Digital staining for histopathology multispectral images by the combined application of spectral enhancement and spectral transformation.

PubMed

Bautista, Pinky A; Yagi, Yukako

2011-01-01

In this paper we introduced a digital staining method for histopathology images captured with an n-band multispectral camera. The method consisted of two major processes: enhancement of the original spectral transmittance and the transformation of the enhanced transmittance to its target spectral configuration. Enhancement is accomplished by shifting the original transmittance with the scaled difference between the original transmittance and the transmittance estimated with m dominant principal component (PC) vectors;the m-PC vectors were determined from the transmittance samples of the background image. Transformation of the enhanced transmittance to the target spectral configuration was done using an nxn transformation matrix, which was derived by applying a least square method to the enhanced and target spectral training data samples of the different tissue components. Experimental results on the digital conversion of a hematoxylin and eosin (H&E) stained multispectral image to its Masson's trichrome stained (MT) equivalent shows the viability of the method.

Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

PubMed

Roe, Daniel R; Bergonzo, Christina; Cheatham, Thomas E

2014-04-03

Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency.

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

PubMed

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-07-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Enhancing resolution of free-flow zone electrophoresis via a simple sheath-flow sample injection.

PubMed

Yang, Ying; Kong, Fan-Zhi; Liu, Ji; Li, Jun-Min; Liu, Xiao-Ping; Li, Guo-Qing; Wang, Ju-Fang; Xiao, Hua; Fan, Liu-Yin; Cao, Cheng-Xi; Li, Shan

2016-07-01

In this work, a simple and novel sheath-flow sample injection method (SFSIM) is introduced to reduce the band broadening of free-flow zone electrophoresis separation in newly developed self-balance free-flow electrophoresis instrument. A needle injector was placed in the center of the separation inlet, into which the BGE and sample solution were pumped simultaneously. BGE formed sheath flow outside the sample stream, resulting in less band broadening related to hydrodynamics and electrodynamics. Hemoglobin and C-phycocyanin were successfully separated by the proposed method in contrast to the poor separation of free-flow electrophoresis with the traditional injection method without sheath flow. About 3.75 times resolution enhancement could be achieved by sheath-flow sample injection method. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploring RNA structure and dynamics through enhanced sampling simulations.

PubMed

Mlýnský, Vojtěch; Bussi, Giovanni

2018-04-01

RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this timescale to be effectively extended in order to probe biologically relevant conformational changes and chemical reactions. Here, we review the role of enhanced sampling techniques in the study of RNA systems. We discuss the challenges and promises associated with the application of these methods to force-field validation, exploration of conformational landscapes and ion/ligand-RNA interactions, as well as catalytic pathways. Important technical aspects of these methods, such as the choice of the biased collective variables and the analysis of multi-replica simulations, are examined in detail. Finally, a perspective on the role of these methods in the characterization of RNA dynamics is provided. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

PubMed Central

2015-01-01

Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency. PMID:24625009

Surface-enhanced Raman sensor for trace chemical detection in water

NASA Astrophysics Data System (ADS)

Lee, Vincent Y.; Farquharson, Stuart; Rainey, Petrie M.

1999-11-01

Surface-enhanced Raman spectroscopy (SERS) promises to be one of the most sensitive methods for chemical detection and in recent years SERS has been used for chemical, biochemical, environmental, and physiological applications. A variety of methods using various media (electrodes, colloids, and substrates) have been successfully developed to enhance Raman signals by six orders of magnitude and more. However, SERS has not become a routine analytical technique because these methods are unable to provide quantitative measurements. This is largely due to the inability to fabricate a sampling medium that provides reversible chemical adsorption, analysis-to-analysis reproducibility, unrestricted solution requirements (reagent concentration and pH) or sample phase (liquid or solid). In an effort to overcome these restrictions, we have developed metal-doped sol-gels to provide surface-enhancement of Raman scattering.

Enhanced Detection of Surface-Associated Bacteria in Indoor Environments by Quantitative PCR

PubMed Central

Buttner, Mark P.; Cruz-Perez, Patricia; Stetzenbach, Linda D.

2001-01-01

Methods for detecting microorganisms on surfaces are needed to locate biocontamination sources and to relate surface and airborne concentrations. Research was conducted in an experimental room to evaluate surface sampling methods and quantitative PCR (QPCR) for enhanced detection of a target biocontaminant present on flooring materials. QPCR and culture analyses were used to quantitate Bacillus subtilis (Bacillus globigii) endospores on vinyl tile, commercial carpet, and new and soiled residential carpet with samples obtained by four surface sampling methods: a swab kit, a sponge swipe, a cotton swab, and a bulk method. The initial data showed that greater overall sensitivity was obtained with the QPCR than with culture analysis; however, the QPCR results for bulk samples from residential carpet were negative. The swab kit and the sponge swipe methods were then tested with two levels of background biological contamination consisting of Penicillium chrysogenum spores. The B. subtilis values obtained by the QPCR method were greater than those obtained by culture analysis. The differences between the QPCR and culture data were significant for the samples obtained with the swab kit for all flooring materials except soiled residential carpet and with the sponge swipe for commercial carpet. The QPCR data showed that there were no significant differences between the swab kit and sponge swipe sampling methods for any of the flooring materials. Inhibition of QPCR due solely to biological contamination of flooring materials was not evident. However, some degree of inhibition was observed with the soiled residential carpet, which may have been caused by the presence of abiotic contaminants, alone or in combination with biological contaminants. The results of this research demonstrate the ability of QPCR to enhance detection and enumeration of biocontaminants on surface materials and provide information concerning the comparability of currently available surface sampling methods. PMID:11375164

Multispectral and Panchromatic used Enhancement Resolution and Study Effective Enhancement on Supervised and Unsupervised Classification Land – Cover

NASA Astrophysics Data System (ADS)

Salman, S. S.; Abbas, W. A.

2018-05-01

The goal of the study is to support analysis Enhancement of Resolution and study effect on classification methods on bands spectral information of specific and quantitative approaches. In this study introduce a method to enhancement resolution Landsat 8 of combining the bands spectral of 30 meters resolution with panchromatic band 8 of 15 meters resolution, because of importance multispectral imagery to extracting land - cover. Classification methods used in this study to classify several lands -covers recorded from OLI- 8 imagery. Two methods of Data mining can be classified as either supervised or unsupervised. In supervised methods, there is a particular predefined target, that means the algorithm learn which values of the target are associated with which values of the predictor sample. K-nearest neighbors and maximum likelihood algorithms examine in this work as supervised methods. In other hand, no sample identified as target in unsupervised methods, the algorithm of data extraction searches for structure and patterns between all the variables, represented by Fuzzy C-mean clustering method as one of the unsupervised methods, NDVI vegetation index used to compare the results of classification method, the percent of dense vegetation in maximum likelihood method give a best results.

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

PubMed

König, Gerhard; Miller, Benjamin T; Boresch, Stefan; Wu, Xiongwu; Brooks, Bernard R

2012-10-09

One of the key requirements for the accurate calculation of free energy differences is proper sampling of conformational space. Especially in biological applications, molecular dynamics simulations are often confronted with rugged energy surfaces and high energy barriers, leading to insufficient sampling and, in turn, poor convergence of the free energy results. In this work, we address this problem by employing enhanced sampling methods. We explore the possibility of using self-guided Langevin dynamics (SGLD) to speed up the exploration process in free energy simulations. To obtain improved free energy differences from such simulations, it is necessary to account for the effects of the bias due to the guiding forces. We demonstrate how this can be accomplished for the Bennett's acceptance ratio (BAR) and the enveloping distribution sampling (EDS) methods. While BAR is considered among the most efficient methods available for free energy calculations, the EDS method developed by Christ and van Gunsteren is a promising development that reduces the computational costs of free energy calculations by simulating a single reference state. To evaluate the accuracy of both approaches in connection with enhanced sampling, EDS was implemented in CHARMM. For testing, we employ benchmark systems with analytical reference results and the mutation of alanine to serine. We find that SGLD with reweighting can provide accurate results for BAR and EDS where conventional molecular dynamics simulations fail. In addition, we compare the performance of EDS with other free energy methods. We briefly discuss the implications of our results and provide practical guidelines for conducting free energy simulations with SGLD.

Design of the sample cell in near-field surface-enhanced Raman scattering by finite difference time domain method

NASA Astrophysics Data System (ADS)

Li, Yaqin; Jian, Guoshu; Wu, Shifa

2006-11-01

The rational design of the sample cell may improve the sensitivity of surface-enhanced Raman scattering (SERS) detection in a high degree. Finite difference time domain (FDTD) simulations of the configuration of Ag film-Ag particles illuminated by plane wave and evanescent wave are performed to provide physical insight for design of the sample cell. Numerical solutions indicate that the sample cell can provide more "hot spots' and the massive field intensity enhancement occurs in these "hot spots'. More information on the nanometer character of the sample can be got because of gradient-field Raman (GFR) of evanescent wave.

Comparison of field-enhanced and pressure-assisted field-enhanced sample injection techniques for the analysis of water-soluble vitamins using CZE.

PubMed

Liu, Qingqing; Liu, Yaling; Guan, Yu; Jia, Li

2009-04-01

A new online concentration method, namely pressure-assisted field-enhanced sample injection (PA-FESI), was developed and compared with FESI for the analysis of water-soluble vitamins by CZE with UV detection. In PA-FESI, negative voltage and positive pressure were simultaneously applied to initialize PA-FESI. PA-FESI uses the hydrodynamic flow generated by the positive pressure to counterbalance the reverse EOF in the capillary column during electrokinetic sample injection, which allowed a longer injection time than usual FESI mode without compromising the separation efficiency. Using the PA-FESI method, the LODs of the vitamins were at ng/mL level based on the S/N of 3 and the RSDs of migration time and peak area for each vitamin (1 microg/mL) were less than 5.1%. The developed method was applied to the analysis of water-soluble vitamins in corns.

MEASUREMENT OF PYRETHROID RESIDUES IN ENVIRONMENTAL AND FOOD SAMPLES BY ENHANCED SOLVENT EXTRACTION/SUPERCRITICAL FLUID EXTRACTION COUPLED WITH GAS CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY

EPA Science Inventory

The abstract summarizes pyrethorid methods development research. It provides a summary of sample preparation and analytical techniques such as supercritical fluid extraction, enhance solvent extraction, gas chromatography and tandem mass spectrometry.

Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions.

PubMed

Wei, Dongshan; Wang, Feng

2010-08-28

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions

NASA Astrophysics Data System (ADS)

Wei, Dongshan; Wang, Feng

2010-08-01

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Resolution-enhancement and sampling error correction based on molecular absorption line in frequency scanning interferometry

NASA Astrophysics Data System (ADS)

Pan, Hao; Qu, Xinghua; Shi, Chunzhao; Zhang, Fumin; Li, Yating

2018-06-01

The non-uniform interval resampling method has been widely used in frequency modulated continuous wave (FMCW) laser ranging. In the large-bandwidth and long-distance measurements, the range peak is deteriorated due to the fiber dispersion mismatch. In this study, we analyze the frequency-sampling error caused by the mismatch and measure it using the spectroscopy of molecular frequency references line. By using the adjacent points' replacement and spline interpolation technique, the sampling errors could be eliminated. The results demonstrated that proposed method is suitable for resolution-enhancement and high-precision measurement. Moreover, using the proposed method, we achieved the precision of absolute distance less than 45 μm within 8 m.

Monitoring the chemical production of citrus-derived bioactive 5-demethylnobiletin using surface enhanced Raman spectroscopy

PubMed Central

Zheng, Jinkai; Fang, Xiang; Cao, Yong; Xiao, Hang; He, Lili

2013-01-01

To develop an accurate and convenient method for monitoring the production of citrus-derived bioactive 5-demethylnobiletin from demethylation reaction of nobiletin, we compared surface enhanced Raman spectroscopy (SERS) methods with a conventional HPLC method. Our results show that both the substrate-based and solution-based SERS methods correlated with HPLC method very well. The solution method produced lower root mean square error of calibration and higher correlation coefficient than the substrate method. The solution method utilized an ‘affinity chromatography’-like procedure to separate the reactant nobiletin from the product 5-demthylnobiletin based on their different binding affinity to the silver dendrites. The substrate method was found simpler and faster to collect the SERS ‘fingerprint’ spectra of the samples as no incubation between samples and silver was needed and only trace amount of samples were required. Our results demonstrated that the SERS methods were superior to HPLC method in conveniently and rapidly characterizing and quantifying 5-demethylnobiletin production. PMID:23885986

Coupling detergent lysis/clean-up methodology with intact protein fractionation for enhanced proteome characterization

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

Sharma, Ritin; Dill, Brian; Chourey, Karuna

2012-01-01

The expanding use of surfactants for proteome sample preparations has prompted the need to systematically optimize the application and removal of these MS-deleterious agents prior to proteome measurements. Here we compare four different detergent clean-up methods (Trichloroacetic acid (TCA) precipitation, Chloroform/Methanol/Water (CMW) extraction, commercial detergent removal spin column method (DRS) and filter-aided sample preparation(FASP)) with respect to varying amounts of protein biomass in the samples, and provide efficiency benchmarks with respect to protein, peptide, and spectral identifications for each method. Our results show that for protein limited samples, FASP outperforms the other three clean-up methods, while at high protein amountmore » all the methods are comparable. This information was used in a dual strategy of comparing molecular weight based fractionated and unfractionated lysates from three increasingly complex samples (Escherichia coli, a five microbial isolate mixture, and a natural microbial community groundwater sample), which were all lysed with SDS and cleaned up using FASP. The two approaches complemented each other by enhancing the number of protein identifications by 8%-25% across the three samples and provided broad pathway coverage.« less

Selective enhancement of carbohydrate ion abundances by diamond nanoparticles for mass spectrometric analysis.

PubMed

Wu, Chieh-Lin; Wang, Chia-Chen; Lai, Yin-Hung; Lee, Hsun; Lin, Jia-Der; Lee, Yuan Tseh; Wang, Yi-Sheng

2013-04-16

Diamond nanoparticles (DNPs) were incorporated into matrix-assisted laser desorption/ionization (MALDI) samples to enhance the sensitivity of the mass spectrometer to carbohydrates. The DNPs optimize the MALDI sample morphology and thermalize the samples for thermally labile compounds because they have a high thermal conductivity, a low extinction coefficient in UV-vis spectral range, and stable chemical properties. The best enhancement effect was achieved when matrix, DNP, and carbohydrate solutions were deposited and vacuum-dried consecutively to form a trilayer sample morphology. It allows the direct identification of underivatized carbohydrates mixed with equal amount of proteins because no increase in the ion abundance of proteins was achieved. For dextran with an average molecular weight of 1500, the trilayer method typically improves the sensitivity by 79- and 7-fold in comparison to the conventional dried-droplet and thin-layer methods, respectively.

Dynamic nuclear polarization in solid samples by electrical-discharge-induced radicals

NASA Astrophysics Data System (ADS)

Katz, Itai; Blank, Aharon

2015-12-01

Dynamic nuclear polarization (DNP) is a method for enhancing nuclear magnetic resonance (NMR) signals that has many potential applications in chemistry and medicine. Traditionally, DNP signal enhancement is achieved through the use of exogenous radicals mixed in a solution with the molecules of interest. Here we show that proton DNP signal enhancements can be obtained for solid samples without the use of solvent and exogenous radicals. Radicals are generated primarily on the surface of a solid sample using electrical discharges. These radicals are found suitable for DNP. They are stable under moderate vacuum conditions, yet readily annihilate upon compound dissolution or air exposure. This feature makes them attractive for use in medical applications, where the current variety of radicals used for DNP faces regulatory problems. In addition, this solvent-free method may be found useful for analytical NMR of solid samples which cannot tolerate solvents, such as certain pharmaceutical products.

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

PubMed

Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Morishita, Tetsuya; Maragliano, Luca

2015-01-01

Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.

Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

PubMed

Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

2015-10-26

Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improved lossless intra coding for H.264/MPEG-4 AVC.

PubMed

Lee, Yung-Lyul; Han, Ki-Hun; Sullivan, Gary J

2006-09-01

A new lossless intra coding method based on sample-by-sample differential pulse code modulation (DPCM) is presented as an enhancement of the H.264/MPEG-4 AVC standard. The H.264/AVC design includes a multidirectional spatial prediction method to reduce spatial redundancy by using neighboring samples as a prediction for the samples in a block of data to be encoded. In the new lossless intra coding method, the spatial prediction is performed based on samplewise DPCM instead of in the block-based manner used in the current H.264/AVC standard, while the block structure is retained for the residual difference entropy coding process. We show that the new method, based on samplewise DPCM, does not have a major complexity penalty, despite its apparent pipeline dependencies. Experiments show that the new lossless intra coding method reduces the bit rate by approximately 12% in comparison with the lossless intra coding method previously included in the H.264/AVC standard. As a result, the new method is currently being adopted into the H.264/AVC standard in a new enhancement project.

Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.

PubMed

Yang, Yi Isaac; Parrinello, Michele

2018-06-12

Collective variables are used often in many enhanced sampling methods, and their choice is a crucial factor in determining sampling efficiency. However, at times, searching for good collective variables can be challenging. In a recent paper, we combined time-lagged independent component analysis with well-tempered metadynamics in order to obtain improved collective variables from metadynamics runs that use lower quality collective variables [ McCarty, J.; Parrinello, M. J. Chem. Phys. 2017 , 147 , 204109 ]. In this work, we extend these ideas to variationally enhanced sampling. This leads to an efficient scheme that is able to make use of the many advantages of the variational scheme. We apply the method to alanine-3 in water. From an alanine-3 variationally enhanced sampling trajectory in which all the six dihedral angles are biased, we extract much better collective variables able to describe in exquisite detail the protein complex free energy surface in a low dimensional representation. The success of this investigation is helped by a more accurate way of calculating the correlation functions needed in the time-lagged independent component analysis and from the introduction of a new basis set to describe the dihedral angles arrangement.

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.

PubMed

Galvelis, Raimondas; Sugita, Yuji

2017-06-13

The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e., importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbor density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation. The bias potential is constructed iteratively from short biased MD simulations accounting for correlation among CVs. Our method is capable of achieving ergodic sampling and calculating free energy of polypeptides with up to 8-dimensional bias potential.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

PubMed

Gil-Ley, Alejandro; Bussi, Giovanni

2015-03-10

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

Molecular dynamics based enhanced sampling of collective variables with very large time steps.

PubMed

Chen, Pei-Yang; Tuckerman, Mark E

2018-01-14

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Molecular dynamics based enhanced sampling of collective variables with very large time steps

NASA Astrophysics Data System (ADS)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta

PubMed Central

Zhang, Zhe; Schindler, Christina E. M.; Lange, Oliver F.; Zacharias, Martin

2015-01-01

The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC) based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC) was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches. PMID:26053419

Rapid determination of actinides in seawater samples

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

Maxwell, Sherrod L.; Culligan, Brian K.; Hutchison, Jay B.

2014-03-09

A new rapid method for the determination of actinides in seawater samples has been developed at the Savannah River National Laboratory. The actinides can be measured by alpha spectrometry or inductively-coupled plasma mass spectrometry. The new method employs novel pre-concentration steps to collect the actinide isotopes quickly from 80 L or more of seawater. Actinides are co-precipitated using an iron hydroxide co-precipitation step enhanced with Ti +3 reductant, followed by lanthanum fluoride co-precipitation. Stacked TEVA Resin and TRU Resin cartridges are used to rapidly separate Pu, U, and Np isotopes from seawater samples. TEVA Resin and DGA Resin were usedmore » to separate and measure Pu, Am and Cm isotopes in seawater volumes up to 80 L. This robust method is ideal for emergency seawater samples following a radiological incident. It can also be used, however, for the routine analysis of seawater samples for oceanographic studies to enhance efficiency and productivity. In contrast, many current methods to determine actinides in seawater can take 1–2 weeks and provide chemical yields of ~30–60 %. This new sample preparation method can be performed in 4–8 h with tracer yields of ~85–95 %. By employing a rapid, robust sample preparation method with high chemical yields, less seawater is needed to achieve lower or comparable detection limits for actinide isotopes with less time and effort.« less

Review of in situ derivatization techniques for enhanced bioanalysis using liquid chromatography with mass spectrometry.

PubMed

Baghdady, Yehia Z; Schug, Kevin A

2016-01-01

Accurate and specific analysis of target molecules in complex biological matrices remains a significant challenge, especially when ultra-trace detection limits are required. Liquid chromatography with mass spectrometry is often the method of choice for bioanalysis. Conventional sample preparation and clean-up methods prior to the analysis of biological fluids such as liquid-liquid extraction, solid-phase extraction, or protein precipitation are time-consuming, tedious, and can negatively affect target recovery and detection sensitivity. An alternative or complementary strategy is the use of an off-line or on-line in situ derivatization technique. In situ derivatization can be incorporated to directly derivatize target analytes in their native biological matrices, without any prior sample clean-up methods, to substitute or even enhance the extraction and preconcentration efficiency of these traditional sample preparation methods. Designed appropriately, it can reduce the number of sample preparation steps necessary prior to analysis. Moreover, in situ derivatization can be used to enhance the performance of the developed liquid chromatography with mass spectrometry-based bioanalysis methods regarding stability, chromatographic separation, selectivity, and ionization efficiency. This review presents an overview of the commonly used in situ derivatization techniques coupled to liquid chromatography with mass spectrometry-based bioanalysis to guide and to stimulate future research. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Faster protein folding using enhanced conformational sampling of molecular dynamics simulation.

PubMed

Kamberaj, Hiqmet

2018-05-01

In this study, we applied swarm particle-like molecular dynamics (SPMD) approach to enhance conformational sampling of replica exchange simulations. In particular, the approach showed significant improvement in sampling efficiency of conformational phase space when combined with replica exchange method (REM) in computer simulation of peptide/protein folding. First we introduce the augmented dynamical system of equations, and demonstrate the stability of the algorithm. Then, we illustrate the approach by using different fully atomistic and coarse-grained model systems, comparing them with the standard replica exchange method. In addition, we applied SPMD simulation to calculate the time correlation functions of the transitions in a two dimensional surface to demonstrate the enhancement of transition path sampling. Our results showed that folded structure can be obtained in a shorter simulation time using the new method when compared with non-augmented dynamical system. Typically, in less than 0.5 ns using replica exchange runs assuming that native folded structure is known and within simulation time scale of 40 ns in the case of blind structure prediction. Furthermore, the root mean square deviations from the reference structures were less than 2Å. To demonstrate the performance of new method, we also implemented three simulation protocols using CHARMM software. Comparisons are also performed with standard targeted molecular dynamics simulation method. Copyright © 2018 Elsevier Inc. All rights reserved.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

PubMed Central

2015-01-01

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide. PMID:25838811

Detection of tobacco-related biomarkers in urine samples by surface-enhanced Raman spectroscopy coupled with thin-layer chromatography.

PubMed

Huang, Rongfu; Han, Sungyub; Li, Xiao Sheryl

2013-08-01

The nicotine metabolites, cotinine and trans-3'-hydroxycotinine (3HC) are considered as superior biomarkers for identifying tobacco exposure. More importantly, the ratio of 3HC to cotinine is a good indicator to phenotype individuals for cytochrome P450 2A6 activity and to individualize pharmacotherapy for tobacco addiction. In this paper, a simple, robust and novel method based on surface-enhanced Raman spectroscopy coupled with thin-layer chromatography (TLC) was developed to directly quantify the biomarkers in human urine samples. This is the first time surface-enhanced Raman spectroscopy (SERS) was used to detect cotinine and 3HC in urine samples. The linear dynamic range for the detection of cotinine is from 40 nM to 8 μM while that of 3HC is from 1 μM to 15 μM. The detection limits are 10 nM and 0.2 μM for cotinine and 3HC, respectively. The proposed method was further validated by quantifying the concentration of both cotinine and 3HC in smokers' urine samples. This TLC-SERS method allows the direct detection of cotinine in the urine samples of both active and passive smokers and the detection of 3HC in smokers.

Deconvolution imaging of weak reflective pipe defects using guided-wave signals captured by a scanning receiver.

PubMed

Sun, Zeqing; Sun, Anyu; Ju, Bing-Feng

2017-02-01

Guided-wave echoes from weak reflective pipe defects are usually interfered by coherent noise and difficult to interpret. In this paper, a deconvolution imaging method is proposed to reconstruct defect images from synthetically focused guided-wave signals, with enhanced axial resolution. A compact transducer, circumferentially scanning around the pipe, is used to receive guided-wave echoes from discontinuities at a distance. This method achieves a higher circumferential sampling density than arrayed transducers-up to 72 sampling spots per lap for a pipe with a diameter of 180 mm. A noise suppression technique is used to enhance the signal-to-noise ratio. The enhancement in both signal-to-noise ratio and axial resolution of the method is experimentally validated by the detection of two kinds of artificial defects: a pitting defect of 5 mm in diameter and 0.9 mm in maximum depth, and iron pieces attached to the pipe surface. A reconstructed image of the pitting defect is obtained with a 5.87 dB signal-to-noise ratio. It is revealed that a high circumferential sampling density is important for the enhancement of the inspection sensitivity, by comparing the images reconstructed with different down-sampling ratios. A modified full width at half maximum is used as the criterion to evaluate the circumferential extent of the region where iron pieces are attached, which is applicable for defects with inhomogeneous reflection intensity.

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

NASA Astrophysics Data System (ADS)

Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele

2016-05-01

Atomistic simulations play a central role in many fields of science. However, their usefulness is often limited by the fact that many systems are characterized by several metastable states separated by high barriers, leading to kinetic bottlenecks. Transitions between metastable states are thus rare events that occur on significantly longer timescales than one can simulate in practice. Numerous enhanced sampling methods have been introduced to alleviate this timescale problem, including methods based on identifying a few crucial order parameters or collective variables and enhancing the sampling of these variables. Metadynamics is one such method that has proven successful in a great variety of fields. Here we review the conceptual and theoretical foundations of metadynamics. As demonstrated, metadynamics is not just a practical tool but can also be considered an important development in the theory of statistical mechanics.

Integrated Hamiltonian sampling: a simple and versatile method for free energy simulations and conformational sampling.

PubMed

Mori, Toshifumi; Hamers, Robert J; Pedersen, Joel A; Cui, Qiang

2014-07-17

Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and λ-dynamics is also briefly discussed.

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

NASA Astrophysics Data System (ADS)

Ahn, Surl-Hee; Grate, Jay W.; Darve, Eric F.

2017-08-01

Molecular dynamics simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not obtain properties' efficiently because we need to run microseconds or longer simulations using femtosecond time steps. To overcome this time scale barrier, we can use the weighted ensemble (WE) method, a powerful enhanced sampling method that efficiently samples thermodynamic and kinetic properties. However, the WE method requires an appropriate partitioning of phase space into discrete macrostates, which can be problematic when we have a high-dimensional collective space or when little is known a priori about the molecular system. Hence, we developed a new WE-based method, called the "Concurrent Adaptive Sampling (CAS) algorithm," to tackle these issues. The CAS algorithm is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective variables and adaptive macrostates to enhance the sampling in the high-dimensional space. This is especially useful for systems in which we do not know what the right reaction coordinates are, in which case we can use many collective variables to sample conformations and pathways. In addition, a clustering technique based on the committor function is used to accelerate sampling the slowest process in the molecular system. In this paper, we introduce the new method and show results from two-dimensional models and bio-molecules, specifically penta-alanine and a triazine trimer.

Investigation of self-adaptive LED surgical lighting based on entropy contrast enhancing method

NASA Astrophysics Data System (ADS)

Liu, Peng; Wang, Huihui; Zhang, Yaqin; Shen, Junfei; Wu, Rengmao; Zheng, Zhenrong; Li, Haifeng; Liu, Xu

2014-05-01

Investigation was performed to explore the possibility of enhancing contrast by varying the spectral distribution (SPD) of the surgical lighting. The illumination scenes with different SPDs were generated by the combination of a self-adaptive white light optimization method and the LED ceiling system, the images of biological sample are taken by a CCD camera and then processed by an 'Entropy' based contrast evaluation model which is proposed specific for surgery occasion. Compared with the neutral white LED based and traditional algorithm based image enhancing methods, the illumination based enhancing method turns out a better performance in contrast enhancing and improves the average contrast value about 9% and 6%, respectively. This low cost method is simple, practicable, and thus may provide an alternative solution for the expensive visual facility medical instruments.

Determination of Aniline and Its Derivatives in Environmental Water by Capillary Electrophoresis with On-Line Concentration

PubMed Central

Liu, Shuhui; Wang, Wenjun; Chen, Jie; Sun, Jianzhi

2012-01-01

This paper describes a simple, sensitive and environmentally benign method for the direct determination of aniline and its derivatives in environmental water samples by capillary zone electrophoresis (CZE) with field-enhanced sample injection. The parameters that influenced the enhancement and separation efficiencies were investigated. Surprisingly, under the optimized conditions, two linear ranges for the calibration plot, 1–50 ng/mL and 50–1000 ng/mL (R > 0.998), were obtained. The detection limit was in the range of 0.29–0.43 ng/mL. To eliminate the effect of the real sample matrix on the stacking efficiency, the standard addition method was applied to the analysis of water samples from local rivers. PMID:22837668

Decalcification using ethylenediaminetetraacetic acid for clear microstructure imaging of cochlea through optical coherence tomography

NASA Astrophysics Data System (ADS)

Lee, Jaeyul; Kim, Kanghae; Wijesinghe, Ruchire Eranga; Jeon, Doekmin; Lee, Sang Heun; Jeon, Mansik; Jang, Jeong Hun

2016-08-01

The aim of this study was to analyze the effectiveness of decalcification using ethylenediaminetetraacetic acid (EDTA) as an optical clearing method to enhance the depth visibility of internal soft tissues of cochlea. Ex vivo mouse and guinea pig cochlea samples were soaked in EDTA solutions for decalcification, and swept source optical coherence tomography (OCT) was used as imaging modality to monitor the decalcified samples consecutively. The monitored noninvasive cross-sectional images showed that the mouse and guinea pig cochlea samples had to be decalcified for subsequent 7 and 14 days, respectively, to obtain the optimal optical clearing results. Using this method, difficulties in imaging of internal cochlea microstructures of mice could be evaded. The obtained results verified that the depth visibility of the decalcified ex vivo samples was enhanced.

Enhanced efficiency of light emitting diodes with a nano-patterned gallium nitride surface realized by soft UV nanoimprint lithography

NASA Astrophysics Data System (ADS)

Zhou, Weimin; Min, Guoquan; Song, Zhitang; Zhang, Jing; Liu, Yanbo; Zhang, Jianping

2010-05-01

This paper reports a significant enhancement in the extraction efficiency of nano-patterned GaN light emitting diodes (LED) realized by soft UV nanoimprint lithography. The 2 inch soft stamp was fabricated using a replication stamp of anodic alumina oxide (AAO) membrane. The light output power was enhanced by 10.9% compared to that of the LED sample without a nano-patterned surface. Up to 41% enhancement in photoluminescence intensity was obtained from the nano-patterned GaN LED sample. The method is simple, cheap and suitable for mass production.

Evaluating Ethanol-based Sample Preservation to Facilitate Use of DNA Barcoding in Routine Freshwater Biomonitoring Programs Using Benthic Macroinvertebrates

EPA Science Inventory

Molecular methods, such as DNA barcoding, have the potential in enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biom...

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations.

PubMed

Mori, Yoshiharu; Okamoto, Yuko

2013-02-01

A simulated tempering method, which is referred to as simulated-tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed to study the intramolecular proton transfer reaction of malonaldehyde in an aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be calculated accurately. Moreover, the simulated-tempering umbrella sampling provides trajectory data more efficiently than the conventional umbrella sampling method.

A new sampling scheme for developing metamodels with the zeros of Chebyshev polynomials

NASA Astrophysics Data System (ADS)

Wu, Jinglai; Luo, Zhen; Zhang, Nong; Zhang, Yunqing

2015-09-01

The accuracy of metamodelling is determined by both the sampling and approximation. This article proposes a new sampling method based on the zeros of Chebyshev polynomials to capture the sampling information effectively. First, the zeros of one-dimensional Chebyshev polynomials are applied to construct Chebyshev tensor product (CTP) sampling, and the CTP is then used to construct high-order multi-dimensional metamodels using the 'hypercube' polynomials. Secondly, the CTP sampling is further enhanced to develop Chebyshev collocation method (CCM) sampling, to construct the 'simplex' polynomials. The samples of CCM are randomly and directly chosen from the CTP samples. Two widely studied sampling methods, namely the Smolyak sparse grid and Hammersley, are used to demonstrate the effectiveness of the proposed sampling method. Several numerical examples are utilized to validate the approximation accuracy of the proposed metamodel under different dimensions.

On the enhanced sampling over energy barriers in molecular dynamics simulations.

PubMed

Gao, Yi Qin; Yang, Lijiang

2006-09-21

We present here calculations of free energies of multidimensional systems using an efficient sampling method. The method uses a transformed potential energy surface, which allows an efficient sampling of both low and high energy spaces and accelerates transitions over barriers. It allows efficient sampling of the configuration space over and only over the desired energy range(s). It does not require predetermined or selected reaction coordinate(s). We apply this method to study the dynamics of slow barrier crossing processes in a disaccharide and a dipeptide system.

Comparison of hot hydroxylamine hydrochloride and oxalic acid leaching of stream sediment and coated rock samples as anomaly enhancement techniques

USGS Publications Warehouse

Filipek, L.H.; Chao, T.T.; Theobald, P.K.

1982-01-01

A hot hydroxylamine hydrochloride (H-Hxl) extraction in 25% acetic acid is compared with the commonly used oxalic acid extraction as a method of anomaly enhancement for Cu and Zn in samples from two very different metal deposits and climatic environments. Results obtained on minus-80-mesh stream sediments from an area near the Magruder massive sulfide deposit in Lincoln County, Georgia, where the climate is humid subtropical, indicate that H-Hxl enhances the anomaly for Cu by a factor of 2 and for Zn by a factor of 1.5, compared to the oxalic method. Analyses of Fe oxide-coated rock samples from outcrops overlying the North Silver Bell porphyry copper deposit near Tucson, Arizona, where the climate is semi-arid to arid, indicate that both techniques effectively outline the zones of hydrothermal alteration. The H-Hxl extraction can also perform well in high-carbonate or high-clay environments, where other workers have suggested that oxalic acid is not very effective. Therefore, the H-Hxl method is recommended for general exploration use. ?? 1982.

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

PubMed Central

2015-01-01

The establishment of early life microbiota in the human infant gut is highly variable and plays a crucial role in host nutrient availability/uptake and maturation of immunity. Although high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the acquisition of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on double filtering (DF) the raw samples, a method that fractionates microbial from human cells to enhance microbial protein identification and characterization in complex fecal samples from healthy premature infants. This method dramatically improved the overall depth of infant gut proteome measurement, with an increase in the number of identified low-abundance proteins and a greater than 2-fold improvement in microbial protein identification and quantification. This enhancement of proteome measurement depth enabled a more extensive microbiome comparison between infants by not only increasing the confidence of identified microbial functional categories but also revealing previously undetected categories. PMID:25350865

Surfactant-enhanced spectrofluorimetric determination of total aflatoxins from wheat samples after magnetic solid-phase extraction using modified Fe3O4 nanoparticles

NASA Astrophysics Data System (ADS)

Manafi, Mohammad Hanif; Allahyari, Mehdi; Pourghazi, Kamyar; Amoli-Diva, Mitra; Taherimaslak, Zohreh

2015-07-01

The extraction and preconcentration of total aflatoxins (including aflatoxin B1, B2, G1, and G2) using magnetic nanoparticles based solid phase extraction (MSPE) followed by surfactant-enhanced spectrofluorimetric detection was proposed. Ethylene glycol bis-mercaptoacetate modified silica coated Fe3O4 nanoparticles as an efficient antibody-free adsorbent was successfully applied to extract aflatoxins from wheat samples. High surface area and strong magnetization properties of magnetic nanoparticles were utilized to achieve high enrichment factor (97), and satisfactory recoveries (92-105%) using only 100 mg of the adsorbent. Furthermore, the fast separation time (less than 10 min) avoids many time-consuming cartridge loading or column-passing procedures accompany with the conventional SPE. In determination step, signal enhancement was performed by formation of Triton X-100 micelles around the analytes in 15% (v/v) acetonitrile-water which dramatically increase the sensitivity of the method. Main factors affecting the extraction efficiency and signal enhancement of the analytes including pH of sample solution, desorption conditions, extraction time, sample volume, adsorbent amount, surfactant concentration and volume and time of micelle formation were evaluated and optimized. Under the optimum conditions, wide linear range of 0.1-50 ng mL-1 with low detection limit of 0.03 ng mL-1 were obtained. The developed method was successfully applied to the extraction and preconcentration of aflatoxins in three commercially available wheat samples and the results were compared with the official AOAC method.

Flow-based analysis using microfluidics-chemiluminescence systems.

PubMed

Al Lawati, Haider A J

2013-01-01

This review will discuss various approaches and techniques in which analysis using microfluidics-chemiluminescence systems (MF-CL) has been reported. A variety of applications is examined, including environmental, pharmaceutical, biological, food and herbal analysis. Reported uses of CL reagents, sample introduction techniques, sample pretreatment methods, CL signal enhancement and detection systems are discussed. A hydrodynamic pumping system is predominately used for these applications. However, several reports are available in which electro-osmotic (EO) pumping has been implemented. Various sample pretreatment methods have been used, including liquid-liquid extraction, solid-phase extraction and molecularly imprinted polymers. A wide range of innovative techniques has been reported for CL signal enhancement. Most of these techniques are based on enhancement of the mixing process in the microfluidics channels, which leads to enhancement of the CL signal. However, other techniques are also reported, such as mirror reaction, liquid core waveguide, on-line pre-derivatization and the use of an opaque white chip with a thin transparent seal. Photodetectors are the most commonly used detectors; however, other detection systems have also been used, including integrated electrochemiluminescence (ECL) and organic photodiodes (OPDs). Copyright © 2012 John Wiley & Sons, Ltd.

CdS nanoparticles-enhanced chemiluminescence and determination of baicalin in pharmaceutical preparations.

PubMed

Chen, Xiaolan; Tan, Xinmei; Wang, Jianxiu

2013-01-01

CdS nanoparticles (CdS NPs) of different sizes were synthesized by the citrate reduction method. It was found that CdS NPs could enhance the chemiluminescence (CL) of the luminol-potassium ferricyanide system and baicalin could inhibit CdS NPs-enhanced luminol-potassium ferricyanide CL signals in alkaline solution. Based on this inhibition, a flow-injection CL method was established for determination of baicalin in pharmaceutical preparations and human urine samples. Under optimized conditions, the linear range for determination of baicalin was 5.0 x 10(-6) to 1.0 x 10(-3) g/L. The detection limit at a signal-to-noise ratio of 3 was 1.7 x 10(-6) g/L. CL spectra, UV-visible spectra and transmission electron microscopy (TEM) were used to investigate the CL mechanism. The method described is simple, selective and obviates the need of extensive sample pretreatment. Copyright © 2012 John Wiley & Sons, Ltd.

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

DOE PAGES

Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

2016-11-03

Here, we compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchangemore » (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium.« less

Comparing generalized ensemble methods for sampling of systems with many degrees of freedom.

PubMed

Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

2016-11-07

We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium (http://www.omnia.md/).

ENHANCED DAPI STAINING FOR CRYPTOSPORIDIUM IN WATER SAMPLES

EPA Science Inventory

The U.S. Environmental Protection Agency's Method 1623 is used to detect and quantify the presence of {ital Cryptosporidium} spp. oocysts in water. The protocol consists of concentrating a sample, staining this concentrate with a fluorescent antibody, and examining the sample mi...

Integral imaging based light field display with enhanced viewing resolution using holographic diffuser

NASA Astrophysics Data System (ADS)

Yan, Zhiqiang; Yan, Xingpeng; Jiang, Xiaoyu; Gao, Hui; Wen, Jun

2017-11-01

An integral imaging based light field display method is proposed by use of holographic diffuser, and enhanced viewing resolution is gained over conventional integral imaging systems. The holographic diffuser is fabricated with controlled diffusion characteristics, which interpolates the discrete light field of the reconstructed points to approximate the original light field. The viewing resolution can thus be improved and independent of the limitation imposed by Nyquist sampling frequency. An integral imaging system with low Nyquist sampling frequency is constructed, and reconstructed scenes of high viewing resolution using holographic diffuser are demonstrated, verifying the feasibility of the method.

Low-temperature dynamic nuclear polarization of gases in frozen mixtures

PubMed Central

Pourfathi, Mehrdad; Clapp, Justin; Kadlecek, Stephen J.; Keenan, Caroline D.; Ghosh, Rajat K.; Kuzma, Nicholas N.; Rizi, Rahim R.

2015-01-01

Purpose To present a new cryogenic technique for preparing gaseous compounds in solid mixtures for polarization using dynamic nuclear polarization (DNP). Methods 129Xe and 15N2O samples were prepared using the presented method. Samples were hyperpolarized at 1.42K at 5T. 129Xe was polarized at 1.65K and 1.42K to compare enhancement. Polarization levels for both samples and T1 relaxation times for the 129Xe sample were measured. Sample pulverization for the 129Xe and controlled annealing for both samples were introduced as additional steps in sample preparation. Results Enhancement increased by 15% due to a temperature drop from 1.65K to 1.42K for the 129Xe sample. A polarization level of 20±3% for the 129Xe sample was achieved, a 2-fold increase from 10±1% after pulverization of the sample at 1.42K. T1 of the 129Xe sample was increased by more than 3-fold via annealing. In the case of 15N2O, annealing led to a ~2-fold increase in the signal level after DNP. Conclusion The presented technique for producing and manipulating solid gas/glassing agent/radical mixtures for DNP led to high polarization levels in 129Xe and 15N2O samples. These methods show potential for polarizing other gases using DNP technology. PMID:26444315

Spectroscopic and Spectrometric Methods Used for the Screening of Certain Herbal Food Supplements Suspected of Adulteration

PubMed Central

Mateescu, Cristina; Popescu, Anca Mihaela; Radu, Gabriel Lucian; Onisei, Tatiana; Raducanu, Adina Elena

2017-01-01

Purpose: This study was carried out in order to find a reliable method for the fast detection of adulterated herbal food supplements with sexual enhancement claims. As some herbal products are advertised as "all natural", their "efficiency" is often increased by addition of active pharmaceutical ingredients such as PDE-5 inhibitors, which can be a real health threat for the consumer. Methodes: Adulterants, potentially present in 50 herbal food supplements with sexual improvement claims, were detected using 2 spectroscopic methods - Raman and Fourier Transform Infrared - known for reliability, reproductibility, and an easy sample preparation. GC-MS technique was used to confirm the potential adulterants spectra. Results: About 22% (11 out of 50 samples) of herbal food supplements with sexual enhancement claims analyzed by spectroscopic and spectrometric methods proved to be "enriched" with active pharmaceutical compounds such as: sildenafil and two of its analogues, tadalafil and phenolphthalein. The occurence of phenolphthalein could be the reason for the non-relevant results obtained by FTIR method in some samples. 91% of the adulterated herbal food supplements were originating from China. Conclusion: The results of this screening highlighted the necessity for an accurate analysis of all alleged herbal aphrodisiacs on the Romanian market. This is a first such a screening analysis carried out on herbal food supplements with sexual enhancement claims. PMID:28761827

Spectroscopic and Spectrometric Methods Used for the Screening of Certain Herbal Food Supplements Suspected of Adulteration.

PubMed

Mateescu, Cristina; Popescu, Anca Mihaela; Radu, Gabriel Lucian; Onisei, Tatiana; Raducanu, Adina Elena

2017-06-01

Purpose: This study was carried out in order to find a reliable method for the fast detection of adulterated herbal food supplements with sexual enhancement claims. As some herbal products are advertised as "all natural", their "efficiency" is often increased by addition of active pharmaceutical ingredients such as PDE-5 inhibitors, which can be a real health threat for the consumer. Methodes: Adulterants, potentially present in 50 herbal food supplements with sexual improvement claims, were detected using 2 spectroscopic methods - Raman and Fourier Transform Infrared - known for reliability, reproductibility, and an easy sample preparation. GC-MS technique was used to confirm the potential adulterants spectra. Results: About 22% (11 out of 50 samples) of herbal food supplements with sexual enhancement claims analyzed by spectroscopic and spectrometric methods proved to be "enriched" with active pharmaceutical compounds such as: sildenafil and two of its analogues, tadalafil and phenolphthalein. The occurence of phenolphthalein could be the reason for the non-relevant results obtained by FTIR method in some samples. 91% of the adulterated herbal food supplements were originating from China. Conclusion: The results of this screening highlighted the necessity for an accurate analysis of all alleged herbal aphrodisiacs on the Romanian market. This is a first such a screening analysis carried out on herbal food supplements with sexual enhancement claims.

Enhanced conformational sampling using enveloping distribution sampling.

PubMed

Lin, Zhixiong; van Gunsteren, Wilfred F

2013-10-14

To lessen the problem of insufficient conformational sampling in biomolecular simulations is still a major challenge in computational biochemistry. In this article, an application of the method of enveloping distribution sampling (EDS) is proposed that addresses this challenge and its sampling efficiency is demonstrated in simulations of a hexa-β-peptide whose conformational equilibrium encompasses two different helical folds, i.e., a right-handed 2.7(10∕12)-helix and a left-handed 3(14)-helix, separated by a high energy barrier. Standard MD simulations of this peptide using the GROMOS 53A6 force field did not reach convergence of the free enthalpy difference between the two helices even after 500 ns of simulation time. The use of soft-core non-bonded interactions in the centre of the peptide did enhance the number of transitions between the helices, but at the same time led to neglect of relevant helical configurations. In the simulations of a two-state EDS reference Hamiltonian that envelops both the physical peptide and the soft-core peptide, sampling of the conformational space of the physical peptide ensures that physically relevant conformations can be visited, and sampling of the conformational space of the soft-core peptide helps to enhance the transitions between the two helices. The EDS simulations sampled many more transitions between the two helices and showed much faster convergence of the relative free enthalpy of the two helices compared with the standard MD simulations with only a slightly larger computational effort to determine optimized EDS parameters. Combined with various methods to smoothen the potential energy surface, the proposed EDS application will be a powerful technique to enhance the sampling efficiency in biomolecular simulations.

Characterisation of signal enhancements achieved when utilizing a photon diode in deep Raman spectroscopy of tissue

PubMed Central

Vardaki, Martha Z.; Matousek, Pavel; Stone, Nicholas

2016-01-01

We characterise the performance of a beam enhancing element (‘photon diode’) for use in deep Raman spectroscopy (DRS) of biological tissues. The optical component enhances the number of laser photons coupled into a tissue sample by returning escaping photons back into it at the illumination zone. The method is compatible with transmission Raman spectroscopy, a deep Raman spectroscopy concept, and its implementation leads to considerable enhancement of detected Raman photon rates. In the past, the enhancement concept was demonstrated with a variety of samples (pharmaceutical tablets, tissue, etc) but it was not systematically characterized with biological tissues. In this study, we investigate the enhancing properties of the photon diode in the transmission Raman geometry as a function of: a) the depth and b) the optical properties of tissue samples. Liquid tissue phantoms were employed to facilitate systematic variation of optical properties. These were chosen to mimic optical properties of human tissues, including breast and prostate. The obtained results evidence that a photon diode can enhance Raman signals of tissues by a maximum of × 2.4, although it can also decrease the signals created towards the back of samples that exhibit high scattering or absorption properties. PMID:27375932

The impact of science methods courses on preservice elementary teachers' science teaching self-efficacy beliefs: Case studies from Turkey and the United States

NASA Astrophysics Data System (ADS)

Bursal, Murat

Four case studies in two American and two Turkish science methods classrooms were conducted to investigate the changes in preservice elementary teachers' personal science teaching efficacy (PSTE) beliefs during their course periods. The findings indicated that while Turkish preservice elementary teachers (TR sample) started the science methods course semester with higher PSTE than their American peers (US sample), due to a significant increase in the US sample's and an insignificant decline in the TR sample's PSTE scores, both groups completed the science methods course with similar PSTE levels. Consistent with Bandura's social cognitive theory, describing four major sources of self-efficacy, the inclusion of mastery experiences (inquiry activities and elementary school micro-teaching experiences) and vicarious experiences (observation of course instructor and supervisor elementary teacher) into the science methods course, providing positive social persuasion (positive appraisal from the instructor and classmates), and improving physiological states (reduced science anxiety and positive attitudes toward becoming elementary school teachers), were found to contribute to the significant enhancement of the US sample's PSTE beliefs. For the TR sample, although some of the above sources were present, the lack of student teaching experiences and inservice teacher observations, as well as the TR samples' negative attitudes toward becoming elementary school teachers and a lack of positive classroom support were found to make Turkish preservice teachers rely mostly on their mastery in science concepts, and therefore resulted in not benefiting from their science methods course, in terms of enhancing their PSTE beliefs. Calls for reforms in the Turkish education system that will include more mastery experiences in the science methods courses and provide more flexibility for students to choose their high school majors and college programs, and switch between them are made. In addition to the mastery experiences contributing to the PSTE beliefs, this study reported that preservice elementary teachers' unawareness of their science misconceptions also results in enhancing their self-efficacy, which is troublesome. Revisions in science content courses to employ inquiry activities, designed for addressing and correcting students' misconceptions, are recommended to overcome teacher candidates' lack of science competency and negative attitudes toward science.

[TLC-SERS study on evodiamine in evodia rutaecarpa].

PubMed

Zhang, Jin-zhi; Wang, Yuan; Chen, Hui; Shao, Hui-bo

2007-05-01

A new method for analyzing the ingredients of evodiamine (EV), rutaecarpine (RU), hydroxyevodiamine (HYD), evodiamide (ED), dihydrorutaecarpine (DRU) and 14-formyldihydrorutaecarpine (FDRU) in evodia rutaecarpa using high performance thin layer chromatography (TLC) and surface enhanced Raman spectroscopy (SERS) technique is reported. The character of this method is that standard samples are not needed. The results show that the characteristic spectral bands of EV, RU, HYD, and ED can be obtained from the TLC spot with microgramme of sample. The spectral band at 1562 cm(-1) was obtained with great enhancement. Molecule absorbed in surface silver sol by nr electrons in ring. The spectral bands of EV, RU, HYD and ED are obviously different due to their differences in structure. The TLC and SERS techniques standard samples are a convenient and speedy method to analyze chemical ingredients with high sensitivity for the study of the Chinese traditional medicine.

Improvements to sample processing and measurement to enable more widespread environmental application of tritium

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

Moran, James; Alexander, Thomas; Aalseth, Craig

2017-08-01

Previous measurements have demonstrated the wealth of information that tritium (T) can provide on environmentally relevant processes. We present modifications to sample preparation approaches that enable T measurement by proportional counting on small sample sizes equivalent to 120 mg of water and demonstrate the accuracy of these methods on a suite of standardized water samples. This enhanced method should provide the analytical flexibility needed to address persistent knowledge gaps in our understanding of T behavior in the environment.

Contrast enhanced spectroscopic optical coherence tomography

NASA Technical Reports Server (NTRS)

Xu, Chenyang (Inventor); Boppart, Stephen A. (Inventor)

2010-01-01

A method of forming an image of a sample includes performing SOCT on a sample. The sample may include a contrast agent, which may include an absorbing agent and/or a scattering agent. A method of forming an image of tissue may include selecting a contrast agent, delivering the contrast agent to the tissue, acquiring SOCT data from the tissue, and converting the SOCT data into an image. The contributions to the SOCT data of an absorbing agent and a scattering agent in a sample may be quantified separately.

Enhanced genetic analysis of single human bioparticles recovered by simplified micromanipulation from forensic 'touch DNA' evidence.

PubMed

Farash, Katherine; Hanson, Erin K; Ballantyne, Jack

2015-03-09

DNA profiles can be obtained from 'touch DNA' evidence, which comprises microscopic traces of human biological material. Current methods for the recovery of trace DNA employ cotton swabs or adhesive tape to sample an area of interest. However, such a 'blind-swabbing' approach will co-sample cellular material from the different individuals, even if the individuals' cells are located in geographically distinct locations on the item. Thus, some of the DNA mixtures encountered in touch DNA samples are artificially created by the swabbing itself. In some instances, a victim's DNA may be found in significant excess thus masking any potential perpetrator's DNA. In order to circumvent the challenges with standard recovery and analysis methods, we have developed a lower cost, 'smart analysis' method that results in enhanced genetic analysis of touch DNA evidence. We describe an optimized and efficient micromanipulation recovery strategy for the collection of bio-particles present in touch DNA samples, as well as an enhanced amplification strategy involving a one-step 5 µl microvolume lysis/STR amplification to permit the recovery of STR profiles from the bio-particle donor(s). The use of individual or few (i.e., "clumps") bioparticles results in the ability to obtain single source profiles. These procedures represent alternative enhanced techniques for the isolation and analysis of single bioparticles from forensic touch DNA evidence. While not necessary in every forensic investigation, the method could be highly beneficial for the recovery of a single source perpetrator DNA profile in cases involving physical assault (e.g., strangulation) that may not be possible using standard analysis techniques. Additionally, the strategies developed here offer an opportunity to obtain genetic information at the single cell level from a variety of other non-forensic trace biological material.

Enhancement of Permeation in Transdermal Drug Delivery System by 6μm Wavelength Area Using an MIR-FEL

NASA Astrophysics Data System (ADS)

Uchizono, T.; Ishii, K.; Iwao, Y.; Itou, Y.; Maruo, H.; Hori, M.; Awazu, K.

2005-03-01

Ablation of the stratum corneum (SC) by pulsed-laser irradiation is one method of enhancing transdermal drug delivery (TD). For non-invasive laser TD treatment, we have tried to enhance TD without ablation of the SC using an MIR-FEL (6-μm wavelength) (FEL : free electron laser). Lidocaine was used as the drug in this study. The enhancement of TD was measured by HPLC. It was found that the lidocaine TD of the sample irradiated by MIR-FEL was enhanced 10 fold faster than the non-irradiated sample with a flux at 0.5 μg/cm2/h, measured by HPLC. We have demonstrated the effectiveness of TD enhancement by an MIR-FEL (6-μm wavelength) irradiation.

The effect of substrate on electric field enhancement of Tip-enhanced Raman spectroscopy (TERS)

NASA Astrophysics Data System (ADS)

Bahreini, Maryam

2018-01-01

The characterization of materials down to a few-molecule level is a key challenge in nanotechnology. Raman spectroscopy is a powerful method that provides chemical information via nondestructive vibrational fingerprinting. Unfortunately, this method suffers from signal weakness which prevents the study of small quantities. Tip-enhanced Raman spectroscopy (TERS) which combines the chemical sensitivity of Raman spectroscopy (RS) with high spatial resolution of scanning probe microscopy (SPM), provides chemical images of surfaces at the nanometer scale. In this method, irradiation of an SPM tip by a focused laser beam results in enhancement of local electric field via two reasons of localized surface plasmon resonance and lightning rod effect. This enhancement leads to the enhancement in Raman intensity from the sample surface in the vicinity of tip. In all TERS measurements, samples should be located on a substrate. In this paper, the dependence of the electric field enhancement to the substrate has been investigated. In simulations, three-dimensional finite-difference time-domain (3D-FDTD) method is used for numerical solution of Maxwell's equations. Our results show that the electric field enhancement is weak for the tip alone case. Introducing a substrate provides further electric field enhancement via near field electromagnetic dipole-dipole coupling between the tip and substrate. Since the side-illumination geometry is used for laser irradiation, the vertical component of the incident field plays a dominant role in the electric field enhancement. Therefore, the coupling effect between the tip and the substrate is the key contribution to the enhancement. For the case of silicon tip and the gold substrate, the electric field enhancement is improved considerably. There is an optimal tip size for TERS because of the competing effects of the radiation damping and the surface scattering of the tip. The results show the substrate as an effective tool for the improvement of the TERS detection sensitivity.

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

NASA Astrophysics Data System (ADS)

Awasthi, Shalini; Nair, Nisanth N.

2017-03-01

Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques.

Dynamics Sampling in Transition Pathway Space.

PubMed

Zhou, Hongyu; Tao, Peng

2018-01-09

The minimum energy pathway contains important information describing the transition between two states on a potential energy surface (PES). Chain-of-states methods were developed to efficiently calculate minimum energy pathways connecting two stable states. In the chain-of-states framework, a series of structures are generated and optimized to represent the minimum energy pathway connecting two states. However, multiple pathways may exist connecting two existing states and should be identified to obtain a full view of the transitions. Therefore, we developed an enhanced sampling method, named as the direct pathway dynamics sampling (DPDS) method, to facilitate exploration of a PES for multiple pathways connecting two stable states as well as addition minima and their associated transition pathways. In the DPDS method, molecular dynamics simulations are carried out on the targeting PES within a chain-of-states framework to directly sample the transition pathway space. The simulations of DPDS could be regulated by two parameters controlling distance among states along the pathway and smoothness of the pathway. One advantage of the chain-of-states framework is that no specific reaction coordinates are necessary to generate the reaction pathway, because such information is implicitly represented by the structures along the pathway. The chain-of-states setup in a DPDS method greatly enhances the sufficient sampling in high-energy space between two end states, such as transition states. By removing the constraint on the end states of the pathway, DPDS will also sample pathways connecting minima on a PES in addition to the end points of the starting pathway. This feature makes DPDS an ideal method to directly explore transition pathway space. Three examples demonstrate the efficiency of DPDS methods in sampling the high-energy area important for reactions on the PES.

Determination of fluoxetine in pharmaceutical and biological samples based on the silver nanoparticle enhanced fluorescence of fluoxetine-terbium complex.

PubMed

Lotfi, Ali; Manzoori, Jamshid L

2016-11-01

In this study, a simple and sensitive spectrofluorimetric method is presented for the determination of fluoxetine based on the enhancing effect of silver nanoparticles (AgNPs) on the terbium-fluoxetine fluorescence emission. The AgNPs were prepared by a simple reduction method and characterized by UV-Vis spectroscopy and transmission electron microscopy. It was indicated that these AgNPs have a remarkable amplifying effect on the terbium-sensitized fluorescence of fluoxetine. The effects of various parameters such as AgNP and Tb 3+ concentration and the pH of the media were investigated. Under obtained optimal conditions, the fluorescence intensity of the terbium-fluoxetine-AgNP system was enhanced linearly by increasing the concentration of fluoxetine in the range of 0.008 to 19 mg/L. The limit of detection (b + 3s) was 8.3 × 10 -4 mg/L. The interference effects of common species found in real samples were also studied. The method had good linearity, recovery, reproducibility and sensitivity, and was satisfactorily applied for the determination of fluoxetine in tablet formulations, human urine and plasma samples. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

State-dependent biasing method for importance sampling in the weighted stochastic simulation algorithm.

PubMed

Roh, Min K; Gillespie, Dan T; Petzold, Linda R

2010-11-07

The weighted stochastic simulation algorithm (wSSA) was developed by Kuwahara and Mura [J. Chem. Phys. 129, 165101 (2008)] to efficiently estimate the probabilities of rare events in discrete stochastic systems. The wSSA uses importance sampling to enhance the statistical accuracy in the estimation of the probability of the rare event. The original algorithm biases the reaction selection step with a fixed importance sampling parameter. In this paper, we introduce a novel method where the biasing parameter is state-dependent. The new method features improved accuracy, efficiency, and robustness.

Analysis of IAEA Environmental Samples for Plutonium and Uranium by ICP/MS in Support Of International Safeguards

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

Farmer, Orville T.; Olsen, Khris B.; Thomas, May-Lin P.

2008-05-01

A method for the separation and determination of total and isotopic uranium and plutonium by ICP-MS was developed for IAEA samples on cellulose-based media. Preparation of the IAEA samples involved a series of redox chemistries and separations using TRU® resin (Eichrom). The sample introduction system, an APEX nebulizer (Elemental Scientific, Inc), provided enhanced nebulization for a several-fold increase in sensitivity and reduction in background. Application of mass bias (ALPHA) correction factors greatly improved the precision of the data. By combining the enhancements of chemical separation, instrumentation and data processing, detection levels for uranium and plutonium approached high attogram levels.

Candle Soot-Driven Performance Enhancement in Pyroelectric Energy Conversion

NASA Astrophysics Data System (ADS)

Azad, Puneet; Singh, V. P.; Vaish, Rahul

2018-05-01

We observed substantial enhancement in pyroelectric output with the help of candle soot coating on the surface of lead zirconate titanate (PZT). Candle soot of varying thicknesses was coated by directly exposing pyroelectric material to the candle flame. The open-circuit pyroelectric voltage and closed-circuit pyroelectric current were recorded while applying infrared heating across the uncoated and candle soot-coated samples for different heating and cooling cycles. In comparison to the uncoated sample, the maximum open-circuit voltage improves seven times for the candle soot-coated sample and electric current increases by eight times across a resistance of 10Å. Moreover, the harvested energy is enhanced by 50 times for candle soot-coated sample. Results indicate that candle soot coating is an effective and economic method to improve infrared sensing performance of pyroelectric materials.

Enhanced sampling of glutamate receptor ligand-binding domains.

PubMed

Lau, Albert Y

2018-04-14

The majority of excitatory synaptic transmission in the central nervous system is mediated by ionotropic glutamate receptors (iGluRs). These membrane-bound protein assemblies consist of modular domains that can be genetically isolated and expressed, which has resulted in a plethora of crystal structures of individual domains in different conformations bound to different ligands. These structures have presented opportunities for molecular dynamics (MD) simulation studies. To examine the free energies that govern molecular behavior, simulation strategies and algorithms have been developed, collectively called enhanced sampling methods This review focuses on the use of enhanced sampling MD simulations of isolated iGluR ligand-binding domains to characterize thermodynamic properties important to receptor function. Copyright © 2018 Elsevier B.V. All rights reserved.

Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange.

PubMed

Kubitzki, Marcus B; de Groot, Bert L

2007-06-15

Today's standard molecular dynamics simulations of moderately sized biomolecular systems at full atomic resolution are typically limited to the nanosecond timescale and therefore suffer from limited conformational sampling. Efficient ensemble-preserving algorithms like replica exchange (REX) may alleviate this problem somewhat but are still computationally prohibitive due to the large number of degrees of freedom involved. Aiming at increased sampling efficiency, we present a novel simulation method combining the ideas of essential dynamics and REX. Unlike standard REX, in each replica only a selection of essential collective modes of a subsystem of interest (essential subspace) is coupled to a higher temperature, with the remainder of the system staying at a reference temperature, T(0). This selective excitation along with the replica framework permits efficient approximate ensemble-preserving conformational sampling and allows much larger temperature differences between replicas, thereby considerably enhancing sampling efficiency. Ensemble properties and sampling performance of the method are discussed using dialanine and guanylin test systems, with multi-microsecond molecular dynamics simulations of these test systems serving as references.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Peter, Emanuel K.

2017-12-01

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

Magnetic stirrer induced dispersive ionic-liquid microextraction for the determination of vanadium in water and food samples prior to graphite furnace atomic absorption spectrometry.

PubMed

Naeemullah; Kazi, Tasneem Gul; Tuzen, Mustafa

2015-04-01

A new dispersive liquid-liquid microextraction, magnetic stirrer induced dispersive ionic-liquid microextraction (MS-IL-DLLME) was developed to quantify the trace level of vanadium in real water and food samples by graphite furnace atomic absorption spectrometry (GFAAS). In this extraction method magnetic stirrer was applied to obtained a dispersive medium of 1-butyl-3-methylimidazolium hexafluorophosphate [C4MIM][PF6] in aqueous solution of (real water samples and digested food samples) to increase phase transfer ratio, which significantly enhance the recovery of vanadium - 4-(2-pyridylazo) resorcinol (PAR) chelate. Variables having vital role on desired microextraction methods were optimised to obtain the maximum recovery of study analyte. Under the optimised experimental variables, enhancement factor (EF) and limit of detection (LOD) were achieved to be 125 and 18 ng L(-1), respectively. Validity and accuracy of the desired method was checked by analysis of certified reference materials (SLRS-4 Riverine water and NIST SRM 1515 Apple leaves). The relative standard deviation (RSD) for 10 replicate determinations at 0.5 μg L(-1) of vanadium level was found to be <5.0%. This method was successfully applied to real water and acid digested food samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation.

PubMed

Peter, Emanuel K

2017-12-07

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

US Fish and Wildlife Service biomonitoring operations manual, Appendices A--K

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

Gianotto, D.F.; Rope, R.C.; Mondecar, M.

1993-04-01

Volume 2 contains Appendices and Summary Sheets for the following areas: A-Legislative Background and Key to Relevant Legislation, B- Biomonitoring Operations Workbook, C-Air Monitoring, D-Introduction to the Flora and Fauna for Biomonitoring, E-Decontamination Guidance Reference Field Methods, F-Documentation Guidance, Sample Handling, and Quality Assurance/Quality Control Standard Operating Procedures, G-Field Instrument Measurements Reference Field Methods, H-Ground Water Sampling Reference Field Methods, I-Sediment Sampling Reference Field Methods, J-Soil Sampling Reference Field Methods, K-Surface Water Reference Field Methods. Appendix B explains how to set up strategy to enter information on the ``disk workbook``. Appendix B is enhanced by DE97006389, an on-line workbook formore » users to be able to make revisions to their own biomonitoring data.« less

Rapid determination of 226Ra in environmental samples

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

Maxwell, Sherrod L.; Culligan, Brian K.

A new rapid method for the determination of {sup 228}Ra in natural water samples has been developed at the SRNL/EBL (Savannah River National Lab/ Environmental Bioassay Laboratory) that can be used for emergency response or routine samples. While gamma spectrometry can be employed with sufficient detection limits to determine {sup 228}Ra in solid samples (via {sup 228}Ac) , radiochemical methods that employ gas flow proportional counting techniques typically provide lower MDA (Minimal Detectable Activity) levels for the determination of {sup 228}Ra in water samples. Most radiochemical methods for {sup 228}Ra collect and purify {sup 228}Ra and allow for {sup 228}Acmore » daughter ingrowth for ~36 hours. In this new SRNL/EBL approach, {sup 228}Ac is collected and purified from the water sample without waiting to eliminate this delay. The sample preparation requires only about 4 hours so that {sup 228}Ra assay results on water samples can be achieved in < 6 hours. The method uses a rapid calcium carbonate precipitation enhanced with a small amount of phosphate added to enhance chemical yields (typically >90%), followed by rapid cation exchange removal of calcium. Lead, bismuth, uranium, thorium and protactinium isotopes are also removed by the cation exchange separation. {sup 228}Ac is eluted from the cation resin directly onto a DGA Resin cartridge attached to the bottom of the cation column to purify {sup 228}Ac. DGA Resin also removes lead and bismuth isotopes, along with Sr isotopes and {sup 90}Y. La is used to determine {sup 228}Ac chemical yield via ICP-MS, but {sup 133}Ba can also be used instead if ICP-MS assay is not available. Unlike some older methods, no lead or strontium holdback carriers or continual readjustment of sample pH is required.« less

SSAGES: Software Suite for Advanced General Ensemble Simulations.

PubMed

Sidky, Hythem; Colón, Yamil J; Helfferich, Julian; Sikora, Benjamin J; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S; Reid, Daniel R; Sevgen, Emre; Thapar, Vikram; Webb, Michael A; Whitmer, Jonathan K; de Pablo, Juan J

2018-01-28

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques-including adaptive biasing force, string methods, and forward flux sampling-that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

Improvement of light extraction of LYSO scintillator by using a combination of self-assembly of nanospheres and atomic layer deposition.

PubMed

Zhu, Zhichao; Liu, Bo; Zhang, Haifeng; Ren, Weina; Cheng, Chuanwei; Wu, Shuang; Gu, Mu; Chen, Hong

2015-03-23

The self-assembled monolayer periodic array of polystyrene spheres conformally coated with TiO₂ layer using atomic layer deposition is designed to obtain a further enhancement of light extraction for LYSO scintillator. The maximum enhancement is 149% for the sample with polystyrene spheres conformally coated with TiO₂ layer, while the enhancement is only 76% for the sample with only polystyrene spheres. Such further enhancement could be contributed from the additional modes forming by TiO₂ layer due to its high refractive index, which can be approved by the simulation of electric field distribution. The experimental results are agreement with the simulated results. Furthermore, the prepared structured layer exhibits an excellent combination with the surface of scintillator, which is in favor of the practical application. Therefore, it is safely concluded that the combination of self-assembly method and atomic layer deposition is a promising approach to obtain a significant enhancement of light extraction for a large area. This method can be extended to many other luminescent materials and devices.

Comparison of two filtration-elution procedures to improve the standard methods ISO 10705-1 & 2 for bacteriophage detection in groundwater, surface water and finished water samples.

PubMed

Helmi, K; Jacob, P; Charni-Ben-Tabassi, N; Delabre, K; Arnal, C

2011-09-01

To select a reliable method for bacteriophage concentration prior detection by culture from surface water, groundwater and drinking water to enhance the sensitivity of the standard methods ISO 10705-1 & 2. Artificially contaminated (groundwater and drinking water) and naturally contaminated (surface water) 1-litre samples were processed for bacteriophages detection. The spiked samples were inoculated with about 150 PFU of F-specific RNA bacteriophages and somatic coliphages using wastewater. Bacteriophage detection in the water samples was achieved using the standard method without and with a concentration step (electropositive Anodisc membrane or a pretreated electronegative Micro Filtration membrane, MF). For artificially contaminated matrices (drinking and ground waters), recovery rates using the concentration step were superior to 70% whilst analyses without concentration step mainly led to false negative results. Besides, the MF membrane presented higher performances compared with the Anodisc membrane. The concentration of a large volume of water (up to one litre) on a filter membrane avoids false negative results obtained by direct analysis as it allows detecting low number of bacteriophages in water samples. The addition of concentration step before applying the standard method could be useful to enhance the reliability of bacteriophages monitoring in water samples as bio-indicators to highlight faecal pollution. © No claim to French Government works. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

Transparency-enhancing technology allows three-dimensional assessment of gastrointestinal mucosa: A porcine model.

PubMed

Mizutani, Hiroya; Ono, Satoshi; Ushiku, Tetsuo; Kudo, Yotaro; Ikemura, Masako; Kageyama, Natsuko; Yamamichi, Nobutake; Fujishiro, Mitsuhiro; Someya, Takao; Fukayama, Masashi; Koike, Kazuhiko; Onodera, Hiroshi

2018-02-01

Although high-resolution three-dimensional imaging of endoscopically resected gastrointestinal specimens can help elucidating morphological features of gastrointestinal mucosa or tumor, there are no established methods to achieve this without breaking specimens apart. We evaluated the utility of transparency-enhancing technology for three-dimensional assessment of gastrointestinal mucosa in porcine models. Esophagus, stomach, and colon mucosa samples obtained from a sacrificed swine were formalin-fixed and paraffin-embedded, and subsequently deparaffinized for analysis. The samples were fluorescently stained, optically cleared using transparency-enhancing technology: ilLUmination of Cleared organs to IDentify target molecules method (LUCID), and visualized using laser scanning microscopy. After observation, all specimens were paraffin-embedded again and evaluated by conventional histopathological assessment to measure the impact of transparency-enhancing procedures. As a result, microscopic observation revealed horizontal section views of mucosa at deeper levels and enabled the three-dimensional image reconstruction of glandular and vascular structures. Besides, paraffin-embedded specimens after transparency-enhancing procedures were all assessed appropriately by conventional histopathological staining. These results suggest that transparency-enhancing technology may be feasible for clinical application and enable the three-dimensional structural analysis of endoscopic resected specimen non-destructively. Although there remain many limitations or problems to be solved, this promising technology might represent a novel histopathological method for evaluating gastrointestinal cancers. © 2018 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

Research on identification and determination of mixed pesticides in apples using surface enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Zhai, Chen; Li, Yongyu; Peng, Yankun; Xu, Tianfeng; Dhakal, Sagar; Chao, Kuanglin; Qin, Jianwei

2015-05-01

Residual pesticides in fruits and vegetables have become one of the major food safety concerns around the world. At present, routine analytical methods used for the determination of pesticide residue on the surface of fruits and vegetables are destructive, complex, time-consuming, high cost and not environmentally friendly. In this study, a novel Surface Enhanced Raman Spectroscopy (SERS) method with silver colloid was developed for fast and sensitive nondestructive detection of residual pesticides in fruits and vegetables by using a self-developed Raman system. SERS technology is a combination of Raman spectroscopy and nanotechnology. SERS can greatly enhance the Raman signal intensity, achieve single-molecule detection, and has a simple sample pre-treatment characteristic of high sensitivity and no damage; in recent years it has begun to be used in food safety testing research. In this study a rapid and sensitive method was developed to identify and analyze mixed pesticides of chlorpyrifos, deltamethrin and acetamiprid in apple samples by SERS. Silver colloid was used for SERS measurement by hydroxylamine hydrochloride reduced. The advantages of this method are seen in its fast preparation at room temperature, good reproducibility and immediate applicability. Raman spectrum is highly interfered by noise signals and fluorescence background, which make it too complex to get good result. In this study the noise signals and fluorescence background were removed by Savitzky-Golay filter and min-max signal adaptive zooming method. Under optimal conditions, pesticide residues in apple samples can be detected by SERS at 0.005 μg/cm2 and 0.002 μg/cm2 for individual acetamiprid and thiram, respectively. When mixing the two pesticides at low concentrations, their characteristic peaks can still be identified from the SERS spectrum of the mixture. Based on the synthesized material and its application in SERS operation, the method represents an ultrasensitive SERS performance in apple samples detection without sample pre-treatment, which indicates that it could be served as a useful means in monitoring pesticide residues.

Confocal Raman microscopic investigation of the effectiveness of penetration enhancers for procaine delivery to the skin

NASA Astrophysics Data System (ADS)

Lunter, Dominique; Daniels, Rolf

2014-12-01

A methodology that employs confocal Raman microscopy (CRM) on ex vivo skin samples is proposed for the investigation of drug content and distribution in the skin. To this end, the influence of the penetration enhancers propylene glycol and polyoxyethylene-23-lauryl ether on the penetration and permeation of procaine as a model substance was investigated. The drug content of skin samples that had been incubated with semisolid formulations containing one of these enhancers was examined after skin segmentation. The experiments showed that propylene glycol did not affect the procaine content that was delivered to the skin, whereas polyoxyethylene-23-lauryl ether led to higher procaine contents and deeper penetration. Neither substance was found to influence the permeation rate of procaine. It is thereby shown that CRM can provide additional information on drug penetration and permeation. Furthermore, the method was found to enhance the depth from which Raman spectra can be collected and to improve the depth resolution compared to previously proposed methods.

The morphological changes of optically cleared cochlea using optical coherence tomography (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Jaeyul; Song, Jaewon; Jeon, Mansik; Kim, Jeehyun

2017-02-01

In this study, we monitored the optical clearing effects by immersing ex vivo guinea pig cochlea samples in ethylenediaminetetraacetic acid (EDTA) to study the internal microstructures in the morphology of guinea pig cochlea. The imaging limitations due to the guinea pig cochlea structures were overcome by optical clearing technique. Subsequently, the study was carried out to confirm the required approximate immersing duration of cochlea in EDTA-based optical clearing to obtain the best optimal depth visibility for guinea pig cochlea samples. Thus, we implemented a decalcification-based optical clearing effect to guinea pig cochlea samples to enhance the depth visualization of internal microstructures using swept source optical coherence tomography (OCT). The obtained nondestructive two-dimensional OCT images successfully illustrated the feasibility of the proposed method by providing clearly visible microstructures in the depth direction as a result of decalcification. The most optimal clearing outcomes for the guinea pig cochlea were obtained after 14 consecutive days. The quantitative assessment results verified the increase of the intensity as well as the thickness measurements of the internal microstructures. Following this method, difficulties in imaging of internal cochlea microstructures of guinea pigs could be avoided. The obtained results verified that the depth visibility of the decalcified ex vivo guinea pig cochlea samples was enhanced. Therefore, the proposed EDTA-based optical clearing method for guinea pig can be considered as a potential application for depth-enhanced OCT visualization.

Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins.

PubMed

Walczewska-Szewc, Katarzyna; Deplazes, Evelyne; Corry, Ben

2015-07-14

Adequately sampling the large number of conformations accessible to proteins and other macromolecules is one of the central challenges in molecular dynamics (MD) simulations; this activity can be difficult, even for relatively simple systems. An example where this problem arises is in the simulation of dye-labeled proteins, which are now being widely used in the design and interpretation of Förster resonance energy transfer (FRET) experiments. In this study, MD simulations are used to characterize the motion of two commonly used FRET dyes attached to an immobilized chain of polyproline. Even in this simple system, the dyes exhibit complex behavior that is a mixture of fast and slow motions. Consequently, very long MD simulations are required to sufficiently sample the entire range of dye motion. Here, we compare the ability of enhanced sampling methods to reproduce the behavior of fluorescent labels on proteins. In particular, we compared Accelerated Molecular Dynamics (AMD), metadynamics, Replica Exchange Molecular Dynamics (REMD), and High Temperature Molecular Dynamics (HTMD) to equilibrium MD simulations. We find that, in our system, all of these methods improve the sampling of the dye motion, but the most significant improvement is achieved using REMD.

Lead (II) removal from natural soils by enhanced electrokinetic remediation.

PubMed

Altin, Ahmet; Degirmenci, Mustafa

2005-01-20

Electrokinetic remediation is a very effective method to remove metal from fine-grained soils having low adsorption and buffering capacity. However, remediation of soil having high alkali and adsorption capacity via the electrokinetic method is a very difficult process. Therefore, enhancement techniques are required for use in these soil types. In this study, the effect of the presence of minerals having high alkali and cation exchange capacity in natural soil polluted with lead (II) was investigated by means of the efficiency of electrokinetic remediation method. Natural soil samples containing clinoptilolite, gypsum and calcite minerals were used in experimental studies. Moreover, a sample containing kaolinite minerals was studied to compare with the results obtained from other samples. Best results for soils bearing alkali and high sorption capacity minerals were obtained upon addition of 3 mol AcH and application of 20 V constant potential after a remediation period of 220 h. In these test conditions, lead (II) removal efficiencies for these samples varied between 60% and 70% up to 0.55 normalized distance. Under the same conditions, removal efficiencies in kaolinite sample varied between 50% and 95% up to 0.9 normalized distance.

Application of surface enhanced Raman scattering and competitive adaptive reweighted sampling on detecting furfural dissolved in transformer oil

NASA Astrophysics Data System (ADS)

Chen, Weigen; Zou, Jingxin; Wan, Fu; Fan, Zhou; Yang, Dingkun

2018-03-01

Detecting the dissolving furfural in mineral oil is an essential technical method to evaluate the ageing condition of oil-paper insulation and the degradation of mechanical properties. Compared with the traditional detection method, Raman spectroscopy is obviously convenient and timesaving in operation. This study explored the method of applying surface enhanced Raman scattering (SERS) on quantitative analysis of the furfural dissolved in oil. Oil solution with different concentration of furfural were prepared and calibrated by high-performance liquid chromatography. Confocal laser Raman spectroscopy (CLRS) and SERS technology were employed to acquire Raman spectral data. Monte Carlo cross validation (MCCV) was used to eliminate the outliers in sample set, then competitive adaptive reweighted sampling (CARS) was developed to select an optimal combination of informative variables that most reflect the chemical properties of concern. Based on selected Raman spectral features, support vector machine (SVM) combined with particle swarm algorithm (PSO) was used to set up a furfural quantitative analysis model. Finally, the generalization ability and prediction precision of the established method were verified by the samples made in lab. In summary, a new spectral method is proposed to quickly detect furfural in oil, which lays a foundation for evaluating the ageing of oil-paper insulation in oil immersed electrical equipment.

Enhanced amperometric detection of metronidazole in drug formulations and urine samples based on chitosan protected tetrasulfonated copper phthalocyanine thin-film modified glassy carbon electrode.

PubMed

Meenakshi, S; Pandian, K; Jayakumari, L S; Inbasekaran, S

2016-02-01

An enhanced electrocatalytic reduction of metronidazole antibiotic drug molecule using chitosan protected tetrasulfonated copper phthalocyanine (Chit/CuTsPc) thin-film modified glassy carbon electrode (GCE) has been developed. An irreversible reduction occurs at -0.47V (vs. Ag/AgCl) using Chit/CuTsPc modified GCE. A maximum peak current value is obtained at pH1 and the electrochemical reduction reaction is a diffusion controlled one. The detection limit is found to be 0.41nM from differential pulse voltammetry (DPV) method. This present investigation method is adopted for electrochemical detection of metronidazole in drug formulation and urine samples by using DPV method. Copyright © 2015 Elsevier B.V. All rights reserved.

Enhanced Cleaning of Genesis Solar Wind Sample 61348 for Film Residue Removal

NASA Technical Reports Server (NTRS)

Allums, K. K.; Gonzalez, C. P.; Kuhlman, K. R.; Allton, J. H.

2015-01-01

The Genesis mission returned to Earth on September 8, 2004, experiencing a nonnominal reentry. During the recovery of the collector materials from the capsule, many of the collector fragments were placed on the adhesive protion of post-it notes to prevent the fragments from moving during transport back to Johnson Space Center. This unknowingly provided an additional contaminate that would prove difficult to remove with the limited chemistries allowed in the Genesis Curation Laboratory. Generally when collector material samples are prepared for allocation to PIs, the samples are cleaned front side only with Ultra-Pure Water (UPW) via megasonic dispersion to the collector surface to remove crash debris and contamination. While this cleaning method works well on samples that were not placed on post-its during recovery, it has caused movement of the residue on the back of the sample to be deposited on the front in at least two examples. Therefore, samples placed on the adhesive portion on post-it note, require enhanced cleaning methods since post-it residue has proved resistant to UPW cleaning.

Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis

NASA Astrophysics Data System (ADS)

Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

2017-08-01

In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH4+ strategy for ethylene and SO2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO2 from fruits. It was satisfied that trace ethylene and SO2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO2 during the entire LVCC sampling process were proved to be < 4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS.

Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis.

PubMed

Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

2017-08-05

In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH 4 + strategy for ethylene and SO 2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO 2 from fruits. It was satisfied that trace ethylene and SO 2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO 2 during the entire LVCC sampling process were proved to be <4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS. Copyright © 2017 Elsevier B.V. All rights reserved.

Antipsychotic drug poisoning monitoring of clozapine in urine by using coffee ring effect based surface-enhanced Raman spectroscopy.

PubMed

Zhu, Qingxia; Yu, Xiaoyan; Wu, Zebing; Lu, Feng; Yuan, Yongfang

2018-07-19

Antipsychotics are the drugs most often involved in drug poisoning cases, and therefore, therapeutic drug monitoring (TDM) is necessary for safe and effective medication administration of these drugs. In this study, a coffee ring effect-based surface-enhanced Raman spectroscopy (CRE-SERS) method was developed and successfully used to monitor antipsychotic poisoning by using urine samples for the first time. The established method exhibited excellent SERS performance since more hot spots were obtained in the "coffee ring". Using the optimized CRE-SERS method, the sensitivity was improved one order more than that of the conventional method with reasonable reproducibility. The antipsychotic drug clozapine (CLO) spiked into urine samples at 0.5-50 μg mL -1 was quantitatively detected, at concentrations above the thresholds for toxicity. The CRE-SERS method allowed CLO and its metabolites to be ultimately distinguished from real poisoning urine samples. The coffee-ring effect would provide more opportunities for practical applications of the SERS-based method. The frequent occurrence of drug poisoning may have created a new area for the application of the CRE-SERS method. It is anticipated that the developed method will also have great potential for other drug poisoning monitoring. Copyright © 2018 Elsevier B.V. All rights reserved.

Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics

PubMed Central

Wu, Xiongwu; Damjanovic, Ana; Brooks, Bernard R.

2013-01-01

This review provides a comprehensive description of the self-guided Langevin dynamics (SGLD) and the self-guided molecular dynamics (SGMD) methods and their applications. Example systems are included to provide guidance on optimal application of these methods in simulation studies. SGMD/SGLD has enhanced ability to overcome energy barriers and accelerate rare events to affordable time scales. It has been demonstrated that with moderate parameters, SGLD can routinely cross energy barriers of 20 kT at a rate that molecular dynamics (MD) or Langevin dynamics (LD) crosses 10 kT barriers. The core of these methods is the use of local averages of forces and momenta in a direct manner that can preserve the canonical ensemble. The use of such local averages results in methods where low frequency motion “borrows” energy from high frequency degrees of freedom when a barrier is approached and then returns that excess energy after a barrier is crossed. This self-guiding effect also results in an accelerated diffusion to enhance conformational sampling efficiency. The resulting ensemble with SGLD deviates in a small way from the canonical ensemble, and that deviation can be corrected with either an on-the-fly or a post processing reweighting procedure that provides an excellent canonical ensemble for systems with a limited number of accelerated degrees of freedom. Since reweighting procedures are generally not size extensive, a newer method, SGLDfp, uses local averages of both momenta and forces to preserve the ensemble without reweighting. The SGLDfp approach is size extensive and can be used to accelerate low frequency motion in large systems, or in systems with explicit solvent where solvent diffusion is also to be enhanced. Since these methods are direct and straightforward, they can be used in conjunction with many other sampling methods or free energy methods by simply replacing the integration of degrees of freedom that are normally sampled by MD or LD. PMID:23913991

Equilibrium Molecular Thermodynamics from Kirkwood Sampling

PubMed Central

2015-01-01

We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys.2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide. PMID:25915525

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.

PubMed

Hansen, Halvor S; Daura, Xavier; Hünenberger, Philippe H

2010-09-14

A new method, fragment-based local elevation umbrella sampling (FB-LEUS), is proposed to enhance the conformational sampling in explicit-solvent molecular dynamics (MD) simulations of solvated polymers. The method is derived from the local elevation umbrella sampling (LEUS) method [ Hansen and Hünenberger , J. Comput. Chem. 2010 , 31 , 1 - 23 ], which combines the local elevation (LE) conformational searching and the umbrella sampling (US) conformational sampling approaches into a single scheme. In LEUS, an initial (relatively short) LE build-up (searching) phase is used to construct an optimized (grid-based) biasing potential within a subspace of conformationally relevant degrees of freedom, which is then frozen and used in a (comparatively longer) US sampling phase. This combination dramatically enhances the sampling power of MD simulations but, due to computational and memory costs, is only applicable to relevant subspaces of low dimensionalities. As an attempt to expand the scope of the LEUS approach to solvated polymers with more than a few relevant degrees of freedom, the FB-LEUS scheme involves an US sampling phase that relies on a superposition of low-dimensionality biasing potentials optimized using LEUS at the fragment level. The feasibility of this approach is tested using polyalanine (poly-Ala) and polyvaline (poly-Val) oligopeptides. Two-dimensional biasing potentials are preoptimized at the monopeptide level, and subsequently applied to all dihedral-angle pairs within oligopeptides of 4,  6,  8, or 10 residues. Two types of fragment-based biasing potentials are distinguished: (i) the basin-filling (BF) potentials act so as to "fill" free-energy basins up to a prescribed free-energy level above the global minimum; (ii) the valley-digging (VD) potentials act so as to "dig" valleys between the (four) free-energy minima of the two-dimensional maps, preserving barriers (relative to linearly interpolated free-energy changes) of a prescribed magnitude. The application of these biasing potentials may lead to an impressive enhancement of the searching power (volume of conformational space visited in a given amount of simulation time). However, this increase is largely offset by a deterioration of the statistical efficiency (representativeness of the biased ensemble in terms of the conformational distribution appropriate for the physical ensemble). As a result, it appears difficult to engineer FB-LEUS schemes representing a significant improvement over plain MD, at least for the systems considered here.

Enhanced conformational sampling via novel variable transformations and very large time-step molecular dynamics

NASA Astrophysics Data System (ADS)

Tuckerman, Mark

2006-03-01

One of the computational grand challenge problems is to develop methodology capable of sampling conformational equilibria in systems with rough energy landscapes. If met, many important problems, most notably protein folding, could be significantly impacted. In this talk, two new approaches for addressing this problem will be presented. First, it will be shown how molecular dynamics can be combined with a novel variable transformation designed to warp configuration space in such a way that barriers are reduced and attractive basins stretched. This method rigorously preserves equilibrium properties while leading to very large enhancements in sampling efficiency. Extensions of this approach to the calculation/exploration of free energy surfaces will be discussed. Next, a new very large time-step molecular dynamics method will be introduced that overcomes the resonances which plague many molecular dynamics algorithms. The performance of the methods is demonstrated on a variety of systems including liquid water, long polymer chains simple protein models, and oligopeptides.

Ultrasound-assisted surfactant-enhanced emulsification microextraction based on the solidification of a floating organic droplet used for the simultaneous determination of six fungicide residues in juices and red wine.

PubMed

You, Xiangwei; Wang, Suli; Liu, Fengmao; Shi, Kaiwei

2013-07-26

A novel ultrasound-assisted surfactant-enhanced emulsification microextraction technique based on the solidification of a floating organic droplet followed by high performance liquid chromatography with diode array detection was developed for simultaneous determination of six fungicide residues in juices and red wine samples. The low-toxicity solvent, 1-dodecanol, was used as an extraction solvent. For its low density and proper melting point near room temperature, the extractant droplet was collected easily by solidifying it at a low temperature. The surfactant, Tween 80, was used as an emulsifier to enhance the dispersion of the water-immiscible extraction solvent into an aqueous phase, which hastened the mass-transfer of the analytes. Organic dispersive solvent typically required in common dispersive liquid-liquid microextraction methods was not used in the proposed method. Some parameters (e.g., the type and volume of extraction solvent, the type and concentration of surfactant, ultrasound extraction time, salt addition, and volume of samples) that affect the extraction efficiency were optimized. The proposed method showed a good linearity within the range of 5μgL(-1)-1000μgL(-1), with the correlation coefficients (γ) higher than 0.9969. The limits of detection for the method ranged from 0.4μgL(-1) to 1.4μgL(-1). Further, this simple, practical, sensitive, and environmentally friendly method was successfully applied to determine the target fungicides in juice and red wine samples. The recoveries of the target fungicides in red wine and fruit juice samples were 79.5%-113.4%, with relative standard deviations that ranged from 0.4% to 12.3%. Copyright © 2013 Elsevier B.V. All rights reserved.

Polarization Sensitive Coherent Anti-Stokes Raman Spectroscopy of DCVJ in Doped Polymer

NASA Astrophysics Data System (ADS)

Ujj, Laszlo

2014-05-01

Coherent Raman Microscopy is an emerging technic and method to image biological samples such as living cells by recording vibrational fingerprints of molecules with high spatial resolution. The race is on to record the entire image during the shortest time possible in order to increase the time resolution of the recorded cellular events. The electronically enhanced polarization sensitive version of Coherent anti-Stokes Raman scattering is one of the method which can shorten the recording time and increase the sharpness of an image by enhancing the signal level of special molecular vibrational modes. In order to show the effectiveness of the method a model system, a highly fluorescence sample, DCVJ in a polymer matrix is investigated. Polarization sensitive resonance CARS spectra are recorded and analyzed. Vibrational signatures are extracted with model independent methods. Details of the measurements and data analysis will be presented. The author gratefully acknowledge the UWF for financial support.

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.

PubMed

Kasahara, Kota; Ma, Benson; Goto, Kota; Dasgupta, Bhaskar; Higo, Junichi; Fukuda, Ikuo; Mashimo, Tadaaki; Akiyama, Yutaka; Nakamura, Haruki

2016-01-01

Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named "myPresto/omegagene" that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods, e.g. , the virtual-system-coupled multi-canonical MD (V-McMD) method, replace a multi-process parallelized run with multiple independent runs to avoid inter-node communication overhead. In addition, adopting the non-Ewald-based zero-multipole summation method (ZMM) makes it possible to eliminate the Fourier space calculations altogether. The combination of these state-of-the-art techniques realizes efficient and accurate calculations of the conformational ensemble at an equilibrium state. By taking these advantages, myPresto/omegagene is specialized for the single process execution with Graphics Processing Unit (GPU). We performed benchmark simulations for the 20-mer peptide, Trp-cage, with explicit solvent. One of the most thermodynamically stable conformations generated by the V-McMD simulation is very similar to an experimentally solved native conformation. Furthermore, the computation speed is four-times faster than that of our previous simulation engine, myPresto/psygene-G. The new simulator, myPresto/omegagene, is freely available at the following URLs: http://www.protein.osaka-u.ac.jp/rcsfp/pi/omegagene/ and http://presto.protein.osaka-u.ac.jp/myPresto4/.

Enhanced photoelectrochemical and photocatalytic activity in visible-light-driven Ag/BiVO{sub 4} inverse opals

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

Fang, Liang, E-mail: lfang@suda.edu.cn, E-mail: dawei.cao@tu-ilmenau.de; Nan, Feng; Yang, Ying

2016-02-29

BiVO{sub 4} photonic crystal inverse opals (io-BiVO{sub 4}) with highly dispersed Ag nanoparticles (NPs) were prepared by the nanosphere lithography method combining the pulsed current deposition method. The incorporation of the Ag NPs can significantly improve the photoelectrochemical and photocatalytic activity of BiVO{sub 4} inverse opals in the visible light region. The photocurrent density of the Ag/io-BiVO{sub 4} sample is 4.7 times higher than that of the disordered sample without the Ag NPs, while the enhancement factor of the corresponding kinetic constant in photocatalytic experiment is approximately 3. The improved photoelectrochemical and photocatalytic activity is benefited from two reasons: onemore » is the enhanced light harvesting owing to the coupling between the slow light and localized surface plasmon resonance effect; the other is the efficient separation of charge carriers due to the Schottky barriers.« less

[Application of surface-enhanced Raman spectra to the analysis of Chinese Ephedra soup medicines].

PubMed

Zhang, J; Wang, Y

1998-06-01

A new method was developed to analyse the spectra of ephedrine in Chinese ephedra soup medicines, using surface-enhanced technique to combine thin layer chromatographic (TLC) technique with surface-enhanced Raman spectroscopy (SERS). The study indicates that the main vibrant characteristic spec tral band of the ephedrine molecules can be obtained by TLC in the samples of about 8 microg, and expounds char acteristics of the sample molecules and the silica gel. Therefore, it is clarified that the main chemical composi tion of Chinese medicines can be carried as finger-print type appraisal by combining TLC and SERS.

Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.

PubMed

Abella, Jayvee R; Moll, Mark; Kavraki, Lydia E

2018-01-01

The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational sampling, and several of these algorithms promote diversity by keeping track of "coverage" in conformational space based on the local sampling density. However, large proteins present special challenges. In particular, larger systems require running many concurrent instances of these algorithms, but these algorithms can quickly become memory intensive because they typically keep previously sampled conformations in memory to maintain coverage estimates. In addition, robotics-inspired algorithms depend on defining useful perturbation strategies for exploring the conformational space, which is a difficult task for large proteins because such systems are typically more constrained and exhibit complex motions. In this article, we introduce two methodologies for maintaining and enhancing diversity in robotics-inspired conformational sampling. The first method addresses algorithms based on coverage estimates and leverages the use of a low-dimensional projection to define a global coverage grid that maintains coverage across concurrent runs of sampling. The second method is an automatic definition of a perturbation strategy through readily available flexibility information derived from B-factors, secondary structure, and rigidity analysis. Our results show a significant increase in the diversity of the conformations sampled for proteins consisting of up to 500 residues when applied to a specific robotics-inspired algorithm for conformational sampling. The methodologies presented in this article may be vital components for the scalability of robotics-inspired approaches.

Enhancement of low sampling frequency recordings for ECG biometric matching using interpolation.

PubMed

Sidek, Khairul Azami; Khalil, Ibrahim

2013-01-01

Electrocardiogram (ECG) based biometric matching suffers from high misclassification error with lower sampling frequency data. This situation may lead to an unreliable and vulnerable identity authentication process in high security applications. In this paper, quality enhancement techniques for ECG data with low sampling frequency has been proposed for person identification based on piecewise cubic Hermite interpolation (PCHIP) and piecewise cubic spline interpolation (SPLINE). A total of 70 ECG recordings from 4 different public ECG databases with 2 different sampling frequencies were applied for development and performance comparison purposes. An analytical method was used for feature extraction. The ECG recordings were segmented into two parts: the enrolment and recognition datasets. Three biometric matching methods, namely, Cross Correlation (CC), Percent Root-Mean-Square Deviation (PRD) and Wavelet Distance Measurement (WDM) were used for performance evaluation before and after applying interpolation techniques. Results of the experiments suggest that biometric matching with interpolated ECG data on average achieved higher matching percentage value of up to 4% for CC, 3% for PRD and 94% for WDM. These results are compared with the existing method when using ECG recordings with lower sampling frequency. Moreover, increasing the sample size from 56 to 70 subjects improves the results of the experiment by 4% for CC, 14.6% for PRD and 0.3% for WDM. Furthermore, higher classification accuracy of up to 99.1% for PCHIP and 99.2% for SPLINE with interpolated ECG data as compared of up to 97.2% without interpolation ECG data verifies the study claim that applying interpolation techniques enhances the quality of the ECG data. Crown Copyright © 2012. Published by Elsevier Ireland Ltd. All rights reserved.

New method of extracting information of arterial oxygen saturation based on ∑ | 𝚫 |

NASA Astrophysics Data System (ADS)

Dai, Wenting; Lin, Ling; Li, Gang

2017-04-01

Noninvasive detection of oxygen saturation with near-infrared spectroscopy has been widely used in clinics. In order to further enhance its detection precision and reliability, this paper proposes a method of time domain absolute difference summation (∑|Δ|) based on a dynamic spectrum. In this method, the ratio of absolute differences between intervals of two differential sampling points at the same moment on logarithm photoplethysmography signals of red and infrared light was obtained in turn, and then they obtained a ratio sequence which was screened with a statistical method. Finally, use the summation of the screened ratio sequence as the oxygen saturation coefficient Q. We collected 120 reference samples of SpO2 and then compared the result of two methods, which are ∑|Δ| and peak-peak. Average root-mean-square errors of the two methods were 3.02% and 6.80%, respectively, in the 20 cases which were selected randomly. In addition, the average variance of Q of the 10 samples, which were obtained by the new method, reduced to 22.77% of that obtained by the peak-peak method. Comparing with the commercial product, the new method makes the results more accurate. Theoretical and experimental analysis indicates that the application of the ∑|Δ| method could enhance the precision and reliability of oxygen saturation detection in real time.

New method of extracting information of arterial oxygen saturation based on ∑|𝚫 |

NASA Astrophysics Data System (ADS)

Wenting, Dai; Ling, Lin; Gang, Li

2017-04-01

Noninvasive detection of oxygen saturation with near-infrared spectroscopy has been widely used in clinics. In order to further enhance its detection precision and reliability, this paper proposes a method of time domain absolute difference summation (∑|Δ|) based on a dynamic spectrum. In this method, the ratio of absolute differences between intervals of two differential sampling points at the same moment on logarithm photoplethysmography signals of red and infrared light was obtained in turn, and then they obtained a ratio sequence which was screened with a statistical method. Finally, use the summation of the screened ratio sequence as the oxygen saturation coefficient Q. We collected 120 reference samples of SpO2 and then compared the result of two methods, which are ∑|Δ| and peak-peak. Average root-mean-square errors of the two methods were 3.02% and 6.80%, respectively, in the 20 cases which were selected randomly. In addition, the average variance of Q of the 10 samples, which were obtained by the new method, reduced to 22.77% of that obtained by the peak-peak method. Comparing with the commercial product, the new method makes the results more accurate. Theoretical and experimental analysis indicates that the application of the ∑|Δ| method could enhance the precision and reliability of oxygen saturation detection in real time.

Enhanced Conformational Sampling of N-Glycans in Solution with Replica State Exchange Metadynamics.

PubMed

Galvelis, Raimondas; Re, Suyong; Sugita, Yuji

2017-05-09

Molecular dynamics (MD) simulation of a N-glycan in solution is challenging because of high-energy barriers of the glycosidic linkages, functional group rotational barriers, and numerous intra- and intermolecular hydrogen bonds. In this study, we apply different enhanced conformational sampling approaches, namely, metadynamics (MTD), the replica-exchange MD (REMD), and the recently proposed replica state exchange MTD (RSE-MTD), to a N-glycan in solution and compare the conformational sampling efficiencies of the approaches. MTD helps to cross the high-energy barrier along the ω angle by utilizing a bias potential, but it cannot enhance sampling of the other degrees of freedom. REMD ensures moderate-energy barrier crossings by exchanging temperatures between replicas, while it hardly crosses the barriers along ω. In contrast, RSE-MTD succeeds to cross the high-energy barrier along ω as well as to enhance sampling of the other degrees of freedom. We tested two RSE-MTD schemes: in one scheme, 64 replicas were simulated with the bias potential along ω at different temperatures, while simulations of four replicas were performed with the bias potentials for different CVs at 300 K. In both schemes, one unbiased replica at 300 K was included to compute conformational properties of the glycan. The conformational sampling of the former is better than the other enhanced sampling methods, while the latter shows reasonable performance without spending large computational resources. The latter scheme is likely to be useful when a N-glycan-attached protein is simulated.

Adaptive enhanced sampling by force-biasing using neural networks

NASA Astrophysics Data System (ADS)

Guo, Ashley Z.; Sevgen, Emre; Sidky, Hythem; Whitmer, Jonathan K.; Hubbell, Jeffrey A.; de Pablo, Juan J.

2018-04-01

A machine learning assisted method is presented for molecular simulation of systems with rugged free energy landscapes. The method is general and can be combined with other advanced sampling techniques. In the particular implementation proposed here, it is illustrated in the context of an adaptive biasing force approach where, rather than relying on discrete force estimates, one can resort to a self-regularizing artificial neural network to generate continuous, estimated generalized forces. By doing so, the proposed approach addresses several shortcomings common to adaptive biasing force and other algorithms. Specifically, the neural network enables (1) smooth estimates of generalized forces in sparsely sampled regions, (2) force estimates in previously unexplored regions, and (3) continuous force estimates with which to bias the simulation, as opposed to biases generated at specific points of a discrete grid. The usefulness of the method is illustrated with three different examples, chosen to highlight the wide range of applicability of the underlying concepts. In all three cases, the new method is found to enhance considerably the underlying traditional adaptive biasing force approach. The method is also found to provide improvements over previous implementations of neural network assisted algorithms.

Method and apparatus for generating motor current spectra to enhance motor system fault detection

DOEpatents

Linehan, Daniel J.; Bunch, Stanley L.; Lyster, Carl T.

1995-01-01

A method and circuitry for sampling periodic amplitude modulations in a nonstationary periodic carrier wave to determine frequencies in the amplitude modulations. The method and circuit are described in terms of an improved motor current signature analysis. The method insures that the sampled data set contains an exact whole number of carrier wave cycles by defining the rate at which samples of motor current data are collected. The circuitry insures that a sampled data set containing stationary carrier waves is recreated from the analog motor current signal containing nonstationary carrier waves by conditioning the actual sampling rate to adjust with the frequency variations in the carrier wave. After the sampled data is transformed to the frequency domain via the Discrete Fourier Transform, the frequency distribution in the discrete spectra of those components due to the carrier wave and its harmonics will be minimized so that signals of interest are more easily analyzed.

Novel Electrosorption-Enhanced Solid-Phase Microextraction Device for Ultrafast In Vivo Sampling of Ionized Pharmaceuticals in Fish.

PubMed

Qiu, Junlang; Wang, Fuxin; Zhang, Tianlang; Chen, Le; Liu, Yuan; Zhu, Fang; Ouyang, Gangfeng

2018-01-02

Decreasing the tedious sample preparation duration is one of the most important concerns for the environmental analytical chemistry especially for in vivo experiments. However, due to the slow mass diffusion paths for most of the conventional methods, ultrafast in vivo sampling remains challenging. Herein, for the first time, we report an ultrafast in vivo solid-phase microextraction (SPME) device based on electrosorption enhancement and a novel custom-made CNT@PPY@pNE fiber for in vivo sampling of ionized acidic pharmaceuticals in fish. This sampling device exhibited an excellent robustness, reproducibility, matrix effect-resistant capacity, and quantitative ability. Importantly, the extraction kinetics of the targeted ionized pharmaceuticals were significantly accelerated using the device, which significantly improved the sensitivity of the SPME in vivo sampling method (limits of detection ranged from 0.12 ng·g -1 to 0.25 ng·g -1 ) and shorten the sampling time (only 1 min). The proposed approach was successfully applied to monitor the concentrations of ionized pharmaceuticals in living fish, which demonstrated that the device and fiber were suitable for ultrafast in vivo sampling and continuous monitoring. In addition, the bioconcentration factor (BCF) values of the pharmaceuticals were derived in tilapia (Oreochromis mossambicus) for the first time, based on the data of ultrafast in vivo sampling. Therefore, we developed and validated an effective and ultrafast SPME sampling device for in vivo sampling of ionized analytes in living organisms and this state-of-the-art method provides an alternative technique for future in vivo studies.

Enhanced photoconductivity by melt quenching method for amorphous organic photorefractive materials

NASA Astrophysics Data System (ADS)

Tsujimura, S.; Fujihara, T.; Sassa, T.; Kinashi, K.; Sakai, W.; Ishibashi, K.; Tsutsumi, N.

2014-10-01

For many optical semiconductor fields of study, the high photoconductivity of amorphous organic semiconductors has strongly been desired, because they make the manufacture of high-performance devices easy when controlling charge carrier transport and trapping is otherwise difficult. This study focuses on the correlation between photoconductivity and bulk state in amorphous organic photorefractive materials to probe the nature of the performance of photoconductivity and to enhance the response time and diffraction efficiency of photorefractivity. The general cooling processes of the quenching method achieved enhanced photoconductivity and a decreased filling rate for shallow traps. Therefore, sample processing, which was quenching in the present case, for photorefractive composites significantly relates to enhanced photorefractivity.

Exploring protein kinase conformation using swarm-enhanced sampling molecular dynamics.

PubMed

Atzori, Alessio; Bruce, Neil J; Burusco, Kepa K; Wroblowski, Berthold; Bonnet, Pascal; Bryce, Richard A

2014-10-27

Protein plasticity, while often linked to biological function, also provides opportunities for rational design of selective and potent inhibitors of their function. The application of computational methods to the prediction of concealed protein concavities is challenging, as the motions involved can be significant and occur over long time scales. Here we introduce the swarm-enhanced sampling molecular dynamics (sesMD) method as a tool to improve sampling of conformational landscapes. In this approach, a swarm of replica simulations interact cooperatively via a set of pairwise potentials incorporating attractive and repulsive components. We apply the sesMD approach to explore the conformations of the DFG motif in the protein p38α mitogen-activated protein kinase. In contrast to multiple MD simulations, sesMD trajectories sample a range of DFG conformations, some of which map onto existing crystal structures. Simulated structures intermediate between the DFG-in and DFG-out conformations are predicted to have druggable pockets of interest for structure-based ligand design.

Enhanced Genetic Analysis of Single Human Bioparticles Recovered by Simplified Micromanipulation from Forensic ‘Touch DNA’ Evidence

PubMed Central

Farash, Katherine; Hanson, Erin K.; Ballantyne, Jack

2015-01-01

DNA profiles can be obtained from ‘touch DNA’ evidence, which comprises microscopic traces of human biological material. Current methods for the recovery of trace DNA employ cotton swabs or adhesive tape to sample an area of interest. However, such a ‘blind-swabbing’ approach will co-sample cellular material from the different individuals, even if the individuals’ cells are located in geographically distinct locations on the item. Thus, some of the DNA mixtures encountered in touch DNA samples are artificially created by the swabbing itself. In some instances, a victim’s DNA may be found in significant excess thus masking any potential perpetrator’s DNA. In order to circumvent the challenges with standard recovery and analysis methods, we have developed a lower cost, ‘smart analysis’ method that results in enhanced genetic analysis of touch DNA evidence. We describe an optimized and efficient micromanipulation recovery strategy for the collection of bio-particles present in touch DNA samples, as well as an enhanced amplification strategy involving a one-step 5 µl microvolume lysis/STR amplification to permit the recovery of STR profiles from the bio-particle donor(s). The use of individual or few (i.e., “clumps”) bioparticles results in the ability to obtain single source profiles. These procedures represent alternative enhanced techniques for the isolation and analysis of single bioparticles from forensic touch DNA evidence. While not necessary in every forensic investigation, the method could be highly beneficial for the recovery of a single source perpetrator DNA profile in cases involving physical assault (e.g., strangulation) that may not be possible using standard analysis techniques. Additionally, the strategies developed here offer an opportunity to obtain genetic information at the single cell level from a variety of other non-forensic trace biological material. PMID:25867046

Near real time vapor detection and enhancement using aerosol adsorption

DOEpatents

Novick, Vincent J.; Johnson, Stanley A.

1999-01-01

A vapor sample detection method where the vapor sample contains vapor and ambient air and surrounding natural background particles. The vapor sample detection method includes the steps of generating a supply of aerosol that have a particular effective median particle size, mixing the aerosol with the vapor sample forming aerosol and adsorbed vapor suspended in an air stream, impacting the suspended aerosol and adsorbed vapor upon a reflecting element, alternatively directing infrared light to the impacted aerosol and adsorbed vapor, detecting and analyzing the alternatively directed infrared light in essentially real time using a spectrometer and a microcomputer and identifying the vapor sample.

Near real time vapor detection and enhancement using aerosol adsorption

DOEpatents

Novick, V.J.; Johnson, S.A.

1999-08-03

A vapor sample detection method is described where the vapor sample contains vapor and ambient air and surrounding natural background particles. The vapor sample detection method includes the steps of generating a supply of aerosol that have a particular effective median particle size, mixing the aerosol with the vapor sample forming aerosol and adsorbed vapor suspended in an air stream, impacting the suspended aerosol and adsorbed vapor upon a reflecting element, alternatively directing infrared light to the impacted aerosol and adsorbed vapor, detecting and analyzing the alternatively directed infrared light in essentially real time using a spectrometer and a microcomputer and identifying the vapor sample. 13 figs.

Use of Body-Mounted Cameras to Enhance Data Collection: An Evaluation of Two Arthropod Sampling Techniques.

PubMed

Hagler, James R; Thompson, Alison L; Stefanek, Melissa A; Machtley, Scott A

2018-03-01

A study was conducted that compared the effectiveness of a sweepnet versus a vacuum suction device for collecting arthropods in cotton. The study differs from previous research in that body-mounted action cameras (B-MACs) were used to record the activity of the person conducting the arthropod collections. The videos produced by the B-MACs were then analyzed with behavioral event recording software to quantify various aspects of the sampling process. The sampler's speed and the number of sampling sweeps or vacuum suctions taken over a fixed distance (12.2 m) of cotton were two of the more significant sampling characteristics quantified for each method. The arthropod counts obtained, combined with the analyses of the videos, enabled us to estimate arthropod sampling efficiency for each technique based on fixed distance, time, and sample unit measurements. Data revealed that the vacuuming was the most precise method for collecting arthropods in the relatively small cotton research plots. However, data also indicates that the sweepnet method would be more efficient for collecting most of the cotton-dwelling arthropod taxa, especially if the sampler could continuously sweep for at least 1 min or ≥80 m (e.g., in larger research plots). The B-MACs are inexpensive and non-cumbersome, the video images generated are outstanding, and they can be archived to provide permanent documentation of a research project. The methods described here could be useful for other types of field-based research to enhance data collection efficiency.

Metal-enhanced fluorescence exciplex emission.

PubMed

Zhang, Yongxia; Mali, Buddha L; Geddes, Chris D

2012-01-01

In this letter, we report the first observation of metal-enhanced exciplex fluorescence, observed from anthracene in the presence of diethylaniline. Anthracene in the presence of diethylaniline in close proximity to Silver Island Films (SIFs) shows enhanced monomer and exciplex emission as compared to a non-silvered control sample containing no silver nanoparticles. Our findings suggest two complementary methods for the enhancement: (i) surface plasmons can radiate coupled monomer and exciplex fluorescence efficiently, and (ii) enhanced absorption (enhanced electric near-field) further facilitates enhanced emission. Our exciplex studies help us to further understand the complex photophysics of the metal-enhanced fluorescence technology. Copyright © 2011 Elsevier B.V. All rights reserved.

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

PubMed

Mishra, Sushil Kumar; Kara, Mahmut; Zacharias, Martin; Koca, Jaroslav

2014-01-01

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

A general method for bead-enhanced quantitation by flow cytometry

PubMed Central

Montes, Martin; Jaensson, Elin A.; Orozco, Aaron F.; Lewis, Dorothy E.; Corry, David B.

2009-01-01

Flow cytometry provides accurate relative cellular quantitation (percent abundance) of cells from diverse samples, but technical limitations of most flow cytometers preclude accurate absolute quantitation. Several quantitation standards are now commercially available which, when added to samples, permit absolute quantitation of CD4+ T cells. However, these reagents are limited by their cost, technical complexity, requirement for additional software and/or limited applicability. Moreover, few studies have validated the use of such reagents in complex biological samples, especially for quantitation of non-T cells. Here we show that addition to samples of known quantities of polystyrene fluorescence standardization beads permits accurate quantitation of CD4+ T cells from complex cell samples. This procedure, here termed single bead-enhanced cytofluorimetry (SBEC), was equally capable of enumerating eosinophils as well as subcellular fragments of apoptotic cells, moieties with very different optical and fluorescent characteristics. Relative to other proprietary products, SBEC is simple, inexpensive and requires no special software, suggesting that the method is suitable for the routine quantitation of most cells and other particles by flow cytometry. PMID:17067632

Method and apparatus for determining nutrient stimulation of biological processes

DOEpatents

Colwell, F.S.; Geesey, G.G.; Gillis, R.J.; Lehman, R.M.

1997-11-11

A method and apparatus is described for determining the nutrients to stimulate microorganisms in a particular environment. A representative sample of microorganisms from a particular environment are contacted with multiple support means wherein each support means has intimately associated with the surface of the support means a different nutrient composition for said microorganisms in said sample. The multiple support means is allowed to remain in contact with the microorganisms in the sample for a time period sufficient to measure differences in microorganism effects for the multiple support means. Microorganism effects for the multiple support means are then measured and compared. The invention is particularly adaptable to being conducted in situ. The additional steps of regulating nutrients added to the particular environment of microorganisms can enhance the desired results. Biological systems particularly suitable for this invention are bioremediation, biologically enhanced oil recovery, biological leaching of metals, and agricultural bioprocesses. 5 figs.

Method and apparatus for determining nutrient stimulation of biological processes

DOEpatents

Colwell, Frederick S.; Geesey, Gill G.; Gillis, Richard J.; Lehman, R. Michael

1999-01-01

A method and apparatus for determining the nutrients to stimulate microorganisms in a particular environment. A representative sample of microorganisms from a particular environment are contacted with multiple support means wherein each support means has intimately associated with the surface of the support means a different nutrient composition for said microorganisms in said sample. The multiple support means is allowed to remain in contact with the microorganisms in the sample for a time period sufficient to measure difference in microorganism effects for the multiple support means. Microorganism effects for the multiple support means are then measured and compared. The invention is particularly adaptable to being conducted in situ. The additional steps of regulating nutrients added to the particular environment of microorganisms can enhance the desired results. Biological systems particularly suitable for this invention are bioremediation, biologically enhanced oil recovery, biological leaching of metals, and agricultural bioprocesses.

Method and apparatus for determining nutrient stimulation of biological processes

DOEpatents

Colwell, F.S.; Geesey, G.G.; Gillis, R.J.; Lehman, R.M.

1999-07-13

A method and apparatus are disclosed for determining the nutrients to stimulate microorganisms in a particular environment. A representative sample of microorganisms from a particular environment are contacted with multiple support means wherein each support means has intimately associated with the surface of the support means a different nutrient composition for microorganisms in the sample. The multiple support means is allowed to remain in contact with the microorganisms in the sample for a time period sufficient to measure difference in microorganism effects for the multiple support means. Microorganism effects for the multiple support means are then measured and compared. The invention is particularly adaptable to being conducted in situ. The additional steps of regulating nutrients added to the particular environment of microorganisms can enhance the desired results. Biological systems particularly suitable for this invention are bioremediation, biologically enhanced oil recovery, biological leaching of metals, and agricultural bioprocesses. 5 figs.

Method and apparatus for determining nutrient stimulation of biological processes

DOEpatents

Colwell, Frederick S.; Geesey, Gill G.; Gillis, Richard J.; Lehman, R. Michael

1997-01-01

A method and apparatus for determining the nutrients to stimulate microorganisms in a particular environment. A representative sample of microorganisms from a particular environment are contacted with multiple support means wherein each support means has intimately associated with the surface of the support means a different nutrient composition for said microorganisms in said sample. The multiple support means is allowed to remain in contact with the microorganisms in the sample for a time period sufficient to measure differences in microorganism effects for the multiple support means. Microorganism effects for the multiple support means are then measured and compared. The invention is particularly adaptable to being conducted in situ. The additional steps of regulating nutrients added to the particular environment of microorganisms can enhance the desired results. Biological systems particularly suitable for this invention are bioremediation, biologically enhanced oil recovery, biological leaching of metals, and agricultural bioprocesses.

Signal enhancement for gradient reverse-phase high-performance liquid chromatography-electrospray ionization mass spectrometry analysis with trifluoroacetic and other strong acid modifiers by postcolumn addition of propionic acid and isopropanol.

PubMed

Kuhlmann, F E; Apffel, A; Fischer, S M; Goldberg, G; Goodley, P C

1995-12-01

Trifluoroacetic acid (TFA) and other volatile strong acids, used as modifiers in reverse-phase high-performance liquid chromatography, cause signal suppression for basic compounds when analyzed by electrospray ionization mass spectrometry (ESI-MS). Evidence is presented that signal suppression is caused by strong ion pairing between the TFA anion and the protonated sample cation of basic sample molecules. The ion-pairing process "masks" the protonated sample cations from the ESI-MS electric fields by rendering them "neutral. " Weakly basic molecules are not suppressed by this process. The TFA signal suppression effect is independent from the well-known spray problem that electrospray has with highly aqueous solutions that contain TFA. This previously reported spray problem is caused by the high conductivity and surface tension of aqueous TFA solutions. A practical method to enhance the signal for most basic analytes in the presence of signal-suppressing volatile strong acids has been developed. The method employs postcolumn addition of a solution of 75% propionic acid and 25% isopropanol in a ratio 1:2 to the column flow. Signal enhancement is typically 10-50 times for peptides and other small basic molecules. Thus, peptide maps that use ESI-MS for detection can be performed at lower levels, with conventional columns, without the need to use capillary chromatography or reduced mass spectral resolution to achieve satisfactory sensitivity. The method may be used with similar results for heptafluorobutyric acid and hydrochloric acid. A mechanism for TFA signal suppression and signal enhancement by the foregoing method, is proposed.

Pyrosequencing®-Based Identification of Low-Frequency Mutations Enriched Through Enhanced-ice-COLD-PCR.

PubMed

How-Kit, Alexandre; Tost, Jörg

2015-01-01

A number of molecular diagnostic assays have been developed in the last years for mutation detection. Although these methods have become increasingly sensitive, most of them are incompatible with a sequencing-based readout and require prior knowledge of the mutation present in the sample. Consequently, coamplification at low denaturation (COLD)-PCR-based methods have been developed and combine a high analytical sensitivity due to mutation enrichment in the sample with the identification of known or unknown mutations by downstream sequencing experiments. Among these methods, the recently developed Enhanced-ice-COLD-PCR appeared as the most powerful method as it outperformed the other COLD-PCR-based methods in terms of the mutation enrichment and due to the simplicity of the experimental setup of the assay. Indeed, E-ice-COLD-PCR is very versatile as it can be used on all types of PCR platforms and is applicable to different types of samples including fresh frozen, FFPE, and plasma samples. The technique relies on the incorporation of an LNA containing blocker probe in the PCR reaction followed by selective heteroduplex denaturation enabling amplification of the mutant allele while amplification of the wild-type allele is prevented. Combined with Pyrosequencing(®), which is a very quantitative high-resolution sequencing technology, E-ice-COLD-PCR can detect and identify mutations with a limit of detection down to 0.01 %.

SSAGES: Software Suite for Advanced General Ensemble Simulations

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

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniquesmore » as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.« less

SSAGES: Software Suite for Advanced General Ensemble Simulations

NASA Astrophysics Data System (ADS)

Sidky, Hythem; Colón, Yamil J.; Helfferich, Julian; Sikora, Benjamin J.; Bezik, Cody; Chu, Weiwei; Giberti, Federico; Guo, Ashley Z.; Jiang, Xikai; Lequieu, Joshua; Li, Jiyuan; Moller, Joshua; Quevillon, Michael J.; Rahimi, Mohammad; Ramezani-Dakhel, Hadi; Rathee, Vikramjit S.; Reid, Daniel R.; Sevgen, Emre; Thapar, Vikram; Webb, Michael A.; Whitmer, Jonathan K.; de Pablo, Juan J.

2018-01-01

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public.

Measurement of Nanoplasmonic Field Enhancement with Ultrafast Photoemission.

PubMed

Rácz, Péter; Pápa, Zsuzsanna; Márton, István; Budai, Judit; Wróbel, Piotr; Stefaniuk, Tomasz; Prietl, Christine; Krenn, Joachim R; Dombi, Péter

2017-02-08

Probing nanooptical near-fields is a major challenge in plasmonics. Here, we demonstrate an experimental method utilizing ultrafast photoemission from plasmonic nanostructures that is capable of probing the maximum nanoplasmonic field enhancement in any metallic surface environment. Directly measured field enhancement values for various samples are in good agreement with detailed finite-difference time-domain simulations. These results establish ultrafast plasmonic photoelectrons as versatile probes for nanoplasmonic near-fields.

Bi2MoxW1-xO6 solid solutions with tunable band structure and enhanced visible-light photocatalytic activities

NASA Astrophysics Data System (ADS)

Li, Wenqi; Ding, Xingeng; Wu, Huating; Yang, Hui

2018-07-01

Semiconductor photocatalysis is an effective green way to combat water pollution. For the first time, this study reports a novel method to develop Bi2MoxW1-xO6 solid solution with microsphere structure through anion-exchange method. All Bi2MoxW1-xO6 samples exhibit an Aurivillius-type crystal structure without any secondary phase, confirming that in complete solid solutions as the value of x increases, the band gap energy of Bi2MoxW1-xO6 solid solutions decreases, while the optical absorption edge moves to longer wavelength. The Raman spectra research shows an increase in orthorhombic distortion with progressive replacement of W sites in Bi2WO6 with Mo6+ ions. Compared to Bi2MoO6 and Bi2WO6 samples, Bi2Mo0.4W0.6O6 sample displayed best photocatalytic activity and cycling stability for degradation of RhB dye. The enhanced photocatalytic activity of Bi2Mo0.4W0.6O6 sample can be synergetically linked to hierarchical hollow structure, enhanced light absorbance, and high carrier-separation efficiency. Additionally, the hollow Bi2MoxW1-xO6 microspheres formation can be attributed to the Kirkendall effect.

Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space.

PubMed

Kim, Ilsoo; Allen, Toby W

2012-04-28

Free energy perturbation, a method for computing the free energy difference between two states, is often combined with non-Boltzmann biased sampling techniques in order to accelerate the convergence of free energy calculations. Here we present a new extension of the Bennett acceptance ratio (BAR) method by combining it with umbrella sampling (US) along a reaction coordinate in configurational space. In this approach, which we call Bennett acceptance ratio with umbrella sampling (BAR-US), the conditional histogram of energy difference (a mapping of the 3N-dimensional configurational space via a reaction coordinate onto 1D energy difference space) is weighted for marginalization with the associated population density along a reaction coordinate computed by US. This procedure produces marginal histograms of energy difference, from forward and backward simulations, with higher overlap in energy difference space, rendering free energy difference estimations using BAR statistically more reliable. In addition to BAR-US, two histogram analysis methods, termed Bennett overlapping histograms with US (BOH-US) and Bennett-Hummer (linear) least square with US (BHLS-US), are employed as consistency and convergence checks for free energy difference estimation by BAR-US. The proposed methods (BAR-US, BOH-US, and BHLS-US) are applied to a 1-dimensional asymmetric model potential, as has been used previously to test free energy calculations from non-equilibrium processes. We then consider the more stringent test of a 1-dimensional strongly (but linearly) shifted harmonic oscillator, which exhibits no overlap between two states when sampled using unbiased Brownian dynamics. We find that the efficiency of the proposed methods is enhanced over the original Bennett's methods (BAR, BOH, and BHLS) through fast uniform sampling of energy difference space via US in configurational space. We apply the proposed methods to the calculation of the electrostatic contribution to the absolute solvation free energy (excess chemical potential) of water. We then address the controversial issue of ion selectivity in the K(+) ion channel, KcsA. We have calculated the relative binding affinity of K(+) over Na(+) within a binding site of the KcsA channel for which different, though adjacent, K(+) and Na(+) configurations exist, ideally suited to these US-enhanced methods. Our studies demonstrate that the significant improvements in free energy calculations obtained using the proposed methods can have serious consequences for elucidating biological mechanisms and for the interpretation of experimental data.

Tip-enhanced Raman spectroscopy and near-field polarization

NASA Astrophysics Data System (ADS)

Saito, Yuika; Mino, Toshihiro; Verma, Prabhat

2015-12-01

Tip-enhanced Raman spectroscopy (TERS) is a powerful tool for High-resolution Raman spectroscopy. In this method, a metal coated nano-tip acts as a plasmonic antenna to enhance the originally weak Raman scattering from a nanometric volume of a sample. The technique enables to detect Raman scattering light from nano-scale area and also enhance the light intensity with combination of near-filed light and localized surface plasmon generated at a metallized tip apex. Nowadays TERS is used to investigate various nano-scale samples, for examples, carbon nanotubes, graphenes DNA and biomaterials. As the TERS developed, there is high demand to investigate the properties of near-field light e.g. polarization properties. We have analyzed the polarization properties of near-field light in TERS and successfully realized the quantitative nano-imaging by visible light.

Spectral gap optimization of order parameters for sampling complex molecular systems

PubMed Central

Tiwary, Pratyush; Berne, B. J.

2016-01-01

In modern-day simulations of many-body systems, much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CVs) or reaction coordinates. A vast array of enhanced-sampling methods are based on the identification and biasing of these low-dimensional order parameters, whose fluctuations are important in driving rare events of interest. Here, we describe a new algorithm for finding optimal low-dimensional CVs for use in enhanced-sampling biasing methods like umbrella sampling, metadynamics, and related methods, when limited prior static and dynamic information is known about the system, and a much larger set of candidate CVs is specified. The algorithm involves estimating the best combination of these candidate CVs, as quantified by a maximum path entropy estimate of the spectral gap for dynamics viewed as a function of that CV. The algorithm is called spectral gap optimization of order parameters (SGOOP). Through multiple practical examples, we show how this postprocessing procedure can lead to optimization of CV and several orders of magnitude improvement in the convergence of the free energy calculated through metadynamics, essentially giving the ability to extract useful information even from unsuccessful metadynamics runs. PMID:26929365

The enhancement in optical and magnetic properties of Na-doped LaFeO3

NASA Astrophysics Data System (ADS)

Devi, E.; Kalaiselvi, B. J.

2018-04-01

La1-xNaxFeO3(x=0.00 and 0.05) were synthesized by sol-gel auto-combustion method. No evidence of impurity phase and the peak (121) slightly shift towards lower angle is confirmed by X-ray diffraction analysis (XRD). The UV-visible spectra show strong absorption peak centered at approximately 231 nm and the calculated optical band gap are found to be 2.73eV, 2.36eV for x = 0.00 and 0.05, respectively. The M-H loop of pure sample is anti-ferromagnetic, whereas those of the Na doped sample shows enhanced ferromagnetic behavior. The remnant magnetization (Mr), saturation magnetization (Ms) and coercive field (Hc) of Na-doped sample are enhanced to 1.06emu/g, 5.39emu/g and 182.84kOe, respectively.

Enhanced sampling techniques in biomolecular simulations.

PubMed

Spiwok, Vojtech; Sucur, Zoran; Hosek, Petr

2015-11-01

Biomolecular simulations are routinely used in biochemistry and molecular biology research; however, they often fail to match expectations of their impact on pharmaceutical and biotech industry. This is caused by the fact that a vast amount of computer time is required to simulate short episodes from the life of biomolecules. Several approaches have been developed to overcome this obstacle, including application of massively parallel and special purpose computers or non-conventional hardware. Methodological approaches are represented by coarse-grained models and enhanced sampling techniques. These techniques can show how the studied system behaves in long time-scales on the basis of relatively short simulations. This review presents an overview of new simulation approaches, the theory behind enhanced sampling methods and success stories of their applications with a direct impact on biotechnology or drug design. Copyright © 2014 Elsevier Inc. All rights reserved.

Enhancing English Learners' Willingness to Communicate through Debate and Philosophy Inquiry Discussion

ERIC Educational Resources Information Center

Shamsudin, Mardziah; Othman, Moomala; Jahedi, Maryam; Aralas, Dalia

2017-01-01

The present study investigated the impact of two instructional methods, Debate and Philosophy Inquiry (PI), in enhancing Willingness to Communicate (WTC) among two groups of English as a Second Language (ESL) learners who were randomly selected. In each group there were sixteen participants. The researchers used independent samples t-test and…

Enhancing Thinking Skills in Early Childhood

ERIC Educational Resources Information Center

Aubrey, Carol; Ghent, Kathryn; Kanira, Eleni

2012-01-01

A case study approach was adopted to investigate two thinking skills programmes for a maximum variation sample of five- to six-year-olds in four schools, in two local authorities (LAs), in England and Wales, using multiple methods. School staff interviewed felt that thinking skills programmes enhanced critical thinking skills and improved use of…

[Experimental study and correction of the absorption and enhancement effect between Ti, V and Fe].

PubMed

Tuo, Xian-Guo; Mu, Ke-Liang; Li, Zhe; Wang, Hong-Hui; Luo, Hui; Yang, Jian-Bo

2009-11-01

The absorption and enhancement effects in X-ray fluorescence analysis for Ti, V and Fe elements were studied in the present paper. Three bogus duality systems of Ti-V/Ti-Fe/V-Fe samples were confected and measured by X-ray fluorescence analysis technique using HPGe semiconductor detector, and the relation curve between unitary coefficient (R(K)) of element count rate and element content (W(K)) were obtained after the experiment. Having analyzed the degree of absorption and enhancement effect between every two elements, the authors get the result, and that is the absorption and enhancement effect between Ti and V is relatively distinctness, while it's not so distinctness in Ti-Fe and V-Fe. After that, a mathematics correction method of exponential fitting was used to fit the R(K)-W(K) curve and get a function equation of X-ray fluorescence count rate and content. Three groups of Ti-V duality samples were used to test the fitting method and the relative errors of Ti and V were less than 0.2% as compared to the actual results.

Method for Operating a Sensor to Differentiate Between Analytes in a Sample

DOEpatents

Kunt, Tekin; Cavicchi, Richard E; Semancik, Stephen; McAvoy, Thomas J

1998-07-28

Disclosed is a method for operating a sensor to differentiate between first and second analytes in a sample. The method comprises the steps of determining a input profile for the sensor which will enhance the difference in the output profiles of the sensor as between the first analyte and the second analyte; determining a first analyte output profile as observed when the input profile is applied to the sensor; determining a second analyte output profile as observed when the temperature profile is applied to the sensor; introducing the sensor to the sample while applying the temperature profile to the sensor, thereby obtaining a sample output profile; and evaluating the sample output profile as against the first and second analyte output profiles to thereby determine which of the analytes is present in the sample.

Magnetic enhancement and coding in mechanosynthesized Ni{sub 0.3}Zn{sub 0.7}Fe{sub 2}O{sub 4} nanoparticles

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

Majumder, S.; Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata-700064; Dey, S.

2015-06-24

The nanosized Ni{sub 0.3}Zn{sub 0.7}Fe{sub 2}O{sub 4} (∼ 15 nm) has been synthesized by high energy ball milling of the bulk powder sample. The sample has been characterized by powder x-ray diffraction, field emission and transmission electron microscopic and dc magnetic measurement techniques. The dc magnetic measurement on the sample indicates that the sample exhibit enhancement of magnetization compared to its counterparts synthesized by chemical methods. Moreover, the system stores the memory of either decrease or increase of magnetic field enabling a magnetic coding of “0” and “1” which can be profitably used in magnetic storage and sensing devices.

Lactase persistence genotyping on whole blood by loop-mediated isothermal amplification and melting curve analysis.

PubMed

Abildgaard, Anders; Tovbjerg, Sara K; Giltay, Axel; Detemmerman, Liselot; Nissen, Peter H

2018-03-26

The lactase persistence phenotype is controlled by a regulatory enhancer region upstream of the Lactase (LCT) gene. In northern Europe, specifically the -13910C > T variant has been associated with lactase persistence whereas other persistence variants, e.g. -13907C > G and -13915 T > G, have been identified in Africa and the Middle East. The aim of the present study was to compare a previously developed high resolution melting assay (HRM) with a novel method based on loop-mediated isothermal amplification and melting curve analysis (LAMP-MC) with both whole blood and DNA as input material. To evaluate the LAMP-MC method, we used 100 whole blood samples and 93 DNA samples in a two tiered study. First, we studied the ability of the LAMP-MC method to produce specific melting curves for several variants of the LCT enhancer region. Next, we performed a blinded comparison between the LAMP-MC method and our existing HRM method with clinical samples of unknown genotype. The LAMP-MC method produced specific melting curves for the variants at position -13909, -13910, -13913 whereas the -13907C > G and -13915 T > G variants produced indistinguishable melting profiles. The LAMP-MC assay is a simple method for lactase persistence genotyping and compares well with our existing HRM method. Copyright © 2018. Published by Elsevier B.V.

Enhanced sampling simulations of DNA step parameters.

PubMed

Karolak, Aleksandra; van der Vaart, Arjan

2014-12-15

A novel approach for the selection of step parameters as reaction coordinates in enhanced sampling simulations of DNA is presented. The method uses three atoms per base and does not require coordinate overlays or idealized base pairs. This allowed for a highly efficient implementation of the calculation of all step parameters and their Cartesian derivatives in molecular dynamics simulations. Good correlation between the calculated and actual twist, roll, tilt, shift, and slide parameters is obtained, while the correlation with rise is modest. The method is illustrated by its application to the methylated and unmethylated 5'-CATGTGACGTCACATG-3' double stranded DNA sequence. One-dimensional umbrella simulations indicate that the flexibility of the central CG step is only marginally affected by methylation. © 2014 Wiley Periodicals, Inc.

Fuzziness-based active learning framework to enhance hyperspectral image classification performance for discriminative and generative classifiers

PubMed Central

2018-01-01

Hyperspectral image classification with a limited number of training samples without loss of accuracy is desirable, as collecting such data is often expensive and time-consuming. However, classifiers trained with limited samples usually end up with a large generalization error. To overcome the said problem, we propose a fuzziness-based active learning framework (FALF), in which we implement the idea of selecting optimal training samples to enhance generalization performance for two different kinds of classifiers, discriminative and generative (e.g. SVM and KNN). The optimal samples are selected by first estimating the boundary of each class and then calculating the fuzziness-based distance between each sample and the estimated class boundaries. Those samples that are at smaller distances from the boundaries and have higher fuzziness are chosen as target candidates for the training set. Through detailed experimentation on three publically available datasets, we showed that when trained with the proposed sample selection framework, both classifiers achieved higher classification accuracy and lower processing time with the small amount of training data as opposed to the case where the training samples were selected randomly. Our experiments demonstrate the effectiveness of our proposed method, which equates favorably with the state-of-the-art methods. PMID:29304512

New method for detection of gastric cancer by hyperspectral imaging: a pilot study

NASA Astrophysics Data System (ADS)

Kiyotoki, Shu; Nishikawa, Jun; Okamoto, Takeshi; Hamabe, Kouichi; Saito, Mari; Goto, Atsushi; Fujita, Yusuke; Hamamoto, Yoshihiko; Takeuchi, Yusuke; Satori, Shin; Sakaida, Isao

2013-02-01

We developed a new, easy, and objective method to detect gastric cancer using hyperspectral imaging (HSI) technology combining spectroscopy and imaging A total of 16 gastroduodenal tumors removed by endoscopic resection or surgery from 14 patients at Yamaguchi University Hospital, Japan, were recorded using a hyperspectral camera (HSC) equipped with HSI technology Corrected spectral reflectance was obtained from 10 samples of normal mucosa and 10 samples of tumors for each case The 16 cases were divided into eight training cases (160 training samples) and eight test cases (160 test samples) We established a diagnostic algorithm with training samples and evaluated it with test samples Diagnostic capability of the algorithm for each tumor was validated, and enhancement of tumors by image processing using the HSC was evaluated The diagnostic algorithm used the 726-nm wavelength, with a cutoff point established from training samples The sensitivity, specificity, and accuracy rates of the algorithm's diagnostic capability in the test samples were 78.8% (63/80), 92.5% (74/80), and 85.6% (137/160), respectively Tumors in HSC images of 13 (81.3%) cases were well enhanced by image processing Differences in spectral reflectance between tumors and normal mucosa suggested that tumors can be clearly distinguished from background mucosa with HSI technology.

A fast and reliable readout method for quantitative analysis of surface-enhanced Raman scattering nanoprobes on chip surface

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

Chang, Hyejin; Jeong, Sinyoung; Ko, Eunbyeol

2015-05-15

Surface-enhanced Raman scattering techniques have been widely used for bioanalysis due to its high sensitivity and multiplex capacity. However, the point-scanning method using a micro-Raman system, which is the most common method in the literature, has a disadvantage of extremely long measurement time for on-chip immunoassay adopting a large chip area of approximately 1-mm scale and confocal beam point of ca. 1-μm size. Alternative methods such as sampled spot scan with high confocality and large-area scan method with enlarged field of view and low confocality have been utilized in order to minimize the measurement time practically. In this study, wemore » analyzed the two methods in respect of signal-to-noise ratio and sampling-led signal fluctuations to obtain insights into a fast and reliable readout strategy. On this basis, we proposed a methodology for fast and reliable quantitative measurement of the whole chip area. The proposed method adopted a raster scan covering a full area of 100 μm × 100 μm region as a proof-of-concept experiment while accumulating signals in the CCD detector for single spectrum per frame. One single scan with 10 s over 100 μm × 100 μm area yielded much higher sensitivity compared to sampled spot scanning measurements and no signal fluctuations attributed to sampled spot scan. This readout method is able to serve as one of key technologies that will bring quantitative multiplexed detection and analysis into practice.« less

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins.

PubMed

Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

2014-03-28

A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.

Fluctuation Flooding Method (FFM) for accelerating conformational transitions of proteins

NASA Astrophysics Data System (ADS)

Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

2014-03-01

A powerful conformational sampling method for accelerating structural transitions of proteins, "Fluctuation Flooding Method (FFM)," is proposed. In FFM, cycles of the following steps enhance the transitions: (i) extractions of largely fluctuating snapshots along anisotropic modes obtained from trajectories of multiple independent molecular dynamics (MD) simulations and (ii) conformational re-sampling of the snapshots via re-generations of initial velocities when re-starting MD simulations. In an application to bacteriophage T4 lysozyme, FFM successfully accelerated the open-closed transition with the 6 ns simulation starting solely from the open state, although the 1-μs canonical MD simulation failed to sample such a rare event.

Application of dispersive liquid-liquid microextraction coupled with vortex-assisted hydrophobic magnetic nanoparticles based solid-phase extraction for determination of aflatoxin M1 in milk samples by sensitive micelle enhanced spectrofluorimetry.

PubMed

Amoli-Diva, Mitra; Taherimaslak, Zohreh; Allahyari, Mehdi; Pourghazi, Kamyar; Manafi, Mohammad Hanif

2015-03-01

An efficient, simple and fast low-density solvent based dispersive liquid-liquid microextraction (LDS-DLLME) followed by vortex-assisted dispersive solid phase extraction (VA-D-SPE) has been developed as a new approach for extraction and preconcentration of aflatoxin M1 in milk samples prior to its micelle enhanced spectrofluorimetic determination. In this LDS-DLLME coupled VA-D-SPE method, milk samples were first treated with methanol/water (80:20, v/v) after removing the fat layer. This solvent was directly used as the dispersing solvent in DLLME along with using 1-heptanol (as a low-density solvent with respect to water) as the extracting solvent. In VA-D-SPE approach, hydrophobic oleic acid modified Fe3O4 nanoparticles were used to retrieve the analyte from the DLLME step. It is considerably that the target of VA-D-SPE was 1-heptanol rather than the aflatoxin M1 directly. The main parameters affecting the efficiency of LDS-DLLME and VA-D-SPE procedures and signal enhancement of aflatoxin M1 were investigated and optimized. Under the optimum conditions, the method was linear in the range from 0.02 to 200 µg L(-1) with the correlation coefficient (R(2)) of 0.9989 and detection limit of 13 ng L(-1). The intra-day precision was 2.9 and 4.3% and the inter-day precision was 2.1 and 3.3% for concentration of 2 and 50 µg L(-1) respectively. The developed method was applied for extraction and preconcentration of AFM1 in three commercially available milk samples and the results were compared with the official AOAC method. Copyright © 2014 Elsevier B.V. All rights reserved.

Identification of Metal Oxide Nanoparticles in Histological Samples by Enhanced Darkfield Microscopy and Hyperspectral Mapping.

PubMed

Roth, Gary A; Sosa Peña, Maria del Pilar; Neu-Baker, Nicole M; Tahiliani, Sahil; Brenner, Sara A

2015-12-08

Nanomaterials are increasingly prevalent throughout industry, manufacturing, and biomedical research. The need for tools and techniques that aid in the identification, localization, and characterization of nanoscale materials in biological samples is on the rise. Currently available methods, such as electron microscopy, tend to be resource-intensive, making their use prohibitive for much of the research community. Enhanced darkfield microscopy complemented with a hyperspectral imaging system may provide a solution to this bottleneck by enabling rapid and less expensive characterization of nanoparticles in histological samples. This method allows for high-contrast nanoscale imaging as well as nanomaterial identification. For this technique, histological tissue samples are prepared as they would be for light-based microscopy. First, positive control samples are analyzed to generate the reference spectra that will enable the detection of a material of interest in the sample. Negative controls without the material of interest are also analyzed in order to improve specificity (reduce false positives). Samples can then be imaged and analyzed using methods and software for hyperspectral microscopy or matched against these reference spectra in order to provide maps of the location of materials of interest in a sample. The technique is particularly well-suited for materials with highly unique reflectance spectra, such as noble metals, but is also applicable to other materials, such as semi-metallic oxides. This technique provides information that is difficult to acquire from histological samples without the use of electron microscopy techniques, which may provide higher sensitivity and resolution, but are vastly more resource-intensive and time-consuming than light microscopy.

Exploiting LBL-assembled Au nanoparticles to enhance Raman signals for point-of-care testing of osteoporosis with excreta sample

NASA Astrophysics Data System (ADS)

Sun, Jian F.; Liu, Xuan; Guo, Zhi R.; Dong, Jian; Huang, Yawen; Zhang, Jie; Jin, Hui; Gu, Ning

2017-02-01

Due to the intrinsic lack of specific biomarkers, there is an increasing demand for degenerative diseases to develop a testing method independent upon the targeting biomolecules. In this paper, we proposed a novel idea for this issue which was to analyze the characteristic information of metabolites with Raman spectrum. First, we achieved the fabrication of stable, uniform and reproducible substrate to enhance the Raman signals, which is crucial to the following analysis of information. This idea was confirmed with the osteoporosis-modeled mice. Furthermore, the testing results with clinical samples also preliminarily exhibited the feasibility of this strategy. The substrate to enhance Raman signal was fabricated by the layer-by-layer assembly of Au nanoparticles. The osteoporosis modeling was made by bilateral ovariectomy. Ten female mice were randomly divided into two groups. The urine and dejecta samples of mice were collected every week. Clinic urine samples were collected from patients with osteoporosis while the controlled samples were from the young students in our university. The LBL-assembled substrate of Au nanoparticles was uniform, stable and reproducible to significantly enhance the Raman signals from tiny amount of samples. With a simple data processing technique, the Raman signal-based method can effectively reflect the development of osteoporosis by comparison with micro-CT characterization. Moreover, the Raman signal from samples of clinic patients also showed the obvious difference with that of the control. Raman spectrum may be a good tool to convey the pathological information of metabolites in molecular level. Our results manifested that the information-based testing is possibly feasible and promising. Our strategy utilizes the characteristic information rather than the biological recognition to test the diseases which are difficult to find specific biomarkers. This will be greatly beneficial to the prevention and diagnosis of degenerative diseases. Also, we believe the combination of big bio-data and characteristic recognition will change the current paradigm of medical diagnosis essentially.

Enhanced Photocatalytic Property of Cu Doped Sodium Niobate

DOE PAGES

Xu, Jianbin; Zhang, Feng; Sun, Bingyang; ...

2015-01-01

Here, we investigate the photocatalytic activity of Cu doped NaNbO 3 powder sample prepared by the modified polymer complex method. The photocatalytic activity of hydrogen evolution from methanol aqueous solution was improved by Cu 2.6 at% doping. The photocatalytic degradation of rhodamine B (RhB) under visible light irradiation was enhanced in comparison with pristine NaNbO 3. Cu introduction improved the adsorption property of NaNbO 3, judging from the Fourier transform infrared spectra. Moreover, the ultraviolet light excitation in Cu doped sample would accelerate the mineralized process.

Information Theory for Gabor Feature Selection for Face Recognition

NASA Astrophysics Data System (ADS)

Shen, Linlin; Bai, Li

2006-12-01

A discriminative and robust feature—kernel enhanced informative Gabor feature—is proposed in this paper for face recognition. Mutual information is applied to select a set of informative and nonredundant Gabor features, which are then further enhanced by kernel methods for recognition. Compared with one of the top performing methods in the 2004 Face Verification Competition (FVC2004), our methods demonstrate a clear advantage over existing methods in accuracy, computation efficiency, and memory cost. The proposed method has been fully tested on the FERET database using the FERET evaluation protocol. Significant improvements on three of the test data sets are observed. Compared with the classical Gabor wavelet-based approaches using a huge number of features, our method requires less than 4 milliseconds to retrieve a few hundreds of features. Due to the substantially reduced feature dimension, only 4 seconds are required to recognize 200 face images. The paper also unified different Gabor filter definitions and proposed a training sample generation algorithm to reduce the effects caused by unbalanced number of samples available in different classes.

Rapid and prodium iodide-compatible optical clearing method for brain tissue based on sugar/sugar-alcohol

NASA Astrophysics Data System (ADS)

Yu, Tingting; Qi, Yisong; Wang, Jianru; Feng, Wei; Xu, Jianyi; Zhu, Jingtan; Yao, Yingtao; Gong, Hui; Luo, Qingming; Zhu, Dan

2016-08-01

The developed optical clearing methods show great potential for imaging of large-volume tissues, but these methods present some nonnegligible limitations such as complexity of implementation and long incubation times. In this study, we tried to screen out rapid optical clearing agents by means of molecular dynamical simulation and experimental demonstration. According to the optical clearing potential of sugar and sugar-alcohol, we further evaluated the improvement in the optical clearing efficacy of mouse brain samples, imaging depth, fluorescence preservation, and linear deformation. The results showed that drops of sorbitol, sucrose, and fructose could quickly make the mouse brain sample transparent within 1 to 2 min, and induce about threefold enhancement in imaging depth. The former two could evidently enhance the fluorescence intensity of green fluorescent protein (GFP) and prodium iodide (PI) nuclear dye. Fructose could significantly increase the fluorescence intensity of PI, but slightly decrease the fluorescence intensity of GFP. Even though the three agents caused some shrinkage in samples, the contraction in horizontal and longitudinal directions are almost the same.

A convenient method for determination of malathion based on the resonance Rayleigh scattering enhancement

NASA Astrophysics Data System (ADS)

Wu, Huan; Zhao, Yanmei; Tan, Xuanping; Huang, Yunmei; Yuan, Haiyan; Yang, Jidong

2017-09-01

A convenient method for determination of malathion (Mala) based on resonance Rayleigh scattering (RRS) enhancement of L-Tryptophan (L-Try)-Pd(II)-Mala system was proposed in this paper. The interaction between L-Try, Pd(II) and malathion in the system was investigated by fluorescence, RRS and UV-Vis absorption spectroscopy. In the optimum conditions, the RRS intensity of L-Try-Pd(II)-Mala system had a remarkable enhancement because the hydrolysis products of malathion would interact with Pd(II) and L-Try each other formed new complexes, which enhanced intensity was directly proportional to the malathion concentration within a certain range. Based on the RRS enhancement of L-Try-Pd(II) system by Mala, a novel, convenient and specific method for Mala determination was developed. To our knowledge, the method is the first RRS method for determination of Mala was reported. The detection limit for Mala was 6.7 ng/mL and the quantitative determination range was 0.06-0.6 μg/mL. The influence of coexisting substances on RRS was also investigated, and the RRS method exhibited good anti-interference ability. The new analytical method has been applied to determine of malathion in real samples with satisfactory results.

Cryptosporidium Oocyst Detection in Water Samples: Floatation Technique Enhanced with Immunofluorescence Is as Effective as Immunomagnetic Separation Method

PubMed Central

Koompapong, Khuanchai; Sutthikornchai, Chantira

2009-01-01

Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 101, 102, and 103 per 10 µl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 102 per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting. PMID:19967082

Cryptosporidium oocyst detection in water samples: floatation technique enhanced with immunofluorescence is as effective as immunomagnetic separation method.

PubMed

Koompapong, Khuanchai; Sutthikornchai, Chantira; Sukthana, Yowalark

2009-12-01

Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 10(1), 10(2), and 10(3) per 10 microl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 10(2) per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting.

An assessment of the potential of laser-induced breakdown spectroscopy (LIBS) for the analysis of cesium in liquid samples of biological origin.

PubMed

Metzinger, Anikó; Kovács-Széles, Eva; Almási, István; Galbács, Gábor

2014-01-01

The present study describes the development of an analytical method for the determination of cesium in biological fluid samples (human urine and blood samples) by laser-induced breakdown spectroscopy (LIBS). The developed method is based on sample presentation by liquid-to-solid conversion, enhancing the emission signal by drying the liquid into small "pockets" created in a metal support (zinc plate), and allows the analysis to be carried out on as little as 1 μL of sample volume, in a closed sample cell. Absolute detection limits on the Cs I 852.1 nm spectral line were calculated by the IUPAC 3σ method to be 6 ng in the urine sample and 27 ng in the blood serum sample. It is estimated that LIBS may be used to detect highly elevated concentration levels of Cs in fluid samples taken from people potentially exposed to surges of Cs from non-natural sources.

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Application of Ultrasound-Assisted Surfactant-Enhanced Emulsification Microextraction Based on Solidification of Floating Organic Droplets and High Performance Liquid Chromatography for Preconcentration and Determination of Alprazolam and Chlordiazepoxide in Human Serum Samples.

PubMed

Goudarzi, Nasser; Amirnavaee, Monavar; Arab Chamjangali, Mansour; Farsimadan, Sahar

2017-07-01

An improved microextraction method is proposed on the basis of ultrasound-assisted surfactant-enhanced emulsification and solidification of a floating organic droplet procedure combined with high performance liquid chromatography for the preconcentration and quantification of alprazolam (ALP) and chlordiazepoxide (CHL) present in a number of human serum samples. Several parameters affecting the extraction efficiency were investigated by the Plackett -Burman factorial design as the screening design. Then the response surface methodology based on the Box-Behnken design was used to optimize the effective parameters in the proposed procedure. The limits of detection for the proposed method were found to be 3.0 and 3.1 ng mL-1 for CHL and ALP, respectively. The calibration curves obtained for the method were linear in the ranges of 10.0-3,500.0 and 10.0-3,000.0 ng mL-1 for CHL and ALP, respectively, with a good determination coefficient. The recoveries of the drugs in the spiked human serum samples were above 93.0%. The developed method was successfully applied to the analysis of these studied drugs in human serum samples. The pre-treatment of the serum samples was performed using acetonitrile to remove the proteins. The proposed procedure was an accurate and reliable one for the determination and preconcentration of these drugs in blood samples. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Effects of receiving-water quality and wastewater treatment on injury, survival, and regrowth of fecal-indicator bacteria and implications for assessment of recreational water quality

USGS Publications Warehouse

Francy, D.S.; Hart, T.L.; Virosteck, C.M.

1996-01-01

Bacterial injury, survival, and regrowth were investigated by use of replicate flow-through incubation chambers placed in the Cuyahoga River or Lake Erie in the greater Cleveland metropolitan area during seven 4-day field studies. The chambers contained wastewater or combined-sewer-overflow (CSO) effluents treated three ways-unchlorinated, chlorinated, and dechlorinated. At timestep intervals, the chamber contents were analyzed for concentrations of injured and healthy fecal coliforms by use of standard selective and enhanced-recovery membrane-filtration methods. Mean percent injuries and survivals were calculated from the fecal-coliform concentration data for each field study. The results of analysis of variance (ANOVA) indicated that treatment affected mean percent injury and survival, whereas site did not. In the warm-weather Lake Erie field study, but not in the warm-weather Cuyahoga River studies, the results of ANOVA indicated that dechlorination enhanced the repair of injuries and regrowth of chlorine-injured fecal coliforms on culture media over chlorination alone. The results of ANOVA on the percent injury from CSO effluent field studies indicated that dechlorination reduced the ability of organisms to recover and regrow on culture media over chlorination alone. However, because of atypical patterns of concentration increases and decreases in some CSO effluent samples, more work needs to be done before the effect of dechlorination and chlorination on reducing fecal-coliform concentrations in CSO effluents can be confirmed. The results of ANOVA on percent survivals found statistically significant differences among the three treatment methods for all but one study. Dechlorination was found to be less effective than chlorination alone in reducing the survival of fecal coliforms in wastewater effluent, but not in CSO effluent. If the concentration of fecal coliforms determined by use of the enhanced-recovery method can be predicted accurately from the concentration found by use of the standard method, then increased monitoring and expense to detect chlorine-injured organisms would be unnecessary. The results of linear regression analysis, however, indicated that the relation between enhanced-recovery and standard-method concentrations was best represented when the data were grouped by treatment. The model generated from linear regression of the unchlorinated data set provided an accurate estimate of enhanced-recovery concentrations from standard-method concentrations, whereas the models generated from the chlorinated and dechlorinated data sets did not. In addition, evaluation of fecal-coliform concentrations found in field studies in terms of Ohio recreational water-quality standards showed that concentrations obtained by standard and enhanced-recovery methods were not comparable. Sample treatment and analysis methods were found to affect the percentage of samples meeting and exceeding Ohio's bathing-water, primary-contact, and secondary-contact standards. Therefore, determining the health risk of swimming in receiving waters was often difficult without information on enhanced-recovery method concentrations and was especially difficult in waters receiving high proportions of chlorinated or dechlorinated effluents.

Highly sensitive spectrofluorimetric determination of trace amounts NADP using Europium ion-doxycycline complex probe

NASA Astrophysics Data System (ADS)

Peng, Qian; Hou, Faju; Jiang, Chongqiu

2006-09-01

A new spectrofluorimetric method was developed for determination of trace amount of Coenzyme II (NADP). Using europium ion-doxycycline (DC) as a fluorescent probe, in the buffer solution of pH 8.44, NADP can remarkably enhance the fluorescence intensity of the Eu 3+-DC complex at λ = 612 nm and the enhanced fluorescence intensity is in proportion to the concentration of NADP. Optimum conditions for the determination of NADP were also investigated. The dynamic range for the determination of NADP is 3.3 × 10 -7 to 6.1 × 10 -6 mol l -1 with detection limit of 6.8 × 10 -8 mol l -1. This method is simple, practical and relatively free interference from coexisting substances and can be successfully applied to determination of NADP in synthetic water samples and in serum samples. Moreover, the enhancement mechanisms of the fluorescence intensity in the Eu 3+-DC system and the Eu 3+-DC-NADP system have been also discussed.

Method and apparatus for generating motor current spectra to enhance motor system fault detection

DOEpatents

Linehan, D.J.; Bunch, S.L.; Lyster, C.T.

1995-10-24

A method and circuitry are disclosed for sampling periodic amplitude modulations in a nonstationary periodic carrier wave to determine frequencies in the amplitude modulations. The method and circuit are described in terms of an improved motor current signature analysis. The method insures that the sampled data set contains an exact whole number of carrier wave cycles by defining the rate at which samples of motor current data are collected. The circuitry insures that a sampled data set containing stationary carrier waves is recreated from the analog motor current signal containing nonstationary carrier waves by conditioning the actual sampling rate to adjust with the frequency variations in the carrier wave. After the sampled data is transformed to the frequency domain via the Discrete Fourier Transform, the frequency distribution in the discrete spectra of those components due to the carrier wave and its harmonics will be minimized so that signals of interest are more easily analyzed. 29 figs.

Enhancing the Equating of Item Difficulty Metrics: Estimation of Reference Distribution. Research Report. ETS RR-14-07

ERIC Educational Resources Information Center

Ali, Usama S.; Walker, Michael E.

2014-01-01

Two methods are currently in use at Educational Testing Service (ETS) for equating observed item difficulty statistics. The first method involves the linear equating of item statistics in an observed sample to reference statistics on the same items. The second method, or the item response curve (IRC) method, involves the summation of conditional…

A new framework to enhance the interpretation of external validation studies of clinical prediction models.

PubMed

Debray, Thomas P A; Vergouwe, Yvonne; Koffijberg, Hendrik; Nieboer, Daan; Steyerberg, Ewout W; Moons, Karel G M

2015-03-01

It is widely acknowledged that the performance of diagnostic and prognostic prediction models should be assessed in external validation studies with independent data from "different but related" samples as compared with that of the development sample. We developed a framework of methodological steps and statistical methods for analyzing and enhancing the interpretation of results from external validation studies of prediction models. We propose to quantify the degree of relatedness between development and validation samples on a scale ranging from reproducibility to transportability by evaluating their corresponding case-mix differences. We subsequently assess the models' performance in the validation sample and interpret the performance in view of the case-mix differences. Finally, we may adjust the model to the validation setting. We illustrate this three-step framework with a prediction model for diagnosing deep venous thrombosis using three validation samples with varying case mix. While one external validation sample merely assessed the model's reproducibility, two other samples rather assessed model transportability. The performance in all validation samples was adequate, and the model did not require extensive updating to correct for miscalibration or poor fit to the validation settings. The proposed framework enhances the interpretation of findings at external validation of prediction models. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Rapid and direct determination of glyphosate, glufosinate, and aminophosphonic acid by online preconcentration CE with contactless conductivity detection.

PubMed

See, Hong Heng; Hauser, Peter C; Ibrahim, Wan Aini Wan; Sanagi, Mohd Marsin

2010-01-01

Rapid and direct online preconcentration followed by CE with capacitively coupled contactless conductivity detection (CE-C(4)D) is evaluated as a new approach for the determination of glyphosate, glufosinate (GLUF), and aminophosphonic acid (AMPA) in drinking water. Two online preconcentration techniques, namely large volume sample stacking without polarity switching and field-enhanced sample injection, coupled with CE-C(4)D were successfully developed and optimized. Under optimized conditions, LODs in the range of 0.01-0.1 microM (1.7-11.1 microg/L) and sensitivity enhancements of 48- to 53-fold were achieved with the large volume sample stacking-CE-C(4)D method. By performing the field-enhanced sample injection-CE-C(4)D procedure, excellent LODs down to 0.0005-0.02 microM (0.1-2.2 microg/L) as well as sensitivity enhancements of up to 245- to 1002-fold were obtained. Both techniques showed satisfactory reproducibility with RSDs of peak height of better than 10%. The newly established approaches were successfully applied to the analysis of glyphosate, glufosinate, and aminophosphonic acid in spiked tap drinking water.

Determination of finasteride and its metabolite in urine by dispersive liquid-liquid microextraction combined with field-enhanced sample stacking and sweeping.

PubMed

Chen, Chun-Hsien; Chao, Yu-Ying; Lin, Yi-Hui; Chen, Yen-Ling

2018-04-27

The on-line preconcentration technique of field-enhanced sample stacking and sweeping (FESS-sweeping) are combined with dispersive liquid-liquid microextraction (DLLME) to monitor the concentrations of finasteride, which is used in the treatment of androgenetic alopecia, and its metabolite, finasteride carboxylic acid (M3), in urine samples. DLLME is used to concentrate and eliminate the interferences of urine samples and uses chloroform as an extracting solvent and acetonitrile as a disperser solvent. A high conductivity buffer (HCB) was introduced into capillary and then sample plug (90.7% capillary length) was injected into capillary. After applying voltage, the sodium dodecyl sulfate (SDS) swept the analytes from the low conductivity sample solution into HCB. The analytes were concentrated on the field-enhanced sample stacking boundary. The limit of detection for the analytes is 20 ng mL -1 . The sensitivity enrichment of finasteride and M3 are 362-fold and 480-fold, respectively, compared with the conventional MEKC method. The on-line preconcentration technique of field-enhanced sample stacking and sweeping possess good selectivity because the endogenous steroid did not interfere the detection of finasteride and M3. The analytical technique is applied to investigate the concentrations in urine samples from patients who have been administered finasteride for the treatment of androgenetic alopecia; the amount of M3 detected in 12 h was 72.69 ± 4.18 μg. Copyright © 2018 Elsevier B.V. All rights reserved.

Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.

PubMed

Curuksu, Jeremy; Zacharias, Martin

2009-03-14

Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simulations performed at different temperatures (T-RexMD) can achieve improved conformational sampling. However, in the case of T-RexMD the computational demand grows rapidly with system size. A Hamiltonian RexMD method that specifically enhances coupled dihedral angle transitions has been developed. The method employs added biasing potentials as replica parameters that destabilize available dihedral substates and was applied to study coupled dihedral transitions in nucleic acid molecules. The biasing potentials can be either fixed at the beginning of the simulation or optimized during an equilibration phase. The method was extensively tested and compared to conventional MD simulations and T-RexMD simulations on an adenine dinucleotide system and on a DNA abasic site. The biasing potential RexMD method showed improved sampling of conformational substates compared to conventional MD simulations similar to T-RexMD simulations but at a fraction of the computational demand. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules.

Au nanostructure arrays for plasmonic applications: annealed island films versus nanoimprint lithography

NASA Astrophysics Data System (ADS)

Lopatynskyi, Andrii M.; Lytvyn, Vitalii K.; Nazarenko, Volodymyr I.; Guo, L. Jay; Lucas, Brandon D.; Chegel, Volodymyr I.

2015-03-01

This paper attempts to compare the main features of random and highly ordered gold nanostructure arrays (NSA) prepared by thermally annealed island film and nanoimprint lithography (NIL) techniques, respectively. Each substrate possesses different morphology in terms of plasmonic enhancement. Both methods allow such important features as spectral tuning of plasmon resonance position depending on size and shape of nanostructures; however, the time and cost is quite different. The respective comparison was performed experimentally and theoretically for a number of samples with different geometrical parameters. Spectral characteristics of fabricated NSA exhibited an expressed plasmon peak in the range from 576 to 809 nm for thermally annealed samples and from 606 to 783 nm for samples prepared by NIL. Modelling of the optical response for nanostructures with typical shapes associated with these techniques (parallelepiped for NIL and semi-ellipsoid for annealed island films) was performed using finite-difference time-domain calculations. Mathematical simulations have indicated the dependence of electric field enhancement on the shape and size of the nanoparticles. As an important point, the distribution of electric field at so-called `hot spots' was considered. Parallelepiped-shaped nanoparticles were shown to yield maximal enhancement values by an order of magnitude greater than their semi-ellipsoid-shaped counterparts; however, both nanoparticle shapes have demonstrated comparable effective electrical field enhancement values. Optimized Au nanostructures with equivalent diameters ranging from 85 to 143 nm and height equal to 35 nm were obtained for both techniques, resulting in the largest electrical field enhancement. The application of island film thermal annealing method for nanochips fabrication can be considered as a possible cost-effective platform for various surface-enhanced spectroscopies; while the NIL-fabricated NSA looks like more effective for sensing of small-size objects.

Rapid detection of acetamiprid in foods using surface-enhanced Raman spectroscopy (SERS).

PubMed

Wijaya, Wisiani; Pang, Shintaro; Labuza, Theodore P; He, Lili

2014-04-01

Acetamiprid is a neonicotinoid pesticide that is commonly used in modern farming. Acetamiprid residue in food commodities can be a potential harm to human and has been implicated in the honey bee hive die off crisis. In this study, we developed rapid, simple, and sensitive methods to detect acetamiprid in apple juice and on apple surfaces using surface-enhanced Raman spectroscopy (SERS). No pretreatment of apple juice sample was performed. A simple surface swab method was used to recover acetamiprid from the apple surface. Samples were incubated with silver dendrites for several minutes and SERS spectra were taken directly from the silver surface. Detection of a set of 5 apple juice samples can be done within 10 min. The swab-SERS method took 15 min for a set of 5 samples. Resulting spectral data were analyzed using principal component analysis. The highest acetamiprid peak at 634 cm(-1) was used to detect and quantify the amount of acetamiprid spiked in 1:1 water-methanol solvent, apple juice, and on apple surface. The SERS method was able to successfully detect acetamiprid at 0.5 μg/mL (0.5 ppm) in solvent, 3 μg/mL (3 ppm) in apple juice, and 0.125 μg/cm(2) on apple surfaces. The SERS methods provide simple, rapid, and sensitive ways to detect acetamiprid in beverages and on the surfaces of thick skinned fruits and vegetables. © 2014 Institute of Food Technologists®

Online sample concentration and analysis of drugs of abuse in human urine by micelle to solvent stacking in capillary zone electrophoresis.

PubMed

Aturki, Zeineb; Fanali, Salvatore; Rocco, Anna

2016-10-01

A sensitive and rapid CZE-UV method was developed to determine drugs and their metabolites' presence in human urine. Ten drugs of abuse were analyzed including four amphetamines, cocaine, cocaethylene, heroin, morphine, 6-monoacetylmorphine, and 4-methylmethcathinone. An MSS (micelle to solvent stacking) approach was evaluated to enhance method sensitivity. This method considers composition of the micellar sample solution matrix and the injection time. Several analytical conditions influencing the resolution of the drugs mixture as pH and buffer concentration, organic solvent content, were also investigated. The base-line separation of all studied analytes in the same run was achieved within 18 min in an uncoated fused silica capillary (50 μm id × 60 cm) using a background solution containing 50 mM phosphate buffer pH 2.5 and 30% ACN v/v. Other experimental parameters such as applied voltage and capillary temperature were set up at 20 kV and 20°C, respectively. LOD values ranging between 15 and 75 ng/mL for all studied compounds were obtained. From a comparison with conventional CZE, the proposed method provides an increase of sensitivity (39- to 55-fold enhancement factor). Under optimal MSS-CZE conditions, good linearity was achieved (R 2 ≤ 0.9998). The method was finally applied to the analysis of urine samples spiked with a standard mixture after a sample pretreatment, reaching satisfactory recovery values. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Manipulation of surface morphology of flower-like Ag/ZnO nanorods to enhance photocatalytic performance

NASA Astrophysics Data System (ADS)

U-thaipan, Kasira; Tedsree, Karaked

2018-06-01

The surface morphology of flower-like Ag/ZnO nanorod can be manipulated by adopting different synthetic routes and also loading different levels of Ag in order to alter their surface structures to achieve the maximum photocatalytic efficiency. In a single-step preparation method Ag/ZnO was prepared by heating directly a mixture of Zn2+ and Ag+ precursors in an aqueous NaOH-ethylene glycol solution, while in the two-step preparation method an intermediate of flower-shaped ZnO nanorod was obtained by a hydrothermal process before depositing Ag particles on the ZnO surfaces by chemical reduction. The structure, morphology and optical properties of the synthesized samples were characterized using TEM, SEM, XRD, DRS and PL techniques. The sample prepared by single-step method are characterized with agglomeration of Ag atoms as clusters on the surface of ZnO, whereas in the sample prepared by two-step method Ag atoms are found uniformly dispersed and deposited as discrete Ag nanoparticles on the surface of ZnO. A significant enhancement in the adsorption of visible light was evident for Ag/ZnO samples prepared by two-step method especially with low Ag content (0.5 mol%). The flower-like Ag/ZnO nanorod prepared with 0.5 mol% Ag by two-step process was found to be the most efficient photocatalyst for the degradation of phenol, which can decompose 90% of phenol within 120 min.

Shockwave-Loading-Induced Enhancement of T c in Superconducting Bi 2Sr 2CaCu 2O 8+δ

DOE PAGES

Liu, Tiansheng; He, Chao; Wang, Fengying; ...

2017-07-27

Here, we report a shockwave method for altering the properties of the superconductor material Bi 2Sr 2CaCu 2O 8+δ (Bi2212). We find that the superconducting transition temperature (T c) increases from 84 K for the pristine sample to 94 K for the sample treated at a temperature and pressure of ~1200 K and ~31 GPa, respectively. X-ray diffraction and transmission electron microscopy characterizations indicate that this T c enhancement arises from a phase transition from pristine Bi2212 to a mixture of superconducting Bi2212 and semiconducting Bi 2Sr 2CuO 6+δ (Bi2201) during the shockwave treatment. The shockwave-treated sample exhibits n-type semiconductormore » properties (with an on-off ratio ~5), in contrast to the pure metallic pristine sample. This study offers an alternative route for modifying the superconducting properties via a shockwave treatment. Furthermore, this method may provide a new approach for studying other temperature- and pressure-sensitive materials.« less

Excellent field emission properties of vertically oriented CuO nanowire films

NASA Astrophysics Data System (ADS)

Feng, Long; Yan, Hui; Li, Heng; Zhang, Rukang; Li, Zhe; Chi, Rui; Yang, Shuaiyu; Ma, Yaya; Fu, Bin; Liu, Jiwen

2018-04-01

Oriented CuO nanowire films were synthesized on a large scale using simple method of direct heating copper grids in air. The field emission properties of the sample can be enhanced by improving the aspect ratio of the nanowires just through a facile method of controlling the synthesis conditions. Although the density of the nanowires is large enough, the screen effect is not an important factor in this field emission process because few nanowires sticking out above the rest. Benefiting from the unique geometrical and structural features, the CuO nanowire samples show excellent field emission (FE) properties. The FE measurements of CuO nanowire films illustrate that the sample synthesized at 500 °C for 8 h has a comparatively low turn-on field of 0.68 V/μm, a low threshold field of 1.1 V/μm, and a large field enhancement factor β of 16782 (a record high value for CuO nanostructures, to the best of our knowledge), indicating that the samples are promising candidates for field emission applications.

Convolutional neural networks based on augmented training samples for synthetic aperture radar target recognition

NASA Astrophysics Data System (ADS)

Yan, Yue

2018-03-01

A synthetic aperture radar (SAR) automatic target recognition (ATR) method based on the convolutional neural networks (CNN) trained by augmented training samples is proposed. To enhance the robustness of CNN to various extended operating conditions (EOCs), the original training images are used to generate the noisy samples at different signal-to-noise ratios (SNRs), multiresolution representations, and partially occluded images. Then, the generated images together with the original ones are used to train a designed CNN for target recognition. The augmented training samples can contrapuntally improve the robustness of the trained CNN to the covered EOCs, i.e., the noise corruption, resolution variance, and partial occlusion. Moreover, the significantly larger training set effectively enhances the representation capability for other conditions, e.g., the standard operating condition (SOC), as well as the stability of the network. Therefore, better performance can be achieved by the proposed method for SAR ATR. For experimental evaluation, extensive experiments are conducted on the Moving and Stationary Target Acquisition and Recognition dataset under SOC and several typical EOCs.

Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath

PubMed Central

Malc, Ewa P.; Jayakody, Chatura N.; Tsuruta, James K.; Mieczkowski, Piotr A.; Janzen, William P.; Dayton, Paul A.

2015-01-01

A perfluorocarbon nanodroplet formulation is shown to be an effective cavitation enhancement agent, enabling rapid and consistent fragmentation of genomic DNA in a standard ultrasonic water bath. This nanodroplet-enhanced method produces genomic DNA libraries and next-generation sequencing results indistinguishable from DNA samples fragmented in dedicated commercial acoustic sonication equipment, and with higher throughput. This technique thus enables widespread access to fast bench-top genomic DNA fragmentation. PMID:26186461

Enhanced Photocatalytic Activity of La3+-Doped TiO2 Nanotubes with Full Wave-Band Absorption

NASA Astrophysics Data System (ADS)

Xia, Minghao; Huang, Lingling; Zhang, Yubo; Wang, Yongqian

2018-06-01

TiO2 nanotubes doped with La3+ were synthesized by anodic oxidation method and the photocatalytic activity was detected by photodegrading methylene blue. As-prepared samples improved the absorption of both ultraviolet light and visible light and have a great enhancement on the photocatalytic activity while contrasting with the pristine TiO2 nanotubes. A tentative mechanism for the enhancement of photocatalytic activity with full wave-band absorption is proposed.

Enhancing forensic science with spectroscopic imaging

NASA Astrophysics Data System (ADS)

Ricci, Camilla; Kazarian, Sergei G.

2006-09-01

This presentation outlines the research we are developing in the area of Fourier Transform Infrared (FTIR) spectroscopic imaging with the focus on materials of forensic interest. FTIR spectroscopic imaging has recently emerged as a powerful tool for characterisation of heterogeneous materials. FTIR imaging relies on the ability of the military-developed infrared array detector to simultaneously measure spectra from thousands of different locations in a sample. Recently developed application of FTIR imaging using an ATR (Attenuated Total Reflection) mode has demonstrated the ability of this method to achieve spatial resolution beyond the diffraction limit of infrared light in air. Chemical visualisation with enhanced spatial resolution in micro-ATR mode broadens the range of materials studied with FTIR imaging with applications to pharmaceutical formulations or biological samples. Macro-ATR imaging has also been developed for chemical imaging analysis of large surface area samples and was applied to analyse the surface of human skin (e.g. finger), counterfeit tablets, textile materials (clothing), etc. This approach demonstrated the ability of this imaging method to detect trace materials attached to the surface of the skin. This may also prove as a valuable tool in detection of traces of explosives left or trapped on the surfaces of different materials. This FTIR imaging method is substantially superior to many of the other imaging methods due to inherent chemical specificity of infrared spectroscopy and fast acquisition times of this technique. Our preliminary data demonstrated that this methodology will provide the means to non-destructive detection method that could relate evidence to its source. This will be important in a wider crime prevention programme. In summary, intrinsic chemical specificity and enhanced visualising capability of FTIR spectroscopic imaging open a window of opportunities for counter-terrorism and crime-fighting, with applications ranging from analysis of trace evidence (e.g. in soil), tablets, drugs, fibres, tape explosives, biological samples to detection of gunshot residues and imaging of fingerprints.

Application of Super-Resolution Convolutional Neural Network for Enhancing Image Resolution in Chest CT.

PubMed

Umehara, Kensuke; Ota, Junko; Ishida, Takayuki

2017-10-18

In this study, the super-resolution convolutional neural network (SRCNN) scheme, which is the emerging deep-learning-based super-resolution method for enhancing image resolution in chest CT images, was applied and evaluated using the post-processing approach. For evaluation, 89 chest CT cases were sampled from The Cancer Imaging Archive. The 89 CT cases were divided randomly into 45 training cases and 44 external test cases. The SRCNN was trained using the training dataset. With the trained SRCNN, a high-resolution image was reconstructed from a low-resolution image, which was down-sampled from an original test image. For quantitative evaluation, two image quality metrics were measured and compared to those of the conventional linear interpolation methods. The image restoration quality of the SRCNN scheme was significantly higher than that of the linear interpolation methods (p < 0.001 or p < 0.05). The high-resolution image reconstructed by the SRCNN scheme was highly restored and comparable to the original reference image, in particular, for a ×2 magnification. These results indicate that the SRCNN scheme significantly outperforms the linear interpolation methods for enhancing image resolution in chest CT images. The results also suggest that SRCNN may become a potential solution for generating high-resolution CT images from standard CT images.

The porous TiO2 nanotubes/Ag3PO4 heterojunction for enhancing sunlight photocatalytic activity

NASA Astrophysics Data System (ADS)

Chi, Chunyan; Pan, Jiaqi; You, Mingzhu; Dong, Zongjun; Zhao, Weijie; Song, Changsheng; Zheng, Yingying; Li, Chaorong

2018-03-01

The porous TiO2 nanotubes/Ag3PO4 heterojunction are synthesized via simple electrospining and chemical co-deposition method. The results of SEM, XRD, TEM and XPS imply that the Ag3PO4 nanoparticles have been introduced on to the surface of TiO2 nanotubes successfully. Compared with the unmodified samples, the photocatalytic activity of the as-prepared porous TiO2 nanotubes/Ag3PO4 heterojunction exhibit a remarkable enhancement by the degradation of methylene blue (MB) under the sunlight. Further, the Z-Scheme structure of the samples and the porous-tubular structure of the TiO2 are considered as the main reasons for the enhancement.

Highly concentrated, ring-shaped phase conversion laser-induced breakdown spectroscopy technology for liquid sample analysis.

PubMed

Lin, Qingyu; Wei, Zhimei; Guo, Hongli; Wang, Shuai; Guo, Guangmeng; Zhang, Zhi; Duan, Yixiang

2017-06-10

A highly concentrated, ring-shaped phase conversion (RSPC) method was developed for liquid sample analysis using the laser-induced breakdown spectroscopy (LIBS) technique. In this work, test samples were prepared by mixing the metal particles with polyvinyl alcohol (PVA) supporter in liquid phase. With heat, the PVA solution solidified inside a modified glass petri dish, forming a metal-enriched polymer ring film. Distinguished from other traditional liquid-to-solid conversing methods, the proposed new method takes advantage of enhanced homogeneity for the target elements inside the ring film. The modified glass petri dish was used to control the ring-shaped concentration. Due to the specially designed circular groove at the bottom of this dish, where the PVA solution and liquid sample mixture accumulated, the target elements were concentrated in this small ring, which is beneficial for enhancing and stabilizing the plasma signals compared to the direct liquid sample analysis using LIBS. The limits of detection for Ag, Cu, Cr, and Ba obtained with the RSPC-LIBS technology were 0.098  μg·mL -1 , 0.18  μg·mL -1 , 0.83  μg·mL -1 , and 0.046  μg·mL -1 , respectively, which provided greater improvement than the direct bulk liquid analysis using LIBS.

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

PubMed

Lu, Qing; Kim, Jaegil; Straub, John E

2013-03-14

The generalized Replica Exchange Method (gREM) is extended into the isobaric-isothermal ensemble, and applied to simulate a vapor-liquid phase transition in Lennard-Jones fluids. Merging an optimally designed generalized ensemble sampling with replica exchange, gREM is particularly well suited for the effective simulation of first-order phase transitions characterized by "backbending" in the statistical temperature. While the metastable and unstable states in the vicinity of the first-order phase transition are masked by the enthalpy gap in temperature replica exchange method simulations, they are transformed into stable states through the parameterized effective sampling weights in gREM simulations, and join vapor and liquid phases with a succession of unimodal enthalpy distributions. The enhanced sampling across metastable and unstable states is achieved without the need to identify a "good" order parameter for biased sampling. We performed gREM simulations at various pressures below and near the critical pressure to examine the change in behavior of the vapor-liquid phase transition at different pressures. We observed a crossover from the first-order phase transition at low pressure, characterized by the backbending in the statistical temperature and the "kink" in the Gibbs free energy, to a continuous second-order phase transition near the critical pressure. The controlling mechanisms of nucleation and continuous phase transition are evident and the coexistence properties and phase diagram are found in agreement with literature results.

Automatic segmentation of Leishmania parasite in microscopic images using a modified CV level set method

NASA Astrophysics Data System (ADS)

Farahi, Maria; Rabbani, Hossein; Talebi, Ardeshir; Sarrafzadeh, Omid; Ensafi, Shahab

2015-12-01

Visceral Leishmaniasis is a parasitic disease that affects liver, spleen and bone marrow. According to World Health Organization report, definitive diagnosis is possible just by direct observation of the Leishman body in the microscopic image taken from bone marrow samples. We utilize morphological and CV level set method to segment Leishman bodies in digital color microscopic images captured from bone marrow samples. Linear contrast stretching method is used for image enhancement and morphological method is applied to determine the parasite regions and wipe up unwanted objects. Modified global and local CV level set methods are proposed for segmentation and a shape based stopping factor is used to hasten the algorithm. Manual segmentation is considered as ground truth to evaluate the proposed method. This method is tested on 28 samples and achieved 10.90% mean of segmentation error for global model and 9.76% for local model.

DNA-PK assay

DOEpatents

Anderson, Carl W.; Connelly, Margery A.

2004-10-12

The present invention provides a method for detecting DNA-activated protein kinase (DNA-PK) activity in a biological sample. The method includes contacting a biological sample with a detectably-labeled phosphate donor and a synthetic peptide substrate defined by the following features to provide specific recognition and phosphorylation by DNA-PK: (1) a phosphate-accepting amino acid pair which may include serine-glutamine (Ser-Gln) (SQ), threonine-glutamine (Thr-Gln) (TQ), glutamine-serine (Gln-Ser) (QS), or glutamine-threonine (Gln-Thr) (QT); (2) enhancer amino acids which may include glutamic acid or glutamine immediately adjacent at the amino- or carboxyl- side of the amino acid pair and forming an amino acid pair-enhancer unit; (3) a first spacer sequence at the amino terminus of the amino acid pair-enhancer unit; (4) a second spacer sequence at the carboxyl terminus of the amino acid pair-enhancer unit, which spacer sequences may include any combination of amino acids that does not provide a phosphorylation site consensus sequence motif; and, (5) a tag moiety, which may be an amino acid sequence or another chemical entity that permits separating the synthetic peptide from the phosphate donor. A compostion and a kit for the detection of DNA-PK activity are also provided. Methods for detecting DNA, protein phosphatases and substances that alter the activity of DNA-PK are also provided. The present invention also provides a method of monitoring protein kinase and DNA-PK activity in living cells. -A composition and a kit for monitoring protein kinase activity in vitro and a composition and a kit for monitoring DNA-PK activities in living cells are also provided. A method for identifying agents that alter protein kinase activity in vitro and a method for identifying agents that alter DNA-PK activity in living cells are also provided.

Synthesis of n-type Bi4-xLaxTi3O12 (x=0 to 0.45) by alternative mechanochemical method

NASA Astrophysics Data System (ADS)

Sharanappa, Nagbasavanna

2017-05-01

Lanthanum doped bismuth titanate ceramic samples have been successfully synthesized by mechanochemical method showed good properties and have investigated the structure, microstructure, dielectric, Curie-Weiss behavior, thermoelectric properties, which resulted from substitution of La-ions in bismuth titanate. Plate-like shape with enhanced density is observed in the SEM micrographs. Ceramic samples exhibiting relaxor ferroelectric behavior by satisfying Curie-Weiss law. Thermoelectric studies reveal n-type semiconducting behavior of these samples. Synthesized compounds explored these desirable properties for innovative semiconductor based device applications.

Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment

NASA Astrophysics Data System (ADS)

Lv, Chao; Zheng, Lianqing; Yang, Wei

2012-01-01

Molecular dynamics sampling can be enhanced via the promoting of potential energy fluctuations, for instance, based on a Hamiltonian modified with the addition of a potential-energy-dependent biasing term. To overcome the diffusion sampling issue, which reveals the fact that enlargement of event-irrelevant energy fluctuations may abolish sampling efficiency, the essential energy space random walk (EESRW) approach was proposed earlier. To more effectively accelerate the sampling of solute conformations in aqueous environment, in the current work, we generalized the EESRW method to a two-dimension-EESRW (2D-EESRW) strategy. Specifically, the essential internal energy component of a focused region and the essential interaction energy component between the focused region and the environmental region are employed to define the two-dimensional essential energy space. This proposal is motivated by the general observation that in different conformational events, the two essential energy components have distinctive interplays. Model studies on the alanine dipeptide and the aspartate-arginine peptide demonstrate sampling improvement over the original one-dimension-EESRW strategy; with the same biasing level, the present generalization allows more effective acceleration of the sampling of conformational transitions in aqueous solution. The 2D-EESRW generalization is readily extended to higher dimension schemes and employed in more advanced enhanced-sampling schemes, such as the recent orthogonal space random walk method.

Improved accuracy of quantitative parameter estimates in dynamic contrast-enhanced CT study with low temporal resolution

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

Kim, Sun Mo, E-mail: Sunmo.Kim@rmp.uhn.on.ca; Haider, Masoom A.; Jaffray, David A.

Purpose: A previously proposed method to reduce radiation dose to patient in dynamic contrast-enhanced (DCE) CT is enhanced by principal component analysis (PCA) filtering which improves the signal-to-noise ratio (SNR) of time-concentration curves in the DCE-CT study. The efficacy of the combined method to maintain the accuracy of kinetic parameter estimates at low temporal resolution is investigated with pixel-by-pixel kinetic analysis of DCE-CT data. Methods: The method is based on DCE-CT scanning performed with low temporal resolution to reduce the radiation dose to the patient. The arterial input function (AIF) with high temporal resolution can be generated with a coarselymore » sampled AIF through a previously published method of AIF estimation. To increase the SNR of time-concentration curves (tissue curves), first, a region-of-interest is segmented into squares composed of 3 × 3 pixels in size. Subsequently, the PCA filtering combined with a fraction of residual information criterion is applied to all the segmented squares for further improvement of their SNRs. The proposed method was applied to each DCE-CT data set of a cohort of 14 patients at varying levels of down-sampling. The kinetic analyses using the modified Tofts’ model and singular value decomposition method, then, were carried out for each of the down-sampling schemes between the intervals from 2 to 15 s. The results were compared with analyses done with the measured data in high temporal resolution (i.e., original scanning frequency) as the reference. Results: The patients’ AIFs were estimated to high accuracy based on the 11 orthonormal bases of arterial impulse responses established in the previous paper. In addition, noise in the images was effectively reduced by using five principal components of the tissue curves for filtering. Kinetic analyses using the proposed method showed superior results compared to those with down-sampling alone; they were able to maintain the accuracy in the quantitative histogram parameters of volume transfer constant [standard deviation (SD), 98th percentile, and range], rate constant (SD), blood volume fraction (mean, SD, 98th percentile, and range), and blood flow (mean, SD, median, 98th percentile, and range) for sampling intervals between 10 and 15 s. Conclusions: The proposed method of PCA filtering combined with the AIF estimation technique allows low frequency scanning for DCE-CT study to reduce patient radiation dose. The results indicate that the method is useful in pixel-by-pixel kinetic analysis of DCE-CT data for patients with cervical cancer.« less

Surface-Tension Replica-Exchange Molecular Dynamics Method for Enhanced Sampling of Biological Membrane Systems.

PubMed

Mori, Takaharu; Jung, Jaewoon; Sugita, Yuji

2013-12-10

Conformational sampling is fundamentally important for simulating complex biomolecular systems. The generalized-ensemble algorithm, especially the temperature replica-exchange molecular dynamics method (T-REMD), is one of the most powerful methods to explore structures of biomolecules such as proteins, nucleic acids, carbohydrates, and also of lipid membranes. T-REMD simulations have focused on soluble proteins rather than membrane proteins or lipid bilayers, because explicit membranes do not keep their structural integrity at high temperature. Here, we propose a new generalized-ensemble algorithm for membrane systems, which we call the surface-tension REMD method. Each replica is simulated in the NPγT ensemble, and surface tensions in a pair of replicas are exchanged at certain intervals to enhance conformational sampling of the target membrane system. We test the method on two biological membrane systems: a fully hydrated DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine) lipid bilayer and a WALP23-POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane system. During these simulations, a random walk in surface tension space is realized. Large-scale lateral deformation (shrinking and stretching) of the membranes takes place in all of the replicas without collapse of the lipid bilayer structure. There is accelerated lateral diffusion of DPPC lipid molecules compared with conventional MD simulation, and a much wider range of tilt angle of the WALP23 peptide is sampled due to large deformation of the POPC lipid bilayer and through peptide-lipid interactions. Our method could be applicable to a wide variety of biological membrane systems.

The Effect of WhatsApp Chat Group in Enhancing EFL Learners' Verbal Interaction outside Classroom Contexts

ERIC Educational Resources Information Center

Minalla, Amir Abdalla

2018-01-01

This study was mainly conducted to examine the possibility of utilizing "WhatsApp Group" in enhancing EFL learners' verbal interaction. To do this experimental and descriptive methods were used to achieve the objective of this study. A questionnaire and pre- and post-test were adopted as tools for data collection. Samples of two groups…

Improvements to sample processing and measurement to enable more widespread environmental application of tritium.

PubMed

Moran, James; Alexander, Thomas; Aalseth, Craig; Back, Henning; Mace, Emily; Overman, Cory; Seifert, Allen; Freeburg, Wilcox

2017-08-01

Previous measurements have demonstrated the wealth of information that tritium (T) can provide on environmentally relevant processes. We present modifications to sample preparation approaches that enable T measurement by proportional counting on small sample sizes equivalent to 120mg of water and demonstrate the accuracy of these methods on a suite of standardized water samples. We identify a current quantification limit of 92.2 TU which, combined with our small sample sizes, correlates to as little as 0.00133Bq of total T activity. This enhanced method should provide the analytical flexibility needed to address persistent knowledge gaps in our understanding of both natural and artificial T behavior in the environment. Copyright © 2017. Published by Elsevier Ltd.

Improvements to sample processing and measurement to enable more widespread environmental application of tritium

DOE PAGES

Moran, James; Alexander, Thomas; Aalseth, Craig; ...

2017-01-26

Previous measurements have demonstrated the wealth of information that tritium (T) can provide on environmentally relevant processes. Here, we present modifications to sample preparation approaches that enable T measurement by proportional counting on small sample sizes equivalent to 120 mg of water and demonstrate the accuracy of these methods on a suite of standardized water samples. We also identify a current quantification limit of 92.2 TU which, combined with our small sample sizes, correlates to as little as 0.00133 Bq of total T activity. Furthermore, this enhanced method should provide the analytical flexibility needed to address persistent knowledge gaps inmore » our understanding of both natural and artificial T behavior in the environment.« less

Combined optical coherence tomography and hyper-spectral imaging using a double clad fiber coupler

NASA Astrophysics Data System (ADS)

Guay-Lord, Robin; Lurie, Kristen L.; Attendu, Xavier; Mageau, Lucas; Godbout, Nicolas; Ellerbee Bowden, Audrey K.; Strupler, Mathias; Boudoux, Caroline

2016-03-01

This proceedings shows the combination of Optical Coherence Tomography (OCT) and Hyper-Spectral Imaging (HSI) using a double-clad optical fiber. The single mode core of the fiber is used to transmit OCT signals, while the cladding, with its large collection area, provides an efficient way to capture the reflectance spectrum of the sample. The combination of both methods enables three-dimensional acquisition of sample morphology with OCT, enhanced by the molecular information contained in its hyper-spectral image. We believe that the combination of these techniques could result in endoscopes with enhanced tissue identification capability.

Studying the Global Bifurcation Involving Wada Boundary Metamorphosis by a Method of Generalized Cell Mapping with Sampling-Adaptive Interpolation

NASA Astrophysics Data System (ADS)

Liu, Xiao-Ming; Jiang, Jun; Hong, Ling; Tang, Dafeng

In this paper, a new method of Generalized Cell Mapping with Sampling-Adaptive Interpolation (GCMSAI) is presented in order to enhance the efficiency of the computation of one-step probability transition matrix of the Generalized Cell Mapping method (GCM). Integrations with one mapping step are replaced by sampling-adaptive interpolations of third order. An explicit formula of interpolation error is derived for a sampling-adaptive control to switch on integrations for the accuracy of computations with GCMSAI. By applying the proposed method to a two-dimensional forced damped pendulum system, global bifurcations are investigated with observations of boundary metamorphoses including full to partial and partial to partial as well as the birth of fully Wada boundary. Moreover GCMSAI requires a computational time of one thirtieth up to one fiftieth compared to that of the previous GCM.

Towards ultrasensitive malaria diagnosis using surface enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Keren; Yuen, Clement; Aniweh, Yaw; Preiser, Peter; Liu, Quan

2016-02-01

We report two methods of surface enhanced Raman spectroscopy (SERS) for hemozoin detection in malaria infected human blood. In the first method, silver nanoparticles were synthesized separately and then mixed with lysed blood; while in the second method, silver nanoparticles were synthesized directly inside the parasites of Plasmodium falciparum. It was observed that the first method yields a smaller variation in SERS measurements and stronger correlation between the estimated contribution of hemozoin and the parasitemia level, which is preferred for the quantification of the parasitemia level. In contrast, the second method yields a higher sensitivity to a low parasitemia level thus could be more effective in the early malaria diagnosis to determine whether a given blood sample is positive.

Enhanced cellular infiltration of human adipose-derived stem cells in allograft menisci using a needle-punch method.

PubMed

Nordberg, Rachel C; Charoenpanich, Adisri; Vaughn, Christopher E; Griffith, Emily H; Fisher, Matthew B; Cole, Jacqueline H; Spang, Jeffrey T; Loboa, Elizabeth G

2016-10-28

The meniscus plays a crucial role in knee joint stability, load transmission, and stress distribution. Meniscal tears are the most common reported knee injuries, and the current standard treatment for meniscal deficiency is meniscal allograft transplantation. A major limitation of this approach is that meniscal allografts do not have the capacity to remodel and maintain tissue homeostasis due to a lack of cellular infiltration. The purpose of this study was to provide a new method for enhanced cellular infiltration in meniscal allografts. Twenty medial menisci were collected from cadaveric human sources and split into five experimental groups: (1) control native menisci, (2) decellularized menisci, (3) decellularized menisci seeded with human adipose-derived stem cells (hASC), (4) decellularized needle-punched menisci, and (5) decellularized needle-punched menisci seeded with hASC. All experimental allografts were decellularized using a combined method with trypsin EDTA and peracetic acid. Needle punching (1-mm spacing, 28 G microneedle) was utilized to improve porosity of the allograft. Samples were recellularized with hASC at a density of 250 k/g of tissue. After 28 days of in vitro culture, menisci were analyzed for mechanical, biochemical, and histological characteristics. Menisci maintained structural integrity and material properties (compressive equilibrium and dynamic moduli) throughout preparations. Increased DNA content was observed in the needle-punched menisci but not in the samples without needle punching. Histology confirmed these results, showing enhanced cellular infiltration in needle-punched samples. The enhanced infiltration achieved in this study could help meniscal allografts better remodel post-surgery. The integration of autologous adipose-derived stem cells could improve long-term efficacy of meniscal transplantation procedures by helping to maintain the meniscus in vivo.

Indirect antiglobulin test-crossmatch using low-ionic-strength saline-albumin enhancement medium and reduced incubation time: effectiveness in the detection of most clinically significant antibodies and impact on blood utilization.

PubMed

Dinardo, C L; Bonifácio, S L; Mendrone, A

2014-01-01

Indirect antiglobulin test-crossmatch (IAT-XM) using enhancement media such as low-ionic-strength saline (LISS) and polyethylene glycol (PEG) usually requires 15 minutes of incubation. These methods are necessary when testing samples from blood recipients who have a higher risk of alloimmunization. In emergency situations, IAT-XM can be time-consuming and can influence presurgery routine, resulting in more red blood cell (RBC) units being tested and stored to avoid the transfusion of uncrossmatched ones. The objective of this study was to evaluate the performance of a LISS-albumin enhancer to intensify antigen-antibody reaction after 5 minutes of 37oC incubation and compare this performance with that of other enhancers, gel, and conventional tube testing. Second, the study evaluated the impact of this method's implementation in the C:T ratio (crossmatched to transfused RBC units) of a transfusion laboratory. Ninety serum samples containing alloantibodies of potential clinical significance were tested against phenotyped RBCs using four different methods: (1) tube with LISS-albumin enhancer (5 minutes of incubation), (2) tube with LISS-albumin and PEG (15 minutes of incubation), (3) gel, and (4) conventional tube method (60 minutes of incubation). In parallel, the study compared the C:T ratio of a tertiary-hospital transfusion laboratory in two different periods: 3 months before and 3 months after the implementation of the 5-minute IAT-XM protocol. The use of LISS-albumin with 5 minutes of incubation exhibited the same performance as LISS-albumin, PEG, and gel with 15 minutes of incubation. Conventional tube method results were equally comparable, but reactions were significantly less intense, except for anti-c (p = 0.406). Accuracy was 100 percent for all selected methods. After the implementation of the 5-minute IAT-XM protocol, the C:T ratio fell from 2.74 to 1.29 (p < 0.001). IAT-XM can have its incubation time reduced to 5 minutes with the use of LISS-albumin enhancement. We suggest this strategy should be used to quickly prepare RBC units for surgical patients, keeping transfusion safety without compromising blood supplies.

Enhancing analysis throughput, sensitivity and specificity in LC/ESI-MS/MS assay of plasma 25-hydroxyvitamin D3 by derivatization with triplex 4-(4-dimethylaminophenyl)-1,2,4-triazoline-3,5-dione (DAPTAD) isotopologues.

PubMed

Ogawa, Shoujiro; Kittaka, Hiroki; Nakata, Akiho; Komatsu, Kenji; Sugiura, Takahiro; Satoh, Mamoru; Nomura, Fumio; Higashi, Tatsuya

2017-03-20

The plasma/serum concentration of 25-hydroxyvitamin D 3 [25(OH)D 3 ] is a diagnostic index for vitamin D deficiency/insufficiency, which is associated with a wide range of diseases, such as rickets, cancer and diabetes. We have reported that the derivatization with 4-(4-dimethylaminophenyl)-1,2,4-triazoline-3,5-dione (DAPTAD) works well in the liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) assay of the serum/plasma 25(OH)D 3 for enhancing the sensitivity and the separation from a potent interfering metabolite, 3-epi-25-hydroxyvitamin D 3 [3-epi-25(OH)D 3 ]. However, enhancing the analysis throughput remains an issue in the LC/ESI-MS/MS assay of 25(OH)D 3 . The most obvious restriction of the LC/MS/MS throughput is the chromatographic run time. In this study, we developed an enhanced throughput method for the determination of the plasma 25(OH)D 3 by LC/ESI-MS/MS combined with the derivatization using the triplex ( 2 H 0 -, 2 H 3 - and 2 H 6 -) DAPTAD isotopologues. After separate derivatization with 1 of 3 different isotopologues, the 3 samples were combined and injected together into LC/ESI-MS/MS. Based on the mass differences between the isotopologues, the derivatized 25(OH)D 3 in the 3 different samples were quantified within a single run. The developed method tripled the hourly analysis throughput without sacrificing assay performance, i.e., ease of pretreatment of plasma sample (only deproteinization), limit of quantification (1.0ng/mL when a 5μL-plasma was used), precision (intra-assay RSD≤5.9% and inter-assay RSD≤5.5%), accuracy (98.7-102.2%), matrix effects, and capability of separating from an interfering metabolite, 3-epi-25(OH)D 3 . The multiplexing of samples by the isotopologue derivatization was applied to the analysis of plasma samples of healthy subjects and the developed method was proven to have a satisfactory applicability. Copyright © 2016 Elsevier B.V. All rights reserved.

Spatial resolution enhancement of terrestrial features using deconvolved SSM/I microwave brightness temperatures

NASA Technical Reports Server (NTRS)

Farrar, Michael R.; Smith, Eric A.

1992-01-01

A method for enhancing the 19, 22, and 37 GHz measurements of the SSM/I (Special Sensor Microwave/Imager) to the spatial resolution and sampling density of the high resolution 85-GHz channel is presented. An objective technique for specifying the tuning parameter, which balances the tradeoff between resolution and noise, is developed in terms of maximizing cross-channel correlations. Various validation procedures are performed to demonstrate the effectiveness of the method, which hopefully will provide researchers with a valuable tool in multispectral applications of satellite radiometer data.

Achieving high thermoelectric performance of Cu1.8S composites with WSe2 nanoparticles.

PubMed

Qin, Peng; Ge, Zhen-Hua; Chen, Yue-Xing; Chong, Xiaoyu; Feng, Jing; He, Jiaqing

2018-08-24

Polycrystalline p-type Cu 1.8 S composites with WSe 2 nanoparticles were fabricated by the mechanical alloying method combined with the spark plasma sintering technique. The Seebeck coefficient was significantly enhanced by the optimized carrier concentration, while the thermal conductivity was simultaneously decreased due to the refined grain and WSe 2 nanoparticles. An enhanced Seebeck coefficient of 110 μV K -1 and a reduced thermal conductivity of 0.68 W m -1 K -1 were obtained for the Cu 1.8 S + 1 wt% WSe 2 sample at 773 K, resulting in a remarkably enhanced peak ZT of 1.22 at 773 K, which is 2.5 times higher than that (0.49 at 773 K) of a pristine Cu 1.8 S sample. The cheap and environmentally friendly Cu 1.8 S-based materials with enhanced properties may find promising applications in thermoelectric devices.

Statistical CT noise reduction with multiscale decomposition and penalized weighted least squares in the projection domain

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

Tang Shaojie; Tang Xiangyang; School of Automation, Xi'an University of Posts and Telecommunications, Xi'an, Shaanxi 710121

2012-09-15

Purposes: The suppression of noise in x-ray computed tomography (CT) imaging is of clinical relevance for diagnostic image quality and the potential for radiation dose saving. Toward this purpose, statistical noise reduction methods in either the image or projection domain have been proposed, which employ a multiscale decomposition to enhance the performance of noise suppression while maintaining image sharpness. Recognizing the advantages of noise suppression in the projection domain, the authors propose a projection domain multiscale penalized weighted least squares (PWLS) method, in which the angular sampling rate is explicitly taken into consideration to account for the possible variation ofmore » interview sampling rate in advanced clinical or preclinical applications. Methods: The projection domain multiscale PWLS method is derived by converting an isotropic diffusion partial differential equation in the image domain into the projection domain, wherein a multiscale decomposition is carried out. With adoption of the Markov random field or soft thresholding objective function, the projection domain multiscale PWLS method deals with noise at each scale. To compensate for the degradation in image sharpness caused by the projection domain multiscale PWLS method, an edge enhancement is carried out following the noise reduction. The performance of the proposed method is experimentally evaluated and verified using the projection data simulated by computer and acquired by a CT scanner. Results: The preliminary results show that the proposed projection domain multiscale PWLS method outperforms the projection domain single-scale PWLS method and the image domain multiscale anisotropic diffusion method in noise reduction. In addition, the proposed method can preserve image sharpness very well while the occurrence of 'salt-and-pepper' noise and mosaic artifacts can be avoided. Conclusions: Since the interview sampling rate is taken into account in the projection domain multiscale decomposition, the proposed method is anticipated to be useful in advanced clinical and preclinical applications where the interview sampling rate varies.« less

Modulation infrared thermometry of caloric effects at up to kHz frequencies

NASA Astrophysics Data System (ADS)

Döntgen, Jago; Rudolph, Jörg; Waske, Anja; Hägele, Daniel

2018-03-01

We present a novel non-contact method for the direct measurement of caloric effects in low volume samples. The adiabatic temperature change ΔT of a magnetocaloric sample is very sensitively determined from thermal radiation. Rapid modulation of ΔT is induced by an oscillating external magnetic field. Detection of thermal radiation with a mercury-cadmium-telluride detector allows for measurements at field frequencies exceeding 1 kHz. In contrast to thermoacoustic methods, our method can be employed in vacuum which enhances adiabatic conditions especially in the case of small volume samples. Systematic measurements of the magnetocaloric effect as a function of temperature, magnetic field amplitude, and modulation frequency give a detailed picture of the thermal behavior of the sample. Highly sensitive measurements of the magnetocaloric effect are demonstrated on a 2 mm thick sample of gadolinium and a 60 μm thick Fe80B12Nb8 ribbon.

Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways

PubMed Central

Wu, Dongsheng; Fajer, Mikolai I.; Cao, Liaoran; Cheng, Xiaolin; Yang, Wei

2016-01-01

Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this mini presentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study. PMID:27498634

[Spectral scatter correction of coal samples based on quasi-linear local weighted method].

PubMed

Lei, Meng; Li, Ming; Ma, Xiao-Ping; Miao, Yan-Zi; Wang, Jian-Sheng

2014-07-01

The present paper puts forth a new spectral correction method based on quasi-linear expression and local weighted function. The first stage of the method is to search 3 quasi-linear expressions to replace the original linear expression in MSC method, such as quadratic, cubic and growth curve expression. Then the local weighted function is constructed by introducing 4 kernel functions, such as Gaussian, Epanechnikov, Biweight and Triweight kernel function. After adding the function in the basic estimation equation, the dependency between the original and ideal spectra is described more accurately and meticulously at each wavelength point. Furthermore, two analytical models were established respectively based on PLS and PCA-BP neural network method, which can be used for estimating the accuracy of corrected spectra. At last, the optimal correction mode was determined by the analytical results with different combination of quasi-linear expression and local weighted function. The spectra of the same coal sample have different noise ratios while the coal sample was prepared under different particle sizes. To validate the effectiveness of this method, the experiment analyzed the correction results of 3 spectral data sets with the particle sizes of 0.2, 1 and 3 mm. The results show that the proposed method can eliminate the scattering influence, and also can enhance the information of spectral peaks. This paper proves a more efficient way to enhance the correlation between corrected spectra and coal qualities significantly, and improve the accuracy and stability of the analytical model substantially.

Typing DNA profiles from previously enhanced fingerprints using direct PCR.

PubMed

Templeton, Jennifer E L; Taylor, Duncan; Handt, Oliva; Linacre, Adrian

2017-07-01

Fingermarks are a source of human identification both through the ridge patterns and DNA profiling. Typing nuclear STR DNA markers from previously enhanced fingermarks provides an alternative method of utilising the limited fingermark deposit that can be left behind during a criminal act. Dusting with fingerprint powders is a standard method used in classical fingermark enhancement and can affect DNA data. The ability to generate informative DNA profiles from powdered fingerprints using direct PCR swabs was investigated. Direct PCR was used as the opportunity to generate usable DNA profiles after performing any of the standard DNA extraction processes is minimal. Omitting the extraction step will, for many samples, be the key to success if there is limited sample DNA. DNA profiles were generated by direct PCR from 160 fingermarks after treatment with one of the following dactyloscopic fingerprint powders: white hadonite; silver aluminium; HiFi Volcano silk black; or black magnetic fingerprint powder. This was achieved by a combination of an optimised double-swabbing technique and swab media, omission of the extraction step to minimise loss of critical low-template DNA, and additional AmpliTaq Gold ® DNA polymerase to boost the PCR. Ninety eight out of 160 samples (61%) were considered 'up-loadable' to the Australian National Criminal Investigation DNA Database (NCIDD). The method described required a minimum of working steps, equipment and reagents, and was completed within 4h. Direct PCR allows the generation of DNA profiles from enhanced prints without the need to increase PCR cycle numbers beyond manufacturer's recommendations. Particular emphasis was placed on preventing contamination by applying strict protocols and avoiding the use of previously used fingerprint brushes. Based on this extensive survey, the data provided indicate minimal effects of any of these four powders on the chance of obtaining DNA profiles from enhanced fingermarks. Copyright © 2017 Elsevier B.V. All rights reserved.

A Novel Qualitative Method to Improve Access, Elicitation, and Sample Diversification for Enhanced Transferability Applied to Studying Chemistry Outreach

ERIC Educational Resources Information Center

Pratt, Justin M.; Yezierski, Ellen J.

2018-01-01

Conducting qualitative research in any discipline warrants two actions: accessing participants and eliciting their ideas. In chemistry education research (CER), survey techniques have been used to increase access to participants and diversify samples. Interview tasks (such as card sorting, using demonstrations, and using simulations) have been…

Derivatization reaction-based surface-enhanced Raman scattering (SERS) for detection of trace acetone.

PubMed

Zheng, Ying; Chen, Zhuo; Zheng, Chengbin; Lee, Yong-Ill; Hou, Xiandeng; Wu, Li; Tian, Yunfei

2016-08-01

A facile method was developed for determination of trace volatile acetone by coupling a derivatization reaction to surface-enhanced Raman scattering (SERS). With iodide modified Ag nanoparticles (Ag IMNPs) as the SERS substrate, acetone without obvious Raman signal could be converted to SERS-sensitive species via a chemical derivatization reaction with 2,4-dinitrophenylhydrazine (2,4-DNPH). In addition, acetone can be effectively separated from liquid phase with a purge-sampling device and then any serious interference from sample matrices can be significantly reduced. The optimal conditions for the derivatization reaction and the SERS analysis were investigated in detail, and the selectivity and reproducibility of this method were also evaluated. Under the optimal conditions, the limit of detection (LOD) for acetone was 5mgL(-1) or 0.09mM (3σ). The relative standard deviation (RSD) for 80mgL(-1) acetone (n=9) was 1.7%. This method was successfully used for the determination of acetone in artificial urine and human urine samples with spiked recoveries ranging from 92% to 110%. The present method is convenient, sensitive, selective, reliable and suitable for analysis of trace acetone, and it could have a promising clinical application in early diabetes diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Combining Different Conceptual Change Methods within 5E Model: A Sample Teaching Design of "Cell" Concept and its Organelles

ERIC Educational Resources Information Center

Urey, Mustafa; Calik, Muammer

2008-01-01

Since students' misconceptions are not completely remedied by means of only one conceptual change method, the authors assume that using different conceptual methods embedded within the 5E model will not only be more effective in enhancing students' conceptual understanding, but also may eliminate all students' misconceptions. The aim of this study…

Ion-pairing HPLC methods to determine EDTA and DTPA in small molecule and biological pharmaceutical formulations.

PubMed

Wang, George; Tomasella, Frank P

2016-06-01

Ion-pairing high-performance liquid chromatography-ultraviolet (HPLC-UV) methods were developed to determine two commonly used chelating agents, ethylenediaminetetraacetic acid (EDTA) in Abilify® (a small molecule drug with aripiprazole as the active pharmaceutical ingredient) oral solution and diethylenetriaminepentaacetic acid (DTPA) in Yervoy® (a monoclonal antibody drug with ipilimumab as the active pharmaceutical ingredient) intravenous formulation. Since the analytes, EDTA and DTPA, do not contain chromophores, transition metal ions (Cu 2+ , Fe 3+ ) which generate highly stable metallocomplexes with the chelating agents were added into the sample preparation to enhance UV detection. The use of metallocomplexes with ion-pairing chromatography provides the ability to achieve the desired sensitivity and selectivity in the development of the method. Specifically, the sample preparation involving metallocomplex formation allowed sensitive UV detection. Copper was utilized for the determination of EDTA and iron was utilized for the determination of DTPA. In the case of EDTA, a gradient mobile phase separated the components of the formulation from the analyte. In the method for DTPA, the active drug substance, ipilimumab, was eluted in the void. In addition, the optimization of the concentration of the ion-pairing reagent was discussed as a means of enhancing the retention of the aminopolycarboxylic acids (APCAs) including EDTA and DTPA and the specificity of the method. The analytical method development was designed based on the chromatographic properties of the analytes, the nature of the sample matrix and the intended purpose of the method. Validation data were presented for the two methods. Finally, both methods were successfully utilized in determining the fate of the chelates.

Permeability enhancement by shock cooling

NASA Astrophysics Data System (ADS)

Griffiths, Luke; Heap, Michael; Reuschlé, Thierry; Baud, Patrick; Schmittbuhl, Jean

2015-04-01

The permeability of an efficient reservoir, e.g. a geothermal reservoir, should be sufficient to permit the circulation of fluids. Generally speaking, permeability decreases over the life cycle of the geothermal system. As a result, is usually necessary to artificially maintain and enhance the natural permeability of these systems. One of the methods of enhancement -- studied here -- is thermal stimulation (injecting cold water at low pressure). This goal of this method is to encourage new thermal cracks within the reservoir host rocks, thereby increasing reservoir permeability. To investigate the development of thermal microcracking in the laboratory we selected two granites: a fine-grained (Garibaldi Grey granite, grain size = 0.5 mm) and a course-grained granite (Lanhelin granite, grain size = 2 mm). Both granites have an initial porosity of about 1%. Our samples were heated to a range of temperatures (100-1000 °C) and were either cooled slowly (1 °C/min) or shock cooled (100 °C/s). A systematic microstructural (2D crack area density, using standard stereological techniques, and 3D BET specific surface area measurements) and rock physical property (porosity, P-wave velocity, uniaxial compressive strength, and permeability) analysis was undertaken to understand the influence of slow and shock cooling on our reservoir granites. Microstructurally, we observe that the 2D crack surface area per unit volume and the specific surface area increase as a result of thermal stressing, and, for the same maximum temperature, crack surface area is higher in the shock cooled samples. This observation is echoed by our rock physical property measurements: we see greater changes for the shock cooled samples. We can conclude that shock cooling is an extremely efficient method of generating thermal microcracks and modifying rock physical properties. Our study highlights that thermal treatments are likely to be an efficient method for the "matrix" permeability enhancement of granitic geothermal reservoirs.

New approaches to the analysis of complex samples using fluorescence lifetime techniques and organized media

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

Hertz, P.R.

Fluorescence spectroscopy is a highly sensitive and selective tool for the analysis of complex systems. In order to investigate the efficacy of several steady state and dynamic techniques for the analysis of complex systems, this work focuses on two types of complex, multicomponent samples: petrolatums and coal liquids. It is shown in these studies dynamic, fluorescence lifetime-based measurements provide enhanced discrimination between complex petrolatum samples. Additionally, improved quantitative analysis of multicomponent systems is demonstrated via incorporation of organized media in coal liquid samples. This research provides the first systematic studies of (1) multifrequency phase-resolved fluorescence spectroscopy for dynamic fluorescence spectralmore » fingerprinting of complex samples, and (2) the incorporation of bile salt micellar media to improve accuracy and sensitivity for characterization of complex systems. In the petroleum studies, phase-resolved fluorescence spectroscopy is used to combine spectral and lifetime information through the measurement of phase-resolved fluorescence intensity. The intensity is collected as a function of excitation and emission wavelengths, angular modulation frequency, and detector phase angle. This multidimensional information enhances the ability to distinguish between complex samples with similar spectral characteristics. Examination of the eigenvalues and eigenvectors from factor analysis of phase-resolved and steady state excitation-emission matrices, using chemometric methods of data analysis, confirms that phase-resolved fluorescence techniques offer improved discrimination between complex samples as compared with conventional steady state methods.« less

Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field.

PubMed

Abella, Jayvee R; Cheng, Sara Y; Wang, Qiantao; Yang, Wei; Ren, Pengyu

2014-07-08

The orthogonal space random walk (OSRW) method has shown enhanced sampling efficiency in free energy calculations from previous studies. In this study, the implementation of OSRW in accordance with the polarizable AMOEBA force field in TINKER molecular modeling software package is discussed and subsequently applied to the hydration free energy calculation of 20 small organic molecules, among which 15 are positively charged and five are neutral. The calculated hydration free energies of these molecules are compared with the results obtained from the Bennett acceptance ratio method using the same force field, and overall an excellent agreement is obtained. The convergence and the efficiency of the OSRW are also discussed and compared with BAR. Combining enhanced sampling techniques such as OSRW with polarizable force fields is very promising for achieving both accuracy and efficiency in general free energy calculations.

Nanoscale surface modification of glass using a 1064 nm pulsed laser

NASA Astrophysics Data System (ADS)

Theppakuttai, Senthil; Chen, Shaochen

2003-07-01

We report a method to produce nanopatterns on borosilicate glass by a Nd:yttrium-aluminum-garnet laser (10 ns, 1064 nm), using silica nanospheres. Nonlinear absorption of the enhanced optical field between the spheres and glass sample is believed to be the primary reason for the creation of nanofeatures on the glass substrate. By shining the laser beam from the backside of the glass sample, the scattering effects are minimized and only the direct field enhancement due to the spheres is utilized for surface patterning. To confirm this, calculations based on the Mie scattering theory were performed, and the resulting intensity as a function of scattering angles are presented. The nanofeatures thus obtained by this method are 350 nm in diameter and the distance between them is around 640 nm, which is same as the size of spheres used.

Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations.

PubMed

Cuendet, Michel A; Tuckerman, Mark E

2014-08-12

In molecular dynamics simulations, most enhanced sampling methods are traditionally associated with one particular estimator to calculate the free energy surface (FES), such as the histogram, the mean force, or the bias potential. Here, we start from the realization that four enhanced sampling methods, metadynamics and well-tempered metadynamics (in their extended Lagrangian form), as well as driven adiabatic free energy dynamics (dAFED) and unified free energy dynamics (UFED), can be used in combination with any of the three above-mentioned FES estimators. We compare the convergence properties of these estimators on the alanine dipeptide and a sodium ion solvation shell. We find that the mean force estimator is superior in all cases. We also show that it can be marginally beneficial to combine information from the histogram and the force, provided that both are of comparable accuracy.

Conformational Entropy as Collective Variable for Proteins.

PubMed

Palazzesi, Ferruccio; Valsson, Omar; Parrinello, Michele

2017-10-05

Many enhanced sampling methods rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate descriptors has proven challenging. Here we suggest that the NMR S 2 order parameter can be used to this effect. We trace the validity of this statement to the suggested relation between S 2 and conformational entropy. Using the S 2 order parameter and a surrogate for the protein enthalpy in conjunction with metadynamics or variationally enhanced sampling, we are able to reversibly fold and unfold a small protein and draw its free energy at a fraction of the time that is needed in unbiased simulations. We also use S 2 in combination with the free energy flooding method to compute the unfolding rate of this peptide. We repeat this calculation at different temperatures to obtain the unfolding activation energy.

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

PubMed Central

Rothrock, Michael J.; Hiett, Kelli L.; Gamble, John; Caudill, Andrew C.; Cicconi-Hogan, Kellie M.; Caporaso, J. Gregory

2014-01-01

The efficacy of DNA extraction protocols can be highly dependent upon both the type of sample being investigated and the types of downstream analyses performed. Considering that the use of new bacterial community analysis techniques (e.g., microbiomics, metagenomics) is becoming more prevalent in the agricultural and environmental sciences and many environmental samples within these disciplines can be physiochemically and microbiologically unique (e.g., fecal and litter/bedding samples from the poultry production spectrum), appropriate and effective DNA extraction methods need to be carefully chosen. Therefore, a novel semi-automated hybrid DNA extraction method was developed specifically for use with environmental poultry production samples. This method is a combination of the two major types of DNA extraction: mechanical and enzymatic. A two-step intense mechanical homogenization step (using bead-beating specifically formulated for environmental samples) was added to the beginning of the “gold standard” enzymatic DNA extraction method for fecal samples to enhance the removal of bacteria and DNA from the sample matrix and improve the recovery of Gram-positive bacterial community members. Once the enzymatic extraction portion of the hybrid method was initiated, the remaining purification process was automated using a robotic workstation to increase sample throughput and decrease sample processing error. In comparison to the strict mechanical and enzymatic DNA extraction methods, this novel hybrid method provided the best overall combined performance when considering quantitative (using 16S rRNA qPCR) and qualitative (using microbiomics) estimates of the total bacterial communities when processing poultry feces and litter samples. PMID:25548939

Constant pressure-assisted head-column field-amplified sample injection in combination with in-capillary derivatization for enhancing the sensitivity of capillary electrophoresis.

PubMed

Yan, Na; Zhou, Lei; Zhu, Zaifang; Zhang, Huige; Zhou, Ximin; Chen, Xingguo

2009-05-15

In this work, a novel method combining constant pressure-assisted head-column field-amplified sample injection (PA-HC-FASI) with in-capillary derivatization was developed for enhancing the sensitivity of capillary electrophoresis. PA-HC-FASI uses an appropriate positive pressure to counterbalance the electroosmotic flow in the capillary column during electrokinetic injection, while taking advantage of the field amplification in the sample matrix and the water of the "head column". Accordingly, the analytes were stacked at the stationary boundary between water and background electrolyte. After 600s PA-HC-FASI, 4-fluoro-7-nitro-2,1,3-benzoxadiazole as derivatization reagent was injected, followed by an electrokinetic step (5kV, 45s) to enhance the mixing efficiency of analytes and reagent plugs. Standing a specified time of 10min for derivatization reaction under 35 degrees C, then the capillary temperature was cooled to 25 degrees C and the derivatives were immediately separated and determined under 25 degrees C. By investigating the variables of the presented approach in detail, on-line preconcentration, derivatization and separation could be automatically operated in one run and required no modification of current CE commercial instrument. Moreover, the sensitivity enhancement factor of 520 and 800 together with the detection limits of 16.32 and 6.34pg/mL was achieved for model compounds: glufosinate and aminomethylphosphonic acid, demonstrating the high detection sensitivity of the presented method.

Photovoltaic Enhancement with Ferroelectric HfO2Embedded in the Structure of Solar Cells

NASA Astrophysics Data System (ADS)

Eskandari, Rahmatollah; Malkinski, Leszek

Enhancing total efficiency of the solar cells is focused on the improving one or all of the three main stages of the photovoltaic effect: absorption of the light, generation of the carriers and finally separation of the carriers. Ferroelectric photovoltaic designs target the last stage with large electric forces from polarized ferroelectric films that can be larger than band gap of the material and the built-in electric fields in semiconductor bipolar junctions. In this project we have fabricated very thin ferroelectric HfO2 films ( 10nm) doped with silicon using RF sputtering method. Doped HfO2 films were capped between two TiN layers ( 20nm) and annealed at temperatures of 800ºC and 1000ºC and Si content was varied between 6-10 mol. % using different size of mounted Si chip on hafnium target. Piezoforce microscopy (PFM) method proved clear ferroelectric properties in samples with 6 mol. % of Si that were annealed at 800ºC. Ferroelectric samples were poled in opposite directions and embedded in the structure of a cell and an enhancement in photovoltaic properties were observed on the poled samples vs unpoled ones with KPFM and I-V measurements. The current work is funded by the NSF EPSCoR LA-SiGMA project under award #EPS-1003897.

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

NASA Astrophysics Data System (ADS)

Arya, Gaurav; Schlick, Tamar

2007-01-01

We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other Monte Carlo moves. Our method extends traditional configurational bias by deleting a repeating motif (monomer) from one end of the biopolymer and regrowing it at the opposite end using the standard Rosenbluth scheme. The method's sampling efficiency compared to local moves, pivot rotations, and standard configurational bias is assessed by parameters relating to translational, rotational, and internal degrees of freedom of the oligonucleosome. Our results show that the end-transfer method is superior in sampling every degree of freedom of the oligonucleosomes over other methods at high salt concentrations (weak electrostatics) but worse than the pivot rotations in terms of sampling internal and rotational sampling at low-to-moderate salt concentrations (strong electrostatics). Under all conditions investigated, however, the end-transfer method is several orders of magnitude more efficient than the standard configurational bias approach. This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially for the traditional configurational-bias method. Thus, the method we propose can significantly improve performance for global biomolecular applications, especially in condensed systems with weak nonbonded interactions and may be combined with local enhancements to improve local sampling.

Rapid multiplexed genotyping for hereditary thrombophilia by SELDI-TOF mass spectrometry.

PubMed

Yang, Shangbin; Xu, Lihui; Wu, Haifeng M

2010-03-01

Approximately 50% of patients with venous thromboembolism also present with hereditary predisposition. The most common genetic factors are single nucleotide polymorphisms (SNPs) of factor V Leiden, prothrombin G20210A, and methylenetetrahydrofolate reductase C677T. Genotyping these SNPs helps clinicians to correctly diagnose the disease and properly manage patients. In this study, we report a novel method using surface-enhanced laser desorption and ionization time of flight mass spectrometry to rapidly genotype, in a multiplex fashion, 3 SNPs that predispose patients to thrombosis. First, patient DNA samples were subjected to polymerase chain reaction to amplify and extend the DNA products with masses corresponding to specific genotypes. Polymerase chain reaction products were then applied to Q10 anionic protein chips, undergoing on-chip sample enrichment and clean-up. Finally, the genotypes of the SNPs were determined by surface-enhanced laser desorption and ionization time of flight mass spectrometry. This method offers a rapid turnaround time of less than 5 hours from sample collection to result reporting. The analytical accuracy of each SNP genotyping result has been confirmed by DNA sequencing. In addition, the genotype results produced by this method were validated by comparing them with results obtained by the approved method in the clinical reference laboratory. This novel method is fast, accurate, and reproducible, and thus provides an excellent platform to promote personalized medicine in the management of clotting disorders.

Electro-enhanced hollow fiber membrane liquid phase microextraction of Cr(VI) oxoanions in drinking water samples.

PubMed

Chanthasakda, Nattaporn; Nitiyanontakit, Sira; Varanusupakul, Pakorn

2016-02-01

Hollow fiber membrane liquid phase microextraction (HF-LPME) of metal oxoanions was studied using an ionic carrier enhanced by the application of an electric field (electro-enhanced HF-LPME). The Cr(VI) oxoanion was used as the model. The transportation of Cr(VI) oxoanions across the supported liquid membrane (SLM) was explored via the ion-exchange process and electrokinetic migration. The type of SLM, type of acceptor solution, extraction time, electric potential, and stirring rate were investigated and optimized using MilliQ water. Electro-enhanced HF-LPME provided a much higher enrichment factor compared to conventional HF-LPME (no electric potential) for the same extraction time. A mixture of an anion exchange carrier (methyltrialkyl-ammonium chloride, Aliquat 336) in the SLM facilitated the transportation of Cr(VI) oxoanions. The SLM that gave the best performance was 1-heptanol mixed with 5% Aliquat 336 with 1M NaOH as the acceptor. Linearity was obtained in the working range of 3-15 µg L(-1) Cr(VI) (R(2)>0.99) at 30 V with a 5 min extraction time. The limit of detection was below 5 µg L(-1). The relative standard deviation was less than 12%. The method was applied to drinking water samples. The recoveries of spiked Cr(VI) in drinking water samples were in the range of 96-101% based on the matrix-matched calibration curves. The method was limited to samples containing low levels of ions due to the occurrence of electrolysis. The type of SLM, particularly regarding its resistance, should be tuned to control this problematic phenomenon. Copyright © 2015 Elsevier B.V. All rights reserved.

Dissolution enhancement of gliclazide using pH change approach in presence of twelve stabilizers with various physico-chemical properties.

PubMed

Talari, Roya; Varshosaz, Jaleh; Mostafavi, Seyed Abolfazl; Nokhodchi, Ali

2009-01-01

The micronization using milling process to enhance dissolution rate is extremely inefficient due to a high energy input, and disruptions in the crystal lattice which can cause physical or chemical instability. Therefore, the aim of the present study is to use in situ micronization process through pH change method to produce micron-size gliclazide particles for fast dissolution hence better bioavailability. Gliclazide was recrystallized in presence of 12 different stabilizers and the effects of each stabilizer on micromeritic behaviors, morphology of microcrystals, dissolution rate and solid state of recrystallized drug particles were investigated. The results showed that recrystallized samples showed faster dissolution rate than untreated gliclazide particles and the fastest dissolution rate was observed for the samples recrystallized in presence of PEG 1500. Some of the recrystallized drug samples in presence of stabilizers dissolved 100% within the first 5 min showing at least 10 times greater dissolution rate than the dissolution rate of untreated gliclazide powders. Micromeritic studies showed that in situ micronization technique via pH change method is able to produce smaller particle size with a high surface area. The results also showed that the type of stabilizer had significant impact on morphology of recrystallized drug particles. The untreated gliclazide is rod or rectangular shape, whereas the crystals produced in presence of stabilizers, depending on the type of stabilizer, were very fine particles with irregular, cubic, rectangular, granular and spherical/modular shape. The results showed that crystallization of gliclazide in presence of stabilizers reduced the crystallinity of the samples as confirmed by XRPD and DSC results. In situ micronization of gliclazide through pH change method can successfully be used to produce micron-sized drug particles to enhance dissolution rate.

Combined micro-droplet and thin-film-assisted pre-concentration of lead traces for on-line monitoring using anodic stripping voltammetry.

PubMed

Belostotsky, Inessa; Gridin, Vladimir V; Schechter, Israel; Yarnitzky, Chaim N

2003-02-01

An improved analytical method for airborne lead traces is reported. It is based on using a Venturi scrubber sampling device for simultaneous thin-film stripping and droplet entrapment of aerosol influxes. At least threefold enhancement of the lead-trace pre-concentration is achieved. The sampled traces are analyzed by square-wave anodic stripping voltammetry. The method was tested by a series of pilot experiments. These were performed using contaminant-controlled air intakes. Reproducible calibration plots were obtained. The data were validated by traditional analysis using filter sampling. LODs are comparable with the conventional techniques. The method was successfully applied to on-line and in situ environmental monitoring of lead.

Ultrasonic-energy enhance the ionic liquid-based dual microextraction to preconcentrate the lead in ground and stored rain water samples as compared to conventional shaking method.

PubMed

Nizamani, Sooraj; Kazi, Tasneem G; Afridi, Hassan I

2018-01-01

An efficient preconcentration technique based on ultrasonic-assisted ionic liquid-based dual microextraction (UA-ILDµE) method has been developed to preconcentrate the lead (Pb +2 ) in ground and stored rain water. In the current proposed method, Pb +2 was complexed with a chelating agent (dithizone), whereas an ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate) was used for extraction purpose. The ultrasonic irradiation and electrical shaking system were applied to enhance the dispersion and extraction of Pb +2 complex in aqueous samples. For second phase, dual microextraction (DµE phase), the enriched Pb +2 complex in ionic liquid, extracted back into the acidic aqueous solution and finally determined by flame atomic absorption spectrometry. Some major analytical parameters that influenced the extraction efficiency of developed method, such as pH, concentration of ligand, volume of ionic liquid and samples, time of shaking in thermostatic electrical shaker and ultrasonic bath, effect of back extracting HNO 3 volume, matrix effect, centrifugation time and rate were optimized. At the sample volume of 25mL, the calculated preconcentration factor was 62.2. The limit of detection of proposed procedure for Pb +2 ions was found to be 0.54μgL -1 . The validation of developed method was performed by the analysis of certified sample of water SRM 1643e and standard addition method in a real water sample. The extraction recovery of Pb +2 was enhanced≥2% with shaking time of 80s in ultrasonic bath as compared to used thermostatic electrical shaker, where for optimum recovery up to 10min was required. The developed procedure was successfully used for the enrichment of Pb +2 in ground and stored rain water (surface water) samples of an endemic region of Pakistan. The resulted data indicated that the ground water samples were highly contaminated with Pb +2 , while some of the surface water samples were also have higher values of Pb +2 than permissible limit of WHO. The concentration of Pb +2 in surface and ground water samples was found in the range of 17.5-24.5 and 25.6-99.1μgL - 1 respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Thermal Desorption Capability Development for Enhanced On-site Health Risk Assessment: HAPSITE (registered trademark) ER Passive Sampling in the Field

DTIC Science & Technology

2015-06-07

Field-Portable Gas Chromatograph-Mass Spectrometer.” Forensic Toxicol, 2006, 24, 17-22. Smith, P. “Person-Portable Gas Chromatography : Rapid Temperature...bench-top Gas Chromatograph-Mass Spectrometer (GC-MS) system (ISQ). Nine sites were sampled and analyzed for compounds using Environmental Protection...extraction methods for Liquid Chromatography -MS (LC- MS). Additionally, TD is approximately 1000X more sensitive, requires minimal sample preparation

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.

PubMed

Higo, Junichi; Dasgupta, Bhaskar; Mashimo, Tadaaki; Kasahara, Kota; Fukunishi, Yoshifumi; Nakamura, Haruki

2015-07-30

A novel enhanced conformational sampling method, virtual-system-coupled adaptive umbrella sampling (V-AUS), was proposed to compute 300-K free-energy landscape for flexible molecular docking, where a virtual degrees of freedom was introduced to control the sampling. This degree of freedom interacts with the biomolecular system. V-AUS was applied to complex formation of two disordered amyloid-β (Aβ30-35 ) peptides in a periodic box filled by an explicit solvent. An interpeptide distance was defined as the reaction coordinate, along which sampling was enhanced. A uniform conformational distribution was obtained covering a wide interpeptide distance ranging from the bound to unbound states. The 300-K free-energy landscape was characterized by thermodynamically stable basins of antiparallel and parallel β-sheet complexes and some other complex forms. Helices were frequently observed, when the two peptides contacted loosely or fluctuated freely without interpeptide contacts. We observed that V-AUS converged to uniform distribution more effectively than conventional AUS sampling did. © 2015 Wiley Periodicals, Inc.

Contrast Enhanced Microscopy Digital Image Correlation: A General Method to Contact-Free Coefficient of Thermal Expansion Measurement of Polymer Films

Treesearch

Jairo A. Diaz; Robert J. Moon; Jeffrey P. Youngblood

2014-01-01

Thermal expansion represents a vital indicator of the processing history and dimensional stability of materials. Solvent-sensitive, thin, and compliant samples are particularly challenging to test. Here we describe how textures highlighted by contrast enhanced optical microscopy modes (i.e., polarized light (PL), phase contrast (PC)) and bright field (BF) can be used...

Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.

PubMed

Higo, Junichi; Ikebe, Jinzen; Kamiya, Narutoshi; Nakamura, Haruki

2012-03-01

Protein folding and protein-ligand docking have long persisted as important subjects in biophysics. Using multicanonical molecular dynamics (McMD) simulations with realistic expressions, i.e., all-atom protein models and an explicit solvent, free-energy landscapes have been computed for several systems, such as the folding of peptides/proteins composed of a few amino acids up to nearly 60 amino-acid residues, protein-ligand interactions, and coupled folding and binding of intrinsically disordered proteins. Recent progress in conformational sampling and its applications to biophysical systems are reviewed in this report, including descriptions of several outstanding studies. In addition, an algorithm and detailed procedures used for multicanonical sampling are presented along with the methodology of adaptive umbrella sampling. Both methods control the simulation so that low-probability regions along a reaction coordinate are sampled frequently. The reaction coordinate is the potential energy for multicanonical sampling and is a structural identifier for adaptive umbrella sampling. One might imagine that this probability control invariably enhances conformational transitions among distinct stable states, but this study examines the enhanced conformational sampling of a simple system and shows that reasonably well-controlled sampling slows the transitions. This slowing is induced by a rapid change of entropy along the reaction coordinate. We then provide a recipe to speed up the sampling by loosening the rapid change of entropy. Finally, we report all-atom McMD simulation results of various biophysical systems in an explicit solvent.

Application of enhanced gas chromatography/triple quadrupole mass spectrometry for monitoring petroleum weathering and forensic source fingerprinting in samples impacted by the Deepwater Horizon oil spill.

PubMed

Adhikari, Puspa L; Wong, Roberto L; Overton, Edward B

2017-10-01

Accurate characterization of petroleum hydrocarbons in complex and weathered oil residues is analytically challenging. This is primarily due to chemical compositional complexity of both the oil residues and environmental matrices, and the lack of instrumental selectivity due to co-elution of interferences with the target analytes. To overcome these analytical selectivity issues, we used an enhanced resolution gas chromatography coupled with triple quadrupole mass spectrometry in Multiple Reaction Monitoring (MRM) mode (GC/MS/MS-MRM) to eliminate interferences within the ion chromatograms of target analytes found in environmental samples. This new GC/MS/MS-MRM method was developed and used for forensic fingerprinting of deep-water and marsh sediment samples containing oily residues from the Deepwater Horizon oil spill. The results showed that the GC/MS/MS-MRM method increases selectivity, eliminates interferences, and provides more accurate quantitation and characterization of trace levels of alkyl-PAHs and biomarker compounds, from weathered oil residues in complex sample matrices. The higher selectivity of the new method, even at low detection limits, provides greater insights on isomer and homolog compositional patterns and the extent of oil weathering under various environmental conditions. The method also provides flat chromatographic baselines for accurate and unambiguous calculation of petroleum forensic biomarker compound ratios. Thus, this GC/MS/MS-MRM method can be a reliable analytical strategy for more accurate and selective trace level analyses in petroleum forensic studies, and for tacking continuous weathering of oil residues. Copyright © 2017 Elsevier Ltd. All rights reserved.

DNP enhanced NMR with flip-back recovery

NASA Astrophysics Data System (ADS)

Björgvinsdóttir, Snædís; Walder, Brennan J.; Pinon, Arthur C.; Yarava, Jayasubba Reddy; Emsley, Lyndon

2018-03-01

DNP methods can provide significant sensitivity enhancements in magic angle spinning solid-state NMR, but in systems with long polarization build up times long recycling periods are required to optimize sensitivity. We show how the sensitivity of such experiments can be improved by the classic flip-back method to recover bulk proton magnetization following continuous wave proton heteronuclear decoupling. Experiments were performed on formulations with characteristic build-up times spanning two orders of magnitude: a bulk BDPA radical doped o-terphenyl glass and microcrystalline samples of theophylline, L-histidine monohydrochloride monohydrate, and salicylic acid impregnated by incipient wetness. For these systems, addition of flip-back is simple, improves the sensitivity beyond that provided by modern heteronuclear decoupling methods such as SPINAL-64, and provides optimal sensitivity at shorter recycle delays. We show how to acquire DNP enhanced 2D refocused CP-INADEQUATE spectra with flip-back recovery, and demonstrate that the flip-back recovery method is particularly useful in rapid recycling regimes. We also report Overhauser effect DNP enhancements of over 70 at 592.6 GHz/900 MHz.

Enhanced Imaging of Building Interior for Portable MIMO Through-the-wall Radar

NASA Astrophysics Data System (ADS)

Song, Yongping; Zhu, Jiahua; Hu, Jun; Jin, Tian; Zhou, Zhimin

2018-01-01

Portable multi-input multi-output (MIMO) radar system is able to imaging the building interior through aperture synthesis. However, significant grating lobes are invoked in the directly imaging results, which may deteriorate the imaging quality of other targets and influence the detail information extraction of imaging scene. In this paper, a two-stage coherence factor (CF) weighting method is proposed to enhance the imaging quality. After obtaining the sub-imaging results of each spatial sampling position using conventional CF approach, a window function is employed to calculate the proposed “enhanced CF” adaptive to the spatial variety effect behind the wall for the combination of these sub-images. The real data experiment illustrates the better performance of proposed method on grating lobes suppression and imaging quality enhancement compare to the traditional radar imaging approach.

Vortex-assisted surfactant-enhanced emulsification microextraction combined with LC-MS/MS for the determination of glucocorticoids in water with the aid of experimental design.

PubMed

Asati, Ankita; Satyanarayana, G N V; Patel, Devendra K

2017-04-01

An efficient and inexpensive method using vortex-assisted surfactant-enhanced emulsification microextraction (VASEME) based on solidification of floating organic droplet coupled with ultraperformance liquid chromatography-tandem mass spectrometry is proposed for the analysis of glucocorticoids in water samples (river water and hospital wastewater). VASEME was optimized by the experimental validation of Plackett-Burman design and central composite design, which has been co-related to experimental design. Plackett-Burman design showed that factors such as vortex time, surfactant concentration, and pH significantly affect the extraction efficiency of the method. Method validation was characterized by an acceptable calibration range of 1-1000 ng L -1 , and the limit of detection was in the range from 2.20 to 8.12 ng L -1 for glucocorticoids. The proposed method was applied to determine glucocorticoids in river water and hospital wastewater in Lucknow, India. It is reliable and rapid and has potential application for analysis of glucocorticoids in environmental aqueous samples. Graphical Abstract Low density based extraction of gluococorticoids by using design of experiment.

[The actual possibilities of robotic microscopy in analysis automation and laboratory telemedicine].

PubMed

Medovyĭ, V S; Piatnitskiĭ, A M; Sokolinskiĭ, B Z; Balugian, R Sh

2012-10-01

The article discusses the possibilities of automation microscopy complexes manufactured by Cellavision and MEKOS to perform the medical analyses of blood films and other biomaterials. The joint work of the complex and physician in the regimen of automatic load stages, screening, sampling and sorting on types with simple morphology, visual sorting of sub-sample with complex morphology provides significant increase of method sensitivity, load decrease and enhancement of physician work conditions. The information technologies, the virtual slides and laboratory telemedicine included permit to develop the representative samples of rare types and pathologies to promote automation methods and medical research targets.

System and method for controlling depth of imaging in tissues using fluorescence microscopy under ultraviolet excitation following staining with fluorescing agents

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

Demos, Stavros; Levenson, Richard

The present disclosure relates to a method for analyzing tissue specimens. In one implementation the method involves obtaining a tissue sample and exposing the sample to one or more fluorophores as contrast agents to enhance contrast of subcellular compartments of the tissue sample. The tissue sample is illuminated by an ultraviolet (UV) light having a wavelength between about 200 nm to about 400 nm, with the wavelength being selected to result in penetration to only a specified depth below a surface of the tissue sample. Inter-image operations between images acquired under different imaging parameters allow for improvement of the imagemore » quality via removal of unwanted image components. A microscope may be used to image the tissue sample and provide the image to an image acquisition system that makes use of a camera. The image acquisition system may create a corresponding image that is transmitted to a display system for processing and display.« less

Single-pulse enhanced coherent diffraction imaging of bacteria with an X-ray free-electron laser

NASA Astrophysics Data System (ADS)

Fan, Jiadong; Sun, Zhibin; Wang, Yaling; Park, Jaehyun; Kim, Sunam; Gallagher-Jones, Marcus; Kim, Yoonhee; Song, Changyong; Yao, Shengkun; Zhang, Jian; Zhang, Jianhua; Duan, Xiulan; Tono, Kensuke; Yabashi, Makina; Ishikawa, Tetsuya; Fan, Chunhai; Zhao, Yuliang; Chai, Zhifang; Gao, Xueyun; Earnest, Thomas; Jiang, Huaidong

2016-09-01

High-resolution imaging offers one of the most promising approaches for exploring and understanding the structure and function of biomaterials and biological systems. X-ray free-electron lasers (XFELs) combined with coherent diffraction imaging can theoretically provide high-resolution spatial information regarding biological materials using a single XFEL pulse. Currently, the application of this method suffers from the low scattering cross-section of biomaterials and X-ray damage to the sample. However, XFELs can provide pulses of such short duration that the data can be collected using the “diffract and destroy” approach before the effects of radiation damage on the data become significant. These experiments combine the use of enhanced coherent diffraction imaging with single-shot XFEL radiation to investigate the cellular architecture of Staphylococcus aureus with and without labeling by gold (Au) nanoclusters. The resolution of the images reconstructed from these diffraction patterns were twice as high or more for gold-labeled samples, demonstrating that this enhancement method provides a promising approach for the high-resolution imaging of biomaterials and biological systems.

Enhancement and stabilization of plasma using collinear long-short double-pulse laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Cui, Minchao; Deguchi, Yoshihiro; Wang, Zhenzhen; Fujita, Yuki; Liu, Renwei; Shiou, Fang-Jung; Zhao, Shengdun

2018-04-01

A collinear long-short dual-pulse laser-induced breakdown spectroscopy (DP-LIBS) method was employed to enhance and stabilize the laser-induced plasma from steel sample. The long-pulse-width laser beam with the pulse width of 60 μs was generated by a Nd: YAG laser which was operated at FR (free running) mode. The comparative experiments were carried out between single pulse LIBS (SP-LIBS) and long-short DP-LIBS. The recorded results showed that the emission intensities and the temperature of plasma were enhanced by long-short DP-LIBS. The plasma images showed that the plasma was bigger and had a longer lifetime in long-short DP-LIBS situation. Through the calculation of time-resolved plasma temperature and intensity ratio, it can be concluded that the plasma was stabilized by the long-pulse-width laser beam. The long-short DP-LIBS method also generated the stable plasma condition from the samples with different initial temperatures, which overcame the difficulties of LIBS in the online measurement for steel production line.

Single-pulse enhanced coherent diffraction imaging of bacteria with an X-ray free-electron laser

PubMed Central

Fan, Jiadong; Sun, Zhibin; Wang, Yaling; Park, Jaehyun; Kim, Sunam; Gallagher-Jones, Marcus; Kim, Yoonhee; Song, Changyong; Yao, Shengkun; Zhang, Jian; Zhang, Jianhua; Duan, Xiulan; Tono, Kensuke; Yabashi, Makina; Ishikawa, Tetsuya; Fan, Chunhai; Zhao, Yuliang; Chai, Zhifang; Gao, Xueyun; Earnest, Thomas; Jiang, Huaidong

2016-01-01

High-resolution imaging offers one of the most promising approaches for exploring and understanding the structure and function of biomaterials and biological systems. X-ray free-electron lasers (XFELs) combined with coherent diffraction imaging can theoretically provide high-resolution spatial information regarding biological materials using a single XFEL pulse. Currently, the application of this method suffers from the low scattering cross-section of biomaterials and X-ray damage to the sample. However, XFELs can provide pulses of such short duration that the data can be collected using the “diffract and destroy” approach before the effects of radiation damage on the data become significant. These experiments combine the use of enhanced coherent diffraction imaging with single-shot XFEL radiation to investigate the cellular architecture of Staphylococcus aureus with and without labeling by gold (Au) nanoclusters. The resolution of the images reconstructed from these diffraction patterns were twice as high or more for gold-labeled samples, demonstrating that this enhancement method provides a promising approach for the high-resolution imaging of biomaterials and biological systems. PMID:27659203

Single-pulse enhanced coherent diffraction imaging of bacteria with an X-ray free-electron laser.

PubMed

Fan, Jiadong; Sun, Zhibin; Wang, Yaling; Park, Jaehyun; Kim, Sunam; Gallagher-Jones, Marcus; Kim, Yoonhee; Song, Changyong; Yao, Shengkun; Zhang, Jian; Zhang, Jianhua; Duan, Xiulan; Tono, Kensuke; Yabashi, Makina; Ishikawa, Tetsuya; Fan, Chunhai; Zhao, Yuliang; Chai, Zhifang; Gao, Xueyun; Earnest, Thomas; Jiang, Huaidong

2016-09-23

High-resolution imaging offers one of the most promising approaches for exploring and understanding the structure and function of biomaterials and biological systems. X-ray free-electron lasers (XFELs) combined with coherent diffraction imaging can theoretically provide high-resolution spatial information regarding biological materials using a single XFEL pulse. Currently, the application of this method suffers from the low scattering cross-section of biomaterials and X-ray damage to the sample. However, XFELs can provide pulses of such short duration that the data can be collected using the "diffract and destroy" approach before the effects of radiation damage on the data become significant. These experiments combine the use of enhanced coherent diffraction imaging with single-shot XFEL radiation to investigate the cellular architecture of Staphylococcus aureus with and without labeling by gold (Au) nanoclusters. The resolution of the images reconstructed from these diffraction patterns were twice as high or more for gold-labeled samples, demonstrating that this enhancement method provides a promising approach for the high-resolution imaging of biomaterials and biological systems.

Pressurized capillary electrochromatographic analysis of water-soluble vitamins by combining with on-line concentration technique.

PubMed

Jia, Li; Liu, Yaling; Du, Yanyan; Xing, Da

2007-06-22

A pressurized capillary electrochromatography (pCEC) system was developed for the separation of water-soluble vitamins, in which UV absorbance was used as the detection method and a monolithic silica-ODS column as the separation column. The parameters (type and content of organic solvent in the mobile phase, type and concentration of electrolyte, pH of the electrolyte buffer, applied voltage and flow rate) affecting the separation resolution were evaluated. The combination of two on-line concentration techniques, namely, solvent gradient zone sharpening effect and field-enhanced sample stacking, was utilized to improve detection sensitivity, which proved to be beneficial to enhance the detection sensitivity by enabling the injection of large volumes of samples. Coupling electrokinetic injection with the on-line concentration techniques was much more beneficial for the concentration of positively charged vitamins. Comparing with the conventional injection mode, the enhancement in the detection sensitivities of water-soluble vitamins using the on-line concentration technique is in the range of 3 to 35-fold. The developed pCEC method was applied to evaluate water-soluble vitamins in corns.

Sensitivity and specificity enhanced enzyme-linked immunosorbent assay by rational hapten modification and heterogeneous antibody/coating antigen combinations for the detection of melamine in milk, milk powder and feed samples.

PubMed

Cao, Biyun; Yang, Hong; Song, Juan; Chang, Huafang; Li, Shuqun; Deng, Anping

2013-11-15

The adulteration of food products with melamine has led to an urgent requirement for sensitive, specific, rapid and reliable quantitative/screening methods. To enhance the sensitivity and specificity of the enzyme-linked immunosorbent assay (ELISA) for the detection of melamine in milk, milk powder and feed samples, rational hapten modification and heterogeneous antibody/coating antigen combinations were adopted. Three melamine derivatives with different length of carboxylic spacer at the end were synthesized and linked to carrier proteins for the production of immunogens and coating antigens. Monoclonal antibody against melamine was produced by hybridoma technology. Under optimal experimental conditions, the standard curves of the ELISAs for melamine were constructed in range of 0.1-100 ng mL(-1). The sensitivity was 10-300 times enhanced compared to those in the published literatures. The cross-reactivity values of the ELISAs also demonstrated the assays exhibited high specificity. Five samples were spiked with melamine at different concentrations and detected by the ELISA. The recovery rates of 72.8-123.0% and intra-assay coefficients of variation of 0.8-18.9% (n=3) were obtained. The ELISA for milk sample was confirmed by high-performance liquid chromatography with a high correlation coefficient of 0.9902 (n=6). The proposed ELISA was proven to be a feasible quantitative/screening method for melamine analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

Determination of nicotine by surface-enhanced Raman scattering (SERS)

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

Barber, T.E.; List, M.S.; Haas, J.W. III

1994-11-01

The analytical application of surface-enhanced Raman spectroscopy (SERS) to the determination of nicotine is demonstrated. A simple spectroelectrochemical method using a copper or silver electrode as the SERS substrate has been developed, consisting of three steps: polishing a working electrode to a mirror finish; roughening the electrode in an electrolyte solution; and, finally, depositing the nicotine analyte onto the roughened electrode after immersion in a sample solution. During the reduction cycle, a large enhancement in nicotine Raman scattering is observed at the electrode surface. The intensity of the SERS signal on a silver electrode is linear with concentration from 10more » to 900 ppb, with an estimated detection limit of 7 ppb. The total analysis time per sample is approximately five minutes. This procedure has been used to analyze the extract from a cigarette side-stream smoke sample (environmental tobacco smoke); the SERS results agree well with those of conventional gas chromatographic analysis.« less

PLUMED 2: New feathers for an old bird

NASA Astrophysics Data System (ADS)

Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni

2014-02-01

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Super-Enhancers and Broad H3K4me3 Domains Form Complex Gene Regulatory Circuits Involving Chromatin Interactions.

PubMed

Cao, Fan; Fang, Yiwen; Tan, Hong Kee; Goh, Yufen; Choy, Jocelyn Yeen Hui; Koh, Bryan Thean Howe; Hao Tan, Jiong; Bertin, Nicolas; Ramadass, Aroul; Hunter, Ewan; Green, Jayne; Salter, Matthew; Akoulitchev, Alexandre; Wang, Wilson; Chng, Wee Joo; Tenen, Daniel G; Fullwood, Melissa J

2017-05-19

Stretched histone regions, such as super-enhancers and broad H3K4me3 domains, are associated with maintenance of cell identity and cancer. We connected super-enhancers and broad H3K4me3 domains in the K562 chronic myelogenous leukemia cell line as well as the MCF-7 breast cancer cell line with chromatin interactions. Super-enhancers and broad H3K4me3 domains showed higher association with chromatin interactions than their typical counterparts. Interestingly, we identified a subset of super-enhancers that overlap with broad H3K4me3 domains and show high association with cancer-associated genes including tumor suppressor genes. Besides cell lines, we could observe chromatin interactions by a Chromosome Conformation Capture (3C)-based method, in primary human samples. Several chromatin interactions involving super-enhancers and broad H3K4me3 domains are constitutive and can be found in both cancer and normal samples. Taken together, these results reveal a new layer of complexity in gene regulation by super-enhancers and broad H3K4me3 domains.

Complete urinary tract infection (UTI) diagnosis and antibiogram using surface enhanced Raman spectroscopy (SERS)

NASA Astrophysics Data System (ADS)

Hadjigeorgiou, Katerina; Kastanos, Evdokia; Kyriakides, Alexandros; Pitris, Costas

2012-03-01

There are three stages to a complete UTI diagnosis: (1) identification of a urine sample as positive/negative for an infection, (2) identification of the responsible bacterium, (3) antibiogram to determine the antibiotic to which the bacteria are most sensitive to. Using conventional methods, all three stages require bacterial cultures in order to provide results. This long delay in diagnosis causes a rise in ineffective treatments, chronic infections, health care costs and antibiotic resistance. In this work, SERS is used to identify a sample as positive/negative for a UTI as well as to obtain an antibiogram against different antibiotics. SERS spectra of serial dilutions of E. coli bacteria mixed with silver nanoparticles, showed a linear correlation between spectral intensity and concentration. For antibiotic sensitivity testing, SERS spectra of three species of gram negative bacteria were collected four hours after exposure to the antibiotics ciprofloxacin and amoxicillin. Spectral analysis revealed clear separation between bacterial samples exposed to antibiotics to which they were sensitive and samples exposed to antibiotics to which they were resistant. With the enhancement provided by SERS, the technique can be applied directly to urine samples leading to the development of a new, rapid method for UTI diagnosis and antibiogram.

Sample processing approach for detection of ricin in surface samples.

PubMed

Kane, Staci; Shah, Sanjiv; Erler, Anne Marie; Alfaro, Teneile

2017-12-01

With several ricin contamination incidents reported over the past decade, rapid and accurate methods are needed for environmental sample analysis, especially after decontamination. A sample processing method was developed for common surface sampling devices to improve the limit of detection and avoid false negative/positive results for ricin analysis. Potential assay interferents from the sample matrix (bleach residue, sample material, wetting buffer), including reference dust, were tested using a Time-Resolved Fluorescence (TRF) immunoassay. Test results suggested that the sample matrix did not cause the elevated background fluorescence sometimes observed when analyzing post-bleach decontamination samples from ricin incidents. Furthermore, sample particulates (80mg/mL Arizona Test Dust) did not enhance background fluorescence or interfere with ricin detection by TRF. These results suggested that high background fluorescence in this immunoassay could be due to labeled antibody quality and/or quantity issues. Centrifugal ultrafiltration devices were evaluated for ricin concentration as a part of sample processing. Up to 30-fold concentration of ricin was observed by the devices, which serve to remove soluble interferents and could function as the front-end sample processing step to other ricin analytical methods. The procedure has the potential to be used with a broader range of environmental sample types and with other potential interferences and to be followed by other ricin analytical methods, although additional verification studies would be required. Published by Elsevier B.V.

Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics.

PubMed

Alibay, Irfan; Burusco, Kepa K; Bruce, Neil J; Bryce, Richard A

2018-03-08

Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4 C 1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.

Contrast enhancement of biological nanoporous materials with zinc oxide infiltration for electron and X-ray nanoscale microscopy

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

Ocola, L. E.; Sampathkumar, V.; Kasthuri, N.

Here, we show that using infiltration of ZnO metal oxide can be useful for high resolution imaging of biological samples in electron and X-ray microscopy. This method is compatible with standard fixation techniques that leave the sample dry, such as finishing with super critical CO 2 drying, or simple vacuum drying at 95°C. We demonstrate this technique can be applied on tooth and brain tissue samples. We also show that high resolution X-ray tomography can be performed on biological systems using Zn K edge (1s) absorption to enhance internal structures, and obtained the first nanoscale 10 KeV X-ray absorption imagesmore » of the interior regions of a tooth.« less

Contrast enhancement of biological nanoporous materials with zinc oxide infiltration for electron and X-ray nanoscale microscopy

DOE PAGES

Ocola, L. E.; Sampathkumar, V.; Kasthuri, N.; ...

2017-07-19

Here, we show that using infiltration of ZnO metal oxide can be useful for high resolution imaging of biological samples in electron and X-ray microscopy. This method is compatible with standard fixation techniques that leave the sample dry, such as finishing with super critical CO 2 drying, or simple vacuum drying at 95°C. We demonstrate this technique can be applied on tooth and brain tissue samples. We also show that high resolution X-ray tomography can be performed on biological systems using Zn K edge (1s) absorption to enhance internal structures, and obtained the first nanoscale 10 KeV X-ray absorption imagesmore » of the interior regions of a tooth.« less

SERS diagnostic platforms, methods and systems microarrays, biosensors and biochips

DOEpatents

Vo-Dinh, Tuan [Knoxville, TN

2007-09-11

A Raman integrated sensor system for the detection of targets including biotargets includes at least one sampling platform, at least one receptor probe disposed on the sampling platform, and an integrated circuit detector system communicably connected to the receptor. The sampling platform is preferably a Raman active surface-enhanced scattering (SERS) platform, wherein the Raman sensor is a SERS sensor. The receptors can include at least one protein receptor and at least one nucleic acid receptor.

Indices of polarimetric purity for biological tissues inspection

NASA Astrophysics Data System (ADS)

Van Eeckhout, Albert; Lizana, Angel; Garcia-Caurel, Enric; Gil, José J.; Sansa, Adrià; Rodríguez, Carla; Estévez, Irene; González, Emilio; Escalera, Juan C.; Moreno, Ignacio; Campos, Juan

2018-02-01

We highlight the interest of using the Indices of Polarimetric Purity (IPPs) for the biological tissue inspection. These are three polarimetric metrics focused on the study of the depolarizing behaviour of the sample. The IPPs have been recently proposed in the literature and provide different and synthetized information than the commonly used depolarizing indices, as depolarization index (PΔ) or depolarization power (Δ). Compared with the standard polarimetric images of biological samples, IPPs enhance the contrast between different tissues of the sample and show differences between similar tissues which are not observed using the other standard techniques. Moreover, they present further physical information related to the depolarization mechanisms inherent to different tissues. In addition, the algorithm does not require advanced calculations (as in the case of polar decompositions), being the indices of polarimetric purity fast and easy to implement. We also propose a pseudo-coloured image method which encodes the sample information as a function of the different indices weights. These images allow us to customize the visualization of samples and to highlight certain of their constitutive structures. The interest and potential of the IPP approach are experimentally illustrated throughout the manuscript by comparing polarimetric images of different ex-vivo samples obtained with standard polarimetric methods with those obtained from the IPPs analysis. Enhanced contrast and retrieval of new information are experimentally obtained from the different IPP based images.

Nanoscale effects in the characterization of viscoelastic materials with atomic force microscopy: coupling of a quasi-three-dimensional standard linear solid model with in-plane surface interactions.

PubMed

Solares, Santiago D

2016-01-01

Significant progress has been accomplished in the development of experimental contact-mode and dynamic-mode atomic force microscopy (AFM) methods designed to measure surface material properties. However, current methods are based on one-dimensional (1D) descriptions of the tip-sample interaction forces, thus neglecting the intricacies involved in the material behavior of complex samples (such as soft viscoelastic materials) as well as the differences in material response between the surface and the bulk. In order to begin to address this gap, a computational study is presented where the sample is simulated using an enhanced version of a recently introduced model that treats the surface as a collection of standard-linear-solid viscoelastic elements. The enhanced model introduces in-plane surface elastic forces that can be approximately related to a two-dimensional (2D) Young's modulus. Relevant cases are discussed for single- and multifrequency intermittent-contact AFM imaging, with focus on the calculated surface indentation profiles and tip-sample interaction force curves, as well as their implications with regards to experimental interpretation. A variety of phenomena are examined in detail, which highlight the need for further development of more physically accurate sample models that are specifically designed for AFM simulation. A multifrequency AFM simulation tool based on the above sample model is provided as supporting information.

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

Ogura, Toshihiko, E-mail: t-ogura@aist.go.jp

Highlights: • We developed a high-sensitive frequency transmission electric-field (FTE) system. • The output signal was highly enhanced by applying voltage to a metal layer on SiN. • The spatial resolution of new FTE method is 41 nm. • New FTE system enables observation of the intact bacteria and virus in water. - Abstract: The high-resolution structural analysis of biological specimens by scanning electron microscopy (SEM) presents several advantages. Until now, wet bacterial specimens have been examined using atmospheric sample holders. However, images of unstained specimens in water using these holders exhibit very poor contrast and heavy radiation damage. Recently,more » we developed the frequency transmission electric-field (FTE) method, which facilitates the SEM observation of biological specimens in water without radiation damage. However, the signal detection system presents low sensitivity. Therefore, a high EB current is required to generate clear images, and thus reducing spatial resolution and inducing thermal damage to the samples. Here a high-sensitivity detection system is developed for the FTE method, which enhances the output signal amplitude by hundredfold. The detection signal was highly enhanced when voltage was applied to the metal layer on silicon nitride thin film. This enhancement reduced the EB current and improved the spatial resolution as well as the signal-to-noise ratio. The spatial resolution of a high-sensitive FTE system is 41 nm, which is considerably higher than previous FTE system. New FTE system can easily be utilised to examine various unstained biological specimens in water, such as living bacteria and viruses.« less

Structural Features, Antitumor and Antioxidant Activities of Rice Bran Polysaccharides Using Different Extraction Methods.

PubMed

Han, Wenfang; Li, Jiangtao; Ding, Yuqin; Xiong, Shanbai; Zhao, Siming

2017-10-01

In this study, rice bran polysaccharides (RBP) were extracted using the hydrothermal method (RBP-H), microwave-assisted extraction (RBP-M) and enzyme-assisted extraction (RBP-E). The prepared RBP samples exhibited the typical spectral patterns of polysaccharides, but differed in chemical composition, molecular features, antitumor and antioxidant activities. The molecular weights (Mw) of RBP-H, RBP-M, and RBP-E were 1.03 × 10 5 , 2.62 × 10 5 , and 0.46 × 10 5 g/mol, respectively. In vitro, all RBP samples significantly inhibited mouse sarcoma S180 cells viability in a dose-dependent manner. In vivo, RBP-M or RBP-E could not only inhibit the growth of the tumor, but also enhance the spleen index. In addition, RBP-E could induce an enhancement of superoxide dismutase (SOD) and glutathione peroxidase activities and a scavenging effect on malondialdehyde. This study demonstrated that the effective antitumor activity of RBP may be owed to its enhancement of antioxidant activity function. The present work suggested that RBP, especially RBP-E could be a safe and effective antitumor, bioactive agent or functional food. Polysaccharides is extracted from rice bran (RBP) using hydrothermal, microwave-assisted and enzyme-assisted extraction methods. The results suggested that the antitumor activity of RBP was associated with enhancement of immunization and antioxidant. RBP could be explored as a natural antitumor and antioxidant agent applied in medicines and functional foods. © 2017 Institute of Food Technologists®.

A Novel Method to Handle the Effect of Uneven Sampling Effort in Biodiversity Databases

PubMed Central

Pardo, Iker; Pata, María P.; Gómez, Daniel; García, María B.

2013-01-01

How reliable are results on spatial distribution of biodiversity based on databases? Many studies have evidenced the uncertainty related to this kind of analysis due to sampling effort bias and the need for its quantification. Despite that a number of methods are available for that, little is known about their statistical limitations and discrimination capability, which could seriously constrain their use. We assess for the first time the discrimination capacity of two widely used methods and a proposed new one (FIDEGAM), all based on species accumulation curves, under different scenarios of sampling exhaustiveness using Receiver Operating Characteristic (ROC) analyses. Additionally, we examine to what extent the output of each method represents the sampling completeness in a simulated scenario where the true species richness is known. Finally, we apply FIDEGAM to a real situation and explore the spatial patterns of plant diversity in a National Park. FIDEGAM showed an excellent discrimination capability to distinguish between well and poorly sampled areas regardless of sampling exhaustiveness, whereas the other methods failed. Accordingly, FIDEGAM values were strongly correlated with the true percentage of species detected in a simulated scenario, whereas sampling completeness estimated with other methods showed no relationship due to null discrimination capability. Quantifying sampling effort is necessary to account for the uncertainty in biodiversity analyses, however, not all proposed methods are equally reliable. Our comparative analysis demonstrated that FIDEGAM was the most accurate discriminator method in all scenarios of sampling exhaustiveness, and therefore, it can be efficiently applied to most databases in order to enhance the reliability of biodiversity analyses. PMID:23326357

A novel method to handle the effect of uneven sampling effort in biodiversity databases.

PubMed

Pardo, Iker; Pata, María P; Gómez, Daniel; García, María B

2013-01-01

How reliable are results on spatial distribution of biodiversity based on databases? Many studies have evidenced the uncertainty related to this kind of analysis due to sampling effort bias and the need for its quantification. Despite that a number of methods are available for that, little is known about their statistical limitations and discrimination capability, which could seriously constrain their use. We assess for the first time the discrimination capacity of two widely used methods and a proposed new one (FIDEGAM), all based on species accumulation curves, under different scenarios of sampling exhaustiveness using Receiver Operating Characteristic (ROC) analyses. Additionally, we examine to what extent the output of each method represents the sampling completeness in a simulated scenario where the true species richness is known. Finally, we apply FIDEGAM to a real situation and explore the spatial patterns of plant diversity in a National Park. FIDEGAM showed an excellent discrimination capability to distinguish between well and poorly sampled areas regardless of sampling exhaustiveness, whereas the other methods failed. Accordingly, FIDEGAM values were strongly correlated with the true percentage of species detected in a simulated scenario, whereas sampling completeness estimated with other methods showed no relationship due to null discrimination capability. Quantifying sampling effort is necessary to account for the uncertainty in biodiversity analyses, however, not all proposed methods are equally reliable. Our comparative analysis demonstrated that FIDEGAM was the most accurate discriminator method in all scenarios of sampling exhaustiveness, and therefore, it can be efficiently applied to most databases in order to enhance the reliability of biodiversity analyses.

Fluorimetric detection of Sn(2+) ion in aqueous medium using Salicylaldehyde based nanoparticles and application to natural samples analysis.

PubMed

Patil, Kishor S; Mahajan, Prasad G; Patil, Shivajirao R

2017-01-05

The fluorescent 2-[(E)-(2-phenylhydrazinylidene)methyl]phenol nanoparticles (PHPNPs) were prepared by a simple reprecipitation method. The prepared PHPNPs examined by Dynamic Light Scattering show narrower particle size distribution having an average particle size of 93.3nm. The Scanning Electron Microphotograph shows distinct spherical shaped morphology of nanoparticles. The blue shift in UV-absorption and fluorescence spectra of PHPNPs with respect to corresponding spectra of PHP in acetone solution indicates H- aggregates and Aggregation Induced Enhanced Emission (AIEE) for nanoparticles. The nanoparticles show selective tendency towards the recognition of Sn(2+) ions by enhancing the fluorescence intensity preference to Cu(2+), Fe(3+), Fe(2+), Ni(2+), NH4(+), Ca(2+), Pb(2+), Hg(2+) and Zn(2+) ions, which actually seem to quench the fluorescence of nanoparticles. The studies on Langmuir adsorption plot, fluorescence lifetime of PHPNPs, DLS-Zeta sizer, UV-visible and fluorescence titration with and without Sn(2+) helped to propose a suitable mechanism of fluorescence enhancement of nanoparticles by Sn(2+) and their binding ability during complexation. The fluorescence enhancement effect of PHPNPs induced by Sn(2+) is further used to develop an analytical method for detection of Sn(2+) from aqueous medium in environmental samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Fluorimetric detection of Sn2 + ion in aqueous medium using Salicylaldehyde based nanoparticles and application to natural samples analysis

NASA Astrophysics Data System (ADS)

Patil, Kishor S.; Mahajan, Prasad G.; Patil, Shivajirao R.

2017-01-01

The fluorescent 2-[(E)-(2-phenylhydrazinylidene)methyl]phenol nanoparticles (PHPNPs) were prepared by a simple reprecipitation method. The prepared PHPNPs examined by Dynamic Light Scattering show narrower particle size distribution having an average particle size of 93.3 nm. The Scanning Electron Microphotograph shows distinct spherical shaped morphology of nanoparticles. The blue shift in UV-absorption and fluorescence spectra of PHPNPs with respect to corresponding spectra of PHP in acetone solution indicates H- aggregates and Aggregation Induced Enhanced Emission (AIEE) for nanoparticles. The nanoparticles show selective tendency towards the recognition of Sn2 + ions by enhancing the fluorescence intensity preference to Cu2 +, Fe3 +, Fe2 +, Ni2 +, NH4+, Ca2 +, Pb2 +, Hg2 + and Zn2 + ions, which actually seem to quench the fluorescence of nanoparticles. The studies on Langmuir adsorption plot, fluorescence lifetime of PHPNPs, DLS-Zeta sizer, UV-visible and fluorescence titration with and without Sn2 + helped to propose a suitable mechanism of fluorescence enhancement of nanoparticles by Sn2 + and their binding ability during complexation. The fluorescence enhancement effect of PHPNPs induced by Sn2 + is further used to develop an analytical method for detection of Sn2 + from aqueous medium in environmental samples.

Effect of dactyloscopic powders on DNA profiling from enhanced fingerprints: results from an experimental study.

PubMed

Tozzo, Pamela; Giuliodori, Alice; Rodriguez, Daniele; Caenazzo, Luciana

2014-03-01

We conducted a study on the effect of fingerprint enhancement methods on subsequent short tandem repeat profiling. First, we performed a study typing blood traces deposited on 5 different surfaces, treated with 8 types of dactyloscopic powders. Three different DNA extraction methods were used. Subsequently, we analyzed latent fingerprints on the same 5 surfaces enhanced with the 8 different powders used in the first part of the study. This study has demonstrated that DNA profiling can be performed on fingerprints left on different substrates, and the substrate will affect the amount of DNA that can be recovered for DNA typing. In the first phase of the study, a profile was obtained in 92% of the 120 samples analyzed; in the second part, in 55% of the 80 samples analyzed, we obtained a profile complete in 32.5% of the cases. From the results obtained, it seems that the powders used in latent fingerprints enhancement, rather than having a direct inhibitory effect on extraction and amplification of DNA, may cause partial degradation of DNA, reducing the efficiency of amplification reaction. It should not be forgotten that these results were obtained under laboratory conditions, and in real caseworks, there may still be different problems involved.

Millennial's perspective of clicker technology in a nursing classroom: A Mixed methods research study.

PubMed

Toothaker, Rebecca

2018-03-01

Nursing education is facing challenges and a shift in paradigm within the nursing classroom. Educators need to explore innovative strategies that engage students. Clickers are one tool that can enhance participation, protect anonymity, and promote learning of concepts. This mixed methods study evaluated nursing student's perceptions of clicker technology during lecture. This study uses a 9-item questionnaire to explore perceived levels of student perception of the technology of clickers in a nursing classroom. The sample consisted of ninety-nine sophomore and senior level nursing students. Participants were recruited using convenience sampling. Ninety-one percent of the students agreed or strongly agreed that the use of clickers helped them to develop a better understanding of the subject matter when compared to traditional lecture based class. The findings portray a positive correlation of learning and an enhanced pedagogical approach for nursing students. Copyright © 2017 Elsevier Ltd. All rights reserved.

Resonance light scattering determination of 6-mercaptopurine coupled with HPLC technique

NASA Astrophysics Data System (ADS)

Li, Ai Ping; Peng, Jing Dong; Zhou, MingQiong; Zhang, Jin

2016-02-01

A simple, fast, costless, sensitive and selective method of resonance light scattering coupled with HPLC was established for the determination of 6-mercaptopurine in human urine sample. In a Britton-Robinson buffer solution of pH 5.5, the formation of coordination complex between 6-mercaptopurine and metal palladium (II) led to enhance the RLS intensity of the system. The RLS signal was detected by fluorescence detector at λex = λem = 315 nm. The analytical parameters were provided by the coupled system, the linear of 6-mercaptopurine response from 0.0615 to 2.40 μg L- 1 and the limit of detection (S/N = 3) was 0.05 μg L- 1. The presented method has been applied to determine 6-mercaptopurine in human urine samples which obtained satisfactory results. Moreover, the reaction mechanism and possible reasons for enhancement of RLS were fully discussed.

Resonance light scattering determination of 6-mercaptopurine coupled with HPLC technique.

PubMed

Li, Ai Ping; Peng, Jing Dong; Zhou, MingQiong; Zhang, Jin

2016-02-05

A simple, fast, costless, sensitive and selective method of resonance light scattering coupled with HPLC was established for the determination of 6-mercaptopurine in human urine sample. In a Britton-Robinson buffer solution of pH5.5, the formation of coordination complex between 6-mercaptopurine and metal palladium (II) led to enhance the RLS intensity of the system. The RLS signal was detected by fluorescence detector at λ(ex)=λ(em)=315 nm. The analytical parameters were provided by the coupled system, the linear of 6-mercaptopurine response from 0.0615 to 2.40 μg L(-1) and the limit of detection (S/N=3) was 0.05 μg L(-1). The presented method has been applied to determine 6-mercaptopurine in human urine samples which obtained satisfactory results. Moreover, the reaction mechanism and possible reasons for enhancement of RLS were fully discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Capillary-valve-based fabrication of ion-selective membrane junction for electrokinetic sample preconcentration in PDMS chip.

PubMed

Liu, Vincent; Song, Yong-Ak; Han, Jongyoon

2010-06-07

In this paper, we report a novel method for fabricating ion-selective membranes in poly(dimethylsiloxane) (PDMS)/glass-based microfluidic preconcentrators. Based on the concept of capillary valves, this fabrication method involves filling a lithographically patterned junction between two microchannels with an ion-selective material such as Nafion resin; subsequent curing results in a high aspect-ratio membrane for use in electrokinetic sample preconcentration. To demonstrate the concentration performance of this high-aspect-ratio, ion-selective membrane, we integrated the preconcentrator with a surface-based immunoassay for R-Phycoerythrin (RPE). Using a 1x PBS buffer system, the preconcentrator-enhanced immunoassay showed an approximately 100x improvement in sensitivity within 30 min. This is the first time that an electrokinetic microfluidic preconcentrator based on ion concentration polarization (ICP) has been used in high ionic strength buffer solutions to enhance the sensitivity of a surface-based immunoassay.

A comparison of four porewater sampling methods for metal mixtures and dissolved organic carbon and the implications for sediment toxicity evaluations

USGS Publications Warehouse

Cleveland, Danielle; Brumbaugh, William G.; MacDonald, Donald D.

2017-01-01

Evaluations of sediment quality conditions are commonly conducted using whole-sediment chemistry analyses but can be enhanced by evaluating multiple lines of evidence, including measures of the bioavailable forms of contaminants. In particular, porewater chemistry data provide information that is directly relevant for interpreting sediment toxicity data. Various methods for sampling porewater for trace metals and dissolved organic carbon (DOC), which is an important moderator of metal bioavailability, have been employed. The present study compares the peeper, push point, centrifugation, and diffusive gradients in thin films (DGT) methods for the quantification of 6 metals and DOC. The methods were evaluated at low and high concentrations of metals in 3 sediments having different concentrations of total organic carbon and acid volatile sulfide and different particle-size distributions. At low metal concentrations, centrifugation and push point sampling resulted in up to 100 times higher concentrations of metals and DOC in porewater compared with peepers and DGTs. At elevated metal levels, the measured concentrations were in better agreement among the 4 sampling techniques. The results indicate that there can be marked differences among operationally different porewater sampling methods, and it is unclear if there is a definitive best method for sampling metals and DOC in porewater.

How [NOT] to Measure a Solar Cell to Get the Highest Efficiency

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

Emery, Keith

The multibillion-dollar photovoltaic (PV) industry sells products by the watt; the calibration labs measure this parameter at the cell and module level with the lowest possible uncertainty of 1-2 percent. The methods and procedures to achieve a measured 50 percent efficiency on a thin-film solar cell are discussed. This talk will describe methods that ignore procedures that increase the uncertainty. Your questions will be answered concerning 'Everything you Always Wanted to Know about Efficiency Enhancements But Were Afraid to Ask.' The talk will cover a step-by-step procedure using examples found in literature or encountered in customer samples by the Nationalmore » Renewable Energy Laboratory's (NREL's) PV Performance Characterization Group on how to artificially enhance the efficiency. The procedures will describe methods that have been used to enhance the current voltage and fill factor.« less

Flow-injection chemiluminescence determination of melamine in urine and plasma.

PubMed

Tang, Xiaoshuang; Shi, Xiyan; Tang, Yuhai; Yue, Zhongjin; He, Qiqi

2012-01-01

A novel flow-injection chemiluminescence method for the determination of melamine in urine and plasma was developed. It was found that melamine can remarkably enhance chemiluminescence emission from the luminol-K(3) Fe(CN)(6) system in an alkaline medium. Under the optimum conditions, chemiluminescence intensity had a good linear relationship with the concentration of melamine in the range 9.0 × 10(-9) -7.0 × 10(-6) g/mL, with a correlation coefficient of 0.9992. The detection limit (3σ) was 3.5 ng/mL. The method has been applied to determine the concentration of melamine in samples using liquid-liquid extraction. Average recoveries of melamine were 102.6% in urine samples and 95.1% in plasma samples. The method provided a reproducible and stable approach for the sensitive detection of melamine in urine and plasma samples. Copyright © 2011 John Wiley & Sons, Ltd.

Postmortem aging and freezing and thawing storage enhance ability of early deboned chicken pectoralis major muscle to hold added salt water.

PubMed

Zhuang, H; Savage, E M

2012-05-01

The effects of postdeboning aging and frozen storage on water-holding capacity (WHC) of chicken breast pectoralis major muscle were investigated. Broiler breast muscle was removed from carcasses either early postmortem (2 h) or later postmortem (24 h). Treatments included: no postdeboning aging; 1-d postdeboning aging at 2°C, 7-d postdeboning aging (2-h deboned meat only), and 6-d storage at -20°C plus 1-d thawing at 2°C (freezing and thawing treatment, 2-h deboned meat only). The WHC was determined by cooking loss, drip loss, a filter paper press method (results were presented as expressible fluid), and a salt-induced swelling and centrifugation method (results were presented as percentage of salt-induced water gain). There were no differences for WHC estimated by cooking loss and expressible fluid between the treatments. Only the freezing and thawing treatment resulted in a significant increase in drip loss. The average percentage of salt-induced water gains by the 24-h deboned samples, postdeboning aged 2 h samples, and frozen 2 h sample, which did not differ from each other, were significantly higher than that by the 2-h deboned sample. These results indicate that regardless of method (carcass aging vs. postdeboning aging) and time (aging for 1 d vs. for 7 d), postmortem aging more than 1 d does not affect WHC of the early deboned samples measured by dripping, cooking, and pressing. However, postmortem carcass aging, postdeboning aging, and freezing and thawing storage can significantly enhance the ability of chicken breast meat to hold added salt water or WHC measured by the salt-induced swelling and centrifuge method.

Rapid Sampling of Molecules via Skin for Diagnostic and Forensic Applications

PubMed Central

Paliwal, Sumit; Ogura, Makoto

2010-01-01

ABSTRACT Purpose Skin provides an excellent portal for diagnostic monitoring of a variety of entities; however, there is a dearth of reliable methods for patient-friendly sampling of skin constituents. This study describes the use of low-frequency ultrasound as a one-step methodology for rapid sampling of molecules from the skin. Methods Sampling was performed using a brief exposure of 20 kHz ultrasound to skin in the presence of a sampling fluid. In vitro sampling from porcine skin was performed to assess the effectiveness of the method and its ability to sample drugs and endogenous epidermal biomolecules from the skin. Dermal presence of an antifungal drug—fluconazole and an abused substance, cocaine—was assessed in rats. Results Ultrasonic sampling captured the native profile of various naturally occurring moisturizing factors in skin. A high sampling efficiency (79 ± 13%) of topically delivered drug was achieved. Ultrasound consistently sampled greater amounts of drug from the skin compared to tape stripping. Ultrasonic sampling also detected sustained presence of cocaine in rat skin for up to 7 days as compared to its rapid disappearance from the urine. Conclusions Ultrasonic sampling provides significant advantages including enhanced sampling from deeper layers of skin and high temporal sampling sensitivity. PMID:20238151

Measuring of electrical changes induced by in situ combustion through flow-through electrodes in a laboratory sample of core material

DOEpatents

Lee, D.O.; Montoya, P.C.; Wayland, J.R. Jr.

1986-12-09

Method and apparatus are provided for obtaining accurate dynamic measurements for passage of phase fronts through a core sample in a test fixture. Flow-through grid structures are provided for electrodes to permit data to be obtained before, during and after passage of a front there through. Such electrodes are incorporated in a test apparatus for obtaining electrical characteristics of the core sample. With the inventive structure a method is provided for measurement of instabilities in a phase front progressing through the medium. Availability of accurate dynamic data representing parameters descriptive of material characteristics before, during and after passage of a front provides a more efficient method for enhanced recovery of oil using a fire flood technique. 12 figs.

Measuring of electrical changes induced by in situ combustion through flow-through electrodes in a laboratory sample of core material

DOEpatents

Lee, David O.; Montoya, Paul C.; Wayland, Jr., James R.

1986-01-01

Method and apparatus are provided for obtaining accurate dynamic measurements for passage of phase fronts through a core sample in a test fixture. Flow-through grid structures are provided for electrodes to permit data to be obtained before, during and after passage of a front therethrough. Such electrodes are incorporated in a test apparatus for obtaining electrical characteristics of the core sample. With the inventive structure a method is provided for measurement of instabilities in a phase front progressing through the medium. Availability of accurate dynamic data representing parameters descriptive of material characteristics before, during and after passage of a front provides a more efficient method for enhanced recovery of oil using a fire flood technique.

Convergent Inquiry in Science & Engineering: The Use of Atomic Force Microscopy in a Biology Class

ERIC Educational Resources Information Center

Lee, Il-Sun; Byeon, Jung-Ho; Kwon, Yong-Ju

2013-01-01

The purpose of this study was to design a teaching method suitable for science high school students using atomic force microscopy. During their scientific inquiry procedure, high school students observed a micro-nanostructure of a biological sample, which is unobservable via an optical microscope. The developed teaching method enhanced students'…

A new flexible forest inventory in France

Treesearch

C. Vidal; T. Belouard; J.-C. Herve; N. Robert; J. Wolsack

2007-01-01

The French National Forest Inventory was created in 1958 to assess metropolitan forest resources. To stick to new national and international requirements as well as to enhance reactivity, a new inventory method was implemented in 2004. This new method is based on a systematic sampling grid covering the whole territory every year. The size of the mesh is variable,...

Determination of alcohol and extract concentration in beer samples using a combined method of near-infrared (NIR) spectroscopy and refractometry.

PubMed

Castritius, Stefan; Kron, Alexander; Schäfer, Thomas; Rädle, Matthias; Harms, Diedrich

2010-12-22

A new approach of combination of near-infrared (NIR) spectroscopy and refractometry was developed in this work to determine the concentration of alcohol and real extract in various beer samples. A partial least-squares (PLS) regression, as multivariate calibration method, was used to evaluate the correlation between the data of spectroscopy/refractometry and alcohol/extract concentration. This multivariate combination of spectroscopy and refractometry enhanced the precision in the determination of alcohol, compared to single spectroscopy measurements, due to the effect of high extract concentration on the spectral data, especially of nonalcoholic beer samples. For NIR calibration, two mathematical pretreatments (first-order derivation and linear baseline correction) were applied to eliminate light scattering effects. A sample grouping of the refractometry data was also applied to increase the accuracy of the determined concentration. The root mean squared errors of validation (RMSEV) of the validation process concerning alcohol and extract concentration were 0.23 Mas% (method A), 0.12 Mas% (method B), and 0.19 Mas% (method C) and 0.11 Mas% (method A), 0.11 Mas% (method B), and 0.11 Mas% (method C), respectively.

Supersampling multiframe blind deconvolution resolution enhancement of adaptive-optics-compensated imagery of LEO satellites

NASA Astrophysics Data System (ADS)

Gerwe, David R.; Lee, David J.; Barchers, Jeffrey D.

2000-10-01

A post-processing methodology for reconstructing undersampled image sequences with randomly varying blur is described which can provide image enhancement beyond the sampling resolution of the sensor. This method is demonstrated on simulated imagery and on adaptive optics compensated imagery taken by the Starfire Optical Range 3.5 meter telescope that has been artificially undersampled. Also shown are the results of multiframe blind deconvolution of some of the highest quality optical imagery of low earth orbit satellites collected with a ground based telescope to date. The algorithm used is a generalization of multiframe blind deconvolution techniques which includes a representation of spatial sampling by the focal plane array elements in the forward stochastic model of the imaging system. This generalization enables the random shifts and shape of the adaptive compensated PSF to be used to partially eliminate the aliasing effects associated with sub- Nyquist sampling of the image by the focal plane array. The method could be used to reduce resolution loss which occurs when imaging in wide FOV modes.

Supersampling multiframe blind deconvolution resolution enhancement of adaptive optics compensated imagery of low earth orbit satellites

NASA Astrophysics Data System (ADS)

Gerwe, David R.; Lee, David J.; Barchers, Jeffrey D.

2002-09-01

We describe a postprocessing methodology for reconstructing undersampled image sequences with randomly varying blur that can provide image enhancement beyond the sampling resolution of the sensor. This method is demonstrated on simulated imagery and on adaptive-optics-(AO)-compensated imagery taken by the Starfire Optical Range 3.5-m telescope that has been artificially undersampled. Also shown are the results of multiframe blind deconvolution of some of the highest quality optical imagery of low earth orbit satellites collected with a ground-based telescope to date. The algorithm used is a generalization of multiframe blind deconvolution techniques that include a representation of spatial sampling by the focal plane array elements based on a forward stochastic model. This generalization enables the random shifts and shape of the AO- compensated point spread function (PSF) to be used to partially eliminate the aliasing effects associated with sub-Nyquist sampling of the image by the focal plane array. The method could be used to reduce resolution loss that occurs when imaging in wide- field-of-view (FOV) modes.

Subnanogram determination of aniracetam in pharmaceutical preparations and biofluids by flow injection analysis with chemiluminescence detection based on its enhancement of the myoglobin-luminol reaction.

PubMed

Shao, Xiaodong; Li, Ying; Li, Fagen; Liu, Yangqin; Song, Zhenghua

2011-01-01

A novel flow injection chemiluminescence method with a myoglobin-luminol system is described for determining aniracetam. Myoglobin-bound aniracetam produced a complex that catalyzed the chemiluminescence reaction between luminol and myoglobin, leading to fast chemiluminescence. The chemiluminescence intensity in the presence of aniracetam was remarkably enhanced compared with that in the absence of aniracetam. Under the optimum reaction conditions the chemiluminescence increment produced was proportional to the concentration of aniracetam in the range of 0.1-1000.0 ng/mL (R2 = 0.9992), with a detection limit of 0.03 ng/mL (3delta). At a flow rate of 2.0 mL/min, the whole process, including sampling and washing, could be completed in 0.5 min, offering a sampling efficiency of 120/h; the RSD was less than 3.0% (n = 5). The method was satisfactory for determination of aniracetam in pharmaceutical preparations and human urine and serum samples. A possible mechanism of the reaction is also discussed.

Combined different dehydration pretreatments and torrefaction to upgrade fuel properties of hybrid pennisetum (Pennisetum americanum ×P. purpureum).

PubMed

Yu, Yan; Wang, Guanghui; Bai, Xiaopeng; Liu, Jude; Wang, Decheng; Wang, Zhiqin

2018-05-16

Different dehydrating methods combined with torrefaction were investigated to find the underlying mechanism that how dehydration process influence the degree of hornification. Hybrid pennisetum was selected as the experiment material. Oven-dried sample (ODS), crushed dried sample (CDS), and sun-cured dried sample (SDS) were torrefied under the temperature of 275 °C and 300 °C with the duration time of 60 min. The results showed that, changes in elevated carbon content and higher heating value (HHV) and reduced oxygen content of SDS were the most obvious under identical torrefaction conditions. Fuel ratio of SDS was enhanced most under 300 °C. It also had the highest devolatilization index (D i ). The combination of sun-cured dried with torrefaction under 300 °C caused lowest degree of irreversible hornification happened during dehydrating process, and different hornification degrees caused by different dehydrating methods effect the enhancement of fuel properties of lignocellulosic biomass material. Copyright © 2018 Elsevier Ltd. All rights reserved.

Enhanced magneto-optical imaging of internal stresses in the removed surface layer

NASA Astrophysics Data System (ADS)

Agalidi, Yuriy; Kozhukhar, Pavlo; Levyi, Sergii; Turbin, Dmitriy

2015-10-01

The paper describes a software method of reconstructing the state of the removed surface layer by visualising internal stresses in the underlying layers of the sample. Such a problem typically needs to be solved as part of forensic investigation that aims to reveal original marking of a sample with removed surface layer. For example, one may be interested in serial numbers of weapons or vehicles that had the surface layer of metal removed from the number plate. Experimental results of studying gradient internal stress fields in ferromagnetic sample using the NDI method of magneto-optical imaging (MOI) are presented. Numerical modelling results of internal stresses enclosed in the surface marking region are analysed and compared to the experimental results of magneto-optical imaging (MOI). MOI correction algorithm intended for reconstructing internal stress fields in the removed surface layer by extracting stresses retained by the underlying layers is described. Limiting ratios between parameters of a marking font are defined for the considered correction algorithm. Enhanced recognition properties for hidden stresses left by marking symbols are experimentally verified and confirmed.

Ultrasound-enhanced ocular delivery of dexamethasone sodium phosphate: an in vivo study

PubMed Central

2014-01-01

Background The eye's unique anatomy and its physiological and anatomical barriers can limit effective drug delivery into the eye. Methods An in vivo study was designed to determine the effectiveness and safety of ultrasound application in enhancing drug delivery in a rabbit model. Permeability of a steroid ophthalmic drug, dexamethasone sodium phosphate, was investigated in ultrasound- and sham-treated cases. For this study, an eye cup filled with dexamethasone sodium phosphate was placed on the cornea. Ultrasound was applied at intensity of 0.8 W/cm2 and frequency of 400 or 600 kHz for 5 min. The drug concentration in aqueous humor samples, collected 90 min after the treatment, was determined using chromatography methods. Light microscopy observations were done to determine the structural changes in the cornea as a result of ultrasound application. Results An increase in drug concentration in aqueous humor samples of 2.8 times (p < 0.05) with ultrasound application at 400 kHz and 2.4 times (p < 0.01) with ultrasound application at 600 kHz was observed as compared to sham-treated samples. Histological analysis showed that the structural changes in the corneas exposed to ultrasound predominantly consisted of minor epithelial disorganization. Conclusions Ultrasound application enhanced the delivery of an anti-inflammatory ocular drug, dexamethasone sodium phosphate, through the cornea in vivo. Ultrasound-enhanced ocular drug delivery appears to be a promising area of research with a potential future application in a clinical setting. PMID:24921047

An enhanced cerium(IV)-rhodamine 6G chemiluminescence system using guest-host interactions in a lab-on-a-chip platform for estimating the total phenolic content in food samples.

PubMed

Al Haddabi, Buthaina; Al Lawati, Haider A J; Suliman, FakhrEldin O

2016-04-01

Two chemiluminescence-microfluidic (CL-MF) systems, e.g., Ce(IV)-rhodamine B (RB) and Ce(IV)-rhodamine 6G (R6G), for the determination of the total phenolic content in teas and some sweeteners were evaluated. The results indicated that the Ce(IV)-R6G system was more sensitive in comparison to the Ce(IV)-RB CL system. Therefore, a simple (CL-MF) method based on the CL of Ce(IV)-R6G was developed, and the sensitivity, selectivity and stability of this system were evaluated. Selected phenolic compounds (PCs), such as quercetin (QRC), catechin (CAT), rutin (RUT), gallic acid (GA), caffeic acid (CA) and syringic acid (SA), produced analytically useful chemiluminescence signals with low detection limits ranging from 0.35 nmol L(-1) for QRC to 11.31 nmol L(-1) for SA. The mixing sequence and the chip design were crucial, as the sensitivity and reproducibility could be substantially affected by these two factors. In addition, the anionic surfactant (i.e., sodium dodecyl sulfate (SDS)) can significantly enhance the CL signal intensity by as much as 300% for the QRC solution. Spectroscopic studies indicated that the enhancement was due to a strong guest-host interaction between the cationic R6G molecules and the anionic amphiphilic environment. Other parameters that could affect the CL intensities of the PCs were carefully optimized. Finally, the method was successfully applied to tea and sweetener samples. Six different tea samples exhibited total phenolic/antioxidant levels from 7.32 to 13.5 g per 100g of sample with respect to GA. Four different sweetener samples were also analyzed and exhibited total phenolic/antioxidant levels from 500.9 to 3422.9 mg kg(-1) with respect to GA. The method was selective, rapid and sensitive when used to estimate the total phenolic/antioxidant level, and the results were in good agreement with those reported for honey and tea samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Practicable group testing method to evaluate weight/weight GMO content in maize grains.

PubMed

Mano, Junichi; Yanaka, Yuka; Ikezu, Yoko; Onishi, Mari; Futo, Satoshi; Minegishi, Yasutaka; Ninomiya, Kenji; Yotsuyanagi, Yuichi; Spiegelhalter, Frank; Akiyama, Hiroshi; Teshima, Reiko; Hino, Akihiro; Naito, Shigehiro; Koiwa, Tomohiro; Takabatake, Reona; Furui, Satoshi; Kitta, Kazumi

2011-07-13

Because of the increasing use of maize hybrids with genetically modified (GM) stacked events, the established and commonly used bulk sample methods for PCR quantification of GM maize in non-GM maize are prone to overestimate the GM organism (GMO) content, compared to the actual weight/weight percentage of GM maize in the grain sample. As an alternative method, we designed and assessed a group testing strategy in which the GMO content is statistically evaluated based on qualitative analyses of multiple small pools, consisting of 20 maize kernels each. This approach enables the GMO content evaluation on a weight/weight basis, irrespective of the presence of stacked-event kernels. To enhance the method's user-friendliness in routine application, we devised an easy-to-use PCR-based qualitative analytical method comprising a sample preparation step in which 20 maize kernels are ground in a lysis buffer and a subsequent PCR assay in which the lysate is directly used as a DNA template. This method was validated in a multilaboratory collaborative trial.

75 FR 6332 - Wyoming Regulatory Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-09

... practices, shrub reclamation standards, fish and wildlife enhancement measures, cultural and historic... normal husbandry practices, reorganize and clarify species diversity and shrub density requirements, and... vegetation sampling methods and reclamation success standards for shrubs on reclaimed lands. In August of...

Nonlinear inversion of electrical resistivity imaging using pruning Bayesian neural networks

NASA Astrophysics Data System (ADS)

Jiang, Fei-Bo; Dai, Qian-Wei; Dong, Li

2016-06-01

Conventional artificial neural networks used to solve electrical resistivity imaging (ERI) inversion problem suffer from overfitting and local minima. To solve these problems, we propose to use a pruning Bayesian neural network (PBNN) nonlinear inversion method and a sample design method based on the K-medoids clustering algorithm. In the sample design method, the training samples of the neural network are designed according to the prior information provided by the K-medoids clustering results; thus, the training process of the neural network is well guided. The proposed PBNN, based on Bayesian regularization, is used to select the hidden layer structure by assessing the effect of each hidden neuron to the inversion results. Then, the hyperparameter α k , which is based on the generalized mean, is chosen to guide the pruning process according to the prior distribution of the training samples under the small-sample condition. The proposed algorithm is more efficient than other common adaptive regularization methods in geophysics. The inversion of synthetic data and field data suggests that the proposed method suppresses the noise in the neural network training stage and enhances the generalization. The inversion results with the proposed method are better than those of the BPNN, RBFNN, and RRBFNN inversion methods as well as the conventional least squares inversion.

Adaptive single-pixel imaging with aggregated sampling and continuous differential measurements

NASA Astrophysics Data System (ADS)

Huo, Yaoran; He, Hongjie; Chen, Fan; Tai, Heng-Ming

2018-06-01

This paper proposes an adaptive compressive imaging technique with one single-pixel detector and single arm. The aggregated sampling (AS) method enables the reduction of resolutions of the reconstructed images. It aims to reduce the time and space consumption. The target image with a resolution up to 1024 × 1024 can be reconstructed successfully at the 20% sampling rate. The continuous differential measurement (CDM) method combined with a ratio factor of significant coefficient (RFSC) improves the imaging quality. Moreover, RFSC reduces the human intervention in parameter setting. This technique enhances the practicability of single-pixel imaging with the benefits from less time and space consumption, better imaging quality and less human intervention.

Enhanced photocatalytic performance of Er-doped Bi{sub 24}O{sub 31}Br{sub 10}: Facile synthesis and photocatalytic mechanism

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

Liu, Zhang Sheng, E-mail: lzsliu2008@hotmail.com; Liu, Zhi Lin; Liu, Jin Long

2016-04-15

Highlights: • Er-doped Bi{sub 24}O{sub 31}Br{sub 10} have been prepared via a one-pot solvothermal method. • Er doping drastically improves the photocatalytic activity of Bi{sub 24}O{sub 31}Br{sub 10}. • The enhanced activity is attributed to effective electron trapping and up-conversion process resulting from Er{sup 3+}. • Holes and super-oxide radicals are main active species. - Abstract: Erbium (Er) doped Bi{sub 24}O{sub 31}Br{sub 10} samples were successfully prepared by using a solvothermal method. The samples were characterized by XRD, XPS, SEM, TEM, BET, DRS, PL and EIS. The photocatalytic activity was evaluated by the degradation of rhodamine B (RhB) and methylmore » orange (MO) under visible light irradiation. The result shows that Er dopant induces a significant improvement in the photocatalytic activity. 1.0% Er–Bi{sub 24}O{sub 31}Br{sub 10} sample exhibits the best photocatalytic performance. The enhanced photocatalytic activity is attributed to the effective trapping of photogenerated electron by Er{sup 3+} ion and the up-conversion process resulting from Er dopant. In addition, it is found that holes and super-oxide radicals play main role in the photocatalytic degradation of RhB and MO.« less

Methods for Multiplex Template Sampling in Digital PCR Assays

PubMed Central

Petriv, Oleh I.; Heyries, Kevin A.; VanInsberghe, Michael; Walker, David; Hansen, Carl L.

2014-01-01

The efficient use of digital PCR (dPCR) for precision copy number analysis requires high concentrations of target molecules that may be difficult or impossible to obtain from clinical samples. To solve this problem we present a strategy, called Multiplex Template Sampling (MTS), that effectively increases template concentrations by detecting multiple regions of fragmented target molecules. Three alternative assay approaches are presented for implementing MTS analysis of chromosome 21, providing a 10-fold concentration enhancement while preserving assay precision. PMID:24854517

Methods for multiplex template sampling in digital PCR assays.

PubMed

Petriv, Oleh I; Heyries, Kevin A; VanInsberghe, Michael; Walker, David; Hansen, Carl L

2014-01-01

The efficient use of digital PCR (dPCR) for precision copy number analysis requires high concentrations of target molecules that may be difficult or impossible to obtain from clinical samples. To solve this problem we present a strategy, called Multiplex Template Sampling (MTS), that effectively increases template concentrations by detecting multiple regions of fragmented target molecules. Three alternative assay approaches are presented for implementing MTS analysis of chromosome 21, providing a 10-fold concentration enhancement while preserving assay precision.

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

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

Ahn, Surl-Hee; Grate, Jay W.; Darve, Eric F.

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run microseconds or longer simulations using femtoseconds time steps. While there are several existing methods to overcome this timescale barrier and efficiently sample thermodynamic and/or kinetic properties, problems remain in regard to being able to sample un- known systems, deal with high-dimensional space of collective variables, and focus the computational effort on slow timescales. Hence, a new sampling method, called the “Concurrent Adaptive Sampling (CAS) algorithm,”more » has been developed to tackle these three issues and efficiently obtain conformations and pathways. The method is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective vari- ables and uses macrostates (a partition of the collective variable space) to enhance the sampling. The exploration is done by running a large number of short simula- tions, and a clustering technique is used to accelerate the sampling. In this paper, we introduce the new methodology and show results from two-dimensional models and bio-molecules, such as penta-alanine and triazine polymer« less

Decontamination methods for samples preserved in cetylpyridinium chloride and cultured on thin-layer agar.

PubMed

Ardizzoni, E; Mulders, W; Sanchez-Padilla, E; Varaine, F; de Jong, B C; Rigouts, L

2014-08-01

Long transportation times of samples to culture laboratories can lead to higher contamination rates and significant loss of viability, resulting in lower culture positivity rates. Thin-layer agar (TLA) is a sensitive culture method for the isolation of Mycobacterium tuberculosis that has been optimised with N-acetyl-L-cysteine-sodium hydroxide (NALC-NaOH) decontaminated samples. The combination of the TLA culture method and other decontamination procedures has not been extensively validated. Among 390 smear-positive samples, we compared the culture positivity of samples decontaminated using the Petroff method vs. NALC-NaOH neutralised with phosphate buffer (PBS), applied to samples preserved with cetylpyridinium chloride (CPC) or CPC-free, and then of CPC-preserved samples decontaminated with NALC-NaOH neutralised using Difco neutralising buffer. The sediments were inoculated on TLA, and then on MGIT 960 or Löwenstein-Jensen (LJ) as gold standards. Decontamination with NALC-NaOH yielded higher culture positivity in TLA than in the Petroff method, which was further enhanced by neutralising CPC with the Difco buffer. Surprisingly, culture positivity on LJ also increased after using Difco buffer, suggesting that CPC may not be completely neutralised in egg-based medium. After transportation in CPC, decontamination using NALC-NaOH followed by neutralisation using Difco buffer resulted in the best recovery rates for samples inoculated on TLA and on LJ.

Localized-surface-plasmon enhanced emission from porous silicon by gold nanoparticles.

PubMed

Wang, Hui; An, Zhenghua; Ren, Qijun; Wang, Hengliang; Mao, Feilong; Chen, Zhanghai; Shen, Xuechu

2011-12-01

The porous silicon (PS) samples, decorated by Au nanoparticles (NPs) possessing localized-surface-plasmon (LSP) resonance, are prepared by the conventional anodization method. Photoluminescence (PL) is studied systematically, in particular, its dependence on the excitation power. It is found that undecorated PS samples exhibit a saturation behavior in PL intensity with increasing the pumping laser power, while the luminescence of Au-decorated PS hybrid samples have a purely linear dependence on the excitation power. In the linear response region of PS samples, addition of metal NPs layer moderately suppresses the emission while, in the saturation region, the net emission is enhanced by approximately up to 4-fold. Several possible mechanisms are discussed. We believe that the observed PL enhancement in saturation region is dominantly due to the resonant coupling between the LSP of Au NPs and the electronic excitation of PS, which inhibits the nonradiative Auger recombination process at high excitation power. These results indicate that the plasmon effect could be useful for designing even more efficient optoelectronic devices such as super bright light emitting devices and solar cells with high efficiencies. Despite many challenges, Au NPs can potentially be applied to introduce LSP resonance for the future silicon-based optoelectronics or photonics.

Transmittance enhancement of sapphires with antireflective subwavelength grating patterned UV polymer surface structures by soft lithography.

PubMed

Lee, Soo Hyun; Leem, Jung Woo; Yu, Jae Su

2013-12-02

We report the total and diffuse transmission enhancement of sapphires with the ultraviolet curable SU8 polymer surface structures consisting of conical subwavelength gratings (SWGs) at one- and both-side surfaces for different periods. The SWGs patterns on the silicon templates were transferred into the SU8 polymer film surface on sapphires by a simple and cost-effective soft lithography technique. For the fabricated samples, the surface morphologies, wetting behaviors, and optical characteristics were investigated. For theoretical optical analysis, a rigorous coupled-wave analysis method was used. At a period of 350 nm, the sample with SWGs on SU8 film/sapphire exhibited a hydrophobic surface and higher total transmittance compared to the bare sapphire over a wide wavelength of 450-1000 nm. As the period of SWGs was increased, the low total transmittance region of < 85% was shifted towards the longer wavelengths and became broader while the diffuse transmittance was increased (i.e., larger haze ratio). For the samples with SWGs at both-side surfaces, the total and diffuse transmittance spectra were further enhanced compared to the samples with SWGs at one-side surface. The theoretical optical calculation results showed a similar trend to the experimentally measured data.

Improvement of the Laser-Induced Breakdown Spectroscopy method sensitivity by the usage of combination of Ag-nanoparticles and vacuum conditions

NASA Astrophysics Data System (ADS)

Sládková, Lucia; Prochazka, David; Pořízka, Pavel; Škarková, Pavlína; Remešová, Michaela; Hrdlička, Aleš; Novotný, Karel; Čelko, Ladislav; Kaiser, Jozef

2017-01-01

In this work we studied the effect of vacuum (low pressure) conditions on the behavior of laser-induced plasma (LIP) created on a sample surface covered with silver nanoparticles (Ag-NPs), i.e. Nanoparticles-Enhanced Laser-Induced Breakdown Spectroscopy (NELIBS) experiment in a vacuum. The focus was put on the step by step optimization of the measurement parameters, such as energy of the laser pulse, temporally resolved detection, ambient pressure, and different content of Ag-NPs applied on the sample surface. The measurement parameters were optimized in order to achieve the greatest enhancement represented as the signal-to-noise ratio (SNR) of NELIBS signal to the SNR of LIBS signal. The presence of NPs involved in the ablation process enhances LIP intensity; hence the improvement in the analytical sensitivity was yielded. A leaded brass standard was analyzed with the emphasis on the signal enhancement of Pb traces. We gained enhancement by a factor of four. Although the low pressure had no significant influence on the LIP signal enhancement compared to that under ambient conditions, the SNR values were noticeably improved with the implementation of the NPs.

Enhancement of acid treated g-C3N4sbnd Cu2O photocatalytic activity by PEG under visible light irradiation

NASA Astrophysics Data System (ADS)

Zuo, Shiyu; Xu, Haiming; Liao, Wei; Sun, Lei; Li, Qiang; Zan, Jie; Zhang, Binyang; Li, Dongya; Xia, Dongsheng

2018-05-01

In this study, g-C3N4sbnd Cu2O was successfully synthesized in the presence of PEG-400 surfactant via an acid treatment hydrothermal method and a high-temperature calcination method. The structures and properties of as-synthesized samples were characterized using a range of techniques, such as XPS, TEM, PL and BET. The g-C3N4sbnd Cu2O heterojunction exhibits the enhanced photocatalytic performance and high stability. It is revealed that the addition of PEG can promote the heterojunction effect of g-C3N4sbnd Cu2O, effectively improving the crystallinity and specific surface area of the photocatalyst, separation efficiency of photocarriers, and light absorption, thus enhancing the photocatalytic performance.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.

PubMed

Yang, Y Isaac; Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin

2016-03-07

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C-H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

NASA Astrophysics Data System (ADS)

Yang, Y. Isaac; Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin

2016-03-01

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

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

Yang, Y. Isaac; Zhang, Jun; Che, Xing

2016-03-07

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence ofmore » the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ − ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.« less

Online analysis of five organic ultraviolet filters in environmental water samples using magnetism-enhanced monolith-based in-tube solid phase microextraction coupled with high-performance liquid chromatography.

PubMed

Mei, Meng; Huang, Xiaojia

2017-11-24

Due to the endocrine disrupting properties, organic UV filters have been a great risk for humans and other organisms. Therefore, development of accurate and effective analytical methods is needed for the determination of UV filters in environmental waters. In this work, a fast, sensitive and environmentally friendly method combining magnetism-enhanced monolith-based in-tube solid phase microextraction with high-performance liquid chromatography with diode array detection (DAD) (ME-MB-IT/SPME-HPLC-DAD) for the online analysis of five organic UV filters in environmental water samples was developed. To extract UV filters effectively, an ionic liquid-based monolithic capillary column doped with magnetic nanoparticles was prepared by in-situ polymerization and used as extraction medium of online ME-MB-IT/SPME-HPLC-DAD system. Several extraction conditions including the intensity of magnetic field, sampling and desorption flow rate, volume of sample and desorption solvent, pH value and ionic strength of sample matrix were optimized thoroughly. Under the optimized conditions, the extraction efficiencies for five organic UV filters were in the range of 44.0-100%. The limits of detection (S/N=3) and limits of quantification (S/N=10) were 0.04-0.26μg/L and 0.12-0.87μg/L, respectively. The precisions indicated by relative standard deviations (RSDs) were less than 10% for both intra- and inter-day variabilities. Finally, the developed method was successfully applied to the determination of UV filters in three environmental water samples and satisfactory results were obtained. Copyright © 2017 Elsevier B.V. All rights reserved.

Laser vaporization of trace explosives for enhanced non-contact detection

NASA Astrophysics Data System (ADS)

Furstenberg, Robert; Papantonakis, Michael; Kendziora, Christopher A.; Bubb, Daniel M.; Corgan, Jeffrey; McGill, R. Andrew

2010-04-01

Trace explosives contamination is found primarily in the form of solid particulates on surfaces, due to the low vapor pressure of most explosives materials. Today, the standard sampling procedure involves physical removal of particulate matter from surfaces of interest. A variety of collection methods have been used including air-jetting or swabbing surfaces of interest. The sampled particles are typically heated to generate vapor for analysis in hand held, bench top, or portal detection systems. These sampling methods are time-consuming (and hence costly), require a skilled technician for optimal performance, and are inherently non-selective, allowing non-explosives particles to be co-sampled and analyzed. This can adversely affect the sensitivity and selectivity of detectors, especially those with a limited dynamic range. We present a new approach to sampling solid particles on a solid surface that is targeted, non-contact, and which selectively enhances trace explosive signatures thus improving the selectivity and sensitivity of existing detectors. Our method involves the illumination of a surface of interest with infrared laser light with a wavelength that matches a distinctive vibrational mode of an explosive. The resonant coupling of laser energy results in rapid heating of explosive particles and rapid release of a vapor plume. Neighboring particles unrelated to explosives are generally not directly heated as their vibrational modes are not resonant with the laser. As a result, the generated vapor plume includes a higher concentration of explosives than if the particles were heated with a non-selective light source (e.g. heat lamp). We present results with both benchtop infrared lasers as well as miniature quantum cascade lasers.

A method for nitrate collection for δ15N and δ18O analysis from waters with low nitrate concentrations

USGS Publications Warehouse

Chang, Cecily C.Y.; Langston, J.; Riggs, M.; Campbell, D.H.; Silva, S.R.; Kendall, C.

1999-01-01

 Recently, methods have been developed to analyze NO3- for δ15N and δ18O, improving our ability to identify NO3- sources and transformations. However, none of the existing methods are suited for waters with low NO3- concentrations (0.7-10 µM). We describe an improved method for collecting and recovering NO3- on exchange columns. To overcome the lengthy collection loading times imposed by the large sample volumes (7-70 L), the sample was prefiltered (0.45 µm) with a large surface area filter. Switching to AG2X anion resin and using a coarser mesh size (100-200) than previous methods also enhanced sample flow. Placement of a cation column in front of the anion column minimized clogging of the anion column by dissolved organic carbon (DOC) accumulation. This also served to minimize transfer of unwanted oxygen atoms from DOC to the 18O portion of the NO3- sample, thereby contaminating the sample and shifting δ18O. The cat-AG2X method is suited for on-site sample collection, making it possible to collect and recover NO3- from low ionic strength waters with modest DOC concentrations (80-800 µM), relieves the investigator of transporting large volumes of water back to the laboratory, and offers a means of sampling rain, snow, snowmelt, and stream samples from access-limited sites.

A Stability Enhancement Method for Centrifugal Compressors using Active Control Casing Treatment System

NASA Astrophysics Data System (ADS)

Zhao, Yuanyang; Xiao, Jun; Li, Liansheng; Yang, Qichao; Liu, Guangbin; Wang, Le

2015-08-01

The centrifugal compressors are widely used in many fields. When the centrifugal compressors operate at the edge of the surge line, the compressor will be unstable. In addition, if the centrifugal compressor runs at this situation long time, the damage will be occurred on compressor. There are some kinds of method to improve and enlarge the range of the centrifugal compressors, such as inlet guide vane, and casing treatment. For casing treatment method, some structures have been researched, such as holed recirculation, basic slot casing treatment and groove casing treatment. All these researches are the passive methods. This paper present a new stability enhancement method based Active Control Casing Treatment (ACCT). All parts of this new method are introduced in detail. The control strategy of the system is mentioned in the paper. As a research sample, a centrifugal compressor having this system is researched using CFD method. The study focuses on the effect of the active control system on the impeller flow. The vortex in impeller is changed by the active control system. And this leads to the suppression of the extension of vortex blockage in impeller and to contribute to the enhancement of the compressor operating range.

Accelerated Brain DCE-MRI Using Iterative Reconstruction With Total Generalized Variation Penalty for Quantitative Pharmacokinetic Analysis: A Feasibility Study.

PubMed

Wang, Chunhao; Yin, Fang-Fang; Kirkpatrick, John P; Chang, Zheng

2017-08-01

To investigate the feasibility of using undersampled k-space data and an iterative image reconstruction method with total generalized variation penalty in the quantitative pharmacokinetic analysis for clinical brain dynamic contrast-enhanced magnetic resonance imaging. Eight brain dynamic contrast-enhanced magnetic resonance imaging scans were retrospectively studied. Two k-space sparse sampling strategies were designed to achieve a simulated image acquisition acceleration factor of 4. They are (1) a golden ratio-optimized 32-ray radial sampling profile and (2) a Cartesian-based random sampling profile with spatiotemporal-regularized sampling density constraints. The undersampled data were reconstructed to yield images using the investigated reconstruction technique. In quantitative pharmacokinetic analysis on a voxel-by-voxel basis, the rate constant K trans in the extended Tofts model and blood flow F B and blood volume V B from the 2-compartment exchange model were analyzed. Finally, the quantitative pharmacokinetic parameters calculated from the undersampled data were compared with the corresponding calculated values from the fully sampled data. To quantify each parameter's accuracy calculated using the undersampled data, error in volume mean, total relative error, and cross-correlation were calculated. The pharmacokinetic parameter maps generated from the undersampled data appeared comparable to the ones generated from the original full sampling data. Within the region of interest, most derived error in volume mean values in the region of interest was about 5% or lower, and the average error in volume mean of all parameter maps generated through either sampling strategy was about 3.54%. The average total relative error value of all parameter maps in region of interest was about 0.115, and the average cross-correlation of all parameter maps in region of interest was about 0.962. All investigated pharmacokinetic parameters had no significant differences between the result from original data and the reduced sampling data. With sparsely sampled k-space data in simulation of accelerated acquisition by a factor of 4, the investigated dynamic contrast-enhanced magnetic resonance imaging pharmacokinetic parameters can accurately estimate the total generalized variation-based iterative image reconstruction method for reliable clinical application.

Stochastic resonance algorithm applied to quantitative analysis for weak chromatographic signals of alkyl halides and alkyl benzenes in water samples.

PubMed

Xiang, Suyun; Wang, Wei; Xia, Jia; Xiang, Bingren; Ouyang, Pingkai

2009-09-01

The stochastic resonance algorithm is applied to the trace analysis of alkyl halides and alkyl benzenes in water samples. Compared to encountering a single signal when applying the algorithm, the optimization of system parameters for a multicomponent is more complex. In this article, the resolution of adjacent chromatographic peaks is first involved in the optimization of parameters. With the optimized parameters, the algorithm gave an ideal output with good resolution as well as enhanced signal-to-noise ratio. Applying the enhanced signals, the method extended the limit of detection and exhibited good linearity, which ensures accurate determination of the multicomponent.

Method and apparatus for improved observation of in-situ combustion processes

DOEpatents

Lee, D.O.; Montoya, P.C.; Wayland, J.R. Jr.

Method and apparatus are provided for obtaining accurate dynamic measurements for passage of phase fronts through a core sample in a test fixture. Flow-through grid structures are provided for electrodes to permit data to be obtained before, during and after passage of a front there-through. Such electrodes are incorporated in a test apparatus for obtaining electrical characteristics of the core sample. With the inventive structure a method is provided for measurement of instabilities in a phase front progressing through the medium. Availability of accurate dynamic data representing parameters descriptive of material characteristics before, during and after passage of a front provides a more efficient method for enhanced recovery of oil using a fire flood technique. 6 figures, 2 tables.

Sensitive diagnosis of cutaneous leishmaniasis by lesion swab sampling coupled to qPCR

PubMed Central

ADAMS, EMILY R.; GOMEZ, MARIA ADELAIDA; SCHESKE, LAURA; RIOS, RUBY; MARQUEZ, RICARDO; COSSIO, ALEXANDRA; ALBERTINI, AUDREY; SCHALLIG, HENK; SARAVIA, NANCY GORE

2015-01-01

SUMMARY Variation in clinical accuracy of molecular diagnostic methods for cutaneous leishmaniasis (CL) is commonly observed depending on the sample source, the method of DNA recovery and the molecular test. Few attempts have been made to compare these variables. Two swab and aspirate samples from lesions of patients with suspected CL (n = 105) were evaluated alongside standard diagnosis by microscopic detection of amastigotes or culture of parasites from lesion material. Three DNA extraction methods were compared: Qiagen on swab and aspirate specimens, Isohelix on swabs and Boil/Spin of lesion aspirates. Recovery of Leishmania DNA was evaluated for each sample type by real-time polymerase chain reaction detection of parasitic 18S rDNA, and the diagnostic accuracy of the molecular method determined. Swab sampling combined with Qiagen DNA extraction was the most efficient recovery method for Leishmania DNA, and was the most sensitive (98%; 95% CI: 91–100%) and specific (84%; 95% CI: 64–95%) approach. Aspirated material was less sensitive at 80% (95% CI: 70–88%) and 61% (95% CI: 50–72%) when coupled to Qiagen or Boil-Spin DNA extraction, respectively. Swab sampling of lesions was painless, simple to perform and coupled with standardized DNA extraction enhances the feasibility of molecular diagnosis of CL. PMID:25111885

Multi-bacteria multi-antibiotic testing using surface enhanced Raman spectroscopy (SERS) for urinary tract infection (UTI) diagnosis

NASA Astrophysics Data System (ADS)

Hadjigeorgiou, Katerina; Kastanos, Evdokia; Pitris, Costas

2013-06-01

The inappropriate use of antibiotics leads to antibiotic resistance, which is a major health care problem. The current method for determination of bacterial susceptibility to antibiotics requires overnight cultures. However most of the infections cannot wait for the results to receive treatment, so physicians administer general spectrum antibiotics. This results in ineffective treatments and aggravates the rising problem of antibiotic resistance. In this work, a rapid method for diagnosis and antibiogram for a bacterial infection was developed using Surface Enhanced Raman Spectroscopy (SERS) with silver nanoparticles. The advantages of this novel method include its rapidness and efficiency which will potentially allow doctors to prescribe the most appropriate antibiotic for an infection. SERS spectra of three species of gram negative bacteria, Escherichia coli, Proteus spp., and Klebsiella spp. were obtained after 0 and 4 hour exposure to the seven different antibiotics. Bacterial strains were diluted in order to reach the concentration of (2x105 cfu/ml), cells/ml which is equivalent to the minimum concentration found in urine samples from UTIs. Even though the concentration of bacteria was low, species classification was achieved with 94% accuracy using spectra obtained at 0 hours. Sensitivity or resistance to antibiotics was predicted with 81%-100% accuracy from spectra obtained after 4 hours of exposure to the different antibiotics. This technique can be applied directly to urine samples, and with the enhancement provided by SERS, this method has the potential to be developed into a rapid method for same day UTI diagnosis and antibiogram.

Combining Cloud Networks and Course Management Systems for Enhanced Analysis in Teaching Laboratories

ERIC Educational Resources Information Center

Abrams, Neal M.

2012-01-01

A cloud network system is combined with standard computing applications and a course management system to provide a robust method for sharing data among students. This system provides a unique method to improve data analysis by easily increasing the amount of sampled data available for analysis. The data can be shared within one course as well as…

Vital sign sensing method based on EMD in terahertz band

NASA Astrophysics Data System (ADS)

Xu, Zhengwu; Liu, Tong

2014-12-01

Non-contact respiration and heartbeat rates detection could be applied to find survivors trapped in the disaster or the remote monitoring of the respiration and heartbeat of a patient. This study presents an improved algorithm that extracts the respiration and heartbeat rates of humans by utilizing the terahertz radar, which further lessens the effects of noise, suppresses the cross-term, and enhances the detection accuracy. A human target echo model for the terahertz radar is first presented. Combining the over-sampling method, low-pass filter, and Empirical Mode Decomposition improves the signal-to-noise ratio. The smoothed pseudo Wigner-Ville distribution time-frequency technique and the centroid of the spectrogram are used to estimate the instantaneous velocity of the target's cardiopulmonary motion. The down-sampling method is adopted to prevent serious distortion. Finally, a second time-frequency analysis is applied to the centroid curve to extract the respiration and heartbeat rates of the individual. Simulation results show that compared with the previously presented vital sign sensing method, the improved algorithm enhances the signal-to-noise ratio to 1 dB with a detection accuracy of 80%. The improved algorithm is an effective approach for the detection of respiration and heartbeat signal in a complicated environment.

Sample-based engine noise synthesis using an enhanced pitch-synchronous overlap-and-add method.

PubMed

Jagla, Jan; Maillard, Julien; Martin, Nadine

2012-11-01

An algorithm for the real time synthesis of internal combustion engine noise is presented. Through the analysis of a recorded engine noise signal of continuously varying engine speed, a dataset of sound samples is extracted allowing the real time synthesis of the noise induced by arbitrary evolutions of engine speed. The sound samples are extracted from a recording spanning the entire engine speed range. Each sample is delimitated such as to contain the sound emitted during one cycle of the engine plus the necessary overlap to ensure smooth transitions during the synthesis. The proposed approach, an extension of the PSOLA method introduced for speech processing, takes advantage of the specific periodicity of engine noise signals to locate the extraction instants of the sound samples. During the synthesis stage, the sound samples corresponding to the target engine speed evolution are concatenated with an overlap and add algorithm. It is shown that this method produces high quality audio restitution with a low computational load. It is therefore well suited for real time applications.

Surface Preparation Methods to Enhance Dynamic Surface Property Measurements of Shocked Metal Surfaces

NASA Astrophysics Data System (ADS)

Zellner, Michael; McNeil, Wendy; Gray, George, III; Huerta, David; King, Nicholas; Neal, George; Payton, Jeremy; Rubin, Jim; Stevens, Gerald; Turley, William; Buttler, William

2008-03-01

This effort investigates surface-preparation methods to enhance dynamic surface-property measurements of shocked metal surfaces. To assess the ability of making reliable and consistent dynamic surface-property measurements, the amount of material ejected from the free-surface upon shock release to vacuum (ejecta) was monitored for shocked Al-1100 and Sn targets. Four surface preparation methods were considered: fly-cut machined finish, diamond-turned machine finish, polished finish, and ball-rolled. The samples were shock loaded by in-contact detonation of HE PBX-9501 on the front-side of the metal coupons. Ejecta production at the back-side or free-side of the metal coupons was monitored using piezoelectric pins, optical shadowgraphy, and x-ray attenuation radiography.

Surface preparation methods to enhance dynamic surface property measurements of shocked metal surfaces

NASA Astrophysics Data System (ADS)

Zellner, M. B.; Vogan McNeil, W.; Gray, G. T.; Huerta, D. C.; King, N. S. P.; Neal, G. E.; Valentine, S. J.; Payton, J. R.; Rubin, J.; Stevens, G. D.; Turley, W. D.; Buttler, W. T.

2008-04-01

This effort investigates surface-preparation methods to enhance dynamic surface-property measurements of shocked metal surfaces. To assess the ability of making reliable and consistent dynamic surface-property measurements, the amount of material ejected from the free surface upon shock release to vacuum (ejecta) was monitored for shocked Al-1100 and Sn targets. Four surface-preparation methods were considered: Fly-cut machine finish, diamond-turned machine finish, polished finish, and ball rolled. The samples were shock loaded by in-contact detonation of HE PBX-9501 on the front side of the metal coupons. Ejecta production at the back side or free side of the metal coupons was monitored using piezoelectric pins, optical shadowgraphy, and x-ray attenuation radiography.

Combined Dynamic Contrast Enhanced Liver MRI and MRA Using Interleaved Variable Density Sampling

PubMed Central

Rahimi, Mahdi Salmani; Korosec, Frank R.; Wang, Kang; Holmes, James H.; Motosugi, Utaroh; Bannas, Peter; Reeder, Scott B.

2014-01-01

Purpose To develop and evaluate a method for volumetric contrast-enhanced MR imaging of the liver, with high spatial and temporal resolutions, for combined dynamic imaging and MR angiography using a single injection of contrast. Methods An interleaved variable density (IVD) undersampling pattern was implemented in combination with a real-time-triggered, time-resolved, dual-echo 3D spoiled gradient echo sequence. Parallel imaging autocalibration lines were acquired only once during the first time-frame. Imaging was performed in ten subjects with focal nodular hyperplasia (FNH) and compared with their clinical MRI. The angiographic phase of the proposed method was compared to a dedicated MR angiogram acquired during a second injection of contrast. Results A total of 21 FNH, 3 cavernous hemangiomas, and 109 arterial segments were visualized in 10 subjects. The temporally-resolved images depicted the characteristic arterial enhancement pattern of the lesions with a 4 s update rate. Images were graded as having significantly higher quality compared to the clinical MRI. Angiograms produced from the IVD method provided non-inferior diagnostic assessment compared to the dedicated MRA. Conclusion Using an undersampled IVD imaging method, we have demonstrated the feasibility of obtaining high spatial and temporal resolution dynamic contrast-enhanced imaging and simultaneous MRA of the liver. PMID:24639130

Multi-class multi-residue analysis of veterinary drugs in meat using enhanced matrix removal lipid cleanup and liquid chromatography-tandem mass spectrometry.

PubMed

Zhao, Limian; Lucas, Derick; Long, David; Richter, Bruce; Stevens, Joan

2018-05-11

This study presents the development and validation of a quantitation method for the analysis of multi-class, multi-residue veterinary drugs using lipid removal cleanup cartridges, enhanced matrix removal lipid (EMR-Lipid), for different meat matrices by liquid chromatography tandem mass spectrometry detection. Meat samples were extracted using a two-step solid-liquid extraction followed by pass-through sample cleanup. The method was optimized based on the buffer and solvent composition, solvent additive additions, and EMR-Lipid cartridge cleanup. The developed method was then validated in five meat matrices, porcine muscle, bovine muscle, bovine liver, bovine kidney and chicken liver to evaluate the method performance characteristics, such as absolute recoveries and precision at three spiking levels, calibration curve linearity, limit of quantitation (LOQ) and matrix effect. The results showed that >90% of veterinary drug analytes achieved satisfactory recovery results of 60-120%. Over 97% analytes achieved excellent reproducibility results (relative standard deviation (RSD) < 20%), and the LOQs were 1-5 μg/kg in the evaluated meat matrices. The matrix co-extractive removal efficiency by weight provided by EMR-lipid cartridge cleanup was 42-58% in samples. The post column infusion study showed that the matrix ion suppression was reduced for samples with the EMR-Lipid cartridge cleanup. The reduced matrix ion suppression effect was also confirmed with <15% frequency of compounds with significant quantitative ion suppression (>30%) for all tested veterinary drugs in all of meat matrices. The results showed that the two-step solid-liquid extraction provides efficient extraction for the entire spectrum of veterinary drugs, including the difficult classes such as tetracyclines, beta-lactams etc. EMR-Lipid cartridges after extraction provided efficient sample cleanup with easy streamlined protocol and minimal impacts on analytes recovery, improving method reliability and consistency. Copyright © 2018 Elsevier B.V. All rights reserved.

Advanced glycation end products, physico-chemical and sensory characteristics of cooked lamb loins affected by cooking method and addition of flavour precursors.

PubMed

Roldan, Mar; Loebner, Jürgen; Degen, Julia; Henle, Thomas; Antequera, Teresa; Ruiz-Carrascal, Jorge

2015-02-01

The influence of the addition of a flavour enhancer solution (FES) (d-glucose, d-ribose, l-cysteine and thiamin) and of sous-vide cooking or roasting on moisture, cooking loss, instrumental colour, sensory characteristics and formation of Maillard reaction (MR) compounds in lamb loins was studied. FES reduced cooking loss and increased water content in sous-vide samples. FES and cooking method showed a marked effect on browning development, both on the meat surface and within. FES led to tougher and chewier texture in sous-vide cooked lamb, and enhanced flavour scores of sous-vide samples more markedly than in roasted ones. FES added meat showed higher contents of furosine; 1,2-dicarbonyl compounds and 5-hydroxymethylfurfural did not reach detectable levels. N-ε-carboxymethyllysine amounts were rather low and not influenced by the studied factors. Cooked meat seems to be a minor dietary source of MR products, regardless the presence of reducing sugars and the cooking method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Super resolution PLIF demonstrated in turbulent jet flows seeded with I2

NASA Astrophysics Data System (ADS)

Xu, Wenjiang; Liu, Ning; Ma, Lin

2018-05-01

Planar laser induced fluorescence (PLIF) represents an indispensable tool for flow and flame imaging. However, the PLIF technique suffers from limited spatial resolution or blurring in many situations, which restricts its applicability and capability. This work describes a new method, named SR-PLIF (super-resolution PLIF), to overcome these limitations and enhance the capability of PLIF. The method uses PLIF images captured simultaneously from two (or more) orientations to reconstruct a final PLIF image with resolution enhanced or blurring removed. This paper reports the development of the reconstruction algorithm, and the experimental demonstration of the SR-PLIF method both with controlled samples and with turbulent flows seeded with iodine vapor. Using controlled samples with two cameras, the spatial resolution in the best case was improved from 0.06 mm in the projections to 0.03 mm in the SR image, in terms of the spreading width of a sharp edge. With turbulent flows, an image sharpness measure was developed to quantify the spatial resolution, and SR reconstruction with two cameras can effectively improve the spatial resolution compared to the projections in terms of the sharpness measure.

Noninvasive prostate cancer screening based on serum surface-enhanced Raman spectroscopy and support vector machine

NASA Astrophysics Data System (ADS)

Li, Shaoxin; Zhang, Yanjiao; Xu, Junfa; Li, Linfang; Zeng, Qiuyao; Lin, Lin; Guo, Zhouyi; Liu, Zhiming; Xiong, Honglian; Liu, Songhao

2014-09-01

This study aims to present a noninvasive prostate cancer screening methods using serum surface-enhanced Raman scattering (SERS) and support vector machine (SVM) techniques through peripheral blood sample. SERS measurements are performed using serum samples from 93 prostate cancer patients and 68 healthy volunteers by silver nanoparticles. Three types of kernel functions including linear, polynomial, and Gaussian radial basis function (RBF) are employed to build SVM diagnostic models for classifying measured SERS spectra. For comparably evaluating the performance of SVM classification models, the standard multivariate statistic analysis method of principal component analysis (PCA) is also applied to classify the same datasets. The study results show that for the RBF kernel SVM diagnostic model, the diagnostic accuracy of 98.1% is acquired, which is superior to the results of 91.3% obtained from PCA methods. The receiver operating characteristic curve of diagnostic models further confirm above research results. This study demonstrates that label-free serum SERS analysis technique combined with SVM diagnostic algorithm has great potential for noninvasive prostate cancer screening.

Chromatographic separation and detection of contaminants from whole milk powder using a chitosan-modified silver nanoparticles surface-enhanced Raman scattering device.

PubMed

Li, Dan; Lv, Di Y; Zhu, Qing X; Li, Hao; Chen, Hui; Wu, Mian M; Chai, Yi F; Lu, Feng

2017-06-01

Methods for the on-site analysis of food contaminants are in high demand. Although portable Raman spectroscopy is commonly used to test food on-site, it can be challenge to achieve this goal with rapid detection and inexpensive substrate. In this study, we detected trace food contaminants in samples of whole milk powder using the methods that combined chromatography with surface-enhanced Raman scattering detection (SERS). We developed a simple and efficient technique to fabricate the paper with chitosan-modified silver nanoparticles as a SERS-active substrate. The soaking time of paper and the concentration of chitosan solution were optimized for chromatographic separation and SERS detection. We then studied the separation properties for real applications including complex sample matrices, and detected melamine at 1mg/L, dicyandiamide at 100mg/L and sodium sulfocyanate at 10mg/L in whole milk powder. As such, our methods have great potential for field-based detection of milk contaminants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Efficient free energy calculations by combining two complementary tempering sampling methods.

PubMed

Xie, Liangxu; Shen, Lin; Chen, Zhe-Ning; Yang, Mingjun

2017-01-14

Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling. To address the sampling in this so-called hidden barrier situation, here we propose an effective approach to combine temperature accelerated molecular dynamics (TAMD), an efficient RC-guided sampling method, with the integrated tempering sampling (ITS), a generalized ensemble sampling method. In this combined ITS-TAMD method, the sampling along the major RCs with high energy barriers is guided by TAMD and the sampling of the rest of the DOFs with lower but not negligible barriers is enhanced by ITS. The performance of ITS-TAMD to three systems in the processes with hidden barriers has been examined. In comparison to the standalone TAMD or ITS approach, the present hybrid method shows three main improvements. (1) Sampling efficiency can be improved at least five times even if in the presence of hidden energy barriers. (2) The canonical distribution can be more accurately recovered, from which the thermodynamic properties along other collective variables can be computed correctly. (3) The robustness of the selection of major RCs suggests that the dimensionality of necessary RCs can be reduced. Our work shows more potential applications of the ITS-TAMD method as the efficient and powerful tool for the investigation of a broad range of interesting cases.

Efficient free energy calculations by combining two complementary tempering sampling methods

NASA Astrophysics Data System (ADS)

Xie, Liangxu; Shen, Lin; Chen, Zhe-Ning; Yang, Mingjun

2017-01-01

Although energy barriers can be efficiently crossed in the reaction coordinate (RC) guided sampling, this type of method suffers from identification of the correct RCs or requirements of high dimensionality of the defined RCs for a given system. If only the approximate RCs with significant barriers are used in the simulations, hidden energy barriers with small to medium height would exist in other degrees of freedom (DOFs) relevant to the target process and consequently cause the problem of insufficient sampling. To address the sampling in this so-called hidden barrier situation, here we propose an effective approach to combine temperature accelerated molecular dynamics (TAMD), an efficient RC-guided sampling method, with the integrated tempering sampling (ITS), a generalized ensemble sampling method. In this combined ITS-TAMD method, the sampling along the major RCs with high energy barriers is guided by TAMD and the sampling of the rest of the DOFs with lower but not negligible barriers is enhanced by ITS. The performance of ITS-TAMD to three systems in the processes with hidden barriers has been examined. In comparison to the standalone TAMD or ITS approach, the present hybrid method shows three main improvements. (1) Sampling efficiency can be improved at least five times even if in the presence of hidden energy barriers. (2) The canonical distribution can be more accurately recovered, from which the thermodynamic properties along other collective variables can be computed correctly. (3) The robustness of the selection of major RCs suggests that the dimensionality of necessary RCs can be reduced. Our work shows more potential applications of the ITS-TAMD method as the efficient and powerful tool for the investigation of a broad range of interesting cases.

Preparation of amorphous solid dispersions by rotary evaporation and KinetiSol Dispersing: approaches to enhance solubility of a poorly water-soluble gum extract.

PubMed

Bennett, Ryan C; Brough, Chris; Miller, Dave A; O'Donnell, Kevin P; Keen, Justin M; Hughey, Justin R; Williams, Robert O; McGinity, James W

2015-03-01

Acetyl-11-keto-β-boswellic acid (AKBA), a gum resin extract, possesses poor water-solubility that limits bioavailability and a high melting point making it difficult to successfully process into solid dispersions by fusion methods. The purpose of this study was to investigate solvent and thermal processing techniques for the preparation of amorphous solid dispersions (ASDs) exhibiting enhanced solubility, dissolution rates and bioavailability. Solid dispersions were successfully produced by rotary evaporation (RE) and KinetiSol® Dispersing (KSD). Solid state and chemical characterization revealed that ASD with good potency and purity were produced by both RE and KSD. Results of the RE studies demonstrated that AQOAT®-LF, AQOAT®-MF, Eudragit® L100-55 and Soluplus with the incorporation of dioctyl sulfosuccinate sodium provided substantial solubility enhancement. Non-sink dissolution analysis showed enhanced dissolution properties for KSD-processed solid dispersions in comparison to RE-processed solid dispersions. Variances in release performance were identified when different particle size fractions of KSD samples were analyzed. Selected RE samples varying in particle surface morphologies were placed under storage and exhibited crystalline growth following solid-state stability analysis at 12 months in comparison to stored KSD samples confirming amorphous instability for RE products. In vivo analysis of KSD-processed solid dispersions revealed significantly enhanced AKBA absorption in comparison to the neat, active substance.

Nanoshell-Enhanced Raman Spectroscopy on a Microplate for Staphylococcal Enterotoxin B Sensing.

PubMed

Wang, Wenbin; Wang, Weiwei; Liu, Liqiang; Xu, Liguang; Kuang, Hua; Zhu, Jianping; Xu, Chuanlai

2016-06-22

A sensitive surface-enhanced Raman scattering (SERS) immunosensor based on the Au nanoparticle (Au NP) shell structure was developed to detect staphylococcal enterotoxin B (SEB) on a microplate. Au NPs modified with 4-nitrothiophenol (4-NTP) and coated with Ag shell of controlled thickness at 6.6 nm exhibited excellent SERS intensity and were used as signal reporters in the detection of SEB. The engaged 4-NTP allowed the significant electromagnetic enhancement between Au NPs and the Ag shell and prevented the dissociation of the Raman reporter. More importantly, 4-NTP-differentiated SERS signals between the sample and microplate. The SERS-based immunosensor had a limit of detection of 1.3 pg/mL SEB. Analysis of SEB-spiked milk samples revealed that the developed method had high accuracy. Therefore, the SERS-encoded Au@Ag core-shell structure-based immunosensor is promising for the detection of biotoxins, pathogens, and environmental pollutants.

Ultrafast Bilateral DCE-MRI of the Breast with Conventional Fourier Sampling: Preliminary Evaluation of Semi-quantitative Analysis.

PubMed

Pineda, Federico D; Medved, Milica; Wang, Shiyang; Fan, Xiaobing; Schacht, David V; Sennett, Charlene; Oto, Aytekin; Newstead, Gillian M; Abe, Hiroyuki; Karczmar, Gregory S

2016-09-01

The study aimed to evaluate the feasibility and advantages of a combined high temporal and high spatial resolution protocol for dynamic contrast-enhanced magnetic resonance imaging of the breast. Twenty-three patients with enhancing lesions were imaged at 3T. The acquisition protocol consisted of a series of bilateral, fat-suppressed "ultrafast" acquisitions, with 6.9- to 9.9-second temporal resolution for the first minute following contrast injection, followed by four high spatial resolution acquisitions with 60- to 79.5-second temporal resolution. All images were acquired with standard uniform Fourier sampling. A filtering method was developed to reduce noise and detect significant enhancement in the high temporal resolution images. Time of arrival (TOA) was defined as the time at which each voxel first satisfied all the filter conditions, relative to the time of initial arterial enhancement. Ultrafast images improved visualization of the vasculature feeding and draining lesions. A small percentage of the entire field of view (<6%) enhanced significantly in the 30 seconds following contrast injection. Lesion conspicuity was highest in early ultrafast images, especially in cases with marked parenchymal enhancement. Although the sample size was relatively small, the average TOA for malignant lesions was significantly shorter than the TOA for benign lesions. Significant differences were also measured in other parameters descriptive of early contrast media uptake kinetics (P < 0.05). Ultrafast imaging in the first minute of dynamic contrast-enhanced magnetic resonance imaging of the breast has the potential to add valuable information on early contrast dynamics. Ultrafast imaging could allow radiologists to confidently identify lesions in the presence of marked background parenchymal enhancement. Copyright © 2016 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

lop-DWI: A Novel Scheme for Pre-Processing of Diffusion-Weighted Images in the Gradient Direction Domain.

PubMed

Sepehrband, Farshid; Choupan, Jeiran; Caruyer, Emmanuel; Kurniawan, Nyoman D; Gal, Yaniv; Tieng, Quang M; McMahon, Katie L; Vegh, Viktor; Reutens, David C; Yang, Zhengyi

2014-01-01

We describe and evaluate a pre-processing method based on a periodic spiral sampling of diffusion-gradient directions for high angular resolution diffusion magnetic resonance imaging. Our pre-processing method incorporates prior knowledge about the acquired diffusion-weighted signal, facilitating noise reduction. Periodic spiral sampling of gradient direction encodings results in an acquired signal in each voxel that is pseudo-periodic with characteristics that allow separation of low-frequency signal from high frequency noise. Consequently, it enhances local reconstruction of the orientation distribution function used to define fiber tracks in the brain. Denoising with periodic spiral sampling was tested using synthetic data and in vivo human brain images. The level of improvement in signal-to-noise ratio and in the accuracy of local reconstruction of fiber tracks was significantly improved using our method.

Contamination-free Ge-based graphene as revealed by graphene enhanced secondary ion mass spectrometry (GESIMS)

NASA Astrophysics Data System (ADS)

Michałowski, P. P.; Pasternak, I.; Strupiński, W.

2018-01-01

In this study, we demonstrate that graphene grown on Ge does not contain any copper contamination, and identify some of the errors affecting the accuracy of commonly used measurement methods. Indeed, one of these, the secondary ion mass spectrometry (SIMS) technique, reveals copper contamination in Ge-based graphene but does not take into account the effect of the presence of the graphene layer. We have shown that this layer increases negative ionization significantly, and thus yields false results, but also that the graphene enhances, by an order of two, the magnitude of the intensity of SIMS signals when compared with a similar graphene-free sample, enabling much better detection limits. This forms the basis of a new measurement procedure, graphene enhanced SIMS (GESIMS) (pending European patent application no. EP 16461554.4), which allows for the precise estimation of the realistic distribution of dopants and contamination in graphene. In addition, we present evidence that the GESIMS effect leads to unexpected mass interferences with double-ionized species, and that these interferences are negligible in samples without graphene. The GESIMS method also shows that graphene transferred from Cu results in increased copper contamination.

Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods.

PubMed

Lesot, Philippe; Kazimierczuk, Krzysztof; Trébosc, Julien; Amoureux, Jean-Paul; Lafon, Olivier

2015-11-01

Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years. Copyright © 2015 John Wiley & Sons, Ltd.

Application of COLD-PCR for improved detection of KRAS mutations in clinical samples.

PubMed

Zuo, Zhuang; Chen, Su S; Chandra, Pranil K; Galbincea, John M; Soape, Matthew; Doan, Steven; Barkoh, Bedia A; Koeppen, Hartmut; Medeiros, L Jeffrey; Luthra, Rajyalakshmi

2009-08-01

KRAS mutations have been detected in approximately 30% of all human tumors, and have been shown to predict response to some targeted therapies. The most common KRAS mutation-detection strategy consists of conventional PCR and direct sequencing. This approach has a 10-20% detection sensitivity depending on whether pyrosequencing or Sanger sequencing is used. To improve detection sensitivity, we compared our conventional method with the recently described co-amplification-at-lower denaturation-temperature PCR (COLD-PCR) method, which selectively amplifies minority alleles. In COLD-PCR, the critical denaturation temperature is lowered to 80 degrees C (vs 94 degrees C in conventional PCR). The sensitivity of COLD-PCR was determined by assessing serial dilutions. Fifty clinical samples were used, including 20 fresh bone-marrow aspirate specimens and the formalin-fixed paraffin-embedded (FFPE) tissue of 30 solid tumors. Implementation of COLD-PCR was straightforward and required no additional cost for reagents or instruments. The method was specific and reproducible. COLD-PCR successfully detected mutations in all samples that were positive by conventional PCR, and enhanced the mutant-to-wild-type ratio by >4.74-fold, increasing the mutation detection sensitivity to 1.5%. The enhancement of mutation detection by COLD-PCR inversely correlated with the tumor-cell percentage in a sample. In conclusion, we validated the utility and superior sensitivity of COLD-PCR for detecting KRAS mutations in a variety of hematopoietic and solid tumors using either fresh or fixed, paraffin-embedded tissue.

High temporal resolution dynamic contrast-enhanced MRI using compressed sensing-combined sequence in quantitative renal perfusion measurement.

PubMed

Chen, Bin; Zhao, Kai; Li, Bo; Cai, Wenchao; Wang, Xiaoying; Zhang, Jue; Fang, Jing

2015-10-01

To demonstrate the feasibility of the improved temporal resolution by using compressed sensing (CS) combined imaging sequence in dynamic contrast-enhanced MRI (DCE-MRI) of kidney, and investigate its quantitative effects on renal perfusion measurements. Ten rabbits were included in the accelerated scans with a CS-combined 3D pulse sequence. To evaluate the image quality, the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were compared between the proposed CS strategy and the conventional full sampling method. Moreover, renal perfusion was estimated by using the separable compartmental model in both CS simulation and realistic CS acquisitions. The CS method showed DCE-MRI images with improved temporal resolution and acceptable image contrast, while presenting significantly higher SNR than the fully sampled images (p<.01) at 2-, 3- and 4-X acceleration. In quantitative measurements, renal perfusion results were in good agreement with the fully sampled one (concordance correlation coefficient=0.95, 0.91, 0.88) at 2-, 3- and 4-X acceleration in CS simulation. Moreover, in realistic acquisitions, the estimated perfusion by the separable compartmental model exhibited no significant differences (p>.05) between each CS-accelerated acquisition and the full sampling method. The CS-combined 3D sequence could improve the temporal resolution for DCE-MRI in kidney while yielding diagnostically acceptable image quality, and it could provide effective measurements of renal perfusion. Copyright © 2015 Elsevier Inc. All rights reserved.

A general soft label based linear discriminant analysis for semi-supervised dimensionality reduction.

PubMed

Zhao, Mingbo; Zhang, Zhao; Chow, Tommy W S; Li, Bing

2014-07-01

Dealing with high-dimensional data has always been a major problem in research of pattern recognition and machine learning, and Linear Discriminant Analysis (LDA) is one of the most popular methods for dimension reduction. However, it only uses labeled samples while neglecting unlabeled samples, which are abundant and can be easily obtained in the real world. In this paper, we propose a new dimension reduction method, called "SL-LDA", by using unlabeled samples to enhance the performance of LDA. The new method first propagates label information from the labeled set to the unlabeled set via a label propagation process, where the predicted labels of unlabeled samples, called "soft labels", can be obtained. It then incorporates the soft labels into the construction of scatter matrixes to find a transformed matrix for dimension reduction. In this way, the proposed method can preserve more discriminative information, which is preferable when solving the classification problem. We further propose an efficient approach for solving SL-LDA under a least squares framework, and a flexible method of SL-LDA (FSL-LDA) to better cope with datasets sampled from a nonlinear manifold. Extensive simulations are carried out on several datasets, and the results show the effectiveness of the proposed method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Use of a Novel Fluidics Microbead Trap/Flow-cell Enhances Speed and Sensitivity of Bead-Based Bioassays

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

Ozanich, Rich M.; Antolick, Kathryn C.; Bruckner-Lea, Cindy J.

2007-09-15

Automated devices and methods for biological sample preparation often utilize surface functionalized microbeads (superparamagnetic or non-magnetic) to allow capture, purification and pre-concentration of trace amounts of proteins, cells, or nucleic acids (DNA/RNA) from complex samples. We have developed unique methods and hardware for trapping either magnetic or non-magnetic functionalized beads that allow samples and reagents to be efficiently perfused over a micro-column of beads. This approach yields enhanced mass transport and up to 5-fold improvements in assay sensitivity or speed, dramatically improving assay capability relative to assays conducted in more traditional “batch modes” (i.e., in tubes or microplate wells). Summarymore » results are given that highlight the analytical performance improvements obtained for automated microbead processing systems utilizing novel microbead trap/flow-cells for various applications, including: 1) simultaneous capture of multiple cytokines using an antibody-coupled polystyrene bead assay with subsequent flow cytometry detection; 2) capture of nucleic acids using oligonucleotide coupled polystyrene beads with flow cytometry detection; and 3) capture of Escherichia coli 0157:H7 (E. coli) from 50 mL sample volumes using antibody-coupled superparamagnetic microbeads with subsequent culturing to assess capture efficiency.« less

Laser Ablation Surface-Enhanced Raman Spectroscopy (LA-SERS) for the Characterization of Organic Colorants in Cultural Heritage

NASA Astrophysics Data System (ADS)

Londero, Pablo

The characterization of artistic practice throughout history often requires measurements of material composition with microscopic resolution, either due to the fine detail of the material composition or to the amount of sample available. This problem is exacerbated for the detection of organic colorants, which are often embedded in a complex matrix (e.g. oil, natural fibers) and in low concentration due to their high tinting strength. Surface-Enhanced Raman Spectroscopy (SERS) is increasingly used in detection of organic colorants in cultural heritage due to its high sensitivity and inherent preferential sensitivity to small organic molecules. This talk will discuss recent results from a new SERS measurement technique, in which laser ablation is used as a micro-sampling method onto a SERS-active film to characterize art samples with microscopic precision and sensitivity comparable to many mass spectrometry measurements. Furthermore, the nature of the sampling method provides built-in benefits to other SERS-based techniques, such as more quantitative characterization of mixtures, improved sensitivity to some analytes, and reduced background interference. Examples will be shown for measurements of reference materials and art objects, including a restored 16th-century dish and a Renaissance fresco, The Incredulity of San Thomas, by Luca Signorelli. Supported by the National Science Foundation (NSF-CHE-1402750).

Nanoscale effects in the characterization of viscoelastic materials with atomic force microscopy: Coupling of a quasi-three-dimensional standard linear solid model with in-plane surface interactions

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

Solares, Santiago D.

Significant progress has been accomplished in the development of experimental contact-mode and dynamic-mode atomic force microscopy (AFM) methods designed to measure surface material properties. However, current methods are based on one-dimensional (1D) descriptions of the tip-sample interaction forces, thus neglecting the intricacies involved in the material behavior of complex samples (such as soft viscoelastic materials) as well as the differences in material response between the surface and the bulk. In order to begin to address this gap, a computational study is presented where the sample is simulated using an enhanced version of a recently introduced model that treats the surfacemore » as a collection of standard-linear-solid viscoelastic elements. The enhanced model introduces in-plane surface elastic forces that can be approximately related to a two-dimensional (2D) Young's modulus. Relevant cases are discussed for single-and multifrequency intermittent-contact AFM imaging, with focus on the calculated surface indentation profiles and tip-sample interaction force curves, as well as their implications with regards to experimental interpretation. A variety of phenomena are examined in detail, which highlight the need for further development of more physically accurate sample models that are specifically designed for AFM simulation. As a result, a multifrequency AFM simulation tool based on the above sample model is provided as supporting information.« less

Nanoscale effects in the characterization of viscoelastic materials with atomic force microscopy: Coupling of a quasi-three-dimensional standard linear solid model with in-plane surface interactions

DOE PAGES

Solares, Santiago D.

2016-04-15

Significant progress has been accomplished in the development of experimental contact-mode and dynamic-mode atomic force microscopy (AFM) methods designed to measure surface material properties. However, current methods are based on one-dimensional (1D) descriptions of the tip-sample interaction forces, thus neglecting the intricacies involved in the material behavior of complex samples (such as soft viscoelastic materials) as well as the differences in material response between the surface and the bulk. In order to begin to address this gap, a computational study is presented where the sample is simulated using an enhanced version of a recently introduced model that treats the surfacemore » as a collection of standard-linear-solid viscoelastic elements. The enhanced model introduces in-plane surface elastic forces that can be approximately related to a two-dimensional (2D) Young's modulus. Relevant cases are discussed for single-and multifrequency intermittent-contact AFM imaging, with focus on the calculated surface indentation profiles and tip-sample interaction force curves, as well as their implications with regards to experimental interpretation. A variety of phenomena are examined in detail, which highlight the need for further development of more physically accurate sample models that are specifically designed for AFM simulation. As a result, a multifrequency AFM simulation tool based on the above sample model is provided as supporting information.« less

A method for measuring total thiaminase activity in fish tissues

USGS Publications Warehouse

Zajicek, James L.; Tillitt, Donald E.; Honeyfield, Dale C.; Brown, Scott B.; Fitzsimons, John D.

2005-01-01

An accurate, quantitative, and rapid method for the measurement of thiaminase activity in fish samples is required to provide sufficient information to characterize the role of dietary thiaminase in the onset of thiamine deficiency in Great Lakes salmonines. A radiometric method that uses 14C-thiamine was optimized for substrate and co-substrate (nicotinic acid) concentrations, incubation time, and sample dilution. Total thiaminase activity was successfully determined in extracts of selected Great Lakes fishes and invertebrates. Samples included whole-body and selected tissues of forage fishes. Positive control material prepared from frozen alewives Alosa pseudoharengus collected in Lake Michigan enhanced the development and application of the method. The method allowed improved discrimination of thiaminolytic activity among forage fish species and their tissues. The temperature dependence of the thiaminase activity observed in crude extracts of Lake Michigan alewives followed a Q10 = 2 relationship for the 1-37??C temperature range, which is consistent with the bacterial-derived thiaminase I protein. ?? Copyright by the American Fisheries Society 2005.

Dynamic surface-enhanced Raman spectroscopy and Chemometric methods for fast detection and intelligent identification of methamphetamine and 3, 4-Methylenedioxy methamphetamine in human urine

NASA Astrophysics Data System (ADS)

Weng, Shizhuang; Dong, Ronglu; Zhu, Zede; Zhang, Dongyan; Zhao, Jinling; Huang, Linsheng; Liang, Dong

2018-01-01

Conventional Surface-Enhanced Raman Spectroscopy (SERS) for fast detection of drugs in urine on the portable Raman spectrometer remains challenges because of low sensitivity and unreliable Raman signal, and spectra process with manual intervention. Here, we develop a novel detection method of drugs in urine using chemometric methods and dynamic SERS (D-SERS) with mPEG-SH coated gold nanorods (GNRs). D-SERS combined with the uniform GNRs can obtain giant enhancement, and the signal is also of high reproducibility. On the basis of the above advantages, we obtained the spectra of urine, urine with methamphetamine (MAMP), urine with 3, 4-Methylenedioxy Methamphetamine (MDMA) using D-SERS. Simultaneously, some chemometric methods were introduced for the intelligent and automatic analysis of spectra. Firstly, the spectra at the critical state were selected through using K-means. Then, the spectra were proposed by random forest (RF) with feature selection and principal component analysis (PCA) to develop the recognition model. And the identification accuracy of model were 100%, 98.7% and 96.7%, respectively. To validate the effect in practical issue further, the drug abusers'urine samples with 0.4, 3, 30 ppm MAMP were detected using D-SERS and identified by the classification model. The high recognition accuracy of > 92.0% can meet the demand of practical application. Additionally, the parameter optimization of RF classification model was simple. Compared with the general laboratory method, the detection process of urine's spectra using D-SERS only need 2 mins and 2 μL samples volume, and the identification of spectra based on chemometric methods can be finish in seconds. It is verified that the proposed approach can provide the accurate, convenient and rapid detection of drugs in urine.

The magnetic introduction of magnetite nanoparticles into live cells for radiosensibility enhancement

NASA Astrophysics Data System (ADS)

Yurenya, Anton Y.; Polikarpov, Mikhail A.; Chukalova, Aynur A.; Moskaleva, Elizaveta Y.; Taldenkov, Alexander N.; Panchenko, Vladislav Y.

2017-04-01

Earlier we proposed a new radiotherapy enhancement method that entails the administration of 57Fe iron-oxide nanoparticles into the cells [5]. Within this work we were prompt to investigate the capability of iron oxide nanoparticles with monolayer coating to penetrate into live cells. Magnetite particle samples were synthesized and stabilized with HCl or citric acid. The cells were incubated in the presence of nanoparticles for 1 h, washed and dried. To distinguish inside-cell particles from outside ones a set of experiments with low temperature incubation was carried out. Several cell samples were prepared in the presence of an external magnetic field in order to study the possibility of the nanoparticle uptake enhancement. To evaluate the amount of particles in each cell sample we used a SQUID-magnetometer. The nanoparticle suspension with HCl stabilization turned to be inadequate for intracellular introduction. Approximately 2·105 particles with citric acid covering conjugated with each cell after incubation at normal conditions. An application of an external magnetic field increased this amount up to 107 particles/cell. Most probably much of these particles penetrated into cells.

Glycerol dehydration of native and diabetic animal tissues studied by THz-TDS and NMR methods

PubMed Central

Smolyanskaya, O. A.; Schelkanova, I. J.; Kulya, M. S.; Odlyanitskiy, E. L.; Goryachev, I. S.; Tcypkin, A. N.; Grachev, Ya. V.; Toropova, Ya. G.; Tuchin, V. V.

2018-01-01

The optical clearing method has been widely used for different spectral ranges where it provides tissue transparency. In this work, we observed the enhanced penetration of the terahertz waves inside biological samples (skin, kidney, and cornea) treated with glycerol solutions inducing changes of optical and dielectric properties. It was supported by the observed trend of free-to-bound water ratio measured by the nuclear magnetic resonance (NMR) method. The terahertz clearing efficiency was found to be less for diabetic samples than for normal ones. Results of the numerical simulation proved that pulse deformation is due to bigger penetration depth caused by the reduction of absorption and refraction at optical clearing. PMID:29541513

A Freeze Substitution Fixation-Based Gold Enlarging Technique for EM Studies of Endocytosed Nanogold-Labeled Molecules

PubMed Central

He, Wanzhong; Kivork, Christine; Machinani, Suman; Morphew, Mary K.; Gail, Anna M.; Tesar, Devin B.; Tiangco, Noreen E.; McIntosh, J. Richard; Bjorkman, Pamela J.

2007-01-01

We have developed methods to locate individual ligands that can be used for electron microscopy studies of dynamic events during endocytosis and subsequent intracellular trafficking. The methods are based on enlargement of 1.4 nm Nanogold attached to an endocytosed ligand. Nanogold, a small label that does not induce misdirection of ligand-receptor complexes, is ideal for labeling ligands endocytosed by live cells, but is too small to be routinely located in cells by electron microscopy. Traditional pre-embedding enhancement protocols to enlarge Nanogold are not compatible with high pressure freezing/freeze substitution fixation (HPF/FSF), the most accurate method to preserve ultrastructure and dynamic events during trafficking. We have developed an improved enhancement procedure for chemically-fixed samples that reduced autonucleation, and a new pre-embedding gold-enlarging technique for HPF/FSF samples that preserved contrast and ultrastructure and can be used for high-resolution tomography. We evaluated our methods using labeled Fc as a ligand for the neonatal Fc receptor. Attachment of Nanogold to Fc did not interfere with receptor binding or uptake, and gold-labeled Fc could be specifically enlarged to allow identification in 2D projections and in tomograms. These methods should be broadly applicable to many endocytosis and transcytosis studies. PMID:17723309

Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

PubMed Central

2013-01-01

The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling. PMID:24634618

ACCELERATED SOLVENT EXTRACTION COMBINED WITH ...

EPA Pesticide Factsheets

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

Experimental investigation on variation of physical properties of coal samples subjected to microwave irradiation

NASA Astrophysics Data System (ADS)

Hu, Guozhong; Yang, Nan; Xu, Guang; Xu, Jialin

2018-03-01

The gas drainage rate of low-permeability coal seam is generally less than satisfactory. This leads to the gas disaster of coal mine, and largely restricts the extraction of coalbed methane (CBM), and increases the emission of greenhouse gases in the mining area. Consequently, enhancing the gas drainage rate is an urgent challenge. To solve this problem, a new approach of using microwave irradiation (MWR) as a non-contact physical field excitation method to enhance gas drainage has been attempted. In order to evaluate the feasibility of this method, the methane adsorption, diffusion and penetrability of coal subjected to MWR were experimentally investigated. The variation of methane adsorbed amount, methane diffusion speed and absorption loop for the coal sample before and after MWR were obtained. The findings show that the MWR can change the adsorption property and reduce the methane adsorption capacity of coal. Moreover, the methane diffusion characteristic curves for both the irradiated coal samples and theoriginal coal samples present the same trend. The irradiated coal samples have better methane diffusion ability than the original ones. As the adsorbed methane decreases, the methane diffusion speed increases or remain the same for the sample subjected to MWR. Furthermore, compared to the original coal samples, the area of the absorption loop for irradiated samples increases, especially for the micro-pore and medium-pore stage. This leads to the increase of open pores in the coal, thus improving the gas penetrability of coal. This study provides supports for positive MWR effects on changing the methane adsorption and improving the methane diffusion and the gas penetrability properties of coal samples.

ENHANCED CONCENTRATION AND ISOLATION OF CYCLOSPORA CAYETANENSIS OOCYSTS FROM HUMAN FECAL SAMPLES

EPA Science Inventory

Cyclospora cayetanensis is the causative agent of cyclosporiasis, an emerging infections disease. A new method for the purification of Cycloposra cayetanensis oocysts from fecal matter has been developed, using a modified detachment solution and a Renocal-sucrose gradient sedimen...

Nature's Art.

ERIC Educational Resources Information Center

Sterling, Vicki; And Others

Over 60 art activities, designed to enhance environmental awareness and incorporate environmental concepts, are outlined in this document. A sample of the activities presented are: decorated notepaper and cards with feathers or weeds; wall plaques of prairie plants; methods of flower preservation; water plant prints; construction of dolls,…

Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

PubMed

Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

2017-05-04

Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C 1 mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast, the interaction energy between the cellulose and water is too weak to dissolve cellulose in water.

Enhanced catalytic performance for light-olefins production from chloromethane over hierarchical porous ZSM-5 zeolite synthesized by a growth-inhibition strategy

NASA Astrophysics Data System (ADS)

Liu, Qing; Wen, Dafen; Yang, Yanran; Fei, Zhaoyang; Zhang, Zhuxiu; Chen, Xian; Tang, Jihai; Cui, Mifen; Qiao, Xu

2018-03-01

Hierarchical porous ZSM-5 (HP-ZSM-5) zeolites were synthesized by hydrothermal crystallization method adding triethoxyvinylsilane as the growth-inhibitor at different hydrothermal crystallized temperatures. The properties of the obtained samples were characterized by XRD, SEM, N2-sorption, uptake of ethylene, 27Al MAS NMR, NH3-TPD, and Py-IR. It was found that the mesopore was introduced and the acidity was adjusted over HP-ZSM-5 samples successfully. The hydrothermal crystallized temperature had an important influence on the porous structure and surface properties. The catalytic performance for chloromethane to light-olefins (CMTO) were also investigated. Compared with ZSM-5 samples, HP-ZSM-5 samples exhibited enhanced stability and increased selectivity of light-olefins for CMTO reaction because of the introduction of the abundant mesopore and appropriate acidity. The lifetime (the duration of chloromethane conversion >98%) and selectivity of light-olefins reached 115 h and 69.3%, respectively.

Strain modulation-enhanced Mg acceptor activation efficiency of Al0.14Ga0.86N/GaN superlattices with AlN interlayer

NASA Astrophysics Data System (ADS)

Wang, Lei; Li, Rui; Li, Ding; Liu, Ningyang; Liu, Lei; Chen, Weihua; Wang, Cunda; Yang, Zhijian; Hu, Xiaodong

2010-02-01

AlN layer was grown as interlayer between undoped GaN and Mg doped Al0.14Ga0.86N/GaN superlattices (SLs) epilayer to modulate the strain distribution between Al0.14Ga0.86N barrier and GaN well layers in SLs sample. Strain relaxation was observed in the SLs sample with AlN interlayer by x-ray diffraction reciprocal space mapping method. The measured hole concentration of SLs sample with AlN interlayer at room temperature was over 1.6×1018 cm-3 but that was only 6.6×1016 cm-3 obtained in SLs sample without AlN interlayer. Variable temperature Hall-effect measurement showed that the acceptor activation energy decreased from 150 to 70 meV after inserting the AlN layer, which indicated that the strain modulation of SLs induced by AlN interlayer was beneficial to the Mg acceptor activation and hole concentration enhancement.

Advanced Computational Methods for High-accuracy Refinement of Protein Low-quality Models

NASA Astrophysics Data System (ADS)

Zang, Tianwu

Predicting the 3-dimentional structure of protein has been a major interest in the modern computational biology. While lots of successful methods can generate models with 3˜5A root-mean-square deviation (RMSD) from the solution, the progress of refining these models is quite slow. It is therefore urgently needed to develop effective methods to bring low-quality models to higher-accuracy ranges (e.g., less than 2 A RMSD). In this thesis, I present several novel computational methods to address the high-accuracy refinement problem. First, an enhanced sampling method, named parallel continuous simulated tempering (PCST), is developed to accelerate the molecular dynamics (MD) simulation. Second, two energy biasing methods, Structure-Based Model (SBM) and Ensemble-Based Model (EBM), are introduced to perform targeted sampling around important conformations. Third, a three-step method is developed to blindly select high-quality models along the MD simulation. These methods work together to make significant refinement of low-quality models without any knowledge of the solution. The effectiveness of these methods is examined in different applications. Using the PCST-SBM method, models with higher global distance test scores (GDT_TS) are generated and selected in the MD simulation of 18 targets from the refinement category of the 10th Critical Assessment of Structure Prediction (CASP10). In addition, in the refinement test of two CASP10 targets using the PCST-EBM method, it is indicated that EBM may bring the initial model to even higher-quality levels. Furthermore, a multi-round refinement protocol of PCST-SBM improves the model quality of a protein to the level that is sufficient high for the molecular replacement in X-ray crystallography. Our results justify the crucial position of enhanced sampling in the protein structure prediction and demonstrate that a considerable improvement of low-accuracy structures is still achievable with current force fields.

Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

NASA Astrophysics Data System (ADS)

Grazioli, Gianmarc

Calculating the kinetics of conformational changes in macromolecules, such as proteins and nucleic acids, is still very much an open problem in theoretical chemistry and computational biophysics. If it were feasible to run large sets of molecular dynamics trajectories that begin in one configuration and terminate when reaching another configuration of interest, calculating kinetics from molecular dynamics simulations would be simple, but in practice, configuration spaces encompassing all possible configurations for even the simplest of macromolecules are far too vast for such a brute force approach. In fact, many problems related to searches of configuration spaces, such as protein structure prediction, are considered to be NP-hard. Two approaches to addressing this problem are to either develop methods for enhanced sampling of trajectories that confine the search to productive trajectories without loss of temporal information, or coarse-grained methodologies that recast the problem in reduced spaces that can be exhaustively searched. This thesis will begin with a description of work carried out in the vein of the second approach, where a Smoluchowski diffusion equation model was developed that accurately reproduces the rate vs. force relationship observed in the mechano-catalytic disulphide bond cleavage observed in thioredoxin-catalyzed reduction of disulphide bonds. Next, three different novel enhanced sampling methods developed in the vein of the first approach will be described, which can be employed either separately or in conjunction with each other to autonomously define a set of energetically relevant subspaces in configuration space, accelerate trajectories between the interfaces dividing the subspaces while preserving the distribution of unassisted transition times between subspaces, and approximate time correlation functions from the kinetic data collected from the transitions between interfaces.

Novel methodology developments in modern molecular simulations

NASA Astrophysics Data System (ADS)

Minary, Peter

The present thesis aims to summarize novel methodological developments and their uses in the rapidly expanding field of molecular simulations. A new formalism designed to treat long range interactions on surfaces/wires, systems which are infinitely replicated in two/one spatial directions but have finite extent in the remaining dimensions, is developed in the first part of this thesis. The method is tested on both model and realistic problems and is found to be accurate, efficient and a marked improvement over existing formulations in speed, accuracy and utility. In the second part of this thesis, a novel ab initio molecular dynamics technique capable of treating metallic systems and highly exothermic chemical reactions is presented. The combination of the aforementioned methods are applied in the next part to study functionalization reactions at the Si(100)-2x1 semiconductor interface. Here, a set of forty finite temperature ab initio molecular dynamics trajectories is employed to investigate the microscopic mechanism of the addition of 1,3-butadiene to the Si(100)-2x1 surface. The detailed study of the trajectories indicate a common non-concerted stepwise mechanism that proceeds via an intermediate carbocation. In the remaining parts of the thesis, a novel set of methods is introduced to significantly enhance conformational sampling in molecular dynamics simulations of biomolecular systems. First, a new set of equations of motion and a reversible, resonance free, integrator are developed which permits step sizes on the order of 100 fs to be used. The new technique provides sufficient sampling to impact studies of the 200--300 residue proteins of greatest interest. Second, it is shown that combining molecular dynamics with novel variable transformations designed to warp configuration space so as to reduce barrier regions and enhance attractive basins lead to substantial gains in conformational sampling efficiency. Here, new transformations designed to overcome barriers induced by intermolecular interactions are introduced. The method is shown to substantially enhance conformational sampling in long alkane chains and in a model protein over standard molecular dynamics as well as parallel tempering.

Towards optical brain imaging: getting light through a bone

NASA Astrophysics Data System (ADS)

Thompson, J. V.; Hokr, B. H.; Nodurft, D. T.; Yakovlev, V. V.

2018-06-01

Optical imaging and detection in biological samples is severely limited by scattering effects. In particular, optical techniques for measuring conditions beneath the skull and within the bone marrow hold significant promise when it comes to speed, sensitivity and specificity. However, the strong optical scattering due to bone hinders the realization of these methods. In this article, we propose a technique to enhance the transmittance of light through bone. This is achieved by injecting light below the top surface of the bone and utilizing multiple scattering to increase transmittance. This technique suggests that enhancements of 2-6 times may be realized by injection of light 1 mm below the surface of the bone. By enhancing the transmittance of light through bone, we will greatly improve our ability to utilize optical methods to better understand and diagnose conditions within biological media.

Striving and Thriving in a Foreign Culture: A Mixed Method Approach on Adult International Students' Experience in U.S.A.

ERIC Educational Resources Information Center

Chen, Dianbing; Yang, Xinxiao

2014-01-01

In this mixed method study, we examined the experience of a sample of international students in four American universities to identify the factors that might enhance their ability in surviving and thriving in a foreign country within the context of university internationalization. The research explored the concepts of cultural values, behaviors,…

The Effectiveness of Emotionally Focused Couples Therapy on Sexual Satisfaction and Marital Adjustment of Infertile Couples with Marital Conflicts

PubMed Central

Soleimani, Ali Akbar; Najafi, Maryam; Ahmadi, Khodabakhsh; Javidi, Nasirudin; Hoseini Kamkar, Elnaz; Mahboubi, Mohamad

2015-01-01

Background The purpose of this investigation is to determine the efficacy of emotionally focused couples therapy (EFT-C) on enhancement of marital adjustment in infertile couples. Materials and Methods This was a semi-experimental study with a pre- and post-test design. We selected 30 infertile couples (60 subjects) by purposive sampling. Couples were randomly assigned to two groups, sample and control. Each group consisted of 15 couples who had marital maladjustment and low sexual satisfaction. Couples answered the marital adjustment and sexual satisfaction questionnaires at baseline after which the sample group received 10 sessions of EFT-C. Results Results of pre-test and post-test showed that EFT-C significantly impacted marital adjustment and sexual satisfaction. Conclusion EFT-C had a significant effect on enhancement of satisfaction, cohesion and affectional expression. This approach impacted physical and emotional sexual satisfaction of infertile couples. PMID:26644864

Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance

PubMed Central

Liu, Yuefeng; Luo, Jingjie; Shin, Yooleemi; Moldovan, Simona; Ersen, Ovidiu; Hébraud, Anne; Schlatter, Guy; Pham-Huu, Cuong; Meny, Christian

2016-01-01

Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields. PMID:27156575

Speckle noise attenuation in optical coherence tomography by compounding images acquired at different positions of the sample

NASA Astrophysics Data System (ADS)

Popescu, Dan P.; Hewko, Mark D.; Sowa, Michael G.

2007-01-01

This study demonstrates a simple method for attenuating the speckle noise generated by coherent multiple-scattered photons in optical-coherence tomography images. The method could be included among the space-diversity techniques used for speckle reduction. It relies on displacing the sample along a weakly focused beam in the sample arm of the interferometer, acquiring a coherent image for each sample position and adding the individual images to form a compounded image. It is proven that the compounded image displays a reduction in the speckle noise generated by multiple scattered photons and an enhancement in the intensity signal caused by single-backscattered photons. To evaluate its potential biomedical applications, the method is used to investigate in vitro a caries lesion affecting the enamel layer of a wisdom tooth. Because of the uncorrelated nature of the speckle noise the compounded image provides a better mapping of the lesion compared to a single (coherent) image.

A LDR-PCR approach for multiplex polymorphisms genotyping of severely degraded DNA with fragment sizes <100 bp.

PubMed

Zhang, Zhen; Wang, Bao-Jie; Guan, Hong-Yu; Pang, Hao; Xuan, Jin-Feng

2009-11-01

Reducing amplicon sizes has become a major strategy for analyzing degraded DNA typical of forensic samples. However, amplicon sizes in current mini-short tandem repeat-polymerase chain reaction (PCR) and mini-sequencing assays are still not suitable for analysis of severely degraded DNA. In this study, we present a multiplex typing method that couples ligase detection reaction with PCR that can be used to identify single nucleotide polymorphisms and small-scale insertion/deletions in a sample of severely fragmented DNA. This method adopts thermostable ligation for allele discrimination and subsequent PCR for signal enhancement. In this study, four polymorphic loci were used to assess the ability of this technique to discriminate alleles in an artificially degraded sample of DNA with fragment sizes <100 bp. Our results showed clear allelic discrimination of single or multiple loci, suggesting that this method might aid in the analysis of extremely degraded samples in which allelic drop out of larger fragments is observed.

Enhanced Resolution of Chiral Amino Acids with Capillary Electrophoresis for Biosignature Detection in Extraterrestrial Samples.

PubMed

Creamer, Jessica S; Mora, Maria F; Willis, Peter A

2017-01-17

Amino acids are fundamental building blocks of terrestrial life as well as ubiquitous byproducts of abiotic reactions. In order to distinguish between amino acids formed by abiotic versus biotic processes it is possible to use chemical distributions to identify patterns unique to life. This article describes two capillary electrophoresis methods capable of resolving 17 amino acids found in high abundance in both biotic and abiotic samples (seven enantiomer pairs d/l-Ala, -Asp, -Glu, -His, -Leu, -Ser, -Val and the three achiral amino acids Gly, β-Ala, and GABA). To resolve the 13 neutral amino acids one method utilizes a background electrolyte containing γ-cyclodextrin and sodium taurocholate micelles. The acidic amino acid enantiomers were resolved with γ-cyclodextrin alone. These methods allow detection limits down to 5 nM for the neutral amino acids and 500 nM for acidic amino acids and were used to analyze samples collected from Mono Lake with minimal sample preparation.

Enhancing the sensitivity of Dengue virus serotype detection by RT-PCR among infected children in India.

PubMed

Ahamed, Syed Fazil; Vivek, Rosario; Kotabagi, Shalini; Nayak, Kaustuv; Chandele, Anmol; Kaja, Murali-Krishna; Shet, Anita

2017-06-01

Dengue surveillance relies on reverse transcription-polymerase chain reaction (RT-PCR), for confirmation of dengue virus (DENV) serotypes. We compared efficacies of published and modified primer sets targeting envelope (Env) and capsid-premembrane (C-prM) genes for detection of circulating DENV serotypes in southern India. Acute samples from children with clinically-diagnosed dengue were used for RT-PCR testing. All samples were also subjected to dengue serology (NS1 antigen and anti-dengue-IgM/IgG rapid immunochromatographic assay). Nested RT-PCR was performed on viral RNA using three methods targeting 654bp C-prM, 511bp C-prM and 641bp Env regions, respectively. RT-PCR-positive samples were validated by population sequencing. Among 171 children with suspected dengue, 121 were dengue serology-positive and 50 were dengue serology-negative. Among 121 serology-positives, RT-PCR detected 91 (75.2%) by CprM654, 72 (59.5%) by CprM511, and 74 (61.1%) by Env641. Among 50 serology-negatives, 10 (20.0%) were detected by CprM654, 12 (24.0%) by CprM511, and 11 (22.0%) by Env641. Overall detection rate using three methods sequentially was 82.6% (100/121) among serology-positive and 40.0% (20/50) among serology-negative samples; 6.6% (8/120) had co-infection with multiple DENV serotypes. We conclude that detection of acute dengue was enhanced by a modified RT-PCR method targeting the 654bp C-prM region, and further improved by using all three methods sequentially. Copyright © 2017 Elsevier B.V. All rights reserved.

Digital enhancement of haematoxylin- and eosin-stained histological images for red-green colour-blind observers.

PubMed

Landini, G; Perryer, G

2009-06-01

Individuals with red-green colour-blindness (CB) commonly experience great difficulty differentiating between certain histological stain pairs, notably haematoxylin-eosin (H&E). The prevalence of red-green CB is high (6-10% of males), including among medical and laboratory personnel, and raises two major concerns: first, accessibility and equity issues during the education and training of individuals with this disability, and second, the likelihood of errors in critical tasks such as interpreting histological images. Here we show two methods to enhance images of H&E-stained samples so the differently stained tissues can be well discriminated by red-green CBs while remaining usable by people with normal vision. Method 1 involves rotating and stretching the range of H&E hues in the image to span the perceptual range of the CB observers. Method 2 digitally unmixes the original dyes using colour deconvolution into two separate images and repositions the information into hues that are more distinctly perceived. The benefits of these methods were tested in 36 volunteers with normal vision and 11 with red-green CB using a variety of H&E stained tissue sections paired with their enhanced versions. CB subjects reported they could better perceive the different stains using the enhanced images for 85% of preparations (method 1: 90%, method 2: 73%), compared to the H&E-stained original images. Many subjects with normal vision also preferred the enhanced images to the original H&E. The results suggest that these colour manipulations confer considerable advantage for those with red-green colour vision deficiency while not disadvantaging people with normal colour vision.

Enhanced spot preparation for liquid extractive sampling and analysis

DOEpatents

Van Berkel, Gary J.; King, Richard C.

2015-09-22

A method for performing surface sampling of an analyte, includes the step of placing the analyte on a stage with a material in molar excess to the analyte, such that analyte-analyte interactions are prevented and the analyte can be solubilized for further analysis. The material can be a matrix material that is mixed with the analyte. The material can be provided on a sample support. The analyte can then be contacted with a solvent to extract the analyte for further processing, such as by electrospray mass spectrometry.

Chemical analysis of acoustically levitated drops by Raman spectroscopy.

PubMed

Tuckermann, Rudolf; Puskar, Ljiljana; Zavabeti, Mahta; Sekine, Ryo; McNaughton, Don

2009-07-01

An experimental apparatus combining Raman spectroscopy with acoustic levitation, Raman acoustic levitation spectroscopy (RALS), is investigated in the field of physical and chemical analytics. Whereas acoustic levitation enables the contactless handling of microsized samples, Raman spectroscopy offers the advantage of a noninvasive method without complex sample preparation. After carrying out some systematic tests to probe the sensitivity of the technique to drop size, shape, and position, RALS has been successfully applied in monitoring sample dilution and preconcentration, evaporation, crystallization, an acid-base reaction, and analytes in a surface-enhanced Raman spectroscopy colloidal suspension.

A novel in-situ method for real-time monitoring of gas transport in soil

NASA Astrophysics Data System (ADS)

Laemmel, Thomas; Maier, Martin; Schack-Kirchner, Helmer; Lang, Friederike

2017-04-01

Gas exchange between soil and atmosphere is important for the biogeochemistry of soils. Gas transport in soil is commonly assumed to be governed by molecular diffusion and is usually described by the soil gas diffusion coefficient DS characterizing the ability of the soil to "transport passively" gas through the soil. One way to determine DS is sampling soil cores in the field and measuring DS in the lab. Unfortunately this method is destructive and laborious. Moreover, a few previous field studies identified other gas transport processes in soil to significantly enhance the diffusive gas transport. However, until now, no method is available to measure gas transport in situ in the soil. We developed a novel method to monitor gas transport in soil in situ. The method includes a custom made gas sampling device, the continuous injection of an inert tracer gas and inverse gas transport modelling in the soil. The gas sampling device has several sampling depths and can be easily installed into a vertical hole drilled by an auger, which allows for fast installation of the system. Helium (He) as inert tracer gas was injected continuously at the lower end of the device. The resulting steady state distribution of He was used to deduce the depth profile of DS. Gas transport in the soil surrounding the gas-sampling-device/soil system was modeled using the Finite Element Modeling program COMSOL . We tested our new method both in the lab and during two short field studies and compared the results with a reference method using soil cores. DS profiles obtained by our in-situ method were consistent with DS profiles determined based on soil core analyses. During a longer monitoring field campaign, typical soil-moisture effects upon gas diffusivity such as an increase during a drying period or a decrease after rain could be observed consistently. Under windy conditions we additionally measured for the first time the direct enhancement of gas transport in soil due to wind-induced pressure-pumping which could increase the effective DS up to 30% in the topsoil. Our novel monitoring method can be quickly and easily installed and allows for monitoring continuously soil gas transport over a long time. It allows monitoring physical modifications of soil gas diffusivity due to rain events or evaporation but it also allows studying non-diffusive gas transport processes in the soil.

Rapid analysis of malachite green and leucomalachite green in fish muscles with surface-enhanced resonance Raman scattering.

PubMed

Zhang, Yuanyuan; Yu, Wansong; Pei, Lu; Lai, Keqiang; Rasco, Barbara A; Huang, Yiqun

2015-02-15

Surface-enhanced resonance Raman scattering (SERRS) coupled with gold nanospheres was applied for rapid analysis of the hazardous substances malachite green (MG) and leucomalachite green (LMG) in fish muscle tissues. The lowest concentration of MG that could be detected was 0.5ngmL(-1) with high linear correlation (R(2)=0.970-0.998) between MG concentration and intensities of characteristic Raman peaks. A simplified sample preparation method taking less than 1h for recovering MG and LMG in fish fillets was developed for SERRS analysis, and 4-8 samples could be handled in parallel. MG and LMG could be detected in extracts of tilapia fish fillets at as low as 2ngg(-1) with SERRS and a simple principle component analysis method. For six other fish species, the lowest detectable concentration of MG ranged from 1ngg(-1) to 10ngg(-1). This study provides a new sensitive approach for the detection of trace amounts of the prohibited drugs MG and LMG in muscle food, which has the potential for rapidly screening a large number of samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

A new cloud point extraction procedure for determination of inorganic antimony species in beverages and biological samples by flame atomic absorption spectrometry.

PubMed

Altunay, Nail; Gürkan, Ramazan

2015-05-15

A new cloud-point extraction (CPE) for the determination of antimony species in biological and beverages samples has been established with flame atomic absorption spectrometry (FAAS). The method is based on the fact that formation of the competitive ion-pairing complex of Sb(III) and Sb(V) with Victoria Pure Blue BO (VPB(+)) at pH 10. The antimony species were individually detected by FAAS. Under the optimized conditions, the calibration range for Sb(V) is 1-250 μg L(-1) with a detection limit of 0.25 μg L(-1) and sensitive enhancement factor of 76.3 while the calibration range for Sb(III) is 10-400 μg L(-1) with a detection limit of 5.15 μg L(-1) and sensitive enhancement factor of 48.3. The precision as a relative standard deviation is in range of 0.24-2.35%. The method was successfully applied to the speciative determination of antimony species in the samples. The validation was verified by analysis of certified reference materials (CRMs). Copyright © 2014 Elsevier Ltd. All rights reserved.

Capillary Electrophoresis Sensitivity Enhancement Based on Adaptive Moving Average Method.

PubMed

Drevinskas, Tomas; Telksnys, Laimutis; Maruška, Audrius; Gorbatsova, Jelena; Kaljurand, Mihkel

2018-06-05

In the present work, we demonstrate a novel approach to improve the sensitivity of the "out of lab" portable capillary electrophoretic measurements. Nowadays, many signal enhancement methods are (i) underused (nonoptimal), (ii) overused (distorts the data), or (iii) inapplicable in field-portable instrumentation because of a lack of computational power. The described innovative migration velocity-adaptive moving average method uses an optimal averaging window size and can be easily implemented with a microcontroller. The contactless conductivity detection was used as a model for the development of a signal processing method and the demonstration of its impact on the sensitivity. The frequency characteristics of the recorded electropherograms and peaks were clarified. Higher electrophoretic mobility analytes exhibit higher-frequency peaks, whereas lower electrophoretic mobility analytes exhibit lower-frequency peaks. On the basis of the obtained data, a migration velocity-adaptive moving average algorithm was created, adapted, and programmed into capillary electrophoresis data-processing software. Employing the developed algorithm, each data point is processed depending on a certain migration time of the analyte. Because of the implemented migration velocity-adaptive moving average method, the signal-to-noise ratio improved up to 11 times for sampling frequency of 4.6 Hz and up to 22 times for sampling frequency of 25 Hz. This paper could potentially be used as a methodological guideline for the development of new smoothing algorithms that require adaptive conditions in capillary electrophoresis and other separation methods.

Layered double hydroxide-enhanced luminescence in a Fenton-like system for selective sensing of cobalt in Hela cells

NASA Astrophysics Data System (ADS)

Yu, Mei; Yuan, Zhiqin; Lu, Chao

2017-09-01

This work presented a facile and eco-friendly method for the determination of cobalt ions (Co(II)) in living cells based on layered double hydroxides (Mg-Al CO3-LDHs) enhanced chemiluminescence (CL) emission of a Co(II)-hydrogen peroxide-sodium hydroxide system. The enhanced CL emission was attributed to the large specific surface area of Mg-Al CO3-LDHs, which facilitates the generation of an excited-stated intermediate. The proposed method displayed high selectivity toward Co(II) over other metal ions. Under the optimal conditions, the increased CL intensity showed a linear response versus Co(II) concentration in the range of 5.0-1000 nM with a detection limit of 3.7 nM (S/N = 3). The relative standard deviation for nine repeated measurements of 100 nM Co(II) was 3.2%. Furthermore, the proposed method was successfully applied to detect Co(II) in living cell samples, and the results were agreed with those obtained by the standard ICP-MS method.

Surface Modification of Silicon Pillar Arrays To Enhance Fluorescence Detection of Uranium and DNA

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

Lincoln, Danielle R.; Charlton, Jennifer J.; Hatab, Nahla A.

There is an ever-growing need for detection methods that are both sensitive and efficient, such that reagent and sample consumption is minimized. Nanopillar arrays offer an attractive option to fill this need by virtue of their small scale in conjunction with their field enhancement intensity gains. This work investigates the use of nanopillar substrates for the detection of the uranyl ion and DNA, two analytes unalike but for their low quantum efficiencies combined with the need for high-throughput analyses. Here in this paper, the adaptability of these platforms was explored, as methods for the successful surface immobilization of both analytesmore » were developed and compared, resulting in a limit of detection for the uranyl ion of less than 1 ppm with a 0.2 μL sample volume. Moreover, differentiation between single-stranded and double-stranded DNA was possible, including qualitative identification between double-stranded DNA and DNA of the same sequence, but with a 10-base-pair mismatch.« less

Surface Modification of Silicon Pillar Arrays To Enhance Fluorescence Detection of Uranium and DNA

DOE PAGES

Lincoln, Danielle R.; Charlton, Jennifer J.; Hatab, Nahla A.; ...

2017-10-27

There is an ever-growing need for detection methods that are both sensitive and efficient, such that reagent and sample consumption is minimized. Nanopillar arrays offer an attractive option to fill this need by virtue of their small scale in conjunction with their field enhancement intensity gains. This work investigates the use of nanopillar substrates for the detection of the uranyl ion and DNA, two analytes unalike but for their low quantum efficiencies combined with the need for high-throughput analyses. Here in this paper, the adaptability of these platforms was explored, as methods for the successful surface immobilization of both analytesmore » were developed and compared, resulting in a limit of detection for the uranyl ion of less than 1 ppm with a 0.2 μL sample volume. Moreover, differentiation between single-stranded and double-stranded DNA was possible, including qualitative identification between double-stranded DNA and DNA of the same sequence, but with a 10-base-pair mismatch.« less

Green design application on campus to enhance student’s quality of life

NASA Astrophysics Data System (ADS)

Tamiami, H.; Khaira, F.; Fachrudin, A.

2018-02-01

Green design becomes an important thing to applied in the building. Green building will provide comfortability and enhance Quality of Life (QoL) for the users. The purpose of this research is to analyze how green design application on campus to enhance student’s QoL. This research conducted in three campuses which located in North Sumatera Province, namely Universitas Sumatera Utara (USU), Universitas Negeri Medan (Unimed) and Universitas Medan Area (UMA) which have a lot of vegetation, open space, and multi-mass buildings. This research compared the green design application to QoL from three universities. Green design in this research that become independent variables focus on the energy efficiency and conservation (EEC), indoor health and comfort (IHC) and building environment management (BEM) with dependent variable is QoL. This research uses quantitative methods with questionnaire survey techniques. The population is students from the three universities with the sample of each University is 50 samples. The analysis uses multiple regression analysis. The results show that green design application may enhance QoL of students. The campus should have a good green design application to enhance QoL of students and give them comfortability.

Enhanced Raman spectroscopy of 2,4,6-TNT in anatase and rutile titania nanocrystals

NASA Astrophysics Data System (ADS)

De La Cruz-Montoya, Edwin; Jeréz, Jaqueline I.; Balaguera-Gelves, Marcia; Luna-Pineda, Tatiana; Castro, Miguel E.; Hernández-Rivera, Samuel P.

2006-05-01

The majority of explosives found in antipersonnel and antitank landmines contain 2,4,6-trinitrotoluene (TNT). Chemical sensing of landmines and Improvised Explosive Devices (IED) requires detecting the chemical signatures of the explosive components in these devices. Nanotechnology is ideally suited to needs in microsensors development by providing new materials and methods that can be employed for trace explosive detection. This work is focused on modification of nano-scaled colloids of titanium dioxide (Titania: anatase, rutile and brookite) and thin layer of the oxides as substrates for use in Enhanced Raman Scattering (ERS) spectroscopy. Ultrafine particles have been generated by hydrothermally treating the sol-gel derived hydrous oxides. ERS spectra of nanocrystalline anatase Titania samples prepared with different average sizes: 38 nm (without acid), 24 nm (without acid) and 7 nm (with HCl). Bulk phase (commercial) and KBr were also used to prepare mixtures with TNT to look for Enhanced Raman Effect of the nitroaromatic explosive on the test surfaces. The studies clearly indicated that the anatase crystal size affects the enhancement of the TNT Raman signal. This enhancement was highest for the samples with Titania average crystal size of 7 nm.

Magnetically assisted surface-enhanced raman scattering selective determination of dopamine in an artificial cerebrospinal fluid and a mouse striatum using Fe(3)O(4)/Ag nanocomposite.

PubMed

Ranc, Vaclav; Markova, Zdenka; Hajduch, Marian; Prucek, Robert; Kvitek, Libor; Kaslik, Josef; Safarova, Klara; Zboril, Radek

2014-03-18

The dopaminergic neural system is a crucial part of the brain responsible for many of its functions including mood, arousal, and other roles. Dopamine is the key neurotransmitter of this system, and a determination of its level presents a demanding task needed for a deeper understanding of the processes, even pathological, involving this brain part. In this work, we present a method for a fast analysis of dopamine levels in samples of cerebrospinal fluid and mouse striatum. The method is based on a nanocomposite composed of magnetite and silver nanoparticles, whose surface is modified with iron nitriloacetic acid (Fe-NTA)-a dopamine-selective compound. The magnetic properties of this nanocomposite enable simple separation of targeted molecules from a complex matrix while the silver acts as a platform for surface-enhanced Raman scattering (SERS). Silver and magnetite nanoparticles are joined by carboxymethyl chitosan, useful in biological environments and enhancing the sensitivity due to the presence of carboxyl groups. This system reveals a good stability and reproducibility. Moreover, rapid and simple quantitative experiments show an improvement in the detection of dopamine levels in biological assays at low femtomolar concentrations. The comparative data performed with clinical samples of mouse striatum show that the developed magnetic SERS is a strong alternative to conventional high-performance liquid chromatography-mass spectrometry (HPLC-MS) with even several superior aspects including faster and cheaper analysis and no necessity of sample preconcentration or derivatization.

Direct Electrospray Ionization Mass Spectrometric Profiling of Real-World Samples via a Solid Sampling Probe

NASA Astrophysics Data System (ADS)

Yu, Zhan; Chen, Lee Chuin; Mandal, Mridul Kanti; Yoshimura, Kentaro; Takeda, Sen; Hiraoka, Kenzo

2013-10-01

This study presents a novel direct analysis strategy for rapid mass spectrometric profiling of biochemicals in real-world samples via a direct sampling probe (DSP) without sample pretreatments. Chemical modification is applied to a disposable stainless steel acupuncture needle to enhance its surface area and hydrophilicity. After insertion into real-world samples, biofluid can be attached on the DSP surface. With the presence of a high DC voltage and solvent vapor condensing on the tip of the DSP, analyte can be dissolved and electrosprayed. The simplicity in design, versatility in application aspects, and other advantages such as low cost and disposability make this new method a competitive tool for direct analysis of real-world samples.

Surface-enhanced Raman scattering spectroscopy characterization and identification of foodborne bacteria

NASA Astrophysics Data System (ADS)

Liu, Yongliang; Chen, Yud-Ren; Nou, Xiangwu; Chao, Kaunglin

2007-09-01

Rapid and routine identification of foodborne bacteria are considerably important, because of bio- / agro- terrorism threats, public health concerns, and economic loss. Conventional, PCR, and immunoassay methods for the detection of bacteria are generally time-consuming, chemical reagent necessary and multi-step procedures. Fast microbial detection requires minimal sample preparation, permits the routine analysis of large numbers of samples with negligible reagent costs, and is easy to operate. Therefore, we have developed silver colloidal nanoparticle based surface-enhanced Raman scattering (SERS) spectroscopy as a potential tool for the rapid and routine detection of E. coli and L. monocytogenes. This study presents the further results of our examination on S. typhimonium, one of the most commonly outbreak bacteria, for the characteristic bands and subsequent identification.

Exploitation of microbes for enhancing bacoside content and reduction of Meloidogyne incognita infestation in Bacopa monnieri L.

PubMed

Gupta, Rupali; Tiwari, Sudeep; Saikia, Shilpi K; Shukla, Virendra; Singh, Rashmi; Singh, S P; Kumar, P V Ajay; Pandey, Rakesh

2015-01-01

Despite the vast exploration of rhizospheric microbial wealth for crop yield enhancement, knowledge about the efficacy of microbial agents as biocontrol weapons against root-knot disease is scarce, especially in medicinal plants, viz., Bacopa monnieri. In the present investigation, rhizospheric microbes, viz., Bacillus megaterium, Glomus intraradices, Trichoderma harzianum ThU, and their combinations were evaluated for the management of Meloidogyne incognita (Kofoid and White) Chitwood and bacoside content enhancement in B. monnieri var CIM-Jagriti. A novel validated method Fourier transform near infrared was used for rapid estimation of total bacoside content. A significant reduction (2.75-fold) in root-knot indices was observed in the combined treatment of B. megaterium and T. harzianum ThU in comparison to untreated control plants. The same treatment also showed significant enhancement (1.40-fold) in total bacoside contents (plant active molecule) content using Fourier transform near-infrared (FT-NIR) method that analyses samples rapidly in an hour without solvent usage and provides ample scope for natural product studies.

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

PubMed

Gill, Samuel C; Lim, Nathan M; Grinaway, Patrick B; Rustenburg, Ariën S; Fass, Josh; Ross, Gregory A; Chodera, John D; Mobley, David L

2018-05-31

Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes. In this technique, the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over 2 orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step toward applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding modes of ligands using enhanced sampling (BLUES) package which is freely available on GitHub.

Mapping Conformational Dynamics of Proteins Using Torsional Dynamics Simulations

PubMed Central

Gangupomu, Vamshi K.; Wagner, Jeffrey R.; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-01-01

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein’s experimentally established conformational substates. Conformational transition of calmodulin from the Ca2+-bound to the Ca2+-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. PMID:23663843

Mapping conformational dynamics of proteins using torsional dynamics simulations.

PubMed

Gangupomu, Vamshi K; Wagner, Jeffrey R; Park, In-Hee; Jain, Abhinandan; Vaidehi, Nagarajan

2013-05-07

All-atom molecular dynamics simulations are widely used to study the flexibility of protein conformations. However, enhanced sampling techniques are required for simulating protein dynamics that occur on the millisecond timescale. In this work, we show that torsional molecular dynamics simulations enhance protein conformational sampling by performing conformational search in the low-frequency torsional degrees of freedom. In this article, we use our recently developed torsional-dynamics method called Generalized Newton-Euler Inverse Mass Operator (GNEIMO) to study the conformational dynamics of four proteins. We investigate the use of the GNEIMO method in simulations of the conformationally flexible proteins fasciculin and calmodulin, as well as the less flexible crambin and bovine pancreatic trypsin inhibitor. For the latter two proteins, the GNEIMO simulations with an implicit-solvent model reproduced the average protein structural fluctuations and sample conformations similar to those from Cartesian simulations with explicit solvent. The application of GNEIMO with replica exchange to the study of fasciculin conformational dynamics produced sampling of two of this protein's experimentally established conformational substates. Conformational transition of calmodulin from the Ca(2+)-bound to the Ca(2+)-free conformation occurred readily with GNEIMO simulations. Moreover, the GNEIMO method generated an ensemble of conformations that satisfy about half of both short- and long-range interresidue distances obtained from NMR structures of holo to apo transitions in calmodulin. Although unconstrained all-atom Cartesian simulations have failed to sample transitions between the substates of fasciculin and calmodulin, GNEIMO simulations show the transitions in both systems. The relatively short simulation times required to capture these long-timescale conformational dynamics indicate that GNEIMO is a promising molecular-dynamics technique for studying domain motion in proteins. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Enhancement in sample collection for the detection of MDMA using a novel planar SPME (PSPME) device coupled to ion mobility spectrometry (IMS).

PubMed

Gura, Sigalit; Guerra-Diaz, Patricia; Lai, Hanh; Almirall, José R

2009-07-01

Trace detection of illicit drugs challenges the scientific community to develop improved sensitivity and selectivity in sampling and detection techniques. Ion mobility spectrometry (IMS) is one of the prominent trace detectors for illicit drugs and explosives, mostly due to its portability, high sensitivity and fast analysis. Current sampling methods for IMS rely on wiping suspected surfaces or withdrawing air through filters to collect particulates. These methods depend greatly on the particulates being bound onto surfaces or having sufficient vapour pressure to be airborne. Many of these compounds are not readily available in the headspace due to their low vapour pressure. This research presents a novel SPME device for enhanced air sampling and shows the use of optimized IMS by genetic algorithms to target volatile markers and/or odour signatures of illicit substances. The sampling method was based on unique static samplers, planar substrates coated with sol-gel polydimethyl siloxane (PDMS) nanoparticles, also known as planar solid-phase microextraction (PSPME). Due to its surface chemistry, high surface area and capacity, PSPME provides significant increases in sensitivity over conventional fibre SPME. The results show a 50-400 times increase in the detection capacity for piperonal, the odour signature of 3,4-methylenedioxymethamphetamine (MDMA). The PSPME-IMS technique was able to detect 600 ng of piperonal in a 30 s extraction from a quart-sized can containing 5 MDMA tablets, while detection using fibre SPME-IMS was not attainable. In a blind study of six cases suspected to contain varying amounts of MDMA in the tablets, PSPME-IMS successfully detected five positive cases and also produced no false positives or false negatives. One positive case had minimal amounts of MDMA resulting in a false negative response for fibre SPME-IMS.

Solid phase microextraction applied to the analysis of organophosphorus insecticides in fruits.

PubMed

Fytianos, K; Raikos, N; Theodoridis, G; Velinova, Z; Tsoukali, H

2006-12-01

Trace amounts of organophosphorus pesticides (OPs) were determined in various fruits by headspace solid phase microextraction (HS-SPME) and gas chromatography-nitrogen phosphorous detection (GC-NPD). Sampling from the headspace enhanced method selectivity, whereas at the same time improved fiber life time and method sensitivity. Diazinon, parathion, methyl parathion, malathion and fenithrothion were determined in various fruits: more than 150 samples of 21 types of fruits were studied. SPME-GC-NPD provided a useful and very efficient analytical tool: method linearity ranged from 1.2 to 700 ng/ml. Limits of detection (LODs) and quantitation (LOQs) ranged from 0.03 to 3 ng/ml and 0.12 to 10 ng/ml respectively, values well below the residue limits set by the EU. Less than 2% of the samples were found positive containing amounts higher than the EU limits. The effect of fruit peeling and washing was also investigated.

Enhanced Wang Landau sampling of adsorbed protein conformations.

PubMed

Radhakrishna, Mithun; Sharma, Sumit; Kumar, Sanat K

2012-03-21

Using computer simulations to model the folding of proteins into their native states is computationally expensive due to the extraordinarily low degeneracy of the ground state. In this paper, we develop an efficient way to sample these folded conformations using Wang Landau sampling coupled with the configurational bias method (which uses an unphysical "temperature" that lies between the collapse and folding transition temperatures of the protein). This method speeds up the folding process by roughly an order of magnitude over existing algorithms for the sequences studied. We apply this method to study the adsorption of intrinsically disordered hydrophobic polar protein fragments on a hydrophobic surface. We find that these fragments, which are unstructured in the bulk, acquire secondary structure upon adsorption onto a strong hydrophobic surface. Apparently, the presence of a hydrophobic surface allows these random coil fragments to fold by providing hydrophobic contacts that were lost in protein fragmentation. © 2012 American Institute of Physics

Pressure dependence of thermal conductivity and specific heat in CeRh2Si2 measured by an extended thermal relaxation method

NASA Astrophysics Data System (ADS)

Nishigori, Shijo; Seida, Osamu

2018-05-01

We have developed a new technique for measuring thermal conductivity and specific heat under pressure by improving a thermal relaxation method. In this technique, a cylindrical sample with a small disc heater is embedded in the pressure-transmitting medium, then temperature variations of the sample and heater were directly measured by thermocouples during a heating and cooling process. Thermal conductivity and specific heat are estimated by comparing the experimental data with temperature variations simulated by a finite element method. The obtained thermal conductivity and specific heat of the test sample CeRh2Si2 exhibit a small enhancement and a clear peak arising from antiferromagnetic transition, respectively. The observation of these typical behaviors for magnetic compounds indicate that the technique is valid for the study on thermal properties under pressure.

Scalable free energy calculation of proteins via multiscale essential sampling

NASA Astrophysics Data System (ADS)

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2010-12-01

A multiscale simulation method, "multiscale essential sampling (MSES)," is proposed for calculating free energy surface of proteins in a sizable dimensional space with good scalability. In MSES, the configurational sampling of a full-dimensional model is enhanced by coupling with the accelerated dynamics of the essential degrees of freedom. Applying the Hamiltonian exchange method to MSES can remove the biasing potential from the coupling term, deriving the free energy surface of the essential degrees of freedom. The form of the coupling term ensures good scalability in the Hamiltonian exchange. As a test application, the free energy surface of the folding process of a miniprotein, chignolin, was calculated in the continuum solvent model. Results agreed with the free energy surface derived from the multicanonical simulation. Significantly improved scalability with the MSES method was clearly shown in the free energy calculation of chignolin in explicit solvent, which was achieved without increasing the number of replicas in the Hamiltonian exchange.

[Development of selective determination methods for quinones with fluorescence and chemiluminescence detection and their application to environmental and biological samples].

PubMed

Kishikawa, Naoya

2010-10-01

Quinones are compounds that have various characteristics such as a biological electron transporter, an industrial product and a harmful environmental pollutant. Therefore, an effective determination method for quinones is required in many fields. This review describes the development of sensitive and selective determination methods for quinones based on some detection principles and their application to analyses in environmental, pharmaceutical and biological samples. Firstly, a fluorescence method was developed based on fluorogenic derivatization of quinones and applied to environmental analysis. Secondly, a luminol chemiluminescence method was developed based on generation of reactive oxygen species through the redox cycle of quinone and applied to pharmaceutical analysis. Thirdly, a photo-induced chemiluminescence method was developed based on formation of reactive oxygen species and fluorophore or chemiluminescence enhancer by the photoreaction of quinones and applied to biological and environmental analyses.

Polyol-enhanced dispersive liquid-liquid microextraction coupled with gas chromatography and nitrogen phosphorous detection for the determination of organophosphorus pesticides from aqueous samples, fruit juices, and vegetables.

PubMed

Farajzadeh, Mir Ali; Afshar Mogaddam, Mohammad Reza; Alizadeh Nabil, Ali Akbar

2015-12-01

Polyol-enhanced dispersive liquid-liquid microextraction has been proposed for the extraction and preconcentration of some organophosphorus pesticides from different samples. In the present study, a high volume of an aqueous phase containing a polyol (sorbitol) is prepared and then a disperser solvent along with an extraction solvent is rapidly injected into it. Sorbitol showed the best results and it was more effective on the extraction recoveries of the analytes than inorganic salts such as sodium chloride, potassium chloride, and sodium sulfate. Under the optimum extraction conditions, the method showed low limits of detection and quantification within the ranges of 12-56 and 44-162 pg/mL, respectively. Enrichment factors and extraction recoveries were in the ranges of 2799-3033 and 84-92%, respectively. The method precision was evaluated at a concentration of 10 ng/mL of each analyte, and relative standard deviations were found to be less than 5.9% for intraday (n = 6) and less than 7.8% for interday (n = 4). Finally, some aqueous samples were successfully analyzed using the proposed method and four analytes (diazinon, dimethoate, chlorpyrifos, and phosalone) were determined, some of them at ng/mL level. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Silver nanoparticle assisted urine sugar determination using thermal lens spectroscopy

NASA Astrophysics Data System (ADS)

Thomas, Lincy; John, Jisha; George, Nibu A.; Kurian, Achamma

2014-11-01

Nanotechnology plays a vital role in the development of biosensors by enhancing their sensitivity and performance. In this paper, we report a novel urine sugar sensing method that makes use of the unique properties of silver-nanofluids in combination with the laser induced photothermal lens technique. The thermal lens signal decreases with increase in sugar levels in urine samples, which may be attributed to the enhanced interaction of glucose and conduction electrons of silver-nanoparticles, thereby changing the surface plasmon energy.

[Study on the surface-enhanced Raman spectrum of trimethoprim].

PubMed

Zhang, Jin-zhi; Wang, Yuan

2003-02-01

A new method is given in this paper to study the spectra of trimethoprim by using the surface-enhanced Raman spectrum (SERS) technology and the highly efficient thin layer chromatography (TLC) dissociation technology. The results of SERS indicate that the main vibrant spectral band can be obtained by TLC in the samples of about 6 micrograms. The expansion and contraction of pyrimidine ring can be obviously increased and the molecule information can be exactly presented under the action of silver particles.

Protocol Improvements for Low Concentration DNA-Based Bioaerosol Sampling and Analysis

PubMed Central

Ng, Chun Kiat; Miller, Dana; Cao, Bin

2015-01-01

Introduction As bioaerosol research attracts increasing attention, there is a need for additional efforts that focus on method development to deal with different environmental samples. Bioaerosol environmental samples typically have very low biomass concentrations in the air, which often leaves researchers with limited options in choosing the downstream analysis steps, especially when culture-independent methods are intended. Objectives This study investigates the impacts of three important factors that can influence the performance of culture-independent DNA-based analysis in dealing with bioaerosol environmental samples engaged in this study. The factors are: 1) enhanced high temperature sonication during DNA extraction; 2) effect of sampling duration on DNA recoverability; and 3) an alternative method for concentrating composite samples. In this study, DNA extracted from samples was analysed using the Qubit fluorometer (for direct total DNA measurement) and quantitative polymerase chain reaction (qPCR). Results and Findings The findings suggest that additional lysis from high temperature sonication is crucial: DNA yields from both high and low biomass samples increased up to 600% when the protocol included 30-min sonication at 65°C. Long air sampling duration on a filter media was shown to have a negative impact on DNA recoverability with up to 98% of DNA lost over a 20-h sampling period. Pooling DNA from separate samples during extraction was proven to be feasible with margins of error below 30%. PMID:26619279

Enhancing students’ mathematical representation and selfefficacy through situation-based learning assisted by geometer’s sketchpad program

NASA Astrophysics Data System (ADS)

Sowanto; Kusumah, Y. S.

2018-05-01

This research was conducted based on the problem of a lack of students’ mathematical representation ability as well as self-efficacy in accomplishing mathematical tasks. To overcome this problem, this research used situation-based learning (SBL) assisted by geometer’s sketchpad program (GSP). This research investigated students’ improvement of mathematical representation ability who were taught under situation-based learning (SBL) assisted by geometer’s sketchpad program (GSP) and regular method that viewed from the whole students’ prior knowledge (high, average, and low level). In addition, this research investigated the difference of students’ self-efficacy after learning was given. This research belongs to quasi experiment research using non-equivalent control group design with purposive sampling. The result of this research showed that students’ enhancement in their mathematical representation ability taught under SBL assisted by GSP was better than the regular method. Also, there was no interaction between learning methods and students prior knowledge in student’ enhancement of mathematical representation ability. There was significant difference of students’ enhancement of mathematical representation ability taught under SBL assisted by GSP viewed from students’ prior knowledge. Furthermore, there was no significant difference in terms of self-efficacy between those who were taught by SBL assisted by GSP with the regular method.

Feasibility Assessment of CO2 Sequestration and Enhanced Recovery in Gas Shale Reservoirs

NASA Astrophysics Data System (ADS)

Vermylen, J. P.; Hagin, P. N.; Zoback, M. D.

2008-12-01

CO2 sequestration and enhanced methane recovery may be feasible in unconventional, organic-rich, gas shale reservoirs in which the methane is stored as an adsorbed phase. Previous studies have shown that organic-rich, Appalachian Devonian shales adsorb approximately five times more carbon dioxide than methane at reservoir conditions. However, the enhanced recovery and sequestration concept has not yet been tested for gas shale reservoirs under realistic flow and production conditions. Using the lessons learned from previous studies on enhanced coalbed methane (ECBM) as a starting point, we are conducting laboratory experiments, reservoir modeling, and fluid flow simulations to test the feasibility of sequestration and enhanced recovery in gas shales. Our laboratory work investigates both adsorption and mechanical properties of shale samples to use as inputs for fluid flow simulation. Static and dynamic mechanical properties of shale samples are measured using a triaxial press under realistic reservoir conditions with varying gas saturations and compositions. Adsorption is simultaneously measured using standard, static, volumetric techniques. Permeability is measured using pulse decay methods calibrated to standard Darcy flow measurements. Fluid flow simulations are conducted using the reservoir simulator GEM that has successfully modeled enhanced recovery in coal. The results of the flow simulation are combined with the laboratory results to determine if enhanced recovery and CO2 sequestration is feasible in gas shale reservoirs.

Sensitive spectrophotometric determination of Co(II) using dispersive liquid-liquid micro-extraction method in soil samples.

PubMed

Hasanpour, Foroozan; Hadadzadeh, Hassan; Taei, Masoumeh; Nekouei, Mohsen; Mozafari, Elmira

2016-05-01

Analytical performance of conventional spectrophotometer was developed by coupling of effective dispersive liquid-liquid micro-extraction method with spectrophotometric determination for ultra-trace determination of cobalt. The method was based on the formation of Co(II)-alpha-benzoin oxime complex and its extraction using a dispersive liquid-liquid micro-extraction technique. During the present work, several important variables such as pH, ligand concentration, amount and type of dispersive, and extracting solvent were optimized. It was found that the crucial factor for the Co(II)-alpha benzoin oxime complex formation is the pH of the alkaline alcoholic medium. Under the optimized condition, the calibration graph was linear in the ranges of 1.0-110 μg L(-1) with the detection limit (S/N = 3) of 0.5 μg L(-1). The preconcentration operation of 25 mL of sample gave enhancement factor of 75. The proposed method was applied for determination of Co(II) in soil samples.

Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2014-2016).

PubMed

Breadmore, Michael C; Wuethrich, Alain; Li, Feng; Phung, Sui Ching; Kalsoom, Umme; Cabot, Joan M; Tehranirokh, Masoomeh; Shallan, Aliaa I; Abdul Keyon, Aemi S; See, Hong Heng; Dawod, Mohamed; Quirino, Joselito P

2017-01-01

One of the most cited limitations of capillary (and microchip) electrophoresis is the poor sensitivity. This review continues to update this series of biennial reviews, first published in Electrophoresis in 2007, on developments in the field of on-line/in-line concentration methods in capillaries and microchips, covering the period July 2014-June 2016. It includes developments in the field of stacking, covering all methods from field amplified sample stacking and large volume sample stacking, through to isotachophoresis, dynamic pH junction, and sweeping. Attention is also given to on-line or in-line extraction methods that have been used for electrophoresis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Teaching the Rules of Debit and Credit

ERIC Educational Resources Information Center

Potts, Andrew J.

1974-01-01

A fundamental method of explaining the basic accounting principles and concepts (debit, credit, basic accounting equation) which includes visual aids, reference to local businesses, and drill, does much toward increasing the student's skill and enhancing his understanding of the subject matter. (Sample transparencies are included.) (Author/AJ)

OBT analysis method using polyethylene beads for limited quantities of animal tissue.

PubMed

Kim, S B; Stuart, M

2015-08-01

This study presents a polyethylene beads method for OBT determination in animal tissues and animal products for cases where the amount of water recovered by combustion is limited by sample size or quantity. In the method, the amount of water recovered after combustion is enhanced by adding tritium-free polyethylene beads to the sample prior to combustion in an oxygen bomb. The method reduces process time by allowing the combustion water to be easily collected with a pipette. Sufficient water recovery was achieved using the polyethylene beads method when 2 g of dry animal tissue or animal product were combusted with 2 g of polyethylene beads. Correction factors, which account for the dilution due to the combustion water of the beads, are provided for beef, chicken, pork, fish and clams, as well as egg, milk and cheese. The method was tested by comparing its OBT results with those of the conventional method using animal samples collected on the Chalk River Laboratories (CRL) site. The results determined that the polyethylene beads method added no more than 25% uncertainty when appropriate correction factors are used. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Compound parabolic concentrator probe for efficient light collection in spectroscopy of biological tissue

NASA Astrophysics Data System (ADS)

Tanaka, Kazunori; Pacheco, Marcos T. T.; Brennan, James F., III; Itzkan, Irving; Berger, Andrew J.; Dasari, Ramachandra R.; Feld, Michael S.

1996-02-01

We describe a compound parabolic concentrator (CPC)-based probe for enhanced signal collection in the spectroscopy of biological tissues. Theoretical considerations governing signal enhancement compared with conventional collection methods are given. A ray-tracing program was used to analyze the throughput of CPC's with shape deviations and surface imperfections. A modified CPC shape with 99% throughput was discovered. A 4.4-mm-long CPC was manufactured and incorporated into an optical fiber-based near-infrared Raman spectrometer system. For human tissue samples, light collection was enhanced by a factor of 7 compared with collection with 0.29-NA optical fibers.

High performance of visible-NIR broad spectral photocurrent application of monodisperse PbSe nanocubes decorated on rGO sheets

NASA Astrophysics Data System (ADS)

Ghorban Shiravizadeh, A.; Elahi, S. M.; Sebt, S. A.; Yousefi, Ramin

2018-02-01

In this work, the photoresponse performance of monodisperse PbSe nanocubes in the range of visible and near-infrared (NIR) (400-1500 nm) regions was enhanced by reduced graphene oxide (rGO). A simple cost-effective method is presented to synthesize monodisperse PbSe nanocubes (NCs) that are decorated on the rGO sheets. By the addition of PbSe/rGO nanocomposites with different rGO concentrations, pristine PbSe NCs were synthesized with the same method. Microscopy images showed that the size of NCs was smaller than the exciton Bohr radius (46 nm) of PbSe bulk. Therefore, the UV-Vis-IR spectroscopy result revealed that the PbSe/rGO samples had absorption peaks in the NIR region around 1650 nm and showed a blue shift compared to the absorption peak of the PbSe bulk. J-V measurements of the samples indicated that monodisperse PbSe/rGO nanocomposites had a higher resistance than the other samples under dark condition. On the other hand, the resistance of the monodisperse PbSe/rGO nanocomposites decreased under different light source illuminations while the resistance of the other samples was increased under illumination. Photodetector measurements indicated that the monodisperse morphology of the PbSe NCs enhanced the photoresponse speed and photocurrent intensity. In addition, responsivity (R) and detectivity (D*) of the samples were higher in the NIR region.

Re-construction layer effect of LiNi0.8Co0.15Mn0.05O2 with solvent evaporation process

NASA Astrophysics Data System (ADS)

Park, Kwangjin; Park, Jun-Ho; Hong, Suk-Gi; Choi, Byungjin; Heo, Sung; Seo, Seung-Woo; Min, Kyoungmin; Park, Jin-Hwan

2017-03-01

The solvent evaporation method on the structural changes and surface chemistry of the cathode and the effect of electrochemical performance of Li1.0Ni0.8Co0.15Mn0.05O2 (NCM) has been investigated. After dissolving of Li residuals using minimum content of solvent in order to minimize the damage of pristine material and the evaporation time, the solvent was evaporated without filtering and remaining powder was re-heated at 700 °C in oxygen environment. Two kinds of solvent, de-ionized water and diluted nitric acid, were used as a solvent. The almost 40% of Li residuals were removed using solvent evaporation method. The NCM sample after solvent evaporation process exhibited an increase in the initial capacity (214.3 mAh/g) compared to the pristine sample (207.4 mAh/g) at 0.1C because of enhancement of electric conductivity caused by decline of Li residuals. The capacity retention of NCM sample after solvent evaporation process (96.0% at the 50th cycle) was also improved compared to that of the pristine NCM sample (90.6% at the 50th cycle). The uniform Li residual layer after solvent treated and heat treatment acted like a coating layer, leading to enhance the cycle performance. The NCM sample using diluted nitric acid showed better performance than that using de-ionized water.

Radiation detection method and system using the sequential probability ratio test

DOEpatents

Nelson, Karl E [Livermore, CA; Valentine, John D [Redwood City, CA; Beauchamp, Brock R [San Ramon, CA

2007-07-17

A method and system using the Sequential Probability Ratio Test to enhance the detection of an elevated level of radiation, by determining whether a set of observations are consistent with a specified model within a given bounds of statistical significance. In particular, the SPRT is used in the present invention to maximize the range of detection, by providing processing mechanisms for estimating the dynamic background radiation, adjusting the models to reflect the amount of background knowledge at the current point in time, analyzing the current sample using the models to determine statistical significance, and determining when the sample has returned to the expected background conditions.

Method and apparatus for implementing material thermal property measurement by flash thermal imaging

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

Sun, Jiangang

A method and apparatus are provided for implementing measurement of material thermal properties including measurement of thermal effusivity of a coating and/or film or a bulk material of uniform property. The test apparatus includes an infrared camera, a data acquisition and processing computer coupled to the infrared camera for acquiring and processing thermal image data, a flash lamp providing an input of heat onto the surface of a two-layer sample with an enhanced optical filter covering the flash lamp attenuating an entire infrared wavelength range with a series of thermal images is taken of the surface of the two-layer sample.

Analysis of chlorophenoxy acid herbicides in water by large-volume on-line derivatization and gas chromatography-mass spectrometry.

PubMed

Ding, W H; Liu, C H; Yeh, S P

2000-10-27

This work presents a modified method to analyze chlorophenoxy acid herbicides in water samples. The herbicides 2,4-D (2,4-dichlorophenoxyacetic acid). Silvex (2,4,5-trichlorophenoxypropionic acid) and 2,4,5-T (2,4,5-trichlorophenoxyacetic acid) were used to evaluate the method. The method involves extraction of samples by a graphitized carbon black cartridge, and on-line derivatization in the GC injection port using a large-volume (10-20 microl) direct sample introduction (DSI) device with tetraalkylammonium salts. The analytes were then identified and quantitated by ion-trap gas chromatography-mass spectrometry. The large-volume DSI injection-port derivatization technique provides sensitivity, fast and reproducible results for chlorophenoxy acid herbicides residues, to quantitation at 0.1 to 0.2 microg/l in 500-ml water samples. An enhanced characteristic mass chromatogram of molecular ions of butylated chlorophenoxy acid herbicides with a significant chlorine isotope pattern by electron impact ionization MS allows us to determine herbicides residues at trace levels in aqueous samples. Recovery of the herbicide residues in spiked various water samples ranged from 70 to 99% while RSDs ranged from 1 to 13%.

Novel synthesis of nanocomposite for the extraction of Sildenafil Citrate (Viagra) from water and urine samples: Process screening and optimization.

PubMed

Asfaram, Arash; Ghaedi, Mehrorang; Purkait, Mihir Kumar

2017-09-01

A sensitive analytical method is investigated to concentrate and determine trace level of Sildenafil Citrate (SLC) present in water and urine samples. The method is based on a sample treatment using dispersive solid-phase micro-extraction (DSPME) with laboratory-made Mn@ CuS/ZnS nanocomposite loaded on activated carbon (Mn@ CuS/ZnS-NCs-AC) as a sorbent for the target analyte. The efficiency was enhanced by ultrasound-assisted (UA) with dispersive nanocomposite solid-phase micro-extraction (UA-DNSPME). Four significant variables affecting SLC recovery like; pH, eluent volume, sonication time and adsorbent mass were selected by the Plackett-Burman design (PBD) experiments. These selected factors were optimized by the central composite design (CCD) to maximize extraction of SLC. The results exhibited that the optimum conditions for maximizing extraction of SLC were 6.0 pH, 300μL eluent (acetonitrile) volume, 10mg of adsorbent and 6min sonication time. Under optimized conditions, virtuous linearity of SLC was ranged from 30 to 4000ngmL -1 with R 2 of 0.99. The limit of detection (LOD) was 2.50ngmL -1 and the recoveries at two spiked levels were ranged from 97.37 to 103.21% with the relative standard deviation (RSD) less than 4.50% (n=15). The enhancement factor (EF) was 81.91. The results show that the combination UAE with DNSPME is a suitable method for the determination of SLC in water and urine samples. Copyright © 2017 Elsevier B.V. All rights reserved.

A simple and rapid method for direct determination of Al(III) based on the enhanced resonance Rayleigh scattering of hemin-functionalized graphene-Al(III) system

NASA Astrophysics Data System (ADS)

Ling, Yu; Chen, Ling Xiao; Dong, Jiang Xue; Li, Nian Bing; Luo, Hong Qun

2016-03-01

A novel method for direct determination of Al(III) by using hemin-functionalized graphene (H-GO) has been established based on the enhancement of resonance Rayleigh scattering (RRS) intensity. The characteristics of RRS spectra, the optimum reaction conditions, and the reaction mechanism have been investigated. In this experiment, the Al(III) would exist in sol-gel Al(OH)3 species under the condition of pH 5.9 in aqueous solutions. When H-GO existed in the solution, the sol-gel Al(OH)3 would react with H-GO and result in enhancement of RRS intensity, owing to the enhanced hydrophobicity of H-GO surface. Therefore, a simple and rapid sensor for Al(III) was developed. The increased intensity of RRS is directly proportional to the concentration of Al(III) in the range of 10 nM-6 μM, along with a detection limit of 0.87 nM. Moreover, the sensor has been applied to determination of Al(III) concentration in real water and aspirin tablet samples with satisfactory results. Therefore, the proposed method is promising as an effective means for selective and sensitive determination of Al(III).

Optimization of the elution buffer and concentration method for detecting hepatitis E virus in swine liver using a nested reverse transcription-polymerase chain reaction and real-time reverse transcription-polymerase chain reaction.

PubMed

Son, Na Ry; Seo, Dong Joo; Lee, Min Hwa; Seo, Sheungwoo; Wang, Xiaoyu; Lee, Bog-Hieu; Lee, Jeong-Su; Joo, In-Sun; Hwang, In-Gyun; Choi, Changsun

2014-09-01

The aim of this study was to develop an optimal technique for detecting hepatitis E virus (HEV) in swine livers. Here, three elution buffers and two concentration methods were compared with respect to enhancing recovery of HEV from swine liver samples. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and nested RT-PCR were performed to detect HEV RNA. When phosphate-buffered saline (PBS, pH 7.4) was used to concentrate HEV in swine liver samples using ultrafiltration, real-time RT-PCR detected HEV in 6 of the 26 samples. When threonine buffer was used to concentrate HEV using polyethylene glycol (PEG) precipitation and ultrafiltration, real-time RT-PCR detected HEV in 1 and 3 of the 26 samples, respectively. When glycine buffer was used to concentrate HEV using ultrafiltration and PEG precipitation, real-time RT-PCR detected HEV in 1 and 3 samples of the 26 samples, respectively. When nested RT-PCR was used to detect HEV, all samples tested negative regardless of the type of elution buffer or concentration method used. Therefore, the combination of real-time RT-PCR and ultrafiltration with PBS buffer was the most sensitive and reliable method for detecting HEV in swine livers. Copyright © 2014 Elsevier B.V. All rights reserved.

Enhanced chemiluminescence of carminic acid-permanganate by CdS quantum dots and its application for sensitive quenchometric flow injection assays of cloxacillin.

PubMed

Khataee, Alireza; Hasanzadeh, Aliyeh; Lotfi, Roya; Joo, Sang Woo

2016-05-15

A novel chemiluminescence (CL) system is introduced based on the oxidation of carminic acid by KMnO4 in acidic conditions. CdS quantum dots (QDs) were synthesized using a facile hydrothermal method which efficiently enhanced the intensity of the CL system. A possible mechanism for the proposed system is presented using the kinetic curves, CL spectra, photoluminescence (PL), and ultraviolet-visible (UV-Vis) analysis. The emission intensity of the KMnO4-carminic acid-CdS QDs system was quenched in the presence of a trace level of cloxacillin. Based on this quenching effect, a novel and sensitive flow injection CL method was developed for determining cloxacillin concentrations. At optimal experimental conditions, the decreased CL intensity had a good linear relation with the cloxacillin concentration in the range of 0.008 to 22.0 mg L(-1). The detection limit (3σ) was 5.8 µg L(-1). The precision of the method was calculated by analyzing samples containing 4.0 mg L(-1) of cloxacillin (n=11), and the relative standard deviations (RSD%) were 2.08%. The feasibility of the method is also demonstrated for determining cloxacillin concentrations in environmental water samples and a pharmaceutical formulation. Copyright © 2016 Elsevier B.V. All rights reserved.

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins.

PubMed

Andersen, Ole Juul; Grouleff, Julie; Needham, Perri; Walker, Ross C; Jensen, Frank

2015-11-19

Current enhanced sampling molecular dynamics methods for studying large conformational changes in proteins suffer from certain limitations. These include, among others, the need for user defined collective variables, the prerequisite of both start and end point structures of the conformational change, and the need for a priori knowledge of the amount by which to boost specific parts of the potential. In this paper, a framework is proposed for a molecular dynamics method for studying ligand-induced conformational changes, in which the nonbonded interactions between the ligand and the protein are used to calculate a biasing force. The method requires only a single input structure, and does not entail the use of collective variables. We provide a proof-of-concept for accelerating conformational changes in three simple test molecules, as well as promising results for two proteins known to undergo domain closure upon ligand binding. For the ribose-binding protein, backbone root-mean-square deviations as low as 0.75 Å compared to the crystal structure of the closed conformation are obtained within 50 ns simulations, whereas no domain closures are observed in unbiased simulations. A skewed closed structure is obtained for the glutamine-binding protein at high bias values, indicating that specific protein-ligand interactions might suppress important protein-protein interactions.

Flexible binding simulation by a novel and improved version of virtual-system coupled adaptive umbrella sampling

NASA Astrophysics Data System (ADS)

Dasgupta, Bhaskar; Nakamura, Haruki; Higo, Junichi

2016-10-01

Virtual-system coupled adaptive umbrella sampling (VAUS) enhances sampling along a reaction coordinate by using a virtual degree of freedom. However, VAUS and regular adaptive umbrella sampling (AUS) methods are yet computationally expensive. To decrease the computational burden further, improvements of VAUS for all-atom explicit solvent simulation are presented here. The improvements include probability distribution calculation by a Markov approximation; parameterization of biasing forces by iterative polynomial fitting; and force scaling. These when applied to study Ala-pentapeptide dimerization in explicit solvent showed advantage over regular AUS. By using improved VAUS larger biological systems are amenable.

Determination of Total Petroleum Hydrocarbons in Australian Groundwater Through the Improvised Gas Chromatography-Flame Ionization Detection Technique.

PubMed

Faustorilla, Maria Vilma; Chen, Zuliang; Dharmarajan, Rajarathnam; Naidu, Ravendra

2017-09-01

Assessment of total petroleum hydrocarbons (TPHs) from contaminated sites demands routine and reliable measurement at trace levels. However, the detection limits of these methods need to be improved. This study developed the programmable temperature vaporization-large volume injection (PTV-LVI) method to quantify TPHs through gas chromatography-flame ionization detection. This configuration enhances the method sensitivity for trace level detections through large volume injections and pre-concentration of analytes along the injection liner. The method was evaluated for the three commonly observed hydrocarbon fractions: C10-C14, C15-C28 and C29-C36. In comparison with conventional injection methods (splitless and pulsed splitless), PTV-LVI showed R2 values > 0.999 with enhanced limits of detection and limits of quantification values. The method was applied to real samples for routine environmental monitoring of TPHs in an Australian contaminated site characterized by refueling station. Analysis of groundwater samples in the area showed a wide range of TPH concentrations as follows: 66-1,546,000 (C10-C14), 216-22,762 (C15-C28) and 105-2,103 (C29-C36) μg/L. This method has detected trace levels, thereby measuring a wider concentration range of TPHs. These more accurate measurements can lead to the appropriate application of risk assessments and remediation techniques. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Core needle biopsy of soft tissue tumors, CEUS vs US guided: a pilot study.

PubMed

Coran, Alessandro; Di Maggio, Antonio; Rastrelli, Marco; Alberioli, Enrico; Attar, Shady; Ortolan, Paolo; Bortolanza, Carlo; Tosi, Annalisa; Montesco, Maria Cristina; Bezzon, Elisabetta; Rossi, Carlo Riccardo; Stramare, Roberto

2015-12-01

The purpose of this study was to evaluate the usefulness of contrast-enhanced ultrasonography (CEUS) in the bioptic sampling of soft tissue tumors (STT) compared with unenhanced ultrasonography alone. This is a prospective longitudinal study of 40 patients subjected to ultrasonography (US)-guided core needle biopsy (CNB) to characterize a suspected STT. Three series of bioptic samplings were carried out on each patient, respectively using unenhanced US alone and CEUS in both the areas of the tumor enhanced or not by the contrast medium. All bioptic samples underwent a histological evaluation and the results were analyzed by comparing the histology of the biopsy with the definitive diagnosis in 15 surgically excised samples. 27 (67.5 %) of the 40 patients completed the entire study procedure; in 19 cases (70.3 %) the three bioptic samplings gave unanimous results, also when compared to the surgical specimen; in seven cases (25.9 %) use of CEUS allowed to obtain additional or more accurate information about the mass in question, compared to simple US guidance without contrast; in one patient (3.7 %) sampling obtained using unenhanced ultrasonography guidance and in the areas enhanced by the contrast agent had precisely the same results of the surgical specimen. CEUS, due to its ability to evaluate microvascular areas, has proven to be a promising method in guiding bioptic sampling of soft tissue tumor, directing the needle to the most significant areas of the tumor. Given the small number of patients evaluated in our study, to achieve statistically significant results, it would be appropriate to obtain a larger sample size, since the very first results seem to be encouraging and to justify the increase of the population.

Evaluation of Two Surface Sampling Methods for Detection of Erwinia herbicola on a Variety of Materials by Culture and Quantitative PCR▿

PubMed Central

Buttner, Mark P.; Cruz, Patricia; Stetzenbach, Linda D.; Cronin, Tracy

2007-01-01

This research was designed to evaluate surface sampling protocols for use with culture and quantitative PCR (QPCR) amplification assay for detection of the gram-negative bacterial biothreat simulant Erwinia herbicola on a variety of surface materials. Surfaces selected for evaluation were wood laminate, glass and computer monitor screens, metal file cabinets, plastic arena seats, nylon seat cushions, finished concrete flooring, and vinyl tile flooring. Laboratory and test chamber studies were performed to evaluate two sampling methods, a sponge and a macrofoam swab, for detection of E. herbicola on surface materials. In laboratory trials, seven materials were inoculated with a known concentration of E. herbicola cells and samples were collected from the surfaces of the materials to determine sampling efficiencies. Culture analysis was ineffective for assessing E. herbicola collection efficiency because very few culturable cells were obtained from surface samples. QPCR demonstrated that E. herbicola DNA was present in high concentrations on all of the surface samples, and sampling efficiencies ranged from 0.7 to 52.2%, depending on the sampling method and the surface material. The swab was generally more efficient than the sponge for collection of E. herbicola from surfaces. Test chamber trials were also performed in which E. herbicola was aerosolized into the chamber and allowed to settle onto test materials. Surface sampling results supported those obtained in laboratory trials. The results of this study demonstrate the capabilities of QPCR to enhance the detection and enumeration of biocontaminants on surface materials and provide information on the comparability of sampling methods. PMID:17416685

Evaluation of two surface sampling methods for detection of Erwinia herbicola on a variety of materials by culture and quantitative PCR.

PubMed

Buttner, Mark P; Cruz, Patricia; Stetzenbach, Linda D; Cronin, Tracy

2007-06-01

This research was designed to evaluate surface sampling protocols for use with culture and quantitative PCR (QPCR) amplification assay for detection of the gram-negative bacterial biothreat simulant Erwinia herbicola on a variety of surface materials. Surfaces selected for evaluation were wood laminate, glass and computer monitor screens, metal file cabinets, plastic arena seats, nylon seat cushions, finished concrete flooring, and vinyl tile flooring. Laboratory and test chamber studies were performed to evaluate two sampling methods, a sponge and a macrofoam swab, for detection of E. herbicola on surface materials. In laboratory trials, seven materials were inoculated with a known concentration of E. herbicola cells and samples were collected from the surfaces of the materials to determine sampling efficiencies. Culture analysis was ineffective for assessing E. herbicola collection efficiency because very few culturable cells were obtained from surface samples. QPCR demonstrated that E. herbicola DNA was present in high concentrations on all of the surface samples, and sampling efficiencies ranged from 0.7 to 52.2%, depending on the sampling method and the surface material. The swab was generally more efficient than the sponge for collection of E. herbicola from surfaces. Test chamber trials were also performed in which E. herbicola was aerosolized into the chamber and allowed to settle onto test materials. Surface sampling results supported those obtained in laboratory trials. The results of this study demonstrate the capabilities of QPCR to enhance the detection and enumeration of biocontaminants on surface materials and provide information on the comparability of sampling methods.

Enhancement of problem solving ability of high school students through learning with real engagement in active problem solving (REAPS) model on the concept of heat transfer

NASA Astrophysics Data System (ADS)

Yulindar, A.; Setiawan, A.; Liliawati, W.

2018-05-01

This study aims to influence the enhancement of problem solving ability before and after learning using Real Engagement in Active Problem Solving (REAPS) model on the concept of heat transfer. The research method used is quantitative method with 35 high school students in Pontianak as sample. The result of problem solving ability of students is obtained through the test in the form of 3 description questions. The instrument has tested the validity by the expert judgment and field testing that obtained the validity value of 0.84. Based on data analysis, the value of N-Gain is 0.43 and the enhancement of students’ problem solving ability is in medium category. This was caused of students who are less accurate in calculating the results of answers and they also have limited time in doing the questions given.

[Monolithic column-gold composite substrate preparation and application to SERS detection of pigment].

PubMed

Xie, Yun-Fei; Li, Yan; Yu, Hui; Qian, He; Yao, Wei-Rong

2014-03-01

In the present study, we developed a novel SERS substrate with the porous monolith material combined with classic gold nanoparticles, and erythrosine as the research object, by adjusting the different experimental conditions for optimal SERS enhancements, including system pH and mixing time, and ultimately selected the optimum pH value 5.06 and mixing time 25 min. Compared with the traditional gold plastic substrate enhancement effect, the experimental conditions were applied to the monolith substrate SERS detection of dye erythrosine, different concentrations of samples were used for erythrosine SERS detection, and the detection limit reached 0.1 g x mL(-1). The method uses the payload of gold nanoparticles in mesoporous materials to effectively enhance the SERS signal. And this method has the advantages of simpleness and good stability, which provides a favorable theoretical basis for the rapid prohibited colorings screening.

Adsorption of NO on alumina-supported oxides and oxide-hydroxides of manganese.

PubMed

Spasova, I; Nikolov, P; Mehandjiev, D

2005-10-15

The adsorption capacity for NO of alumina-supported oxides and oxide-hydroxides of manganese have been studied. Two series of samples have been prepared by precipitation on gamma-alumina and appropriate thermal treatment. The samples have been characterized by adsorption methods, magnetic methods, electronic paramagnetic resonance (EPR), transient response technique, and temperature-programmed desorption (TPD). The influence of the concentration of the initial manganese-containing solution has been investigated. The sample, prepared with a solution with Mn concentration of 4 g/100 ml, has been shown to be the best adsorbent for NO under the conditions of the experiment. It has been found that the presence mainly of Mn3+ ions on the surface of the support is probably responsible for the enhanced adsorption capacity.

Convolutional neural network using generated data for SAR ATR with limited samples

NASA Astrophysics Data System (ADS)

Cong, Longjian; Gao, Lei; Zhang, Hui; Sun, Peng

2018-03-01

Being able to adapt all weather at all times, it has been a hot research topic that using Synthetic Aperture Radar(SAR) for remote sensing. Despite all the well-known advantages of SAR, it is hard to extract features because of its unique imaging methodology, and this challenge attracts the research interest of traditional Automatic Target Recognition(ATR) methods. With the development of deep learning technologies, convolutional neural networks(CNNs) give us another way out to detect and recognize targets, when a huge number of samples are available, but this premise is often not hold, when it comes to monitoring a specific type of ships. In this paper, we propose a method to enhance the performance of Faster R-CNN with limited samples to detect and recognize ships in SAR images.

Cloud point extraction and flame atomic absorption spectrometric determination of cadmium and nickel in drinking and wastewater samples.

PubMed

Naeemullah; Kazi, Tasneem G; Shah, Faheem; Afridi, Hassan I; Baig, Jameel Ahmed; Soomro, Abdul Sattar

2013-01-01

A simple method for the preconcentration of cadmium (Cd) and nickel (Ni) in drinking and wastewater samples was developed. Cloud point extraction has been used for the preconcentration of both metals, after formation of complexes with 8-hydroxyquinoline (8-HQ) and extraction with the surfactant octylphenoxypolyethoxyethanol (Triton X-114). Dilution of the surfactant-rich phase with acidified ethanol was performed after phase separation, and the Cd and Ni contents were measured by flame atomic absorption spectrometry. The experimental variables, such as pH, amounts of reagents (8-HQ and Triton X-114), temperature, incubation time, and sample volume, were optimized. After optimization of the complexation and extraction conditions, enhancement factors of 80 and 61, with LOD values of 0.22 and 0.52 microg/L, were obtained for Cd and Ni, respectively. The proposed method was applied satisfactorily for the determination of both elements in drinking and wastewater samples.

Optimization of a Viability PCR Method for the Detection of Listeria monocytogenes in Food Samples.

PubMed

Agustí, Gemma; Fittipaldi, Mariana; Codony, Francesc

2018-06-01

Rapid detection of Listeria and other microbial pathogens in food is an essential part of quality control and it is critical for ensuring the safety of consumers. Culture-based methods for detecting foodborne pathogens are time-consuming, laborious and cannot detect viable but non-culturable microorganism, whereas viability PCR methodology provides quick results; it is able to detect viable but non-culturable cells, and allows for easier handling of large amount of samples. Although the most critical point to use viability PCR technique is achieving the complete exclusion of dead cell amplification signals, many improvements are being introduced to overcome this. In the present work, the yield of dead cell DNA neutralization was enhanced by incorporating two new sample treatment strategies: tube change combined with a double light treatment. This procedure was successfully tested using artificially contaminated food samples, showing improved neutralization of dead cell DNA.

Emission spectrographic determination of volatile trace elements in geologic materials by a carrier distillation technique

USGS Publications Warehouse

Barton, H.N.

1986-01-01

Trace levels of chalcophile elements that form volatile sulfide minerals are determined in stream sediments and in the nonmagnetic fraction of a heavy-mineral concentrate of stream sediments by a carrier distillation emission spectrographic method. Photographically recorded spectra of samples are visually compared with those of synthetic standards for the two sample types. Rock and soil samples may also be analyzed by comparison with the stream-sediment standards. A gallium oxide spectrochemical carrier/buffer enhances the early emission of the volatile elements. Detection limits in parts per million attained are: Sb 5, As 20, Bi 0.1, Cd 1, Cu 1, Pb 2, Ag 0.1, Zn 2, and Sn 0.1. A comparison with other methods of analysis, total-burn emission and atomic absorption spectroscopy, shows good correlation for standard reference for materials and samples from a variety of geologic terranes. ?? 1986.

Variational Approach to Enhanced Sampling and Free Energy Calculations

NASA Astrophysics Data System (ADS)

Valsson, Omar; Parrinello, Michele

2014-08-01

The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

Enhanced room temperature ferromagnetism in Cr-doped ZnO nanoparticles prepared by auto-combustion method

NASA Astrophysics Data System (ADS)

Haq, Khizar-ul; Irfan, M.; Masood, Muhammad; Saleem, Murtaza; Iqbal, Tahir; Ahmad, Ishaq; Khan, M. A.; Zaffar, M.; Irfan, Muhammad

2018-04-01

Zn1‑x Cr x O (x = 0.00, 0.01, 0.03, 0.05, 0.07, and 0.09) nanoparticles were synthesized, by an auto-combustion method. Structural, optical, and magnetic characteristics of Cr-doped ZnO samples calcined at 600 °C have been analyzed by using X-ray diffraction (XRD), field emission scanning electron microscope (FESEM), UV–Vis spectroscopy and vibrating sample magnetometer (VSM). The XRD data confirmed the hexagonal wurtzite structure of pure and Cr-doped ZnO nanoparticles. The calculated values of grain size using Scherrer's formula are in the range of 30.7–9.2 nm. The morphology of nanopowders has been observed by FESEM, and EDS results confirmed a systematic increase of Cr content in the samples and clearly indicate with no impurity element. The band gaps, computed by UV–Vis spectroscopy, are in the range of 2.83–2.35 eV for different doping concentrations. By analyzing VSM data, significantly enhanced room temperature ferromagnetism is identified in Cr-doped ZnO samples. The value of magnetization is a 12 times increased of the value reported by Daunet al. (2010). Room temperature ferromagnetism of the nanoparticles is of vital prominence for spintronics applications. Project supported by the Office of Research, Innovation, and Commercialization (ORIC), MUST Mirpur (AJK).

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation.

PubMed

Kasahara, Kota; Sakuraba, Shun; Fukuda, Ikuo

2018-03-08

We investigate the problem of artifacts caused by the periodic boundary conditions (PBC) used in molecular simulation studies. Despite the long history of simulations with PBCs, the existence of measurable artifacts originating from PBCs applied to inherently nonperiodic physical systems remains controversial. Specifically, these artifacts appear as differences between simulations of the same system but with different simulation-cell sizes. Earlier studies have implied that, even in the simple case of a small model peptide in water, sampling inefficiency is a major obstacle to understanding these artifacts. In this study, we have resolved the sampling issue using the replica exchange molecular dynamics (REMD) enhanced-sampling method to explore PBC artifacts. Explicitly solvated zwitterionic polyalanine octapeptides with three different cubic-cells, having dimensions of L = 30, 40, and 50 Å, were investigated to elucidate the differences with 64 replica × 500 ns REMD simulations using the AMBER parm99SB force field. The differences among them were not large overall, and the results for the L = 30 and 40 Å simulations in the conformational free energy landscape were found to be very similar at room temperature. However, a small but statistically significant difference was seen for L = 50 Å. We observed that extended conformations were slightly overstabilized in the smaller systems. The origin of these artifacts is discussed by comparison to an electrostatic calculation method without PBCs.

Effect of microstructure on the thermoelectric performance of La{sub 1−x}Sr{sub x}CoO{sub 3}

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

Viskadourakis, Z.; Department of Mechanical and Manufacturing Engineering, University of Cypruss, 75 Kallipoleos Avenue, P.O. Box 20537, 1678 Nicosia; Athanasopoulos, G.I.

We present a case where the microstructure has a profound effect on the thermoelectric properties of oxide compounds. Specifically, we have investigated the effect of different sintering treatments on La{sub 1−x}Sr{sub x}CoO{sub 3} samples synthesized using the Pechini method. We found that the samples, which are dense and consist of inhomogeneously-mixed grains of different size, exhibit both higher Seebeck coefficient and thermoelectric figure of merit than the samples, which are porous and consist of grains with almost identical size. The enhancement of Seebeck coefficient in the dense samples is attributed to the so-called “energy-filtering” mechanism that is related to themore » energy barrier of the grain boundary. On the other hand, the thermal conductivity for the porous compounds is significantly reduced in comparison to the dense compounds. It is suggested that a fine-manipulation of grain size ratio combined with a fine-tuning of porosity could considerably enhance the thermoelectric performance of oxides. - Graphical abstract: The enhancement of the dimensionless thermoelectric figure ZT of merit is presented for two equally Sr-doped LaCoO3 compounds, possessing different microstructure, indicating the effect of the latter to the thermoelectric performance of the La{sub 1−x}Sr{sub x}CoO{sub 3} solid solution. - Highlights: • Electrical and thermal transport properties are affected by the microstructure in La{sub 1−x}Sr{sub x}CoO{sub 3} polycrystalline materials. • Coarse/fine grain size distribution enhances the Seebeck coefficient. • Porosity reduces the thermal conductivity in La{sub 1−x}Sr{sub x}CoO{sub 3} polycrystalline samples. • The combination of large/small grain ratio distribution with the high porosity may result to the enhancement of the thermoelectric performance of the material.« less

Using pseudoalignment and base quality to accurately quantify microbial community composition

PubMed Central

Novembre, John

2018-01-01

Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference. We also assess performance in real 16S data, where we reanalyze previous genetic association data to show our method discovers a larger number of quantitative trait associations than other widely used methods. We implement our method in the software Karp, for k-mer based analysis of read pools, to provide a novel combination of speed and accuracy that is uniquely suited for enhancing discoveries in microbial studies. PMID:29659582

Determination of refractive and volatile elements in sediment using laser ablation inductively coupled plasma mass spectrometry.

PubMed

Duodu, Godfred Odame; Goonetilleke, Ashantha; Allen, Charlotte; Ayoko, Godwin A

2015-10-22

Wet-milling protocol was employed to produce pressed powder tablets with excellent cohesion and homogeneity suitable for laser ablation (LA) analysis of volatile and refractive elements in sediment. The influence of sample preparation on analytical performance was also investigated, including sample homogeneity, accuracy and limit of detection. Milling in volatile solvent for 40 min ensured sample is well mixed and could reasonably recover both volatile (Hg) and refractive (Zr) elements. With the exception of Cr (-52%) and Nb (+26%) major, minor and trace elements in STSD-1 and MESS-3 could be analysed within ±20% of the certified values. Comparison of the method with total digestion method using HF was tested by analysing 10 different sediment samples. The laser method recovers significantly higher amounts of analytes such as Ag, Cd, Sn and Sn than the total digestion method making it a more robust method for elements across the periodic table. LA-ICP-MS also eliminates the interferences from chemical reagents as well as the health and safety risks associated with digestion processes. Therefore, it can be considered as an enhanced method for the analysis of heterogeneous matrices such as river sediments. Copyright © 2015 Elsevier B.V. All rights reserved.

Highly sensitive on-site detection of drugs adulterated in botanical dietary supplements using thin layer chromatography combined with dynamic surface enhanced Raman spectroscopy.

PubMed

Fang, Fang; Qi, Yunpeng; Lu, Feng; Yang, Liangbao

2016-01-01

The phenomenon of botanical dietary supplements (BDS) doped with illegal adulterants has become a serious problem all over the world, which could cause great threat to human's health. Therefore, it is of great value to identify BDS. Herein, we put forward a highly sensitive method for on-site detection of antitussive and antiasthmatic drugs adulterated in BDS using thin layer chromatography (TLC) combined with dynamic surface enhanced Raman spectroscopy (DSERS). Adulterants in BDS were separated on a TLC plate and located under UV illumination. Then DSERS detection was performed using a portable Raman spectrometer with 50% glycerol silver colloid serving as DSERS active substrate. Here, the effects of different solvents on detection efficacy were evaluated using phenformin hydrochloride (PHE) as a probe. It was shown that 50% glycerol resulted in higher SERS enhancement and relatively higher stability. Moreover, practical application of this novel TLC-DSERS method was demonstrated with rapid analysis of real BDS samples and one sample adulterated with benproperine phosphate (BEN) was found. Furthermore, the obtained result was verified by ultra performance liquid chromatography-quadrupole time of flight mass spectrometry (UPLC-QTOF/MS). The sensitivity of the TLC-DSERS technique is 1-2 orders of magnitude higher than that of TLC-SERS technique. The results turned out that this combined method would have good prospects for on-site and sensitive detection of adulterated BDS. Copyright © 2015 Elsevier B.V. All rights reserved.

Real-time spectrum estimation–based dual-channel speech-enhancement algorithm for cochlear implant

PubMed Central

2012-01-01

Background Improvement of the cochlear implant (CI) front-end signal acquisition is needed to increase speech recognition in noisy environments. To suppress the directional noise, we introduce a speech-enhancement algorithm based on microphone array beamforming and spectral estimation. The experimental results indicate that this method is robust to directional mobile noise and strongly enhances the desired speech, thereby improving the performance of CI devices in a noisy environment. Methods The spectrum estimation and the array beamforming methods were combined to suppress the ambient noise. The directivity coefficient was estimated in the noise-only intervals, and was updated to fit for the mobile noise. Results The proposed algorithm was realized in the CI speech strategy. For actual parameters, we use Maxflat filter to obtain fractional sampling points and cepstrum method to differentiate the desired speech frame and the noise frame. The broadband adjustment coefficients were added to compensate the energy loss in the low frequency band. Discussions The approximation of the directivity coefficient is tested and the errors are discussed. We also analyze the algorithm constraint for noise estimation and distortion in CI processing. The performance of the proposed algorithm is analyzed and further be compared with other prevalent methods. Conclusions The hardware platform was constructed for the experiments. The speech-enhancement results showed that our algorithm can suppresses the non-stationary noise with high SNR. Excellent performance of the proposed algorithm was obtained in the speech enhancement experiments and mobile testing. And signal distortion results indicate that this algorithm is robust with high SNR improvement and low speech distortion. PMID:23006896

Anisotropic tubular filtering for automatic detection of acid-fast bacilli in Ziehl-Neelsen stained sputum smear samples

NASA Astrophysics Data System (ADS)

Raza, Shan-e.-Ahmed; Marjan, M. Q.; Arif, Muhammad; Butt, Farhana; Sultan, Faisal; Rajpoot, Nasir M.

2015-03-01

One of the main factors for high workload in pulmonary pathology in developing countries is the relatively large proportion of tuberculosis (TB) cases which can be detected with high throughput using automated approaches. TB is caused by Mycobacterium tuberculosis, which appears as thin, rod-shaped acid-fast bacillus (AFB) in Ziehl-Neelsen (ZN) stained sputum smear samples. In this paper, we present an algorithm for automatic detection of AFB in digitized images of ZN stained sputum smear samples under a light microscope. A key component of the proposed algorithm is the enhancement of raw input image using a novel anisotropic tubular filter (ATF) which suppresses the background noise while simultaneously enhancing strong anisotropic features of AFBs present in the image. The resulting image is then segmented using color features and candidate AFBs are identified. Finally, a support vector machine classifier using morphological features from candidate AFBs decides whether a given image is AFB positive or not. We demonstrate the effectiveness of the proposed ATF method with two different feature sets by showing that the proposed image analysis pipeline results in higher accuracy and F1-score than the same pipeline with standard median filtering for image enhancement.

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

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

Xiong, Weili; Richard J. Giannone; Morowitz, Michael J.

The early-life microbiota establishment in the human infant gut is highly variable and plays a crucial role in host nutrients and immunity maturation. While high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the construction of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on Double Filtering (DF) to enhance microbial protein characterization in complex fecal samples from healthy premature infants. We improved the overall depth of infant gut proteome measurement, withmore » an increase in the number of identified low abundance proteins, and observed greater than twofold improvement in metrics for microbial protein identifications and quantifications with a relatively high rank correlation to control. We further showed the substantial enhancement of this approach for extensively interpreting microbial functional categories between infants by affording more detailed and confident identified categories. This approach provided an avenue for in-depth measurement in the microbial component of infant fecal samples and thus comprehensive characterization of infant gut microbiome functionality.« less

Upconversion improvement in KLaF4:Yb3+/Er3+ nanoparticles by doping Al3+ ions

NASA Astrophysics Data System (ADS)

Zhou, Haifang; Wang, Xiechun; Lai, Yunfeng; Cheng, Shuying; Zheng, Qiao; Yu, Jinlin

2017-10-01

Rare-earth ion-doped upconversion (UC) materials show great potential applications in optical and optoelectronic devices due to their novel optical properties. In this work, hexagonal KLaF4:Yb3+/Er3+ nanoparticles (NPs) were successfully synthesized by a hydrothermal method, and remarkably enhanced upconversion luminescence in green and red emission bands in KLaF4:Yb3+/Er3+ NPs has been achieved by doping Al3+ ions under 980 nm excitation. Compared to the aluminum-free KLaF4:Yb3+/Er3+ NPs sample, the UC fluorescence intensities of the green and red emissions of NPs doped with 10 at.% Al3+ ions were significantly enhanced by 5.9 and 7.3 times, respectively. Longer lifetimes of the doped samples were observed for the 4S3/2 state and 4F9/2 state. The underlying reason for the UC enhancement by doping Al3+ ions was mainly ascribed to distortion of the local symmetry around Er3+ ions and adsorption reduction of organic ligands on the surface of NPs. In addition, the influence of doping Al3+ ions on the structure and morphology of the NPs samples was also discussed.

Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut

DOE PAGES

Xiong, Weili; Richard J. Giannone; Morowitz, Michael J.; ...

2014-10-28

The early-life microbiota establishment in the human infant gut is highly variable and plays a crucial role in host nutrients and immunity maturation. While high-performance mass spectrometry (MS)-based metaproteomics is a powerful method for the functional characterization of complex microbial communities, the construction of comprehensive metaproteomic information in human fecal samples is inhibited by the presence of abundant human proteins. To alleviate this restriction, we have designed a novel metaproteomic strategy based on Double Filtering (DF) to enhance microbial protein characterization in complex fecal samples from healthy premature infants. We improved the overall depth of infant gut proteome measurement, withmore » an increase in the number of identified low abundance proteins, and observed greater than twofold improvement in metrics for microbial protein identifications and quantifications with a relatively high rank correlation to control. We further showed the substantial enhancement of this approach for extensively interpreting microbial functional categories between infants by affording more detailed and confident identified categories. This approach provided an avenue for in-depth measurement in the microbial component of infant fecal samples and thus comprehensive characterization of infant gut microbiome functionality.« less

Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design.

PubMed

Sinko, William; Lindert, Steffen; McCammon, J Andrew

2013-01-01

Protein flexibility plays a major role in biomolecular recognition. In many cases, it is not obvious how molecular structure will change upon association with other molecules. In proteins, these changes can be major, with large deviations in overall backbone structure, or they can be more subtle as in a side-chain rotation. Either way the algorithms that predict the favorability of biomolecular association require relatively accurate predictions of the bound structure to give an accurate assessment of the energy involved in association. Here, we review a number of techniques that have been proposed to accommodate receptor flexibility in the simulation of small molecules binding to protein receptors. We investigate modifications to standard rigid receptor docking algorithms and also explore enhanced sampling techniques, and the combination of free energy calculations and enhanced sampling techniques. The understanding and allowance for receptor flexibility are helping to make computer simulations of ligand protein binding more accurate. These developments may help improve the efficiency of drug discovery and development. Efficiency will be essential as we begin to see personalized medicine tailored to individual patients, which means specific drugs are needed for each patient's genetic makeup. © 2012 John Wiley & Sons A/S.

3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography

Treesearch

Michael C. Martin; Charlotte Dabat-Blondeau; Miriam Unger; Julia Sedlmair; Dilworth Y. Parkinson; Hans A. Bechtel; Barbara Illman; Jonathan M. Castro; Marco Keiluweit; David Buschke; Brenda Ogle; Michael J. Nasse; Carol J. Hirschmugl

2013-01-01

We report Fourier transform infrared spectro-microtomography, a nondestructive three-dimensional imaging approach that reveals the distribution of distinctive chemical compositions throughout an intact biological or materials sample. The method combines mid-infrared absorption contrast with computed tomographic data acquisition and reconstruction to enhance chemical...

Structured-illumination reflectance imaging for enhanced detection of subsurface tissue bruising in apples

USDA-ARS?s Scientific Manuscript database

In this research, a novel method of fresh bruise detection was developed using a structured illumination reflectance imaging (SIRI) system. The SIRI system projects sinusoidal patterns of illumination onto samples, and image demodulation is then used to recover depth-specific information through var...

Using National Coastal Condition Assessment Underwater Video to Investigate Nearshore Substrate Type

EPA Science Inventory

A comprehensive method for describing bottom types in Great Lakes nearshore regions (<30 m deep and <5 km from shore) would enhance our ability to target monitoring efforts. Dredges are ineffective at sampling hard bottoms (bedrock/boulder/cobble) and other habitat features. We a...

Enhancing Creative Thinking through Designing Electronic Slides

ERIC Educational Resources Information Center

Mokaram, Al-Ali Khaled; Al-Shabatat, Ahmad Mohammad; Fong, Fook Soon; Abdallah, Andaleeb Ahmad

2011-01-01

During the shifting of teaching and learning methods using computer technologies, much emphasis was paid on the knowledge content more than the thinking skills. Thus, this study investigated the effects of a computer application, namely, designing electronic slides on the development of creative thinking skills of a sample of undergraduate…

Room temperature synthesis and highly enhanced visible light photocatalytic activity of porous BiOI/BiOCl composites nanoplates microflowers.

PubMed

Dong, Fan; Sun, Yanjuan; Fu, Min; Wu, Zhongbiao; Lee, S C

2012-06-15

This research represents a highly enhanced visible light photocatalytic removal of 450 ppb level of nitric oxide (NO) in air by utilizing flower-like hierarchical porous BiOI/BiOCl composites synthesized by a room temperature template free method for the first time. The facile synthesis method avoids high temperature treatment, use of organic precursors and production of undesirable organic byproducts during synthesis process. The result indicated that the as-prepared BiOI/BiOCl composites samples were solid solution and were self-assembled hierarchically with single-crystal nanoplates. The aggregation of the self-assembled nanoplates resulted in the formation of 3D hierarchical porous architecture containing tri-model mesopores. The coupling to BiOI with BiOCl led to down-lowered valence band (VB) and up-lifted conduction band (CB) in contrast to BiOI, making the composites suitable for visible light excitation. The BiOI/BiOCl composites samples exhibited highly enhanced visible light photocatalytic activity for removal of NO in air due to the large surface areas and pore volume, hierarchical structure and modified band structure, exceeding that of P25, BiOI, C-doped TiO(2) and Bi(2)WO(6). This research results could provide a cost-effective approach for the synthesis of porous hierarchical materials and enhancement of photocatalyst performance for environmental and energetic applications owing to its low cost and easy scaling up. Copyright © 2012 Elsevier B.V. All rights reserved.

RAPID SEPARATION METHOD FOR EMERGENCY WATER AND URINE SAMPLES

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

Maxwell, S.; Culligan, B.

2008-08-27

The Savannah River Site Environmental Bioassay Lab participated in the 2008 NRIP Emergency Response program administered by the National Institute for Standards and Technology (NIST) in May, 2008. A new rapid column separation method was used for analysis of actinides and {sup 90}Sr the NRIP 2008 emergency water and urine samples. Significant method improvements were applied to reduce analytical times. As a result, much faster analysis times were achieved, less than 3 hours for determination of {sup 90}Sr and 3-4 hours for actinides. This represents a 25%-33% improvement in analysis times from NRIP 2007 and a {approx}100% improvement compared tomore » NRIP 2006 report times. Column flow rates were increased by a factor of two, with no significant adverse impact on the method performance. Larger sample aliquots, shorter count times, faster cerium fluoride microprecipitation and streamlined calcium phosphate precipitation were also employed. Based on initial feedback from NIST, the SRS Environmental Bioassay Lab had the most rapid analysis times for actinides and {sup 90}Sr analyses for NRIP 2008 emergency urine samples. High levels of potential matrix interferences may be present in emergency samples and rugged methods are essential. Extremely high levels of {sup 210}Po were found to have an adverse effect on the uranium results for the NRIP-08 urine samples, while uranium results for NRIP-08 water samples were not affected. This problem, which was not observed for NRIP-06 or NRIP-07 urine samples, was resolved by using an enhanced {sup 210}Po removal step, which will be described.« less

Feasibility of Using Gluconolactone, Trehalose and Hydroxy-Propyl Gamma Cyclodextrin to Enhance Bendroflumethiazide Dissolution Using Lyophilisation and Physical Mixing Techniques.

PubMed

Saleh, Ashraf; McGarry, Kenneth; Chaw, Cheng Shu; Elkordy, Amal Ali

2018-02-01

Hydrophobic drugs are facing a major challenge in dissolution rate enhancement and solubility in aqueous solutions; therefore, a variety of methods have been used to improve dissolution rate and/or solubility of bendroflumethiazide as a model hydrophobic drug. In this study, two main methods (physical mixing and lyophilisation) were used with gluconolactone, hydroxyl propyl γ-ccyclodextrin, and trehalose to explore this challenge. Bendroflumethiazide, practically insoluble in water, was mixed with one of the three excipients gluconolactone, hydroxyl propyl γ-cyclodextrin, and trehalose in three different ratios 1:1, 1:2, 1:5. To the best of our knowledge, the dissolution of the drug has not been previously enhanced by using either these methods or any of the used excipients. Samples containing drug and each of the excipients were characterized via dissolution testing, Fourier Transform infra-red spectroscopy, differential scanning calorimetry, and scanning electron microscopy. The used methods showed a significant enhancement in dug dissolution rate; physical mixing significantly, p < 0.05, increased the percentage of the drug released with time; for example, bendroflumethiazide dissolution in distilled water was improved from less than 20% to 99.79% within 90 min for physically mixed drug-cyclodextrin 1:5. The lyophilisation process was enhanced and the drug dissolution rate and the highest drug dissolution was achieved for (drug-gluconolactone 1:1) with 98.98% drug release within 90 min. the physical mixing and freeze drying processes significantly increased the percentage of drug release with time.

Determination of pharmaceutical compounds in surface- and ground-water samples by solid-phase extraction and high-performance liquid chromatography-electrospray ionization mass spectrometry

USGS Publications Warehouse

Cahill, J.D.; Furlong, E.T.; Burkhardt, M.R.; Kolpin, D.; Anderson, L.G.

2004-01-01

Commonly used prescription and over-the-counter pharmaceuticals are possibly present in surface- and ground-water samples at ambient concentrations less than 1 μg/L. In this report, the performance characteristics of a combined solid-phase extraction isolation and high-performance liquid chromatography–electrospray ionization mass spectrometry (HPLC–ESI-MS) analytical procedure for routine determination of the presence and concentration of human-health pharmaceuticals are described. This method was developed and used in a recent national reconnaissance of pharmaceuticals in USA surface waters. The selection of pharmaceuticals evaluated for this method was based on usage estimates, resulting in a method that contains compounds from diverse chemical classes, which presents challenges and compromises when applied as a single routine analysis. The method performed well for the majority of the 22 pharmaceuticals evaluated, with recoveries greater than 60% for 12 pharmaceuticals. The recoveries of angiotensin-converting enzyme inhibitors, a histamine (H2) receptor antagonist, and antihypoglycemic compound classes were less than 50%, but were retained in the method to provide information describing the potential presence of these compounds in environmental samples and to indicate evidence of possible matrix enhancing effects. Long-term recoveries, evaluated from reagent-water fortifications processed over 2 years, were similar to initial method performance. Method detection limits averaged 0.022 μg/L, sufficient for expected ambient concentrations. Compound-dependent matrix effects on HPLC/ESI-MS analysis, including enhancement and suppression of ionization, were observed as a 20–30% increase in measured concentrations for three compounds and greater than 50% increase for two compounds. Changing internal standard and more frequent ESI source maintenance minimized matrix effects. Application of the method in the national survey demonstrates that several pharmaceuticals are routinely detected at 0.010–0.100 μg/L concentrations.

Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.

PubMed

Chodera, John D; Shirts, Michael R

2011-11-21

The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in discovering new ways to enhance the phase space mixing of these protocols in order to improve sampling of uncorrelated configurations. Here, we demonstrate how both of these classes of algorithms can be considered as special cases of Gibbs sampling within a Markov chain Monte Carlo framework. Gibbs sampling is a well-studied scheme in the field of statistical inference in which different random variables are alternately updated from conditional distributions. While the update of the conformational degrees of freedom by Metropolis Monte Carlo or molecular dynamics unavoidably generates correlated samples, we show how judicious updating of the thermodynamic state indices--corresponding to thermodynamic parameters such as temperature or alchemical coupling variables--can substantially increase mixing while still sampling from the desired distributions. We show how state update methods in common use can lead to suboptimal mixing, and present some simple, inexpensive alternatives that can increase mixing of the overall Markov chain, reducing simulation times necessary to obtain estimates of the desired precision. These improved schemes are demonstrated for several common applications, including an alchemical expanded ensemble simulation, parallel tempering, and multidimensional replica exchange umbrella sampling.

The holy grail of soil metal contamination site assessment: reducing risk and increasing confidence of decision making using infield portable X-ray Fluorescence (pXRF) technology

NASA Astrophysics Data System (ADS)

Rouillon, M.; Taylor, M. P.; Dong, C.

2016-12-01

This research assesses the advantages of integrating field portable X-ray Fluorescence (pXRF) technology for reducing the risk and increase confidence of decision making for metal-contaminated site assessments. Metal-contaminated sites are often highly heterogeneous and require a high sampling density to accurately characterize the distribution and concentration of contaminants. The current regulatory assessment approaches rely on a small number of samples processed using standard wet-chemistry methods. In New South Wales (NSW), Australia, the current notification trigger for characterizing metal-contaminated sites require the upper 95% confidence interval of the site mean to equal or exceed the relevant guidelines. The method's low `minimum' sampling requirements can misclassify sites due to the heterogeneous nature of soil contamination, leading to inaccurate decision making. To address this issue, we propose integrating infield pXRF analysis with the established sampling method to overcome sampling limitations. This approach increases the minimum sampling resolution and reduces the 95% CI of the site mean. Infield pXRF analysis at contamination hotspots enhances sample resolution efficiently and without the need to return to the site. In this study, the current and proposed pXRF site assessment methods are compared at five heterogeneous metal-contaminated sites by analysing the spatial distribution of contaminants, 95% confidence intervals of site means, and the sampling and analysis uncertainty associated with each method. Finally, an analysis of costs associated with both the current and proposed methods is presented to demonstrate the advantages of incorporating pXRF into metal-contaminated site assessments. The data shows that pXRF integrated site assessments allows for faster, cost-efficient, characterisation of metal-contaminated sites with greater confidence for decision making.

Enhanced kinetics of Al{sub 0.97}Ga{sub 0.03}As wet oxidation through the use of hydrogenation

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

Le Du, M.; Sagnes, I.; Beaudoin, G.

2006-09-11

This letter reports on a different kinetic behavior of the wet thermal oxidation process resulting in Al{sub x}O{sub y} material depending on the AlAs material growth method, molecular beam epitaxy (MBE) or metal organic vapor phase epitaxy (MOVPE). A higher oxidation rate for MOVPE-grown materia is systemically found. Considering the major role of hydrogen in the wet oxidation reaction, it is believed this observation could be linked with the higher hydrogen residual concentration in MOVPE layers. Using a hydrogen plasma, MBE-grown Al{sub 0.97}Ga{sub 0.03}As layers were hydrogened prior to oxidation. This hydrogenated sample showed a ten times enhanced oxidation ratemore » as compared to the nonhydrogenated Al{sub 0.97}Ga{sub 0.03}As sample. This behavior is mainly attributed to a hydrogen induced modification of the diffusion limited regime, enhancing the diffusion length of oxidizing species and reaction products in the oxidized layers.« less

Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

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

Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun

In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO- d 6) and hexamethylphosphoramide (HMPA- d 18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO- d 6/HMPA-d 18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass,more » facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less

Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

DOE PAGES

Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; ...

2016-04-26

In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO- d 6) and hexamethylphosphoramide (HMPA- d 18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO- d 6/HMPA-d 18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass,more » facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less

The synthesis of four-layer gold-silver-polymer-silver core-shell nanomushroom with inbuilt Raman molecule for surface-enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Jiang, Tao; Wang, Xiaolong; Zhou, Jun

2017-12-01

A facial two-step reduction method was proposed to synthesize four-layer gold-silver-polymer-silver (Au@Ag@PSPAA@Ag) core-shell nanomushrooms (NMs) with inbuilt Raman molecule. The surface-enhanced Raman scattering (SERS) intensity of 4MBA adhered on the surface of Au core gradually increased with the modification of middle Ag shell and then Ag mushroom cap due to the formation of two kinds of ultra-small interior nanogap. Compared with the initial Au nanoparticles, the SERS enhancement ratio of the Au@Ag@PSPAA@Ag NMs approached to nearly 40. The novel core-shell NMs also exhibited homogeneous SERS signals for only one sample and reproducible signals for 10 different samples, certified by the low relative standard deviation values of less than 10% and 15% for the character peaks of 4-mercaptobenzoic acid, respectively. Such a novel four-layer core-shell nanostructure with reliable SERS performance has great potential application in quantitative SERS-based immunoassay.

Elucidating Structural Characteristics of Biomass using Solution-State 2 D NMR with a Mixture of Deuterated Dimethylsulfoxide and Hexamethylphosphoramide.

PubMed

Yoo, Chang Geun; Pu, Yunqiao; Li, Mi; Ragauskas, Arthur J

2016-05-23

Recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6 ) and hexamethylphosphoramide (HMPA-d18 ). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. The structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6 /HMPA-d18 ; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. It also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Room-temperature in situ nuclear spin hyperpolarization from optically pumped nitrogen vacancy centres in diamond

DOE PAGES

King, Jonathan P.; Jeong, Keunhong; Vassiliou, Christophoros C.; ...

2015-12-07

Low detection sensitivity stemming from the weak polarization of nuclear spins is a primary limitation of magnetic resonance spectroscopy and imaging. Methods have been developed to enhance nuclear spin polarization but they typically require high magnetic fields, cryogenic temperatures or sample transfer between magnets. Here we report bulk, room-temperature hyperpolarization of 13C nuclear spins observed via high-field magnetic resonance. The technique harnesses the high optically induced spin polarization of diamond nitrogen vacancy centres at room temperature in combination with dynamic nuclear polarization. We observe bulk nuclear spin polarization of 6%, an enhancement of ~170,000 over thermal equilibrium. The signal ofmore » the hyperpolarized spins was detected in situ with a standard nuclear magnetic resonance probe without the need for sample shuttling or precise crystal orientation. In conclusion, hyperpolarization via optical pumping/dynamic nuclear polarization should function at arbitrary magnetic fields enabling orders of magnitude sensitivity enhancement for nuclear magnetic resonance of solids and liquids under ambient conditions.« less

Determination of sulpiride in pharmaceutical preparations and biological fluids using a Cr (III) enhanced chemiluminescence method.

PubMed

Khan, Muhammad Naeem; Jan, Muhammad Rasul; Shah, Jasmin; Lee, Sang Hak; Kim, Young Ho

2013-01-01

A highly sensitive and simple method for identifying sulpiride in pharmaceutical formulations and biological fluids is presented. The method is based on increased chemiluminescence (CL) intensity of a luminol-H2O2 system in response to the addition of Cr (III) under alkaline conditions. The CL intensity of the luminol-H2O2-Cr (III) system was greatly enhanced by the addition of sulpiride and the CL intensity was proportional to the concentration of sulpiride in a sample solution. Various parameters affecting the CL intensity were systematically investigated and optimized for determination of the sulpiride in a sample. Under the optimum conditions, the CL intensity was proportional to the concentration of sulpiride in the range of 0.068-4.0 µg/mL, with a good correlation coefficient of 0.997. The limit of detection (LOD) and limit of quantification (LOQ) were found to be 8.50 × 10(-6) µg/mL and 2.83 × 10(-5) µg/mL, respectively. The method presented here produced good reproducibility with a relative standard deviation (RSD) of 2.70% (n = 7). The effects of common excipients and metal ions were studied for their interference effect. The method was validated statistically through recovery studies and successfully applied for the determination of sulpiride in pure form, pharmaceutical preparations and spiked human plasma samples. The percentage recoveries were found to range from 99.10 to 100.05% for pure form, 98.12 to 100.18% for pharmaceutical preparations and 97.9 to 101.4% for spiked human plasma. Copyright © 2012 John Wiley & Sons, Ltd.

Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy

NASA Astrophysics Data System (ADS)

Zheng, Lianqing; Yang, Wei

2008-07-01

Recently, accelerated molecular dynamics (AMD) technique was generalized to realize essential energy space random walks so that further sampling enhancement and effective localized enhanced sampling could be achieved. This method is especially meaningful when essential coordinates of the target events are not priori known; moreover, the energy space metadynamics method was also introduced so that biasing free energy functions can be robustly generated. Despite the promising features of this method, due to the nonequilibrium nature of the metadynamics recursion, it is challenging to rigorously use the data obtained at the recursion stage to perform equilibrium analysis, such as free energy surface mapping; therefore, a large amount of data ought to be wasted. To resolve such problem so as to further improve simulation convergence, as promised in our original paper, we are reporting an alternate approach: the adaptive-length self-healing (ALSH) strategy for AMD simulations; this development is based on a recent self-healing umbrella sampling method. Here, the unit simulation length for each self-healing recursion is increasingly updated based on the Wang-Landau flattening judgment. When the unit simulation length for each update is long enough, all the following unit simulations naturally run into the equilibrium regime. Thereafter, these unit simulations can serve for the dual purposes of recursion and equilibrium analysis. As demonstrated in our model studies, by applying ALSH, both fast recursion and short nonequilibrium data waste can be compromised. As a result, combining all the data obtained from all the unit simulations that are in the equilibrium regime via the weighted histogram analysis method, efficient convergence can be robustly ensured, especially for the purpose of free energy surface mapping.

Comparison of linear and nonlinear implementation of the compartmental tissue uptake model for dynamic contrast-enhanced MRI.

PubMed

Kallehauge, Jesper F; Sourbron, Steven; Irving, Benjamin; Tanderup, Kari; Schnabel, Julia A; Chappell, Michael A

2017-06-01

Fitting tracer kinetic models using linear methods is much faster than using their nonlinear counterparts, although this comes often at the expense of reduced accuracy and precision. The aim of this study was to derive and compare the performance of the linear compartmental tissue uptake (CTU) model with its nonlinear version with respect to their percentage error and precision. The linear and nonlinear CTU models were initially compared using simulations with varying noise and temporal sampling. Subsequently, the clinical applicability of the linear model was demonstrated on 14 patients with locally advanced cervical cancer examined with dynamic contrast-enhanced magnetic resonance imaging. Simulations revealed equal percentage error and precision when noise was within clinical achievable ranges (contrast-to-noise ratio >10). The linear method was significantly faster than the nonlinear method, with a minimum speedup of around 230 across all tested sampling rates. Clinical analysis revealed that parameters estimated using the linear and nonlinear CTU model were highly correlated (ρ ≥ 0.95). The linear CTU model is computationally more efficient and more stable against temporal downsampling, whereas the nonlinear method is more robust to variations in noise. The two methods may be used interchangeably within clinical achievable ranges of temporal sampling and noise. Magn Reson Med 77:2414-2423, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Matrix-enhanced degradation of p,p'-DDT during gas chromatographic analysis: A consideration

USGS Publications Warehouse

Foreman, W.T.; Gates, Paul M.

1997-01-01

Analysis of p,p‘-DDT in environmental samples requires monitoring the GC-derived breakdown of this insecticide, which produces p,p‘-DDD and/or p,p‘-DDE, both also primary environmental degradation products. A performance evaluation standard (PES) containing p,p‘-DDT but notp,p‘-DDD or p,p‘-DDE can be injected at regular intervals throughout an analytical sequence to monitor GC degradation. Some U.S. EPA methods limit GC breakdown of DDT in the PES to ≤20%. GC/MS analysis of large-volume natural water samples fortified with deuterium- and 13C-labeled p,p‘-DDT exhibited up to 65% DDT breakdown by the GC inlet. These matrix-enhanced GC degradation amounts substantially exceeded the <20% breakdown levels indicated by bracketing injections of the PES containing unlabeled and labeled DDT. Substantial matrix-enhanced GC degradation was not observed during analysis of a limited number of fractionated bed-sediment extracts containing labeled DDT. Use of isotopically labeled DDT seems to provide an effective tool for monitoring sample-specific DDT breakdown during GC/MS analysis. However, analyte co-elutions render impractical their use in GC/ECD analysis. The oc currence of matrix-enhanced GC degradation might have important implications on data quality and the resultant interpretations of the environmental degradation of DDT and other thermolabile contaminants.

Polyaniline-coated cigarette filters as a solid-phase extraction sorbent for the extraction and enrichment of polycyclic aromatic hydrocarbon in water samples.

PubMed

Bunkoed, Opas; Rueankaew, Thanaschaphorn; Nurerk, Piyaluk; Kanatharana, Proespichaya

2016-06-01

Polyaniline coated cigarette filters were successfully synthesized and used as a solid-phase extraction sorbent for the extraction and preconcentration of polycyclic aromatic hydrocarbons in water samples. The polyaniline helped to enhance the adsorption ability of polycyclic aromatic hydrocarbons on the sorbent through π-π interactions. The high porosity and large surface area of the cigarette filters helped to reduce backpressure and can be operated with high sample flow rate without loss of extraction efficiency. The developed sorbent was characterized by Fourier transform infrared spectroscopy and scanning electron microscopy. The parameters that affected the extraction efficiencies, i.e. polymerization time, type of desorption solvent and its volume, sample flow rate, sample volume, sample pH, ionic strength, and organic modifier were investigated. Under the optimal conditions, the method was linear over the range of 0.5-10 μg/L and a detection limit of 0.5 ng/L. This simple, rapid, and cost-effective method was successfully applied to the preconcentration of polycyclic aromatic hydrocarbons from water samples. The developed method provided a high enrichment factor with good extraction efficiency (85-98%) and a relative standard deviation <10%. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Novel hybrid cryo-radial method: an emerging alternative to CT-guided biopsy in suspected lung cancer. A prospective case series and description of technique.

PubMed

Herath, Samantha; Yap, Elaine

2018-02-01

In diagnosing peripheral pulmonary lesions (PPL), radial endobronchial ultrasound (R-EBUS) is emerging as a safer method in comparison to CT-guided biopsy. Despite the better safety profile, the yield of R-EBUS remains lower (73%) than CT-guided biopsy (90%) due to the smaller size of samples. We adopted a hybrid method by adding cryobiopsy via the R-EBUS Guide Sheath (GS) to produce larger, non-crushed samples to improve diagnostic capability and enhance molecular testing. We report six prospective patients who underwent this procedure in our institution. R-EBUS samples were obtained via conventional sampling methods (needle aspiration, forceps biopsy, and cytology brush), followed by a cryobiopsy. An endobronchial blocker was placed near the planned area of biopsy in advance and inflated post-biopsy to minimize the risk of bleeding in all patients. A chest X-ray was performed 1 h post-procedure. All the PPLs were visualized with R-EBUS. The mean diameter of cryobiopsy samples was twice the size of forceps biopsy samples. In four patients, cryobiopsy samples were superior in size and the number of malignant cells per high power filed and was the preferred sample selected for mutation analysis and molecular testing. There was no pneumothorax or significant bleeding to report. Cryobiopsy samples were consistently larger and were the preferred samples for molecular testing, with an increase in the diagnostic yield and reduction in the need for repeat procedures, without hindering the marked safety profile of R-EBUS. Using an endobronchial blocker improves the safety of this procedure.

A Novel Method for Characterization of Superconductors: Physical Measurements and Modeling of Thin Films

NASA Technical Reports Server (NTRS)

Kim, B. F.; Moorjani, K.; Phillips, T. E.; Adrian, F. J.; Bohandy, J.; Dolecek, Q. E.

1993-01-01

A method for characterization of granular superconducting thin films has been developed which encompasses both the morphological state of the sample and its fabrication process parameters. The broad scope of this technique is due to the synergism between experimental measurements and their interpretation using numerical simulation. Two novel technologies form the substance of this system: the magnetically modulated resistance method for characterizing superconductors; and a powerful new computer peripheral, the Parallel Information Processor card, which provides enhanced computing capability for PC computers. This enhancement allows PC computers to operate at speeds approaching that of supercomputers. This makes atomic scale simulations possible on low cost machines. The present development of this system involves the integration of these two technologies using mesoscale simulations of thin film growth. A future stage of development will incorporate atomic scale modeling.

Sampling of atmospheric carbonyl compounds for determination by liquid chromatography after 2,4-dinitrophenylhydrazine labelling

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

Vairavamurthy, A.; Roberts, J.M.; Newman, L.

1991-06-01

Carbonyl compounds are both primary (directly emitted) and secondary (formed in situ) atmospheric species, which play a major role in tropospheric photochemistry. Because of trace concentrations (parts-per-billion and lower), ambient air measurements of carbonyls pose serious analytical problems. Generally, chromatographic approaches combined with chemical derivatization have been used to enhance sensitivity and selectivity in analysis. Currently, the liquid chromatographic method coupled to 2,4-dinitrophenylhydrazine derivatization (DNPH-LC) is in widespread use. Interferences arising from similar compounds are greatly minimized by chromatographic separation; however, those in the air sampling step, especially with ozone, continue to be problematic and remain to be resolved. Wemore » discuss here the different sampling techniques used for time-integrated collection of carbonyls in the DNPH-LC methods. Emphasis is placed on addressing: (1) the principles, advantages, and limitations of sampling techniques; (2) problems associated with reagent blank and sampling instrument; and (3) effects of atmospheric co-pollutants, especially ozone. 58 refs., 8 figs., 3 tabs.« less

Tackling sampling challenges in biomolecular simulations.

PubMed

Barducci, Alessandro; Pfaendtner, Jim; Bonomi, Massimiliano

2015-01-01

Molecular dynamics (MD) simulations are a powerful tool to give an atomistic insight into the structure and dynamics of proteins. However, the time scales accessible in standard simulations, which often do not match those in which interesting biological processes occur, limit their predictive capabilities. Many advanced sampling techniques have been proposed over the years to overcome this limitation. This chapter focuses on metadynamics, a method based on the introduction of a time-dependent bias potential to accelerate sampling and recover equilibrium properties of a few descriptors that are able to capture the complexity of a process at a coarse-grained level. The theory of metadynamics and its combination with other popular sampling techniques such as the replica exchange method is briefly presented. Practical applications of these techniques to the study of the Trp-Cage miniprotein folding are also illustrated. The examples contain a guide for performing these calculations with PLUMED, a plugin to perform enhanced sampling simulations in combination with many popular MD codes.

Q-controlled amplitude modulation atomic force microscopy in liquids: An analysis

NASA Astrophysics Data System (ADS)

Hölscher, H.; Schwarz, U. D.

2006-08-01

An analysis of amplitude modulation atomic force microscopy in liquids is presented with respect to the application of the Q-Control technique. The equation of motion is solved by numerical and analytic methods with and without Q-Control in the presence of a simple model interaction force adequate for many liquid environments. In addition, the authors give an explicit analytical formula for the tip-sample indentation showing that higher Q factors reduce the tip-sample force. It is found that Q-Control suppresses unwanted deformations of the sample surface, leading to the enhanced image quality reported in several experimental studies.

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

PubMed Central

Bonomi, Massimiliano; Camilloni, Carlo; Vendruscolo, Michele

2016-01-01

Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conformational sampling, which represents a separate challenge. To address such challenge and to exhaustively and efficiently generate structural ensembles we combine metainference with metadynamics and illustrate its application to the calculation of the free energy landscape of the alanine dipeptide. PMID:27561930

Dual-stage trapped-flux magnet cryostat for measurements at high magnetic fields

DOEpatents

Islam, Zahirul; Das, Ritesh K.; Weinstein, Roy

2015-04-14

A method and a dual-stage trapped-flux magnet cryostat apparatus are provided for implementing enhanced measurements at high magnetic fields. The dual-stage trapped-flux magnet cryostat system includes a trapped-flux magnet (TFM). A sample, for example, a single crystal, is adjustably positioned proximate to the surface of the TFM, using a translation stage such that the distance between the sample and the surface is selectively adjusted. A cryostat is provided with a first separate thermal stage provided for cooling the TFM and with a second separate thermal stage provided for cooling sample.

Selectivity enhancement in photoacoustic gas analysis via phase-sensitive detection at high modulation frequency

NASA Technical Reports Server (NTRS)

Kosterev, Anatoliy (Inventor)

2010-01-01

A method for detecting a target fluid in a fluid sample comprising a first fluid and the target fluid using photoacoustic spectroscopy (PAS), comprises a) providing a light source configured to introduce an optical signal having at least one wavelength into the fluid sample; b) modulating the optical signal at a desired modulation frequency such that the optical signal generates an acoustic signal in the fluid sample; c) measuring the acoustic signal in a resonant acoustic detector; and d) using the phase of the acoustic signal to detect the presence of the target fluid.

Combining Deep and Handcrafted Image Features for Presentation Attack Detection in Face Recognition Systems Using Visible-Light Camera Sensors

PubMed Central

Nguyen, Dat Tien; Pham, Tuyen Danh; Baek, Na Rae; Park, Kang Ryoung

2018-01-01

Although face recognition systems have wide application, they are vulnerable to presentation attack samples (fake samples). Therefore, a presentation attack detection (PAD) method is required to enhance the security level of face recognition systems. Most of the previously proposed PAD methods for face recognition systems have focused on using handcrafted image features, which are designed by expert knowledge of designers, such as Gabor filter, local binary pattern (LBP), local ternary pattern (LTP), and histogram of oriented gradients (HOG). As a result, the extracted features reflect limited aspects of the problem, yielding a detection accuracy that is low and varies with the characteristics of presentation attack face images. The deep learning method has been developed in the computer vision research community, which is proven to be suitable for automatically training a feature extractor that can be used to enhance the ability of handcrafted features. To overcome the limitations of previously proposed PAD methods, we propose a new PAD method that uses a combination of deep and handcrafted features extracted from the images by visible-light camera sensor. Our proposed method uses the convolutional neural network (CNN) method to extract deep image features and the multi-level local binary pattern (MLBP) method to extract skin detail features from face images to discriminate the real and presentation attack face images. By combining the two types of image features, we form a new type of image features, called hybrid features, which has stronger discrimination ability than single image features. Finally, we use the support vector machine (SVM) method to classify the image features into real or presentation attack class. Our experimental results indicate that our proposed method outperforms previous PAD methods by yielding the smallest error rates on the same image databases. PMID:29495417

Combining Deep and Handcrafted Image Features for Presentation Attack Detection in Face Recognition Systems Using Visible-Light Camera Sensors.

PubMed

Nguyen, Dat Tien; Pham, Tuyen Danh; Baek, Na Rae; Park, Kang Ryoung

2018-02-26

Although face recognition systems have wide application, they are vulnerable to presentation attack samples (fake samples). Therefore, a presentation attack detection (PAD) method is required to enhance the security level of face recognition systems. Most of the previously proposed PAD methods for face recognition systems have focused on using handcrafted image features, which are designed by expert knowledge of designers, such as Gabor filter, local binary pattern (LBP), local ternary pattern (LTP), and histogram of oriented gradients (HOG). As a result, the extracted features reflect limited aspects of the problem, yielding a detection accuracy that is low and varies with the characteristics of presentation attack face images. The deep learning method has been developed in the computer vision research community, which is proven to be suitable for automatically training a feature extractor that can be used to enhance the ability of handcrafted features. To overcome the limitations of previously proposed PAD methods, we propose a new PAD method that uses a combination of deep and handcrafted features extracted from the images by visible-light camera sensor. Our proposed method uses the convolutional neural network (CNN) method to extract deep image features and the multi-level local binary pattern (MLBP) method to extract skin detail features from face images to discriminate the real and presentation attack face images. By combining the two types of image features, we form a new type of image features, called hybrid features, which has stronger discrimination ability than single image features. Finally, we use the support vector machine (SVM) method to classify the image features into real or presentation attack class. Our experimental results indicate that our proposed method outperforms previous PAD methods by yielding the smallest error rates on the same image databases.

Development of a New Apparatus for Investigating Acoustic Effects on Hydraulic Properties of Low-Permeability Geo-Materials

NASA Astrophysics Data System (ADS)

Nakajima, H.; Sawada, A.; Sugita, H.; Takeda, M.; Komai, T.; Zhang, M.

2006-12-01

Remediation of polluted soils and groundwater contaminated by heavy metals and non-aqueous phase liquids has been one of the challenging issues in the field of geo-environments. In-situ removal of the contaminants from low permeable soils, such as clay strata, is particularly difficult because of the low mobility, strong adsorption, and/or other various interactions within soils. Thus current remediation techniques, such as pump- and-treat method and even eletrokinetic method, generally suffer from low recovery rates and/or economically unacceptable long remediation periods. A perspective improvement in remediation technology is to couple the electrokinetic method with an application of acoustic waves. This so-called Electro-Acoustic Soil Decontamination (EASD) method has been proposed by Battelle Columbus Labs.(Muralidhara et al. 1990). Simultaneous application of an electric field and an acoustic field may produce a synergistic effect and result in further enhancement of water transport by electro-osmosis in principle, but there is still no fundamental data for the design of EASD method in practical applications. A number of investigations have shown that an application of acoustic waves can increase hydraulic conductivity and mobility of non-aqueous phase liquids in porous media. Most of the prior and ongoing researches in this area have been focused on increasing production from declining oil and gas reservoirs. During several field tests by the oil and gas industries, increases in oil production rates by 20% or more have been reported. However, underlying physical mechanisms for acoustically enhanced fluid transport are not adequately understood. In addition, majority of the past investigations has dealt with applications of large amplitude of acoustic waves to relatively permeable soils or fractured rocks, and there is little information if acoustic wave effectively enhances flow and contaminant transport for less permeable clayey soils. To evaluate the feasibility of the EASD method and to obtain the fundamental but important knowledge for the design of this method, it is first necessary to understand the effects of acoustic wave application on pore water flow behavior. A new apparatus is developed to investigate the effects of acoustic wave on hydraulic properties of soil sample. This test apparatus enables to confine a cylindrical specimen under hydrostatic pressure conditions and to apply acoustic wave simultaneously. Preliminary results associated with the effects of acoustic wave frequency on changes of permeability of kaolin clay samples are illustrated in this report. A program investigating the effects of electricity and pore water chemistry on efficiency of decontamination using the same samples is also ongoing and briefly presented. The two strategies for enhancing the efficiency of remediation for low permeable soils will be combined in the near future

Sensitive elemental detection using microwave-assisted laser-induced breakdown imaging

NASA Astrophysics Data System (ADS)

Iqbal, Adeel; Sun, Zhiwei; Wall, Matthew; Alwahabi, Zeyad T.

2017-10-01

This study reports a sensitive spectroscopic method for quantitative elemental detection by manipulating the temporal and spatial parameters of laser-induced plasma. The method was tested for indium detection in solid samples, in which laser ablation was used to generate a tiny plasma. The lifetime of the laser-induced plasma can be extended to hundreds of microseconds using microwave injection to remobilize the electrons. In this novel method, temporal integrated signal of indium emission was significantly enhanced. Meanwhile, the projected detectable area of the excited indium atoms was also significantly improved using an interference-, instead of diffraction-, based technique, achieved by directly imaging microwave-enhanced plasma through a novel narrow-bandpass filter, exactly centered at the indium emission line. Quantitative laser-induce breakdown spectroscopy was also recorded simultaneously with the new imaging method. The intensities recorded from both methods exhibit very good mutual linear relationship. The detection intensity was improved to 14-folds because of the combined improvements in the plasma lifetime and the area of detection.

Tuneable surface enhanced Raman spectroscopy hyphenated to chemically derivatized thin-layer chromatography plates for screening histamine in fish.

PubMed

Xie, Zhengjun; Wang, Yang; Chen, Yisheng; Xu, Xueming; Jin, Zhengyu; Ding, Yunlian; Yang, Na; Wu, Fengfeng

2017-09-01

Reliable screening of histamine in fish was of urgent importance for food safety. This work presented a highly selective surface enhanced Raman spectroscopy (SERS) method mediated by thin-layer chromatography (TLC), which was tailored for identification and quantitation of histamine. Following separation and derivatization with fluram, plates were assayed with SERS, jointly using silver nanoparticle and NaCl. The latter dramatically suppressed the masking effect caused by excessive fluram throughout the plate, thus offering clear baseline and intensive Raman fingerprints specific to the analyte. Under optimized conditions, the usability of this method was validated by identifying the structural fingerprints of both targeted and unknown compounds in fish samples. Meanwhile, the quantitative results of this method agreed with those by an HPLC method officially suggested by EU for histamine determination. Showing remarkable cost-efficiency and user-friendliness, this facile TLC-SERS method was indeed screening-oriented and may be more attractive to controlling laboratories of limited resource. Copyright © 2017 Elsevier Ltd. All rights reserved.

Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath.

PubMed

Chen, Changjun; Huang, Yanzhao; Xiao, Yi

2013-01-01

Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of freedom in the molecule to environment temperature, like dihedrals in generalized coordinates or nonhydrogen atoms in Cartesian coordinate. After applying to ALA dipeptide model, we find that this modified molecular dynamics greatly enhances the sampling behavior in the conformational space and provides more information about the state-to-state transition, while conventional molecular dynamics fails to do so. Moreover, from the results of 16 independent 100 ns simulations by the new method, it shows that trpzip2 has one-half chances to reach the naive state in all the trajectories, which is greatly higher than conventional molecular dynamics. Such an improvement would provide a potential way for searching the conformational space or predicting the most stable states of peptides and proteins.

[Method of fused sample preparation after nitrify-determination of primary and minor elements in manganese ore by X-ray fluorescence spectrometry].

PubMed

Song, Yi; Guo, Fen; Gu, Song-hai

2007-02-01

Eight components, i. e. Mn, SiO2, Fe, P, Al2O3, CaO, MgO and S, in manganese ore were determined by X-ray fluorescence spectrometer. Because manganese ore sample releases a lot of air bubbles during fusion which effect accuracy and reproducibility of determination, nitric acid was added to the sample to destroy organic matter before fusion by the mixture flux at 1000 degrees C. This method solved the problem that the flux splashed during fusion because organic matter volatilized brought out a lot of air bubbles, eliminated particle size effects and mineral effect, while solved the problem of volatilization of sulfur during fusion. The experiments for the selection of the sample preparation conditions, i. e. fusion flux, fusion time and volume of HNO3, were carried out. The matrix effects on absorption and enhancement were corrected by variable theoretical alpha coefficient to expand the range of determination. Moreover, the precision and accuracy experiments were performed. In comparison with chemical analysis method, the quantitative analytical results for each component are satisfactory. The method has proven rapid, precise and simple.

Gas discharge plasma treatment of poly(ethylene glycol-co-1,3/1,4 cyclohexanedimethanol terephthalate) for enhanced paint adhesion

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

Salapare, Hernando S., E-mail: hssalapare@up.edu.ph; Department of Physical Sciences and Mathematics, College of Arts and Sciences, University of the Philippines Manila, Manila City 1000; College of Science, Pamantasan ng Lungsod ng Maynila, Intramuros, Manila City 1002

Low-energy hydrogen-ions and tetrafluoromethane-ions produced from a gas discharge ion source were irradiated to poly(ethylene glycol-co-1,3/1,4 cyclohexanedimethanol terephthalate) (PETG) sheets for enhancing paint adhesion. The ion beams were characterized using a cast steel mass spectrometer, while the untreated and treated samples were characterized using Fourier transform infrared spectroscopy, scanning electron microscopy, contact angle measurements, and profilometry. The paint adhesion was determined by using the standard method for evaluating adhesion by knife [ASTM D6677-07, Standard Test Method for Evaluating Adhesion by Knife (ASTM International, West Conshohocken, PA, 2012)] and was correlated with the calculation of the work of adhesion derived frommore » the Young–Dupré equation. After plasma treatment, a significant decrease in the contact angle was observed in all samples, except for the CF{sub 4} ion-treated samples with the discharge current of 3 mA and an irradiation time of 30 min. At longer irradiation times, the treated samples showed lesser changes in the contact angle measurement. The increase in the average and root-mean-square surface roughness was observed on the samples after plasma treatment. The samples treated with either H{sub 2} or CF{sub 4} ions for 15 min showed a direct correlation between the discharge current and surface roughness. The samples treated for 30 min showed no significant correlation between the surface roughness and discharge current, which can be attributed to the possible melting of the samples since PETG has a low melting point. The observation made in this study on the relationship of wettability and surface roughness is consistent with the Wenzel wetting mode. Scanning electron micrographs showed surface etching on the hydrogen ion-treated samples while no significant surface changes were observed for the CF{sub 4} ion-treated samples. In general, paint adhesion was stronger for samples that exhibited enhanced wettability and high work of adhesion. The optimal work of adhesion to double the paint adhesion performance was at least 84.79 mN/m. The increase in the surface roughness after the treatment provided an increased friction between the paint and the PETG surface. The increase in the paint adhesion was also due to the covalent, hydrogen, and van der Waals bonding that are typically observed for highly wettable surfaces.« less

Clinical performance of a free-breathing spatiotemporally accelerated 3-D time-resolved contrast-enhanced pediatric abdominal MR angiography

PubMed Central

Yousaf, Ufra; Hsiao, Albert; Cheng, Joseph Y.; Alley, Marcus T.; Lustig, Michael; Pauly, John M.; Vasanawala, Shreyas S.

2015-01-01

Background Pediatric contrast-enhanced MR angiography is often limited by respiration, other patient motion and compromised spatiotemporal resolution. Objective To determine the reliability of a free-breathing spatiotemporally accelerated 3-D time-resolved contrast enhanced MR angiography method for depicting abdominal arterial anatomy in young children. Materials and methods With IRB approval and informed consent, we retrospectively identified 27 consecutive children (16 males and 11 females; mean age: 3.8 years, range: 14 days to 8.4 years) referred for contrast enhanced MR angiography at our institution, who had undergone free-breathing spatiotemporally accelerated time-resolved contrast enhanced MR angiography studies. An radio-frequency-spoiled gradient echo sequence with Cartesian variable density k-space sampling and radial view ordering, intrinsic motion navigation and intermittent fat suppression was developed. Images were reconstructed with soft-gated parallel imaging locally low-rank method to achieve both motion correction and high spatiotemporal resolution. Quality of delineation of 13 abdominal arteries in the reconstructed images was assessed independently by two radiologists on a five-point scale. Ninety-five percent confidence intervals of the proportion of diagnostically adequate cases were calculated. Interobserver agreements were also analyzed. Results Eleven out of 13 arteries achieved acceptable image quality (mean score range: 3.9–5.0) for both readers. Fair to substantial interobserver agreement was reached on nine arteries. Conclusion Free-breathing spatiotemporally accelerated 3-D time-resolved contrast enhanced MR angiography frequently yields diagnostic image quality for most abdominal arteries for pediatric contrast enhanced MR angiography. PMID:26040509

Enhancement of concentration range of chromatographically detectable components with array detector mass spectrometry

DOEpatents

Enke, Christie

2013-02-19

Methods and instruments for high dynamic range analysis of sample components are described. A sample is subjected to time-dependent separation, ionized, and the ions dispersed with a constant integration time across an array of detectors according to the ions m/z values. Each of the detectors in the array has a dynamically adjustable gain or a logarithmic response function, producing an instrument capable of detecting a ratio of responses or 4 or more orders of magnitude.

Development and validation of a liquid chromatography-tandem mass spectrometry method for the determination of pyridostigmine bromide from guinea pig plasma.

PubMed

Needham, Shane R; Ye, Binying; Smith, J Richard; Korte, William D

2003-11-05

An HPLC/MS/MS method was validated for the low level analysis of pyridostigmine bromide (PB) from guinea pig plasma. An advantage of this strong-cation exchange HPLC/MS/MS method was the enhancement of the ESI-MS signal by providing good retention and good peak shape of PB with a mobile phase of 70% acetonitrile. In addition, the use of 70% acetonitrile in the mobile phase allowed the direct injection of the supernant from the protein precipitated extracted sample. The assay was linear from the range of 0.1 to 50 ng/ml using only 25 microl of sample. The precision and accuracy of the assay was better than 9.1 and 113%, respectively.

Constructing a MoS₂ QDs/CdS Core/Shell Flowerlike Nanosphere Hierarchical Heterostructure for the Enhanced Stability and Photocatalytic Activity.

PubMed

Liang, Shijing; Zhou, Zhouming; Wu, Xiuqin; Zhu, Shuying; Bi, Jinhong; Zhou, Limin; Liu, Minghua; Wu, Ling

2016-02-15

MoS₂ quantum dots (QDs)/CdS core/shell nanospheres with a hierarchical heterostructure have been prepared by a simple microwave hydrothermal method. The as-prepared samples are characterized by XRD, TEM, SEM, UV-VIS diffuse reflectance spectra (DRS) and N₂-sorption in detail. The photocatalytic activities of the samples are evaluated by water splitting into hydrogen. Results show that the as-prepared MoS₂ QDs/CdS core/shell nanospheres with a diameter of about 300 nm are composed of the shell of CdS nanorods and the core of MoS₂ QDs. For the photocatalytic reaction, the samples exhibit a high stability of the photocatalytic activity and a much higher hydrogen evolution rate than the pure CdS, the composite prepared by a physical mixture, and the Pt-loaded CdS sample. In addition, the stability of CdS has also been greatly enhanced. The effect of the reaction time on the formations of nanospheres, the photoelectric properties and the photocatalytic activities of the samples has been investigated. Finally, a possible photocatalytic reaction process has also been proposed.

Potential of cancer screening with serum surface-enhanced Raman spectroscopy and a support vector machine

NASA Astrophysics Data System (ADS)

Li, S. X.; Zhang, Y. J.; Zeng, Q. Y.; Li, L. F.; Guo, Z. Y.; Liu, Z. M.; Xiong, H. L.; Liu, S. H.

2014-06-01

Cancer is the most common disease to threaten human health. The ability to screen individuals with malignant tumours with only a blood sample would be greatly advantageous to early diagnosis and intervention. This study explores the possibility of discriminating between cancer patients and normal subjects with serum surface-enhanced Raman spectroscopy (SERS) and a support vector machine (SVM) through a peripheral blood sample. A total of 130 blood samples were obtained from patients with liver cancer, colonic cancer, esophageal cancer, nasopharyngeal cancer, gastric cancer, as well as 113 blood samples from normal volunteers. Several diagnostic models were built with the serum SERS spectra using SVM and principal component analysis (PCA) techniques. The results show that a diagnostic accuracy of 85.5% is acquired with a PCA algorithm, while a diagnostic accuracy of 95.8% is obtained using radial basis function (RBF), PCA-SVM methods. The results prove that a RBF kernel PCA-SVM technique is superior to PCA and conventional SVM (C-SVM) algorithms in classification serum SERS spectra. The study demonstrates that serum SERS, in combination with SVM techniques, has great potential for screening cancerous patients with any solid malignant tumour through a peripheral blood sample.

[TLC-FT-SERS study on ingredients of Isrhynchophylline].

PubMed

Wang, Yuan; Wang, Song-ying; Zhao, Yi-xue; Ren, Gui-fen; Zi, Feng-lan

2002-02-01

A new method for analysing the ingredients of Isrhynchophylline in Uncaria Rhynchophylla Jacks by thin layer chromatography (TLC) and the surface-enhanced Raman spectroscopy (SERS) is reported in this paper. The results show that the characteristic spectra bands of Isrhynchophylline situated at the thin layer with the amount of sample about 2.5 micrograms were obtained. The difference between SERS and solid spectra was found. Great enhancement of the 1,615 cm-1 spectral band was abstained. Molecule was absorbed in surface silver sol by pi electrons in phenyl and by pair of electrons in N together. An absorption model of Isrhynchophylline and silver sol was proposed. This method can be used to analyse the chemical ingredients with high sensitivity.

A Modified LC/MS/MS Method with Enhanced Sensitivity for the Determination of Scopolamine in Human Plasma

NASA Technical Reports Server (NTRS)

Wang, Zuwei; Vaksman, Zalman; Putcha, Lakshmi

2008-01-01

Intranasal scopolamine is a choice drug for the treatment of motion sickness during space flight because of its quick onset of action, short half-life and favorable sideeffects profile. The dose administered usually ranges between 0.1 and 0.4 mg. Such small doses make it difficult to detect concentrations of scopolamine in biological fluids using existing sensitive LC/MS/MS method, especially when the biological sample volumes are limited. To measure scopolamine in human plasma to facilitate pharmacokinetic evaluation of the drug, we developed a sensitive LC/MS/MS method using 96 well micro elution plates for solid phase extraction (SPE) of scopolamine in human plasma. Human plasma (100-250 micro L) were loaded onto Waters Oasis HLB 96 well micro elution plate and eluted with 50 L of organic solvent without evaporation and reconstitution. HPLC separation of the eluted sample was performed using an Agilent Zorbax SB-CN column (50 x 2.1 mm) at a flow rate of 0.2 mL/min for 3 minutes. The mobile phase for separation was 80:20 (v/v) methanol: ammonium acetate (30 mM) in water. Concentrations of scopolamine were determined using a Micromass Quattro Micro(TM) mass spectrometer with electrospray ionization (ESI). ESI mass spectra were acquired in positive ion mode with multiple reaction monitoring for the determination of scopolamine m/z = 304.2 right arrow 138.1 and internal standard hyoscyamine m/z = 290.2 right arrow 124.1. The method is rapid, reproducible, specific and has the following parameters: scopolamine and the IS are eluted at about 1.1 and 1.7 min respectively. The linear range is 25-10000 pg/mL for scopolamine in human plasma with correlation coefficients greater than 0.99 and CV less than 0.5%. The intra-day and inter-day CVs are less than 15% for quality control samples with concentrations of 75,300, and 750 pg/mL of scopolamine in human plasma. SPE using 96 well micro elution plates allows rapid sample preparation and enhanced sensitivity for the LC/MS/MS determination of scopolamine in a small volume of biological samples. The new method is also cost effective since it uses a small volume of organic solvents compared to the methods using SPE cartridges or regular 96 well SPE plates. This method can be successfully used for bioavailability and pharmacokinetic evaluations of scopolamine, especially when volumes of biological samples are limited. Further investigation to use automated SPE system with 96 well micro elution plates is planned.

A Novel Tri-Enzyme System in Combination with Laser-Driven NMR Enables Efficient Nuclear Polarization of Biomolecules in Solution

PubMed Central

Lee, Jung Ho; Cavagnero, Silvia

2013-01-01

NMR is an extremely powerful, yet insensitive technique. Many available nuclear polarization methods that address sensitivity are not directly applicable to low-concentration biomolecules in liquids and are often too invasive. Photochemically induced dynamic nuclear polarization (photo-CIDNP) is no exception. It needs high-power laser irradiation, which often leads to sample degradation, and photosensitizer reduction. Here, we introduce a novel tri-enzyme system that significantly overcomes the above challenges rendering photo-CIDNP a practically applicable technique for NMR sensitivity enhancement in solution. The specificity of the nitrate reductase (NR) enzyme is exploited to selectively in situ re-oxidize the reduced photo-CIDNP dye FMNH2. At the same time, the oxygen-scavenging ability of glucose oxidase (GO) and catalase (CAT) is synergistically employed to prevent sample photodegradation. The resulting tri-enzyme system (NR-GO-CAT) enables prolonged sensitivity-enhanced data collection in 1D and 2D heteronuclear NMR, leading to the highest photo-CIDNP sensitivity enhancement (48-fold relative to SE-HSQC) achieved to date for amino acids and polypeptides in solution. NR-GO-CAT extends the concentration limit of photo-CIDNP NMR down to the low micromolar range. In addition, sensitivity (relative to the reference SE-HSQC) is found to be inversely proportional to sample concentration, paving the way to the future analysis of even more diluted samples. PMID:23560683

On-site Rapid Detection of Trace Non-volatile Inorganic Explosives by Stand-alone Ion Mobility Spectrometry via Acid-enhanced Evaporization

PubMed Central

Peng, Liying; Hua, Lei; Wang, Weiguo; Zhou, Qinghua; Li, Haiyang

2014-01-01

New techniques for the field detection of inorganic improvised explosive devices (IEDs) are urgently developed. Although ion mobility spectrometry (IMS) has been proved to be the most effective method for screening organic explosives, it still faces a major challenge to detect inorganic explosives owing to their low volatilities. Herein, we proposed a strategy for detecting trace inorganic explosives by thermal desorption ion mobility spectrometry (TD-IMS) with sample-to-sample analysis time less than 5 s based on in-situ acidification on the sampling swabs. The responses for typical oxidizers in inorganic explosives, such as KNO3, KClO3 and KClO4 were at least enhanced by a factor of 3000 and their limits of detection were found to be subnanogram. The common organic explosives and their mixtures with inorganic oxidizers were detected, indicating that the acidification process did not affect the detection of organic explosives. Moreover, the typical inorganic explosives such as black powders, firecrackers and match head could be sensitively detected as well. These results demonstrated that this method could be easily employed in the current deployed IMS for on-site sensitive detection of either inorganic explosives or organic ones. PMID:25318960

Vortex-assisted surfactant-enhanced emulsification microextraction based on solidification of floating organic drop combined with high performance liquid chromatography for determination of naproxen and nabumetone.

PubMed

Asadi, Mohammad; Haji Shabani, Ali Mohammad; Dadfarnia, Shayessteh; Abbasi, Bijan

2015-12-18

A novel, rapid, simple and green vortex-assisted surfactant-enhanced emulsification microextraction method based on solidification of floating organic drop was developed for simultaneous separation/preconcentration and determination of ultra trace amounts of naproxen and nabumetone with high performance liquid chromatography-fluorescence detection. Some parameters influencing the extraction efficiency of analytes such as type and volume of extractant, type and concentration of surfactant, sample pH, KCl concentration, sample volume, and vortex time were investigated and optimized. Under optimal conditions, the calibration graph exhibited linearity in the range of 3.0-300.0ngL(-1) for naproxen and 7.0-300.0ngL(-1) for nabumetone with a good coefficient of determination (R(2)>0.999). The limits of detection were 0.9 and 2.1ngL(-1). The relative standard deviations for inter- and intra-day assays were in the range of 5.8-10.1% and 3.8-6.1%, respectively. The method was applied to the determination of naproxen and nabumetone in urine, water, wastewater and milk samples and the accuracy was evaluated through recovery experiments. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison of two thin-film microextractions for the analysis of estrogens in aqueous tea extract and environmental water samples by high performance liquid chromatography-ultraviolet detection.

PubMed

Cai, Pei-Shan; Li, Dan; Chen, Jing; Xiong, Chao-Mei; Ruan, Jin-Lan

2015-04-15

Two thin-film microextractions (TFME), octadecylsilane (ODS)-polyacrylonitrile (PAN)-TFME and polar enhanced phase (PEP)-PAN-TFME have been proposed for the analysis of bisphenol-A, diethylstilbestrol and 17β-estradiol in aqueous tea extract and environmental water samples followed by high performance liquid chromatography-ultraviolet detection. Both thin-films were prepared by spraying. The influencing factors including pH, extraction time, desorption solvent, desorption volume, desorption time, ion strength and reusability were investigated. Under the optimal conditions, the two TFME methods are similar in terms of the analytical performance evaluated by standard addition method. The limits of detection for three estrogens in environmental water and aqueous tea extract matrix ranged from 1.3 to 1.6 and 2.8 to 7.1 ng mL(-1) by the two TFME methods, respectively. Both approaches were applied for the analysis of analytes in real aqueous tea extract and environmental water samples, presenting satisfactory recoveries ranged from 87.3% to 109.4% for the spiked samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of an analytical microbial consortia method for enhancing performance monitoring at aerobic wastewater treatment plants.

PubMed

Razban, Behrooz; Nelson, Kristina Y; McMartin, Dena W; Cullimore, D Roy; Wall, Michelle; Wang, Dunling

2012-01-01

An analytical method to produce profiles of bacterial biomass fatty acid methyl esters (FAME) was developed employing rapid agitation followed by static incubation (RASI) using selective media of wastewater microbial communities. The results were compiled to produce a unique library for comparison and performance analysis at a Wastewater Treatment Plant (WWTP). A total of 146 samples from the aerated WWTP, comprising 73 samples of each secondary and tertiary effluent, were included analyzed. For comparison purposes, all samples were evaluated via a similarity index (SI) with secondary effluents producing an SI of 0.88 with 2.7% variation and tertiary samples producing an SI 0.86 with 5.0% variation. The results also highlighted significant differences between the fatty acid profiles of the tertiary and secondary effluents indicating considerable shifts in the bacterial community profile between these treatment phases. The WWTP performance results using this method were highly replicable and reproducible indicating that the protocol has potential as a performance-monitoring tool for aerated WWTPs. The results quickly and accurately reflect shifts in dominant bacterial communities that result when processes operations and performance change.

Enhanced performance of a structured cyclo olefin copolymer-based amorphous silicon solar cell

NASA Astrophysics Data System (ADS)

Zhan, Xinghua; Chen, Fei; Gao, Mengyu; Tie, Shengnian; Gao, Wei

2017-07-01

The submicron array was fabricated onto a cyclo olefin copolymer (COC) film by a hot embossing method. An amorphous silicon p-i-n junction and transparent conductive layers were then deposited onto it through a plasma enhanced chemical vapor deposition (PECVD) and magnetron sputtering. The efficiency of the fabricated COC-based solar cell was measured and the result demonstrated 18.6% increase of the solar cell efficiency when compared to the sample without array structure. The imprinted polymer solar cells with submicron array indeed increase their efficiency.

Bio-sensing with butterfly wings: naturally occurring nano-structures for SERS-based malaria parasite detection.

PubMed

Garrett, Natalie L; Sekine, Ryo; Dixon, Matthew W A; Tilley, Leann; Bambery, Keith R; Wood, Bayden R

2015-09-07

Surface enhanced Raman scattering (SERS) is a powerful tool with great potential to provide improved bio-sensing capabilities. The current 'gold-standard' method for diagnosis of malaria involves visual inspection of blood smears using light microscopy, which is time consuming and can prevent early diagnosis of the disease. We present a novel surface-enhanced Raman spectroscopy substrate based on gold-coated butterfly wings, which enabled detection of malarial hemozoin pigment within lysed blood samples containing 0.005% and 0.0005% infected red blood cells.

The microstructure and photoluminescence of ZnO-MoS2 core shell nano-materials

NASA Astrophysics Data System (ADS)

Yu, H.; Liu, C. M.; Huang, X. Y.; Lei, M. Y.

2017-01-01

In this paper, ZnO-MoS2-FT (FT is the fabrication temperature of MoS2) core shell nano-material samples (with ZnO as a core and MoS2 as a shell material) were fabricated on ITO substrate using hydrothermal method. The crystal structure, morphology, optical absorption and photoluminescence (PL) of samples were investigated. Compared with that of pure ZnO nanorods, ZnO-MoS2-FT samples show an enhanced light absorption. In addition, ultraviolet (UV) and visible (Vis) PL intensity of ZnO-MoS2-FT samples excited by 325 nm laser are greatly weakened. The UV PL peak position is not changed obviously. However, the Vis PL peak position is changed visibly. The Vis PL of ZnO-MoS2-FT samples under UV excitation indicates that the ratio of oxygen interstitial to oxygen vacancy is decreased. The suppression of UV PL of ZnO-MoS2-FT samples may be related to the weakening of crystal quality of ZnO, easier separation of electron-hole pairs, enhancement of light absorption, and newly introduced defects in the interface between ZnO and MoS2. Under 514 nm laser excitation, the PL peak position of ZnO-MoS2-FT samples has a red shift with FT being increased from 80 to 160 °C. The influence of excitation power (EP) on the PL of ZnO-MoS2-FT samples was also investigated. The PL of ZnO-MoS2-FT samples have a red shift with EP being increased. This may be due to the sample temperature is increased with EP, resulting an enhancement of electron-phonon interaction. A schematic diagram of charge generation and transfer is presented to understand the mechanism of PL of ZnO-MoS2 under UV and Vis excitation.

Rapid surface enhanced Raman scattering detection method for chloramphenicol residues

NASA Astrophysics Data System (ADS)

Ji, Wei; Yao, Weirong

2015-06-01

Chloramphenicol (CAP) is a widely used amide alcohol antibiotics, which has been banned from using in food producing animals in many countries. In this study, surface enhanced Raman scattering (SERS) coupled with gold colloidal nanoparticles was used for the rapid analysis of CAP. Density functional theory (DFT) calculations were conducted with Gaussian 03 at the B3LYP level using the 3-21G(d) and 6-31G(d) basis sets to analyze the assignment of vibrations. Affirmatively, the theoretical Raman spectrum of CAP was in complete agreement with the experimental spectrum. They both exhibited three strong peaks characteristic of CAP at 1104 cm-1, 1344 cm-1, 1596 cm-1, which were used for rapid qualitative analysis of CAP residues in food samples. The use of SERS as a method for the measurements of CAP was explored by comparing use of different solvents, gold colloidal nanoparticles concentration and absorption time. The method of the detection limit was determined as 0.1 μg/mL using optimum conditions. The Raman peak at 1344 cm-1 was used as the index for quantitative analysis of CAP in food samples, with a linear correlation of R2 = 0.9802. Quantitative analysis of CAP residues in foods revealed that the SERS technique with gold colloidal nanoparticles was sensitive and of a good stability and linear correlation, and suited for rapid analysis of CAP residue in a variety of food samples.

Rapid surface enhanced Raman scattering detection method for chloramphenicol residues.

PubMed

Ji, Wei; Yao, Weirong

2015-06-05

Chloramphenicol (CAP) is a widely used amide alcohol antibiotics, which has been banned from using in food producing animals in many countries. In this study, surface enhanced Raman scattering (SERS) coupled with gold colloidal nanoparticles was used for the rapid analysis of CAP. Density functional theory (DFT) calculations were conducted with Gaussian 03 at the B3LYP level using the 3-21G(d) and 6-31G(d) basis sets to analyze the assignment of vibrations. Affirmatively, the theoretical Raman spectrum of CAP was in complete agreement with the experimental spectrum. They both exhibited three strong peaks characteristic of CAP at 1104 cm(-1), 1344 cm(-1), 1596 cm(-1), which were used for rapid qualitative analysis of CAP residues in food samples. The use of SERS as a method for the measurements of CAP was explored by comparing use of different solvents, gold colloidal nanoparticles concentration and absorption time. The method of the detection limit was determined as 0.1 μg/mL using optimum conditions. The Raman peak at 1344 cm(-1) was used as the index for quantitative analysis of CAP in food samples, with a linear correlation of R(2)=0.9802. Quantitative analysis of CAP residues in foods revealed that the SERS technique with gold colloidal nanoparticles was sensitive and of a good stability and linear correlation, and suited for rapid analysis of CAP residue in a variety of food samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Substrate transport pathway inside outward open conformation of EmrD: a molecular dynamics simulation study.

PubMed

Xianwei, Tan; Diannan, Lu; Boxiong, Wang

2016-07-19

The EmrD transporter, which is a classical major facilitator superfamily (MFS) protein, can extrude a range of drug molecules out of E. coil. The drug molecules transport through the channel of MFS in an outward open state, an important issue in research about bacterial drug resistance, which however, is still unknown. In this paper, we construct a starting outward-open model of the EmrD transporter using a state transition method. The starting model is refined by a conventional molecular dynamics simulation. Locally enhanced sampling simulation (LES) is used to validate the outward-open model of EmrD. In the locally enhanced sampling simulation, ten substrates are placed along the channel of the outward-open EmrD, and these substrates are sampled in the outward-open center cavity. It is found that the translocation pathway of these substrates from the inside to the outside of the cell through the EmrD transporter is composed of two sub-pathways, one sub-pathway, including H2, H4, and H5, and another sub-pathway, including H8, H10, and H11. The results give us have a further insight to the ways of substrate translocation of an MFS protein. The model method is based on common features of an MFS protein, so this modeling method can be used to construct various MFS protein models which have a desired state with other conformations not known in the alternating-access mechanism.

Method to make accurate concentration and isotopic measurements for small gas samples

NASA Astrophysics Data System (ADS)

Palmer, M. R.; Wahl, E.; Cunningham, K. L.

2013-12-01

Carbon isotopic ratio measurements of CO2 and CH4 provide valuable insight into carbon cycle processes. However, many of these studies, like soil gas, soil flux, and water head space experiments, provide very small gas sample volumes, too small for direct measurement by current constant-flow Cavity Ring-Down (CRDS) isotopic analyzers. Previously, we addressed this issue by developing a sample introduction module which enabled the isotopic ratio measurement of 40ml samples or smaller. However, the system, called the Small Sample Isotope Module (SSIM), does dilute the sample during the delivery with inert carrier gas which causes a ~5% reduction in concentration. The isotopic ratio measurements are not affected by this small dilution, but researchers are naturally interested accurate concentration measurements. We present the accuracy and precision of a new method of using this delivery module which we call 'double injection.' Two portions of the 40ml of the sample (20ml each) are introduced to the analyzer, the first injection of which flushes out the diluting gas and the second injection is measured. The accuracy of this new method is demonstrated by comparing the concentration and isotopic ratio measurements for a gas sampled directly and that same gas measured through the SSIM. The data show that the CO2 concentration measurements were the same within instrument precision. The isotopic ratio precision (1σ) of repeated measurements was 0.16 permil for CO2 and 1.15 permil for CH4 at ambient concentrations. This new method provides a significant enhancement in the information provided by small samples.