Virtual substrate method for nanomaterials characterization

PubMed Central

Da, Bo; Liu, Jiangwei; Yamamoto, Mahito; Ueda, Yoshihiro; Watanabe, Kazuyuki; Cuong, Nguyen Thanh; Li, Songlin; Tsukagoshi, Kazuhito; Yoshikawa, Hideki; Iwai, Hideo; Tanuma, Shigeo; Guo, Hongxuan; Gao, Zhaoshun; Sun, Xia; Ding, Zejun

2017-01-01

Characterization techniques available for bulk or thin-film solid-state materials have been extended to substrate-supported nanomaterials, but generally non-quantitatively. This is because the nanomaterial signals are inevitably buried in the signals from the underlying substrate in common reflection-configuration techniques. Here, we propose a virtual substrate method, inspired by the four-point probe technique for resistance measurement as well as the chop-nod method in infrared astronomy, to characterize nanomaterials without the influence of underlying substrate signals from four interrelated measurements. By implementing this method in secondary electron (SE) microscopy, a SE spectrum (white electrons) associated with the reflectivity difference between two different substrates can be tracked and controlled. The SE spectrum is used to quantitatively investigate the covering nanomaterial based on subtle changes in the transmission of the nanomaterial with high efficiency rivalling that of conventional core-level electrons. The virtual substrate method represents a benchmark for surface analysis to provide ‘free-standing' information about supported nanomaterials. PMID:28548114

FIELD EVALUATION OF IN-SITU BIODEGRADATION OF CHLORINATED ETHENES: PART I, METHODOLOGY AND FIELD SITE CHARACTERIZATION

EPA Science Inventory

Careful site characterization and implementation of quantitative monitoring methods are prerequisites for a convincing evaluation of enhanced biostimulation for aquifer restoration. his paper describes the characterization of a site at Moffett Naval Air Station, Mountain View, Ca...

Development of a method for urine bikunin/urinary trypsin inhibitor (UTI) quantitation and structural characterization: Application to type 1 and type 2 diabetes.

PubMed

Lepedda, Antonio Junior; Nieddu, Gabriele; Rocchiccioli, Silvia; Fresu, Pietro; De Muro, Pierina; Formato, Marilena

2013-12-01

Bikunin is a plasma proteinase inhibitor often associated with inflammatory conditions. It has a half-life of few minutes and it is rapidly excreted into urine as urinary trypsin inhibitor (UTI). UTI levels are usually low in healthy individuals but they can increase up to tenfold in both acute and chronic inflammatory diseases. This article describes a sensitive method for both direct UTI quantitation and structural characterization. UTI purification was performed by anion exchange micro-chromatography followed by SDS-PAGE. A calibration curve for protein quantitation was set up by using a purified UTI fraction. UTI identification and structural characterization was performed by Nano-LC-MS/MS analysis. The method was applied on urine samples from 9 patients with type 1 diabetes, 11 patients with type 2 diabetes, and 28 healthy controls, matched for age and sex with patients, evidencing higher UTI levels in both groups of patients with respect to controls (p < 0.001 and p = 0.001, respectively). Spearman's correlation tests highlighted no association between UTI levels and age in each group tested. Owing to the elevated sensitivity and specificity, the described method allows UTI quantitation from very low quantities of specimen. Furthermore, as UTI concentration is normalized for creatinine level, the analysis could be also performed on randomly collected urine samples. Finally, MS/MS analysis prospects the possibility of characterizing PTM sites potentially able to affect UTI localization, function, and pathophysiological activity. Preliminary results suggest that UTI levels could represent a useful marker of chronic inflammatory condition in type 1 and 2 diabetes. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A FIELD EVALUATION OF IN-SITU BIODEGRADATION OF CHLORINATED ETHENES: PART I, METHODOLOGY AND FIELD SITE CHARACTERIZATION

EPA Science Inventory

Careful site characterization and implementation of quantitative monitoring methods are prerequisites for a convincing evaluation of enhanced biostimulation for aquifer restoration. This paper describes the characterization of a site at Moffett Naval Air Station, Mountain View, C...

Automatic 3D segmentation of multiphoton images: a key step for the quantification of human skin.

PubMed

Decencière, Etienne; Tancrède-Bohin, Emmanuelle; Dokládal, Petr; Koudoro, Serge; Pena, Ana-Maria; Baldeweck, Thérèse

2013-05-01

Multiphoton microscopy has emerged in the past decade as a useful noninvasive imaging technique for in vivo human skin characterization. However, it has not been used until now in evaluation clinical trials, mainly because of the lack of specific image processing tools that would allow the investigator to extract pertinent quantitative three-dimensional (3D) information from the different skin components. We propose a 3D automatic segmentation method of multiphoton images which is a key step for epidermis and dermis quantification. This method, based on the morphological watershed and graph cuts algorithms, takes into account the real shape of the skin surface and of the dermal-epidermal junction, and allows separating in 3D the epidermis and the superficial dermis. The automatic segmentation method and the associated quantitative measurements have been developed and validated on a clinical database designed for aging characterization. The segmentation achieves its goals for epidermis-dermis separation and allows quantitative measurements inside the different skin compartments with sufficient relevance. This study shows that multiphoton microscopy associated with specific image processing tools provides access to new quantitative measurements on the various skin components. The proposed 3D automatic segmentation method will contribute to build a powerful tool for characterizing human skin condition. To our knowledge, this is the first 3D approach to the segmentation and quantification of these original images. © 2013 John Wiley & Sons A/S. Published by Blackwell Publishing Ltd.

A High Resolution/Accurate Mass (HRAM) Data-Dependent MS3 Neutral Loss Screening, Classification, and Relative Quantitation Methodology for Carbonyl Compounds in Saliva

NASA Astrophysics Data System (ADS)

Dator, Romel; Carrà, Andrea; Maertens, Laura; Guidolin, Valeria; Villalta, Peter W.; Balbo, Silvia

2017-04-01

Reactive carbonyl compounds (RCCs) are ubiquitous in the environment and are generated endogenously as a result of various physiological and pathological processes. These compounds can react with biological molecules inducing deleterious processes believed to be at the basis of their toxic effects. Several of these compounds are implicated in neurotoxic processes, aging disorders, and cancer. Therefore, a method characterizing exposures to these chemicals will provide insights into how they may influence overall health and contribute to disease pathogenesis. Here, we have developed a high resolution accurate mass (HRAM) screening strategy allowing simultaneous identification and relative quantitation of DNPH-derivatized carbonyls in human biological fluids. The screening strategy involves the diagnostic neutral loss of hydroxyl radical triggering MS3 fragmentation, which is only observed in positive ionization mode of DNPH-derivatized carbonyls. Unique fragmentation pathways were used to develop a classification scheme for characterizing known and unanticipated/unknown carbonyl compounds present in saliva. Furthermore, a relative quantitation strategy was implemented to assess variations in the levels of carbonyl compounds before and after exposure using deuterated d 3 -DNPH. This relative quantitation method was tested on human samples before and after exposure to specific amounts of alcohol. The nano-electrospray ionization (nano-ESI) in positive mode afforded excellent sensitivity with detection limits on-column in the high-attomole levels. To the best of our knowledge, this is the first report of a method using HRAM neutral loss screening of carbonyl compounds. In addition, the method allows simultaneous characterization and relative quantitation of DNPH-derivatized compounds using nano-ESI in positive mode.

The Role of Extracellular Vesicles in Metastasis

DTIC Science & Technology

2017-10-01

quantitative characterization of each cancerous ESV subpopulation’s role in cargo transfer. Specifically, we aim to (1) optimize an existing...the first quantitative data on which ESV subpopulations (exosomes, MVs, or oncosomes) manipulate the tumor microenvironment, the ESV cargo transferred...without cellular contaminants or without damaging the cargo. A second hindrance has been the lack of quantitative methods for measuring very small

Nonparticipatory Stiffness in the Male Perioral Complex

ERIC Educational Resources Information Center

Chu, Shin-Ying; Barlow, Steven M.; Lee, Jaehoon

2009-01-01

Purpose: The objective of this study was to extend previous published findings in the authors' laboratory using a new automated technology to quantitatively characterize nonparticipatory perioral stiffness in healthy male adults. Method: Quantitative measures of perioral stiffness were sampled during a nonparticipatory task using a…

Ultrasonic NDE Simulation for Composite Manufacturing Defects

NASA Technical Reports Server (NTRS)

Leckey, Cara A. C.; Juarez, Peter D.

2016-01-01

The increased use of composites in aerospace components is expected to continue into the future. The large scale use of composites in aerospace necessitates the development of composite-appropriate nondestructive evaluation (NDE) methods to quantitatively characterize defects in as-manufactured parts and damage incurred during or post manufacturing. Ultrasonic techniques are one of the most common approaches for defect/damage detection in composite materials. One key technical challenge area included in NASA's Advanced Composite's Project is to develop optimized rapid inspection methods for composite materials. Common manufacturing defects in carbon fiber reinforced polymer (CFRP) composites include fiber waviness (in-plane and out-of-plane), porosity, and disbonds; among others. This paper is an overview of ongoing work to develop ultrasonic wavefield based methods for characterizing manufacturing waviness defects. The paper describes the development and implementation of a custom ultrasound simulation tool that is used to model ultrasonic wave interaction with in-plane fiber waviness (also known as marcelling). Wavefield data processing methods are applied to the simulation data to explore possible routes for quantitative defect characterization.

Methods for Characterization of Alternative RNA Splicing.

PubMed

Harvey, Samuel E; Cheng, Chonghui

2016-01-01

Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.

Study Of Nondestructive Techniques For Testing Composites

NASA Technical Reports Server (NTRS)

Roth, D.; Kautz, H.; Draper, S.; Bansal, N.; Bowles, K.; Bashyam, M.; Bishop, C.

1995-01-01

Study evaluates some nondestructive methods for characterizing ceramic-, metal-, and polymer-matrix composite materials. Results demonstrated utility of two ultrasonic methods for obtaining quantitative data on microstructural anomalies in composite materials.

Toxicoproteomics in Aquatic Toxicology: iTRAQ Reveals Insight into Proteins Affected by 17alpha-ethinylestradiol, Dieldrin, and 17â-trenbolone

EPA Science Inventory

Toxicoproteomics is an emerging discipline in toxicology for characterizing chemical modes of action at the molecular level. We have successfully utilized a quantitative proteomics method termed isobaric tagging for relative and absolute quantitation (iTRAQ) to measure protein re...

Assessment and monitoring of forest ecosystem structure

Treesearch

Oscar A. Aguirre Calderón; Javier Jiménez Pérez; Horst Kramer

2006-01-01

Characterization of forest ecosystems structure must be based on quantitative indices that allow objective analysis of human influences or natural succession processes. The objective of this paper is the compilation of diverse quantitative variables to describe structural attributes from the arboreal stratum of the ecosystem, as well as different methods of forest...

A novel image-based quantitative method for the characterization of NETosis

PubMed Central

Zhao, Wenpu; Fogg, Darin K.; Kaplan, Mariana J.

2015-01-01

NETosis is a newly recognized mechanism of programmed neutrophil death. It is characterized by a stepwise progression of chromatin decondensation, membrane rupture, and release of bactericidal DNA-based structures called neutrophil extracellular traps (NETs). Conventional ‘suicidal’ NETosis has been described in pathogenic models of systemic autoimmune disorders. Recent in vivo studies suggest that a process of ‘vital’ NETosis also exists, in which chromatin is condensed and membrane integrity is preserved. Techniques to assess ‘suicidal’ or ‘vital’ NET formation in a specific, quantitative, rapid and semiautomated way have been lacking, hindering the characterization of this process. Here we have developed a new method to simultaneously assess both ‘suicidal’ and ‘vital’ NETosis, using high-speed multi-spectral imaging coupled to morphometric image analysis, to quantify spontaneous NET formation observed ex-vivo or stimulus-induced NET formation triggered in vitro. Use of imaging flow cytometry allows automated, quantitative and rapid analysis of subcellular morphology and texture, and introduces the potential for further investigation using NETosis as a biomarker in pre-clinical and clinical studies. PMID:26003624

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding.

PubMed

Shahi, Payam; Kim, Samuel C; Haliburton, John R; Gartner, Zev J; Abate, Adam R

2017-03-14

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

NASA Astrophysics Data System (ADS)

Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

2017-03-01

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

PubMed Central

Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

2017-01-01

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing. PMID:28290550

Diffuse Reflectance Infrared Fourier Transform Spectroscopy for the Determination of Asbestos Species in Bulk Building Materials

PubMed Central

Accardo, Grazia; Cioffi, Raffaeke; Colangelo, Francesco; d’Angelo, Raffaele; De Stefano, Luca; Paglietti, Fderica

2014-01-01

Diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy is a well-known technique for thin film characterization. Since all asbestos species exhibit intense adsorptions peaks in the 4000–400 cm−1 region of the infrared spectrum, a quantitative analysis of asbestos in bulk samples by DRIFT is possible. In this work, different quantitative analytical procedures have been used to quantify chrysotile content in bulk materials produced by building requalification: partial least squares (PLS) chemometrics, the Linear Calibration Curve Method (LCM) and the Method of Additions (MoA). Each method has its own pros and cons, but all give affordable results for material characterization: the amount of asbestos (around 10%, weight by weight) can be determined with precision and accuracy (errors less than 0.1). PMID:28788467

Validation of a Spectral Method for Quantitative Measurement of Color in Protein Drug Solutions.

PubMed

Yin, Jian; Swartz, Trevor E; Zhang, Jian; Patapoff, Thomas W; Chen, Bartolo; Marhoul, Joseph; Shih, Norman; Kabakoff, Bruce; Rahimi, Kimia

2016-01-01

A quantitative spectral method has been developed to precisely measure the color of protein solutions. In this method, a spectrophotometer is utilized for capturing the visible absorption spectrum of a protein solution, which can then be converted to color values (L*a*b*) that represent human perception of color in a quantitative three-dimensional space. These quantitative values (L*a*b*) allow for calculating the best match of a sample's color to a European Pharmacopoeia reference color solution. In order to qualify this instrument and assay for use in clinical quality control, a technical assessment was conducted to evaluate the assay suitability and precision. Setting acceptance criteria for this study required development and implementation of a unique statistical method for assessing precision in 3-dimensional space. Different instruments, cuvettes, protein solutions, and analysts were compared in this study. The instrument accuracy, repeatability, and assay precision were determined. The instrument and assay are found suitable for use in assessing color of drug substances and drug products and is comparable to the current European Pharmacopoeia visual assessment method. In the biotechnology industry, a visual assessment is the most commonly used method for color characterization, batch release, and stability testing of liquid protein drug solutions. Using this method, an analyst visually determines the color of the sample by choosing the closest match to a standard color series. This visual method can be subjective because it requires an analyst to make a judgment of the best match of color of the sample to the standard color series, and it does not capture data on hue and chroma that would allow for improved product characterization and the ability to detect subtle differences between samples. To overcome these challenges, we developed a quantitative spectral method for color determination that greatly reduces the variability in measuring color and allows for a more precise understanding of color differences. In this study, we established a statistical method for assessing precision in 3-dimensional space and demonstrated that the quantitative spectral method is comparable with respect to precision and accuracy to the current European Pharmacopoeia visual assessment method. © PDA, Inc. 2016.

Characterization of Cerebral White Matter Properties Using Quantitative Magnetic Resonance Imaging Stains

PubMed Central

Hurley, Samuel A.; Samsonov, Alexey A.; Adluru, Nagesh; Hosseinbor, Ameer Pasha; Mossahebi, Pouria; Tromp, Do P.M.; Zakszewski, Elizabeth; Field, Aaron S.

2011-01-01

Abstract The image contrast in magnetic resonance imaging (MRI) is highly sensitive to several mechanisms that are modulated by the properties of the tissue environment. The degree and type of contrast weighting may be viewed as image filters that accentuate specific tissue properties. Maps of quantitative measures of these mechanisms, akin to microstructural/environmental-specific tissue stains, may be generated to characterize the MRI and physiological properties of biological tissues. In this article, three quantitative MRI (qMRI) methods for characterizing white matter (WM) microstructural properties are reviewed. All of these measures measure complementary aspects of how water interacts with the tissue environment. Diffusion MRI, including diffusion tensor imaging, characterizes the diffusion of water in the tissues and is sensitive to the microstructural density, spacing, and orientational organization of tissue membranes, including myelin. Magnetization transfer imaging characterizes the amount and degree of magnetization exchange between free water and macromolecules like proteins found in the myelin bilayers. Relaxometry measures the MRI relaxation constants T1 and T2, which in WM have a component associated with the water trapped in the myelin bilayers. The conduction of signals between distant brain regions occurs primarily through myelinated WM tracts; thus, these methods are potential indicators of pathology and structural connectivity in the brain. This article provides an overview of the qMRI stain mechanisms, acquisition and analysis strategies, and applications for these qMRI stains. PMID:22432902

Three-dimensional characterization of pigment dispersion in dried paint films using focused ion beam-scanning electron microscopy.

PubMed

Lin, Jui-Ching; Heeschen, William; Reffner, John; Hook, John

2012-04-01

The combination of integrated focused ion beam-scanning electron microscope (FIB-SEM) serial sectioning and imaging techniques with image analysis provided quantitative characterization of three-dimensional (3D) pigment dispersion in dried paint films. The focused ion beam in a FIB-SEM dual beam system enables great control in slicing paints, and the sectioning process can be synchronized with SEM imaging providing high quality serial cross-section images for 3D reconstruction. Application of Euclidean distance map and ultimate eroded points image analysis methods can provide quantitative characterization of 3D particle distribution. It is concluded that 3D measurement of binder distribution in paints is effective to characterize the order of pigment dispersion in dried paint films.

Stable isotope dimethyl labelling for quantitative proteomics and beyond

PubMed Central

Hsu, Jue-Liang; Chen, Shu-Hui

2016-01-01

Stable-isotope reductive dimethylation, a cost-effective, simple, robust, reliable and easy-to- multiplex labelling method, is widely applied to quantitative proteomics using liquid chromatography-mass spectrometry. This review focuses on biological applications of stable-isotope dimethyl labelling for a large-scale comparative analysis of protein expression and post-translational modifications based on its unique properties of the labelling chemistry. Some other applications of the labelling method for sample preparation and mass spectrometry-based protein identification and characterization are also summarized. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644970

Epitope mapping and targeted quantitation of the cardiac biomarker troponin by SID-MRM mass spectrometry.

PubMed

Zhao, Cheng; Trudeau, Beth; Xie, Helen; Prostko, John; Fishpaugh, Jeffrey; Ramsay, Carol

2014-06-01

The absolute quantitation of the targeted protein using MS provides a promising method to evaluate/verify biomarkers used in clinical diagnostics. In this study, a cardiac biomarker, troponin I (TnI), was used as a model protein for method development. The epitope peptide of TnI was characterized by epitope excision followed with LC/MS/MS method and acted as the surrogate peptide for the targeted protein quantitation. The MRM-based MS assay using a stable internal standard that improved the selectivity, specificity, and sensitivity of the protein quantitation. Also, plasma albumin depletion and affinity enrichment of TnI by anti-TnI mAb-coated microparticles reduced the sample complexity, enhanced the dynamic range, and further improved the detecting sensitivity of the targeted protein in the biological matrix. Therefore, quantitation of TnI, a low abundant protein in human plasma, has demonstrated the applicability of the targeted protein quantitation strategy through its epitope peptide determined by epitope mapping method. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analytical robustness of quantitative NIR chemical imaging for Islamic paper characterization

NASA Astrophysics Data System (ADS)

Mahgoub, Hend; Gilchrist, John R.; Fearn, Thomas; Strlič, Matija

2017-07-01

Recently, spectral imaging techniques such as Multispectral (MSI) and Hyperspectral Imaging (HSI) have gained importance in the field of heritage conservation. This paper explores the analytical robustness of quantitative chemical imaging for Islamic paper characterization by focusing on the effect of different measurement and processing parameters, i.e. acquisition conditions and calibration on the accuracy of the collected spectral data. This will provide a better understanding of the technique that can provide a measure of change in collections through imaging. For the quantitative model, special calibration target was devised using 105 samples from a well-characterized reference Islamic paper collection. Two material properties were of interest: starch sizing and cellulose degree of polymerization (DP). Multivariate data analysis methods were used to develop discrimination and regression models which were used as an evaluation methodology for the metrology of quantitative NIR chemical imaging. Spectral data were collected using a pushbroom HSI scanner (Gilden Photonics Ltd) in the 1000-2500 nm range with a spectral resolution of 6.3 nm using a mirror scanning setup and halogen illumination. Data were acquired at different measurement conditions and acquisition parameters. Preliminary results showed the potential of the evaluation methodology to show that measurement parameters such as the use of different lenses and different scanning backgrounds may not have a great influence on the quantitative results. Moreover, the evaluation methodology allowed for the selection of the best pre-treatment method to be applied to the data.

Collection of quantitative chemical release field data.

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

Demirgian, J.; Macha, S.; Loyola Univ.

1999-01-01

Detection and quantitation of chemicals in the environment requires Fourier-transform infrared (FTIR) instruments that are properly calibrated and tested. This calibration and testing requires field testing using matrices that are representative of actual instrument use conditions. Three methods commonly used for developing calibration files and training sets in the field are a closed optical cell or chamber, a large-scale chemical release, and a small-scale chemical release. There is no best method. The advantages and limitations of each method should be considered in evaluating field results. Proper calibration characterizes the sensitivity of an instrument, its ability to detect a component inmore » different matrices, and the quantitative accuracy and precision of the results.« less

Relationship between Plaque Echo, Thickness and Neovascularization Assessed by Quantitative and Semi-quantitative Contrast-Enhanced Ultrasonography in Different Stenosis Groups.

PubMed

Song, Yan; Feng, Jun; Dang, Ying; Zhao, Chao; Zheng, Jie; Ruan, Litao

2017-12-01

The aim of this study was to determine the relationship between plaque echo, thickness and neovascularization in different stenosis groups using quantitative and semi-quantitative contrast-enhanced ultrasound (CEUS) in patients with carotid atherosclerosis plaque. A total of 224 plaques were divided into mild stenosis (<50%; 135 plaques, 60.27%), moderate stenosis (50%-69%; 39 plaques, 17.41%) and severe stenosis (70%-99%; 50 plaques, 22.32%) groups. Quantitative and semi-quantitative methods were used to assess plaque neovascularization and determine the relationship between plaque echo, thickness and neovascularization. Correlation analysis revealed no relationship of neovascularization with plaque echo in the groups using either quantitative or semi-quantitative methods. Furthermore, there was no correlation of neovascularization with plaque thickness using the semi-quantitative method. The ratio of areas under the curve (RAUC) was negatively correlated with plaque thickness (r = -0.317, p = 0.001) in the mild stenosis group. With the quartile method, plaque thickness of the mild stenosis group was divided into four groups, with significant differences between the 1.5-2.2 mm and ≥3.5 mm groups (p = 0.002), 2.3-2.8 mm and ≥3.5 mm groups (p <0.001) and 2.9-3.4 mm and ≥3.5 mm groups (p <0.001). Both semi-quantitative and quantitative CEUS methods characterizing neovascularization of plaque are equivalent with respect to assessing relationships between neovascularization, echogenicity and thickness. However, the quantitative method could fail for plaque <3.5 mm because of motion artifacts. Copyright © 2017 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

Nonlinear optical microscopy: use of second harmonic generation and two-photon microscopy for automated quantitative liver fibrosis studies.

PubMed

Sun, Wanxin; Chang, Shi; Tai, Dean C S; Tan, Nancy; Xiao, Guangfa; Tang, Huihuan; Yu, Hanry

2008-01-01

Liver fibrosis is associated with an abnormal increase in an extracellular matrix in chronic liver diseases. Quantitative characterization of fibrillar collagen in intact tissue is essential for both fibrosis studies and clinical applications. Commonly used methods, histological staining followed by either semiquantitative or computerized image analysis, have limited sensitivity, accuracy, and operator-dependent variations. The fibrillar collagen in sinusoids of normal livers could be observed through second-harmonic generation (SHG) microscopy. The two-photon excited fluorescence (TPEF) images, recorded simultaneously with SHG, clearly revealed the hepatocyte morphology. We have systematically optimized the parameters for the quantitative SHG/TPEF imaging of liver tissue and developed fully automated image analysis algorithms to extract the information of collagen changes and cell necrosis. Subtle changes in the distribution and amount of collagen and cell morphology are quantitatively characterized in SHG/TPEF images. By comparing to traditional staining, such as Masson's trichrome and Sirius red, SHG/TPEF is a sensitive quantitative tool for automated collagen characterization in liver tissue. Our system allows for enhanced detection and quantification of sinusoidal collagen fibers in fibrosis research and clinical diagnostics.

A typology of street patterns.

PubMed

Louf, Rémi; Barthelemy, Marc

2014-12-06

We propose a quantitative method to classify cities according to their street pattern. We use the conditional probability distribution of shape factor of blocks with a given area and define what could constitute the 'fingerprint' of a city. Using a simple hierarchical clustering method, these fingerprints can then serve as a basis for a typology of cities. We apply this method to a set of 131 cities in the world, and at an intermediate level of the dendrogram, we observe four large families of cities characterized by different abundances of blocks of a certain area and shape. At a lower level of the classification, we find that most European cities and American cities in our sample fall in their own sub-category, highlighting quantitatively the differences between the typical layouts of cities in both regions. We also show with the example of New York and its different boroughs, that the fingerprint of a city can be seen as the sum of the ones characterizing the different neighbourhoods inside a city. This method provides a quantitative comparison of urban street patterns, which could be helpful for a better understanding of the causes and mechanisms behind their distinct shapes. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry.

PubMed

Walzthoeni, Thomas; Joachimiak, Lukasz A; Rosenberger, George; Röst, Hannes L; Malmström, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi

2015-12-01

Chemical cross-linking in combination with mass spectrometry generates distance restraints of amino acid pairs in close proximity on the surface of native proteins and protein complexes. In this study we used quantitative mass spectrometry and chemical cross-linking to quantify differences in cross-linked peptides obtained from complexes in spatially discrete states. We describe a generic computational pipeline for quantitative cross-linking mass spectrometry consisting of modules for quantitative data extraction and statistical assessment of the obtained results. We used the method to detect conformational changes in two model systems: firefly luciferase and the bovine TRiC complex. Our method discovers and explains the structural heterogeneity of protein complexes using only sparse structural information.

Quantitative Urine Culture Method Using a Plastic „Paddle” Containing Dual Media

PubMed Central

Craig, William A.; Kunin, Calvin M.

1972-01-01

A new dip-inoculum method for quantitative urine culture is described which utilizes a dual-chambered plastic „paddle” housing both a general purpose and differential medium. Comparative bacterial counts of 1,000 clinical specimens using the pour plate and this device were identical in 82.9% and within a factor of five in 95.6%. The „paddle” detected all but 19 of 258 specimens (92.6%) with 100,000 or greater colonies per ml. This simple, convenient method should allow more extensive use of quantitative urine culture in the diagnosis and follow-up of patients with urinary tract infections in office practice. It should not be considered as a substitute for the more definitive pour plate method or for standard methods for characterization of bacteriological species when more exact information is required. PMID:4555636

Improved method for HPLC analysis of polyamines, agmatine and aromatic monoamines in plant tissue

NASA Technical Reports Server (NTRS)

Slocum, R. D.; Flores, H. E.; Galston, A. W.; Weinstein, L. H.

1989-01-01

The high performance liquid chromatographic (HPLC) method of Flores and Galston (1982 Plant Physiol 69: 701) for the separation and quantitation of benzoylated polyamines in plant tissues has been widely adopted by other workers. However, due to previously unrecognized problems associated with the derivatization of agmatine, this important intermediate in plant polyamine metabolism cannot be quantitated using this method. Also, two polyamines, putrescine and diaminopropane, also are not well resolved using this method. A simple modification of the original HPLC procedure greatly improves the separation and quantitation of these amines, and further allows the simulation analysis of phenethylamine and tyramine, which are major monoamine constituents of tobacco and other plant tissues. We have used this modified HPLC method to characterize amine titers in suspension cultured carrot (Daucas carota L.) cells and tobacco (Nicotiana tabacum L.) leaf tissues.

[Quantitative characterization of nuclear polymorphism of the epithelial cells in fibroadenomatosis and cancer of the breast].

PubMed

Ganina, K P; Petunin, Iu I; Timoshenko, Ia G

1989-01-01

A method for quantitative analysis of epithelial cell nuclear polymorphism was suggested, viz. identification of general statistical population using Petunin's criterion. This criterion was employed to assess heterogeneity of visible surface of interphase epithelial cell nuclei and to assay nuclear DNA level in fibroadenomatous hyperplasia and cancer of the breast. Heterogeneity index (h), alongside with other parameters, appeared useful for quantitative assessment of the disease: heterogeneity index values ranging 0.1-0.4 point to pronounced heterogeneity of epithelial cell nucleus surface and DNA level, and are suggestive of malignant transformation of tissue, whereas benign proliferation of the epithelium is usually characterized by 0.4 less than h less than or equal to 0.9.

Analytical Characterization of an Oil-in-Water Adjuvant Emulsion.

PubMed

Sun, Jenny; Remmele, Richard L; Sanyal, Gautam

2017-07-01

Adjuvants are typically used in subunit vaccine formulations to enhance immune responses elicited by individual antigens. Physical chemical characterization of novel adjuvants is an important step in ensuring their effective use in vaccine formulations. This paper reports application of a panel of quantitative assays developed to analyze and characterize an oil-in-water adjuvant emulsion, which contains glucopyranosyl lipid A (GLA) and is a squalene-based emulsion. GLA is a fully synthetic analogue of monophosphoryl lipid A, which is a Toll-like receptor type 4 agonist and an FDA-approved adjuvant. The GLA-stable emulsion (GLA-SE) is currently being used for a respiratory syncytial virus vaccine in a phase 2 clinical trial. GLA was quantitated using reverse-phased high-performance liquid chromatography (RP-HPLC) coupled to a mass spectrometric detector, achieving higher assay sensitivity than the charged aerosol detection routinely used. Quantitation of the excipients of GLA-SE, including squalene, egg phosphatidyl choline, and Poloxamer 188, was achieved using a simple and rapid RP-HPLC method with evaporative light scattering detection, eliminating chemical derivatization typically required for these chromophore-lacking compounds. DL-α-tocopherol, the antioxidant of the GLA-SE, was quantitated using a RP-HPLC method with conventional UV detection. The experimental results compared well with values expected for these compounds based on targeted composition of the adjuvant. The assays were applied to identify degradation of individual components in a GLA-SE sample that degraded into distinct aqueous and oil phases. The methods developed and reported here are effective tools in monitoring physicochemical integrity of the adjuvant, as well as in formulation studies.

Simple and rapid method for isolation and quantitation of polyhydroxyalkanoate by SDS-sonication treatment.

PubMed

Arikawa, Hisashi; Sato, Shunsuke; Fujiki, Tetsuya; Matsumoto, Keiji

2017-08-01

We developed a new method for isolation and quantitation of polyhydroxyalkanoate (PHA) from culture broth. In this method, the cells were sonicated in sodium dodecyl sulfate (SDS) solution and centrifuged to recover PHA. The recovered PHA was rinsed with deionized water and ethanol, and then weighed after drying. Hazardous chemicals such as chloroform, methanol, and sulfuric acid were not used, and no expensive analytical instruments were needed. We applied this method to Cupriavidus necator culture broths that included various amounts of poly(3-hydroxybutyrate) (PHB) or poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx) from flasks and jar fermentors. The quantitation by this method was practical for use with a wide range of production amounts and PHA monomer compositions compared to the conventional whole-cell methanolysis method with gas chromatographic analysis, and besides, the recovered PHAs were adequately pure (≥96% purity). Therefore, this new method would be valuable not only for quantitation of PHA but also for preparation of samples to characterize their mechanical properties. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A fluorescent-photochrome method for the quantitative characterization of solid phase antibody orientation.

PubMed

Ahluwalia, Arti; De Rossi, Danilo; Giusto, Giuseppe; Chen, Oren; Papper, Vladislav; Likhtenshtein, Gertz I

2002-06-15

A fluorescent-photochrome method of quantifying the orientation and surface density of solid phase antibodies is described. The method is based on measurements of quenching and rates of cis-trans photoisomerization and photodestruction of a stilbene-labeled hapten by a quencher in solution. These experimental parameters enable a quantitative description of the order of binding sites of antibodies immobilized on a surface and can be used to characterize the microviscosity and steric hindrance in the vicinity of the binding site. Furthermore, a theoretical method for the determination of the depth of immersion of the fluorescent label in a two-phase system was developed. The model exploits the concept of dynamic interactions and is based on the empirical dependence of parameters of static exchange interactions on distances between exchangeable centers. In the present work, anti-dinitrophenyl (DNP) antibodies and stilbene-labeled DNP were used to investigate three different protein immobilization methods: physical adsorption, covalent binding, and the Langmuir-Blodgett technique. Copyright 2002 Elsevier Science (USA).

Developing Non-Targeted Measurement Methods to Characterize the Human Exposome

EPA Science Inventory

The exposome represents all exposures experienced by an individual during their lifetime. Registered chemicals currently number in the tens-of-thousands, and therefore comprise a significant portion of the human exposome. To date, quantitative monitoring methods have been develop...

Novel quantitative methods for characterization of chemical induced functional alteration in developing neuronal cultures

EPA Science Inventory

ABSTRACT BODY: Thousands of chemicals lack adequate testing for adverse effects on nervous system development, stimulating research into alternative methods to screen chemicals for potential developmental neurotoxicity. Microelectrode arrays (MEA) collect action potential spiking...

Combinatorial modification of human histone H4 quantitated by two-dimensional liquid chromatography coupled with top down mass spectrometry.

PubMed

Pesavento, James J; Bullock, Courtney R; LeDuc, Richard D; Mizzen, Craig A; Kelleher, Neil L

2008-05-30

Quantitative proteomics has focused heavily on correlating protein abundances, ratios, and dynamics by developing methods that are protein expression-centric (e.g. isotope coded affinity tag, isobaric tag for relative and absolute quantification, etc.). These methods effectively detect changes in protein abundance but fail to provide a comprehensive perspective of the diversity of proteins such as histones, which are regulated by post-translational modifications. Here, we report the characterization of modified forms of HeLa cell histone H4 with a dynamic range >10(4) using a strictly Top Down mass spectrometric approach coupled with two dimensions of liquid chromatography. This enhanced dynamic range enabled the precise characterization and quantitation of 42 forms uniquely modified by combinations of methylation and acetylation, including those with trimethylated Lys-20, monomethylated Arg-3, and the novel dimethylated Arg-3 (each <1% of all H4 forms). Quantitative analyses revealed distinct trends in acetylation site occupancy depending on Lys-20 methylation state. Because both modifications are dynamically regulated through the cell cycle, we simultaneously investigated acetylation and methylation kinetics through three cell cycle phases and used these data to statistically assess the robustness of our quantitative analysis. This work represents the most comprehensive analysis of histone H4 forms present in human cells reported to date.

Vessel wall characterization using quantitative MRI: what's in a number?

PubMed

Coolen, Bram F; Calcagno, Claudia; van Ooij, Pim; Fayad, Zahi A; Strijkers, Gustav J; Nederveen, Aart J

2018-02-01

The past decade has witnessed the rapid development of new MRI technology for vessel wall imaging. Today, with advances in MRI hardware and pulse sequences, quantitative MRI of the vessel wall represents a real alternative to conventional qualitative imaging, which is hindered by significant intra- and inter-observer variability. Quantitative MRI can measure several important morphological and functional characteristics of the vessel wall. This review provides a detailed introduction to novel quantitative MRI methods for measuring vessel wall dimensions, plaque composition and permeability, endothelial shear stress and wall stiffness. Together, these methods show the versatility of non-invasive quantitative MRI for probing vascular disease at several stages. These quantitative MRI biomarkers can play an important role in the context of both treatment response monitoring and risk prediction. Given the rapid developments in scan acceleration techniques and novel image reconstruction, we foresee the possibility of integrating the acquisition of multiple quantitative vessel wall parameters within a single scan session.

Enumeration of viable and non-viable larvated Ascaris eggs with quantitative PCR

EPA Science Inventory

Aims: The goal of the study was to further develop an incubation-qPCR method for quantifying viable Ascaris eggs. The specific objectives were to characterize the detection limit and number of template copies per egg, determine the specificity of the method, and test the method w...

Characterization of 3D joint space morphology using an electrostatic model (with application to osteoarthritis)

NASA Astrophysics Data System (ADS)

Cao, Qian; Thawait, Gaurav; Gang, Grace J.; Zbijewski, Wojciech; Reigel, Thomas; Brown, Tyler; Corner, Brian; Demehri, Shadpour; Siewerdsen, Jeffrey H.

2015-02-01

Joint space morphology can be indicative of the risk, presence, progression, and/or treatment response of disease or trauma. We describe a novel methodology of characterizing joint space morphology in high-resolution 3D images (e.g. cone-beam CT (CBCT)) using a model based on elementary electrostatics that overcomes a variety of basic limitations of existing 2D and 3D methods. The method models each surface of a joint as a conductor at fixed electrostatic potential and characterizes the intra-articular space in terms of the electric field lines resulting from the solution of Gauss’ Law and the Laplace equation. As a test case, the method was applied to discrimination of healthy and osteoarthritic subjects (N = 39) in 3D images of the knee acquired on an extremity CBCT system. The method demonstrated improved diagnostic performance (area under the receiver operating characteristic curve, AUC > 0.98) compared to simpler methods of quantitative measurement and qualitative image-based assessment by three expert musculoskeletal radiologists (AUC = 0.87, p-value = 0.007). The method is applicable to simple (e.g. the knee or elbow) or multi-axial joints (e.g. the wrist or ankle) and may provide a useful means of quantitatively assessing a variety of joint pathologies.

Development of Mass Spectrometric Ionization Methods for Fullerenes and Fullerene Derivatives

EPA Science Inventory

Currently investigations into the environmental behavior of fullerenes and fullerene derivatives is hampered by the lack of well characterized standards and by the lack of readily available quantitative analytical methods. Reported herein are investigations into the utility of ma...

Calculating Confidence, Uncertainty, and Numbers of Samples When Using Statistical Sampling Approaches to Characterize and Clear Contaminated Areas

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

Piepel, Gregory F.; Matzke, Brett D.; Sego, Landon H.

2013-04-27

This report discusses the methodology, formulas, and inputs needed to make characterization and clearance decisions for Bacillus anthracis-contaminated and uncontaminated (or decontaminated) areas using a statistical sampling approach. Specifically, the report includes the methods and formulas for calculating the • number of samples required to achieve a specified confidence in characterization and clearance decisions • confidence in making characterization and clearance decisions for a specified number of samples for two common statistically based environmental sampling approaches. In particular, the report addresses an issue raised by the Government Accountability Office by providing methods and formulas to calculate the confidence that amore » decision area is uncontaminated (or successfully decontaminated) if all samples collected according to a statistical sampling approach have negative results. Key to addressing this topic is the probability that an individual sample result is a false negative, which is commonly referred to as the false negative rate (FNR). The two statistical sampling approaches currently discussed in this report are 1) hotspot sampling to detect small isolated contaminated locations during the characterization phase, and 2) combined judgment and random (CJR) sampling during the clearance phase. Typically if contamination is widely distributed in a decision area, it will be detectable via judgment sampling during the characterization phrase. Hotspot sampling is appropriate for characterization situations where contamination is not widely distributed and may not be detected by judgment sampling. CJR sampling is appropriate during the clearance phase when it is desired to augment judgment samples with statistical (random) samples. The hotspot and CJR statistical sampling approaches are discussed in the report for four situations: 1. qualitative data (detect and non-detect) when the FNR = 0 or when using statistical sampling methods that account for FNR > 0 2. qualitative data when the FNR > 0 but statistical sampling methods are used that assume the FNR = 0 3. quantitative data (e.g., contaminant concentrations expressed as CFU/cm2) when the FNR = 0 or when using statistical sampling methods that account for FNR > 0 4. quantitative data when the FNR > 0 but statistical sampling methods are used that assume the FNR = 0. For Situation 2, the hotspot sampling approach provides for stating with Z% confidence that a hotspot of specified shape and size with detectable contamination will be found. Also for Situation 2, the CJR approach provides for stating with X% confidence that at least Y% of the decision area does not contain detectable contamination. Forms of these statements for the other three situations are discussed in Section 2.2. Statistical methods that account for FNR > 0 currently only exist for the hotspot sampling approach with qualitative data (or quantitative data converted to qualitative data). This report documents the current status of methods and formulas for the hotspot and CJR sampling approaches. Limitations of these methods are identified. Extensions of the methods that are applicable when FNR = 0 to account for FNR > 0, or to address other limitations, will be documented in future revisions of this report if future funding supports the development of such extensions. For quantitative data, this report also presents statistical methods and formulas for 1. quantifying the uncertainty in measured sample results 2. estimating the true surface concentration corresponding to a surface sample 3. quantifying the uncertainty of the estimate of the true surface concentration. All of the methods and formulas discussed in the report were applied to example situations to illustrate application of the methods and interpretation of the results.« less

Tuned apatitic materials: Synthesis, characterization and potential antimicrobial applications

NASA Astrophysics Data System (ADS)

Fierascu, Irina; Fierascu, Radu Claudiu; Somoghi, Raluca; Ion, Rodica Mariana; Moanta, Adriana; Avramescu, Sorin Marius; Damian, Celina Maria; Ditu, Lia Mara

2018-04-01

Inorganic antimicrobial materials can be viable for multiple applications (related to its use for new buildings with special requirements related to microbiological loading, such as hospital buildings and for consolidation of cultural heritage constructions); also the use of substituted hydroxyapatites for protection of stone artefacts against environmental factors (acidic rain) and biodeterioration it's an option to no longer use of toxic substances. This paper presents methods of synthesis and characterization of the material from the point of view of the obtained structures and final applications. The materials were characterized in terms of composition and morphology (using X-ray Diffraction, X-ray Fluorescence, Inductively coupled plasma-atomic emission spectrometry, Fourier Transform Infrared Spectroscopy, X-ray Photoelectron Spectroscopy, Surface area and pore size determination). Antimicrobial activity was tested against filamentous fungi strains and pathogenic bacteria strains, using both spot on lawn qualitative method (on agar medium) and serial microdilution quantitative method (in broth medium). Further, it was evaluated the anti-biofilm activity of the tested samples toward the most important microbial strains implicated in biofilm development, using crystal violet stained biofilms microtiter assay, followed by spectrophotometric quantitative evaluation.

Characterization of European sword blades through neutron imaging techniques

NASA Astrophysics Data System (ADS)

Salvemini, F.; Grazzi, F.; Peetermans, S.; Gener, M.; Lehmann, E. H.; Zoppi, M.

2014-09-01

In the present work, we have studied two European rapier blades, dating back to the period ranging from the Late Renaissance to the Early Modern Age (about 17th to 18th century). In order to determine variation in quality and differences in technology, a study was undertaken with the purpose to observe variations in the blade microstructure (and consequently in the construction processes). The samples, which in the present case were expendable, have been investigated, preliminarily, through standard metallography and then by means of white beam and energy-selective neutron imaging. The comparison of the results, using the two techniques, turned out to be satisfactory, with a substantial quantitative agreement of the results obtained with the two techniques, and show the complementarity of the two methods. Metallography has been considered up to now the method of choice for metal material characterization. The correspondence between the two methods, as well as the non-invasive character of the neutron-based techniques and its possibility to obtain 3D reconstruction, candidate neutron imaging as an important and quantitatively reliable technique for metal characterization.

A First Laboratory Utilizing NMR for Undergraduate Education: Characterization of Edible Fats and Oils by Quantitative [superscript 13]C NMR

ERIC Educational Resources Information Center

Fry, Charles G.; Hofstetter, Heike; Bowman, Matthew D.

2017-01-01

Quantitative [superscript 13]C NMR provides a straightforward method of analyzing edible oils in undergraduate chemistry laboratories. [superscript 13]C spectra are relatively easy to understand, and are much simpler to analyze and workup than corresponding [superscript 1]H spectra. Average chain length, degree of saturation, and average…

A method to characterize the roughness of 2-D line features: recrystallization boundaries.

PubMed

Sun, J; Zhang, Y B; Dahl, A B; Conradsen, K; Juul Jensen, D

2017-03-01

A method is presented, which allows quantification of the roughness of nonplanar boundaries of objects for which the neutral plane is not known. The method provides quantitative descriptions of both the local and global characteristics. How the method can be used to estimate the sizes of rough features and local curvatures is also presented. The potential of the method is illustrated by quantification of the roughness of two recrystallization boundaries in a pure Al specimen characterized by scanning electron microscopy. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Optofluidic time-stretch quantitative phase microscopy.

PubMed

Guo, Baoshan; Lei, Cheng; Wu, Yi; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Lee, Sangwook; Isozaki, Akihiro; Li, Ming; Jiang, Yiyue; Yasumoto, Atsushi; Di Carlo, Dino; Tanaka, Yo; Yatomi, Yutaka; Ozeki, Yasuyuki; Goda, Keisuke

2018-03-01

Innovations in optical microscopy have opened new windows onto scientific research, industrial quality control, and medical practice over the last few decades. One of such innovations is optofluidic time-stretch quantitative phase microscopy - an emerging method for high-throughput quantitative phase imaging that builds on the interference between temporally stretched signal and reference pulses by using dispersive properties of light in both spatial and temporal domains in an interferometric configuration on a microfluidic platform. It achieves the continuous acquisition of both intensity and phase images with a high throughput of more than 10,000 particles or cells per second by overcoming speed limitations that exist in conventional quantitative phase imaging methods. Applications enabled by such capabilities are versatile and include characterization of cancer cells and microalgal cultures. In this paper, we review the principles and applications of optofluidic time-stretch quantitative phase microscopy and discuss its future perspective. Copyright © 2017 Elsevier Inc. All rights reserved.

Onset dynamics of action potentials in rat neocortical neurons and identified snail neurons: quantification of the difference.

PubMed

Volgushev, Maxim; Malyshev, Aleksey; Balaban, Pavel; Chistiakova, Marina; Volgushev, Stanislav; Wolf, Fred

2008-04-09

The generation of action potentials (APs) is a key process in the operation of nerve cells and the communication between neurons. Action potentials in mammalian central neurons are characterized by an exceptionally fast onset dynamics, which differs from the typically slow and gradual onset dynamics seen in identified snail neurons. Here we describe a novel method of analysis which provides a quantitative measure of the onset dynamics of action potentials. This method captures the difference between the fast, step-like onset of APs in rat neocortical neurons and the gradual, exponential-like AP onset in identified snail neurons. The quantitative measure of the AP onset dynamics, provided by the method, allows us to perform quantitative analyses of factors influencing the dynamics.

Onset Dynamics of Action Potentials in Rat Neocortical Neurons and Identified Snail Neurons: Quantification of the Difference

PubMed Central

Volgushev, Maxim; Malyshev, Aleksey; Balaban, Pavel; Chistiakova, Marina; Volgushev, Stanislav; Wolf, Fred

2008-01-01

The generation of action potentials (APs) is a key process in the operation of nerve cells and the communication between neurons. Action potentials in mammalian central neurons are characterized by an exceptionally fast onset dynamics, which differs from the typically slow and gradual onset dynamics seen in identified snail neurons. Here we describe a novel method of analysis which provides a quantitative measure of the onset dynamics of action potentials. This method captures the difference between the fast, step-like onset of APs in rat neocortical neurons and the gradual, exponential-like AP onset in identified snail neurons. The quantitative measure of the AP onset dynamics, provided by the method, allows us to perform quantitative analyses of factors influencing the dynamics. PMID:18398478

Robust and fast characterization of OCT-based optical attenuation using a novel frequency-domain algorithm for brain cancer detection

NASA Astrophysics Data System (ADS)

Yuan, Wu; Kut, Carmen; Liang, Wenxuan; Li, Xingde

2017-03-01

Cancer is known to alter the local optical properties of tissues. The detection of OCT-based optical attenuation provides a quantitative method to efficiently differentiate cancer from non-cancer tissues. In particular, the intraoperative use of quantitative OCT is able to provide a direct visual guidance in real time for accurate identification of cancer tissues, especially these without any obvious structural layers, such as brain cancer. However, current methods are suboptimal in providing high-speed and accurate OCT attenuation mapping for intraoperative brain cancer detection. In this paper, we report a novel frequency-domain (FD) algorithm to enable robust and fast characterization of optical attenuation as derived from OCT intensity images. The performance of this FD algorithm was compared with traditional fitting methods by analyzing datasets containing images from freshly resected human brain cancer and from a silica phantom acquired by a 1310 nm swept-source OCT (SS-OCT) system. With graphics processing unit (GPU)-based CUDA C/C++ implementation, this new attenuation mapping algorithm can offer robust and accurate quantitative interpretation of OCT images in real time during brain surgery.

Light scattering application for quantitative estimation of apoptosis

NASA Astrophysics Data System (ADS)

Bilyy, Rostyslav O.; Stoika, Rostyslav S.; Getman, Vasyl B.; Bilyi, Olexander I.

2004-05-01

Estimation of cell proliferation and apoptosis are in focus of instrumental methods used in modern biomedical sciences. Present study concerns monitoring of functional state of cells, specifically the development of their programmed death or apoptosis. The available methods for such purpose are either very expensive, or require time-consuming operations. Their specificity and sensitivity are frequently not sufficient for making conclusions which could be used in diagnostics or treatment monitoring. We propose a novel method for apoptosis measurement based on quantitative determination of cellular functional state taking into account their physical characteristics. This method uses the patented device -- laser microparticle analyser PRM-6 -- for analyzing light scattering by the microparticles, including cells. The method gives an opportunity for quick, quantitative, simple (without complicated preliminary cell processing) and relatively cheap measurement of apoptosis in cellular population. The elaborated method was used for studying apoptosis expression in murine leukemia cells of L1210 line and human lymphoblastic leukemia cells of K562 line. The results obtained by the proposed method permitted measuring cell number in tested sample, detecting and quantitative characterization of functional state of cells, particularly measuring the ratio of the apoptotic cells in suspension.

In-focal-plane characterization of excitation distribution for quantitative fluorescence microscopy applications

NASA Astrophysics Data System (ADS)

Dietrich, Klaus; Brülisauer, Martina; ćaǧin, Emine; Bertsch, Dietmar; Lüthi, Stefan; Heeb, Peter; Stärker, Ulrich; Bernard, André

2017-06-01

The applications of fluorescence microscopy span medical diagnostics, bioengineering and biomaterial analytics. Full exploitation of fluorescent microscopy is hampered by imperfections in illumination, detection and filtering. Mainly, errors stem from deviations induced by real-world components inducing spatial or angular variations of propagation properties along the optical path, and they can be addressed through consistent and accurate calibration. For many applications, uniform signal to noise ratio (SNR) over the imaging area is required. Homogeneous SNR can be achieved by quantifying and compensating for the signal bias. We present a method to quantitatively characterize novel reference materials as a calibration reference for biomaterials analytics. The reference materials under investigation comprise thin layers of fluorophores embedded in polymer matrices. These layers are highly homogeneous in their fluorescence response, where cumulative variations do not exceed 1% over the field of view (1.5 x 1.1 mm). An automated and reproducible measurement methodology, enabling sufficient correction for measurement artefacts, is reported. The measurement setup is equipped with an autofocus system, ensuring that the measured film quality is not artificially increased by out-of-focus reduction of the system modulation transfer function. The quantitative characterization method is suitable for analysis of modified bio-materials, especially through patterned protein decoration. The imaging method presented here can be used to statistically analyze protein patterns, thereby increasing both precision and throughput. Further, the method can be developed to include a reference emitter and detector pair on the image surface of the reference object, in order to provide traceable measurements.

Low angle light scattering analysis: a novel quantitative method for functional characterization of human and murine platelet receptors.

PubMed

Mindukshev, Igor; Gambaryan, Stepan; Kehrer, Linda; Schuetz, Claudia; Kobsar, Anna; Rukoyatkina, Natalia; Nikolaev, Viacheslav O; Krivchenko, Alexander; Watson, Steve P; Walter, Ulrich; Geiger, Joerg

2012-07-01

Determinations of platelet receptor functions are indispensable diagnostic indicators of cardiovascular and hemostatic diseases including hereditary and acquired receptor defects and receptor responses to drugs. However, presently available techniques for assessing platelet function have some disadvantages, such as low sensitivity and the requirement of large sample sizes and unphysiologically high agonist concentrations. Our goal was to develop and initially characterize a new technique designed to quantitatively analyze platelet receptor activation and platelet function on the basis of measuring changes in low angle light scattering. We developed a novel technique based on low angle light scattering registering changes in light scattering at a range of different angles in platelet suspensions during activation. The method proved to be highly sensitive for simultaneous real time detection of changes in size and shape of platelets during activation. Unlike commonly-used methods, the light scattering method could detect platelet shape change and aggregation in response to nanomolar concentrations of extracellular nucleotides. Furthermore, our results demonstrate that the advantages of the light scattering method make it a choice method for platelet receptor monitoring and for investigation of both murine and human platelets in disease models. Our data demonstrate the suitability and superiority of this new low angle light scattering method for comprehensive analyses of platelet receptors and functions. This highly sensitive, quantitative, and online detection of essential physiological, pathophysiological and pharmacological-response properties of human and mouse platelets is a significant improvement over conventional techniques.

Characterization of Vocal Fold Vibration in Sulcus Vocalis Using High-Speed Digital Imaging

ERIC Educational Resources Information Center

Yamauchi, Akihito; Yokonishi, Hisayuki; Imagawa, Hiroshi; Sakakibara, Ken-Ichi; Nito, Takaharu; Tayama, Niro; Yamasoba, Tatsuya

2017-01-01

Purpose: The aim of the present study was to qualitatively and quantitatively characterize vocal fold vibrations in sulcus vocalis by high-speed digital imaging (HSDI) and to clarify the correlations between HSDI-derived parameters and traditional vocal parameters. Method: HSDI was performed in 20 vocally healthy subjects (8 men and 12 women) and…

A Novel Method for Measurement and Characterization of Soil Macroporosity

Treesearch

Christopher Barton; Tasos Karathanasis

2002-01-01

Quantitative macropore characterizations were performed in large zero-tension soil lysimeters of a Maury silt loam (fine, mixed, mesic Typic Paleudalf) and a Loradale silt loam (fine, silty, mixed, mesic Typic Axgiudoll) soil in an effort to assess potential colloid transport. Steel pipe sections (50 cm diameter X 100 cm length) were hydraulically driven into the soil...

New method for the temperature-programmed desorption (TPD) of ammonia experiment for characterization of zeolite acidity: a review.

PubMed

Niwa, Miki; Katada, Naonobu

2013-10-01

In this review, a method for the temperature-programmed desorption (TPD) of ammonia experiment for the characterization of zeolite acidity and its improvement by simultaneous IR measurement and DFT calculation are described. First, various methods of ammonia TPD are explained, since the measurements have been conducted under the concepts of kinetics, equilibrium, or diffusion control. It is however emphasized that the ubiquitous TPD experiment is governed by the equilibrium between ammonia molecules in the gas phase and on the surface. Therefore, a method to measure quantitatively the strength of the acid site (∆H upon ammonia desorption) under equilibrium-controlled conditions is elucidated. Then, a quantitative relationship between ∆H and H0 function is proposed, based on which the acid strength ∆H can be converted into the H0 function. The identification of the desorption peaks and the quantitative measurement of the number of acid sites are then explained. In order to overcome a serious disadvantage of the method (i.e., no information is provided about the structure of acid sites), the simultaneous measurement of IR spectroscopy with ammonia TPD, named IRMS-TPD (infrared spectroscopy/mass spectrometry-temperature-programmed desorption), is proposed. Based on this improved measurement, Brønsted and Lewis acid sites were differentiated and the distribution of Brønsted OH was revealed. The acidity characterized by IRMS-TPD was further supported by the theoretical DFT calculation. Thus, the advanced study of zeolite acidity at the molecular level was made possible. Advantages and disadvantages of the ammonia TPD experiment are discussed, and understanding of the catalytic cracking activity based on the derived acidic profile is explained. Copyright © 2013 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative characterization of gold nanoparticles by size-exclusion and hydrodynamic chromatography, coupled to inductively coupled plasma mass spectrometry and quasi-elastic light scattering.

PubMed

Pitkänen, Leena; Montoro Bustos, Antonio R; Murphy, Karen E; Winchester, Michael R; Striegel, André M

2017-08-18

The physicochemical characterization of nanoparticles (NPs) is of paramount importance for tailoring and optimizing the properties of these materials as well as for evaluating the environmental fate and impact of the NPs. Characterizing the size and chemical identity of disperse NP sample populations can be accomplished by coupling size-based separation methods to physical and chemical detection methods. Informed decisions regarding the NPs can only be made, however, if the separations themselves are quantitative, i.e., if all or most of the analyte elutes from the column within the course of the experiment. We undertake here the size-exclusion chromatographic characterization of Au NPs spanning a six-fold range in mean size. The main problem which has plagued the size-exclusion chromatography (SEC) analysis of Au NPs, namely lack of quantitation accountability due to generally poor NP recovery from the columns, is overcome by carefully matching eluent formulation with the appropriate stationary phase chemistry, and by the use of on-line inductively coupled plasma mass spectrometry (ICP-MS) detection. Here, for the first time, we demonstrate the quantitative analysis of Au NPs by SEC/ICP-MS, including the analysis of a ternary NP blend. The SEC separations are contrasted to HDC/ICP-MS (HDC: hydrodynamic chromatography) separations employing the same stationary phase chemistry. Additionally, analysis of Au NPs by HDC with on-line quasi-elastic light scattering (QELS) allowed for continuous determination of NP size across the chromatographic profiles, circumventing issues related to the shedding of fines from the SEC columns. The use of chemically homogeneous reference materials with well-defined size range allowed for better assessment of the accuracy and precision of the analyses, and for a more direct interpretation of results, than would be possible employing less rigorously characterized analytes. Published by Elsevier B.V.

Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources

EPA Science Inventory

The state of California has mandated the preparation of a guidance document on the application of fecal source identification methods for recreational water quality management. California contains the fifth highest population of cattle in the United States, making the inclusio...

Tannin structural elucidation and quantitative ³¹P NMR analysis. 2. Hydrolyzable tannins and proanthocyanidins.

PubMed

Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

2013-10-02

An unprecedented analytical method that allows simultaneous structural and quantitative characterization of all functional groups present in tannins is reported. In situ labeling of all labile H groups (aliphatic and phenolic hydroxyls and carboxylic acids) with a phosphorus-containing reagent (Cl-TMDP) followed by quantitative ³¹P NMR acquisition constitutes a novel fast and reliable analytical tool for the analysis of tannins and proanthocyanidins with significant implications for the fields of food and feed analyses, tannery, and the development of natural polyphenolics containing products.

A-TEEMTM, a new molecular fingerprinting technique: simultaneous absorbance-transmission and fluorescence excitation-emission matrix method

NASA Astrophysics Data System (ADS)

Quatela, Alessia; Gilmore, Adam M.; Steege Gall, Karen E.; Sandros, Marinella; Csatorday, Karoly; Siemiarczuk, Alex; (Ben Yang, Boqian; Camenen, Loïc

2018-04-01

We investigate the new simultaneous absorbance-transmission and fluorescence excitation-emission matrix method for rapid and effective characterization of the varying components from a mixture. The absorbance-transmission and fluorescence excitation-emission matrix method uniquely facilitates correction of fluorescence inner-filter effects to yield quantitative fluorescence spectral information that is largely independent of component concentration. This is significant because it allows one to effectively monitor quantitative component changes using multivariate methods and to generate and evaluate spectral libraries. We present the use of this novel instrument in different fields: i.e. tracking changes in complex mixtures including natural water, wine as well as monitoring stability and aggregation of hormones for biotherapeutics.

Noncontact quantitative biomechanical characterization of cardiac muscle using shear wave imaging optical coherence tomography

PubMed Central

Wang, Shang; Lopez, Andrew L.; Morikawa, Yuka; Tao, Ge; Li, Jiasong; Larina, Irina V.; Martin, James F.; Larin, Kirill V.

2014-01-01

We report on a quantitative optical elastographic method based on shear wave imaging optical coherence tomography (SWI-OCT) for biomechanical characterization of cardiac muscle through noncontact elasticity measurement. The SWI-OCT system employs a focused air-puff device for localized loading of the cardiac muscle and utilizes phase-sensitive OCT to monitor the induced tissue deformation. Phase information from the optical interferometry is used to reconstruct 2-D depth-resolved shear wave propagation inside the muscle tissue. Cross-correlation of the displacement profiles at various spatial locations in the propagation direction is applied to measure the group velocity of the shear waves, based on which the Young’s modulus of tissue is quantified. The quantitative feature and measurement accuracy of this method is demonstrated from the experiments on tissue-mimicking phantoms with the verification using uniaxial compression test. The experiments are performed on ex vivo cardiac muscle tissue from mice with normal and genetically altered myocardium. Our results indicate this optical elastographic technique is useful as a noncontact tool to assist the cardiac muscle studies. PMID:25071943

Three-dimensional cardiac architecture determined by two-photon microtomy

NASA Astrophysics Data System (ADS)

Huang, Hayden; MacGillivray, Catherine; Kwon, Hyuk-Sang; Lammerding, Jan; Robbins, Jeffrey; Lee, Richard T.; So, Peter

2009-07-01

Cardiac architecture is inherently three-dimensional, yet most characterizations rely on two-dimensional histological slices or dissociated cells, which remove the native geometry of the heart. We previously developed a method for labeling intact heart sections without dissociation and imaging large volumes while preserving their three-dimensional structure. We further refine this method to permit quantitative analysis of imaged sections. After data acquisition, these sections are assembled using image-processing tools, and qualitative and quantitative information is extracted. By examining the reconstructed cardiac blocks, one can observe end-to-end adjacent cardiac myocytes (cardiac strands) changing cross-sectional geometries, merging and separating from other strands. Quantitatively, representative cross-sectional areas typically used for determining hypertrophy omit the three-dimensional component; we show that taking orientation into account can significantly alter the analysis. Using fast-Fourier transform analysis, we analyze the gross organization of cardiac strands in three dimensions. By characterizing cardiac structure in three dimensions, we are able to determine that the α crystallin mutation leads to hypertrophy with cross-sectional area increases, but not necessarily via changes in fiber orientation distribution.

Sibling recurrence and the genetic epidemiology of autism

PubMed Central

Constantino, John N.; Zhang, Yi; Frazier, Thomas; Abbacchi, Anna M.; Law, Paul

2010-01-01

Objective Although the symptoms of autism exhibit quantitative distributions in nature, estimates of recurrence risk in families have never previously considered or incorporated quantitative characterization of the autistic phenotype among siblings. Method We report the results of quantitative characterization of 2,920 children from 1,235 families participating in a national volunteer register who met the criteria of having at least one child clinically-affected by an autism spectrum disorder (ASD) and at least one full biological sibling. Results The occurrence of a traditionally-defined ASD in an additional child occurred in 10.9% of the families. An additional 20% of non-ASD-affected siblings had a history of language delay, half of whom had exhibited autistic qualities of speech. Quantitative characterization using the Social Responsiveness Scale (SRS) supported previously-reported aggregation of a wide range of subclinical (quantitative) autistic traits among otherwise unaffected children in multiple-incidence families, and a relative absence of quantitative autistic traits among siblings in single-incidence autism families. Girls whose standardized severity ratings fell above a first percentile severity threshold (relative to the general population distribution) were significantly less likely to have elicited community diagnoses than their male counterparts. Conclusions These data suggest that, depending on how it is defined, sibling recurrence in ASD may exceed previously-published estimates, and varies as a function of family type. The results support differences in mechanisms of genetic transmission between simplex and multiplex autism, and advance current understanding of the genetic epidemiology of autism. PMID:20889652

Quantitative characterization of the carbon/carbon composites components based on video of polarized light microscope.

PubMed

Li, Yixian; Qi, Lehua; Song, Yongshan; Chao, Xujiang

2017-06-01

The components of carbon/carbon (C/C) composites have significant influence on the thermal and mechanical properties, so a quantitative characterization of component is necessary to study the microstructure of C/C composites, and further to improve the macroscopic properties of C/C composites. Considering the extinction crosses of the pyrocarbon matrix have significant moving features, the polarized light microscope (PLM) video is used to characterize C/C composites quantitatively because it contains sufficiently dynamic and structure information. Then the optical flow method is introduced to compute the optical flow field between the adjacent frames, and segment the components of C/C composites from PLM image by image processing. Meanwhile the matrix with different textures is re-segmented by the length difference of motion vectors, and then the component fraction of each component and extinction angle of pyrocarbon matrix are calculated directly. Finally, the C/C composites are successfully characterized from three aspects of carbon fiber, pyrocarbon, and pores by a series of image processing operators based on PLM video, and the errors of component fractions are less than 15%. © 2017 Wiley Periodicals, Inc.

Orthogonal analytical methods for botanical standardization: Determination of green tea catechins by qNMR and LC-MS/MS

PubMed Central

Napolitano, José G.; Gödecke, Tanja; Lankin, David C.; Jaki, Birgit U.; McAlpine, James B.; Chen, Shao-Nong; Pauli, Guido F.

2013-01-01

The development of analytical methods for parallel characterization of multiple phytoconstituents is essential to advance the quality control of herbal products. While chemical standardization is commonly carried out by targeted analysis using gas or liquid chromatography-based methods, more universal approaches based on quantitative 1H NMR (qHNMR) measurements are being used increasingly in the multi-targeted assessment of these complex mixtures. The present study describes the development of a 1D qHNMR-based method for simultaneous identification and quantification of green tea constituents. This approach utilizes computer-assisted 1H iterative Full Spin Analysis (HiFSA) and enables rapid profiling of seven catechins in commercial green tea extracts. The qHNMR results were cross-validated against quantitative profiles obtained with an orthogonal LC-MS/MS method. The relative strengths and weaknesses of both approaches are discussed, with special emphasis on the role of identical reference standards in qualitative and quantitative analyses. PMID:23870106

Quantitative analysis of fracture surface by roughness and fractal method

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

Li, X.W.; Tian, J.F.; Kang, Y.

1995-09-01

In recent years there has been extensive research and great development in Quantitative Fractography, which acts as an integral part of fractographic analysis. A prominent technique for studying the fracture surface is based on fracture profile generation and the major means for characterizing the profile quantitatively are roughness and fractal methods. By this way, some quantitative indexes such as the roughness parameters R{sub L} for profile and R{sub S} for surface, fractal dimensions D{sub L} for profile and D{sub S} for surface can be measured. Given the relationships between the indexes and the mechanical properties of materials, it is possiblemore » to achieve the goal of protecting materials from fracture. But, as the case stands, the theory and experimental technology of quantitative fractography are still imperfect and remain to be studied further. Recently, Gokhale and Underwood et al have proposed an assumption-free method for estimating the surface roughness by vertically sectioning the fracture surface with sections at an angle of 120 deg with each other, which could be expressed as follows: R{sub S} = {ovr R{sub L}{center_dot}{Psi}} where {Psi} is the profile structure factor. This method is based on the classical sterological principles and verified with the aid of computer simulations for some ruled surfaces. The results are considered to be applicable to fracture surfaces with any arbitrary complexity and anisotropy. In order to extend the detail applications to this method in quantitative fractography, the authors made a study on roughness and fractal methods dependent on this method by performing quantitative measurements on some typical low-temperature impact fractures.« less

Allele-specific methylated multiplex real-time quantitative PCR (ASMM RTQ-PCR), a powerful method for diagnosing loss of imprinting of the 11p15 region in Russell Silver and Beckwith Wiedemann syndromes.

PubMed

Azzi, Salah; Steunou, Virginie; Rousseau, Alexandra; Rossignol, Sylvie; Thibaud, Nathalie; Danton, Fabienne; Le Jule, Marilyne; Gicquel, Christine; Le Bouc, Yves; Netchine, Irène

2011-02-01

Many human syndromes involve a loss of imprinting (LOI) due to a loss (LOM) or a gain of DNA methylation (GOM). Most LOI occur as mosaics and can therefore be difficult to detect with conventional methods. The human imprinted 11p15 region is crucial for the control of fetal growth, and LOI at this locus is associated with two clinical disorders with opposite phenotypes: Beckwith-Wiedemann syndrome (BWS), characterized by fetal overgrowth and a high risk of tumors, and Russell-Silver syndrome (RSS), characterized by intrauterine and postnatal growth restriction. Until recently, we have been using Southern blotting for the diagnosis of RSS and BWS. We describe here a powerful quantitative technique, allele-specific methylated multiplex real-time quantitative PCR (ASMM RTQ-PCR), for the diagnosis of these two complex disorders. We first checked the specificity of the probes and primers used for ASMM RTQ-PCR. We then carried out statistical validation for this method, on both retrospective and prospective populations of patients. This analysis demonstrated that ASMM RTQ-PCR is more sensitive than Southern blotting for detecting low degree of LOI. Moreover, ASMM RTQ-PCR is a very rapid, reliable, simple, safe, and cost effective method. © 2011 Wiley-Liss, Inc.

Analysis of Natural Toxins by Liquid Chromatography-Chemiluminescence Nitrogen Detection and Application to the Preparation of Certified Reference Materials.

PubMed

Thomas, Krista; Wechsler, Dominik; Chen, Yi-Min; Crain, Sheila; Quilliam, Michael A

2016-09-01

The implementation of instrumental analytical methods such as LC-MS for routine monitoring of toxins requires the availability of accurate calibration standards. This is a challenge because many toxins are rare, expensive, dangerous to handle, and/or unstable, and simple gravimetric procedures are not reliable for establishing accurate concentrations in solution. NMR has served as one method of qualitative and quantitative characterization of toxin calibration solution Certified Reference Materials (CRMs). LC with chemiluminescence N detection (LC-CLND) was selected as a complementary method for comprehensive characterization of CRMs because it provides a molar response to N. Here we report on our investigation of LC-CLND as a method suitable for quantitative analysis of nitrogenous toxins. It was demonstrated that a wide range of toxins could be analyzed quantitatively by LC-CLND. Furthermore, equimolar responses among diverse structures were established and it was shown that a single high-purity standard such as caffeine could be used for instrument calibration. The limit of detection was approximately 0.6 ng N. Measurement of several of Canada's National Research Council toxin CRMs with caffeine as the calibrant showed precision averaging 2% RSD and accuracy ranging from 97 to 102%. Application of LC-CLND to the production of calibration solution CRMs and the establishment of traceability of measurement results are presented.

Automatic registration of ICG images using mutual information and perfusion analysis

NASA Astrophysics Data System (ADS)

Kim, Namkug; Seo, Jong-Mo; Lee, June-goo; Kim, Jong Hyo; Park, Kwangsuk; Yu, Hyeong-Gon; Yu, Young Suk; Chung, Hum

2005-04-01

Introduction: Indocyanin green fundus angiographic images (ICGA) of the eyes is useful method in detecting and characterizing the choroidal neovascularization (CNV), which is the major cause of the blindness over 65 years of age. To investigate the quantitative analysis of the blood flow on ICGA, systematic approach for automatic registration of using mutual information and a quantitative analysis was developed. Methods: Intermittent sequential images of indocyanin green angiography were acquired by Heidelberg retinal angiography that uses the laser scanning system for the image acquisition. Misalignment of the each image generated by the minute eye movement of the patients was corrected by the mutual information method because the distribution of the contrast media on image is changing throughout the time sequences. Several region of interest (ROI) were selected by a physician and the intensities of the selected region were plotted according to the time sequences. Results: The registration of ICGA time sequential images is required not only translate transform but also rotational transform. Signal intensities showed variation based on gamma-variate function depending on ROIs and capillary vessels show more variance of signal intensity than major vessels. CNV showed intermediate variance of signal intensity and prolonged transit time. Conclusion: The resulting registered images can be used not only for quantitative analysis, but also for perfusion analysis. Various investigative approached on CNV using this method will be helpful in the characterization of the lesion and follow-up.

Evaluation of fecal indicator and pathogenic bacteria originating from swine manure applied to agricultural lands using culture-based and quantitative real-time PCR methods.

EPA Science Inventory

Fecal bacteria, including those originating from concentrated animal feeding operations, are a leading contributor to water quality impairments in agricultural areas. Rapid and reliable methods are needed that can accurately characterize fecal pollution in agricultural settings....

Evaluation of Fecal Indicator and Pathogenic Bacteria Originating from Swine Manure Applied to Agricultural Lands Using Culture-Based and Quantitative Real-Time PCR Methods

EPA Science Inventory

Fecal bacteria, including those originating from concentrated animal feeding operations, are a leading contributor to water quality impairments in agricultural areas. Rapid and reliable methods are needed that can accurately characterize fecal pollution in agricultural settings....

Semi-quantitative estimation by IR of framework, extraframework and defect Al species of HBEA zeolites.

PubMed

Marques, João P; Gener, Isabelle; Ayrault, Philippe; Lopes, José M; Ribeiro, F Ramôa; Guisnet, Michel

2004-10-21

A simple method based on the characterization (composition, Bronsted and Lewis acidities) of acid treated HBEA zeolites was developed for estimating the concentrations of framework, extraframework and defect Al species.

THE PRACTICE OF STRUCTURE ACTIVITY RELATIONSHIPS (SAR) IN TOXICOLOGY

EPA Science Inventory

Both qualitative and quantitative modeling methods relating chemical structure to biological activity, called structure-activity relationship analyses or SAR, are applied to the prediction and characterization of chemical toxicity. This minireview will discuss some generic issue...

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

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

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Analysis of defect structure in silicon. Silicon sheet growth development for the large area silicon sheet task of the Low-Cost Solar array Project

NASA Technical Reports Server (NTRS)

Natesh, R.; Mena, M.; Plichta, M.; Smith, J. M.; Sellani, M. A.

1982-01-01

One hundred ninety-three silicon sheet samples, approximately 880 square centimeters, were analyzed for twin boundary density, dislocation pit density, and grain boundary length. One hundred fifteen of these samples were manufactured by a heat exchanger method, thirty-eight by edge defined film fed growth, twenty-three by the silicon on ceramics process, and ten by the dendritic web process. Seven solar cells were also step-etched to determine the internal defect distribution on these samples. Procedures were developed or the quantitative characterization of structural defects such as dislocation pits, precipitates, twin & grain boundaries using a QTM 720 quantitative image analyzing system interfaced with a PDP 11/03 mini computer. Characterization of the grain boundary length per unit area for polycrystalline samples was done by using the intercept method on an Olympus HBM Microscope.

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

Tannin structural elucidation and quantitative ³¹P NMR analysis. 1. Model compounds.

PubMed

Melone, Federica; Saladino, Raffaele; Lange, Heiko; Crestini, Claudia

2013-10-02

Tannins and flavonoids are secondary metabolites of plants that display a wide array of biological activities. This peculiarity is related to the inhibition of extracellular enzymes that occurs through the complexation of peptides by tannins. Not only the nature of these interactions, but more fundamentally also the structure of these heterogeneous polyphenolic molecules are not completely clear. This first paper describes the development of a new analytical method for the structural characterization of tannins on the basis of tannin model compounds employing an in situ labeling of all labile H groups (aliphatic OH, phenolic OH, and carboxylic acids) with a phosphorus reagent. The ³¹P NMR analysis of ³¹P-labeled samples allowed the unprecedented quantitative and qualitative structural characterization of hydrolyzable tannins, proanthocyanidins, and catechin tannin model compounds, forming the foundations for the quantitative structural elucidation of a variety of actual tannin samples described in part 2 of this series.

Tissue Characterization with Quantitative High-Resolution Magic Angle Spinning Chemical Exchange Saturation Transfer Z-Spectroscopy.

PubMed

Zhou, Iris Yuwen; Fuss, Taylor L; Igarashi, Takahiro; Jiang, Weiping; Zhou, Xin; Cheng, Leo L; Sun, Phillip Zhe

2016-11-01

Chemical exchange saturation transfer (CEST) provides sensitive magnetic resonance (MR) contrast for probing dilute compounds via exchangeable protons, serving as an emerging molecular imaging methodology. CEST Z-spectrum is often acquired by sweeping radiofrequency saturation around bulk water resonance, offset by offset, to detect CEST effects at characteristic chemical shift offsets, which requires prolonged acquisition time. Herein, combining high-resolution magic angle spinning (HRMAS) with concurrent application of gradient and rf saturation to achieve fast Z-spectral acquisition, we demonstrated the feasibility of fast quantitative HRMAS CEST Z-spectroscopy. The concept was validated with phantoms, which showed excellent agreement with results obtained from conventional HRMAS MR spectroscopy (MRS). We further utilized the HRMAS Z-spectroscopy for fast ex vivo quantification of ischemic injury with rodent brain tissues after ischemic stroke. This method allows rapid and quantitative CEST characterization of biological tissues and shows potential for a host of biomedical applications.

Quantitative Analysis of Cancer Cell Migration in Gradients Of EGF, HGF, and SDF-alpha Using a Microfluidic Chemotaxis Device

DTIC Science & Technology

2005-01-01

Quantitative Analysis of Cancer Cell Migration in Gradients of EGF, HGF, and SDF-alpha Using a Microfluidic Chemotaxis Device The University of California...allowing for parallel analysis . Additionally, simple methods of localizing gels into microdevices are demonstrated. The device was characterized by...To overcome some of these drawbacks, several approaches have utilized free diffusion to produce gradients in static environ - ments.5-9 However

High-resolution gas chromatography/mass spectrometry method for characterization and quantitative analysis of ginkgolic acids in Ginkgo biloba plants, extracts, and dietary supplements.

PubMed

Wang, Mei; Zhao, Jianping; Avula, Bharathi; Wang, Yan-Hong; Avonto, Cristina; Chittiboyina, Amar G; Wylie, Philip L; Parcher, Jon F; Khan, Ikhlas A

2014-12-17

A high-resolution gas chromatography/mass spectrometry (GC/MS) with selected ion monitor method focusing on the characterization and quantitative analysis of ginkgolic acids (GAs) in Ginkgo biloba L. plant materials, extracts, and commercial products was developed and validated. The method involved sample extraction with (1:1) methanol and 10% formic acid, liquid-liquid extraction with n-hexane, and derivatization with trimethylsulfonium hydroxide (TMSH). Separation of two saturated (C13:0 and C15:0) and six unsaturated ginkgolic acid methyl esters with different positional double bonds (C15:1 Δ8 and Δ10, C17:1 Δ8, Δ10, and Δ12, and C17:2) was achieved on a very polar (88% cyanopropyl) aryl-polysiloxane HP-88 capillary GC column. The double bond positions in the GAs were determined by ozonolysis. The developed GC/MS method was validated according to ICH guidelines, and the quantitation results were verified by comparison with a standard high-performance liquid chromatography method. Nineteen G. biloba authenticated and commercial plant samples and 21 dietary supplements purported to contain G. biloba leaf extracts were analyzed. Finally, the presence of the marker compounds, terpene trilactones and flavonol glycosides for Ginkgo biloba in the dietary supplements was determined by UHPLC/MS and used to confirm the presence of G. biloba leaf extracts in all of the botanical dietary supplements.

Quantitative NDE of Composite Structures at NASA

NASA Technical Reports Server (NTRS)

Cramer, K. Elliott; Leckey, Cara A. C.; Howell, Patricia A.; Johnston, Patrick H.; Burke, Eric R.; Zalameda, Joseph N.; Winfree, William P.; Seebo, Jeffery P.

2015-01-01

The use of composite materials continues to increase in the aerospace community due to the potential benefits of reduced weight, increased strength, and manufacturability. Ongoing work at NASA involves the use of the large-scale composite structures for spacecraft (payload shrouds, cryotanks, crew modules, etc). NASA is also working to enable the use and certification of composites in aircraft structures through the Advanced Composites Project (ACP). The rapid, in situ characterization of a wide range of the composite materials and structures has become a critical concern for the industry. In many applications it is necessary to monitor changes in these materials over a long time. The quantitative characterization of composite defects such as fiber waviness, reduced bond strength, delamination damage, and microcracking are of particular interest. The research approaches of NASA's Nondestructive Evaluation Sciences Branch include investigation of conventional, guided wave, and phase sensitive ultrasonic methods, infrared thermography and x-ray computed tomography techniques. The use of simulation tools for optimizing and developing these methods is also an active area of research. This paper will focus on current research activities related to large area NDE for rapidly characterizing aerospace composites.

Characterization and quantification of flavonoids and saponins in adzuki bean (Vigna angularis L.) by HPLC-DAD-ESI-MSn analysis.

PubMed

Liu, Rui; Cai, Zongwei; Xu, Baojun

2017-09-22

Bioactive activities of adzuki bean have been widely reported, however, the phytochemical information of adzuki bean is incomplete. The aim of this study was to characterize and quantify flavonoids and saponins in adzuki bean. High performance liquid chromatography with diode array detection and electro spray ionization-tandem multi-stage mass spectrometry (HPLC-DAD-ESI-MS n ) were applied to do qualitative and quantitative analyses. A total of 15 compounds from adzuki bean were identified by HPLC-DAD-ESI-MS n . Among 15 compounds identified, four flavonoids (catechin, vitexin-4″-O-glucoside, quercetin-3-O-glucoside, and quercetin-3-O-rutinoside) and six saponins (azukisaponin I, II, III, IV, V, and VI) in adzuki bean were further quantified by external calibration method using HPLC-MS with the program of time segment and extract ion chromatogram (EIC) analysis. Current qualitative and quantitative method based on HPLC and MS technique provides a scientific basis for in vitro and in vivo pharmacological study in the future. Graphical abstract Isolation and characterization of flavonoids and saponins from adzuki bean.

Quantitative photoacoustic elasticity and viscosity imaging for cirrhosis detection

NASA Astrophysics Data System (ADS)

Wang, Qian; Shi, Yujiao; Yang, Fen; Yang, Sihua

2018-05-01

Elasticity and viscosity assessments are essential for understanding and characterizing the physiological and pathological states of tissue. In this work, by establishing a photoacoustic (PA) shear wave model, an approach for quantitative PA elasticity imaging based on measurement of the rise time of the thermoelastic displacement was developed. Thus, using an existing PA viscoelasticity imaging method that features a phase delay measurement, quantitative PA elasticity imaging and viscosity imaging can be obtained in a simultaneous manner. The method was tested and validated by imaging viscoelastic agar phantoms prepared at different agar concentrations, and the imaging data were in good agreement with rheometry results. Ex vivo experiments on liver pathological models demonstrated the capability for cirrhosis detection, and the results were consistent with the corresponding histological results. This method expands the scope of conventional PA imaging and has potential to become an important alternative imaging modality.

Three-dimensional modeling and quantitative analysis of gap junction distributions in cardiac tissue.

PubMed

Lackey, Daniel P; Carruth, Eric D; Lasher, Richard A; Boenisch, Jan; Sachse, Frank B; Hitchcock, Robert W

2011-11-01

Gap junctions play a fundamental role in intercellular communication in cardiac tissue. Various types of heart disease including hypertrophy and ischemia are associated with alterations of the spatial arrangement of gap junctions. Previous studies applied two-dimensional optical and electron-microscopy to visualize gap junction arrangements. In normal cardiomyocytes, gap junctions were primarily found at cell ends, but can be found also in more central regions. In this study, we extended these approaches toward three-dimensional reconstruction of gap junction distributions based on high-resolution scanning confocal microscopy and image processing. We developed methods for quantitative characterization of gap junction distributions based on analysis of intensity profiles along the principal axes of myocytes. The analyses characterized gap junction polarization at cell ends and higher-order statistical image moments of intensity profiles. The methodology was tested in rat ventricular myocardium. Our analysis yielded novel quantitative data on gap junction distributions. In particular, the analysis demonstrated that the distributions exhibit significant variability with respect to polarization, skewness, and kurtosis. We suggest that this methodology provides a quantitative alternative to current approaches based on visual inspection, with applications in particular in characterization of engineered and diseased myocardium. Furthermore, we propose that these data provide improved input for computational modeling of cardiac conduction.

Analysis of atomic force microscopy data for surface characterization using fuzzy logic

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

Al-Mousa, Amjed, E-mail: aalmousa@vt.edu; Niemann, Darrell L.; Niemann, Devin J.

2011-07-15

In this paper we present a methodology to characterize surface nanostructures of thin films. The methodology identifies and isolates nanostructures using Atomic Force Microscopy (AFM) data and extracts quantitative information, such as their size and shape. The fuzzy logic based methodology relies on a Fuzzy Inference Engine (FIE) to classify the data points as being top, bottom, uphill, or downhill. The resulting data sets are then further processed to extract quantitative information about the nanostructures. In the present work we introduce a mechanism which can consistently distinguish crowded surfaces from those with sparsely distributed structures and present an omni-directional searchmore » technique to improve the structural recognition accuracy. In order to demonstrate the effectiveness of our approach we present a case study which uses our approach to quantitatively identify particle sizes of two specimens each with a unique gold nanoparticle size distribution. - Research Highlights: {yields} A Fuzzy logic analysis technique capable of characterizing AFM images of thin films. {yields} The technique is applicable to different surfaces regardless of their densities. {yields} Fuzzy logic technique does not require manual adjustment of the algorithm parameters. {yields} The technique can quantitatively capture differences between surfaces. {yields} This technique yields more realistic structure boundaries compared to other methods.« less

Characterization, thermal stability studies, and analytical method development of Paromomycin for formulation development.

PubMed

Khan, Wahid; Kumar, Neeraj

2011-06-01

Paromomycin (PM) is an aminoglycoside antibiotic, first isolated in the 1950s, and approved in 2006 for treatment of visceral leishmaniasis. Although isolated six decades back, sufficient information essential for development of pharmaceutical formulation is not available for PM. The purpose of this paper was to determine thermal stability and development of new analytical method for formulation development of PM. PM was characterized by thermoanalytical (DSC, TGA, and HSM) and by spectroscopic (FTIR) techniques and these techniques were used to establish thermal stability of PM after heating PM at 100, 110, 120, and 130 °C for 24 h. Biological activity of these heated samples was also determined by microbiological assay. Subsequently, a simple, rapid and sensitive RP-HPLC method for quantitative determination of PM was developed using pre-column derivatization with 9-fluorenylmethyl chloroformate. The developed method was applied to estimate PM quantitatively in two parenteral dosage forms. PM was successfully characterized by various stated techniques. These techniques indicated stability of PM for heating up to 120 °C for 24 h, but when heated at 130 °C, PM is liable to degradation. This degradation is also observed in microbiological assay where PM lost ∼30% of its biological activity when heated at 130 °C for 24 h. New analytical method was developed for PM in the concentration range of 25-200 ng/ml with intra-day and inter-day variability of < 2%RSD. Characterization techniques were established and stability of PM was determined successfully. Developed analytical method was found sensitive, accurate, and precise for quantification of PM. Copyright © 2010 John Wiley & Sons, Ltd. Copyright © 2010 John Wiley & Sons, Ltd.

Ratiometric spectral imaging for fast tumor detection and chemotherapy monitoring in vivo

PubMed Central

Hwang, Jae Youn; Gross, Zeev; Gray, Harry B.; Medina-Kauwe, Lali K.; Farkas, Daniel L.

2011-01-01

We report a novel in vivo spectral imaging approach to cancer detection and chemotherapy assessment. We describe and characterize a ratiometric spectral imaging and analysis method and evaluate its performance for tumor detection and delineation by quantitatively monitoring the specific accumulation of targeted gallium corrole (HerGa) into HER2-positive (HER2 +) breast tumors. HerGa temporal accumulation in nude mice bearing HER2 + breast tumors was monitored comparatively by a. this new ratiometric imaging and analysis method; b. established (reflectance and fluorescence) spectral imaging; c. more commonly used fluorescence intensity imaging. We also tested the feasibility of HerGa imaging in vivo using the ratiometric spectral imaging method for tumor detection and delineation. Our results show that the new method not only provides better quantitative information than typical spectral imaging, but also better specificity than standard fluorescence intensity imaging, thus allowing enhanced in vivo outlining of tumors and dynamic, quantitative monitoring of targeted chemotherapy agent accumulation into them. PMID:21721808

Normalized Temperature Contrast Processing in Infrared Flash Thermography

NASA Technical Reports Server (NTRS)

Koshti, Ajay M.

2016-01-01

The paper presents further development in normalized contrast processing used in flash infrared thermography method. Method of computing normalized image or pixel intensity contrast, and normalized temperature contrast are provided. Methods of converting image contrast to temperature contrast and vice versa are provided. Normalized contrast processing in flash thermography is useful in quantitative analysis of flash thermography data including flaw characterization and comparison of experimental results with simulation. Computation of normalized temperature contrast involves use of flash thermography data acquisition set-up with high reflectivity foil and high emissivity tape such that the foil, tape and test object are imaged simultaneously. Methods of assessing other quantitative parameters such as emissivity of object, afterglow heat flux, reflection temperature change and surface temperature during flash thermography are also provided. Temperature imaging and normalized temperature contrast processing provide certain advantages over normalized image contrast processing by reducing effect of reflected energy in images and measurements, therefore providing better quantitative data. Examples of incorporating afterglow heat-flux and reflection temperature evolution in flash thermography simulation are also discussed.

Composition and Quantitation of Microalgal Lipids by ERETIC 1H NMR Method

PubMed Central

Nuzzo, Genoveffa; Gallo, Carmela; d’Ippolito, Giuliana; Cutignano, Adele; Sardo, Angela; Fontana, Angelo

2013-01-01

Accurate characterization of biomass constituents is a crucial aspect of research in the biotechnological application of natural products. Here we report an efficient, fast and reproducible method for the identification and quantitation of fatty acids and complex lipids (triacylglycerols, glycolipids, phospholipids) in microalgae under investigation for the development of functional health products (probiotics, food ingredients, drugs, etc.) or third generation biofuels. The procedure consists of extraction of the biological matrix by modified Folch method and direct analysis of the resulting material by proton nuclear magnetic resonance (1H NMR). The protocol uses a reference electronic signal as external standard (ERETIC method) and allows assessment of total lipid content, saturation degree and class distribution in both high throughput screening of algal collection and metabolic analysis during genetic or culturing studies. As proof of concept, the methodology was applied to the analysis of three microalgal species (Thalassiosira weissflogii, Cyclotella cryptica and Nannochloropsis salina) which drastically differ for the qualitative and quantitative composition of their fatty acid-based lipids. PMID:24084790

The Integral Method, a new approach to quantify bactericidal activity.

PubMed

Gottardi, Waldemar; Pfleiderer, Jörg; Nagl, Markus

2015-08-01

The bactericidal activity (BA) of antimicrobial agents is generally derived from the results of killing assays. A reliable quantitative characterization and particularly a comparison of these substances, however, are impossible with this information. We here propose a new method that takes into account the course of the complete killing curve for assaying BA and that allows a clear-cut quantitative comparison of antimicrobial agents with only one number. The new Integral Method, based on the reciprocal area below the killing curve, reliably calculates an average BA [log10 CFU/min] and, by implementation of the agent's concentration C, the average specific bactericidal activity SBA=BA/C [log10 CFU/min/mM]. Based on experimental killing data, the pertaining BA and SBA values of exemplary active halogen compounds were established, allowing quantitative assertions. N-chlorotaurine (NCT), chloramine T (CAT), monochloramine (NH2Cl), and iodine (I2) showed extremely diverging SBA values of 0.0020±0.0005, 1.11±0.15, 3.49±0.22, and 291±137log10 CFU/min/mM, respectively, against Staphylococcus aureus. This immediately demonstrates an approximately 550-fold stronger activity of CAT, 1730-fold of NH2Cl, and 150,000-fold of I2 compared to NCT. The inferred quantitative assertions and conclusions prove the new method suitable for characterizing bactericidal activity. Its application comprises the effect of defined agents on various bacteria, the consequence of temperature shifts, the influence of varying drug structure, dose-effect relationships, ranking of isosteric agents, comparison of competing commercial antimicrobial formulations, and the effect of additives. Copyright © 2015 Elsevier B.V. All rights reserved.

A method of combined single-cell electrophysiology and electroporation.

PubMed

Graham, Lyle J; Del Abajo, Ricardo; Gener, Thomas; Fernandez, Eduardo

2007-02-15

This paper describes a method of extracellular recording and subsequent electroporation with the same electrode in single retinal ganglion cells in vitro. We demonstrate anatomical identification of neurons whose receptive fields were measured quantitatively. We discuss how this simple method should also be applicable for the delivery of a variety of intracellular agents, including gene delivery, to physiologically characterized neurons, both in vitro and in vivo.

Three-dimensional Hessian matrix-based quantitative vascular imaging of rat iris with optical-resolution photoacoustic microscopy in vivo

NASA Astrophysics Data System (ADS)

Zhao, Huangxuan; Wang, Guangsong; Lin, Riqiang; Gong, Xiaojing; Song, Liang; Li, Tan; Wang, Wenjia; Zhang, Kunya; Qian, Xiuqing; Zhang, Haixia; Li, Lin; Liu, Zhicheng; Liu, Chengbo

2018-04-01

For the diagnosis and evaluation of ophthalmic diseases, imaging and quantitative characterization of vasculature in the iris are very important. The recently developed photoacoustic imaging, which is ultrasensitive in imaging endogenous hemoglobin molecules, provides a highly efficient label-free method for imaging blood vasculature in the iris. However, the development of advanced vascular quantification algorithms is still needed to enable accurate characterization of the underlying vasculature. We have developed a vascular information quantification algorithm by adopting a three-dimensional (3-D) Hessian matrix and applied for processing iris vasculature images obtained with a custom-built optical-resolution photoacoustic imaging system (OR-PAM). For the first time, we demonstrate in vivo 3-D vascular structures of a rat iris with a the label-free imaging method and also accurately extract quantitative vascular information, such as vessel diameter, vascular density, and vascular tortuosity. Our results indicate that the developed algorithm is capable of quantifying the vasculature in the 3-D photoacoustic images of the iris in-vivo, thus enhancing the diagnostic capability of the OR-PAM system for vascular-related ophthalmic diseases in vivo.

Histological Image Processing Features Induce a Quantitative Characterization of Chronic Tumor Hypoxia

PubMed Central

Grabocka, Elda; Bar-Sagi, Dafna; Mishra, Bud

2016-01-01

Hypoxia in tumors signifies resistance to therapy. Despite a wealth of tumor histology data, including anti-pimonidazole staining, no current methods use these data to induce a quantitative characterization of chronic tumor hypoxia in time and space. We use image-processing algorithms to develop a set of candidate image features that can formulate just such a quantitative description of xenographed colorectal chronic tumor hypoxia. Two features in particular give low-variance measures of chronic hypoxia near a vessel: intensity sampling that extends radially away from approximated blood vessel centroids, and multithresholding to segment tumor tissue into normal, hypoxic, and necrotic regions. From these features we derive a spatiotemporal logical expression whose truth value depends on its predicate clauses that are grounded in this histological evidence. As an alternative to the spatiotemporal logical formulation, we also propose a way to formulate a linear regression function that uses all of the image features to learn what chronic hypoxia looks like, and then gives a quantitative similarity score once it is trained on a set of histology images. PMID:27093539

Quantitative characterization of colloidal assembly of graphene oxide-silver nanoparticle hybrids using aerosol differential mobility-coupled mass analyses.

PubMed

Nguyen, Thai Phuong; Chang, Wei-Chang; Lai, Yen-Chih; Hsiao, Ta-Chih; Tsai, De-Hao

2017-10-01

In this work, we develop an aerosol-based, time-resolved ion mobility-coupled mass characterization method to investigate colloidal assembly of graphene oxide (GO)-silver nanoparticle (AgNP) hybrid nanostructure on a quantitative basis. Transmission electron microscopy (TEM) and zeta potential (ZP) analysis were used to provide visual information and elemental-based particle size distributions, respectively. Results clearly show a successful controlled assembly of GO-AgNP by electrostatic-directed heterogeneous aggregation between GO and bovine serum albumin (BSA)-functionalized AgNP under an acidic environment. Additionally, physical size, mass, and conformation (i.e., number of AgNP per nanohybrid) of GO-AgNP were shown to be proportional to the number concentration ratio of AgNP to GO (R) and the selected electrical mobility diameter. An analysis of colloidal stability of GO-AgNP indicates that the stability increased with its absolute ZP, which was dependent on R and environmental pH. The work presented here provides a proof of concept for systematically synthesizing hybrid colloidal nanomaterials through the tuning of surface chemistry in aqueous phase with the ability in quantitative characterization. Graphical Abstract Colloidal assembly of graphene oxide-silver nanoparticle hybrids characterized by aerosol differential mobility-coupled mass analyses.

Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy.

PubMed

Giss, Dominic; Kemmerling, Simon; Dandey, Venkata; Stahlberg, Henning; Braun, Thomas

2014-05-20

Multimolecular protein complexes are important for many cellular processes. However, the stochastic nature of the cellular interactome makes the experimental detection of complex protein assemblies difficult and quantitative analysis at the single molecule level essential. Here, we present a fast and simple microfluidic method for (i) the quantitative isolation of endogenous levels of untagged protein complexes from minute volumes of cell lysates under close to physiological conditions and (ii) the labeling of specific components constituting these complexes. The method presented uses specific antibodies that are conjugated via a photocleavable linker to magnetic beads that are trapped in microcapillaries to immobilize the target proteins. Proteins are released by photocleavage, eluted, and subsequently analyzed by quantitative transmission electron microscopy at the single molecule level. Additionally, before photocleavage, immunogold can be employed to label proteins that interact with the primary target protein. Thus, the presented method provides a new way to study the interactome and, in combination with single molecule transmission electron microscopy, to structurally characterize the large, dynamic, heterogeneous multimolecular protein complexes formed.

Characterization of Nanopipettes.

PubMed

Perry, David; Momotenko, Dmitry; Lazenby, Robert A; Kang, Minkyung; Unwin, Patrick R

2016-05-17

Nanopipettes are widely used in electrochemical and analytical techniques as tools for sizing, sequencing, sensing, delivery, and imaging. For all of these applications, the response of a nanopipette is strongly affected by its geometry and surface chemistry. As the size of nanopipettes becomes smaller, precise geometric characterization is increasingly important, especially if nanopipette probes are to be used for quantitative studies and analysis. This contribution highlights the combination of data from voltage-scanning ion conductivity experiments, transmission electron microscopy and finite element method simulations to fully characterize nanopipette geometry and surface charge characteristics, with an accuracy not achievable using existing approaches. Indeed, it is shown that presently used methods for characterization can lead to highly erroneous information on nanopipettes. The new approach to characterization further facilitates high-level quantification of the behavior of nanopipettes in electrochemical systems, as demonstrated herein for a scanning ion conductance microscope setup.

Methodology for quantifying uncertainty in coal assessments with an application to a Texas lignite deposit

USGS Publications Warehouse

Olea, R.A.; Luppens, J.A.; Tewalt, S.J.

2011-01-01

A common practice for characterizing uncertainty in coal resource assessments has been the itemization of tonnage at the mining unit level and the classification of such units according to distance to drilling holes. Distance criteria, such as those used in U.S. Geological Survey Circular 891, are still widely used for public disclosure. A major deficiency of distance methods is that they do not provide a quantitative measure of uncertainty. Additionally, relying on distance between data points alone does not take into consideration other factors known to have an influence on uncertainty, such as spatial correlation, type of probability distribution followed by the data, geological discontinuities, and boundary of the deposit. Several geostatistical methods have been combined to formulate a quantitative characterization for appraising uncertainty. Drill hole datasets ranging from widespread exploration drilling to detailed development drilling from a lignite deposit in Texas were used to illustrate the modeling. The results show that distance to the nearest drill hole is almost completely unrelated to uncertainty, which confirms the inadequacy of characterizing uncertainty based solely on a simple classification of resources by distance classes. The more complex statistical methods used in this study quantify uncertainty and show good agreement between confidence intervals in the uncertainty predictions and data from additional drilling. ?? 2010.

Development and validation of a single robust HPLC method for the characterization of a pharmaceutical starting material and impurities from three suppliers using three separate synthetic routes.

PubMed

Sheldon, E M; Downar, J B

2000-08-15

Novel approaches to the development of analytical procedures for monitoring incoming starting material in support of chemical/pharmaceutical processes are described. High technology solutions were utilized for timely process development and preparation of high quality clinical supplies. A single robust HPLC method was developed and characterized for the analysis of the key starting material from three suppliers. Each supplier used a different process for the preparation of this material and, therefore, each suppliers' material exhibited a unique impurity profile. The HPLC method utilized standard techniques acceptable for release testing in a QC/manufacturing environment. An automated experimental design protocol was used to characterize the robustness of the HPLC method. The method was evaluated for linearity, limit of quantitation, solution stability, and precision of replicate injections. An LC-MS method that emulated the release HPLC method was developed and the identities of impurities were mapped between the two methods.

Quantitative 3D determination of self-assembled structures on nanoparticles using small angle neutron scattering.

PubMed

Luo, Zhi; Marson, Domenico; Ong, Quy K; Loiudice, Anna; Kohlbrecher, Joachim; Radulescu, Aurel; Krause-Heuer, Anwen; Darwish, Tamim; Balog, Sandor; Buonsanti, Raffaella; Svergun, Dmitri I; Posocco, Paola; Stellacci, Francesco

2018-04-09

The ligand shell (LS) determines a number of nanoparticles' properties. Nanoparticles' cores can be accurately characterized; yet the structure of the LS, when composed of mixture of molecules, can be described only qualitatively (e.g., patchy, Janus, and random). Here we show that quantitative description of the LS' morphology of monodisperse nanoparticles can be obtained using small-angle neutron scattering (SANS), measured at multiple contrasts, achieved by either ligand or solvent deuteration. Three-dimensional models of the nanoparticles' core and LS are generated using an ab initio reconstruction method. Characteristic length scales extracted from the models are compared with simulations. We also characterize the evolution of the LS upon thermal annealing, and investigate the LS morphology of mixed-ligand copper and silver nanoparticles as well as gold nanoparticles coated with ternary mixtures. Our results suggest that SANS combined with multiphase modeling is a versatile approach for the characterization of nanoparticles' LS.

Preparation of surface enhanced Raman substrate and its characterization

NASA Astrophysics Data System (ADS)

Liu, Y.; Wang, J. Y.; Wang, J. Q.

2017-10-01

Surface enhanced Raman spectroscopy (SERS) is a fast, convenient and highly sensitive detection technique, and preparing the good effect and repeatable substrate is the key to realize the trace amount and quantitative detection in the field of food safety detection. In this paper, a surface enhanced Raman substrate based on submicrometer silver particles structure was prepared by chemical deposition method, and characterized its structure and optical properties.

Spectroscopic characterization and quantitative determination of atorvastatin calcium impurities by novel HPLC method

NASA Astrophysics Data System (ADS)

Gupta, Lokesh Kumar

2012-11-01

Seven process related impurities were identified by LC-MS in the atorvastatin calcium drug substance. These impurities were identified by LC-MS. The structure of impurities was confirmed by modern spectroscopic techniques like 1H NMR and IR and physicochemical studies conducted by using synthesized authentic reference compounds. The synthesized reference samples of the impurity compounds were used for the quantitative HPLC determination. These impurities were detected by newly developed gradient, reverse phase high performance liquid chromatographic (HPLC) method. The system suitability of HPLC analysis established the validity of the separation. The analytical method was validated according to International Conference of Harmonization (ICH) with respect to specificity, precision, accuracy, linearity, robustness and stability of analytical solutions to demonstrate the power of newly developed HPLC method.

A case of Pitt-Hopkins syndrome with absence of hyperventilation.

PubMed

Inati, Adlette; Abbas, Hussein A; Korjian, Serge; Daaboul, Yazan; Harajeily, Mohamad; Saab, Raya

2013-12-01

Pitt-Hopkins syndrome is characterized by mental retardation, hyperventilation, and dysmorphic features due to TCF4 mutations. We report a case of Pitt-Hopkins syndrome in a 2½-year-old boy presenting with psychomotor retardation, recurrent respiratory tract infections, and dysmorphic features with absence of hyperventilation or other breathing abnormalities. Comparative genomic hybridization and quantitative real-time polymerase chain reaction were used to confirm TCF4 haploinsufficiency. Pitt-Hopkins syndrome is a rare debilitating disease that should be in the differential diagnosis of other neurodevelopmental disorders characterized by mental retardation and hypotonicity despite the absence of hyperapnea and seizures. Quantitative real-time polymerase chain reaction is another method to identify TCF4 and to confirm Pitt-Hopkins syndrome diagnosis.

Devising tissue ingrowth metrics: a contribution to the computational characterization of engineered soft tissue healing.

PubMed

Alves, Antoine; Attik, Nina; Bayon, Yves; Royet, Elodie; Wirth, Carine; Bourges, Xavier; Piat, Alexis; Dolmazon, Gaëlle; Clermont, Gaëlle; Boutrand, Jean-Pierre; Grosgogeat, Brigitte; Gritsch, Kerstin

2018-03-14

The paradigm shift brought about by the expansion of tissue engineering and regenerative medicine away from the use of biomaterials, currently questions the value of histopathologic methods in the evaluation of biological changes. To date, the available tools of evaluation are not fully consistent and satisfactory for these advanced therapies. We have developed a new, simple and inexpensive quantitative digital approach that provides key metrics for structural and compositional characterization of the regenerated tissues. For example, metrics provide the tissue ingrowth rate (TIR) which integrates two separate indicators; the cell ingrowth rate (CIR) and the total collagen content (TCC) as featured in the equation, TIR% = CIR% + TCC%. Moreover a subset of quantitative indicators describing the directional organization of the collagen (relating structure and mechanical function of tissues), the ratio of collagen I to collagen III (remodeling quality) and the optical anisotropy property of the collagen (maturity indicator) was automatically assessed as well. Using an image analyzer, all metrics were extracted from only two serial sections stained with either Feulgen & Rossenbeck (cell specific) or Picrosirius Red F3BA (collagen specific). To validate this new procedure, three-dimensional (3D) scaffolds were intraperitoneally implanted in healthy and in diabetic rats. It was hypothesized that quantitatively, the healing tissue would be significantly delayed and of poor quality in diabetic rats in comparison to healthy rats. In addition, a chemically modified 3D scaffold was similarly implanted in a third group of healthy rats with the assumption that modulation of the ingrown tissue would be quantitatively present in comparison to the 3D scaffold-healthy group. After 21 days of implantation, both hypotheses were verified by use of this novel computerized approach. When the two methods were run in parallel, the quantitative results revealed fine details and differences not detected by the semi-quantitative assessment, demonstrating the importance of quantitative analysis in the performance evaluation of soft tissue healing. This automated and supervised method reduced operator dependency and proved to be simple, sensitive, cost-effective and time-effective. It supports objective therapeutic comparisons and helps to elucidate regeneration and the dynamics of a functional tissue.

A Method to Measure and Estimate Normalized Contrast in Infrared Flash Thermography

NASA Technical Reports Server (NTRS)

Koshti, Ajay M.

2016-01-01

The paper presents further development in normalized contrast processing used in flash infrared thermography method. Method of computing normalized image or pixel intensity contrast, and normalized temperature contrast are provided. Methods of converting image contrast to temperature contrast and vice versa are provided. Normalized contrast processing in flash thermography is useful in quantitative analysis of flash thermography data including flaw characterization and comparison of experimental results with simulation. Computation of normalized temperature contrast involves use of flash thermography data acquisition set-up with high reflectivity foil and high emissivity tape such that the foil, tape and test object are imaged simultaneously. Methods of assessing other quantitative parameters such as emissivity of object, afterglow heat flux, reflection temperature change and surface temperature during flash thermography are also provided. Temperature imaging and normalized temperature contrast processing provide certain advantages over normalized image contrast processing by reducing effect of reflected energy in images and measurements, therefore providing better quantitative data. Examples of incorporating afterglow heat-flux and reflection temperature evolution in flash thermography simulation are also discussed.

Quantitative characterization of the spatial distribution of particles in materials: Application to materials processing

NASA Technical Reports Server (NTRS)

Parse, Joseph B.; Wert, J. A.

1991-01-01

Inhomogeneities in the spatial distribution of second phase particles in engineering materials are known to affect certain mechanical properties. Progress in this area has been hampered by the lack of a convenient method for quantitative description of the spatial distribution of the second phase. This study intends to develop a broadly applicable method for the quantitative analysis and description of the spatial distribution of second phase particles. The method was designed to operate on a desktop computer. The Dirichlet tessellation technique (geometrical method for dividing an area containing an array of points into a set of polygons uniquely associated with the individual particles) was selected as the basis of an analysis technique implemented on a PC. This technique is being applied to the production of Al sheet by PM processing methods; vacuum hot pressing, forging, and rolling. The effect of varying hot working parameters on the spatial distribution of aluminum oxide particles in consolidated sheet is being studied. Changes in distributions of properties such as through-thickness near-neighbor distance correlate with hot-working reduction.

[Application and Integration of Qualitative and Quantitative Research Methods in Intervention Studies in Rehabilitation Research].

PubMed

Wirtz, M A; Strohmer, J

2016-06-01

In order to develop and evaluate interventions in rehabilitation research a wide range of empirical research methods may be adopted. Qualitative research methods emphasize the relevance of an open research focus and a natural proximity to research objects. Accordingly, using qualitative methods special benefits may arise if researchers strive to identify and organize unknown information aspects (inductive purpose). Particularly, quantitative research methods require a high degree of standardization and transparency of the research process. Furthermore, a clear definition of efficacy and effectiveness exists (deductive purpose). These paradigmatic approaches are characterized by almost opposite key characteristics, application standards, purposes and quality criteria. Hence, specific aspects have to be regarded if researchers aim to select or combine those approaches in order to ensure an optimal gain in knowledge. © Georg Thieme Verlag KG Stuttgart · New York.

Qualitative and quantitative analysis of flavonoids in Sophora tonkinensis by LC/MS and HPLC.

PubMed

He, Chang-Ming; Cheng, Zhi-Hong; Chen, Dao-Feng

2013-11-01

To develop analytical methods for the identification and determination of the flavonoids in Sophora tonkinensis for comprehensive quality evaluation. An HPLC-DAD-ESI-MS method was used for the separation and characterization of the flavonoids in S. tonkinensis, and a liquid chromatographic method was employed to simultaneously determine five major active flavonoids in this crude drug. Seventeen flavonoids were identified, among which, seven were unambiguously identified as trifolirhizin, quercetin, formononetin, macckiain, kurarinone, sophoranone, and sophoranochromene by comparing their retention times, and UV and MS spectra with those of the authentic compounds, and the other ten flavonoids were tentatively identified by comparing their UV and MS/MS spectra with those of literature data. Furthermore, five major active flavonoids, including trifolirhizin, quercetin, maackiain, sophoranone, and sophoranochromene were determined in S. tonkinensis. All calibration curves expressed good linearity (r > 0.999 8) within the test ranges, and the recovery from this method was 96.40%-104.43%. The developed HPLC method was successfully applied to quantitatively determine the five flavonoids in seventeen samples of S. tonkinensis. The developed method rapidly characterized the bioactive flavonoids of S. tonkinensis, and could be readily utilized to enhance the quality assurance approaches for this traditional Chinese medicine. Copyright © 2013 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

Qualitative and quantitative analyses of Epimedium wushanense by high-performance liquid chromatography coupled with diode array detection and electrospray ionization tandem mass spectrometry.

PubMed

Li, Hui-fang; Guan, Xiang-yu; Ye, Min; Xiang, Cheng; Lin, Chang-hu; Sun, Chao; Guo, De-an

2011-06-01

A new HPLC-DAD-ESI-MS(n) method was developed for rapid separation, characterization and quantitation of flavonoids in Epimedium wushanense, a popular Chinese herbal medicine. For qualitative identification, a total of 37 compounds were characterized from the underground and aerial parts of E. wushanense. Among them, 28 compounds were prenylated flavonoids, and 23 were confirmed by comparing with reference standards. For quantitative analysis, 12 major flavonoids including kaempferol glycosides, desmethylicaritin glycosides, and icaritin glycosides were simultaneously determined by HPLC/UV. Samples were separated on a Waters Symmetry C(18) column at 35 °C eluted with a gradient three-component mobile phase of acetonitrile, methanol, and water containing 0.03% v/v formic acid. All the flavonoids showed good linearity (r(2) ≥0.9997). The recoveries varied from 92.6 to 106.1% at three concentration levels. This method was applied to the determination of 20 samples of different geographical sources, harvesting time, and plant parts. Contents of the predominant flavonoid, epimedin C, ranged from 1.4 to 5.1% in aerial parts and 1.0 to 2.8% in underground parts. The methods established in this paper were simple and reliable and could be used for the quality control of E. wushanense. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification, quantitation, and method validation for flavan-3-ols in fermented ready-to-drink teas from the Italian market using HPLC-UV/DAD and LC-MS/MS.

PubMed

Cordero, Chiara; Canale, Francesca; Del Rio, Daniele; Bicchi, Carlo

2009-11-01

The present study is focused on flavan-3-ols characterizing the antioxidant properties of fermented tea (Camellia sinensis). These bioactive compounds, object of nutritional claims in commercial products, should be quantified with rigorous analytical procedures whose accuracy and precision have been stated with a certain level of confidence. An HPLC-UV/DAD method, able to detect and quantify flavan-3-ols in infusions and ready-to-drink teas, has been developed for routine analysis and validated by characterizing several performance parameters. The accuracy assessment has been run through a series of LC-MS/MS analyses. Epigallocatechin, (+)-catechin, (-)-epigallocatechingallate, (-)-epicatechin, (-)-gallocatechingallate, (-)-epicatechingallate, and (-)-catechingallate were chosen as markers of the polyphenolic fraction. Quantitative results showed that samples obtained from tea leaves infusion were richer in polyphenolic antioxidants than those obtained through other industrial processes. The influence of shelf-life and packaging material on the flavan-3-ols content was also considered; markers decreased, with an exponential trend, as a function of time within the shelf life while packaging materials demonstrated to influence differently the flavan-3-ol fraction composition over time. The method presented here provides quantitative results with a certain level of confidence and is suitable for a routine quality control of iced teas whose antioxidant properties are object of nutritional claim.

Automated characterization of normal and pathologic lung tissue by topological texture analysis of multidetector CT

NASA Astrophysics Data System (ADS)

Boehm, H. F.; Fink, C.; Becker, C.; Reiser, M.

2007-03-01

Reliable and accurate methods for objective quantitative assessment of parenchymal alterations in the lung are necessary for diagnosis, treatment and follow-up of pulmonary diseases. Two major types of alterations are pulmonary emphysema and fibrosis, emphysema being characterized by abnormal enlargement of the air spaces distal to the terminal, nonrespiratory bronchiole, accompanied by destructive changes of the alveolar walls. The main characteristic of fibrosis is coursening of the interstitial fibers and compaction of the pulmonary tissue. With the ability to display anatomy free from superimposing structures and greater visual clarity, Multi-Detector-CT has shown to be more sensitive than the chest radiograph in identifying alterations of lung parenchyma. In automated evaluation of pulmonary CT-scans, quantitative image processing techniques are applied for objective evaluation of the data. A number of methods have been proposed in the past, most of which utilize simple densitometric tissue features based on the mean X-ray attenuation coefficients expressed in terms of Hounsfield Units [HU]. Due to partial volume effects, most of the density-based methodologies tend to fail, namely in cases, where emphysema and fibrosis occur within narrow spatial limits. In this study, we propose a methodology based upon the topological assessment of graylevel distribution in the 3D image data of lung tissue which provides a way of improving quantitative CT evaluation. Results are compared to the more established density-based methods.

Methods for collecting algal samples as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Porter, Stephen D.; Cuffney, Thomas F.; Gurtz, Martin E.; Meador, Michael R.

1993-01-01

Benthic algae (periphyton) and phytoplankton communities are characterized in the U.S. Geological Survey's National Water-Quality Assessment Program as part of an integrated physical, chemical, and biological assessment of the Nation's water quality. This multidisciplinary approach provides multiple lines of evidence for evaluating water-quality status and trends, and for refining an understanding of the factors that affect water-quality conditions locally, regionally, and nationally. Water quality can be characterized by evaluating the results of qualitative and quantitative measurements of the algal community. Qualitative periphyton samples are collected to develop of list of taxa present in the sampling reach. Quantitative periphyton samples are collected to measure algal community structure within selected habitats. These samples of benthic algal communities are collected from natural substrates, using the sampling methods that are most appropriate for the habitat conditions. Phytoplankton samples may be collected in large nonwadeable streams and rivers to meet specific program objectives. Estimates of algal biomass (chlorophyll content and ash-free dry mass) also are optional measures that may be useful for interpreting water-quality conditions. A nationally consistent approach provides guidance on site, reach, and habitat selection, as well as information on methods and equipment for qualitative and quantitative sampling. Appropriate quality-assurance and quality-control guidelines are used to maximize the ability to analyze data locally, regionally, and nationally.

DEVELOPMENT OF CHEMICAL METHODS TO CHARACTERIZE EXPOSURE TO EDCS IN THE NEUSE RIVER BASIN

EPA Science Inventory

To develop a quantitative health and environmental risk assessment of endocrine disrupting compounds (EDCs), information on exposures is essential. A full exposure assessment has complex requirements that require preliminary information to direct further research in this area....

Future Issues and Perspectives in the Evaluation of Social Development.

ERIC Educational Resources Information Center

Marsden, David; Oakley, Peter

1991-01-01

An instrumental/technocratic approach to evaluation of social development relies on primarily quantitative methods. An interpretive approach resists claims to legitimacy and authority of "experts" and questions existing interpretations. The latter approach is characterized by cultural relativism and subjectivity. (SK)

Quantitative analysis on collagen of dermatofibrosarcoma protuberans skin by second harmonic generation microscopy.

PubMed

Wu, Shulian; Huang, Yudian; Li, Hui; Wang, Yunxia; Zhang, Xiaoman

2015-01-01

Dermatofibrosarcoma protuberans (DFSP) is a skin cancer usually mistaken as other benign tumors. Abnormal DFSP resection results in tumor recurrence. Quantitative characterization of collagen alteration on the skin tumor is essential for developing a diagnostic technique. In this study, second harmonic generation (SHG) microscopy was performed to obtain images of the human DFSP skin and normal skin. Subsequently, structure and texture analysis methods were applied to determine the differences in skin texture characteristics between the two skin types, and the link between collagen alteration and tumor was established. Results suggest that combining SHG microscopy and texture analysis methods is a feasible and effective method to describe the characteristics of skin tumor like DFSP. © Wiley Periodicals, Inc.

Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance.

PubMed

Wang, Shuo; Poon, Gregory M K; Wilson, W David

2015-01-01

Biosensor-surface plasmon resonance (SPR) technology has emerged as a powerful label-free approach for the study of nucleic acid interactions in real time. The method provides simultaneous equilibrium and kinetic characterization for biomolecular interactions with low sample requirements and without the need for external probes. A detailed and practical guide for protein-DNA interaction analyses using biosensor-SPR methods is presented. Details of SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips and samples, experimental design, quantitative and qualitative data analyses and presentation. A specific example of the interaction of a transcription factor with DNA is provided with results evaluated by both kinetic and steady-state SPR methods.

Microstructural study of the nickel-base alloy WAZ-20 using qualitative and quantitative electron optical techniques

NASA Technical Reports Server (NTRS)

Young, S. G.

1973-01-01

The NASA nickel-base alloy WAZ-20 was analyzed by advanced metallographic techniques to qualitatively and quantitatively characterize its phases and stability. The as-cast alloy contained primary gamma-prime, a coarse gamma-gamma prime eutectic, a gamma-fine gamma prime matrix, and MC carbides. A specimen aged at 870 C for 1000 hours contained these same constituents and a few widely scattered high W particles. No detrimental phases (such as sigma or mu) were observed. Scanning electron microscope, light metallography, and replica electron microscope methods are compared. The value of quantitative electron microprobe techniques such as spot and area analysis is demonstrated.

A New Quantitative 3D Imaging Method for Characterizing Spray in the Near-field of Nozzle Exits

DTIC Science & Technology

2015-01-13

measurements were performed on a flat-panel tabletop cone - beam CT system in the Radiology Department at Stanford University. The X-ray generator (CPI...quantitative measurement technique to examine the dense near-field region of sprays using X-ray computed tomography (CT). An optimized “spray CT system” was...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 X-ray CT, Spray, Hollow Cone Spray, Near Field REPORT DOCUMENTATION PAGE 11. SPONSOR

Three-dimensional quantitative flow diagnostics

NASA Technical Reports Server (NTRS)

Miles, Richard B.; Nosenchuck, Daniel M.

1989-01-01

The principles, capabilities, and practical implementation of advanced measurement techniques for the quantitative characterization of three-dimensional flows are reviewed. Consideration is given to particle, Rayleigh, and Raman scattering; fluorescence; flow marking by H2 bubbles, photochromism, photodissociation, and vibrationally excited molecules; light-sheet volume imaging; and stereo imaging. Also discussed are stereo schlieren methods, holographic particle imaging, optical tomography, acoustic and magnetic-resonance imaging, and the display of space-filling data. Extensive diagrams, graphs, photographs, sample images, and tables of numerical data are provided.

Bioelectrochemical Systems Workshop:Standardized Analyses, Design Benchmarks, and Reporting

DTIC Science & Technology

2012-01-01

related to the exoelectrogenic biofilm activity, and to investigate whether the community structure is a function of design and operational parameters...where should biofilm samples be collected? The most prevalent methods of community characterization in BES studies have entailed phylogenetic ...of function associated with this genetic marker, and in methods that involve polymerase chain reaction (PCR) amplification the quantitative

Retrieval analysis of different orthodontic brackets: the applicability of electron microprobe techniques for determining material heterogeneities and corrosive potential

PubMed Central

HOLST, Alexandra Ioana; HOLST, Stefan; HIRSCHFELDER, Ursula; von SECKENDORFF, Volker

2012-01-01

Objective The objective of this study was to investigate the applicability of micro-analytical methods with high spatial resolution to the characterization of the composition and corrosion behavior of two bracket systems. Material and methods The surfaces of six nickel-free brackets and six nickel-containing brackets were examined for signs of corrosion and qualitative surface analysis using an electron probe microanalyzer (EPMA), prior to bonding to patient's tooth surfaces and four months after clinical use. The surfaces were characterized qualitatively by secondary electron (SE) images and back scattered electron (BSE) images in both compositional and topographical mode. Qualitative and quantitative wavelength-dispersive analyses were performed for different elements, and by utilizing qualitative analysis the relative concentration of selected elements was mapped two-dimensionally. The absolute concentration of the elements was determined in specially prepared brackets by quantitative analysis using pure element standards for calibration and calculating correction-factors (ZAF). Results Clear differences were observed between the different bracket types. The nickel-containing stainless steel brackets consist of two separate pieces joined by a brazing alloy. Compositional analysis revealed two different alloy compositions, and reaction zones on both sides of the brazing alloy. The nickel-free bracket was a single piece with only slight variation in element concentration, but had a significantly rougher surface. After clinical use, no corrosive phenomena were detectable with the methods applied. Traces of intraoral wear at the contact areas between the bracket slot and the arch wire were verified. Conclusion Electron probe microanalysis is a valuable tool for the characterization of element distribution and quantitative analysis for corrosion studies. PMID:23032212

The characterization and certification of a quantitative reference material for Legionella detection and quantification by qPCR.

PubMed

Baume, M; Garrelly, L; Facon, J P; Bouton, S; Fraisse, P O; Yardin, C; Reyrolle, M; Jarraud, S

2013-06-01

The characterization and certification of a Legionella DNA quantitative reference material as a primary measurement standard for Legionella qPCR. Twelve laboratories participated in a collaborative certification campaign. A candidate reference DNA material was analysed through PCR-based limiting dilution assays (LDAs). The validated data were used to statistically assign both a reference value and an associated uncertainty to the reference material. This LDA method allowed for the direct quantification of the amount of Legionella DNA per tube in genomic units (GU) and the determination of the associated uncertainties. This method could be used for the certification of all types of microbiological standards for qPCR. The use of this primary standard will improve the accuracy of Legionella qPCR measurements and the overall consistency of these measurements among different laboratories. The extensive use of this certified reference material (CRM) has been integrated in the French standard NF T90-471 (April 2010) and in the ISO Technical Specification 12 869 (Anon 2012 International Standardisation Organisation) for validating qPCR methods and ensuring the reliability of these methods. © 2013 The Society for Applied Microbiology.

X-ray characterization techniques for the assessment of surface damage in crystalline wafers: A model study in AlN

NASA Astrophysics Data System (ADS)

Bobea, M.; Tweedie, J.; Bryan, I.; Bryan, Z.; Rice, A.; Dalmau, R.; Xie, J.; Collazo, R.; Sitar, Z.

2013-03-01

A high-resolution X-ray diffraction method with enhanced surface sensitivity has been used to investigate the effects of various polishing steps on the near-surface region of single crystal substrates. The method involves the study of a highly asymmetric reflection, observable under grazing incidence conditions. Analysis of rocking curve measurements and reciprocal space maps (RSMs) revealed subtle structural differences between the polished substrates. For aluminum nitride wafers, damage induced from diamond sawing and mechanical polishing was readily identifiable by on-axis rocking curves, but this method was unable to distinguish between sample surfaces subjected to various degrees of chemical mechanical polishing (CMP). To characterize sufficiently these surfaces, (10.3) RSMs were measured to provide both qualitative and quantitative information about the near-surface region. Two features present in the RSMs were utilized to quantitatively assess the polished wafers: the magnitude of the diffuse scatter in the omega-scans and the elongation of the crystal truncation rod. The method is able to distinguish between different degrees of CMP surface preparation and provides metrics to quantify subsurface damage after this polishing step.

Nuclear model calculations and their role in space radiation research

NASA Technical Reports Server (NTRS)

Townsend, L. W.; Cucinotta, F. A.; Heilbronn, L. H.

2002-01-01

Proper assessments of spacecraft shielding requirements and concomitant estimates of risk to spacecraft crews from energetic space radiation requires accurate, quantitative methods of characterizing the compositional changes in these radiation fields as they pass through thick absorbers. These quantitative methods are also needed for characterizing accelerator beams used in space radiobiology studies. Because of the impracticality/impossibility of measuring these altered radiation fields inside critical internal body organs of biological test specimens and humans, computational methods rather than direct measurements must be used. Since composition changes in the fields arise from nuclear interaction processes (elastic, inelastic and breakup), knowledge of the appropriate cross sections and spectra must be available. Experiments alone cannot provide the necessary cross section and secondary particle (neutron and charged particle) spectral data because of the large number of nuclear species and wide range of energies involved in space radiation research. Hence, nuclear models are needed. In this paper current methods of predicting total and absorption cross sections and secondary particle (neutrons and ions) yields and spectra for space radiation protection analyses are reviewed. Model shortcomings are discussed and future needs presented. c2002 COSPAR. Published by Elsevier Science Ltd. All right reserved.

Quantitative methods for structural characterization of proteins based on deep UV resonance Raman spectroscopy.

PubMed

Shashilov, Victor A; Sikirzhytski, Vitali; Popova, Ludmila A; Lednev, Igor K

2010-09-01

Here we report on novel quantitative approaches for protein structural characterization using deep UV resonance Raman (DUVRR) spectroscopy. Specifically, we propose a new method combining hydrogen-deuterium (HD) exchange and Bayesian source separation for extracting the DUVRR signatures of various structural elements of aggregated proteins including the cross-beta core and unordered parts of amyloid fibrils. The proposed method is demonstrated using the set of DUVRR spectra of hen egg white lysozyme acquired at various stages of HD exchange. Prior information about the concentration matrix and the spectral features of the individual components was incorporated into the Bayesian equation to eliminate the ill-conditioning of the problem caused by 100% correlation of the concentration profiles of protonated and deuterated species. Secondary structure fractions obtained by partial least squares (PLS) and least squares support vector machines (LS-SVMs) were used as the initial guess for the Bayessian source separation. Advantages of the PLS and LS-SVMs methods over the classical least squares calibration (CLSC) are discussed and illustrated using the DUVRR data of the prion protein in its native and aggregated forms. Copyright (c) 2010 Elsevier Inc. All rights reserved.

Capillary zone electrophoresis method for a highly glycosylated and sialylated recombinant protein: development, characterization and application for process development.

PubMed

Zhang, Le; Lawson, Ken; Yeung, Bernice; Wypych, Jette

2015-01-06

A purity method based on capillary zone electrophoresis (CZE) has been developed for the separation of isoforms of a highly glycosylated protein. The separation was found to be driven by the number of sialic acids attached to each isoform. The method has been characterized using orthogonal assays and shown to have excellent specificity, precision and accuracy. We have demonstrated the CZE method is a useful in-process assay to support cell culture and purification development of this glycoprotein. Compared to isoelectric focusing (IEF), the CZE method provides more quantitative results and higher sample throughput with excellent accuracy, qualities that are required for process development. In addition, the CZE method has been applied in the stability testing of purified glycoprotein samples.

Classification of cassava genotypes based on qualitative and quantitative data.

PubMed

Oliveira, E J; Oliveira Filho, O S; Santos, V S

2015-02-02

We evaluated the genetic variation of cassava accessions based on qualitative (binomial and multicategorical) and quantitative traits (continuous). We characterized 95 accessions obtained from the Cassava Germplasm Bank of Embrapa Mandioca e Fruticultura; we evaluated these accessions for 13 continuous, 10 binary, and 25 multicategorical traits. First, we analyzed the accessions based only on quantitative traits; next, we conducted joint analysis (qualitative and quantitative traits) based on the Ward-MLM method, which performs clustering in two stages. According to the pseudo-F, pseudo-t2, and maximum likelihood criteria, we identified five and four groups based on quantitative trait and joint analysis, respectively. The smaller number of groups identified based on joint analysis may be related to the nature of the data. On the other hand, quantitative data are more subject to environmental effects in the phenotype expression; this results in the absence of genetic differences, thereby contributing to greater differentiation among accessions. For most of the accessions, the maximum probability of classification was >0.90, independent of the trait analyzed, indicating a good fit of the clustering method. Differences in clustering according to the type of data implied that analysis of quantitative and qualitative traits in cassava germplasm might explore different genomic regions. On the other hand, when joint analysis was used, the means and ranges of genetic distances were high, indicating that the Ward-MLM method is very useful for clustering genotypes when there are several phenotypic traits, such as in the case of genetic resources and breeding programs.

Quantitation of influenza virus using field flow fractionation and multi-angle light scattering for quantifying influenza A particles

PubMed Central

Bousse, Tatiana; Shore, David A.; Goldsmith, Cynthia S.; Hossain, M. Jaber; Jang, Yunho; Davis, Charles T.; Donis, Ruben O.; Stevens, James

2017-01-01

Summary Recent advances in instrumentation and data analysis in field flow fractionation and multi-angle light scattering (FFF-MALS) have enabled greater use of this technique to characterize and quantitate viruses. In this study, the FFF-MALS technique was applied to the characterization and quantitation of type A influenza virus particles to assess its usefulness for vaccine preparation. The use of FFF-MALS for quantitation and measurement of control particles provided data accurate to within 5% of known values, reproducible with a coefficient of variation of 1.9 %. The methods, sensitivity and limit of detection were established by analyzing different volumes of purified virus, which produced a linear regression with fitting value R2 of 0.99. FFF-MALS was further applied to detect and quantitate influenza virus in the supernatant of infected MDCK cells and allantoic fluids of infected eggs. FFF fractograms of the virus present in these different fluids revealed similar distribution of monomeric and oligomeric virions. However, the monomer fraction of cell grown virus has greater size variety. Notably, β-propialactone (BPL) inactivation of influenza viruses did not influence any of the FFF-MALS measurements. Quantitation analysis by FFF-MALS was compared to infectivity assays and real-time RT-PCR (qRT-PCR) and the limitations of each assay were discussed. PMID:23916678

Imprecise Probability Methods for Weapons UQ

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

Picard, Richard Roy; Vander Wiel, Scott Alan

Building on recent work in uncertainty quanti cation, we examine the use of imprecise probability methods to better characterize expert knowledge and to improve on misleading aspects of Bayesian analysis with informative prior distributions. Quantitative approaches to incorporate uncertainties in weapons certi cation are subject to rigorous external peer review, and in this regard, certain imprecise probability methods are well established in the literature and attractive. These methods are illustrated using experimental data from LANL detonator impact testing.

A Method to Quantify Visual Information Processing in Children Using Eye Tracking

PubMed Central

Kooiker, Marlou J.G.; Pel, Johan J.M.; van der Steen-Kant, Sanny P.; van der Steen, Johannes

2016-01-01

Visual problems that occur early in life can have major impact on a child's development. Without verbal communication and only based on observational methods, it is difficult to make a quantitative assessment of a child's visual problems. This limits accurate diagnostics in children under the age of 4 years and in children with intellectual disabilities. Here we describe a quantitative method that overcomes these problems. The method uses a remote eye tracker and a four choice preferential looking paradigm to measure eye movement responses to different visual stimuli. The child sits without head support in front of a monitor with integrated infrared cameras. In one of four monitor quadrants a visual stimulus is presented. Each stimulus has a specific visual modality with respect to the background, e.g., form, motion, contrast or color. From the reflexive eye movement responses to these specific visual modalities, output parameters such as reaction times, fixation accuracy and fixation duration are calculated to quantify a child's viewing behavior. With this approach, the quality of visual information processing can be assessed without the use of communication. By comparing results with reference values obtained in typically developing children from 0-12 years, the method provides a characterization of visual information processing in visually impaired children. The quantitative information provided by this method can be advantageous for the field of clinical visual assessment and rehabilitation in multiple ways. The parameter values provide a good basis to: (i) characterize early visual capacities and consequently to enable early interventions; (ii) compare risk groups and follow visual development over time; and (iii), construct an individual visual profile for each child. PMID:27500922

A Method to Quantify Visual Information Processing in Children Using Eye Tracking.

PubMed

Kooiker, Marlou J G; Pel, Johan J M; van der Steen-Kant, Sanny P; van der Steen, Johannes

2016-07-09

Visual problems that occur early in life can have major impact on a child's development. Without verbal communication and only based on observational methods, it is difficult to make a quantitative assessment of a child's visual problems. This limits accurate diagnostics in children under the age of 4 years and in children with intellectual disabilities. Here we describe a quantitative method that overcomes these problems. The method uses a remote eye tracker and a four choice preferential looking paradigm to measure eye movement responses to different visual stimuli. The child sits without head support in front of a monitor with integrated infrared cameras. In one of four monitor quadrants a visual stimulus is presented. Each stimulus has a specific visual modality with respect to the background, e.g., form, motion, contrast or color. From the reflexive eye movement responses to these specific visual modalities, output parameters such as reaction times, fixation accuracy and fixation duration are calculated to quantify a child's viewing behavior. With this approach, the quality of visual information processing can be assessed without the use of communication. By comparing results with reference values obtained in typically developing children from 0-12 years, the method provides a characterization of visual information processing in visually impaired children. The quantitative information provided by this method can be advantageous for the field of clinical visual assessment and rehabilitation in multiple ways. The parameter values provide a good basis to: (i) characterize early visual capacities and consequently to enable early interventions; (ii) compare risk groups and follow visual development over time; and (iii), construct an individual visual profile for each child.

Office-Based Elastographic Technique for Quantifying Mechanical Properties of Skeletal Muscle

PubMed Central

Ballyns, Jeffrey J.; Turo, Diego; Otto, Paul; Shah, Jay P.; Hammond, Jennifer; Gebreab, Tadesse; Gerber, Lynn H.; Sikdar, Siddhartha

2012-01-01

Objectives Our objectives were to develop a new, efficient, and easy-to-administer approach to ultrasound elastography and assess its ability to provide quantitative characterization of viscoelastic properties of skeletal muscle in an outpatient clinical environment. We sought to show its validity and clinical utility in assessing myofascial trigger points, which are associated with myofascial pain syndrome. Methods Ultrasound imaging was performed while the muscle was externally vibrated at frequencies in the range of 60 to 200 Hz using a handheld vibrator. The spatial gradient of the vibration phase yielded the shear wave speed, which is related to the viscoelastic properties of tissue. The method was validated using a calibrated experimental phantom, the biceps brachii muscle in healthy volunteers (n = 6), and the upper trapezius muscle in symptomatic patients with axial neck pain (n = 13) and asymptomatic (pain-free) control participants (n = 9). Results Using the experimental phantom, our method was able to quantitatively measure the shear moduli with error rates of less than 20%. The mean shear modulus ± SD in the normal biceps brachii measured 12.5 ± 3.4 kPa, within the range of published values using more sophisticated methods. Shear wave speeds in active myofascial trigger points and the surrounding muscle tissue were significantly higher than those in normal tissue at high frequency excitations (>100 Hz; P < .05). Conclusions Off-the-shelf office-based equipment can be used to quantitatively characterize skeletal muscle viscoelastic properties with estimates comparable to those using more sophisticated methods. Our preliminary results using this method indicate that patients with spontaneous neck pain and symptomatic myofascial trigger points have increased tissue heterogeneity at the trigger point site and the surrounding muscle tissue. PMID:22837285

Utilizing Pyrosequencing and Quantitative pCR to Characterize Fungal Populations among House Dust Samples

EPA Science Inventory

Molecular techniques are an alternative to culturing and counting methods in quantifying indoor fungal contamination. Pyrosequencing offers the possibility of identifying unexpected indoor fungi. In this study, 50 house dust samples were collected from homes in the Yakima Valley,...

QUANTITATIVE PESTICIDE EXPOSURE ASSESSMENT OF CHILDREN LIVING IN AN AGRICULTURAL COMMUNITY

EPA Science Inventory

In support of planning efforts for the National Children's Study, we conducted a pilot study to test field methods characterizing pesticide exposures to 20 farmworker children aged 6-24 months living in the Salinas Valley, Monterey County, California. Sample collection included d...

Quantitative Characterization of Tissue Microstructure with Temporal Diffusion Spectroscopy

PubMed Central

Xu, Junzhong; Does, Mark D.; Gore, John C.

2009-01-01

The signals recorded by diffusion-weighted magnetic resonance imaging (DWI) are dependent on the micro-structural properties of biological tissues, so it is possible to obtain quantitative structural information non-invasively from such measurements. Oscillating gradient spin echo (OGSE) methods have the ability to probe the behavior of water diffusion over different time scales and the potential to detect variations in intracellular structure. To assist in the interpretation of OGSE data, analytical expressions have been derived for diffusion-weighted signals with OGSE methods for restricted diffusion in some typical structures, including parallel planes, cylinders and spheres, using the theory of temporal diffusion spectroscopy. These analytical predictions have been confirmed with computer simulations. These expressions suggest how OGSE signals from biological tissues should be analyzed to characterize tissue microstructure, including how to estimate cell nuclear sizes. This approach provides a model to interpret diffusion data obtained from OGSE measurements that can be used for applications such as monitoring tumor response to treatment in vivo. PMID:19616979

Are three generations of quantitative molecular methods sufficient in medical virology? Brief review.

PubMed

Clementi, Massimo; Bagnarelli, Patrizia

2015-10-01

In the last two decades, development of quantitative molecular methods has characterized the evolution of clinical virology more than any other methodological advancement. Using these methods, a great deal of studies has addressed efficiently in vivo the role of viral load, viral replication activity, and viral transcriptional profiles as correlates of disease outcome and progression, and has highlighted the physio-pathology of important virus diseases of humans. Furthermore, these studies have contributed to a better understanding of virus-host interactions and have sharply revolutionized the research strategies in basic and medical virology. In addition and importantly from a medical point of view, quantitative methods have provided a rationale for the therapeutic intervention and therapy monitoring in medically important viral diseases. Despite the advances in technology and the development of three generations of molecular methods within the last two decades (competitive PCR, real-time PCR, and digital PCR), great challenges still remain for viral testing related not only to standardization, accuracy, and precision, but also to selection of the best molecular targets for clinical use and to the identification of thresholds for risk stratification and therapeutic decisions. Future research directions, novel methods and technical improvements could be important to address these challenges.

A Comparison of Multivariate and Pre-Processing Methods for Quantitative Laser-Induced Breakdown Spectroscopy of Geologic Samples

NASA Technical Reports Server (NTRS)

Anderson, R. B.; Morris, R. V.; Clegg, S. M.; Bell, J. F., III; Humphries, S. D.; Wiens, R. C.

2011-01-01

The ChemCam instrument selected for the Curiosity rover is capable of remote laser-induced breakdown spectroscopy (LIBS).[1] We used a remote LIBS instrument similar to ChemCam to analyze 197 geologic slab samples and 32 pressed-powder geostandards. The slab samples are well-characterized and have been used to validate the calibration of previous instruments on Mars missions, including CRISM [2], OMEGA [3], the MER Pancam [4], Mini-TES [5], and Moessbauer [6] instruments and the Phoenix SSI [7]. The resulting dataset was used to compare multivariate methods for quantitative LIBS and to determine the effect of grain size on calculations. Three multivariate methods - partial least squares (PLS), multilayer perceptron artificial neural networks (MLP ANNs) and cascade correlation (CC) ANNs - were used to generate models and extract the quantitative composition of unknown samples. PLS can be used to predict one element (PLS1) or multiple elements (PLS2) at a time, as can the neural network methods. Although MLP and CC ANNs were successful in some cases, PLS generally produced the most accurate and precise results.

Visualization and Hierarchical Analysis of Flow in Discrete Fracture Network Models

NASA Astrophysics Data System (ADS)

Aldrich, G. A.; Gable, C. W.; Painter, S. L.; Makedonska, N.; Hamann, B.; Woodring, J.

2013-12-01

Flow and transport in low permeability fractured rock is primary in interconnected fracture networks. Prediction and characterization of flow and transport in fractured rock has important implications in underground repositories for hazardous materials (eg. nuclear and chemical waste), contaminant migration and remediation, groundwater resource management, and hydrocarbon extraction. We have developed methods to explicitly model flow in discrete fracture networks and track flow paths using passive particle tracking algorithms. Visualization and analysis of particle trajectory through the fracture network is important to understanding fracture connectivity, flow patterns, potential contaminant pathways and fast paths through the network. However, occlusion due to the large number of highly tessellated and intersecting fracture polygons preclude the effective use of traditional visualization methods. We would also like quantitative analysis methods to characterize the trajectory of a large number of particle paths. We have solved these problems by defining a hierarchal flow network representing the topology of particle flow through the fracture network. This approach allows us to analyses the flow and the dynamics of the system as a whole. We are able to easily query the flow network, and use paint-and-link style framework to filter the fracture geometry and particle traces based on the flow analytics. This allows us to greatly reduce occlusion while emphasizing salient features such as the principal transport pathways. Examples are shown that demonstrate the methodology and highlight how use of this new method allows quantitative analysis and characterization of flow and transport in a number of representative fracture networks.

Characterization of a high-spin non-heme Fe(III)-OOH intermediate and its quantitative conversion to an Fe(IV)═O complex.

PubMed

Li, Feifei; Meier, Katlyn K; Cranswick, Matthew A; Chakrabarti, Mrinmoy; Van Heuvelen, Katherine M; Münck, Eckard; Que, Lawrence

2011-05-18

We have generated a high-spin Fe(III)-OOH complex supported by tetramethylcyclam via protonation of its conjugate base and characterized it in detail using various spectroscopic methods. This Fe(III)-OOH species can be converted quantitatively to an Fe(IV)═O complex via O-O bond cleavage; this is the first example of such a conversion. This conversion is promoted by two factors: the strong Fe(III)-OOH bond, which inhibits Fe-O bond lysis, and the addition of protons, which facilitates O-O bond cleavage. This example provides a synthetic precedent for how O-O bond cleavage of high-spin Fe(III)-peroxo intermediates of non-heme iron enzymes may be promoted. © 2011 American Chemical Society

Physiological attributes of 11 Northwest conifer species

Treesearch

Ronni L. Korol

2001-01-01

The quantitative description and simulation of the fundamental processes that characterize forest growth are increasing in importance in forestry research. Predicting future forest growth, however, is compounded by the various combinations of temperature, humidity, precipitation, and atmospheric carbon dioxide concentration that may occur. One method of integrating new...

Non-gel Based Proteomics to Study Steroid Receptor Agonists in the Fathead Minnow

EPA Science Inventory

Toxicoproteomics is an emerging field that is greatly enabled by non-gel based methods using LC MS/MS for biomarker discovery and characterization for endocrine disrupting chemicals. Using iTRAQ (isobaric tagging for relative and absolute quantitation), we quantified a diverse r...

Wildland Fire Prevention: Today, Intuition--Tomorrow, Management

Treesearch

Albert J. Simard; Linda R. Donoghue

1987-01-01

Describes, from a historical perspective, methods used to characterize fire prevention problems and evaluate prevention programs and discusses past research efforts to bolster these analytical and management efforts. Highlights research on the sociological perspectives of the wildfire problem and on quantitative fire occurrence prediction and program evaluation systems...

Characterization of Aspergillus section Nigri species populations in vineyard soil using droplet digital PCR

USDA-ARS?s Scientific Manuscript database

Identification of populations of Aspergillus section Nigri species in environmental samples using traditional methods is laborious and impractical for large numbers of samples. We developed species-specific primers and probes for quantitative droplet digital PCR (ddPCR) to improve sample throughput ...

Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology.

PubMed

Janssen, K A; Sidoli, S; Garcia, B A

2017-01-01

Functional epigenetic regulation occurs by dynamic modification of chromatin, including genetic material (i.e., DNA methylation), histone proteins, and other nuclear proteins. Due to the highly complex nature of the histone code, mass spectrometry (MS) has become the leading technique in identification of single and combinatorial histone modifications. MS has now overcome antibody-based strategies due to its automation, high resolution, and accurate quantitation. Moreover, multiple approaches to analysis have been developed for global quantitation of posttranslational modifications (PTMs), including large-scale characterization of modification coexistence (middle-down and top-down proteomics), which is not currently possible with any other biochemical strategy. Recently, our group and others have simplified and increased the effectiveness of analyzing histone PTMs by improving multiple MS methods and data analysis tools. This review provides an overview of the major achievements in the analysis of histone PTMs using MS with a focus on the most recent improvements. We speculate that the workflow for histone analysis at its state of the art is highly reliable in terms of identification and quantitation accuracy, and it has the potential to become a routine method for systems biology thanks to the possibility of integrating histone MS results with genomics and proteomics datasets. © 2017 Elsevier Inc. All rights reserved.

Technique for Determination of Rational Boundaries in Combining Construction and Installation Processes Based on Quantitative Estimation of Technological Connections

NASA Astrophysics Data System (ADS)

Gusev, E. V.; Mukhametzyanov, Z. R.; Razyapov, R. V.

2017-11-01

The problems of the existing methods for the determination of combining and technologically interlinked construction processes and activities are considered under the modern construction conditions of various facilities. The necessity to identify common parameters that characterize the interaction nature of all the technology-related construction and installation processes and activities is shown. The research of the technologies of construction and installation processes for buildings and structures with the goal of determining a common parameter for evaluating the relationship between technologically interconnected processes and construction works are conducted. The result of this research was to identify the quantitative evaluation of interaction construction and installation processes and activities in a minimum technologically necessary volume of the previous process allowing one to plan and organize the execution of a subsequent technologically interconnected process. The quantitative evaluation is used as the basis for the calculation of the optimum range of the combination of processes and activities. The calculation method is based on the use of the graph theory. The authors applied a generic characterization parameter to reveal the technological links between construction and installation processes, and the proposed technique has adaptive properties which are key for wide use in organizational decisions forming. The article provides a written practical significance of the developed technique.

Computer simulation of schlieren images of rotationally symmetric plasma systems: a simple method.

PubMed

Noll, R; Haas, C R; Weikl, B; Herziger, G

1986-03-01

Schlieren techniques are commonly used methods for quantitative analysis of cylindrical or spherical index of refraction profiles. Many schlieren objects, however, are characterized by more complex geometries, so we have investigated the more general case of noncylindrical, rotationally symmetric distributions of index of refraction n(r,z). Assuming straight ray paths in the schlieren object we have calculated 2-D beam deviation profiles. It is shown that experimental schlieren images of the noncylindrical plasma generated by a plasma focus device can be simulated with these deviation profiles. The computer simulation allows a quantitative analysis of these schlieren images, which yields, for example, the plasma parameters, electron density, and electron density gradients.

Quantitative imaging of aggregated emulsions.

PubMed

Penfold, Robert; Watson, Andrew D; Mackie, Alan R; Hibberd, David J

2006-02-28

Noise reduction, restoration, and segmentation methods are developed for the quantitative structural analysis in three dimensions of aggregated oil-in-water emulsion systems imaged by fluorescence confocal laser scanning microscopy. Mindful of typical industrial formulations, the methods are demonstrated for concentrated (30% volume fraction) and polydisperse emulsions. Following a regularized deconvolution step using an analytic optical transfer function and appropriate binary thresholding, novel application of the Euclidean distance map provides effective discrimination of closely clustered emulsion droplets with size variation over at least 1 order of magnitude. The a priori assumption of spherical nonintersecting objects provides crucial information to combat the ill-posed inverse problem presented by locating individual particles. Position coordinates and size estimates are recovered with sufficient precision to permit quantitative study of static geometrical features. In particular, aggregate morphology is characterized by a novel void distribution measure based on the generalized Apollonius problem. This is also compared with conventional Voronoi/Delauney analysis.

Impact of Oriented Clay Particles on X-Ray Spectroscopy Analysis

NASA Astrophysics Data System (ADS)

Lim, A. J. M. S.; Syazwani, R. N.; Wijeyesekera, D. C.

2016-07-01

Understanding the engineering properties of the mineralogy and microfabic of clayey soils is very complex and thus very difficult for soil characterization. Micromechanics of soils recognize that the micro structure and mineralogy of clay have a significant influence on its engineering behaviour. To achieve a more reliable quantitative evaluation of clay mineralogy, a proper sample preparation technique for quantitative clay mineral analysis is necessary. This paper presents the quantitative evaluation of elemental analysis and chemical characterization of oriented and random oriented clay particles using X-ray spectroscopy. Three different types of clays namely marine clay, bentonite and kaolin clay were studied. The oriented samples were prepared by placing the dispersed clay in water and left to settle on porous ceramic tiles by applying a relatively weak suction through a vacuum pump. Images form a Scanning Electron Microscope (SEM) was also used to show the comparison between the orientation patterns of both the sample preparation techniques. From the quantitative analysis of the X-ray spectroscopy, oriented sampling method showed more accuracy in identifying mineral deposits, because it produced better peak intensity on the spectrum and more mineral content can be identified compared to randomly oriented samples.

Reinventing the ames test as a quantitative lab that connects classical and molecular genetics.

PubMed

Goodson-Gregg, Nathan; De Stasio, Elizabeth A

2009-01-01

While many institutions use a version of the Ames test in the undergraduate genetics laboratory, students typically are not exposed to techniques or procedures beyond qualitative analysis of phenotypic reversion, thereby seriously limiting the scope of learning. We have extended the Ames test to include both quantitative analysis of reversion frequency and molecular analysis of revertant gene sequences. By giving students a role in designing their quantitative methods and analyses, students practice and apply quantitative skills. To help students connect classical and molecular genetic concepts and techniques, we report here procedures for characterizing the molecular lesions that confer a revertant phenotype. We suggest undertaking reversion of both missense and frameshift mutants to allow a more sophisticated molecular genetic analysis. These modifications and additions broaden the educational content of the traditional Ames test teaching laboratory, while simultaneously enhancing students' skills in experimental design, quantitative analysis, and data interpretation.

Quantitative proteomics in biological research.

PubMed

Wilm, Matthias

2009-10-01

Proteomics has enabled the direct investigation of biological material, at first through the analysis of individual proteins, then of lysates from cell cultures, and finally of extracts from tissues and biopsies from entire organisms. Its latest manifestation - quantitative proteomics - allows deeper insight into biological systems. This article reviews the different methods used to extract quantitative information from mass spectra. It follows the technical developments aimed toward global proteomics, the attempt to characterize every expressed protein in a cell by at least one peptide. When applications of the technology are discussed, the focus is placed on yeast biology. In particular, differential quantitative proteomics, the comparison between an experiment and its control, is very discriminating for proteins involved in the process being studied. When trying to understand biological processes on a molecular level, differential quantitative proteomics tends to give a clearer picture than global transcription analyses. As a result, MS has become an even more indispensable tool for biochemically motivated biological research.

A facile one-step fluorescence method for the quantitation of low-content single base deamination impurity in synthetic oligonucleotides.

PubMed

Su, Xiaoye; Liang, Ruiting; Stolee, Jessica A

2018-06-05

Oligonucleotides are being researched and developed as potential drug candidates for the treatment of a broad spectrum of diseases. The characterization of antisense oligonucleotide (ASO) impurities caused by base mutations (e.g. deamination) which are closely related to the target ASO is a significant analytical challenge. Herein, we describe a novel one-step method, utilizing a strategy that combines fluorescence-ON detection with competitive hybridization, to achieve single base mutation quantitation in extensively modified synthetic ASOs. Given that this method is highly specific and sensitive (LoQ = 4 nM), we envision that it will find utility for screening other impurities as well as sequencing modified oligonucleotides. Copyright © 2018 Elsevier B.V. All rights reserved.

Characterizing Corrosion Effects of Weak Organic Acids Using a Modified Bono Test

NASA Astrophysics Data System (ADS)

Zhou, Yuqin; Turbini, Laura J.; Ramjattan, Deepchand; Christian, Bev; Pritzker, Mark

2013-12-01

To meet environmental requirements and achieve benefits of cost-effective manufacturing, no-clean fluxes (NCFs) or low-solids fluxes have become popular in present electronic manufacturing processes. Weak organic acids (WOAs) as the activation ingredients in NCFs play an important role, especially in the current lead-free and halogen-free soldering technology era. However, no standard or uniform method exists to characterize the corrosion effects of WOAs on actual metallic circuits of printed wiring boards (PWBs). Hence, the development of an effective quantitative test method for evaluating the corrosion effects of WOAs on the PWB's metallic circuits is imperative. In this paper, the modified Bono test, which was developed to quantitatively examine the corrosion properties of flux residues, is used to characterize the corrosion effects of five WOAs (i.e., abietic acid, succinic acid, glutaric acid, adipic acid, and malic acid) on PWB metallic circuits. Experiments were performed under three temperature/humidity conditions (85°C/85% RH, 60°C/93% RH, and 40°C/93% RH) using two WOA solution concentrations. The different corrosion effects among the various WOAs were best reflected in the testing results at 40°C and 60°C. Optical microscopy was used to observe the morphology of the corroded copper tracks, and scanning electron microscopy (SEM) energy-dispersive x-ray (EDX) characterization was performed to determine the dendrite composition.

Mass spectrometry as a quantitative tool in plant metabolomics

PubMed Central

Jorge, Tiago F.; Mata, Ana T.

2016-01-01

Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644967

A Simple and Computationally Efficient Approach to Multifactor Dimensionality Reduction Analysis of Gene-Gene Interactions for Quantitative Traits

PubMed Central

Gui, Jiang; Moore, Jason H.; Williams, Scott M.; Andrews, Peter; Hillege, Hans L.; van der Harst, Pim; Navis, Gerjan; Van Gilst, Wiek H.; Asselbergs, Folkert W.; Gilbert-Diamond, Diane

2013-01-01

We present an extension of the two-class multifactor dimensionality reduction (MDR) algorithm that enables detection and characterization of epistatic SNP-SNP interactions in the context of a quantitative trait. The proposed Quantitative MDR (QMDR) method handles continuous data by modifying MDR’s constructive induction algorithm to use a T-test. QMDR replaces the balanced accuracy metric with a T-test statistic as the score to determine the best interaction model. We used a simulation to identify the empirical distribution of QMDR’s testing score. We then applied QMDR to genetic data from the ongoing prospective Prevention of Renal and Vascular End-Stage Disease (PREVEND) study. PMID:23805232

Quantitative phase analysis and microstructure characterization of magnetite nanocrystals obtained by microwave assisted non-hydrolytic sol–gel synthesis

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

Sciancalepore, Corrado, E-mail: corrado.sciancalepore@unimore.it; Bondioli, Federica; INSTM Consortium, Via G. Giusti 9, 51121 Firenze

2015-02-15

An innovative preparation procedure, based on microwave assisted non-hydrolytic sol–gel synthesis, to obtain spherical magnetite nanoparticles was reported together with a detailed quantitative phase analysis and microstructure characterization of the synthetic products. The nanoparticle growth was analyzed as a function of the synthesis time and was described in terms of crystallization degree employing the Rietveld method on the magnetic nanostructured system for the determination of the amorphous content using hematite as internal standard. Product crystallinity increases as the microwave thermal treatment is increased and reaches very high percentages for synthesis times longer than 1 h. Microstructural evolution of nanocrystals wasmore » followed by the integral breadth methods to obtain information on the crystallite size-strain distribution. The results of diffraction line profile analysis were compared with nanoparticle grain distribution estimated by dimensional analysis of the transmission electron microscopy (TEM) images. A variation both in the average grain size and in the distribution of the coherently diffraction domains is evidenced, allowing to suppose a relationship between the two quantities. The traditional integral breadth methods have proven to be valid for a rapid assessment of the diffraction line broadening effects in the above-mentioned nanostructured systems and the basic assumption for the correct use of these methods are discussed as well. - Highlights: • Fe{sub 3}O{sub 4} nanocrystals were obtained by MW-assisted non-hydrolytic sol–gel synthesis. • Quantitative phase analysis revealed that crystallinity up to 95% was reached. • The strategy of Rietveld refinements was discussed in details. • Dimensional analysis showed nanoparticles ranging from 4 to 8 nm. • Results of integral breadth methods were compared with microscopic analysis.« less

Office-based elastographic technique for quantifying mechanical properties of skeletal muscle.

PubMed

Ballyns, Jeffrey J; Turo, Diego; Otto, Paul; Shah, Jay P; Hammond, Jennifer; Gebreab, Tadesse; Gerber, Lynn H; Sikdar, Siddhartha

2012-08-01

Our objectives were to develop a new, efficient, and easy-to-administer approach to ultrasound elastography and assess its ability to provide quantitative characterization of viscoelastic properties of skeletal muscle in an outpatient clinical environment. We sought to show its validity and clinical utility in assessing myofascial trigger points, which are associated with myofascial pain syndrome. Ultrasound imaging was performed while the muscle was externally vibrated at frequencies in the range of 60 to 200 Hz using a handheld vibrator. The spatial gradient of the vibration phase yielded the shear wave speed, which is related to the viscoelastic properties of tissue. The method was validated using a calibrated experimental phantom, the biceps brachii muscle in healthy volunteers (n = 6), and the upper trapezius muscle in symptomatic patients with axial neck pain (n = 13) and asymptomatic (pain-free) control participants (n = 9). Using the experimental phantom, our method was able to quantitatively measure the shear moduli with error rates of less than 20%. The mean shear modulus ± SD in the normal biceps brachii measured 12.5 ± 3.4 kPa, within the range of published values using more sophisticated methods. Shear wave speeds in active myofascial trigger points and the surrounding muscle tissue were significantly higher than those in normal tissue at high frequency excitations (>100 Hz; P < .05). Off-the-shelf office-based equipment can be used to quantitatively characterize skeletal muscle viscoelastic properties with estimates comparable to those using more sophisticated methods. Our preliminary results using this method indicate that patients with spontaneous neck pain and symptomatic myofascial trigger points have increased tissue heterogeneity at the trigger point site and the surrounding muscle tissue.

Characterization of Infrastructure Materials using Nonlinear Ultrasonics

NASA Astrophysics Data System (ADS)

Liu, Minghe

In order to improve the safety, reliability, cost, and performance of civil and mechanical structures/components, it is necessary to develop techniques that are capable of characterizing and quantifying the amount of distributed damage in engineering materials before any detectable discontinuities (cracks, delaminations, voids, etc.) appear. In this dissertation, novel nonlinear ultrasonic NDE methods are developed and applied to characterize cumulative damage such as fatigue damage in metallic materials and degradation of cement-based materials due to chemical reactions. First, nonlinear Rayleigh surface waves are used to measure the near-surface residual stresses in shot-peened aluminum alloy (AA 7075) samples. Results show that the nonlinear Rayleigh wave is very sensitive to near-surface residual stresses, and has the potential to quantitatively detect them. Second, a novel two-wave mixing method is theoretically developed and numerically verified. This method is then successfully applied to detect the fatigue damage in aluminum alloy (AA 6061) samples subjected to monotonic compression. In addition to its high sensitivity to fatigue damage, this collinear wave mixing method allows the measurement over a specific region of interest in the specimen, and this capability makes it possible to obtain spatial distribution of fatigue damage through the thickness direction of the sample by simply timing the transducers. Third, the nonlinear wave mixing method is used to characterize the degradation of cement-based materials caused by alkali-silica reaction (ASR). It is found that the nonlinear ultrasonic method is sensitive to detect ASR damage at very early stage, and has the potential to identify the different damage stages. Finally, a micromechanics-based chemo-mechanical model is developed which relates the acoustic nonlinearity parameter to ASR damage. This model provides a way to quantitatively predict the changes in the acoustic nonlinearity parameter due to ASR damage, which can be used to guide experimental measurements for nondestructive evaluation of ASR damage.

The uniformity study of non-oxide thin film at device level using electron energy loss spectroscopy

NASA Astrophysics Data System (ADS)

Li, Zhi-Peng; Zheng, Yuankai; Li, Shaoping; Wang, Haifeng

2018-05-01

Electron energy loss spectroscopy (EELS) has been widely used as a chemical analysis technique to characterize materials chemical properties, such as element valence states, atoms/ions bonding environment. This study provides a new method to characterize physical properties (i.e., film uniformity, grain orientations) of non-oxide thin films in the magnetic device by using EELS microanalysis on scanning transmission electron microscope. This method is based on analyzing white line ratio of spectra and related extended energy loss fine structures so as to correlate it with thin film uniformity. This new approach can provide an effective and sensitive method to monitor/characterize thin film quality (i.e., uniformity) at atomic level for thin film development, which is especially useful for examining ultra-thin films (i.e., several nanometers) or embedded films in devices for industry applications. More importantly, this technique enables development of quantitative characterization of thin film uniformity and it would be a remarkably useful technique for examining various types of devices for industrial applications.

Quantitative Characterization of Magnetic Mobility of Nanoparticle in Solution-Based Condition.

PubMed

Rodoplu, Didem; Boyaci, Ismail H; Bozkurt, Akif G; Eksi, Haslet; Zengin, Adem; Tamer, Ugur; Aydogan, Nihal; Ozcan, Sadan; Tugcu-Demiröz, Fatmanur

2015-01-01

Magnetic nanoparticles are considered as the ideal substrate to selectively isolate target molecules or organisms from sample solutions in a wide variety of applications including bioassays, bioimaging and environmental chemistry. The broad array of these applications in fields requires the accurate magnetic characterization of nanoparticles for a variety of solution based-conditions. Because the freshly synthesized magnetic nanoparticles demonstrated a perfect magnetization value in solid form, they exhibited a different magnetic behavior in solution. Here, we present simple quantitative method for the measurement of magnetic mobility of nanoparticles in solution-based condition. Magnetic mobility of the nanoparticles was quantified with initial mobility of the particles using UV-vis absorbance spectroscopy in water, ethanol and MES buffer. We demonstrated the efficacy of this method through a systematic characterization of four different core-shell structures magnetic nanoparticles over three different surface modifications. The solid nanoparticles were characterized using transmission electron microscopy (TEM), X-ray diffraction (XRD) and saturation magnetization (Ms). The surfaces of the nanoparticles were functionalized with 11-mercaptoundecanoic acid and bovine serum albumin BSA was selected as biomaterial. The effect of the surface modification and solution media on the stability of the nanoparticles was monitored by zeta potentials and hydrodynamic diameters of the nanoparticles. Results obtained from the mobility experiments indicate that the initial mobility was altered with solution media, surface functionalization, size and shape of the magnetic nanoparticle. The proposed method easily determines the interactions between the magnetic nanoparticles and their surrounding biological media, the magnetophoretic responsiveness of nanoparticles and the initial mobilities of the nanoparticles.

Sampling interval analysis and CDF generation for grain-scale gravel bed topography

USDA-ARS?s Scientific Manuscript database

In river hydraulics, there is a continuing need for characterizing bed elevations to arrive at quantitative roughness measures that can be used in predicting flow depth and for improved prediction of fine-sediment transport over and through coarse beds. Recently published prediction methods require...

Development and Evaluation of a Quantitative PCR Assay Targeting Sandhill Crane (Grus canadensis) Fecal Pollution

EPA Science Inventory

While the microbial water quality in the Platte River is seasonally impacted by excreta from migrating cranes, there are no methods available to study crane fecal contamination. Here we characterized microbial populations in crane feces using phylogenetic analysis of 16S rRNA gen...

Quantitative Assessment of Interutterance Stability: Application to Dysarthria

ERIC Educational Resources Information Center

Cummins, Fred; Lowit, Anja; van Brenk, Frits

2014-01-01

Purpose: Following recent attempts to quantify articulatory impairment in speech, the present study evaluates the usefulness of a novel measure of motor stability to characterize dysarthria. Method: The study included 8 speakers with ataxic dysarthria (AD), 16 speakers with hypokinetic dysarthria (HD) as a result of Parkinson's disease, and…

TRACE-LEVEL MEASUREMENT OF COMPLEX COMBUSTION EFFLUENTS AND RESIDUES USING MULTIDIMENSIONAL GAS CHROMATOGRAPHY-MASS SPECTROMETRY (MDGC-MS). (R828190)

EPA Science Inventory

The identification and quantitation of non-method-specific target analytes have greater importance with respect to EPA's current combustion strategy. The risk associated with combustion process emissions must now be characterized. EPA has recently released draft guidance on pr...

Major advances in testing of dairy products: milk component and dairy product attribute testing.

PubMed

Barbano, D M; Lynch, J M

2006-04-01

Milk component analysis is relatively unusual in the field of quantitative analytical chemistry because an analytical test result determines the allocation of very large amounts of money between buyers and sellers of milk. Therefore, there is high incentive to develop and refine these methods to achieve a level of analytical performance rarely demanded of most methods or laboratory staff working in analytical chemistry. In the last 25 yr, well-defined statistical methods to characterize and validate analytical method performance combined with significant improvements in both the chemical and instrumental methods have allowed achievement of improved analytical performance for payment testing. A shift from marketing commodity dairy products to the development, manufacture, and marketing of value added dairy foods for specific market segments has created a need for instrumental and sensory approaches and quantitative data to support product development and marketing. Bringing together sensory data from quantitative descriptive analysis and analytical data from gas chromatography olfactometry for identification of odor-active compounds in complex natural dairy foods has enabled the sensory scientist and analytical chemist to work together to improve the consistency and quality of dairy food flavors.

Elucidating the Burden of HIV in Tissues Using Multiplexed Immunofluorescence and In Situ Hybridization: Methods for the Single-Cell Phenotypic Characterization of Cells Harboring HIV In Situ.

PubMed

Vasquez, Joshua J; Hussien, Rajaa; Aguilar-Rodriguez, Brandon; Junger, Henrik; Dobi, Dejan; Henrich, Timothy J; Thanh, Cassandra; Gibson, Erica; Hogan, Louise E; McCune, Joseph; Hunt, Peter W; Stoddart, Cheryl A; Laszik, Zoltan G

2018-06-01

Persistent tissue reservoirs of HIV present a major barrier to cure. Defining subsets of infected cells in tissues is a major focus of HIV cure research. Herein, we describe a novel multiplexed in situ hybridization (ISH) (RNAscope) protocol to detect HIV-DNA (vDNA) and HIV-RNA (vRNA) in formalin-fixed paraffin-embedded (FFPE) human tissues in combination with immunofluorescence (IF) phenotyping of the infected cells. We show that multiplexed IF and ISH (mIFISH) is suitable for quantitative assessment of HIV vRNA and vDNA and that multiparameter IF phenotyping allows precise identification of the cellular source of the ISH signal. We also provide semi-quantitative data on the impact of various tissue fixatives on the detectability of vDNA and vRNA with RNAscope technology. Finally, we describe methods to quantitate the ISH signal on whole-slide digital images and validation of the quantitative ISH data with quantitative real-time PCR for vRNA. It is our hope that this approach will provide insight into the biology of HIV tissue reservoirs and to inform strategies aimed at curing HIV.

Rock surface roughness measurement using CSI technique and analysis of surface characterization by qualitative and quantitative results

NASA Astrophysics Data System (ADS)

Mukhtar, Husneni; Montgomery, Paul; Gianto; Susanto, K.

2016-01-01

In order to develop image processing that is widely used in geo-processing and analysis, we introduce an alternative technique for the characterization of rock samples. The technique that we have used for characterizing inhomogeneous surfaces is based on Coherence Scanning Interferometry (CSI). An optical probe is first used to scan over the depth of the surface roughness of the sample. Then, to analyse the measured fringe data, we use the Five Sample Adaptive method to obtain quantitative results of the surface shape. To analyse the surface roughness parameters, Hmm and Rq, a new window resizing analysis technique is employed. The results of the morphology and surface roughness analysis show micron and nano-scale information which is characteristic of each rock type and its history. These could be used for mineral identification and studies in rock movement on different surfaces. Image processing is thus used to define the physical parameters of the rock surface.

Morphological characterization of coral reefs by combining lidar and MBES data: A case study from Yuanzhi Island, South China Sea

NASA Astrophysics Data System (ADS)

Zhang, Kai; Yang, Fanlin; Zhang, Hande; Su, Dianpeng; Li, QianQian

2017-06-01

The correlation between seafloor morphological features and biological complexity has been identified in numerous recent studies. This research focused on the potential for accurate characterization of coral reefs based on high-resolution bathymetry from multiple sources. A standard deviation (STD) based method for quantitatively characterizing terrain complexity was developed that includes robust estimation to correct for irregular bathymetry and a calibration for the depth-dependent variablity of measurement noise. Airborne lidar and shipborne sonar bathymetry measurements from Yuanzhi Island, South China Sea, were merged to generate seamless high-resolution coverage of coral bathymetry from the shoreline to deep water. The new algorithm was applied to the Yuanzhi Island surveys to generate maps of quantitive terrain complexity, which were then compared to in situ video observations of coral abundance. The terrain complexity parameter is significantly correlated with seafloor coral abundance, demonstrating the potential for accurately and efficiently mapping coral abundance through seafloor surveys, including combinations of surveys using different sensors.

Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

DOE PAGES

Perras, Frederic A.

2015-12-15

Here, nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities.

Quantitative ultrasonic evaluation of engineering properties in metals, composites and ceramics

NASA Technical Reports Server (NTRS)

Vary, A.

1980-01-01

Ultrasonic technology from the perspective of nondestructive evaluation approaches to material strength prediction and property verification is reviewed. Emergent advanced technology involving quantitative ultrasonic techniques for materials characterization is described. Ultrasonic methods are particularly useful in this area because they involve mechanical elastic waves that are strongly modulated by the same morphological factors that govern mechanical strength and dynamic failure processes. It is emphasized that the technology is in its infancy and that much effort is still required before all the available techniques can be transferred from laboratory to industrial environments.

Methods to characterize environmental settings of stream and groundwater sampling sites for National Water-Quality Assessment

USGS Publications Warehouse

Nakagaki, Naomi; Hitt, Kerie J.; Price, Curtis V.; Falcone, James A.

2012-01-01

Characterization of natural and anthropogenic features that define the environmental settings of sampling sites for streams and groundwater, including drainage basins and groundwater study areas, is an essential component of water-quality and ecological investigations being conducted as part of the U.S. Geological Survey's National Water-Quality Assessment program. Quantitative characterization of environmental settings, combined with physical, chemical, and biological data collected at sampling sites, contributes to understanding the status of, and influences on, water-quality and ecological conditions. To support studies for the National Water-Quality Assessment program, a geographic information system (GIS) was used to develop a standard set of methods to consistently characterize the sites, drainage basins, and groundwater study areas across the nation. This report describes three methods used for characterization-simple overlay, area-weighted areal interpolation, and land-cover-weighted areal interpolation-and their appropriate applications to geographic analyses that have different objectives and data constraints. In addition, this document records the GIS thematic datasets that are used for the Program's national design and data analyses.

Comparison of dynamic isotope power systems for distributed planet surface applications

NASA Technical Reports Server (NTRS)

Bents, David J.; Mckissock, Barbara I.; Hanlon, James C.; Schmitz, Paul C.; Rodriguez, Carlos D.; Withrow, Colleen A.

1991-01-01

Dynamic isotope power system (DIPS) alternatives were investigated and characterized for the surface mission elements associated with a lunar base and subsequent manned Mars expedition. System designs based on two convertor types were studied. These systems were characterized parametrically and compared over the steady-state electrical output power range 0.2 to 20 kWe. Three methods of thermally integrating the heat source and the Stirling heater head were considered, depending on unit size. Figures of merit were derived from the characterizations and compared over the parametric range. Design impacts of mission environmental factors are discussed and quantitatively assessed.

High Definition Confocal Imaging Modalities for the Characterization of Tissue-Engineered Substitutes.

PubMed

Mayrand, Dominique; Fradette, Julie

2018-01-01

Optimal imaging methods are necessary in order to perform a detailed characterization of thick tissue samples from either native or engineered tissues. Tissue-engineered substitutes are featuring increasing complexity including multiple cell types and capillary-like networks. Therefore, technical approaches allowing the visualization of the inner structural organization and cellular composition of tissues are needed. This chapter describes an optical clearing technique which facilitates the detailed characterization of whole-mount samples from skin and adipose tissues (ex vivo tissues and in vitro tissue-engineered substitutes) when combined with spectral confocal microscopy and quantitative analysis on image renderings.

Quantitative imaging biomarkers: the application of advanced image processing and analysis to clinical and preclinical decision making.

PubMed

Prescott, Jeffrey William

2013-02-01

The importance of medical imaging for clinical decision making has been steadily increasing over the last four decades. Recently, there has also been an emphasis on medical imaging for preclinical decision making, i.e., for use in pharamaceutical and medical device development. There is also a drive towards quantification of imaging findings by using quantitative imaging biomarkers, which can improve sensitivity, specificity, accuracy and reproducibility of imaged characteristics used for diagnostic and therapeutic decisions. An important component of the discovery, characterization, validation and application of quantitative imaging biomarkers is the extraction of information and meaning from images through image processing and subsequent analysis. However, many advanced image processing and analysis methods are not applied directly to questions of clinical interest, i.e., for diagnostic and therapeutic decision making, which is a consideration that should be closely linked to the development of such algorithms. This article is meant to address these concerns. First, quantitative imaging biomarkers are introduced by providing definitions and concepts. Then, potential applications of advanced image processing and analysis to areas of quantitative imaging biomarker research are described; specifically, research into osteoarthritis (OA), Alzheimer's disease (AD) and cancer is presented. Then, challenges in quantitative imaging biomarker research are discussed. Finally, a conceptual framework for integrating clinical and preclinical considerations into the development of quantitative imaging biomarkers and their computer-assisted methods of extraction is presented.

Unpredictability of escape trajectory explains predator evasion ability and microhabitat preference of desert rodents.

PubMed

Moore, Talia Y; Cooper, Kimberly L; Biewener, Andrew A; Vasudevan, Ramanarayan

2017-09-05

Mechanistically linking movement behaviors and ecology is key to understanding the adaptive evolution of locomotion. Predator evasion, a behavior that enhances fitness, may depend upon short bursts or complex patterns of locomotion. However, such movements are poorly characterized by existing biomechanical metrics. We present methods based on the entropy measure of randomness from Information Theory to quantitatively characterize the unpredictability of non-steady-state locomotion. We then apply the method by examining sympatric rodent species whose escape trajectories differ in dimensionality. Unlike the speed-regulated gait use of cursorial animals to enhance locomotor economy, bipedal jerboa (family Dipodidae) gait transitions likely enhance maneuverability. In field-based observations, jerboa trajectories are significantly less predictable than those of quadrupedal rodents, likely increasing predator evasion ability. Consistent with this hypothesis, jerboas exhibit lower anxiety in open fields than quadrupedal rodents, a behavior that varies inversely with predator evasion ability. Our unpredictability metric expands the scope of quantitative biomechanical studies to include non-steady-state locomotion in a variety of evolutionary and ecologically significant contexts.Biomechanical understanding of animal gait and maneuverability has primarily been limited to species with more predictable, steady-state movement patterns. Here, the authors develop a method to quantify movement predictability, and apply the method to study escape-related movement in several species of desert rodents.

Comparison of methods for quantitative evaluation of endoscopic distortion

NASA Astrophysics Data System (ADS)

Wang, Quanzeng; Castro, Kurt; Desai, Viraj N.; Cheng, Wei-Chung; Pfefer, Joshua

2015-03-01

Endoscopy is a well-established paradigm in medical imaging, and emerging endoscopic technologies such as high resolution, capsule and disposable endoscopes promise significant improvements in effectiveness, as well as patient safety and acceptance of endoscopy. However, the field lacks practical standardized test methods to evaluate key optical performance characteristics (OPCs), in particular the geometric distortion caused by fisheye lens effects in clinical endoscopic systems. As a result, it has been difficult to evaluate an endoscope's image quality or assess its changes over time. The goal of this work was to identify optimal techniques for objective, quantitative characterization of distortion that are effective and not burdensome. Specifically, distortion measurements from a commercially available distortion evaluation/correction software package were compared with a custom algorithm based on a local magnification (ML) approach. Measurements were performed using a clinical gastroscope to image square grid targets. Recorded images were analyzed with the ML approach and the commercial software where the results were used to obtain corrected images. Corrected images based on the ML approach and the software were compared. The study showed that the ML method could assess distortion patterns more accurately than the commercial software. Overall, the development of standardized test methods for characterizing distortion and other OPCs will facilitate development, clinical translation, manufacturing quality and assurance of performance during clinical use of endoscopic technologies.

Characterization and Comparison of Galactomannan Enzyme Immunoassay and Quantitative Real-Time PCR Assay for Detection of Aspergillus fumigatus in Bronchoalveolar Lavage Fluid from Experimental Invasive Pulmonary Aspergillosis

PubMed Central

Francesconi, Andrea; Kasai, Miki; Petraitiene, Ruta; Petraitis, Vidmantas; Kelaher, Amy M.; Schaufele, Robert; Hope, William W.; Shea, Yvonne R.; Bacher, John; Walsh, Thomas J.

2006-01-01

Bronchoalveolar lavage (BAL) is widely used for evaluation of patients with suspected invasive pulmonary aspergillosis (IPA). However, the diagnostic yield of BAL for detection of IPA by culture and direct examination is limited. Earlier diagnosis may be facilitated by assays that can detect Aspergillus galactomannan antigen or DNA in BAL fluid. We therefore characterized and compared the diagnostic yields of a galactomannan enzyme immunoassay (GM EIA), quantitative real-time PCR (qPCR), and quantitative cultures in experiments using BAL fluid from neutropenic rabbits with experimentally induced IPA defined as microbiologically and histologically evident invasion. The qPCR assay targeted the rRNA gene complex of Aspergillus fumigatus. The GM EIA and qPCR assay were characterized by receiver operator curve analysis. With an optimal cutoff of 0.75, the GM EIA had a sensitivity and specificity of 100% in untreated controls. A decline in sensitivity (92%) was observed when antifungal therapy (AFT) was administered. The optimal cutoff for qPCR was a crossover of 36 cycles, with sensitivity and specificity of 80% and 100%, respectively. The sensitivity of qPCR also decreased with AFT to 50%. Quantitative culture of BAL had a sensitivity of 46% and a specificity of 100%. The sensitivity of quantitative culture decreased with AFT to 16%. The GM EIA and qPCR assay had greater sensitivity than culture in detection of A. fumigatus in BAL fluid in experimentally induced IPA (P ± 0.04). Use of the GM EIA and qPCR assay in conjunction with culture-based diagnostic methods applied to BAL fluid could facilitate accurate diagnosis and more-timely initiation of specific therapy. PMID:16825367

The dynamic micro computed tomography at SSRF

NASA Astrophysics Data System (ADS)

Chen, R.; Xu, L.; Du, G.; Deng, B.; Xie, H.; Xiao, T.

2018-05-01

Synchrotron radiation micro-computed tomography (SR-μCT) is a critical technique for quantitative characterizing the 3D internal structure of samples, recently the dynamic SR-μCT has been attracting vast attention since it can evaluate the three-dimensional structure evolution of a sample. A dynamic μCT method, which is based on monochromatic beam, was developed at the X-ray Imaging and Biomedical Application Beamline at Shanghai Synchrotron Radiation Facility, by combining the compressed sensing based CT reconstruction algorithm and hardware upgrade. The monochromatic beam based method can achieve quantitative information, and lower dose than the white beam base method in which the lower energy beam is absorbed by the sample rather than contribute to the final imaging signal. The developed method is successfully used to investigate the compression of the air sac during respiration in a bell cricket, providing new knowledge for further research on the insect respiratory system.

Exploitation of immunofluorescence for the quantification and characterization of small numbers of Pasteuria endospores.

PubMed

Costa, Sofia R; Kerry, Brian R; Bardgett, Richard D; Davies, Keith G

2006-12-01

The Pasteuria group of endospore-forming bacteria has been studied as a biocontrol agent of plant-parasitic nematodes. Techniques have been developed for its detection and quantification in soil samples, and these mainly focus on observations of endospore attachment to nematodes. Characterization of Pasteuria populations has recently been performed with DNA-based techniques, which usually require the extraction of large numbers of spores. We describe a simple immunological method for the quantification and characterization of Pasteuria populations. Bayesian statistics were used to determine an extraction efficiency of 43% and a threshold of detection of 210 endospores g(-1) sand. This provided a robust means of estimating numbers of endospores in small-volume samples from a natural system. Based on visual assessment of endospore fluorescence, a quantitative method was developed to characterize endospore populations, which were shown to vary according to their host.

Characterization of molecularly imprinted polymers using a new polar solvent titration method.

PubMed

Song, Di; Zhang, Yagang; Geer, Michael F; Shimizu, Ken D

2014-07-01

A new method of characterizing molecularly imprinted polymers (MIPs) was developed and tested, which provides a more accurate means of identifying and measuring the molecular imprinting effect. In the new polar solvent titration method, a series of imprinted and non-imprinted polymers were prepared in solutions containing increasing concentrations of a polar solvent. The polar solvent additives systematically disrupted the templation and monomer aggregation processes in the prepolymerization solutions, and the extent of disruption was captured by the polymerization process. The changes in binding capacity within each series of polymers were measured, providing a quantitative assessment of the templation and monomer aggregation processes in the imprinted and non-imprinted polymers. The new method was tested using three different diphenyl phosphate imprinted polymers made using three different urea functional monomers. Each monomer had varying efficiencies of templation and monomer aggregation. The new MIP characterization method was found to have several advantages. To independently verify the new characterization method, the MIPs were also characterized using traditional binding isotherm analyses. The two methods appeared to give consistent conclusions. First, the polar solvent titration method is less susceptible to false positives in identifying the imprinting effect. Second, the method is able to differentiate and quantify changes in binding capacity, as measured at a fixed guest and polymer concentration, arising from templation or monomer aggregation processes in the prepolymerization solution. Third, the method was also easy to carry out, taking advantage of the ease of preparing MIPs. Copyright © 2014 John Wiley & Sons, Ltd.

Quantitative Evaluation of the Total Magnetic Moments of Colloidal Magnetic Nanoparticles: A Kinetics-based Method.

PubMed

Liu, Haiyi; Sun, Jianfei; Wang, Haoyao; Wang, Peng; Song, Lina; Li, Yang; Chen, Bo; Zhang, Yu; Gu, Ning

2015-06-08

A kinetics-based method is proposed to quantitatively characterize the collective magnetization of colloidal magnetic nanoparticles. The method is based on the relationship between the magnetic force on a colloidal droplet and the movement of the droplet under a gradient magnetic field. Through computational analysis of the kinetic parameters, such as displacement, velocity, and acceleration, the magnetization of colloidal magnetic nanoparticles can be calculated. In our experiments, the values measured by using our method exhibited a better linear correlation with magnetothermal heating, than those obtained by using a vibrating sample magnetometer and magnetic balance. This finding indicates that this method may be more suitable to evaluate the collective magnetism of colloidal magnetic nanoparticles under low magnetic fields than the commonly used methods. Accurate evaluation of the magnetic properties of colloidal nanoparticles is of great importance for the standardization of magnetic nanomaterials and for their practical application in biomedicine. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantification of Liver Iron with MRI: State of the Art and Remaining Challenges

PubMed Central

Hernando, Diego; Levin, Yakir S; Sirlin, Claude B; Reeder, Scott B

2015-01-01

Liver iron overload is the histological hallmark of hereditary hemochromatosis and transfusional hemosiderosis, and can also occur in chronic hepatopathies. Iron overload can result in liver damage, with the eventual development of cirrhosis, liver failure and hepatocellular carcinoma. Assessment of liver iron levels is necessary for detection and quantitative staging of iron overload, and monitoring of iron-reducing treatments. This article discusses the need for non-invasive assessment of liver iron, and reviews qualitative and quantitative methods with a particular emphasis on MRI. Specific MRI methods for liver iron quantification include signal intensity ratio as well as R2 and R2* relaxometry techniques. Methods that are in clinical use, as well as their limitations, are described. Remaining challenges, unsolved problems, and emerging techniques to provide improved characterization of liver iron deposition are discussed. PMID:24585403

Estimation of Qualitative and Quantitative Parameters of Air Cleaning by a Pulsed Corona Discharge Using Multicomponent Standard Mixtures

NASA Astrophysics Data System (ADS)

Filatov, I. E.; Uvarin, V. V.; Kuznetsov, D. L.

2018-05-01

The efficiency of removal of volatile organic impurities in air by a pulsed corona discharge is investigated using model mixtures. Based on the method of competing reactions, an approach to estimating the qualitative and quantitative parameters of the employed electrophysical technique is proposed. The concept of the "toluene coefficient" characterizing the relative reactivity of a component as compared to toluene is introduced. It is proposed that the energy efficiency of the electrophysical method be estimated using the concept of diversified yield of the removal process. Such an approach makes it possible to substantially intensify the determination of energy parameters of removal of impurities and can also serve as a criterion for estimating the effectiveness of various methods in which a nonequilibrium plasma is used for air cleaning from volatile impurities.

Quantitative CT characterization of pediatric lung development using routine clinical imaging

PubMed Central

Stein, Jill M.; Walkup, Laura L.; Brody, Alan S.; Fleck, Robert J.

2016-01-01

Background The use of quantitative CT analysis in children is limited by lack of normal values of lung parenchymal attenuation. These characteristics are important because normal lung development yields significant parenchymal attenuation changes as children age. Objective To perform quantitative characterization of normal pediatric lung parenchymal X-ray CT attenuation under routine clinical conditions in order to establish a baseline comparison to that seen in pathological lung conditions. Materials and methods We conducted a retrospective query of normal CT chest examinations in children ages 0–7 years from 2004 to 2014 using standard clinical protocol. During these examinations semi-automated lung parenchymal segmentation was performed to measure lung volume and mean lung attenuation. Results We analyzed 42 CT examinations in 39 children, ages 3 days to 83 months (mean ± standard deviation [SD] = 42±27 months). Lung volume ranged 0.10–1.72 liters (L). Mean lung attenuation was much higher in children younger than 12 months, with values as high as −380 Hounsfield units (HU) in neonates (lung volume 0.10 L). Lung volume decreased to approximately −650 HU by age 2 years (lung volume 0.47 L), with subsequently slower exponential decrease toward a relatively constant value of −860 HU as age and lung volume increased. Conclusion Normal lung parenchymal X-ray CT attenuation decreases with increasing lung volume and age; lung attenuation decreases rapidly in the first 2 years of age and more slowly thereafter. This change in normal lung attenuation should be taken into account as quantitative CT methods are translated to pediatric pulmonary imaging. PMID:27576458

Characterization of articular cartilage by combining microscopic analysis with a fibril-reinforced finite-element model.

PubMed

Julkunen, Petro; Kiviranta, Panu; Wilson, Wouter; Jurvelin, Jukka S; Korhonen, Rami K

2007-01-01

Load-bearing characteristics of articular cartilage are impaired during tissue degeneration. Quantitative microscopy enables in vitro investigation of cartilage structure but determination of tissue functional properties necessitates experimental mechanical testing. The fibril-reinforced poroviscoelastic (FRPVE) model has been used successfully for estimation of cartilage mechanical properties. The model includes realistic collagen network architecture, as shown by microscopic imaging techniques. The aim of the present study was to investigate the relationships between the cartilage proteoglycan (PG) and collagen content as assessed by quantitative microscopic findings, and model-based mechanical parameters of the tissue. Site-specific variation of the collagen network moduli, PG matrix modulus and permeability was analyzed. Cylindrical cartilage samples (n=22) were harvested from various sites of the bovine knee and shoulder joints. Collagen orientation, as quantitated by polarized light microscopy, was incorporated into the finite-element model. Stepwise stress-relaxation experiments in unconfined compression were conducted for the samples, and sample-specific models were fitted to the experimental data in order to determine values of the model parameters. For comparison, Fourier transform infrared imaging and digital densitometry were used for the determination of collagen and PG content in the same samples, respectively. The initial and strain-dependent fibril network moduli as well as the initial permeability correlated significantly with the tissue collagen content. The equilibrium Young's modulus of the nonfibrillar matrix and the strain dependency of permeability were significantly associated with the tissue PG content. The present study demonstrates that modern quantitative microscopic methods in combination with the FRPVE model are feasible methods to characterize the structure-function relationships of articular cartilage.

Energy Storage Publications | Transportation Research | NREL

Science.gov Websites

. 367, 1 November 2017 pp. 214-215. Quantitative Microstructure Characterization of a NMC Electrode . NREL/PR-5400-68759. Quantitative Microstructure Characterization of a NMC Electrode Presentation Source . NREL/PR-5400-68339. Microstructure Characterization and Modeling for Improved Electrode Design

Comparison of droplet digital PCR with quantitative real-time PCR for determination of zygosity in transgenic maize.

PubMed

Xu, Xiaoli; Peng, Cheng; Wang, Xiaofu; Chen, Xiaoyun; Wang, Qiang; Xu, Junfeng

2016-12-01

This study evaluated the applicability of droplet digital PCR (ddPCR) as a tool for maize zygosity determination using quantitative real-time PCR (qPCR) as a reference technology. Quantitative real-time PCR is commonly used to determine transgene copy number or GMO zygosity characterization. However, its effectiveness is based on identical reaction efficiencies for the transgene and the endogenous reference gene. Additionally, a calibrator sample should be utilized for accuracy. Droplet digital PCR is a DNA molecule counting technique that directly counts the absolute number of target and reference DNA molecules in a sample, independent of assay efficiency or external calibrators. The zygosity of the transgene can be easily determined using the ratio of the quantity of the target gene to the reference single copy endogenous gene. In this study, both the qPCR and ddPCR methods were used to determine insect-resistant transgenic maize IE034 zygosity. Both methods performed well, but the ddPCR method was more convenient because of its absolute quantification property.

Determination of Grayanotoxins from Rhododendron brachycarpum in Dietary Supplements and Homemade Wine by Liquid Chromatography-Quadrupole Time-of-Flight-Mass Spectrometry and Liquid Chromatography-Tandem Mass Spectrometry.

PubMed

Hwang, Taeik; Noh, Eunyoung; Jeong, Ji Hye; Park, Sung-Kwan; Shin, Dongwoo; Kang, Hoil

2018-02-28

A sensitive and specific high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (LC-QTOF-MS) method combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed for the determination of grayanotoxins I and III in dietary supplements and homemade wine. Grayanotoxins I and III were successfully extracted using solid-phase extraction cartridges, characterized by LC-QTOF-MS, and quantitated by LC-MS/MS. The LC-MS/MS calibration curves were linear over concentrations of 10-100 ng/mL (grayanotoxin I) and 20-400 ng/mL (grayanotoxin III). Grayanotoxins I and III were found in 51 foodstuffs, with quantitative determinations revealing total toxin concentrations of 18.4-101 000 ng/mL (grayanotoxin I) and 15.3-56 000 ng/mL (grayanotoxin III). The potential of the validated method was demonstrated by successful quantitative analysis of grayanotoxins I and III in dietary supplements and homemade wine; the method appears suitable for the routine detection of grayanotoxins I and III from Rhododendron brachycarpum.

ESI-Q-TOF structural characterization of prominent MS/MS product ions of veterinary drugs for improved regulatory monitoring

USDA-ARS?s Scientific Manuscript database

Introduction The misuse of veterinary drugs in animal production could result in a negative impact on food safety, drug resistance, and in the environment. Consequently, countries around the world have regulated their use, which requires effective methods for the qualitative and quantitative residu...

Conflict of Interest and Disclosure Policies in Psychiatry and Medicine: A Comparative Study of Peer-Reviewed Journals

ERIC Educational Resources Information Center

Khurana, Gauri; Henderson, Schuyler; Walter, Garry; Martin, Andres

2012-01-01

Objective: The authors reviewed and characterized conflict of interest (COI) and disclosure policies published in peer-reviewed psychiatric and nonpsychiatric journals. Methods: The authors examined peer-reviewed publications in the psychiatric (N=20) and nonpsychiatric (N=20) literature. Using qualitative and quantitative approaches, they…

Quantitative Study of Vibrational Symmetry of Injured Vocal Folds via Digital Kymography in Excised Canine Larynges

ERIC Educational Resources Information Center

Krausert, Christopher R.; Ying, Di; Zhang, Yu; Jiang, Jack J.

2011-01-01

Purpose: Digital kymography and vocal fold curve fitting are blended with detailed symmetry analysis of kymograms to provide a comprehensive characterization of the vibratory properties of injured vocal folds. Method: Vocal fold vibration of 12 excised canine larynges was recorded under uninjured, unilaterally injured, and bilaterally injured…

Characterization of fecal concentrations in human and other animal sources by physical, culture-based, and quantitative real-time PCR methods

EPA Science Inventory

The characteristics of fecal sources, and the ways in which they are measured, can profoundly influence the interpretation of which sources are contaminating water. Although feces from various hosts are known to differ, it is not well understood how those differences compare acro...

Quantitative phase imaging of arthropods

PubMed Central

Sridharan, Shamira; Katz, Aron; Soto-Adames, Felipe; Popescu, Gabriel

2015-01-01

Abstract. Classification of arthropods is performed by characterization of fine features such as setae and cuticles. An unstained whole arthropod specimen mounted on a slide can be preserved for many decades, but is difficult to study since current methods require sample manipulation or tedious image processing. Spatial light interference microscopy (SLIM) is a quantitative phase imaging (QPI) technique that is an add-on module to a commercial phase contrast microscope. We use SLIM to image a whole organism springtail Ceratophysella denticulata mounted on a slide. This is the first time, to our knowledge, that an entire organism has been imaged using QPI. We also demonstrate the ability of SLIM to image fine structures in addition to providing quantitative data that cannot be obtained by traditional bright field microscopy. PMID:26334858

Analysis of ultrasound pulse-echo images for characterization of muscle disease

NASA Astrophysics Data System (ADS)

Leeman, Sidney; Heckmatt, John Z.

1996-04-01

This study aims to extract quantifiable indices characterizing ultrasound propagation and scattering in skeletal muscle, from data acquired using a real-time linear array scanner in a paediatric muscle clinic, in order to establish early diagnosis of Duchenne muscular dystrophy in young children, as well as to chart the progressive severity of the disease. Approximately 40 patients with gait disorders, aged between 1 and 11 years, were scanned with a real-time linear array ultrasound scanner, at 5 MHz. A control group consisted of approximately 50 boys, in the same age range, with no evidence or history of muscle disease. Results show that ultrasound quantitative methods can provide a tight clustering of normal data, and also provide a basis for charting the degree of change in diseased muscle. The most significant (quantitative) parameters derive from the frequency of the attenuation and the muscle echogenicity. The approach provides a discrimination method that is more sensitive than visual assessment of the corresponding image by even an experienced observer. There are also indications that the need for traumatic muscle biopsy may be obviated in some cases.

p-Type Doping of GaN Nanowires Characterized by Photoelectrochemical Measurements.

PubMed

Kamimura, Jumpei; Bogdanoff, Peter; Ramsteiner, Manfred; Corfdir, Pierre; Feix, Felix; Geelhaar, Lutz; Riechert, Henning

2017-03-08

GaN nanowires (NWs) doped with Mg as a p-type impurity were grown on Si(111) substrates by plasma-assisted molecular beam epitaxy. In a systematic series of experiments, the amount of Mg supplied during NW growth was varied. The incorporation of Mg into the NWs was confirmed by the observation of donor-acceptor pairs and acceptor-bound excitons in low-temperature photoluminescence spectroscopy. Quantitative information about the Mg concentrations was deduced from Raman scattering by local vibrational modes related to Mg. In order to study the type and density of charge carriers present in the NWs, we employed two photoelectrochemical techniques, open-circuit potential and Mott-Schottky measurements. Both methods showed the expected transition from n-type to p-type conductivity with increasing Mg doping level, and the latter characterization technique allowed us to quantify the charge carrier concentration. Beyond the quantitative information obtained for Mg doping of GaN NWs, our systematic and comprehensive investigation demonstrates the benefit of photoelectrochemical methods for the analysis of doping in semiconductor NWs in general.

White-light diffraction phase microscopy at doubled space-bandwidth product.

PubMed

Shan, Mingguang; Kandel, Mikhail E; Majeed, Hassaan; Nastasa, Viorel; Popescu, Gabriel

2016-12-12

White light diffraction microscopy (wDPM) is a quantitative phase imaging method that benefits from both temporal and spatial phase sensitivity, granted, respectively, by the common-path geometry and white light illumination. However, like all off-axis quantitative phase imaging methods, wDPM is characterized by a reduced space-bandwidth product compared to phase shifting approaches. This happens essentially because the ultimate resolution of the image is governed by the period of the interferogram and not just the diffraction limit. As a result, off-axis techniques generates single-shot, i.e., high time-bandwidth, phase measurements, at the expense of either spatial resolution or field of view. Here, we show that combining phase-shifting and off-axis, the original space-bandwidth is preserved. Specifically, we developed phase-shifting diffraction phase microscopy with white light, in which we measure and combine two phase shifted interferograms. Due to the white light illumination, the phase images are characterized by low spatial noise, i.e., <1nm pathlength. We illustrate the operation of the instrument with test samples, blood cells, and unlabeled prostate tissue biopsy.

Discrimination and characterization of strawberry juice based on electronic nose and tongue: comparison of different juice processing approaches by LDA, PLSR, RF, and SVM.

PubMed

Qiu, Shanshan; Wang, Jun; Gao, Liping

2014-07-09

An electronic nose (E-nose) and an electronic tongue (E-tongue) have been used to characterize five types of strawberry juices based on processing approaches (i.e., microwave pasteurization, steam blanching, high temperature short time pasteurization, frozen-thawed, and freshly squeezed). Juice quality parameters (vitamin C, pH, total soluble solid, total acid, and sugar/acid ratio) were detected by traditional measuring methods. Multivariate statistical methods (linear discriminant analysis (LDA) and partial least squares regression (PLSR)) and neural networks (Random Forest (RF) and Support Vector Machines) were employed to qualitative classification and quantitative regression. E-tongue system reached higher accuracy rates than E-nose did, and the simultaneous utilization did have an advantage in LDA classification and PLSR regression. According to cross-validation, RF has shown outstanding and indisputable performances in the qualitative and quantitative analysis. This work indicates that the simultaneous utilization of E-nose and E-tongue can discriminate processed fruit juices and predict quality parameters successfully for the beverage industry.

Facile quantitation of free thiols in a recombinant monoclonal antibody by reversed-phase high performance liquid chromatography with hydrophobicity-tailored thiol derivatization.

PubMed

Welch, Leslie; Dong, Xiao; Hewitt, Daniel; Irwin, Michelle; McCarty, Luke; Tsai, Christina; Baginski, Tomasz

2018-06-02

Free thiol content, and its consistency, is one of the product quality attributes of interest during technical development of manufactured recombinant monoclonal antibodies (mAbs). We describe a new, mid/high-throughput reversed-phase-high performance liquid chromatography (RP-HPLC) method coupled with derivatization of free thiols, for the determination of total free thiol content in an E. coli-expressed therapeutic monovalent monoclonal antibody mAb1. Initial selection of the derivatization reagent used an hydrophobicity-tailored approach. Maleimide-based thiol-reactive reagents with varying degrees of hydrophobicity were assessed to identify and select one that provided adequate chromatographic resolution and robust quantitation of free thiol-containing mAb1 forms. The method relies on covalent derivatization of free thiols in denatured mAb1 with N-tert-butylmaleimide (NtBM) label, followed by RP-HPLC separation with UV-based quantitation of native (disulfide containing) and labeled (free thiol containing) forms. The method demonstrated good specificity, precision, linearity, accuracy and robustness. Accuracy of the method, for samples with a wide range of free thiol content, was demonstrated using admixtures as well as by comparison to an orthogonal LC-MS peptide mapping method with isotope tagging of free thiols. The developed method has a facile workflow which fits well into both R&D characterization and quality control (QC) testing environments. The hydrophobicity-tailored approach to the selection of free thiol derivatization reagent is easily applied to the rapid development of free thiol quantitation methods for full-length recombinant antibodies. Copyright © 2018 Elsevier B.V. All rights reserved.

Probability of Detection (POD) as a statistical model for the validation of qualitative methods.

PubMed

Wehling, Paul; LaBudde, Robert A; Brunelle, Sharon L; Nelson, Maria T

2011-01-01

A statistical model is presented for use in validation of qualitative methods. This model, termed Probability of Detection (POD), harmonizes the statistical concepts and parameters between quantitative and qualitative method validation. POD characterizes method response with respect to concentration as a continuous variable. The POD model provides a tool for graphical representation of response curves for qualitative methods. In addition, the model allows comparisons between candidate and reference methods, and provides calculations of repeatability, reproducibility, and laboratory effects from collaborative study data. Single laboratory study and collaborative study examples are given.

High-throughput label-free screening of euglena gracilis with optofluidic time-stretch quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Guo, Baoshan; Lei, Cheng; Ito, Takuro; Yaxiaer, Yalikun; Kobayashi, Hirofumi; Jiang, Yiyue; Tanaka, Yo; Ozeki, Yasuyuki; Goda, Keisuke

2017-02-01

The development of reliable, sustainable, and economical sources of alternative fuels is an important, but challenging goal for the world. As an alternative to liquid fossil fuels, microalgal biofuel is expected to play a key role in reducing the detrimental effects of global warming since microalgae absorb atmospheric CO2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid contents and fail to characterize a diverse population of microalgal cells with single-cell resolution in a noninvasive and interference-free manner. Here we demonstrate high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy. In particular, we use Euglena gracilis - an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement) within lipid droplets. Our optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch phase-contrast microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase contents of every single cell at a high throughput of 10,000 cells/s. We characterize heterogeneous populations of E. gracilis cells under two different culture conditions to evaluate their lipid production efficiency. Our method holds promise as an effective analytical tool for microalgaebased biofuel production.

A synchrotron-based local computed tomography combined with data-constrained modelling approach for quantitative analysis of anthracite coal microstructure

PubMed Central

Chen, Wen Hao; Yang, Sam Y. S.; Xiao, Ti Qiao; Mayo, Sherry C.; Wang, Yu Dan; Wang, Hai Peng

2014-01-01

Quantifying three-dimensional spatial distributions of pores and material compositions in samples is a key materials characterization challenge, particularly in samples where compositions are distributed across a range of length scales, and where such compositions have similar X-ray absorption properties, such as in coal. Consequently, obtaining detailed information within sub-regions of a multi-length-scale sample by conventional approaches may not provide the resolution and level of detail one might desire. Herein, an approach for quantitative high-definition determination of material compositions from X-ray local computed tomography combined with a data-constrained modelling method is proposed. The approach is capable of dramatically improving the spatial resolution and enabling finer details within a region of interest of a sample larger than the field of view to be revealed than by using conventional techniques. A coal sample containing distributions of porosity and several mineral compositions is employed to demonstrate the approach. The optimal experimental parameters are pre-analyzed. The quantitative results demonstrated that the approach can reveal significantly finer details of compositional distributions in the sample region of interest. The elevated spatial resolution is crucial for coal-bed methane reservoir evaluation and understanding the transformation of the minerals during coal processing. The method is generic and can be applied for three-dimensional compositional characterization of other materials. PMID:24763649

A quantitative approach to evolution of music and philosophy

NASA Astrophysics Data System (ADS)

Vieira, Vilson; Fabbri, Renato; Travieso, Gonzalo; Oliveira, Osvaldo N., Jr.; da Fontoura Costa, Luciano

2012-08-01

The development of new statistical and computational methods is increasingly making it possible to bridge the gap between hard sciences and humanities. In this study, we propose an approach based on a quantitative evaluation of attributes of objects in fields of humanities, from which concepts such as dialectics and opposition are formally defined mathematically. As case studies, we analyzed the temporal evolution of classical music and philosophy by obtaining data for 8 features characterizing the corresponding fields for 7 well-known composers and philosophers, which were treated with multivariate statistics and pattern recognition methods. A bootstrap method was applied to avoid statistical bias caused by the small sample data set, with which hundreds of artificial composers and philosophers were generated, influenced by the 7 names originally chosen. Upon defining indices for opposition, skewness and counter-dialectics, we confirmed the intuitive analysis of historians in that classical music evolved according to a master-apprentice tradition, while in philosophy changes were driven by opposition. Though these case studies were meant only to show the possibility of treating phenomena in humanities quantitatively, including a quantitative measure of concepts such as dialectics and opposition, the results are encouraging for further application of the approach presented here to many other areas, since it is entirely generic.

Total internal reflection holographic microscopy (TIRHM) for quantitative phase characterization of cell-substrate adhesion

NASA Astrophysics Data System (ADS)

Ash, William Mason, III

Total Internal Reflection Holographic Microscopy (TIRHM) combines near-field microscopy with digital holography to produce a new form of near-field phase microscopy. Using a prism in TIR as a near-field imager, the presence of microscopic organisms, cell-substrate interfaces, and adhesions, causes relative refractive index (RRI) and frustrated TIR (f-TIR) to modulate the object beam's evanescent wave phase front. Quantitative phase images of test specimens such as Amoeba proteus, Dictyostelium Discoideum and cells such as SKOV-3 ovarian cancer and 3T3 fibroblasts are produced without the need to introduce stains or fluorophores. The angular spectrum method of digital holography to compensate for tilt anamorphism due to the inclined TIR plane is also discussed. The results of this work conclusively demonstrate, for the first time, the integration of near-field microscopy with digital holography. The cellular images presented show a correlation between the physical extent of the Amoeba proteus plasma membrane and the adhesions that are quantitatively profiled by phase cross-sectioning of the holographic images obtained by digital holography. With its ability to quantitatively characterise cellular adhesion and motility, it is anticipated that TIRHM can be a tool for characterizing and combating cancer metastasis, as well as improving our understanding of morphogenesis and embryogenesis itself.

EBIC Characterization and Hydrogen Passivation in Silicon Sheet

NASA Technical Reports Server (NTRS)

Hanoka, J. I.

1985-01-01

As a general qualitative tool, the electron beam induced current (EBIC) method can be very useful in imaging recombination in silicon sheet used for solar cells. Work using EBIC on EFG silicon ribbon is described. In particular, some efforts at making the technique more quantitative and hence more useful, some limitations of the method, and finally specific application to hydrogen passivation is treated. Some brief remarks are made regarding the technique itself.

Prospective in (Primate) Dental Analysis through Tooth 3D Topographical Quantification

PubMed Central

Guy, Franck; Gouvard, Florent; Boistel, Renaud; Euriat, Adelaïde; Lazzari, Vincent

2013-01-01

The occlusal morphology of the teeth is mostly determined by the enamel-dentine junction morphology; the enamel-dentine junction plays the role of a primer and conditions the formation of the occlusal enamel reliefs. However, the accretion of the enamel cap yields thickness variations that alter the morphology and the topography of the enamel–dentine junction (i.e., the differential deposition of enamel by the ameloblasts create an external surface that does not necessarily perfectly parallel the enamel–dentine junction). This self-reliant influence of the enamel on tooth morphology is poorly understood and still under-investigated. Studies considering the relationship between enamel and dentine morphologies are rare, and none of them tackled this relationship in a quantitative way. Major limitations arose from: (1) the difficulties to characterize the tooth morphology in its comprehensive tridimensional aspect and (2) practical issues in relating enamel and enamel–dentine junction quantitative traits. We present new aspects of form representation based exclusively on 3D analytical tools and procedures. Our method is applied to a set of 21 unworn upper second molars belonging to eight extant anthropoid genera. Using geometrical analysis of polygonal meshes representatives of the tooth form, we propose a 3D dataset that constitutes a detailed characterization of the enamel and of the enamel–dentine junction morphologies. Also, for the first time, to our knowledge, we intend to establish a quantitative method for comparing enamel and enamel–dentine junction surfaces descriptors (elevation, inclination, orientation, etc.). New indices that allow characterizing the occlusal morphology are proposed and discussed. In this note, we present technical aspects of our method with the example of anthropoid molars. First results show notable individual variations and taxonomic heterogeneities for the selected topographic parameters and for the pattern and strength of association between enamel–dentine junction and enamel, the enamel cap altering in different ways the “transcription” of the enamel–dentine junction morphology. PMID:23826088

Practical estimates of field-saturated hydraulic conductivity of bedrock outcrops using a modified bottomless bucket method

USGS Publications Warehouse

Mirus, Benjamin B.; Perkins, Kim S.

2012-01-01

The bottomless bucket (BB) approach (Nimmo et al., 2009a) is a cost-effective method for rapidly characterizing field-saturated hydraulic conductivity Kfs of soils and alluvial deposits. This practical approach is of particular value for quantifying infiltration rates in remote areas with limited accessibility. A similar approach for bedrock outcrops is also of great value for improving quantitative understanding of infiltration and recharge in rugged terrain. We develop a simple modification to the BB method for application to bedrock outcrops, which uses a non-toxic, quick-drying silicone gel to seal the BB to the bedrock. These modifications to the field method require only minor changes to the analytical solution for calculating Kfs on soils. We investigate the reproducibility of the method with laboratory experiments on a previously studied calcarenite rock and conduct a sensitivity analysis to quantify uncertainty in our predictions. We apply the BB method on both bedrock and soil for sites on Pahute Mesa, which is located in a remote area of the Nevada National Security Site. The bedrock BB tests may require monitoring over several hours to days, depending on infiltration rates, which necessitates a cover to prevent evaporative losses. Our field and laboratory results compare well to Kfs values inferred from independent reports, which suggests the modified BB method can provide useful estimates and facilitate simple hypothesis testing. The ease with which the bedrock BB method can be deployed should facilitate more rapid in-situ data collection than is possible with alternative methods for quantitative characterization of infiltration into bedrock.

Quantitative analysis of PEG-functionalized colloidal gold nanoparticles using charged aerosol detection.

PubMed

Smith, Mackensie C; Crist, Rachael M; Clogston, Jeffrey D; McNeil, Scott E

2015-05-01

Surface characteristics of a nanoparticle, such as functionalization with polyethylene glycol (PEG), are critical to understand and achieve optimal biocompatibility. Routine physicochemical characterization such as UV-vis spectroscopy (for gold nanoparticles), dynamic light scattering, and zeta potential are commonly used to assess the presence of PEG. However, these techniques are merely qualitative and are not sensitive enough to distinguish differences in PEG quantity, density, or presentation. As an alternative, two methods are described here which allow for quantitative measurement of PEG on PEGylated gold nanoparticles. The first, a displacement method, utilizes dithiothreitol to displace PEG from the gold surface. The dithiothreitol-coated gold nanoparticles are separated from the mixture via centrifugation, and the excess dithiothreitol and dissociated PEG are separated through reversed-phase high-performance liquid chromatography (RP-HPLC). The second, a dissolution method, utilizes potassium cyanide to dissolve the gold nanoparticles and liberate PEG. Excess CN(-), Au(CN)2 (-), and free PEG are separated using RP-HPLC. In both techniques, the free PEG can be quantified against a standard curve using charged aerosol detection. The displacement and dissolution methods are validated here using 2-, 5-, 10-, and 20-kDa PEGylated 30-nm colloidal gold nanoparticles. Further value in these techniques is demonstrated not only by quantitating the total PEG fraction but also by being able to be adapted to quantitate the free unbound PEG and the bound PEG fractions. This is an important distinction, as differences in the bound and unbound PEG fractions can affect biocompatibility, which would not be detected in techniques that only quantitate the total PEG fraction.

[Morphological characteristics of kidneys connective tissue of mature fetuses and newborns from mothers, whose pregnancy was complicated by preeclampsia of varying degrees of severity].

PubMed

Sorokina, Iryna V; Myroshnychenko, Mykhailo S; Kapustnyk, Nataliia V; Khramova, Tetyana O; Dehtiarova, Oksana V; Danylchenko, Svitlana I

2018-01-01

Introduction: The kidneys connective tissue condition in the antenatal period affects the formation of tissues and it changes with the development of various general pathological processes in this organ. The aim of the study was to identify the morphological features of kidneys connective tissue of fetuses and newborns from mothers whose pregnancy was complicated by preeclampsia of varying degrees of severity. Materials and methods: The material of the study was the tissue of kidneys of mature fetuses and newborns from mothers with physiological pregnancy (28 cases), as well as from mothers whose pregnancy was complicated by preeclampsia of varying degrees of severity (78 cases). Immunohistochemical study was performed by an indirect Coons method according to M. Brosman's technique using monoclonal antibodies to collagen type I, III and IV. Results: The kidneys connective tissue of fetuses and newborns developing under the maternal preeclampsia conditions is characterized by the qualitative and quantitative changes that indicate the development of sclerotic processes in this organ, the severity of which increase with the age and with the increase of the maternal preeclampsia severity. Qualitative changes are characterized by an increase of the fibrous component, thickening of the bundles of connective tissue fibers, and a decrease in the distance between them. Quantitative changes are characterized by a pronounced predominance of collagen fibers over elastic fibers, almost total absence in some field of view elastic fibers and the violation of the content of collagen type I, III and IV. Conclusion: Maternal preeclampsia underlies the development of qualitative and quantitative changes in kidneys connective tissue of fetuses and newborns, which as a result will lead to disruption of the functions of these organs in such children.

Production and certification of NIST Standard Reference Material 2372 Human DNA Quantitation Standard.

PubMed

Kline, Margaret C; Duewer, David L; Travis, John C; Smith, Melody V; Redman, Janette W; Vallone, Peter M; Decker, Amy E; Butler, John M

2009-06-01

Modern highly multiplexed short tandem repeat (STR) assays used by the forensic human-identity community require tight control of the initial amount of sample DNA amplified in the polymerase chain reaction (PCR) process. This, in turn, requires the ability to reproducibly measure the concentration of human DNA, [DNA], in a sample extract. Quantitative PCR (qPCR) techniques can determine the number of intact stretches of DNA of specified nucleotide sequence in an extremely small sample; however, these assays must be calibrated with DNA extracts of well-characterized and stable composition. By 2004, studies coordinated by or reported to the National Institute of Standards and Technology (NIST) indicated that a well-characterized, stable human DNA quantitation certified reference material (CRM) could help the forensic community reduce within- and among-laboratory quantitation variability. To ensure that the stability of such a quantitation standard can be monitored and that, if and when required, equivalent replacement materials can be prepared, a measurement of some stable quantity directly related to [DNA] is required. Using a long-established conventional relationship linking optical density (properly designated as decadic attenuance) at 260 nm with [DNA] in aqueous solution, NIST Standard Reference Material (SRM) 2372 Human DNA Quantitation Standard was issued in October 2007. This SRM consists of three quite different DNA extracts: a single-source male, a multiple-source female, and a mixture of male and female sources. All three SRM components have very similar optical densities, and thus very similar conventional [DNA]. The materials perform very similarly in several widely used gender-neutral assays, demonstrating that the combination of appropriate preparation methods and metrologically sound spectrophotometric measurements enables the preparation and certification of quantitation [DNA] standards that are both maintainable and of practical utility.

Intrinsic property measurement of surfactant-templated mesoporous silica films using time-resolved single-molecule imaging.

PubMed

Kennard, Raymond; DeSisto, William J; Giririjan, Thanu Praba; Mason, Michael D

2008-04-07

Mesoporous silica membranes fabricated by the surfactant-templated sol-gel process have received attention because of the potential to prepare membranes with a narrow pore size distribution and ordering of the interconnected pores. Potential applications include ultrafiltration, biological separations and drug delivery, and separators in lithium-ion batteries. Despite advancements in synthesis and characterization of these membranes, a quantitative description of the membrane microstructure remains a challenge. Currently the membrane microstructure is characterized by the combination of results from several techniques, i.e., gas permeance testing, x-ray diffraction scanning electron microscopy, transmission electron microscopy, and permporometry. The results from these ensemble methods are then compiled and the data fitted to a particular flow model. Although these methods are very effective in determining membrane performance, general pore size distribution, and defect concentration, they are unable to monitor molecular paths through the membrane and quantitatively measure molecular interactions between the molecular specie and pore network. Single-molecule imaging techniques enable optical measurements that probe materials on nanometer length scales through observation of individual molecules without the influence of averaging. Using single-molecule imaging spectroscopy, we can quantitatively characterize the interaction between the probe molecule and the interior of the pore within mesoporous silica membranes. This approach is radically different from typical membrane characterization methods in that it has the potential to spatially sample the underlying pore structure distribution, the surface energy, and the transport properties. Our hope is that this new fundamental knowledge can be quantitatively linked to both the preparation and the performance of membranes, leading to the advancement of membrane science and technology. Fluorescent molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindo-carbocyanine perchlorate, used to interrogate the available free volume in their vicinity, were loaded into the mesoporous silica membranes at subnanomolar concentrations. The mesoporous silica films were prepared using a nonionic ethylene oxide-propylene oxide-ethylene oxide triblock copolymer surfactant, Pluronic P123, on single crystal silicon substrates using dip coating of a silica sol. Membranes were prepared resulting in an average pore diameter of approximately 5 nm as measured by helium, nitrogen permeance, and porosimetry. Fluorescent images and time transient experiments were recorded using a custom built single-molecule scanning confocal microscope at differing temperatures (10, 20, 30, 40, and 50 degrees C). Time-dependent polarization anisotropy was used to obtain the enthalpy of adsorption and Henry's law constant of the probe molecule.

Intrinsic property measurement of surfactant-templated mesoporous silica films using time-resolved single-molecule imaging

NASA Astrophysics Data System (ADS)

Kennard, Raymond; DeSisto, William J.; Giririjan, Thanu Praba; Mason, Michael D.

2008-04-01

Mesoporous silica membranes fabricated by the surfactant-templated sol-gel process have received attention because of the potential to prepare membranes with a narrow pore size distribution and ordering of the interconnected pores. Potential applications include ultrafiltration, biological separations and drug delivery, and separators in lithium-ion batteries. Despite advancements in synthesis and characterization of these membranes, a quantitative description of the membrane microstructure remains a challenge. Currently the membrane microstructure is characterized by the combination of results from several techniques, i.e., gas permeance testing, x-ray diffraction scanning electron microscopy, transmission electron microscopy, and permporometry. The results from these ensemble methods are then compiled and the data fitted to a particular flow model. Although these methods are very effective in determining membrane performance, general pore size distribution, and defect concentration, they are unable to monitor molecular paths through the membrane and quantitatively measure molecular interactions between the molecular specie and pore network. Single-molecule imaging techniques enable optical measurements that probe materials on nanometer length scales through observation of individual molecules without the influence of averaging. Using single-molecule imaging spectroscopy, we can quantitatively characterize the interaction between the probe molecule and the interior of the pore within mesoporous silica membranes. This approach is radically different from typical membrane characterization methods in that it has the potential to spatially sample the underlying pore structure distribution, the surface energy, and the transport properties. Our hope is that this new fundamental knowledge can be quantitatively linked to both the preparation and the performance of membranes, leading to the advancement of membrane science and technology. Fluorescent molecules, 1,1-dioctadecyl-3,3,3,3-tetramethylindo-carbocyanine perchlorate, used to interrogate the available free volume in their vicinity, were loaded into the mesoporous silica membranes at subnanomolar concentrations. The mesoporous silica films were prepared using a nonionic ethylene oxide-propylene oxide-ethylene oxide triblock copolymer surfactant, Pluronic P123, on single crystal silicon substrates using dip coating of a silica sol. Membranes were prepared resulting in an average pore diameter of approximately 5nm as measured by helium, nitrogen permeance, and porosimetry. Fluorescent images and time transient experiments were recorded using a custom built single-molecule scanning confocal microscope at differing temperatures (10, 20, 30, 40, and 50°C). Time-dependent polarization anisotropy was used to obtain the enthalpy of adsorption and Henry's law constant of the probe molecule.

Quantitative proteomics in the field of microbiology.

PubMed

Otto, Andreas; Becher, Dörte; Schmidt, Frank

2014-03-01

Quantitative proteomics has become an indispensable analytical tool for microbial research. Modern microbial proteomics covers a wide range of topics in basic and applied research from in vitro characterization of single organisms to unravel the physiological implications of stress/starvation to description of the proteome content of a cell at a given time. With the techniques available, ranging from classical gel-based procedures to modern MS-based quantitative techniques, including metabolic and chemical labeling, as well as label-free techniques, quantitative proteomics is today highly successful in sophisticated settings of high complexity such as host-pathogen interactions, mixed microbial communities, and microbial metaproteomics. In this review, we will focus on the vast range of techniques practically applied in current research with an introduction of the workflows used for quantitative comparisons, a description of the advantages/disadvantages of the various methods, reference to hallmark publications and presentation of applications in current microbial research. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Method for Label-Free, Differential Top-Down Proteomics.

PubMed

Ntai, Ioanna; Toby, Timothy K; LeDuc, Richard D; Kelleher, Neil L

2016-01-01

Biomarker discovery in the translational research has heavily relied on labeled and label-free quantitative bottom-up proteomics. Here, we describe a new approach to biomarker studies that utilizes high-throughput top-down proteomics and is the first to offer whole protein characterization and relative quantitation within the same experiment. Using yeast as a model, we report procedures for a label-free approach to quantify the relative abundance of intact proteins ranging from 0 to 30 kDa in two different states. In this chapter, we describe the integrated methodology for the large-scale profiling and quantitation of the intact proteome by liquid chromatography-mass spectrometry (LC-MS) without the need for metabolic or chemical labeling. This recent advance for quantitative top-down proteomics is best implemented with a robust and highly controlled sample preparation workflow before data acquisition on a high-resolution mass spectrometer, and the application of a hierarchical linear statistical model to account for the multiple levels of variance contained in quantitative proteomic comparisons of samples for basic and clinical research.

Characterization and Application of a Grazing Angle Objective for Quantitative Infrared Reflection Microspectroscopy

NASA Technical Reports Server (NTRS)

Pepper, Stephen V.

1995-01-01

A grazing angle objective on an infrared microspectrometer is studied for quantitative spectroscopy by considering the angular dependence of the incident intensity within the objective's angular aperture. The assumption that there is no angular dependence is tested by comparing the experimental reflectance of Si and KBr surfaces with the reflectance calculated by integrating the Fresnel reflection coefficient over the angular aperture under this assumption. Good agreement was found, indicating that the specular reflectance of surfaces can straight-forwardly be quantitatively integrated over the angular aperture without considering non-uniform incident intensity. This quantitative approach is applied to the thickness determination of dipcoated Krytox on gold. The infrared optical constants of both materials are known, allowing the integration to be carried out. The thickness obtained is in fair agreement with the value determined by ellipsometry in the visible. Therefore, this paper illustrates a method for more quantitative use of a grazing angle objective for infrared reflectance microspectroscopy.

Quantitative Fluorescence Studies in Living Cells: Extending Fluorescence Fluctuation Spectroscopy to Peripheral Membrane Proteins

NASA Astrophysics Data System (ADS)

Smith, Elizabeth Myhra

The interactions of peripheral membrane proteins with both membrane lipids and proteins are vital for many cellular processes including membrane trafficking, cellular signaling, and cell growth/regulation. Building accurate biophysical models of these processes requires quantitative characterization of the behavior of peripheral membrane proteins, yet methods to quantify their interactions inside living cells are very limited. Because peripheral membrane proteins usually exist both in membrane-bound and cytoplasmic forms, the separation of these two populations is a key challenge. This thesis aims at addressing this challenge by extending fluorescence fluctuation spectroscopy (FFS) to simultaneously measure the oligomeric state of peripheral membrane proteins in the cytoplasm and at the plasma membrane. We developed a new method based on z-scan FFS that accounts for the fluorescence contributions from cytoplasmic and membrane layers by incorporating a fluorescence intensity z-scan through the cell. H-Ras-EGFP served as a model system to demonstrate the feasibility of the technique. The resolvability and stability of z-scanning was determined as well as the oligomeric state of H-Ras-EGFP at the plasma membrane and in the cytoplasm. Further, we successfully characterized the binding affinity of a variety of proteins to the plasma membrane by quantitative analysis of the z-scan fluorescence intensity profile. This analysis method, which we refer to as z-scan fluorescence profile deconvoution, was further used in combination with dual-color competition studies to determine the lipid specificity of protein binding. Finally, we applied z-scan FFS to provide insight into the early assembly steps of the HTLV-1 retrovirus.

Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy.

PubMed

Meroni, Alice; Lazzaro, Federico; Muzi-Falconi, Marco; Podestà, Alessandro

2018-01-01

We describe a method to extract quantitative information on DNA structural and configurational properties from high-resolution topographic maps recorded by atomic force microscopy (AFM). DNA molecules are deposited on mica surfaces from an aqueous solution, carefully dehydrated, and imaged in air in Tapping Mode. Upon extraction of the spatial coordinates of the DNA backbones from AFM images, several parameters characterizing DNA structure and configuration can be calculated. Here, we explain how to obtain the distribution of contour lengths, end-to-end distances, and gyration radii. This modular protocol can be also used to characterize other statistical parameters from AFM topographies.

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

NASA Technical Reports Server (NTRS)

Ansari, R. R.; Suh, K. I.; Dunker, S.; Kitaya, N.; Sebag, J.

2001-01-01

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

High-throughput electrical measurement and microfluidic sorting of semiconductor nanowires.

PubMed

Akin, Cevat; Feldman, Leonard C; Durand, Corentin; Hus, Saban M; Li, An-Ping; Hui, Ho Yee; Filler, Michael A; Yi, Jingang; Shan, Jerry W

2016-05-24

Existing nanowire electrical characterization tools not only are expensive and require sophisticated facilities, but are far too slow to enable statistical characterization of highly variable samples. They are also generally not compatible with further sorting and processing of nanowires. Here, we demonstrate a high-throughput, solution-based electro-orientation-spectroscopy (EOS) method, which is capable of automated electrical characterization of individual nanowires by direct optical visualization of their alignment behavior under spatially uniform electric fields of different frequencies. We demonstrate that EOS can quantitatively characterize the electrical conductivities of nanowires over a 6-order-of-magnitude range (10(-5) to 10 S m(-1), corresponding to typical carrier densities of 10(10)-10(16) cm(-3)), with different fluids used to suspend the nanowires. By implementing EOS in a simple microfluidic device, continuous electrical characterization is achieved, and the sorting of nanowires is demonstrated as a proof-of-concept. With measurement speeds two orders of magnitude faster than direct-contact methods, the automated EOS instrument enables for the first time the statistical characterization of highly variable 1D nanomaterials.

Morphometric Analysis of Chemoreception Organ in Male and Female Ticks (Acari: Ixodidae).

PubMed

Josek, Tanya; Allan, Brian F; Alleyne, Marianne

2018-05-04

The Haller's organ plays a crucial role in a tick's ability to detect hosts. Even though this sensory organ is vital to tick survival, the morphology of this organ is not well understood. The objective of this study was to characterize variation in the morphological components of the Haller's organ of three medically important tick species using quantitative methods. The Haller's organs of Ixodes scapularis Say (Ixodida: Ixodidae) (black-legged tick), Amblyomma americanum (L.) (Ixodida: Ixodidae) (lone star tick), and Dermacentor variabilis (Say) (Ixodida: Ixodidae) (American dog tick) were morphologically analyzed using environmental scanning electron microscopy and geometric morphometrics, and the results were statistically interpreted using canonical variate analysis. Our data reveal significant, quantitative differences in the morphology of the Haller's organ among all three tick species and that in D. variabilis the sensory structure is sexually dimorphic. Studies like this can serve as a quantitative basis for further studies on sensor physiology, behavior, and tick species life history, potentially leading to novel methods for the prevention of tick-borne disease.

Simultaneous characterisation and quantitation of flavonol glycosides and aglycones in noni leaves using a validated HPLC-UV/MS method.

PubMed

Deng, Shixin; West, Brett J; Jensen, C Jarakae

2008-11-15

The leaves of Morinda citrifolia L. (noni) have been utilized in a variety of commercial products marketed for their health benefits. This paper reports on a rapid and selective HPLC method for simultaneous characterization and quantitation of four flavonols in an ethanolic extract of noni leaves by using dual detectors of UV (365nm) and ESI-MS (negative mode). The limits of detection and quantitation were between 0.012 and 0.165μg/mL. The intra- and inter-assay precisions, in terms of percent relative standard deviation, are less than 4.38% and 3.50%, respectively. The accuracy, in terms of recovery percentage, ranged from 96.66% to 100.03%. Good linearity (correlation coefficient >0.999) for each calibration curve of standards was achieved in the range investigated. The contents of four flavonoids in the noni leaves varied from 1.16 to 371.6mg/100g dry weight. Copyright © 2008 Elsevier Ltd. All rights reserved.

Accounting for Limited Detection Efficiency and Localization Precision in Cluster Analysis in Single Molecule Localization Microscopy

PubMed Central

Shivanandan, Arun; Unnikrishnan, Jayakrishnan; Radenovic, Aleksandra

2015-01-01

Single Molecule Localization Microscopy techniques like PhotoActivated Localization Microscopy, with their sub-diffraction limit spatial resolution, have been popularly used to characterize the spatial organization of membrane proteins, by means of quantitative cluster analysis. However, such quantitative studies remain challenged by the techniques’ inherent sources of errors such as a limited detection efficiency of less than 60%, due to incomplete photo-conversion, and a limited localization precision in the range of 10 – 30nm, varying across the detected molecules, mainly depending on the number of photons collected from each. We provide analytical methods to estimate the effect of these errors in cluster analysis and to correct for them. These methods, based on the Ripley’s L(r) – r or Pair Correlation Function popularly used by the community, can facilitate potentially breakthrough results in quantitative biology by providing a more accurate and precise quantification of protein spatial organization. PMID:25794150

Quantitative, Qualitative and Geospatial Methods to Characterize HIV Risk Environments.

PubMed

Conners, Erin E; West, Brooke S; Roth, Alexis M; Meckel-Parker, Kristen G; Kwan, Mei-Po; Magis-Rodriguez, Carlos; Staines-Orozco, Hugo; Clapp, John D; Brouwer, Kimberly C

2016-01-01

Increasingly, 'place', including physical and geographical characteristics as well as social meanings, is recognized as an important factor driving individual and community health risks. This is especially true among marginalized populations in low and middle income countries (LMIC), whose environments may also be more difficult to study using traditional methods. In the NIH-funded longitudinal study Mapa de Salud, we employed a novel approach to exploring the risk environment of female sex workers (FSWs) in two Mexico/U.S. border cities, Tijuana and Ciudad Juárez. In this paper we describe the development, implementation, and feasibility of a mix of quantitative and qualitative tools used to capture the HIV risk environments of FSWs in an LMIC setting. The methods were: 1) Participatory mapping; 2) Quantitative interviews; 3) Sex work venue field observation; 4) Time-location-activity diaries; 5) In-depth interviews about daily activity spaces. We found that the mixed-methodology outlined was both feasible to implement and acceptable to participants. These methods can generate geospatial data to assess the role of the environment on drug and sexual risk behaviors among high risk populations. Additionally, the adaptation of existing methods for marginalized populations in resource constrained contexts provides new opportunities for informing public health interventions.

Quantitative, Qualitative and Geospatial Methods to Characterize HIV Risk Environments

PubMed Central

Conners, Erin E.; West, Brooke S.; Roth, Alexis M.; Meckel-Parker, Kristen G.; Kwan, Mei-Po; Magis-Rodriguez, Carlos; Staines-Orozco, Hugo; Clapp, John D.; Brouwer, Kimberly C.

2016-01-01

Increasingly, ‘place’, including physical and geographical characteristics as well as social meanings, is recognized as an important factor driving individual and community health risks. This is especially true among marginalized populations in low and middle income countries (LMIC), whose environments may also be more difficult to study using traditional methods. In the NIH-funded longitudinal study Mapa de Salud, we employed a novel approach to exploring the risk environment of female sex workers (FSWs) in two Mexico/U.S. border cities, Tijuana and Ciudad Juárez. In this paper we describe the development, implementation, and feasibility of a mix of quantitative and qualitative tools used to capture the HIV risk environments of FSWs in an LMIC setting. The methods were: 1) Participatory mapping; 2) Quantitative interviews; 3) Sex work venue field observation; 4) Time-location-activity diaries; 5) In-depth interviews about daily activity spaces. We found that the mixed-methodology outlined was both feasible to implement and acceptable to participants. These methods can generate geospatial data to assess the role of the environment on drug and sexual risk behaviors among high risk populations. Additionally, the adaptation of existing methods for marginalized populations in resource constrained contexts provides new opportunities for informing public health interventions. PMID:27191846

Characterization of Low-Molecular-Weight Heparins by Strong Anion-Exchange Chromatography.

PubMed

Sadowski, Radosław; Gadzała-Kopciuch, Renata; Kowalkowski, Tomasz; Widomski, Paweł; Jujeczka, Ludwik; Buszewski, Bogusław

2017-11-01

Currently, detailed structural characterization of low-molecular-weight heparin (LMWH) products is an analytical subject of great interest. In this work, we carried out a comprehensive structural analysis of LMWHs and applied a modified pharmacopeial method, as well as methods developed by other researchers, to the analysis of novel biosimilar LMWH products; and, for the first time, compared the qualitative and quantitative composition of commercially available drugs (enoxaparin, nadroparin, and dalteparin). For this purpose, we used strong anion-exchange (SAX) chromatography with spectrophotometric detection because this method is more helpful, easier, and faster than other separation techniques for the detailed disaccharide analysis of new LMWH drugs. In addition, we subjected the obtained results to statistical analysis (factor analysis, t-test, and Newman-Keuls post hoc test).

HPLC method development for evolving applications in the pharmaceutical industry and nanoscale chemistry

NASA Astrophysics Data System (ADS)

Castiglione, Steven Louis

As scientific research trends towards trace levels and smaller architectures, the analytical chemist is often faced with the challenge of quantitating said species in a variety of matricies. The challenge is heightened when the analytes prove to be potentially toxic or possess physical or chemical properties that make traditional analytical methods problematic. In such cases, the successful development of an acceptable quantitative method plays a critical role in the ability to further develop the species under study. This is particularly true for pharmaceutical impurities and nanoparticles (NP). The first portion of the research focuses on the development of a part-per-billion level HPLC method for a substituted phenazine-class pharmaceutical impurity. The development of this method was required due to the need for a rapid methodology to quantitatively determine levels of a potentially toxic phenazine moiety in order to ensure patient safety. As the synthetic pathway for the active ingredient was continuously refined to produce progressively lower amounts of the phenazine impurity, the approach for increasingly sensitive quantitative methods was required. The approaches evolved across four discrete methods, each employing a unique scheme for analyte detection. All developed methods were evaluated with regards to accuracy, precision and linear adherence as well as ancillary benefits and detriments -- e.g., one method in this evolution demonstrated the ability to resolve and detect other species from the phenazine class. The second portion of the research focuses on the development of an HPLC method for the quantitative determination of NP size distributions. The current methodology for the determination of NP sizes employs tunneling electron microscopy (TEM), which requires sample drying without particle size alteration and which, in many cases, may prove infeasible due to cost or availability. The feasibility of an HPLC method for NP size characterizations evolved across three methods, each employing a different approach for size resolution. These methods were evaluated primarily for sensitivity, which proved to be a substantial hurdle to further development, but does not appear to deter future research efforts.

Diffusion and ideal MRI techniques to characterize limb-girdle muscular dystrophy

NASA Astrophysics Data System (ADS)

Hernández-Salazar, G.; Hidalgo-Tobon, S.; Vargas-Cañas, S.; Marrufo-Melendez, O.; Solis-Najera, S.; Taboada-Barajas, J.; Rodríguez, A. O.; Delgado-Hernández, R.

2012-10-01

Limb-girdle muscular dystrophies (LGMD) are a group of autosomal dominantly or recessively inherited muscular dystrophies that also present with primary proximal (limb-girdle) muscle weakness. In the thigh, muscles at the back are affected, with a tendency to preserve the tibialis anterior and gastrocnemius. The aim of this study was to compare quantitative MRI measurements from IDEAL-based imaging and DW imaging in the thigh muscles of adults with LGMDs and healthy volunteers(HC). Six women (three patients and three healthy volunteers) were examined. Imaging experiments were conducted on a 1.5T GE scanner (General Electric Medical Systems. Milwaukee). T1 IDEAL 2D images and diffusion images were acquired. Results demonstrated that the use of noninvasive MRI techniques may provide the means to characterize the muscle through quantitative methods to determine the percentage of fat and ADC values.

Depositional sequence analysis and sedimentologic modeling for improved prediction of Pennsylvanian reservoirs (Annex 1). Annual report, February 1, 1991--January 31, 1992

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

Watney, W.L.

1992-08-01

Interdisciplinary studies of the Upper Pennsylvanian Lansing and Kansas City groups have been undertaken in order to improve the geologic characterization of petroleum reservoirs and to develop a quantitative understanding of the processes responsible for formation of associated depositional sequences. To this end, concepts and methods of sequence stratigraphy are being used to define and interpret the three-dimensional depositional framework of the Kansas City Group. The investigation includes characterization of reservoir rocks in oil fields in western Kansas, description of analog equivalents in near-surface and surface sites in southeastern Kansas, and construction of regional structural and stratigraphic framework to linkmore » the site specific studies. Geologic inverse and simulation models are being developed to integrate quantitative estimates of controls on sedimentation to produce reconstructions of reservoir-bearing strata in an attempt to enhance our ability to predict reservoir characteristics.« less

Depositional sequence analysis and sedimentologic modeling for improved prediction of Pennsylvanian reservoirs (Annex 1)

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

Watney, W.L.

1992-01-01

Interdisciplinary studies of the Upper Pennsylvanian Lansing and Kansas City groups have been undertaken in order to improve the geologic characterization of petroleum reservoirs and to develop a quantitative understanding of the processes responsible for formation of associated depositional sequences. To this end, concepts and methods of sequence stratigraphy are being used to define and interpret the three-dimensional depositional framework of the Kansas City Group. The investigation includes characterization of reservoir rocks in oil fields in western Kansas, description of analog equivalents in near-surface and surface sites in southeastern Kansas, and construction of regional structural and stratigraphic framework to linkmore » the site specific studies. Geologic inverse and simulation models are being developed to integrate quantitative estimates of controls on sedimentation to produce reconstructions of reservoir-bearing strata in an attempt to enhance our ability to predict reservoir characteristics.« less

Semi-automated identification of cones in the human retina using circle Hough transform

PubMed Central

Bukowska, Danuta M.; Chew, Avenell L.; Huynh, Emily; Kashani, Irwin; Wan, Sue Ling; Wan, Pak Ming; Chen, Fred K

2015-01-01

A large number of human retinal diseases are characterized by a progressive loss of cones, the photoreceptors critical for visual acuity and color perception. Adaptive Optics (AO) imaging presents a potential method to study these cells in vivo. However, AO imaging in ophthalmology is a relatively new phenomenon and quantitative analysis of these images remains difficult and tedious using manual methods. This paper illustrates a novel semi-automated quantitative technique enabling registration of AO images to macular landmarks, cone counting and its radius quantification at specified distances from the foveal center. The new cone counting approach employs the circle Hough transform (cHT) and is compared to automated counting methods, as well as arbitrated manual cone identification. We explore the impact of varying the circle detection parameter on the validity of cHT cone counting and discuss the potential role of using this algorithm in detecting both cones and rods separately. PMID:26713186

The effects of tissue processing on markers for T and B cells from solid tissues.

PubMed

Millard, P R; Rabin, B S; Whiteside, T L; Hubbard, J D

1977-03-01

Suspensions of lymphoid cells from tissues have been used for the determination of the quantitative relationship between the T and B cell populations. The distribution of the lymphocytes within a given tissue, however, cannot be demonstrated once such a suspension has been prepared. Various methods of characterizing lymphocytes within tissues were evaluated. The method of tissue preparation can alter the capability of detecting the lymphocyte markers. Fluorescein-labeled anti-immunoglobulin sera reacted equally well with lymphocytes in tissue regardless of the method of tissue preparation. Complement-coated sheep erythrocytes were less effective in detecting lymphocyte markers in tissue sections than in cell suspensions. Quantitative assays of lymphocytes could be done in suspensions only. Unaltered sheep erythrocytes did not bind to T lymphocytes in tissue. T lymphocytes could be identified in tissue sections, however, by the use of anti-human T cell serum.

An Overview of Addiction Research Center Inventory Scales (ARCI): An Appendix and Manual of Scales.

ERIC Educational Resources Information Center

Haertzen, C.A.

The Addiction Research Center Inventory is a 550 item multipurpose test measuring the broad range of physical, emotive, cognitive, and subjective effects of drugs. This manual provides technical information concerning 38 most valid scales, a quantitative method for characterizing the similarity of a profile of scores for the subject, group, or…

Calibration method for spectroscopic systems

DOEpatents

Sandison, David R.

1998-01-01

Calibration spots of optically-characterized material placed in the field of view of a spectroscopic system allow calibration of the spectroscopic system. Response from the calibration spots is measured and used to calibrate for varying spectroscopic system operating parameters. The accurate calibration achieved allows quantitative spectroscopic analysis of responses taken at different times, different excitation conditions, and of different targets.

Calibration method for spectroscopic systems

DOEpatents

Sandison, D.R.

1998-11-17

Calibration spots of optically-characterized material placed in the field of view of a spectroscopic system allow calibration of the spectroscopic system. Response from the calibration spots is measured and used to calibrate for varying spectroscopic system operating parameters. The accurate calibration achieved allows quantitative spectroscopic analysis of responses taken at different times, different excitation conditions, and of different targets. 3 figs.

Differences in Views of School Principals and Teachers Regarding Technology Integration

ERIC Educational Resources Information Center

Claro, Magdalena; Nussbaum, Miguel; López, Ximena; Contardo, Victoria

2017-01-01

This paper studies the similarities and differences among the views of school principals and teachers regarding a mobile computer lab (MCL) initiative implemented in 1,591 public schools in Chile. It also characterizes the aspects in which their views diverge. A mixed methods study was carried out in two stages: first, a quantitative stage, where…

Characterizing the sustainable forestry issue network in thc United States

Treesearch

Steverson O. Moffat; Frederick W. Cubbage; Thomas P. Holmes; Elizabethann O' Sullivan

2001-01-01

Issue network analysis techniques were applied to the issue sustainable forestry in the United States to identify potential public and private outcomes for the issue. A quantitative approach based on work by Laumann and Knoke [(The Organizational State (1987)] was utilized in conjunction with the Delphi method. Results suggest that the parity in the distribution of...

Design and analysis of quantitative differential proteomics investigations using LC-MS technology.

PubMed

Bukhman, Yury V; Dharsee, Moyez; Ewing, Rob; Chu, Peter; Topaloglou, Thodoros; Le Bihan, Thierry; Goh, Theo; Duewel, Henry; Stewart, Ian I; Wisniewski, Jacek R; Ng, Nancy F

2008-02-01

Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is becoming an increasingly important tool in characterizing the abundance of proteins in biological samples of various types and across conditions. Effects of disease or drug treatments on protein abundance are of particular interest for the characterization of biological processes and the identification of biomarkers. Although state-of-the-art instrumentation is available to make high-quality measurements and commercially available software is available to process the data, the complexity of the technology and data presents challenges for bioinformaticians and statisticians. Here, we describe a pipeline for the analysis of quantitative LC-MS data. Key components of this pipeline include experimental design (sample pooling, blocking, and randomization) as well as deconvolution and alignment of mass chromatograms to generate a matrix of molecular abundance profiles. An important challenge in LC-MS-based quantitation is to be able to accurately identify and assign abundance measurements to members of protein families. To address this issue, we implement a novel statistical method for inferring the relative abundance of related members of protein families from tryptic peptide intensities. This pipeline has been used to analyze quantitative LC-MS data from multiple biomarker discovery projects. We illustrate our pipeline here with examples from two of these studies, and show that the pipeline constitutes a complete workable framework for LC-MS-based differential quantitation. Supplementary material is available at http://iec01.mie.utoronto.ca/~thodoros/Bukhman/.

Twoplex 12/13 C6 aniline stable isotope and linkage-specific sialic acid labeling 2D-LC-MS workflow for quantitative N-glycomics.

PubMed

Albrecht, Simone; Mittermayr, Stefan; Smith, Josh; Martín, Silvia Millán; Doherty, Margaret; Bones, Jonathan

2017-01-01

Quantitative glycomics represents an actively expanding research field ranging from the discovery of disease-associated glycan alterations to the quantitative characterization of N-glycans on therapeutic proteins. Commonly used analytical platforms for comparative relative quantitation of complex glycan samples include MALDI-TOF-MS or chromatographic glycan profiling with subsequent data alignment and statistical evaluation. Limitations of such approaches include run-to-run technical variation and the potential introduction of subjectivity during data processing. Here, we introduce an offline 2D LC-MS E workflow for the fractionation and relative quantitation of twoplex isotopically labeled N-linked oligosaccharides using neutral 12 C 6 and 13 C 6 aniline (Δmass = 6 Da). Additional linkage-specific derivatization of sialic acids using 4-(4,6-dimethoxy-1,3,5-trizain-2-yl)-4-methylmorpholinium chloride offered simultaneous and advanced in-depth structural characterization. The potential of the method was demonstrated for the differential analysis of structurally defined N-glycans released from serum proteins of patients diagnosed with various stages of colorectal cancer. The described twoplex 12 C 6 / 13 C 6 aniline 2D LC-MS platform is ideally suited for differential glycomic analysis of structurally complex N-glycan pools due to combination and analysis of samples in a single LC-MS injection and the associated minimization in technical variation. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Bioactive saponins and glycosides. XIII. Horse chestnut. (3): Quantitative analysis of escins Ia, Ib, IIa, and IIb by means of high performance liquid chromatography].

PubMed

Yoshikawa, M; Murakami, T; Otuki, K; Yamahara, J; Matsuda, H

1999-01-01

As a part of our studies on the characterization of bioactive saponin constituents of horse chestnut trees, a quantitative method using high performance liquid chromatography (HPLC) has been developed for four principle saponin constituents, such as escins Ia, Ib, IIa, and IIb, isolated from the seeds of European horse chestnut trees (Aesculus hippocastanum L., Hippocastanaceae). As an application of this HPLC method, we examined the contents and compositions of these escins in the seeds of Japanese horse chestnut trees (A. turbinata BLUME) and in several commercial materials named as "beta-escin". Additionally, the distribution of escins in the Japanese horse chestnut trees was examined, and escins were found to be contained only in the seeds.

Characterizing optical properties and spatial heterogeneity of human ovarian tissue using spatial frequency domain imaging

NASA Astrophysics Data System (ADS)

Nandy, Sreyankar; Mostafa, Atahar; Kumavor, Patrick D.; Sanders, Melinda; Brewer, Molly; Zhu, Quing

2016-10-01

A spatial frequency domain imaging (SFDI) system was developed for characterizing ex vivo human ovarian tissue using wide-field absorption and scattering properties and their spatial heterogeneities. Based on the observed differences between absorption and scattering images of different ovarian tissue groups, six parameters were quantitatively extracted. These are the mean absorption and scattering, spatial heterogeneities of both absorption and scattering maps measured by a standard deviation, and a fitting error of a Gaussian model fitted to normalized mean Radon transform of the absorption and scattering maps. A logistic regression model was used for classification of malignant and normal ovarian tissues. A sensitivity of 95%, specificity of 100%, and area under the curve of 0.98 were obtained using six parameters extracted from the SFDI images. The preliminary results demonstrate the diagnostic potential of the SFDI method for quantitative characterization of wide-field optical properties and the spatial distribution heterogeneity of human ovarian tissue. SFDI could be an extremely robust and valuable tool for evaluation of the ovary and detection of neoplastic changes of ovarian cancer.

Evaluating the reproducibility of quantifying modified nucleosides from ribonucleic acids by LC–UV–MS

PubMed Central

Russell, Susan P.; Limbach, Patrick A.

2013-01-01

Post-transcriptional chemical covalent modification of adenosine, guanosine, uridine and cytidine occurs frequently in all types of ribonucleic acids (RNAs). In ribosomal RNA (rRNA) and transfer RNA (tRNA) these modifications make important contributions to RNA structure and stability and to the accuracy and efficiency of protein translation. The functional dynamics, synergistic nature and regulatory roles of these posttranscriptional nucleoside modifications within the cell are not well characterized. These modifications are present at very low levels and isolation of individual nucleosides for analysis requires a complex multi-step approach. The focus of this study is to characterize the reproducibility of a liquid chromatography method used to isolate and quantitatively characterize modified nucleosides in tRNA and rRNA when nucleoside detection is performed using ultraviolet and mass spectrometric detection (UV and MS, respectively). Despite the analytical challenges of sample isolation and dynamic range, quantitative profiling of modified nucleosides obtained from bacterial tRNAs and rRNAs is feasible at relative standard deviations of 5% RSD or less. PMID:23500350

A spatiotemporal characterization method for the dynamic cytoskeleton.

PubMed

Alhussein, Ghada; Shanti, Aya; Farhat, Ilyas A H; Timraz, Sara B H; Alwahab, Noaf S A; Pearson, Yanthe E; Martin, Matthew N; Christoforou, Nicolas; Teo, Jeremy C M

2016-05-01

The significant gap between quantitative and qualitative understanding of cytoskeletal function is a pressing problem; microscopy and labeling techniques have improved qualitative investigations of localized cytoskeleton behavior, whereas quantitative analyses of whole cell cytoskeleton networks remain challenging. Here we present a method that accurately quantifies cytoskeleton dynamics. Our approach digitally subdivides cytoskeleton images using interrogation windows, within which box-counting is used to infer a fractal dimension (Df ) to characterize spatial arrangement, and gray value intensity (GVI) to determine actin density. A partitioning algorithm further obtains cytoskeleton characteristics from the perinuclear, cytosolic, and periphery cellular regions. We validated our measurement approach on Cytochalasin-treated cells using transgenically modified dermal fibroblast cells expressing fluorescent actin cytoskeletons. This method differentiates between normal and chemically disrupted actin networks, and quantifies rates of cytoskeletal degradation. Furthermore, GVI distributions were found to be inversely proportional to Df , having several biophysical implications for cytoskeleton formation/degradation. We additionally demonstrated detection sensitivity of differences in Df and GVI for cells seeded on substrates with varying degrees of stiffness, and coated with different attachment proteins. This general approach can be further implemented to gain insights on dynamic growth, disruption, and structure of the cytoskeleton (and other complex biological morphology) due to biological, chemical, or physical stimuli. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A spatiotemporal characterization method for the dynamic cytoskeleton

PubMed Central

Alhussein, Ghada; Shanti, Aya; Farhat, Ilyas A. H.; Timraz, Sara B. H.; Alwahab, Noaf S. A.; Pearson, Yanthe E.; Martin, Matthew N.; Christoforou, Nicolas

2016-01-01

The significant gap between quantitative and qualitative understanding of cytoskeletal function is a pressing problem; microscopy and labeling techniques have improved qualitative investigations of localized cytoskeleton behavior, whereas quantitative analyses of whole cell cytoskeleton networks remain challenging. Here we present a method that accurately quantifies cytoskeleton dynamics. Our approach digitally subdivides cytoskeleton images using interrogation windows, within which box‐counting is used to infer a fractal dimension (D f) to characterize spatial arrangement, and gray value intensity (GVI) to determine actin density. A partitioning algorithm further obtains cytoskeleton characteristics from the perinuclear, cytosolic, and periphery cellular regions. We validated our measurement approach on Cytochalasin‐treated cells using transgenically modified dermal fibroblast cells expressing fluorescent actin cytoskeletons. This method differentiates between normal and chemically disrupted actin networks, and quantifies rates of cytoskeletal degradation. Furthermore, GVI distributions were found to be inversely proportional to D f, having several biophysical implications for cytoskeleton formation/degradation. We additionally demonstrated detection sensitivity of differences in D f and GVI for cells seeded on substrates with varying degrees of stiffness, and coated with different attachment proteins. This general approach can be further implemented to gain insights on dynamic growth, disruption, and structure of the cytoskeleton (and other complex biological morphology) due to biological, chemical, or physical stimuli. © 2016 The Authors. Cytoskeleton Published by Wiley Periodicals, Inc. PMID:27015595

Use of local noise power spectrum and wavelet analysis in quantitative image quality assurance for EPIDs

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

Lee, Soyoung

Purpose: To investigate the use of local noise power spectrum (NPS) to characterize image noise and wavelet analysis to isolate defective pixels and inter-subpanel flat-fielding artifacts for quantitative quality assurance (QA) of electronic portal imaging devices (EPIDs). Methods: A total of 93 image sets including custom-made bar-pattern images and open exposure images were collected from four iViewGT a-Si EPID systems over three years. Global quantitative metrics such as modulation transform function (MTF), NPS, and detective quantum efficiency (DQE) were computed for each image set. Local NPS was also calculated for individual subpanels by sampling region of interests within each subpanelmore » of the EPID. The 1D NPS, obtained by radially averaging the 2D NPS, was fitted to a power-law function. The r-square value of the linear regression analysis was used as a singular metric to characterize the noise properties of individual subpanels of the EPID. The sensitivity of the local NPS was first compared with the global quantitative metrics using historical image sets. It was then compared with two commonly used commercial QA systems with images collected after applying two different EPID calibration methods (single-level gain and multilevel gain). To detect isolated defective pixels and inter-subpanel flat-fielding artifacts, Haar wavelet transform was applied on the images. Results: Global quantitative metrics including MTF, NPS, and DQE showed little change over the period of data collection. On the contrary, a strong correlation between the local NPS (r-square values) and the variation of the EPID noise condition was observed. The local NPS analysis indicated image quality improvement with the r-square values increased from 0.80 ± 0.03 (before calibration) to 0.85 ± 0.03 (after single-level gain calibration) and to 0.96 ± 0.03 (after multilevel gain calibration), while the commercial QA systems failed to distinguish the image quality improvement between the two calibration methods. With wavelet analysis, defective pixels and inter-subpanel flat-fielding artifacts were clearly identified as spikes after thresholding the inversely transformed images. Conclusions: The proposed local NPS (r-square values) showed superior sensitivity to the noise level variations of individual subpanels compared with global quantitative metrics such as MTF, NPS, and DQE. Wavelet analysis was effective in detecting isolated defective pixels and inter-subpanel flat-fielding artifacts. The proposed methods are promising for the early detection of imaging artifacts of EPIDs.« less

Quality-by-Design II: Application of Quantitative Risk Analysis to the Formulation of Ciprofloxacin Tablets.

PubMed

Claycamp, H Gregg; Kona, Ravikanth; Fahmy, Raafat; Hoag, Stephen W

2016-04-01

Qualitative risk assessment methods are often used as the first step to determining design space boundaries; however, quantitative assessments of risk with respect to the design space, i.e., calculating the probability of failure for a given severity, are needed to fully characterize design space boundaries. Quantitative risk assessment methods in design and operational spaces are a significant aid to evaluating proposed design space boundaries. The goal of this paper is to demonstrate a relatively simple strategy for design space definition using a simplified Bayesian Monte Carlo simulation. This paper builds on a previous paper that used failure mode and effects analysis (FMEA) qualitative risk assessment and Plackett-Burman design of experiments to identity the critical quality attributes. The results show that the sequential use of qualitative and quantitative risk assessments can focus the design of experiments on a reduced set of critical material and process parameters that determine a robust design space under conditions of limited laboratory experimentation. This approach provides a strategy by which the degree of risk associated with each known parameter can be calculated and allocates resources in a manner that manages risk to an acceptable level.

Quantitative characterization of conformational-specific protein-DNA binding using a dual-spectral interferometric imaging biosensor.

PubMed

Zhang, Xirui; Daaboul, George G; Spuhler, Philipp S; Dröge, Peter; Ünlü, M Selim

2016-03-14

DNA-binding proteins play crucial roles in the maintenance and functions of the genome and yet, their specific binding mechanisms are not fully understood. Recently, it was discovered that DNA-binding proteins recognize specific binding sites to carry out their functions through an indirect readout mechanism by recognizing and capturing DNA conformational flexibility and deformation. High-throughput DNA microarray-based methods that provide large-scale protein-DNA binding information have shown effective and comprehensive analysis of protein-DNA binding affinities, but do not provide information of DNA conformational changes in specific protein-DNA complexes. Building on the high-throughput capability of DNA microarrays, we demonstrate a quantitative approach that simultaneously measures the amount of protein binding to DNA and nanometer-scale DNA conformational change induced by protein binding in a microarray format. Both measurements rely on spectral interferometry on a layered substrate using a single optical instrument in two distinct modalities. In the first modality, we quantitate the amount of binding of protein to surface-immobilized DNA in each DNA spot using a label-free spectral reflectivity technique that accurately measures the surface densities of protein and DNA accumulated on the substrate. In the second modality, for each DNA spot, we simultaneously measure DNA conformational change using a fluorescence vertical sectioning technique that determines average axial height of fluorophores tagged to specific nucleotides of the surface-immobilized DNA. The approach presented in this paper, when combined with current high-throughput DNA microarray-based technologies, has the potential to serve as a rapid and simple method for quantitative and large-scale characterization of conformational specific protein-DNA interactions.

High-throughput, label-free, single-cell, microalgal lipid screening by machine-learning-equipped optofluidic time-stretch quantitative phase microscopy.

PubMed

Guo, Baoshan; Lei, Cheng; Kobayashi, Hirofumi; Ito, Takuro; Yalikun, Yaxiaer; Jiang, Yiyue; Tanaka, Yo; Ozeki, Yasuyuki; Goda, Keisuke

2017-05-01

The development of reliable, sustainable, and economical sources of alternative fuels to petroleum is required to tackle the global energy crisis. One such alternative is microalgal biofuel, which is expected to play a key role in reducing the detrimental effects of global warming as microalgae absorb atmospheric CO 2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid amounts and fail to characterize a diverse population of microalgal cells with single-cell resolution in a non-invasive and interference-free manner. Here high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy was demonstrated. In particular, Euglena gracilis, an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement), within lipid droplets was investigated. The optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch quantitative phase microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase maps of every single cell at a high throughput of 10,000 cells/s, enabling accurate cell classification without the need for fluorescent staining. Specifically, the dataset was used to characterize heterogeneous populations of E. gracilis cells under two different culture conditions (nitrogen-sufficient and nitrogen-deficient) and achieve the cell classification with an error rate of only 2.15%. The method holds promise as an effective analytical tool for microalgae-based biofuel production. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells.

PubMed

D'Antonio, Matteo; Woodruff, Grace; Nathanson, Jason L; D'Antonio-Chronowska, Agnieszka; Arias, Angelo; Matsui, Hiroko; Williams, Roy; Herrera, Cheryl; Reyna, Sol M; Yeo, Gene W; Goldstein, Lawrence S B; Panopoulos, Athanasia D; Frazer, Kelly A

2017-04-11

Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) offers the possibility of studying the molecular mechanisms underlying human diseases in cell types difficult to extract from living patients, such as neurons and cardiomyocytes. To date, studies have been published that use small panels of iPSC-derived cell lines to study monogenic diseases. However, to study complex diseases, where the genetic variation underlying the disorder is unknown, a sizable number of patient-specific iPSC lines and controls need to be generated. Currently the methods for deriving and characterizing iPSCs are time consuming, expensive, and, in some cases, descriptive but not quantitative. Here we set out to develop a set of simple methods that reduce cost and increase throughput in the characterization of iPSC lines. Specifically, we outline methods for high-throughput quantification of surface markers, gene expression analysis of in vitro differentiation potential, and evaluation of karyotype with markedly reduced cost. Published by Elsevier Inc.

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

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

Pidatala, Venkataramana R.; Mahboubi, Amir; Mortimer, Jenny C.

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharidemore » fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.« less

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE.

PubMed

Pidatala, Venkataramana R; Mahboubi, Amir; Mortimer, Jenny C

2017-10-16

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

DOE PAGES

Pidatala, Venkataramana R.; Mahboubi, Amir; Mortimer, Jenny C.

2017-10-16

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharidemore » fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.« less

Probabilistic Exposure Analysis for Chemical Risk Characterization

PubMed Central

Bogen, Kenneth T.; Cullen, Alison C.; Frey, H. Christopher; Price, Paul S.

2009-01-01

This paper summarizes the state of the science of probabilistic exposure assessment (PEA) as applied to chemical risk characterization. Current probabilistic risk analysis methods applied to PEA are reviewed. PEA within the context of risk-based decision making is discussed, including probabilistic treatment of related uncertainty, interindividual heterogeneity, and other sources of variability. Key examples of recent experience gained in assessing human exposures to chemicals in the environment, and other applications to chemical risk characterization and assessment, are presented. It is concluded that, although improvements continue to be made, existing methods suffice for effective application of PEA to support quantitative analyses of the risk of chemically induced toxicity that play an increasing role in key decision-making objectives involving health protection, triage, civil justice, and criminal justice. Different types of information required to apply PEA to these different decision contexts are identified, and specific PEA methods are highlighted that are best suited to exposure assessment in these separate contexts. PMID:19223660

Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer

DOE PAGES

Song, Ehwang; Gao, Yuqian; Wu, Chaochao; ...

2017-07-19

Here, mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are becoming the method of choice for preclinical verification of candidate protein biomarkers. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large set of targeted MS-based assays, and a depository to share assays publicly, providing that assays meet the guidelines proposed bymore » CPTAC. Herein, we report 98 SRM assays covering 70 candidate protein biomarkers previously reported as associated with ovarian cancer that have been thoroughly characterized according to the CPTAC Assay Characterization Guidance Document. The experiments, methods and results for characterizing these SRM assays for their MS response, repeatability, selectivity, stability, and reproducible detection of endogenous analytes are described in detail.« less

Structural Characterization of Ginsenosides from Flower Buds of Panax ginseng by RRLC-Q-TOF MS.

PubMed

Wu, Wei; Lu, Ziyan; Teng, Yaran; Guo, Yingying; Liu, Shuying

2016-02-01

Ginseng flower bud as a part of Panax ginseng has received much attention as a valuable functional food with medicinal potential. A few studies focused on systematic and comprehensive studies on its major ingredients. This study aims to rapidly characterize ginsenosides in ginseng flower buds and provide scientific basis for developing functional food, exploiting pharmaceutical effects and making full use of ginseng resources. A rapid resolution liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (RRLC-Q-TOF-MS) method was developed for rapid qualitative and quantitative analysis of ginsenosides in ginseng flower buds. The compounds were identified by comparing retention time of the reference standards, accurate mass measurement and the fragment ions obtained from RRLC-Q-TOF-MS/MS analyses. A total of 14 kinds of ginsenosides were identified and 5 kinds of malonyl-ginsenosides were first tentatively identified in ginseng flower buds. Ten kinds of main ginsenosides were quantitatively analyzed. The developed RRLC-Q-TOF-MS method was demonstrated as an effective analytical means for rapid characterization of the ginsenosides in flower buds of P. ginseng. The research result is valuable for quality control, assessment of authenticity and stability evaluation of ginseng flower buds. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Characterization and antimicrobial performance of nano silver coatings on leather materials

PubMed Central

Lkhagvajav, N.; Koizhaiganova, M.; Yasa, I.; Çelik, E.; Sari, Ö.

2015-01-01

In this study, the characterization and the antimicrobial properties of nano silver (nAg) coating on leather were investigated. For this purpose, turbidity, viscosity and pH of nAg solutions prepared by the sol-gel method were measured. The formation of films from these solutions was characterized according to temperature by Differential Thermal Analysis-Thermogravimetry (DTA-TG) equipment. The surface morphology of treated leathers was observed using Scanning Electron Microscopy (SEM). The antimicrobial performance of nAg coatings on leather materials to the test microorganisms as Escherichia coli , Staphylococcus aureus , Candida albicans and Aspergillius niger was evaluated by the application of qualitative (Agar overlay method) and quantitative (percentage of microbial reduction) tests. According to qualitative test results it was found that 20 μg/cm 2 and higher concentrations of nAg on the leather samples were effective against all microorganisms tested. Moreover, quantitative test results showed that leather samples treated with 20 μg/cm 2 of nAg demonstrated the highest antibacterial activity against E. coli with 99.25% bacterium removal, whereas a 10 μg/cm 2 concentration of nAg on leather was enough to exhibit the excellent percentage reduction against S. aureus of 99.91%. The results are promising for the use of colloidal nano silver solution on lining leather as antimicrobial coating. PMID:26221087

State of Aircraft Turboshaft Engines by Means of Tribotechnical Diagnostic

NASA Astrophysics Data System (ADS)

Mihalčová, Janka

2018-03-01

The contribution describes concrete example of application of tribotechnical methods for the determination of the bearing wear state in aircraft turboshaft engines. Tribotechnical methods, which will be mentioned, deal with qualitative and quantitative characterization of particles occurred in oil. Here belong method optical emission spectrometry method with rotating disc electrode for determination of chemical elements concentration in oil. Method of optical particles counting for detection of particles distribution according to their scale, determination of their number and ferrographic analysis. Exploitation of these methods make it possible to determine quickly and correctly the friction regime and wearing of friction pair that is washed by oil in observed engines.

Challenges in quantitative crystallographic characterization of 3D thin films by ACOM-TEM.

PubMed

Kobler, A; Kübel, C

2017-02-01

Automated crystal orientation mapping for transmission electron microscopy (ACOM-TEM) has become an easy to use method for the investigation of crystalline materials and complements other TEM methods by adding local crystallographic information over large areas. It fills the gap between high resolution electron microscopy and electron back scatter diffraction in terms of spatial resolution. Recent investigations showed that spot diffraction ACOM-TEM is a quantitative method with respect to sample parameters like grain size, twin density, orientation density and others. It can even be used in combination with in-situ tensile or thermal testing. However, there are limitations of the current method. In this paper we discuss some of the challenges and discuss solutions, e.g. we present an ambiguity filter that reduces the number of pixels with a '180° ambiguity problem'. For that an ACOM-TEM tilt series of nanocrystalline Pd thin films with overlapping crystallites was acquired and analyzed. Copyright © 2017. Published by Elsevier B.V.

Use of quantitative SPECT/CT reconstruction in 99mTc-sestamibi imaging of patients with renal masses.

PubMed

Jones, Krystyna M; Solnes, Lilja B; Rowe, Steven P; Gorin, Michael A; Sheikhbahaei, Sara; Fung, George; Frey, Eric C; Allaf, Mohamad E; Du, Yong; Javadi, Mehrbod S

2018-02-01

Technetium-99m ( 99m Tc)-sestamibi single-photon emission computed tomography/computed tomography (SPECT/CT) has previously been shown to allow for the accurate differentiation of benign renal oncocytomas and hybrid oncocytic/chromophobe tumors (HOCTs) apart from other malignant renal tumor histologies, with oncocytomas/HOCTs showing high uptake and renal cell carcinoma (RCC) showing low uptake based on uptake ratios from non-quantitative single-photon emission computed tomography (SPECT) reconstructions. However, in this study, several tumors fell close to the uptake ratio cutoff, likely due to limitations in conventional SPECT/CT reconstruction methods. We hypothesized that application of quantitative SPECT/CT (QSPECT) reconstruction methods developed by our group would provide more robust separation of hot and cold lesions, serving as an imaging framework on which quantitative biomarkers can be validated for evaluation of renal masses with 99m Tc-sestamibi. Single-photon emission computed tomography data were reconstructed using the clinical Flash 3D reconstruction and QSPECT methods. Two blinded readers then characterized each tumor as hot or cold. Semi-quantitative uptake ratios were calculated by dividing lesion activity by background renal activity for both Flash 3D and QSPECT reconstructions. The difference between median (mean) hot and cold tumor uptake ratios measured 0.655 (0.73) with the QSPECT method and 0.624 (0.67) with the conventional method, resulting in increased separation between hot and cold tumors. Sub-analysis of 7 lesions near the separation point showed a higher absolute difference (0.16) between QPSECT and Flash 3D mean uptake ratios compared to the remaining lesions. Our finding of improved separation between uptake ratios of hot and cold lesions using QSPECT reconstruction lays the foundation for additional quantitative SPECT techniques such as SPECT-UV in the setting of renal 99m Tc-sestamibi and other SPECT/CT exams. With robust quantitative image reconstruction and biomarker analysis, there may be an expanded role for SPECT/CT imaging in renal masses and other pathologic conditions.

Barcode extension for analysis and reconstruction of structures

NASA Astrophysics Data System (ADS)

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L.; Gootenberg, Jonathan S.; Yin, Peng

2017-03-01

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

Barcode extension for analysis and reconstruction of structures.

PubMed

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

2017-03-13

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

Barcode extension for analysis and reconstruction of structures

PubMed Central

Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

2017-01-01

Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures. PMID:28287117

Computer-based objective quantitative assessment of pulmonary parenchyma via x-ray CT

NASA Astrophysics Data System (ADS)

Uppaluri, Renuka; McLennan, Geoffrey; Sonka, Milan; Hoffman, Eric A.

1998-07-01

This paper is a review of our recent studies using a texture- based tissue characterization method called the Adaptive Multiple Feature Method. This computerized method is automated and performs tissue classification based upon the training acquired on a set of representative examples. The AMFM has been applied to several different discrimination tasks including normal subjects, subjects with interstitial lung disease, smokers, asbestos-exposed subjects, and subjects with cystic fibrosis. The AMFM has also been applied to data acquired using different scanners and scanning protocols. The AMFM has shown to be successful and better than other existing techniques in discriminating the tissues under consideration. We demonstrate that the AMFM is considerably more sensitive and specific in characterizing the lung, especially in the presence of mixed pathology, as compared to more commonly used methods. Evidence is presented suggesting that the AMFM is highly sensitive to some of the earliest disease processes.

The change and development of statistical methods used in research articles in child development 1930-2010.

PubMed

Køppe, Simo; Dammeyer, Jesper

2014-09-01

The evolution of developmental psychology has been characterized by the use of different quantitative and qualitative methods and procedures. But how does the use of methods and procedures change over time? This study explores the change and development of statistical methods used in articles published in Child Development from 1930 to 2010. The methods used in every article in the first issue of every volume were categorized into four categories. Until 1980 relatively simple statistical methods were used. During the last 30 years there has been an explosive use of more advanced statistical methods employed. The absence of statistical methods or use of simple methods had been eliminated.

Quantitative characterization of microstructure of asphalt mixtures

DOT National Transportation Integrated Search

2010-10-01

The microstructure of the fine aggregate matrix has a significant influence on the : mechanical properties and evolution of damage in an asphalt mixture. However, very little : work has been done to define and quantitatively characterize the microstr...

Advanced NDE techniques for quantitative characterization of aircraft

NASA Technical Reports Server (NTRS)

Heyman, Joseph S.; Winfree, William P.

1990-01-01

Recent advances in nondestructive evaluation (NDE) at NASA Langley Research Center and their applications that have resulted in quantitative assessment of material properties based on thermal and ultrasonic measurements are reviewed. Specific applications include ultrasonic determination of bolt tension, ultrasonic and thermal characterization of bonded layered structures, characterization of composite materials, and disbonds in aircraft skins.

Three dimensional characterization of laser ablation craters using high resolution X-ray computed tomography

NASA Astrophysics Data System (ADS)

Galmed, A. H.; du Plessis, A.; le Roux, S. G.; Hartnick, E.; Von Bergmann, H.; Maaza, M.

2018-01-01

Laboratory X-ray computed tomography is an emerging technology for the 3D characterization and dimensional analysis of many types of materials. In this work we demonstrate the usefulness of this characterization method for the full three dimensional analysis of laser ablation craters, in the context of a laser induced breakdown spectroscopy setup. Laser induced breakdown spectroscopy relies on laser ablation for sampling the material of interest. We demonstrate here qualitatively (in images) and quantitatively (in terms of crater cone angles, depths, diameters and volume) laser ablation crater analysis in 3D for metal (aluminum) and rock (false gold ore). We show the effect of a Gaussian beam profile on the resulting crater geometry, as well as the first visual evidence of undercutting in the rock sample, most likely due to ejection of relatively large grains. The method holds promise for optimization of laser ablation setups especially for laser induced breakdown spectroscopy.

Tracer Methods for Characterizing Fracture Creation in Engineered Geothermal Systems

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

Rose, Peter; Harris, Joel

2014-05-08

The aim of this proposal is to develop, through novel high-temperature-tracing approaches, three technologies for characterizing fracture creation within Engineered Geothermal Systems (EGS). The objective of a first task is to identify, develop and demonstrate adsorbing tracers for characterizing interwell reservoir-rock surface areas and fracture spacing. The objective of a second task is to develop and demonstrate a methodology for measuring fracture surface areas adjacent to single wells. The objective of a third task is to design, fabricate and test an instrument that makes use of tracers for measuring fluid flow between newly created fractures and wellbores. In one methodmore » of deployment, it will be used to identify qualitatively which fractures were activated during a hydraulic stimulation experiment. In a second method of deployment, it will serve to measure quantitatively the rate of fluid flowing from one or more activated fracture during a production test following a hydraulic stimulation.« less

Quantitative elasticity measurement of urinary bladder wall using laser-induced surface acoustic waves.

PubMed

Li, Chunhui; Guan, Guangying; Zhang, Fan; Song, Shaozhen; Wang, Ruikang K; Huang, Zhihong; Nabi, Ghulam

2014-12-01

The maintenance of urinary bladder elasticity is essential to its functions, including the storage and voiding phases of the micturition cycle. The bladder stiffness can be changed by various pathophysiological conditions. Quantitative measurement of bladder elasticity is an essential step toward understanding various urinary bladder disease processes and improving patient care. As a nondestructive, and noncontact method, laser-induced surface acoustic waves (SAWs) can accurately characterize the elastic properties of different layers of organs such as the urinary bladder. This initial investigation evaluates the feasibility of a noncontact, all-optical method of generating and measuring the elasticity of the urinary bladder. Quantitative elasticity measurements of ex vivo porcine urinary bladder were made using the laser-induced SAW technique. A pulsed laser was used to excite SAWs that propagated on the bladder wall surface. A dedicated phase-sensitive optical coherence tomography (PhS-OCT) system remotely recorded the SAWs, from which the elasticity properties of different layers of the bladder were estimated. During the experiments, series of measurements were performed under five precisely controlled bladder volumes using water to estimate changes in the elasticity in relation to various urinary bladder contents. The results, validated by optical coherence elastography, show that the laser-induced SAW technique combined with PhS-OCT can be a feasible method of quantitative estimation of biomechanical properties.

In-depth quantitative analysis of the microstructures produced by Surface Mechanical Attrition Treatment (SMAT)

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

Samih, Y., E-mail: youssef.samih@univ-lorraine.fr; Université de Lorraine, Laboratory of Excellence on Design of Alloy Metals for low-mAss Structures; Beausir, B.

2013-09-15

Electron BackScattered Diffraction (EBSD) maps are used to characterize quantitatively the graded microstructure formed by Surface Mechanical Attrition Treatment (SMAT) and applied here to the 316L stainless steel. In particular, the analysis of GNDs – coupled with relevant and reliable criteria – was used to depict the thickness of each zone identified in the SMAT-affected layers: (i) the “ultrafine grain” (UFG) zone present at the extreme top surface, (ii), the “transition zone” where grains were fragmented under the heavy plastic deformation and, finally, (iii) the “deformed zone” where initial grains are simply deformed. The interest of this procedure is illustratedmore » through the comparative analysis of the effect of some SMAT processing parameters (amplitude of vibration and treatment duration). The UFG and transition zones are more significantly modified than the overall affected thickness under our tested conditions. - Highlights: • EBSD maps are used to characterize quantitatively the microstructure of SMAT treated samples. • Calculation of the GND density to quantify strain gradients • A new method to depict the different zone thicknesses in the SMAT affected layer • Effects of SMAT processing parameters on the surface microstructure evolution.« less

FDTD-based quantitative analysis of terahertz wave detection for multilayered structures.

PubMed

Tu, Wanli; Zhong, Shuncong; Shen, Yaochun; Zhou, Qing; Yao, Ligang

2014-10-01

Experimental investigations have shown that terahertz pulsed imaging (TPI) is able to quantitatively characterize a range of multilayered media (e.g., biological issues, pharmaceutical tablet coatings, layered polymer composites, etc.). Advanced modeling of the interaction of terahertz radiation with a multilayered medium is required to enable the wide application of terahertz technology in a number of emerging fields, including nondestructive testing. Indeed, there have already been many theoretical analyses performed on the propagation of terahertz radiation in various multilayered media. However, to date, most of these studies used 1D or 2D models, and the dispersive nature of the dielectric layers was not considered or was simplified. In the present work, the theoretical framework of using terahertz waves for the quantitative characterization of multilayered media was established. A 3D model based on the finite difference time domain (FDTD) method is proposed. A batch of pharmaceutical tablets with a single coating layer of different coating thicknesses and different refractive indices was modeled. The reflected terahertz wave from such a sample was computed using the FDTD method, assuming that the incident terahertz wave is broadband, covering a frequency range up to 3.5 THz. The simulated results for all of the pharmaceutical-coated tablets considered were found to be in good agreement with the experimental results obtained using a commercial TPI system. In addition, we studied a three-layered medium to mimic the occurrence of defects in the sample.

Interactions across Multiple Stimulus Dimensions in Primary Auditory Cortex.

PubMed

Sloas, David C; Zhuo, Ran; Xue, Hongbo; Chambers, Anna R; Kolaczyk, Eric; Polley, Daniel B; Sen, Kamal

2016-01-01

Although sensory cortex is thought to be important for the perception of complex objects, its specific role in representing complex stimuli remains unknown. Complex objects are rich in information along multiple stimulus dimensions. The position of cortex in the sensory hierarchy suggests that cortical neurons may integrate across these dimensions to form a more gestalt representation of auditory objects. Yet, studies of cortical neurons typically explore single or few dimensions due to the difficulty of determining optimal stimuli in a high dimensional stimulus space. Evolutionary algorithms (EAs) provide a potentially powerful approach for exploring multidimensional stimulus spaces based on real-time spike feedback, but two important issues arise in their application. First, it is unclear whether it is necessary to characterize cortical responses to multidimensional stimuli or whether it suffices to characterize cortical responses to a single dimension at a time. Second, quantitative methods for analyzing complex multidimensional data from an EA are lacking. Here, we apply a statistical method for nonlinear regression, the generalized additive model (GAM), to address these issues. The GAM quantitatively describes the dependence between neural response and all stimulus dimensions. We find that auditory cortical neurons in mice are sensitive to interactions across dimensions. These interactions are diverse across the population, indicating significant integration across stimulus dimensions in auditory cortex. This result strongly motivates using multidimensional stimuli in auditory cortex. Together, the EA and the GAM provide a novel quantitative paradigm for investigating neural coding of complex multidimensional stimuli in auditory and other sensory cortices.

Glycan reductive isotope labeling for quantitative glycomics.

PubMed

Xia, Baoyun; Feasley, Christa L; Sachdev, Goverdhan P; Smith, David F; Cummings, Richard D

2009-04-15

Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed glycan reductive isotope labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [(12)C(6)]aniline and [(13)C(6)]aniline. These dual-labeled aniline-tagged glycans can be recovered by reverse-phase chromatography and can be quantified based on ultraviolet (UV) absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins, using this method. This technique allows linear relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of glycomics.

GLYCAN REDUCTIVE ISOTOPE LABELING (GRIL) FOR QUANTITATIVE GLYCOMICS

PubMed Central

Xia, Baoyun; Feasley, Christa L.; Sachdev, Goverdhan P.; Smith, David F.; Cummings, Richard D.

2009-01-01

Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed Glycan Reductive Isotope Labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [12C6]-aniline and [13C6]-aniline. These dual-labeled aniline-tagged glycans can be recovered by reversed-phase chromatography and quantified based on UV-absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins using this method. This technique allows for linear, relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of Glycomics. PMID:19454239

Computational characterization of ordered nanostructured surfaces

NASA Astrophysics Data System (ADS)

Mohieddin Abukhdeir, Nasser

2016-08-01

A vital and challenging task for materials researchers is to determine relationships between material characteristics and desired properties. While the measurement and assessment of material properties can be complex, quantitatively characterizing their structure is frequently a more challenging task. This issue is magnified for materials researchers in the areas of nanoscience and nanotechnology, where material structure is further complicated by phenomena such as self-assembly, collective behavior, and measurement uncertainty. Recent progress has been made in this area for both self-assembled and nanostructured surfaces due to increasing accessibility of imaging techniques at the nanoscale. In this context, recent advances in nanomaterial surface structure characterization are reviewed including the development of new theory and image processing methods.

Tracing molecular dephasing in biological tissue

NASA Astrophysics Data System (ADS)

Mokim, M.; Carruba, C.; Ganikhanov, F.

2017-10-01

We demonstrate the quantitative spectroscopic characterization and imaging of biological tissue using coherent time-domain microscopy with a femtosecond resolution. We identify tissue constituents and perform dephasing time (T2) measurements of characteristic Raman active vibrations. This was shown in subcutaneous mouse fat embedded within collagen rich areas of the dermis and the muscle connective tissue. The demonstrated equivalent spectral resolution (<0.3 cm-1) is an order of magnitude better compared to commonly used frequency-domain methods for characterization of biological media. This provides with the important dimensions and parameters in biological media characterization and can become an effective tool in detecting minute changes in the bio-molecular composition and environment that is critical for molecular level diagnosis.

High energy PIXE: A tool to characterize multi-layer thick samples

NASA Astrophysics Data System (ADS)

Subercaze, A.; Koumeir, C.; Métivier, V.; Servagent, N.; Guertin, A.; Haddad, F.

2018-02-01

High energy PIXE is a useful and non-destructive tool to characterize multi-layer thick samples such as cultural heritage objects. In a previous work, we demonstrated the possibility to perform quantitative analysis of simple multi-layer samples using high energy PIXE, without any assumption on their composition. In this work an in-depth study of the parameters involved in the method previously published is proposed. Its extension to more complex samples with a repeated layer is also presented. Experiments have been performed at the ARRONAX cyclotron using 68 MeV protons. The thicknesses and sequences of a multi-layer sample including two different layers of the same element have been determined. Performances and limits of this method are presented and discussed.

Measuring Borrelia burgdorferi Motility and Chemotaxis.

PubMed

Zhang, Kai; Li, Chunhao

2018-01-01

Swimming plate, cell motion tracking, and capillary tube assays are very useful tools to quantitatively measure bacterial motility and chemotaxis. These methods were modified and applied to study Borrelia burgdorferi motility and chemotaxis. By using these methods, numerous motility and chemotaxis mutants have been characterized and several chemoattractants were identified. With the assistance of these tools, the role of motility and chemotaxis in the pathogenicity of B. burgdorferi has been established. In addition, these tools also facilitate the study of motility and chemotaxis in other spirochetes.

Investigation of Post-mortem Tissue Effects Using Long-time Decorrelation Ultrasound

NASA Astrophysics Data System (ADS)

Csány, Gergely; Balogh, Lajos; Gyöngy, Miklós

Decorrelation ultrasound is being increasingly used to investigate long-term biological phenomena. In the current work, ultrasound image sequences of mice who did not survive anesthesia (in a separate investigation) were analyzed and post-mortem tissue effects were observed via decorrelation calculation. A method was developed to obtain a quantitative parameter characterizing the rate of decorrelation. The results show that ultrasound decorrelation imaging is an effective method of observing post-mortem tissue effects and point to further studies elucidating the mechanism behind these effects.

Quantitative shear wave imaging optical coherence tomography for noncontact mechanical characterization of myocardium

NASA Astrophysics Data System (ADS)

Wang, Shang; Lopez, Andrew L.; Morikawa, Yuka; Tao, Ge; Li, Jiasong; Larina, Irina V.; Martin, James F.; Larin, Kirill V.

2015-03-01

Optical coherence elastography (OCE) is an emerging low-coherence imaging technique that provides noninvasive assessment of tissue biomechanics with high spatial resolution. Among various OCE methods, the capability of quantitative measurement of tissue elasticity is of great importance for tissue characterization and pathology detection across different samples. Here we report a quantitative OCE technique, termed quantitative shear wave imaging optical coherence tomography (Q-SWI-OCT), which enables noncontact measurement of tissue Young's modulus based on the ultra-fast imaging of the shear wave propagation inside the sample. A focused air-puff device is used to interrogate the tissue with a low-pressure short-duration air stream that stimulates a localized displacement with the scale at micron level. The propagation of this tissue deformation in the form of shear wave is captured by a phase-sensitive OCT system running with the scan of the M-mode imaging over the path of the wave propagation. The temporal characteristics of the shear wave is quantified based on the cross-correlation of the tissue deformation profiles at all the measurement locations, and linear regression is utilized to fit the data plotted in the domain of time delay versus wave propagation distance. The wave group velocity is thus calculated, which results in the quantitative measurement of the Young's modulus. As the feasibility demonstration, experiments are performed on tissuemimicking phantoms with different agar concentrations and the quantified elasticity values with Q-SWI-OCT agree well with the uniaxial compression tests. For functional characterization of myocardium with this OCE technique, we perform our pilot experiments on ex vivo mouse cardiac muscle tissues with two studies, including 1) elasticity difference of cardiac muscle under relaxation and contract conditions and 2) mechanical heterogeneity of the heart introduced by the muscle fiber orientation. Our results suggest the potential of using Q-SWI-OCT as an essential tool for nondestructive biomechanical evaluation of myocardium.

Quantitation of Bone Growth Rate Variability in Rats Exposed to Micro-(near zero G) and Macrogravity (2G)

NASA Technical Reports Server (NTRS)

Bromage, Timothy G.; Doty, Stephen B.; Smolyar, Igor; Holton, Emily

1997-01-01

Our stated primary objective is to quantify the growth rate variability of rat lamellar bone exposed to micro- (near zero G: e.g., Cosmos 1887 & 2044; SLS-1 & SLS-2) and macrogravity (2G). The primary significance of the proposed work is that an elegant method will be established that unequivocally characterizes the morphological consequences of gravitational factors on developing bone. The integrity of this objective depends upon our successful preparation of thin sections suitable for imaging individual bone lamellae, and our imaging and quantitation of growth rate variability in populations of lamellae from individual bone samples.

Methodology for characterizing potential adversaries of Nuclear Material Safeguards Systems

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

Kirkwood, C.W.; Pollock, S.M.

1978-11-01

The results are described of a study by Woodward--Clyde Consultants to assist the University of California Lawrence Livermore Laboratory in the development of methods to analyze and evaluate Nuclear Material Safeguards (NMS) Systems. The study concentrated on developing a methodology to assist experts in describing, in quantitative form, their judgments about the characteristics of potential adversaries of NMS Systems.

Method for detecting damage in carbon-fibre reinforced plastic-steel structures based on eddy current pulsed thermography

NASA Astrophysics Data System (ADS)

Li, Xuan; Liu, Zhiping; Jiang, Xiaoli; Lodewijks, Gabrol

2018-01-01

Eddy current pulsed thermography (ECPT) is well established for non-destructive testing of electrical conductive materials, featuring the advantages of contactless, intuitive detecting and efficient heating. The concept of divergence characterization of the damage rate of carbon fibre-reinforced plastic (CFRP)-steel structures can be extended to ECPT thermal pattern characterization. It was found in this study that the use of ECPT technology on CFRP-steel structures generated a sizeable amount of valuable information for comprehensive material diagnostics. The relationship between divergence and transient thermal patterns can be identified and analysed by deploying mathematical models to analyse the information about fibre texture-like orientations, gaps and undulations in these multi-layered materials. The developed algorithm enabled the removal of information about fibre texture and the extraction of damage features. The model of the CFRP-glue-steel structures with damage was established using COMSOL Multiphysics® software, and quantitative non-destructive damage evaluation from the ECPT image areas was derived. The results of this proposed method illustrate that damaged areas are highly affected by available information about fibre texture. This proposed work can be applied for detection of impact induced damage and quantitative evaluation of CFRP structures.

Assessing direct analysis in real-time-mass spectrometry (DART-MS) for the rapid identification of additives in food packaging.

PubMed

Ackerman, L K; Noonan, G O; Begley, T H

2009-12-01

The ambient ionization technique direct analysis in real time (DART) was characterized and evaluated for the screening of food packaging for the presence of packaging additives using a benchtop mass spectrometer (MS). Approximate optimum conditions were determined for 13 common food-packaging additives, including plasticizers, anti-oxidants, colorants, grease-proofers, and ultraviolet light stabilizers. Method sensitivity and linearity were evaluated using solutions and characterized polymer samples. Additionally, the response of a model additive (di-ethyl-hexyl-phthalate) was examined across a range of sample positions, DART, and MS conditions (temperature, voltage and helium flow). Under optimal conditions, molecular ion (M+H+) was the major ion for most additives. Additive responses were highly sensitive to sample and DART source orientation, as well as to DART flow rates, temperatures, and MS inlet voltages, respectively. DART-MS response was neither consistently linear nor quantitative in this setting, and sensitivity varied by additive. All additives studied were rapidly identified in multiple food-packaging materials by DART-MS/MS, suggesting this technique can be used to screen food packaging rapidly. However, method sensitivity and quantitation requires further study and improvement.

The concept of culture: a core issue in health disparities.

PubMed

Page, J Bryan

2005-06-01

Contemporary discourse contains numerous examples of use of the concept of culture by social and behavioral scientists. Simple reification, where the speaker makes culture into a thing capable of action exemplifies one usage in public discourse. Some quantitative social scientists attempt to characterize people's cultural identities by means of a single categorical variable, which often "lumps" people into categories such as "Hispanic" or "Black" that in fact have numerous culturally bounded subcategories. Approaches that emphasize cultural process are preferable to those who attempt to categorize; more complex measures of acculturation help investigators to make convincing analyses of circumstances in which health disparities occur. Examples in which investigators make appropriate use of cultural characterizations demonstrate their utility in investigating health disparities in Haitian American women, injecting and noninjecting drug users, Hispanic youth, and adult Hispanics at risk of HIV infection. Focus on culture in the study of health disparities can identify entanglements between structural factors such as poverty and lack of education and cultural factors such as beliefs about health. Qualitative methods coupled with quantitative methods have great potential to improve investigators' grasp of cultural nuance while capturing the distribution of qualitatively derived behaviors.

Least Squares Moving-Window Spectral Analysis.

PubMed

Lee, Young Jong

2017-08-01

Least squares regression is proposed as a moving-windows method for analysis of a series of spectra acquired as a function of external perturbation. The least squares moving-window (LSMW) method can be considered an extended form of the Savitzky-Golay differentiation for nonuniform perturbation spacing. LSMW is characterized in terms of moving-window size, perturbation spacing type, and intensity noise. Simulation results from LSMW are compared with results from other numerical differentiation methods, such as single-interval differentiation, autocorrelation moving-window, and perturbation correlation moving-window methods. It is demonstrated that this simple LSMW method can be useful for quantitative analysis of nonuniformly spaced spectral data with high frequency noise.

Development of a pressurized liquid extraction-solid-phase extraction followed by liquid chromatography-electrospray ionization tandem mass spectrometry method for the quantitative determination of benzoxazolinones and their degradation products in agricultural soil.

PubMed

Villagrasa, M; Guillamón, M; Navarro, A; Eljarrat, E; Barceló, D

2008-02-01

A new analytical method for the quantitative determination of benzoxazolinones and their degradation products in agricultural soils based on the use of pressurized liquid extraction (PLE) followed by solid-phase extraction (SPE) and then instrumental determination using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS-MS) is described. Using this method, the characterization, separation and quantitative detection of a mixture of two benzoxazolinones, benzoxazolin-2-one (BOA) and 6-methoxybenzoxazolin-2-one (MBOA) and their degradation products, 2-aminophenol (APH), N-(2-hydroxyphenyl)malonamic acid (HMPMA), 2-amino-3-H-phenoxazin-3-one (APO), 9-methoxy-2-amino-3-H-phenoxazin-3-one (AMPO), 2-acetylamino-3-H-phenoxazin-3-one (AAPO) and 2-acetylamino-9-methoxy-2-amino-3-H-phenoxazin-3-one (AAMPO) was achieved. The complete LC-ESI-MS-MS precursor-product ion fragmentation pathways for the degradation products of benzoxazolinones are described for the first time. Quantitative analysis was done in the multiple reaction mode using two specific combinations of precursor-product ion transitions for each compound. The optimized method was quality assessed by the measure of parameter as recovery, linearity, sensitivity, repeatability and reproducibility. Recoveries of the analytes ranged from 53 to 123%. The developed method offered improvements to the sensitivity as compared with our previously LC-MS method, with detection limits down to 2.4-21 ng/g of dry weight. This achievement allows us to identify and quantify for the first time degradation products of benzoxazolinones in real agricultural soil samples. Analytes were found in the range of 20.6-149 ng/g dry weight.

Annual distribution of allergenic fungal spores in atmospheric particulate matter in the Eastern Mediterranean; a comparative study between ergosterol and quantitative PCR analysis

NASA Astrophysics Data System (ADS)

Lang-Yona, N.; Dannemiller, K.; Yamamoto, N.; Burshtein, N.; Peccia, J.; Yarden, O.; Rudich, Y.

2012-03-01

Airborne fungal spores are an important fraction of atmospheric particulate matter and are major causative agents of allergenic and infectious diseases. Predicting the variability and species of allergy-causing fungal spores requires detailed and reliable methods for identification and quantification. There are diverse methods for their detection in the atmosphere and in the indoor environments; yet, it is important to optimize suitable methods for characterization of fungal spores in atmospheric samples. In this study we sampled and characterized total and specific airborne fungal spores from PM10 samples collected in Rehovot, Israel over an entire year. The total fungal spore concentrations vary throughout the year although the species variability was nearly the same. Seasonal equivalent spore concentrations analyzed by real-time quantitative-PCR-based methods were fall > winter > spring > summer. Reported concentrations based on ergosterol analysis for the same samples were and fall > spring > winter > summer. Correlation between the two analytical methods was found only for the spring season. These poor associations may be due to the per-spore ergosterol variations that arise from both varying production rates, as well as molecular degradation of ergosterol. While conversion of genome copies to spore concentration is not yet straightforward, the potential for improving this conversion and the ability of qPCR to identify groups of fungi or specific species makes this method preferable for environmental spore quantification. Identifying tools for establishing the relation between the presence of species and the actual ability to induce allergies is still needed in order to predict the effect on human health.

Annual distribution of allergenic fungal spores in atmospheric particulate matter in the eastern mediterranean; a comparative study between ergosterol and quantitative PCR analysis

NASA Astrophysics Data System (ADS)

Lang-Yona, N.; Dannemiller, K.; Yamamoto, N.; Burshtein, N.; Peccia, J.; Yarden, O.; Rudich, Y.

2011-10-01

Airborne fungal spores are an important fraction of atmospheric particulate matter and are major causative agents of allergenic and infectious diseases. Predicting the variability and species of allergy-causing fungal spores requires detailed and reliable methods for identification and quantification. There are diverse methods for their detection in the atmosphere and in the indoor environments; yet, it is important to optimize suitable methods for characterization of fungal spores in atmospheric samples. In this study we sampled and characterized total and specific airborne fungal spores from PM10 samples collected in Rohovot, Israel over an entire year. The total fungal spore concentrations vary throughout the year although the species variability was nearly the same. Seasonal equivalent spore concentrations analyzed by real-time quantitative-PCR-based methods were fall > winter > spring > summer. Reported concentrations based on ergosterol analysis for the same samples were and fall > spring > winter > summer. Correlation between the two analytical methods was found only for the spring season. These poor associations may be due to the per-spore ergosterol variations that arise from both varying production rates, as well as molecular degradation of ergosterol. While conversion of genome copies to spore concentration is not yet straightforward, the potential for improving this conversion and the ability of qPCR to identify groups of fungi or specific species makes this method preferable for environmental spore quantification. Identifying tools for establishing the relation between the presence of species and the actual ability to induce allergies is still needed in order to predict the effect on human health.

Defining glycoprotein cancer biomarkers by MS in conjunction with glycoprotein enrichment.

PubMed

Song, Ehwang; Mechref, Yehia

2015-01-01

Protein glycosylation is an important and common post-translational modification. More than 50% of human proteins are believed to be glycosylated to modulate the functionality of proteins. Aberrant glycosylation has been correlated to several diseases, such as inflammatory skin diseases, diabetes mellitus, cardiovascular disorders, rheumatoid arthritis, Alzheimer's and prion diseases, and cancer. Many approved cancer biomarkers are glycoproteins which are not highly abundant proteins. Therefore, effective qualitative and quantitative assessment of glycoproteins entails enrichment methods. This chapter summarizes glycoprotein enrichment methods, including lectin affinity, immunoaffinity, hydrazide chemistry, hydrophilic interaction liquid chromatography, and click chemistry. The use of these enrichment approaches in assessing the qualitative and quantitative changes of glycoproteins in different types of cancers are presented and discussed. This chapter highlights the importance of glycoprotein enrichment techniques for the identification and characterization of new reliable cancer biomarkers.

Quantitative assessment of submicron scale anisotropy in tissue multifractality by scattering Mueller matrix in the framework of Born approximation

NASA Astrophysics Data System (ADS)

Das, Nandan Kumar; Dey, Rajib; Chakraborty, Semanti; Panigrahi, Prasanta K.; Meglinski, Igor; Ghosh, Nirmalya

2018-04-01

A number of tissue-like disordered media exhibit local anisotropy of scattering in the scaling behavior. Scaling behavior contains wealth of fractal or multifractal properties. We demonstrate that the spatial dielectric fluctuations in a sample of biological tissue exhibit multifractal anisotropy. Multifractal anisotropy encoded in the wavelength variation of the light scattering Mueller matrix and manifesting as an intriguing spectral diattenuation effect. We developed an inverse method for the quantitative assessment of the multifractal anisotropy. The method is based on the processing of relevant Mueller matrix elements in Fourier domain by using Born approximation, followed by the multifractal analysis. The approach promises for probing subtle micro-structural changes in biological tissues associated with the cancer and precancer, as well as for non-destructive characterization of a wide range of scattering materials.

Nanoscale Structure of Type I Collagen Fibrils: Quantitative Measurement of D-spacing

PubMed Central

Erickson, Blake; Fang, Ming; Wallace, Joseph M.; Orr, Bradford G.; Les, Clifford M.; Holl, Mark M. Banaszak

2012-01-01

This paper details a quantitative method to measure the D-periodic spacing of Type I collagen fibrils using Atomic Force Microscopy coupled with analysis using a 2D Fast Fourier Transform approach. Instrument calibration, data sampling and data analysis are all discussed and comparisons of the data to the complementary methods of electron microscopy and X-ray scattering are made. Examples of the application of this new approach to the analysis of Type I collagen morphology in disease models of estrogen depletion and Osteogenesis Imperfecta are provided. We demonstrate that it is the D-spacing distribution, not the D-spacing mean, that showed statistically significant differences in estrogen depletion associated with early stage Osteoporosis and Osteogenesis Imperfecta. The ability to quantitatively characterize nanoscale morphological features of Type I collagen fibrils will provide important structural information regarding Type I collagen in many research areas, including tissue aging and disease, tissue engineering, and gene knock out studies. Furthermore, we also envision potential clinical applications including evaluation of tissue collagen integrity under the impact of diseases or drug treatments. PMID:23027700

Starting from the bench--prevention and control of foodborne and zoonotic diseases.

PubMed

Vongkamjan, Kitiya; Wiedmann, Martin

2015-02-01

Foodborne diseases are estimated to cause around 50 million disease cases and 3000 deaths a year in the US. Worldwide, food and waterborne diseases are estimated to cause more than 2 million deaths per year. Lab-based research is a key component of efforts to prevent and control foodborne diseases. Over the last two decades, molecular characterization of pathogen isolates has emerged as a key component of foodborne and zoonotic disease prevention and control. Characterization methods have evolved from banding pattern-based subtyping methods to sequenced-based approaches, including full genome sequencing. Molecular subtyping methods not only play a key role for characterizing pathogen transmission and detection of disease outbreaks, but also allow for identification of clonal pathogen groups that show distinct transmission characteristics. Importantly, the data generated from molecular characterization of foodborne pathogens also represent critical inputs for epidemiological and modeling studies. Continued and enhanced collaborations between infectious disease related laboratory sciences and epidemiologists, modelers, and other quantitative scientists will be critical to a One-Health approach that delivers societal benefits, including improved surveillance systems and prevention approaches for zoonotic and foodborne pathogens. Copyright © 2014 Elsevier B.V. All rights reserved.

New horizons in selective laser sintering surface roughness characterization

NASA Astrophysics Data System (ADS)

Vetterli, M.; Schmid, M.; Knapp, W.; Wegener, K.

2017-12-01

Powder-based additive manufacturing of polymers and metals has evolved from a prototyping technology to an industrial process for the fabrication of small to medium series of complex geometry parts. Unfortunately due to the processing of powder as a basis material and the successive addition of layers to produce components, a significant surface roughness inherent to the process has been observed since the first use of such technologies. A novel characterization method based on an elastomeric pad coated with a reflective layer, the Gelsight, was found to be reliable and fast to characterize surfaces processed by selective laser sintering (SLS) of polymers. With help of this method, a qualitative and quantitative investigation of SLS surfaces is feasible. Repeatability and reproducibility investigations are performed for both 2D and 3D areal roughness parameters. Based on the good results, the Gelsight is used for the optimization of vertical SLS surfaces. A model built on laser scanning parameters is proposed and after confirmation could achieve a roughness reduction of 10% based on the S q parameter. The Gelsight could be successfully identified as a fast, reliable and versatile surface topography characterization method as it applies to all kind of surfaces.

HPAEC-PAD quantification of Haemophilus influenzae type b polysaccharide in upstream and downstream samples.

PubMed

van der Put, Robert M F; de Haan, Alex; van den IJssel, Jan G M; Hamidi, Ahd; Beurret, Michel

2015-11-27

Due to the rapidly increasing introduction of Haemophilus influenzae type b (Hib) and other conjugate vaccines worldwide during the last decade, reliable and robust analytical methods are needed for the quantitative monitoring of intermediate samples generated during fermentation (upstream processing, USP) and purification (downstream processing, DSP) of polysaccharide vaccine components. This study describes the quantitative characterization of in-process control (IPC) samples generated during the fermentation and purification of the capsular polysaccharide (CPS), polyribosyl-ribitol-phosphate (PRP), derived from Hib. Reliable quantitative methods are necessary for all stages of production; otherwise accurate process monitoring and validation is not possible. Prior to the availability of high performance anion exchange chromatography methods, this polysaccharide was predominantly quantified either with immunochemical methods, or with the colorimetric orcinol method, which shows interference from fermentation medium components and reagents used during purification. Next to an improved high performance anion exchange chromatography-pulsed amperometric detection (HPAEC-PAD) method, using a modified gradient elution, both the orcinol assay and high performance size exclusion chromatography (HPSEC) analyses were evaluated. For DSP samples, it was found that the correlation between the results obtained by HPAEC-PAD specific quantification of the PRP monomeric repeat unit released by alkaline hydrolysis, and those from the orcinol method was high (R(2)=0.8762), and that it was lower between HPAEC-PAD and HPSEC results. Additionally, HPSEC analysis of USP samples yielded surprisingly comparable results to those obtained by HPAEC-PAD. In the early part of the fermentation, medium components interfered with the different types of analysis, but quantitative HPSEC data could still be obtained, although lacking the specificity of the HPAEC-PAD method. Thus, the HPAEC-PAD method has the advantage of giving a specific response compared to the orcinol assay and HPSEC, and does not show interference from various components that can be present in intermediate and purified PRP samples. Copyright © 2014 Elsevier Ltd. All rights reserved.

Spontaneous Focusing on Quantitative Relations: Towards a Characterization

ERIC Educational Resources Information Center

Degrande, Tine; Verschaffel, Lieven; Van Dooren, Wim

2017-01-01

In contrast to previous studies on Spontaneous Focusing on Quantitative Relations (SFOR), the present study investigated not only the "extent" to which children focus on (multiplicative) quantitative relations, but also the "nature" of children's quantitative focus (i.e., the types of quantitative relations that children focus…

Quantitative Raman characterization of cross-linked collagen thin films as a model system for diagnosing early osteoarthritis

NASA Astrophysics Data System (ADS)

Wang, Chao; Durney, Krista M.; Fomovsky, Gregory; Ateshian, Gerard A.; Vukelic, Sinisa

2016-03-01

The onset of osteoarthritis (OA)in articular cartilage is characterized by degradation of extracellular matrix (ECM). Specifically, breakage of cross-links between collagen fibrils in the articular cartilage leads to loss of structural integrity of the bulk tissue. Since there are no broadly accepted, non-invasive, label-free tools for diagnosing OA at its early stage, Raman spectroscopyis therefore proposed in this work as a novel, non-destructive diagnostic tool. In this study, collagen thin films were employed to act as a simplified model system of the cartilage collagen extracellular matrix. Cross-link formation was controlled via exposure to glutaraldehyde (GA), by varying exposure time and concentration levels, and Raman spectral information was collected to quantitatively characterize the cross-link assignments imparted to the collagen thin films during treatment. A novel, quantitative method was developed to analyze the Raman signal obtained from collagen thin films. Segments of Raman signal were decomposed and modeled as the sum of individual bands, providing an optimization function for subsequent curve fitting against experimental findings. Relative changes in the concentration of the GA-induced pyridinium cross-links were extracted from the model, as a function of the exposure to GA. Spatially resolved characterization enabled construction of spectral maps of the collagen thin films, which provided detailed information about the variation of cross-link formation at various locations on the specimen. Results showed that Raman spectral data correlate with glutaraldehyde treatment and therefore may be used as a proxy by which to measure loss of collagen cross-links in vivo. This study proposes a promising system of identifying onset of OA and may enable early intervention treatments that may serve to slow or prevent osteoarthritis progression.

The Specificity of Observational Studies in Physical Activity and Sports Sciences: Moving Forward in Mixed Methods Research and Proposals for Achieving Quantitative and Qualitative Symmetry.

PubMed

Anguera, M Teresa; Camerino, Oleguer; Castañer, Marta; Sánchez-Algarra, Pedro; Onwuegbuzie, Anthony J

2017-01-01

Mixed methods studies are been increasingly applied to a diversity of fields. In this paper, we discuss the growing use-and enormous potential-of mixed methods research in the field of sport and physical activity. A second aim is to contribute to strengthening the characteristics of mixed methods research by showing how systematic observation offers rigor within a flexible framework that can be applied to a wide range of situations. Observational methodology is characterized by high scientific rigor and flexibility throughout its different stages and allows the objective study of spontaneous behavior in natural settings, with no external influence. Mixed methods researchers need to take bold yet thoughtful decisions regarding both substantive and procedural issues. We present three fundamental and complementary ideas to guide researchers in this respect: we show why studies of sport and physical activity that use a mixed methods research approach should be included in the field of mixed methods research, we highlight the numerous possibilities offered by observational methodology in this field through the transformation of descriptive data into quantifiable code matrices, and we discuss possible solutions for achieving true integration of qualitative and quantitative findings.

Wavelet entropy: a new tool for analysis of short duration brain electrical signals.

PubMed

Rosso, O A; Blanco, S; Yordanova, J; Kolev, V; Figliola, A; Schürmann, M; Başar, E

2001-01-30

Since traditional electrical brain signal analysis is mostly qualitative, the development of new quantitative methods is crucial for restricting the subjectivity in the study of brain signals. These methods are particularly fruitful when they are strongly correlated with intuitive physical concepts that allow a better understanding of brain dynamics. Here, new method based on orthogonal discrete wavelet transform (ODWT) is applied. It takes as a basic element the ODWT of the EEG signal, and defines the relative wavelet energy, the wavelet entropy (WE) and the relative wavelet entropy (RWE). The relative wavelet energy provides information about the relative energy associated with different frequency bands present in the EEG and their corresponding degree of importance. The WE carries information about the degree of order/disorder associated with a multi-frequency signal response, and the RWE measures the degree of similarity between different segments of the signal. In addition, the time evolution of the WE is calculated to give information about the dynamics in the EEG records. Within this framework, the major objective of the present work was to characterize in a quantitative way functional dynamics of order/disorder microstates in short duration EEG signals. For that aim, spontaneous EEG signals under different physiological conditions were analyzed. Further, specific quantifiers were derived to characterize how stimulus affects electrical events in terms of frequency synchronization (tuning) in the event related potentials.

Hydro-geomorphological characterization and classification of Chilean river networks using horizontal, vertical and climatological properties

NASA Astrophysics Data System (ADS)

Pereira, A. A.; Gironas, J. A.; Passalacqua, P.; Mejia, A.; Niemann, J. D.

2017-12-01

Previous work has shown that lithological, tectonic and climatic processes have a major influence in shaping the geomorphology of river networks. Accordingly, quantitative classification methods have been developed to identify and characterize network types (dendritic, parallel, pinnate, rectangular and trellis) based solely on the self-affinity of their planform properties, computed from available Digital Elevation Model (DEM) data. In contrast, this research aim is to include both horizontal and vertical properties to evaluate a quantitative classification method for river networks. We include vertical properties to consider the unique surficial conditions (e.g., large and steep height drops, volcanic activity, and complexity of stream networks) of the Andes Mountains. Furthermore, the goal of the research is also to explain the implications and possible relations between the hydro-geomorphological properties and climatic conditions. The classification method is applied to 42 basins in the southern Andes in Chile, ranging in size from 208 Km2 to 8,000 Km2. The planform metrics include the incremental drainage area, stream course irregularity and junction angles, while the vertical metrics include the hypsometric curve and the slope-area relationship. We introduce new network structures (Brush, Funnel and Low Sinuosity Rectangular), possibly unique to the Andes, that can be quantitatively differentiated from previous networks identified in other geographic regions. Then, this research evaluates the effect that excluding different Strahler order streams has on the horizontal properties and therefore in the classification. We found that climatic conditions are not only linked to horizontal parameters, but also to vertical ones, finding significant correlation between climatic variables (average near-surface temperature and rainfall) and vertical measures (parameters associated with the hypsometric curve and slope-area relation). The proposed classification shows differences among basins previously classified as the same type, which are not noticeable in their horizontal properties and helps reduce misclassifications within the old clusters. Additional hydro-geomorphological metrics are to be considered in the classification method to improve the effectiveness of it.

An integrative strategy for quantitative analysis of the N-glycoproteome in complex biological samples.

PubMed

Wang, Ji; Zhou, Chuang; Zhang, Wei; Yao, Jun; Lu, Haojie; Dong, Qiongzhu; Zhou, Haijun; Qin, Lunxiu

2014-01-15

The complexity of protein glycosylation makes it difficult to characterize glycosylation patterns on a proteomic scale. In this study, we developed an integrated strategy for comparatively analyzing N-glycosylation/glycoproteins quantitatively from complex biological samples in a high-throughput manner. This strategy entailed separating and enriching glycopeptides/glycoproteins using lectin affinity chromatography, and then tandem labeling them with 18O/16O to generate a mass shift of 6 Da between the paired glycopeptides, and finally analyzing them with liquid chromatography-mass spectrometry (LC-MS) and the automatic quantitative method we developed based on Mascot Distiller. The accuracy and repeatability of this strategy were first verified using standard glycoproteins; linearity was maintained within a range of 1:10-10:1. The peptide concentration ratios obtained by the self-build quantitative method were similar to both the manually calculated and theoretical values, with a standard deviation (SD) of 0.023-0.186 for glycopeptides. The feasibility of the strategy was further confirmed with serum from hepatocellular carcinoma (HCC) patients and healthy individuals; the expression of 44 glycopeptides and 30 glycoproteins were significantly different between HCC patient and control serum. This strategy is accurate, repeatable, and efficient, and may be a useful tool for identification of disease-related N-glycosylation/glycoprotein changes.

Thermostable 𝜶-Amylase Activity from Thermophilic Bacteria Isolated from Bora Hot Spring, Central Sulawesi

NASA Astrophysics Data System (ADS)

Gazali, F. M.; Suwastika, I. N.

2018-03-01

α-Amylase is one of the most important enzyme in biotechnology field, especially in industrial application. Thermostability of α-Amylase produced by thermophilic bacteria improves industrial process of starch degradation in starch industry. The present study were concerned to the characterization of α-Amylase activity from indigenous thermophilic bacteria isolated from Bora hot spring, Central Sulawesi. There were 18 isolates which had successfully isolated from 90°C sediment samples of Bora hot spring and 13 of them showed amylolytic activity. The α-Amylase activity was measured qualitatively at starch agar and quantitatively based on DNS (3,5-Dinitrosalicylic acid) methods, using maltose as standard solution. Two isolates (out of 13 amylolytic bacteria), BR 002 and BR 015 showed amylolytic index of 0.8 mm and 0.5 mm respectively, after being incubated at 55°C in the 0.002% Starch Agar Medium. The α-Amylase activity was further characterized quantitatively which includes the optimum condition of pH and temperature of α-Amylase crude enzyme from each isolate. To our knowledge, this is the first report on isolation and characterization of a thermostable α-Amylase from thermophilic bacteria isolated from Central Sulawesi particularly from Bora hot spring.

Qualitative and quantitative analysis of the diuretic component ergone in Polyporus umbellatus by HPLC with fluorescence detection and HPLC-APCI-MS/MS.

PubMed

Zhao, Ying-Yong; Zhao, Ye; Zhang, Yong-Min; Lin, Rui-Chao; Sun, Wen-Ji

2009-06-01

Polyporus umbellatus is a widely used anti-aldosteronic diuretic in Traditional Chinese medicine (TCM). A new, sensitive and selective high-performance liquid chromatography-fluorescence detector (HPLC-FLD) and high-performance liquid chromatography-atmospheric pressure chemical ionization-mass spectrometry (HPLC-APCI-MS/MS) method for quantitative and qualitative determination of ergosta-4,6,8(14),22-tetraen-3-one(ergone), which is the main diuretic component, was provided for quality control of P. umbellatus crude drug. The ergone in the ethanolic extract of P. umbellatus was unambiguously characterized by HPLC-APCI, and further confirmed by comparing with a standard compound. The trace ergone was detected by the sensitive and selective HPLC-FLD. Linearity (r2 > 0.9998) and recoveries of low, medium and high concentration (100.5%, 100.2% and 100.4%) were consistent with the experimental criteria. The limit of detection (LOD) of ergone was around 0.2 microg/mL. Our results indicated that the content of ergone in P. umbellatus varied significantly from habitat to habitat with contents ranging from 2.13 +/- 0.02 to 59.17 +/- 0.05 microg/g. Comparison among HPLC-FLD and HPLC-UV or HPLC-APCI-MS/MS demonstrated that the HPLC-FLD and HPLC-APCI-MS/MS methods gave similar quantitative results for the selected herb samples, the HPLC-UV methods gave lower quantitative results than HPLC-FLD and HPLC-APCI-MS/MS methods. The established new HPLC-FLD method has the advantages of being rapid, simple, selective and sensitive, and could be used for the routine analysis of P. umbellatus crude drug.

Breast tumour visualization using 3D quantitative ultrasound methods

NASA Astrophysics Data System (ADS)

Gangeh, Mehrdad J.; Raheem, Abdul; Tadayyon, Hadi; Liu, Simon; Hadizad, Farnoosh; Czarnota, Gregory J.

2016-04-01

Breast cancer is one of the most common cancer types accounting for 29% of all cancer cases. Early detection and treatment has a crucial impact on improving the survival of affected patients. Ultrasound (US) is non-ionizing, portable, inexpensive, and real-time imaging modality for screening and quantifying breast cancer. Due to these attractive attributes, the last decade has witnessed many studies on using quantitative ultrasound (QUS) methods in tissue characterization. However, these studies have mainly been limited to 2-D QUS methods using hand-held US (HHUS) scanners. With the availability of automated breast ultrasound (ABUS) technology, this study is the first to develop 3-D QUS methods for the ABUS visualization of breast tumours. Using an ABUS system, unlike the manual 2-D HHUS device, the whole patient's breast was scanned in an automated manner. The acquired frames were subsequently examined and a region of interest (ROI) was selected in each frame where tumour was identified. Standard 2-D QUS methods were used to compute spectral and backscatter coefficient (BSC) parametric maps on the selected ROIs. Next, the computed 2-D parameters were mapped to a Cartesian 3-D space, interpolated, and rendered to provide a transparent color-coded visualization of the entire breast tumour. Such 3-D visualization can potentially be used for further analysis of the breast tumours in terms of their size and extension. Moreover, the 3-D volumetric scans can be used for tissue characterization and the categorization of breast tumours as benign or malignant by quantifying the computed parametric maps over the whole tumour volume.

Synthesis, spectroscopy and computational studies of some biologically important hydroxyhaloquinolines and their novel derivatives

NASA Astrophysics Data System (ADS)

Malecki, Grzegorz; Nycz, Jacek E.; Ryrych, Ewa; Ponikiewski, Lukasz; Nowak, Maria; Kusz, Joachim; Pikies, Jerzy

2010-04-01

A series crystalline compounds of methyl and phosphinyl derivatives of 2-methylquinolin-8-ol ( 1a) and related 5,7-dichloro-2-methylquinolin-8-ol ( 1b) were quantitatively prepared and characterized by microanalysis, IR, UV-vis and multinuclear NMR spectroscopy. Five of them have been characterized by single crystal X-ray diffraction method. The known compounds, 8-methoxy-2-methylquinoline ( 2a) and 8-methoxyquinoline ( 2d), were synthesised by a new route. NMR solution spectra at ambient temperature, showed readily diagnostic H-1 and C-13 signals from methyl groups. The geometries of the studied compounds were optimized in singlet states using the density functional theory (DFT) method with B3LYP functional. In general, the predicted bond lengths and angles are in a good agreement with the values based on the X-ray crystal structure data. Electronic spectra were calculated by TDDFT method.

Characterization of nucleosides and nucleobases in fruits of Ziziphus jujuba by UPLC-DAD-MS.

PubMed

Guo, Sheng; Duan, Jin-Ao; Tang, Yu-Ping; Zhu, Zhen-Hua; Qian, Ye-Fei; Yang, Nian-Yun; Shang, Er-Xin; Qian, Da-Wei

2010-10-13

The fruit of Ziziphus jujuba , named dazao in Chinese, has been utilized as food as well as crude drugs in China for thousands of years. To explore the profiles of the nucleosides and nucleobases in this fruit, an ultraperformance liquid chromatograph coupled with a photodiode array detector and electrospray ionization-mass spectrometer method (UPLC-DAD-MS) has been established and validated in this paper. The validated method was successfully applied for the simultaneous characterization and quantitation of 9 nucleosides and nucleobases in 49 dazao samples, which comprised 43 cultivars from 26 cultivation regions. Furthermore, principal component analysis (PCA) was performed to classify the samples on the basis of the contents of the nine analyzed compounds. The results showed that almost all of these dazao samples were rich in nucleosides and nucleobases, although their contents were obviously various, and the proposed method could serve as a prerequisite for quality control of jujube products.

Characterization and Developmental History of Problem Solving Methods in Medicine

PubMed Central

Harbort, Robert A.

1980-01-01

The central thesis of this paper is the importance of the framework in which information is structured. It is technically important in the design of systems; it is also important in guaranteeing that systems are usable by clinicians. Progress in medical computing depends on our ability to develop a more quantitative understanding of the role of context in our choice of problem solving techniques. This in turn will help us to design more flexible and responsive computer systems. The paper contains an overview of some models of knowledge and problem solving methods, a characterization of modern diagnostic techniques, and a discussion of skill development in medical practice. Diagnostic techniques are examined in terms of how they are taught, what problem solving methods they use, and how they fit together into an overall theory of interpretation of the medical status of a patient.

Thermographic venous blood flow characterization with external cooling stimulation

NASA Astrophysics Data System (ADS)

Saxena, Ashish; Ng, E. Y. K.; Raman, Vignesh

2018-05-01

Experimental characterization of blood flow in a human forearm is done with the application of continuous external cooling based active thermography method. Qualitative and quantitative detection of the blood vessel in a thermal image is done, along with the evaluation of blood vessel diameter, blood flow direction, and velocity in the target blood vessel. Subtraction based image manipulation is performed to enhance the feature contrast of the thermal image acquired after the removal of external cooling. To demonstrate the effect of occlusion diseases (obstruction), an external cuff based occlusion is applied after the removal of cooling and its effect on the skin rewarming is studied. Using external cooling, a transit time method based blood flow velocity estimation is done. From the results obtained, it is evident that an external cooling based active thermography method can be used to develop a diagnosis tool for superficial blood vessel diseases.

Application of different analytical methods for the characterization of non-spherical micro- and nanoparticles.

PubMed

Mathaes, Roman; Winter, Gerhard; Engert, Julia; Besheer, Ahmed

2013-09-10

Non-spherical micro- and nanoparticles have recently gained considerable attention due to their surprisingly different interaction with biological systems compared to their spherical counterparts, opening new opportunities for drug delivery and vaccination. Up till now, electron microscopy is the only method to quantitatively identify the critical quality attributes (CQAs) of non-spherical particles produced by film-stretching; namely size, morphology and the quality of non-spherical particles (degree of contamination with spherical ones). However, electron microscopy requires expensive instrumentation, demanding sample preparation and non-trivial image analysis. To circumvent these drawbacks, the ability of different particle analysis methods to quantitatively identify the CQA of spherical and non-spherical poly(1-phenylethene-1,2-diyl (polystyrene) particles over a wide size range (40 nm, 2 μm and 10 μm) was investigated. To this end, light obscuration, image-based analysis methods (Microflow imaging, MFI, and Vi-Cell XR Coulter Counter) and flow cytometry were used to study particles in the micron range, while asymmetric flow field fractionation (AF4) coupled to multi-angle laser scattering (MALS) and quasi elastic light scattering (QELS) was used for particles in the nanometer range, and all measurements were benchmarked against electron microscopy. Results show that MFI can reliably identify particle size and aspect ratios of the 10 μm particles, but not the 2 μm ones. Meanwhile, flow cytometry was able to differentiate between spherical and non-spherical 10 or 2 μm particles, and determine the amount of impurities in the sample. As for the nanoparticles, AF4 coupled to MALS and QELS allowed the measurement of the geometric (rg) and hydrodynamic (rh) radii of the particles, as well as their shape factors (rg/rh), confirming their morphology. While this study shows the utility of MFI, flow cytometry and AF4 for quantitative evaluation of the CQA of non-spherical particles over a wide size range, the limitations of the methods are discussed. The use of orthogonal characterization methods can provide a complete picture about the CQA of non-spherical particles over a wide size range. Copyright © 2013 Elsevier B.V. All rights reserved.

Minimizing thermal degradation in gas chromatographic quantitation of pentaerythritol tetranitrate.

PubMed

Lubrano, Adam L; Field, Christopher R; Newsome, G Asher; Rogers, Duane A; Giordano, Braden C; Johnson, Kevin J

2015-05-15

An analytical method for establishing calibration curves for the quantitation of pentaerythriol tetranitrate (PETN) from sorbent-filled thermal desorption tubes by gas chromatography with electron capture detection (TDS-GC-ECD) was developed. As PETN has been demonstrated to thermally degrade under typical GC instrument conditions, peaks corresponding to both PETN degradants and molecular PETN are observed. The retention time corresponding to intact PETN was verified by high-resolution mass spectrometry with a flowing atmospheric pressure afterglow (FAPA) ionization source, which enabled soft ionization of intact PETN eluting the GC and subsequent accurate-mass identification. The GC separation parameters were transferred to a conventional GC-ECD instrument where analytical method-induced PETN degradation was further characterized and minimized. A method calibration curve was established by direct liquid deposition of PETN standard solutions onto the glass frit at the head of sorbent-filled thermal desorption tubes. Two local, linear relationships between detector response and PETN concentration were observed, with a total dynamic range of 0.25-25ng. Published by Elsevier B.V.

Combined use of optical and electron microscopic techniques for the measurement of hygroscopic property, chemical composition, and morphology of individual aerosol particles.

PubMed

Ahn, Kang-Ho; Kim, Sun-Man; Jung, Hae-Jin; Lee, Mi-Jung; Eom, Hyo-Jin; Maskey, Shila; Ro, Chul-Un

2010-10-01

In this work, an analytical method for the characterization of the hygroscopic property, chemical composition, and morphology of individual aerosol particles is introduced. The method, which is based on the combined use of optical and electron microscopic techniques, is simple and easy to apply. An optical microscopic technique was used to perform the visual observation of the phase transformation and hygroscopic growth of aerosol particles on a single particle level. A quantitative energy-dispersive electron probe X-ray microanalysis, named low-Z particle EPMA, was used to perform a quantitative chemical speciation of the same individual particles after the measurement of the hygroscopic property. To validate the analytical methodology, the hygroscopic properties of artificially generated NaCl, KCl, (NH(4))(2)SO(4), and Na(2)SO(4) aerosol particles of micrometer size were investigated. The practical applicability of the analytical method for studying the hygroscopic property, chemical composition, and morphology of ambient aerosol particles is demonstrated.

Quantitative characterization of metastatic disease in the spine. Part I. Semiautomated segmentation using atlas-based deformable registration and the level set method

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

Hardisty, M.; Gordon, L.; Agarwal, P.

2007-08-15

Quantitative assessment of metastatic disease in bone is often considered immeasurable and, as such, patients with skeletal metastases are often excluded from clinical trials. In order to effectively quantify the impact of metastatic tumor involvement in the spine, accurate segmentation of the vertebra is required. Manual segmentation can be accurate but involves extensive and time-consuming user interaction. Potential solutions to automating segmentation of metastatically involved vertebrae are demons deformable image registration and level set methods. The purpose of this study was to develop a semiautomated method to accurately segment tumor-bearing vertebrae using the aforementioned techniques. By maintaining morphology of anmore » atlas, the demons-level set composite algorithm was able to accurately differentiate between trans-cortical tumors and surrounding soft tissue of identical intensity. The algorithm successfully segmented both the vertebral body and trabecular centrum of tumor-involved and healthy vertebrae. This work validates our approach as equivalent in accuracy to an experienced user.« less

Fast-tracking determination of homozygous transgenic lines and transgene stacking using a reliable quantitative real-time PCR assay.

PubMed

Wang, Xianghong; Jiang, Daiming; Yang, Daichang

2015-01-01

The selection of homozygous lines is a crucial step in the characterization of newly generated transgenic plants. This is particularly time- and labor-consuming when transgenic stacking is required. Here, we report a fast and accurate method based on quantitative real-time PCR with a rice gene RBE4 as a reference gene for selection of homozygous lines when using multiple transgenic stacking in rice. Use of this method allowed can be used to determine the stacking of up to three transgenes within four generations. Selection accuracy reached 100 % for a single locus and 92.3 % for two loci. This method confers distinct advantages over current transgenic research methodologies, as it is more accurate, rapid, and reliable. Therefore, this protocol could be used to efficiently select homozygous plants and to expedite time- and labor-consuming processes normally required for multiple transgene stacking. This protocol was standardized for determination of multiple gene stacking in molecular breeding via marker-assisted selection.

Quantifying exciton hopping in disordered media with quenching sites: Application to arrays of quantum dots

NASA Astrophysics Data System (ADS)

Miyazaki, Jun

2013-10-01

We present an analytical method for quantifying exciton hopping in an energetically disordered system with quenching sites. The method is subsequently used to provide a quantitative understanding of exciton hopping in a quantum dot (QD) array. Several statistical quantities that characterize the dynamics (survival probability, average number of distinct sites visited, average hopping distance, and average hopping rate in the initial stage) are obtained experimentally by measuring time-resolved fluorescence intensities at various temperatures. The time evolution of these quantities suggests in a quantitative way that at low temperature an exciton tends to be trapped at a local low-energy site, while at room temperature, exciton hopping occurs repeatedly, leading to a large hopping distance. This method will serve to facilitate highly efficient optoelectronic devices using QDs such as photovoltaic cells and light-emitting diodes, since exciton hopping is considered to strongly influence their operational parameters. The presence of a dark QD (quenching site) that exhibits fast decay is also quantified.

Appreciating the difference between design-based and model-based sampling strategies in quantitative morphology of the nervous system.

PubMed

Geuna, S

2000-11-20

Quantitative morphology of the nervous system has undergone great developments over recent years, and several new technical procedures have been devised and applied successfully to neuromorphological research. However, a lively debate has arisen on some issues, and a great deal of confusion appears to exist that is definitely responsible for the slow spread of the new techniques among scientists. One such element of confusion is related to uncertainty about the meaning, implications, and advantages of the design-based sampling strategy that characterize the new techniques. In this article, to help remove this uncertainty, morphoquantitative methods are described and contrasted on the basis of the inferential paradigm of the sampling strategy: design-based vs model-based. Moreover, some recommendations are made to help scientists judge the appropriateness of a method used for a given study in relation to its specific goals. Finally, the use of the term stereology to label, more or less expressly, only some methods is critically discussed. Copyright 2000 Wiley-Liss, Inc.

Application of ASTAR(TM)/Precession Electron Diffraction Technique to Quantitatively Study Defects in Nanocrystalline Metallic Materials

NASA Astrophysics Data System (ADS)

Ghamarian, Iman

Nanocrystalline metallic materials have the potential to exhibit outstanding performance which leads to their usage in challenging applications such as coatings and biomedical implant devices. To optimize the performance of nanocrystalline metallic materials according to the desired applications, it is important to have a decent understanding of the structure, processing and properties of these materials. Various efforts have been made to correlate microstructure and properties of nanocrystalline metallic materials. Based on these research activities, it is noticed that microstructure and defects (e.g., dislocations and grain boundaries) play a key role in the behavior of these materials. Therefore, it is of great importance to establish methods to quantitatively study microstructures, defects and their interactions in nanocrystalline metallic materials. Since the mechanisms controlling the properties of nanocrystalline metallic materials occur at a very small length scale, it is fairly difficult to study them. Unfortunately, most of the characterization techniques used to explore these materials do not have the high enough spatial resolution required for the characterization of these materials. For instance, by applying complex profile-fitting algorithms to X-ray diffraction patterns, it is possible to get an estimation of the average grain size and the average dislocation density within a relatively large area. However, these average values are not enough for developing meticulous phenomenological models which are able to correlate microstructure and properties of nanocrystalline metallic materials. As another example, electron backscatter diffraction technique also cannot be used widely in the characterization of these materials due to problems such as relative poor spatial resolution (which is 90 nm) and the degradation of Kikuchi diffraction patterns in severely deformed nano-size grain metallic materials. In this study, ASTAR(TM)/precession electron diffraction is introduced as a relatively new orientation microscopy technique to characterize defects (e.g., geometrically necessary dislocations and grain boundaries) in challenging nanocrystalline metallic materials. The capability of this characterization technique to quantitatively determine the dislocation density distributions of geometrically necessary dislocations in severely deformed metallic materials is assessed. Based on the developed method, it is possible to determine the distributions and accumulations of dislocations with respect to the nearest grain boundaries and triple junctions. Also, the competency of this technique to study the grain boundary character distributions of nanocrystalline metallic materials is presented.

Species-Specific Thiol-Disulfide Equilibrium Constant: A Tool To Characterize Redox Transitions of Biological Importance.

PubMed

Mirzahosseini, Arash; Somlyay, Máté; Noszál, Béla

2015-08-13

Microscopic redox equilibrium constants, a new species-specific type of physicochemical parameters, were introduced and determined to quantify thiol-disulfide equilibria of biological significance. The thiol-disulfide redox equilibria of glutathione with cysteamine, cysteine, and homocysteine were approached from both sides, and the equilibrium mixtures were analyzed by quantitative NMR methods to characterize the highly composite, co-dependent acid-base and redox equilibria. The directly obtained, pH-dependent, conditional constants were then decomposed by a new evaluation method, resulting in pH-independent, microscopic redox equilibrium constants for the first time. The 80 different, microscopic redox equilibrium constant values show close correlation with the respective thiolate basicities and provide sound means for the development of potent agents against oxidative stress.

The diagnostic capability of laser induced fluorescence in the characterization of excised breast tissues

NASA Astrophysics Data System (ADS)

Galmed, A. H.; Elshemey, Wael M.

2017-08-01

Differentiating between normal, benign and malignant excised breast tissues is one of the major worldwide challenges that need a quantitative, fast and reliable technique in order to avoid personal errors in diagnosis. Laser induced fluorescence (LIF) is a promising technique that has been applied for the characterization of biological tissues including breast tissue. Unfortunately, only few studies have adopted a quantitative approach that can be directly applied for breast tissue characterization. This work provides a quantitative means for such characterization via introduction of several LIF characterization parameters and determining the diagnostic accuracy of each parameter in the differentiation between normal, benign and malignant excised breast tissues. Extensive analysis on 41 lyophilized breast samples using scatter diagrams, cut-off values, diagnostic indices and receiver operating characteristic (ROC) curves, shows that some spectral parameters (peak height and area under the peak) are superior for characterization of normal, benign and malignant breast tissues with high sensitivity (up to 0.91), specificity (up to 0.91) and accuracy ranking (highly accurate).

Methodology for cork plank characterization (Quercus suber L.) by near-infrared spectroscopy and image analysis

NASA Astrophysics Data System (ADS)

Prades, Cristina; García-Olmo, Juan; Romero-Prieto, Tomás; García de Ceca, José L.; López-Luque, Rafael

2010-06-01

The procedures used today to characterize cork plank for the manufacture of cork bottle stoppers continue to be based on a traditional, manual method that is highly subjective. Furthermore, there is no specific legislation regarding cork classification. The objective of this viability study is to assess the potential of near-infrared spectroscopy (NIRS) technology for characterizing cork plank according to the following variables: aspect or visual quality, porosity, moisture and geographical origin. In order to calculate the porosity coefficient, an image analysis program was specifically developed in Visual Basic language for a desktop scanner. A set comprising 170 samples from two geographical areas of Andalusia (Spain) was classified into eight quality classes by visual inspection. Spectra were obtained in the transverse and tangential sections of the cork planks using an NIRSystems 6500 SY II reflectance spectrophotometer. The quantitative calibrations showed cross-validation coefficients of determination of 0.47 for visual quality, 0.69 for porosity and 0.66 for moisture. The results obtained using NIRS technology are promising considering the heterogeneity and variability of a natural product such as cork in spite of the fact that the standard error of cross validation (SECV) in the quantitative analysis is greater than the standard error of laboratory (SEL) for the three variables. The qualitative analysis regarding geographical origin achieved very satisfactory results. Applying these methods in industry will permit quality control procedures to be automated, as well as establishing correlations between the different classification systems currently used in the sector. These methods can be implemented in the cork chain of custody certification and will also provide a certainly more objective tool for assessing the economic value of the product.

In-depth investigation on quantitative characterization of pyrolysis oil by 31P NMR

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

Ben, Haoxi; Ferrell, III, Jack R.

The characterization of different heteroatom functional groups by employing 31P NMR has been developed for almost 30 years. In this study, an in-depth investigation of this commonly used method has been accomplished for the analysis of pyrolysis oil. Several commonly used internal standards for 31P NMR have been examined by in situ monitoring. The results indicated that endo-N-hydroxy-5-norbornene-2,3-dicarboximide (NHND) is not stable after a long period of storage or experiment (>12 hours), but both cyclohexanol and triphenylphosphine oxide (TPPO) can be used as internal standards if a long experiment or storage is required. The pyrolysis oil has also been investigatedmore » by both short time (16 hours) in situ monitoring and long time (14 days) ex situ monitoring. The results showed that aliphatic OH, carboxylic acids and water contents are not very stable after 2 hours, and thus a short time of preparation, storage, and experiment need to be considered to ensure a precise quantitative measurement. The decomposition products are still unclear, but some preliminary investigations for different acids, (e.g. formic acid) have been accomplished. The results indicated that the aromatic carboxylic acids (benzoic acid and vanillic acid) are more stable than formic acid and acetic acid. Interestingly, the formic acid will even decompose to some other compounds at the very beginning of the in situ monitoring test. Further characterization found that water is one of the major products for the decomposition of formic acid in the 31P NMR solution. Finally, as far as we know, this is the first report on such time-dependent changes when using 31P NMR to analyze the pyrolysis oil, and these results show that proper application of this method is essential to achieve reliable quantitative data.« less

In-depth investigation on quantitative characterization of pyrolysis oil by 31P NMR

DOE PAGES

Ben, Haoxi; Ferrell, III, Jack R.

2016-01-29

The characterization of different heteroatom functional groups by employing 31P NMR has been developed for almost 30 years. In this study, an in-depth investigation of this commonly used method has been accomplished for the analysis of pyrolysis oil. Several commonly used internal standards for 31P NMR have been examined by in situ monitoring. The results indicated that endo-N-hydroxy-5-norbornene-2,3-dicarboximide (NHND) is not stable after a long period of storage or experiment (>12 hours), but both cyclohexanol and triphenylphosphine oxide (TPPO) can be used as internal standards if a long experiment or storage is required. The pyrolysis oil has also been investigatedmore » by both short time (16 hours) in situ monitoring and long time (14 days) ex situ monitoring. The results showed that aliphatic OH, carboxylic acids and water contents are not very stable after 2 hours, and thus a short time of preparation, storage, and experiment need to be considered to ensure a precise quantitative measurement. The decomposition products are still unclear, but some preliminary investigations for different acids, (e.g. formic acid) have been accomplished. The results indicated that the aromatic carboxylic acids (benzoic acid and vanillic acid) are more stable than formic acid and acetic acid. Interestingly, the formic acid will even decompose to some other compounds at the very beginning of the in situ monitoring test. Further characterization found that water is one of the major products for the decomposition of formic acid in the 31P NMR solution. Finally, as far as we know, this is the first report on such time-dependent changes when using 31P NMR to analyze the pyrolysis oil, and these results show that proper application of this method is essential to achieve reliable quantitative data.« less

[On-Orbit Multispectral Sensor Characterization Based on Spectral Tarps].

PubMed

Li, Xin; Zhang, Li-ming; Chen, Hong-yao; Xu, Wei-wei

2016-03-01

The multispectral remote sensing technology has been a primary means in the research of biomass monitoring, climate change, disaster prediction and etc. The spectral sensitivity is essential in the quantitative analysis of remote sensing data. When the sensor is running in the space, it will be influenced by cosmic radiation, severe change of temperature, chemical molecular contamination, cosmic dust and etc. As a result, the spectral sensitivity will degrade by time, which has great implication on the accuracy and consistency of the physical measurements. This paper presents a characterization method of the degradation based on man-made spectral targets. Firstly, a degradation model is established in the paper. Then, combined with equivalent reflectance of spectral targets measured and inverted from image, the degradation characterization can be achieved. The simulation and on orbit experiment results showed that, using the proposed method, the change of center wavelength and band width can be monotored. The method proposed in the paper has great significance for improving the accuracy of long time series remote sensing data product and comprehensive utilization level of multi sensor data products.

Solution-Based Electro-Orientation Spectroscopy (EOS) for Contactless Measurement of Semiconductor Nanowires

NASA Astrophysics Data System (ADS)

Yuan, Wuhan; Mohabir, Amar; Tutuncuoglu, Gozde; Filler, Michael; Feldman, Leonard; Shan, Jerry

2017-11-01

Solution-based, contactless methods for determining the electrical conductivity of nanowires and nanotubes have unique advantages over conventional techniques in terms of high throughput and compatibility with further solution-based processing and assembly methods. Here, we describe the solution-based electro-orientation spectroscopy (EOS) method, in which nanowire conductivity is measured from the AC-electric-field-induced alignment rate of the nanowire in a suspending fluid. The particle conductivity is determined from the measured crossover frequency between conductivity-dominated, low-frequency alignment to the permittivity-dominated, high-frequency regime. We discuss the extension of the EOS measurement range by an order-of-magnitude, taking advantage of the high dielectric constant of deionized water. With water and other fluids, we demonstrate that EOS can quantitatively characterize the electrical conductivities of nanowires over a 7-order-of-magnitude range, 10-5 to 102 S/m. We highlight the efficiency and utility of EOS for nanomaterial characterization by statistically characterizing the variability of semiconductor nanowires of the same nominal composition, and studying the connection between synthesis parameters and properties. NSF CBET-1604931.

Lateral Temperature-Gradient Method for High-Throughput Characterization of Material Processing by Millisecond Laser Annealing.

PubMed

Bell, Robert T; Jacobs, Alan G; Sorg, Victoria C; Jung, Byungki; Hill, Megan O; Treml, Benjamin E; Thompson, Michael O

2016-09-12

A high-throughput method for characterizing the temperature dependence of material properties following microsecond to millisecond thermal annealing, exploiting the temperature gradients created by a lateral gradient laser spike anneal (lgLSA), is presented. Laser scans generate spatial thermal gradients of up to 5 °C/μm with peak temperatures ranging from ambient to in excess of 1400 °C, limited only by laser power and materials thermal limits. Discrete spatial property measurements across the temperature gradient are then equivalent to independent measurements after varying temperature anneals. Accurate temperature calibrations, essential to quantitative analysis, are critical and methods for both peak temperature and spatial/temporal temperature profile characterization are presented. These include absolute temperature calibrations based on melting and thermal decomposition, and time-resolved profiles measured using platinum thermistors. A variety of spatially resolved measurement probes, ranging from point-like continuous profiling to large area sampling, are discussed. Examples from annealing of III-V semiconductors, CdSe quantum dots, low-κ dielectrics, and block copolymers are included to demonstrate the flexibility, high throughput, and precision of this technique.

Differential Variance Analysis: a direct method to quantify and visualize dynamic heterogeneities

NASA Astrophysics Data System (ADS)

Pastore, Raffaele; Pesce, Giuseppe; Caggioni, Marco

2017-03-01

Many amorphous materials show spatially heterogenous dynamics, as different regions of the same system relax at different rates. Such a signature, known as Dynamic Heterogeneity, has been crucial to understand the nature of the jamming transition in simple model systems and is currently considered very promising to characterize more complex fluids of industrial and biological relevance. Unfortunately, measurements of dynamic heterogeneities typically require sophisticated experimental set-ups and are performed by few specialized groups. It is now possible to quantitatively characterize the relaxation process and the emergence of dynamic heterogeneities using a straightforward method, here validated on video microscopy data of hard-sphere colloidal glasses. We call this method Differential Variance Analysis (DVA), since it focuses on the variance of the differential frames, obtained subtracting images at different time-lags. Moreover, direct visualization of dynamic heterogeneities naturally appears in the differential frames, when the time-lag is set to the one corresponding to the maximum dynamic susceptibility. This approach opens the way to effectively characterize and tailor a wide variety of soft materials, from complex formulated products to biological tissues.

Quantum dot nanoparticle conjugation, characterization, and applications in neuroscience

NASA Astrophysics Data System (ADS)

Pathak, Smita

Quantum dot are semiconducting nanoparticles that have been used for decades in a variety of applications such as solar cells, LEDs and medical imaging. Their use in the last area, however, has been extremely limited despite their potential as revolutionary new biological labeling tools. Quantum dots are much brighter and more stable than conventional fluorophores, making them optimal for high resolution imaging and long term studies. Prior work in this area involves synthesizing and chemically conjugating quantum dots to molecules of interest in-house. However this method is both time consuming and prone to human error. Additionally, non-specific binding and nanoparticle aggregation currently prevent researchers from utilizing this system to its fullest capacity. Another critical issue that has not been addressed is determining the number of ligands bound to nanoparticles, which is crucial for proper interpretation of results. In this work, methods to label fixed cells using two types of chemically modified quantum dots are studied. Reproducible non-specific artifact labeling is consistently demonstrated if antibody-quantum dot conditions are less than optimal. In order to explain this, antibodies bound to quantum dots were characterized and quantified. While other groups have qualitatively characterized antibody functionalized quantum dots using TEM, AFM, UV spectroscopy and gel electrophoresis, and in some cases have reported calculated estimates of the putative number of total antibodies bound to quantum dots, no quantitative experimental results had been reported prior to this work. The chemical functionalization and characterization of quantum dot nanocrystals achieved in this work elucidates binding mechanisms of ligands to nanoparticles and allows researchers to not only translate our tools to studies in their own areas of interest but also derive quantitative results from these studies. This research brings ease of use and increased reliability to nanoparticles in medical imaging.

Chemical Characterization and Determination of the Anti-Oxidant Capacity of Two Brown Algae with Respect to Sampling Season and Morphological Structures Using Infrared Spectroscopy and Multivariate Analyses.

PubMed

Beratto, Angelo; Agurto, Cristian; Freer, Juanita; Peña-Farfal, Carlos; Troncoso, Nicolás; Agurto, Andrés; Castillo, Rosario Del P

2017-10-01

Brown algae biomass has been shown to be a highly important industrial source for the production of alginates and different nutraceutical products. The characterization of this biomass is necessary in order to allocate its use to specific applications according to the chemical and biological characteristics of this highly variable resource. The methods commonly used for algae characterization require a long time for the analysis and rigorous pretreatments of samples. In this work, nondestructive and fast analyses of different morphological structures from Lessonia spicata and Macrocystis pyrifera, which were collected during different seasons, were performed using Fourier transform infrared (FT-IR) techniques in combination with chemometric methods. Mid-infrared (IR) and near-infrared (NIR) spectral ranges were tested to evaluate the spectral differences between the species, seasons, and morphological structures of algae using a principal component analysis (PCA). Quantitative analyses of the polyphenol and alginate contents and the anti-oxidant capacity of the samples were performed using partial least squares (PLS) with both spectral ranges in order to build a predictive model for the rapid quantification of these parameters with industrial purposes. The PCA mainly showed differences in the samples based on seasonal sampling, where changes were observed in the bands corresponding to polysaccharides, proteins, and lipids. The obtained PLS models had high correlation coefficients (r) for the polyphenol content and anti-oxidant capacity (r > 0.9) and lower values for the alginate determination (0.7 < r < 0.8). Fourier transform infrared-based techniques were suitable tools for the rapid characterization of algae biomass, in which high variability in the samples was incorporated for the qualitative and quantitative analyses, and have the potential to be used on an industrial scale.

Electric Potential and Electric Field Imaging with Dynamic Applications & Extensions

NASA Technical Reports Server (NTRS)

Generazio, Ed

2017-01-01

The technology and methods for remote quantitative imaging of electrostatic potentials and electrostatic fields in and around objects and in free space is presented. Electric field imaging (EFI) technology may be applied to characterize intrinsic or existing electric potentials and electric fields, or an externally generated electrostatic field made be used for volumes to be inspected with EFI. The baseline sensor technology (e-Sensor) and its construction, optional electric field generation (quasi-static generator), and current e- Sensor enhancements (ephemeral e-Sensor) are discussed. Critical design elements of current linear and real-time two-dimensional (2D) measurement systems are highlighted, and the development of a three dimensional (3D) EFI system is presented. Demonstrations for structural, electronic, human, and memory applications are shown. Recent work demonstrates that phonons may be used to create and annihilate electric dipoles within structures. Phonon induced dipoles are ephemeral and their polarization, strength, and location may be quantitatively characterized by EFI providing a new subsurface Phonon-EFI imaging technology. Results from real-time imaging of combustion and ion flow, and their measurement complications, will be discussed. Extensions to environment, Space and subterranean applications will be presented, and initial results for quantitative characterizing material properties are shown. A wearable EFI system has been developed by using fundamental EFI concepts. These new EFI capabilities are demonstrated to characterize electric charge distribution creating a new field of study embracing areas of interest including electrostatic discharge (ESD) mitigation, manufacturing quality control, crime scene forensics, design and materials selection for advanced sensors, combustion science, on-orbit space potential, container inspection, remote characterization of electronic circuits and level of activation, dielectric morphology of structures, tether integrity, organic molecular memory, atmospheric science, weather prediction, earth quake prediction, and medical diagnostic and treatment efficacy applications such as cardiac polarization wave propagation and electromyography imaging.

Quantitative characterization of viscoelastic behavior in tissue-mimicking phantoms and ex vivo animal tissues.

PubMed

Maccabi, Ashkan; Shin, Andrew; Namiri, Nikan K; Bajwa, Neha; St John, Maie; Taylor, Zachary D; Grundfest, Warren; Saddik, George N

2018-01-01

Viscoelasticity of soft tissue is often related to pathology, and therefore, has become an important diagnostic indicator in the clinical assessment of suspect tissue. Surgeons, particularly within head and neck subsites, typically use palpation techniques for intra-operative tumor detection. This detection method, however, is highly subjective and often fails to detect small or deep abnormalities. Vibroacoustography (VA) and similar methods have previously been used to distinguish tissue with high-contrast, but a firm understanding of the main contrast mechanism has yet to be verified. The contributions of tissue mechanical properties in VA images have been difficult to verify given the limited literature on viscoelastic properties of various normal and diseased tissue. This paper aims to investigate viscoelasticity theory and present a detailed description of viscoelastic experimental results obtained in tissue-mimicking phantoms (TMPs) and ex vivo tissues to verify the main contrast mechanism in VA and similar imaging modalities. A spherical-tip micro-indentation technique was employed with the Hertzian model to acquire absolute, quantitative, point measurements of the elastic modulus (E), long term shear modulus (η), and time constant (τ) in homogeneous TMPs and ex vivo tissue in rat liver and porcine liver and gallbladder. Viscoelastic differences observed between porcine liver and gallbladder tissue suggest that imaging modalities which utilize the mechanical properties of tissue as a primary contrast mechanism can potentially be used to quantitatively differentiate between proximate organs in a clinical setting. These results may facilitate more accurate tissue modeling and add information not currently available to the field of systems characterization and biomedical research.

Three dimensional motion capture applied to violin playing: A study on feasibility and characterization of the motor strategy.

PubMed

Ancillao, Andrea; Savastano, Bernardo; Galli, Manuela; Albertini, Giorgio

2017-10-01

Playing string instruments requires advanced motor skills and a long training that is often spent in uncomfortable postures that may lead to injuries or musculoskeletal disorders. Thus, it is interesting to objectively characterize the motor strategy adopted by the players. In this work, we implemented a method for the quantitative analysis of the motor performance of a violin player. The proposed protocol takes advantage of an optoelectronic system and some infra-red reflecting markers in order to track player's motion. The method was tested on a professional violin player performing a legato bowing task. The biomechanical strategy of the upper limb and bow positioning were described by means of quantitative parameters and motion profiles. Measured quantities were: bow trajectory, angles, tracks, velocity, acceleration and jerk. A good repeatability of the bowing motion (CV < 2%) and high smoothness (jerk < 5 m/s 3 ) were observed. Motion profiles of shoulder, elbow and wrist were repeatable (CV < 7%) and comparable to the curves observed in other studies. Jerk and acceleration profiles demonstrated high smoothness in the ascending and descending phases of bowing. High variability was instead observed for the neck angle (CV ∼56%). "Quantitative" measurements, instead of "qualitative" observation, can support the diagnosis of motor disorders and the accurate evaluation of musicians' skills. The proposed protocol is a powerful tool for the description of musician's performance, that may be useful to document improvements in playing abilities and to adjust training strategies. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative characterization of viscoelastic behavior in tissue-mimicking phantoms and ex vivo animal tissues

PubMed Central

Shin, Andrew; Namiri, Nikan K.; Bajwa, Neha; St. John, Maie; Taylor, Zachary D.; Grundfest, Warren; Saddik, George N.

2018-01-01

Viscoelasticity of soft tissue is often related to pathology, and therefore, has become an important diagnostic indicator in the clinical assessment of suspect tissue. Surgeons, particularly within head and neck subsites, typically use palpation techniques for intra-operative tumor detection. This detection method, however, is highly subjective and often fails to detect small or deep abnormalities. Vibroacoustography (VA) and similar methods have previously been used to distinguish tissue with high-contrast, but a firm understanding of the main contrast mechanism has yet to be verified. The contributions of tissue mechanical properties in VA images have been difficult to verify given the limited literature on viscoelastic properties of various normal and diseased tissue. This paper aims to investigate viscoelasticity theory and present a detailed description of viscoelastic experimental results obtained in tissue-mimicking phantoms (TMPs) and ex vivo tissues to verify the main contrast mechanism in VA and similar imaging modalities. A spherical-tip micro-indentation technique was employed with the Hertzian model to acquire absolute, quantitative, point measurements of the elastic modulus (E), long term shear modulus (η), and time constant (τ) in homogeneous TMPs and ex vivo tissue in rat liver and porcine liver and gallbladder. Viscoelastic differences observed between porcine liver and gallbladder tissue suggest that imaging modalities which utilize the mechanical properties of tissue as a primary contrast mechanism can potentially be used to quantitatively differentiate between proximate organs in a clinical setting. These results may facilitate more accurate tissue modeling and add information not currently available to the field of systems characterization and biomedical research. PMID:29373598

Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea

PubMed Central

Narihiro, Takashi; Sekiguchi, Yuji

2011-01-01

Summary For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α‐subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers. PMID:21375721

Estimating sub-surface dispersed oil concentration using acoustic backscatter response.

PubMed

Fuller, Christopher B; Bonner, James S; Islam, Mohammad S; Page, Cheryl; Ojo, Temitope; Kirkey, William

2013-05-15

The recent Deepwater Horizon disaster resulted in a dispersed oil plume at an approximate depth of 1000 m. Several methods were used to characterize this plume with respect to concentration and spatial extent including surface supported sampling and autonomous underwater vehicles with in situ instrument payloads. Additionally, echo sounders were used to track the plume location, demonstrating the potential for remote detection using acoustic backscatter (ABS). This study evaluated use of an Acoustic Doppler Current Profiler (ADCP) to quantitatively detect oil-droplet suspensions from the ABS response in a controlled laboratory setting. Results from this study showed log-linear ABS responses to oil-droplet volume concentration. However, the inability to reproduce ABS response factors suggests the difficultly in developing meaningful calibration factors for quantitative field analysis. Evaluation of theoretical ABS intensity derived from the particle size distribution provided insight regarding method sensitivity in the presence of interfering ambient particles. Copyright © 2013 Elsevier Ltd. All rights reserved.

From the street to the laboratory: analytical profiles of methoxetamine, 3-methoxyeticyclidine and 3-methoxyphencyclidine and their determination in three biological matrices.

PubMed

De Paoli, Giorgia; Brandt, Simon D; Wallach, Jason; Archer, Roland P; Pounder, Derrick J

2013-06-01

Three psychoactive arylcyclohexylamines, advertised as "research chemicals," were obtained from an online retailer and characterized by gas chromatography ion trap electron and chemical ionization mass spectrometry, nuclear magnetic resonance spectroscopy and diode array detection. The three phencyclidines were identified as 2-(ethylamino)-2-(3-methoxyphenyl)cyclohexanone (methoxetamine), N-ethyl-1-(3-methoxyphenyl)cyclohexanamine and 1-[1-(3-methoxyphenyl)cyclohexyl]piperidine. A qualitative/quantitative method of analysis was developed and validated using liquid chromatography (HPLC) electrospray tandem mass spectrometry and ultraviolet (UV) detection for the determination of these compounds in blood, urine and vitreous humor. HPLC-UV proved to be a robust, accurate and precise method for the qualitative and quantitative analysis of these substances in biological fluids (0.16-5.0 mg/L), whereas the mass spectrometer was useful as a confirmatory tool.

Quantitative fluorescence imaging of protein diffusion and interaction in living cells.

PubMed

Capoulade, Jérémie; Wachsmuth, Malte; Hufnagel, Lars; Knop, Michael

2011-08-07

Diffusion processes and local dynamic equilibria inside cells lead to nonuniform spatial distributions of molecules, which are essential for processes such as nuclear organization and signaling in cell division, differentiation and migration. To understand these mechanisms, spatially resolved quantitative measurements of protein abundance, mobilities and interactions are needed, but current methods have limited capabilities to study dynamic parameters. Here we describe a microscope based on light-sheet illumination that allows massively parallel fluorescence correlation spectroscopy (FCS) measurements and use it to visualize the diffusion and interactions of proteins in mammalian cells and in isolated fly tissue. Imaging the mobility of heterochromatin protein HP1α (ref. 4) in cell nuclei we could provide high-resolution diffusion maps that reveal euchromatin areas with heterochromatin-like HP1α-chromatin interactions. We expect that FCS imaging will become a useful method for the precise characterization of cellular reaction-diffusion processes.

Quantitative mutant analysis of viral quasispecies by chip-based matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry

PubMed Central

Amexis, Georgios; Oeth, Paul; Abel, Kenneth; Ivshina, Anna; Pelloquin, Francois; Cantor, Charles R.; Braun, Andreas; Chumakov, Konstantin

2001-01-01

RNA viruses exist as quasispecies, heterogeneous and dynamic mixtures of mutants having one or more consensus sequences. An adequate description of the genomic structure of such viral populations must include the consensus sequence(s) plus a quantitative assessment of sequence heterogeneities. For example, in quality control of live attenuated viral vaccines, the presence of even small quantities of mutants or revertants may indicate incomplete or unstable attenuation that may influence vaccine safety. Previously, we demonstrated the monitoring of oral poliovirus vaccine with the use of mutant analysis by PCR and restriction enzyme cleavage (MAPREC). In this report, we investigate genetic variation in live attenuated mumps virus vaccine by using both MAPREC and a platform (DNA MassArray) based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Mumps vaccines prepared from the Jeryl Lynn strain typically contain at least two distinct viral substrains, JL1 and JL2, which have been characterized by full length sequencing. We report the development of assays for characterizing sequence variants in these substrains and demonstrate their use in quantitative analysis of substrains and sequence variations in mixed virus cultures and mumps vaccines. The results obtained from both the MAPREC and MALDI-TOF methods showed excellent correlation. This suggests the potential utility of MALDI-TOF for routine quality control of live viral vaccines and for assessment of genetic stability and quantitative monitoring of genetic changes in other RNA viruses of clinical interest. PMID:11593021

X-ray studies of dynamic aging in an aluminum alloy subjected to severe plastic deformation

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

Sitdikov, V.D., E-mail: svil@mail.rb.ru; Laboratory for Mechanics of Bulk Nanomaterials, Saint Petersburg State University, 28 Universitetsky pr., Saint Petersburg 198504; Chizhov, P.S.

In this work, X-ray scattering methods were applied for a quantitative characterization of the microstructure of an aluminum alloy of the Al–Mg–Si system during dynamic aging realized through the high pressure torsion technique. A qualitative and quantitative phase analysis of the alloy was performed, together with Al alloy lattice parameter determination. From the reflections broadening the effective size of the coherent scattering domains and the lattice microstrain were determined in the framework of the Halder–Wagner approach. Using the method of small-angle X-ray scattering, the quantitative characteristics of the size, shape and spatial distribution of the secondary phase particles formed inmore » the Al alloy during dynamic aging were established. In order to validate the obtained results, the method of small-angle X-ray scattering was preliminarily tested on similar samples after artificial aging and compared with the results from small-angle neutron diffraction widely known in literature. - Highlights: • Spherical fcc β-Mg2Si precipitates formed in Al 6201 alloy during dynamic aging in the course of severe plastic deformation. • The size, shape and distribution of the precipitates due to artificial and dynamic aging were revealed by SAXS method. • Monoclinic needle-like β' precipitates and Al5FeSi intermetallic phase were detected in 6201 alloy after T6 treatment.« less

Novel images extraction model using improved delay vector variance feature extraction and multi-kernel neural network for EEG detection and prediction.

PubMed

Ge, Jing; Zhang, Guoping

2015-01-01

Advanced intelligent methodologies could help detect and predict diseases from the EEG signals in cases the manual analysis is inefficient available, for instance, the epileptic seizures detection and prediction. This is because the diversity and the evolution of the epileptic seizures make it very difficult in detecting and identifying the undergoing disease. Fortunately, the determinism and nonlinearity in a time series could characterize the state changes. Literature review indicates that the Delay Vector Variance (DVV) could examine the nonlinearity to gain insight into the EEG signals but very limited work has been done to address the quantitative DVV approach. Hence, the outcomes of the quantitative DVV should be evaluated to detect the epileptic seizures. To develop a new epileptic seizure detection method based on quantitative DVV. This new epileptic seizure detection method employed an improved delay vector variance (IDVV) to extract the nonlinearity value as a distinct feature. Then a multi-kernel functions strategy was proposed in the extreme learning machine (ELM) network to provide precise disease detection and prediction. The nonlinearity is more sensitive than the energy and entropy. 87.5% overall accuracy of recognition and 75.0% overall accuracy of forecasting were achieved. The proposed IDVV and multi-kernel ELM based method was feasible and effective for epileptic EEG detection. Hence, the newly proposed method has importance for practical applications.

Impacts of heterogeneous organic matter on phenanthrene sorption--Different soil and sediment samples

USGS Publications Warehouse

Karapanagioti, Hrissi K.; Childs, Jeffrey; Sabatini, David A.

2001-01-01

Organic petrography has been proposed as a tool for characterizing the heterogeneous organic matter present in soil and sediment samples. A new simplified method is proposed as a quantitative means of interpreting observed sorption behavior for phenanthrene and different soils and sediments based on their organic petrographical characterization. This method is tested under singe solute conditions and at phenanthrene concentration of 1 μg/L. Since the opaque organic matter fraction dominates the sorption process, we propose that by quantifying this fraction one can interpret organic content normalized sorption distribution coefficient (Koc) values for a sample. While this method was developed and tested for various samples within the same aquifer, in the current study the method is validated for soil and sediment samples from different sites that cover a wide range of organic matter origin, age, and organic content. All 10 soil and sediment samples studied had log Koc values for the opaque particles between 5.6 and 6.8. This range of Koc values illustrates the heterogeneity of opaque particles between sites and geological formations and thus the need to characterize the opaque fraction of materials on a site-by-site basis.

Comprehensive Profiling and Quantification of Ginsenosides in the Root, Stem, Leaf, and Berry of Panax ginseng by UPLC-QTOF/MS.

PubMed

Lee, Jae Won; Choi, Bo-Ram; Kim, Young-Chang; Choi, Doo Jin; Lee, Young-Seob; Kim, Geum-Soog; Baek, Nam-In; Kim, Seung-Yu; Lee, Dae Young

2017-12-04

The effective production and usage of ginsenosides, given their distinct pharmacological effects, are receiving increasing amounts of attention. As the ginsenosides content differs in different parts of Panax ginseng, we wanted to assess and compare the ginsenosides content in the ginseng roots, leave, stems, and berries. To extract the ginsenosides, 70% (v/v) methanol was used. The optimal ultra-performance liquid chromatography-quadrupole time of flight mass spectrometry (UPLC-QTOF/MS) method was used to profile various ginsenosides from the different parts of P. ginseng. The datasets were then subjected to multivariate analysis including principal component analysis (PCA) and hierarchical clustering analysis (HCA). A UPLC-QTOF/MS method with an in-house library was constructed to profile 58 ginsenosides. With this method, a total of 39 ginsenosides were successfully identified and quantified in the ginseng roots, leave, stem, and berries. PCA and HCA characterized the different ginsenosides compositions from the different parts. The quantitative ginsenoside contents were also characterized from each plant part. The results of this study indicate that the UPLC-QTOF/MS method can be an effective tool to characterize various ginsenosides from the different parts of P. ginseng.

Quantifying Safety Margin Using the Risk-Informed Safety Margin Characterization (RISMC)

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

Grabaskas, David; Bucknor, Matthew; Brunett, Acacia

2015-04-26

The Risk-Informed Safety Margin Characterization (RISMC), developed by Idaho National Laboratory as part of the Light-Water Reactor Sustainability Project, utilizes a probabilistic safety margin comparison between a load and capacity distribution, rather than a deterministic comparison between two values, as is usually done in best-estimate plus uncertainty analyses. The goal is to determine the failure probability, or in other words, the probability of the system load equaling or exceeding the system capacity. While this method has been used in pilot studies, there has been little work conducted investigating the statistical significance of the resulting failure probability. In particular, it ismore » difficult to determine how many simulations are necessary to properly characterize the failure probability. This work uses classical (frequentist) statistics and confidence intervals to examine the impact in statistical accuracy when the number of simulations is varied. Two methods are proposed to establish confidence intervals related to the failure probability established using a RISMC analysis. The confidence interval provides information about the statistical accuracy of the method utilized to explore the uncertainty space, and offers a quantitative method to gauge the increase in statistical accuracy due to performing additional simulations.« less

Rapid measurement of protein osmotic second virial coefficients by self-interaction chromatography.

PubMed Central

Tessier, Peter M; Lenhoff, Abraham M; Sandler, Stanley I

2002-01-01

Weak protein interactions are often characterized in terms of the osmotic second virial coefficient (B(22)), which has been shown to correlate with protein phase behavior, such as crystallization. Traditional methods for measuring B(22), such as static light scattering, are too expensive in terms of both time and protein to allow extensive exploration of the effects of solution conditions on B(22). In this work we have measured protein interactions using self-interaction chromatography, in which protein is immobilized on chromatographic particles and the retention of the same protein is measured in isocratic elution. The relative retention of the protein reflects the average protein interactions, which we have related to the second virial coefficient via statistical mechanics. We obtain quantitative agreement between virial coefficients measured by self-interaction chromatography and traditional characterization methods for both lysozyme and chymotrypsinogen over a wide range of pH and ionic strengths, yet self-interaction chromatography requires at least an order of magnitude less time and protein than other methods. The method thus holds significant promise for the characterization of protein interactions requiring only commonly available laboratory equipment, little specialized expertise, and relatively small investments of both time and protein. PMID:11867474

Quantitative image analysis for evaluating the coating thickness and pore distribution in coated small particles.

PubMed

Laksmana, F L; Van Vliet, L J; Hartman Kok, P J A; Vromans, H; Frijlink, H W; Van der Voort Maarschalk, K

2009-04-01

This study aims to develop a characterization method for coating structure based on image analysis, which is particularly promising for the rational design of coated particles in the pharmaceutical industry. The method applies the MATLAB image processing toolbox to images of coated particles taken with Confocal Laser Scanning Microscopy (CSLM). The coating thicknesses have been determined along the particle perimeter, from which a statistical analysis could be performed to obtain relevant thickness properties, e.g. the minimum coating thickness and the span of the thickness distribution. The characterization of the pore structure involved a proper segmentation of pores from the coating and a granulometry operation. The presented method facilitates the quantification of porosity, thickness and pore size distribution of a coating. These parameters are considered the important coating properties, which are critical to coating functionality. Additionally, the effect of the coating process variations on coating quality can straight-forwardly be assessed. Enabling a good characterization of the coating qualities, the presented method can be used as a fast and effective tool to predict coating functionality. This approach also enables the influence of different process conditions on coating properties to be effectively monitored, which latterly leads to process tailoring.

Role of white matter lesions, cerebral atrophy, and APOE on cognition in older persons with and without dementia: the Cache County, Utah, study of memory and aging.

PubMed

Bigler, Erin D; Lowry, Christopher M; Kerr, Burton; Tate, David F; Hessel, Cory D; Earl, Heath D; Miller, Michael J; Rice, Sara A; Smith, Kay H; Tschanz, JoAnn T; Welsh-Bohmer, Kathleen; Plassman, Brenda; Victoroff, Jeff

2003-07-01

Neuropsychological, qualitative, and quantitative magnetic resonance imaging findings were examined in subjects with Alzheimer's disease (AD), non-AD dementia or mixed neuropsychiatric disorder, subjects characterized as mild/ambiguous, and controls, all with known apolipoprotein E (APOE) genotype. Neuropsychological tasks included an expanded Consortium to Establish a Registery for Alzheimer's Disease (J. T. Tschanz et al., 2000; K. A. Welsh, J. M. Hoffman, N. L. Earl, & M. W. Hanson 1994) battery and the Mini-Mental Status Examination (M. F. Folstein, S. E. Folstein, & P. R. McHugh, 1975). Periventricular white matter lesions were the most clinically salient, and generalized measures of cerebral atrophy were the most significant quantitative indicators. APOE genotype was unrelated to imaging or neuropsychological performance. Neuropsychological relationships with neuroimaging findings depend on the qualitative or quantitative method used.

Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection.

PubMed

Liu, Yang; Wilson, W David

2010-01-01

Surface plasmon resonance (SPR) technology with biosensor surfaces has become a widely-used tool for the study of nucleic acid interactions without any labeling requirements. The method provides simultaneous kinetic and equilibrium characterization of the interactions of biomolecules as well as small molecule-biopolymer binding. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetic methods for systems with strong binding coupled to small spectroscopic signals and/or reaction heats. A detailed and practical guide for nucleic acid interaction analysis using SPR-biosensor methods is presented. Details of the SPR technology and basic fundamentals are described with recommendations on the preparation of the SPR instrument, sensor chips, and samples, as well as extensive information on experimental design, quantitative and qualitative data analysis and presentation. A specific example of the interaction of a minor-groove-binding agent with DNA is evaluated by both kinetic and steady-state SPR methods to illustrate the technique. Since the molecules that bind cooperatively to specific DNA sequences are attractive for many applications, a cooperative small molecule-DNA interaction is also presented.

Near-infrared fluorescence image quality test methods for standardized performance evaluation

NASA Astrophysics Data System (ADS)

Kanniyappan, Udayakumar; Wang, Bohan; Yang, Charles; Ghassemi, Pejhman; Wang, Quanzeng; Chen, Yu; Pfefer, Joshua

2017-03-01

Near-infrared fluorescence (NIRF) imaging has gained much attention as a clinical method for enhancing visualization of cancers, perfusion and biological structures in surgical applications where a fluorescent dye is monitored by an imaging system. In order to address the emerging need for standardization of this innovative technology, it is necessary to develop and validate test methods suitable for objective, quantitative assessment of device performance. Towards this goal, we develop target-based test methods and investigate best practices for key NIRF imaging system performance characteristics including spatial resolution, depth of field and sensitivity. Characterization of fluorescence properties was performed by generating excitation-emission matrix properties of indocyanine green and quantum dots in biological solutions and matrix materials. A turbid, fluorophore-doped target was used, along with a resolution target for assessing image sharpness. Multi-well plates filled with either liquid or solid targets were generated to explore best practices for evaluating detection sensitivity. Overall, our results demonstrate the utility of objective, quantitative, target-based testing approaches as well as the need to consider a wide range of factors in establishing standardized approaches for NIRF imaging system performance.

A gradient method for the quantitative analysis of cell movement and tissue flow and its application to the analysis of multicellular Dictyostelium development.

PubMed

Siegert, F; Weijer, C J; Nomura, A; Miike, H

1994-01-01

We describe the application of a novel image processing method, which allows quantitative analysis of cell and tissue movement in a series of digitized video images. The result is a vector velocity field showing average direction and velocity of movement for every pixel in the frame. We apply this method to the analysis of cell movement during different stages of the Dictyostelium developmental cycle. We analysed time-lapse video recordings of cell movement in single cells, mounds and slugs. The program can correctly assess the speed and direction of movement of either unlabelled or labelled cells in a time series of video images depending on the illumination conditions. Our analysis of cell movement during multicellular development shows that the entire morphogenesis of Dictyostelium is characterized by rotational cell movement. The analysis of cell and tissue movement by the velocity field method should be applicable to the analysis of morphogenetic processes in other systems such as gastrulation and neurulation in vertebrate embryos.

Phosphoprotein binding agents and methods of their use

DOEpatents

Goshe, Michael B.; Conrads, Thomas P.; Veenstra, Timothy D.; Panisko, Ellen A.

2004-11-16

The invention provides reagents and methods for characterizing (i.e., identification and/or quantitation) the phosphorylation states of proteins. Proteins may be post-transcriptionally modified such that they contain phosphate groups at either some or all of their serine, threonine, tyrosine, histidine, and/or lysine amino acid residues. In many cases the extent to which a protein is phosphorylated determines it bioactivity, i.e., its ability to effect cell functions such as differentiation, division, and metabolism. Hence, a powerful tool for diagnosing various diseases and for furthering the understanding of protein--protein interactions is provided.

Periodate oxidation of nanoscaled magnetic dextran composites

NASA Astrophysics Data System (ADS)

Hong, Xia; Guo, Wei; Yuan, Hang; Li, Jun; Liu, Yanmei; Ma, Lan; Bai, Yubai; Li, Tiejin

2004-02-01

Highly hydrophilic, uniform and nontoxic magnetic fluids consisting of magnetite (Fe 3O 4) and dextran were prepared. A periodate oxidation method was used to further activate the magnetic dextran, forming magnetic polyaldehyde-dextran, which could be conjugated to biomolecules such as proteins or antibodies. Oxidated Magnetic dextran composites were characterized by TEM, XRD and SQUID magnetometry. Moreover, a flexible, rapid and simple method to detect aldehydes was introduced to the magnetic composite system by utilizing 2,4-dinitrophenylhydrazine reagent. The result of the quantitative analysis of aldehyde was given by thermogravimetric analysis and elemental analysis.

Quantitative evaluation of cross correlation between two finite-length time series with applications to single-molecule FRET.

PubMed

Hanson, Jeffery A; Yang, Haw

2008-11-06

The statistical properties of the cross correlation between two time series has been studied. An analytical expression for the cross correlation function's variance has been derived. On the basis of these results, a statistically robust method has been proposed to detect the existence and determine the direction of cross correlation between two time series. The proposed method has been characterized by computer simulations. Applications to single-molecule fluorescence spectroscopy are discussed. The results may also find immediate applications in fluorescence correlation spectroscopy (FCS) and its variants.

Detection of 22 common leukemic fusion genes using a single-step multiplex qRT-PCR-based assay.

PubMed

Lyu, Xiaodong; Wang, Xianwei; Zhang, Lina; Chen, Zhenzhu; Zhao, Yu; Hu, Jieying; Fan, Ruihua; Song, Yongping

2017-07-25

Fusion genes generated from chromosomal translocation play an important role in hematological malignancies. Detection of fusion genes currently employ use of either conventional RT-PCR methods or fluorescent in situ hybridization (FISH), where both methods involve tedious methodologies and require prior characterization of chromosomal translocation events as determined by cytogenetic analysis. In this study, we describe a real-time quantitative reverse transcription PCR (qRT-PCR)-based multi-fusion gene screening method with the capacity to detect 22 fusion genes commonly found in leukemia. This method does not require pre-characterization of gene translocation events, thereby facilitating immediate diagnosis and therapeutic management. We performed fluorescent qRT-PCR (F-qRT-PCR) using a commercially-available multi-fusion gene detection kit on a patient cohort of 345 individuals comprising 108 cases diagnosed with acute myeloid leukemia (AML) for initial evaluation; remaining patients within the cohort were assayed for confirmatory diagnosis. Results obtained by F-qRT-PCR were compared alongside patient analysis by cytogenetic characterization. Gene translocations detected by F-qRT-PCR in AML cases were diagnosed in 69.4% of the patient cohort, which was comparatively similar to 68.5% as diagnosed by cytogenetic analysis, thereby demonstrating 99.1% concordance. Overall gene fusion was detected in 53.7% of the overall patient population by F-qRT-PCR, 52.9% by cytogenetic prediction in leukemia, and 9.1% in non-leukemia patients by both methods. The overall concordance rate was calculated to be 99.0%. Fusion genes were detected by F-qRT-PCR in 97.3% of patients with CML, followed by 69.4% with AML, 33.3% with acute lymphoblastic leukemia (ALL), 9.1% with myelodysplastic syndromes (MDS), and 0% with chronic lymphocytic leukemia (CLL). We describe the use of a F-qRT-PCR-based multi-fusion gene screening method as an efficient one-step diagnostic procedure as an effective alternative to lengthy conventional diagnostic procedures requiring both cytogenetic analysis followed by targeted quantitative reverse transcription (qRT-PCR) methods, thus allowing timely patient management.

Quantitative investigation of non-hydrolytic disruptive activity on crystalline cellulose and application to recombinant swollenin.

PubMed

Wang, Yuguo; Tang, Rentao; Tao, Jin; Gao, Gui; Wang, Xiaonan; Mu, Ying; Feng, Yan

2011-09-01

For the efficient degradation and bioconversion of cellulosic biomass, it is important to efficiently disrupt and convert crystalline regions of cellulose into easily hydrolyzable regions than to simply hydrolyze cellulose. Expansin-like proteins such as swollenins have disruptive functions on lignocellulose, including crystalline cellulose, via non-hydrolytic mechanisms. In this work, we produced the swollenin from Trichoderma asperellum in Escherichia coli. The recombinant protein was then refolded into the bioactive form with simultaneous purification via a novel cellulose-assisted process. We devised a novel, simple, and efficient method to quantitatively determine the non-hydrolytic disruptive activity of swollenin on crystalline cellulose. This method is based on the synergism of the swollenin and the endoglucanase FnCel5A from Fervidobacterium nodosum. The change from crystalline regions into easily hydrolyzable forms, due to non-hydrolytic disruption, might be slight and not easily be observed. However, disrupted regions of cellulose could be hydrolyzed by FnCel5A, and reducing sugars were formed by the synergism. The disruptive function of the swollenin was quantitatively characterized by measuring the release of reducing sugars. These methods and processes will be useful for further research on non-hydrolytic disruptive bioactivities and provide novel approaches for the efficient and economical bioconversion of cellulosic biomass.

Comparative study of quantitative phase imaging techniques for refractometry of optical fibers

NASA Astrophysics Data System (ADS)

de Dorlodot, Bertrand; Bélanger, Erik; Bérubé, Jean-Philippe; Vallée, Réal; Marquet, Pierre

2018-02-01

The refractive index difference profile of optical fibers is the key design parameter because it determines, among other properties, the insertion losses and propagating modes. Therefore, an accurate refractive index profiling method is of paramount importance to their development and optimization. Quantitative phase imaging (QPI) is one of the available tools to retrieve structural characteristics of optical fibers, including the refractive index difference profile. Having the advantage of being non-destructive, several different QPI methods have been developed over the last decades. Here, we present a comparative study of three different available QPI techniques, namely the transport-of-intensity equation, quadriwave lateral shearing interferometry and digital holographic microscopy. To assess the accuracy and precision of those QPI techniques, quantitative phase images of the core of a well-characterized optical fiber have been retrieved for each of them and a robust image processing procedure has been applied in order to retrieve their refractive index difference profiles. As a result, even if the raw images for all the three QPI methods were suffering from different shortcomings, our robust automated image-processing pipeline successfully corrected these. After this treatment, all three QPI techniques yielded accurate, reliable and mutually consistent refractive index difference profiles in agreement with the accuracy and precision of the refracted near-field benchmark measurement.

Quantitative Determination of Fluorinated Alkyl Substances by Large-Volume-Injection LC/MS/MS—Characterization of Municipal Wastewaters

PubMed Central

Schultz, Melissa M.; Barofsky, Douglas F.; Field, Jennifer A.

2008-01-01

A quantitative method was developed for the determination of fluorinated alkyl substances in municipal wastewater influents and effluents. The method consisted of centrifugation followed by large-volume injection (500 μL) of the supernatant onto a liquid chromatograph with a reverse-phase column and detection by electrospray ionization, and tandem mass spectrometry (LC/MS/MS). The fluorinated analytes studied include perfluoroalkyl sulfonates, fluorotelomer sulfonates, perfluorocarboxylates, and select fluorinated alkyl sulfonamides. Recoveries of the fluorinated analytes from wastewater treatment plant (WWTP) raw influents and final effluent ranged from 77% – 96% and 80% – 99%, respectively. The lower limit of quantitation ranged from 0.5 to 3.0 ng/L depending on the analyte. The method was applied to flow-proportional composites of raw influent and final effluent collected over a 24 hr period from ten WWTPs nationwide. Fluorinated alkyl substances were observed in wastewater at all treatment plants and each plant exhibited unique distributions of fluorinated alkyl substances despite similarities in treatment processes. In nine out of the ten plants sampled, at least one class of fluorinated alkyl substances exhibited increased concentrations in the effluent as compared to the influent concentrations. In some instances, decreases in certain fluorinated analyte concentrations were observed and attributed to sorption to sludge. PMID:16433363

A sensitive method for determination of COL-3, a chemically modified tetracycline, in human plasma using high-performance liquid chromatography and ultraviolet detection.

PubMed

Rudek, Michelle A; Hartke, Carol; Zabelina, Yelena; Zhao, Ming; New, Pamela; Baker, Sharyn D

2005-04-01

COL-3, 6-deoxy-6-desmethyl-4-desdimethylamino-tetracycline, is a matrix metalloproteinase inhibitor currently in clinical development. A HPLC-UV method to quantitate COL-3 in human plasma was developed. COL-3 was extracted from plasma using solid-phase extraction cartridges. COL-3 is separated on a Waters Symmetry Shield RP8 (3.9 mm x150 mm, 5 microm) column with EDTA (0.001 M) in sodium acetate (0.01 M, pH 3.5)-acetonitrile mobile phase using a gradient profile at a flow rate of 1 ml/min for 22 min. Carryover was eliminated by using an extended needle wash of methanol:acetonitrile:dichloromethane (1:1:1, v/v/v). Detection of COL-3 and the internal standard, chrysin, was observed at 350 nm. COL-3 and chrysin elute at 8.9 and 9.9 min, respectively. The lower limit of quantitation in human plasma of COL-3 was 75 ng/ml, linearity was observed from 75 to 10,000 ng/ml. A 30,000 ng/ml sample that was diluted 1:50 with plasma was accurately quantitated. This method is rapid, widely applicable, and suitable for quantifying COL-3 in patient samples enabling further clinical pharmacology characterization of COL-3.

Nuclear magnetic resonance and high-performance liquid chromatography techniques for the characterization of bioactive compounds from Humulus lupulus L. (hop).

PubMed

Bertelli, Davide; Brighenti, Virginia; Marchetti, Lucia; Reik, Anna; Pellati, Federica

2018-06-01

Humulus lupulus L. (hop) represents one of the most cultivated crops, it being a key ingredient in the brewing process. Many health-related properties have been described for hop extracts, making this plant gain more interest in the field of pharmaceutical and nutraceutical research. Among the analytical tools available for the phytochemical characterization of plant extracts, quantitative nuclear magnetic resonance (qNMR) represents a new and powerful technique. In this ambit, the present study was aimed at the development of a new, simple, and efficient qNMR method for the metabolite fingerprinting of bioactive compounds in hop cones, taking advantage of the novel ERETIC 2 tool. To the best of our knowledge, this is the first attempt to apply this method to complex matrices of natural origin, such as hop extracts. The qNMR method set up in this study was applied to the quantification of both prenylflavonoids and bitter acids in eight hop cultivars. The performance of this analytical method was compared with that of HPLC-UV/DAD, which represents the most frequently used technique in the field of natural product analysis. The quantitative data obtained for hop samples by means of the two aforementioned techniques highlighted that the amount of bioactive compounds was slightly higher when qNMR was applied, although the order of magnitude of the values was the same. The accuracy of qNMR was comparable to that of the chromatographic method, thus proving to be a reliable tool for the analysis of these secondary metabolites in hop extracts. Graphical abstract Graphical abstract related to the extraction and analytical methods applied in this work for the analysis of bioactive compounds in Humulus lupulus L. (hop) cones.

Joint Stochastic Inversion of Pre-Stack 3D Seismic Data and Well Logs for High Resolution Hydrocarbon Reservoir Characterization

NASA Astrophysics Data System (ADS)

Torres-Verdin, C.

2007-05-01

This paper describes the successful implementation of a new 3D AVA stochastic inversion algorithm to quantitatively integrate pre-stack seismic amplitude data and well logs. The stochastic inversion algorithm is used to characterize flow units of a deepwater reservoir located in the central Gulf of Mexico. Conventional fluid/lithology sensitivity analysis indicates that the shale/sand interface represented by the top of the hydrocarbon-bearing turbidite deposits generates typical Class III AVA responses. On the other hand, layer- dependent Biot-Gassmann analysis shows significant sensitivity of the P-wave velocity and density to fluid substitution. Accordingly, AVA stochastic inversion, which combines the advantages of AVA analysis with those of geostatistical inversion, provided quantitative information about the lateral continuity of the turbidite reservoirs based on the interpretation of inverted acoustic properties (P-velocity, S-velocity, density), and lithotype (sand- shale) distributions. The quantitative use of rock/fluid information through AVA seismic amplitude data, coupled with the implementation of co-simulation via lithotype-dependent multidimensional joint probability distributions of acoustic/petrophysical properties, yields accurate 3D models of petrophysical properties such as porosity and permeability. Finally, by fully integrating pre-stack seismic amplitude data and well logs, the vertical resolution of inverted products is higher than that of deterministic inversions methods.

Post-translational quantitation by SRM/MRM: applications in cardiology.

PubMed

Gianazza, Erica; Banfi, Cristina

2018-06-04

Post-translational modifications (PTMs) have an important role in the regulation of protein function, localization and interaction with other molecules. PTMs apply a dynamic control of proteins both in physiological and pathological conditions. The study of disease-specific PTMs allows identifying potential biomarkers and developing effective drugs. Enrichment techniques combined with high-resolution MS/MS analysis provide attractive results on PTMs characterization. Selected reaction monitoring/multiple reaction monitoring (SRM/MRM) is a powerful targeted assay for the quantitation and validation of PTMs in complex biological samples. Areas covered: The most frequent PTMs are described in terms of biological role and analytical methods commonly used to detect them. The applications of SRM/MRM for the absolute quantitation of PTMs are reported and a specific section is focused on PTMs detection in proteins that are involved in cardiovascular system and heart diseases. Expert commentary: PTMs characterization in relation to disease pathology is still in progress, but targeted proteomics by LC-MS/MS has significantly upgraded the knowledge in the last years. Advances in enrichment strategies and software tools will facilitate the interpretation of high PTMs complexity. Promising studies confirm the great potentiality of SRM/MRM to study PTMs in cardiovascular field and PTMomics could be very useful in a clinical perspective.

Quantitation of Oxidative Modifications of Commercial Human Albumin for Clinical Use.

PubMed

Takahashi, Teppei; Terada, Tomoyoshi; Arikawa, Hajime; Kizaki, Kazuha; Terawaki, Hiroyuki; Imai, Hajime; Itoh, Yoshinori; Era, Seiichi

2016-01-01

We investigated the quantitation of oxidative chemical modifications, such as thiol oxidation and carbonylation, in medical-grade human serum albumin (HSA) preparations, in comparison with those of healthy and diseased subjects. Four kinds of HSA products were obtained from three major suppliers in Japan. Eight male collegiate students and six healthy male volunteers were recruited as the young (21.6 years) and older (57.2 years) groups, respectively. Four male stable patients (64.3 years) treated with regular hemodialysis (HD) also enrolled in this study. Quantitative analyses for thiol oxidation and carbonylation were performed using HPLC and spectroscopic methods, respectively. Structural characterization was further investigated by differential scanning calorimetry (DSC) and circular dichroism (CD) spectropolarimetry. Significantly larger amounts of thiol-oxidized and carbonylated HSA products were observed than HSA obtained from healthy subjects. In the structural characterization, the midpoint temperature of the denaturation curve (Tm) analyzed by DSC was relatively high, and may have been caused by the added albumin-specific stabilizers, and CD-resolved secondary structure showed that HSA products had a helical conformation. Commercial HSA products for clinical use have a more thermally stable state and remain in a helix-rich structure, even though their specific amino acids (mainly Cys and Lys residues) are oxidatively modified.

High-throughput analysis of the protein sequence-stability landscape using a quantitative "yeast surface two-hybrid" system and fragment reconstitution

PubMed Central

Dutta, Sanjib; Koide, Akiko; Koide, Shohei

2008-01-01

Stability evaluation of many mutants can lead to a better understanding of the sequence determinants of a structural motif and of factors governing protein stability and protein evolution. The traditional biophysical analysis of protein stability is low throughput, limiting our ability to widely explore the sequence space in a quantitative manner. In this study, we have developed a high-throughput library screening method for quantifying stability changes, which is based on protein fragment reconstitution and yeast surface display. Our method exploits the thermodynamic linkage between protein stability and fragment reconstitution and the ability of the yeast surface display technique to quantitatively evaluate protein-protein interactions. The method was applied to a fibronectin type III (FN3) domain. Characterization of fragment reconstitution was facilitated by the co-expression of two FN3 fragments, thus establishing a "yeast surface two-hybrid" method. Importantly, our method does not rely on competition between clones and thus eliminates a common limitation of high-throughput selection methods in which the most stable variants are predominantly recovered. Thus, it allows for the isolation of sequences that exhibits a desired level of stability. We identified over one hundred unique sequences for a β-bulge motif, which was significantly more informative than natural sequences of the FN3 family in revealing the sequence determinants for the β-bulge. Our method provides a powerful means to rapidly assess stability of many variants, to systematically assess contribution of different factors to protein stability and to enhance protein stability. PMID:18674545

Development of a GC/MS method for the qualitative and quantitative analysis of mixtures of free fatty acids and metal soaps in paint samples.

PubMed

La Nasa, Jacopo; Modugno, Francesca; Aloisi, Matteo; Lluveras-Tenorio, Anna; Bonaduce, Ilaria

2018-02-25

In this paper we present a new analytical GC/MS method for the analysis of mixtures of free fatty acids and metal soaps in paint samples. This approach is based on the use of two different silylating agents: N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) and 1,1,1,3,3,3-hexamethyldisilazane (HMDS). Our experimentation demonstrated that HMDS does not silylate fatty acid carboxylates, so it can be used for the selective derivatization and GC/MS quantitative analysis of free fatty acids. On the other hand BSTFA is able to silylate both free fatty acids and fatty acids carboxylates. The reaction conditions for the derivatization of carboxylates with BSTFA were thus optimized with a full factorial 3 2 experimental design using lead stearate and lead palmitate as model systems. The analytical method was validated following the ICH guidelines. The method allows the qualitative and quantitative analysis of fatty acid carboxylates of sodium, calcium, magnesium, aluminium, manganese, cobalt, copper, zinc, cadmium, and lead and of lead azelate. In order to exploit the performances of the new analytical method, samples collected from two reference paint layers, from a gilded 16th century marble sculpture, and from a paint tube belonging to the atelier of Edvard Munch, used in the last period of his life (1916-1944), were characterized. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of Self-Potential Response beyond the Fixed Geometry Technique

NASA Astrophysics Data System (ADS)

Mahardika, Harry

2018-03-01

The self-potential (SP) method is one of the oldest geophysical methods that are still available for today’s application. Since its early days SP data interpretation has been done qualitatively until the emerging of the fixed geometry analysis that was used to characterize the orientation and the electric-dipole properties of a mineral ore structure. Through the expansion of fundamental theories, computational methods, field-and-lab experiments in the last fifteen years, SP method has emerge from its low-class reputation to become more respectable. It became a complementary package alongside electric-resistivity tomography (ERT) for detecting groundwater flow in the subsurface, and extends to the hydrothermal flow in geothermal areas. As the analysis of SP data becomes more quantitative, its potential applications become more diverse. In this paper, we will show examples of our current SP studies such as the groundwater flow characterization inside a fault area. Lastly we will introduce the application of the "active" SP method - that is the seismoelectric method - which can be used for 4D real-time monitoring systems.

Database for LDV Signal Processor Performance Analysis

NASA Technical Reports Server (NTRS)

Baker, Glenn D.; Murphy, R. Jay; Meyers, James F.

1989-01-01

A comparative and quantitative analysis of various laser velocimeter signal processors is difficult because standards for characterizing signal bursts have not been established. This leaves the researcher to select a signal processor based only on manufacturers' claims without the benefit of direct comparison. The present paper proposes the use of a database of digitized signal bursts obtained from a laser velocimeter under various configurations as a method for directly comparing signal processors.

Characterization of ceramic powders by an X-ray measuring method

NASA Technical Reports Server (NTRS)

Ziegler, B.

1983-01-01

X-ray line broadening analysis gives quantitative data on structural changes of ceramic powders after different processing steps. Various Al2O3 powders were investigated and the following points are discussed on the basis of these results: X-ray line broadening analysis, structural changes during grinding, structural changes during annealing, influence of structural properties on sintering behavior and application of line broadening analysis to quality control of powders.

[Spectrophotometric determination of prodigiozan in ampule solutions].

PubMed

Shchedrina, L E; Brutko, L I; Rastunova, G A; Shcherbakova, E G

1984-06-01

Based on a study of the absorption properties of prodigiosan it has been shown that its UV absorption spectrum is characterized by an arm at 250-260 nm with an inflection point at 260 nm. The concentration ranges within which the optical density of prodigiosan solution obeyed the Bouguer-Lambert-Beer law were measured. This allowed the development of a quantitative spectrophotometric method for determination of prodigiosan in ampouled solutions.

GENOMIC DIVERSITY AND THE MICROENVIRONMENT AS DRIVERS OF PROGRESSION IN DCIS

DTIC Science & Technology

2017-10-01

stains, including quantitative analysis, 7) Identification of upstaged DCIS cases for the radiology aim, 8) Development of image analysis methods for...goals of the project? Aim 1. Determine whether genetic diversity of DCIS is greater in DCIS with adjacent invasive disease compared to DCIS without... compared to DCIS without IDC. Since genomics is not the sole driver of tumor behavior, we will phenotypically characterize DCIS and its

Spectroscopic Determination of the AC Voltammetric Response.

DTIC Science & Technology

1984-01-06

characterization of electrode processes. More recently, with the advent of linear sweep cyclic AC voltanmetry(12’ 13), it has been shown that AC methods...implemented with the same instrumentation ( 7 ) as previously used in MSRS and retains both the qualitative and quantitative utility of linear sweep ...voltammetric response (eg. peak width at balf-height, peak separation and cross-over potential in cyclic AC voltametry ) apply equally well to the SACRS

Characterization of methanol-oxidizing bacteria by their growth response to various chemicals.

PubMed Central

Kühn, I

1978-01-01

"Fingerprints" of strains of methanol-oxidizing bacteria were obtained by exposing them to a set of chemicals which could stimulate or inhibit the growth. The chemicals gave quantitative results, which were used to calculate the similarities between the strains. The method has been used for establishing identity or nonidentity between isolates, and its use in a search for random mutants is also outlined. PMID:103500

Promoter isolation and characterization of GhAO-like1, a Gossypium hirsutum gene similar to multicopper oxidases that is highly expressed in reproductive organs.

PubMed

Lambret-Frotté, Julia; Artico, Sinara; Muniz Nardeli, Sarah; Fonseca, Fernando; Brilhante Oliveira-Neto, Osmundo; Grossi-de-Sá, Maria Fatima; Alves-Ferreira, Marcio

2016-01-01

Cotton is one of the most economically important cultivated crops. It is the major source of natural fiber for the textile industry and an important target for genetic modification for both biotic stress and herbicide tolerance. Therefore, the characterization of genes and regulatory regions that might be useful for genetic transformation is indispensable. The isolation and characterization of new regulatory regions is of great importance to drive transgene expression in genetically modified crops. One of the major drawbacks in cotton production is pest damage; therefore, the most promising, cost-effective, and sustainable method for pest control is the development of genetically resistant cotton lines. Considering this scenario, our group isolated and characterized the promoter region of a MCO (multicopper oxidase) from Gossypium hirsutum, named GhAO-like1 (ascorbate oxidase-like1). The quantitative expression, together with the in vivo characterization of the promoter region reveals that GhAO-like1 has a flower- and fruit-specific expression pattern. The GUS activity is mainly observed in stamens, as expected considering that the GhAO-like1 regulatory sequence is enriched in cis elements, which have been characterized as a target of reproductive tissue specific transcription factors. Both histological and quantitative analyses in Arabidopsis thaliana have confirmed flower (mainly in stamens) and fruit expression of GhAO-like1. In the present paper, we isolated and characterized both in silico and in vivo the promoter region of the GhAO-like1 gene. The regulatory region of GhAO-like1 might be useful to confer tissue-specific expression in genetically modified plants.

Quantitative Characterization of Major Hepatic UDP-Glucuronosyltransferase Enzymes in Human Liver Microsomes: Comparison of Two Proteomic Methods and Correlation with Catalytic Activity.

PubMed

Achour, Brahim; Dantonio, Alyssa; Niosi, Mark; Novak, Jonathan J; Fallon, John K; Barber, Jill; Smith, Philip C; Rostami-Hodjegan, Amin; Goosen, Theunis C

2017-10-01

Quantitative characterization of UDP-glucuronosyltransferase (UGT) enzymes is valuable in glucuronidation reaction phenotyping, predicting metabolic clearance and drug-drug interactions using extrapolation exercises based on pharmacokinetic modeling. Different quantitative proteomic workflows have been employed to quantify UGT enzymes in various systems, with reports indicating large variability in expression, which cannot be explained by interindividual variability alone. To evaluate the effect of methodological differences on end-point UGT abundance quantification, eight UGT enzymes were quantified in 24 matched liver microsomal samples by two laboratories using stable isotope-labeled (SIL) peptides or quantitative concatemer (QconCAT) standard, and measurements were assessed against catalytic activity in seven enzymes ( n = 59). There was little agreement between individual abundance levels reported by the two methods; only UGT1A1 showed strong correlation [Spearman rank order correlation (Rs) = 0.73, P < 0.0001; R 2 = 0.30; n = 24]. SIL-based abundance measurements correlated well with enzyme activities, with correlations ranging from moderate for UGTs 1A6, 1A9, and 2B15 (Rs = 0.52-0.59, P < 0.0001; R 2 = 0.34-0.58; n = 59) to strong correlations for UGTs 1A1, 1A3, 1A4, and 2B7 (Rs = 0.79-0.90, P < 0.0001; R 2 = 0.69-0.79). QconCAT-based data revealed generally poor correlation with activity, whereas moderate correlations were shown for UGTs 1A1, 1A3, and 2B7. Spurious abundance-activity correlations were identified in the cases of UGT1A4/2B4 and UGT2B7/2B15, which could be explained by correlations of protein expression between these enzymes. Consistent correlation of UGT abundance with catalytic activity, demonstrated by the SIL-based dataset, suggests that quantitative proteomic data should be validated against catalytic activity whenever possible. In addition, metabolic reaction phenotyping exercises should consider spurious abundance-activity correlations to avoid misleading conclusions. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

Comparison of 13C Nuclear Magnetic Resonance and Fourier Transform Infrared spectroscopy for estimating humification and aromatization of soil organic matter

NASA Astrophysics Data System (ADS)

Rogers, K.; Cooper, W. T.; Hodgkins, S. B.; Verbeke, B. A.; Chanton, J.

2017-12-01

Solid state direct polarization 13C NMR spectroscopy (DP-NMR) is generally considered the most quantitatively reliable method for soil organic matter (SOM) characterization, including determination of the relative abundances of carbon functional groups. These functional abundances can then be used to calculate important soil parameters such as degree of humification and extent of aromaticity that reveal differences in reactivity or compositional changes along gradients (e.g. thaw chronosequence in permafrost). Unfortunately, the 13C NMR DP-NMR experiment is time-consuming, with a single sample often requiring over 24 hours of instrument time. Alternatively, solid state cross polarization 13C NMR (CP-NMR) can circumvent this problem, reducing analyses times to 4-6 hours but with some loss of quantitative reliability. Attenuated Total Reflectance Fourier Transform Infrared spectroscopy (ATR-FTIR) is a quick and relatively inexpensive method for characterizing solid materials, and has been suggested as an alternative to NMR for analysis of soil organic matter and determination of humification (HI) and aromatization (AI) indices. However, the quantitative reliability of ATR-FTIR for SOM analyses has never been verified, nor have any ATR-FTIR data been compared to similar measurements by NMR. In this work we focused on FTIR vibrational bands that correspond to the three functional groups used to calculate HI and AI values: carbohydrates (1030 cm-1), aromatics (1510, 1630 cm-1), and aliphatics (2850, 2920 cm-1). Data from ATR-FTIR measurements were compared to analogous quantitation by DP- and CP-NMR using peat samples from Sweden, Minnesota, and North Carolina. DP- and CP-NMR correlate very strongly, although the correlations are not always 1:1. Direct comparison of relative abundances of the three functional groups determined by NMR and ATR-FTIR yielded satisfactory results for carbohydrates (r2= 0.78) and aliphatics (r2=0.58), but less so for aromatics (r2= 0.395). ATR-FTIR has to this point been used primarily for relative abundance analyses (e.g. calculating HI and AI values), but these results suggest FTIR can provide quantitative reliability that approaches that of NMR.

Analyzing the Evolution of Membrane Fouling via a Novel Method Based on 3D Optical Coherence Tomography Imaging.

PubMed

Li, Weiyi; Liu, Xin; Wang, Yi-Ning; Chong, Tzyy Haur; Tang, Chuyang Y; Fane, Anthony G

2016-07-05

The development of novel tools for studying the fouling behavior during membrane processes is critical. This work explored optical coherence tomography (OCT) to quantitatively interpret the formation of a cake layer during a membrane process; the quantitative analysis was based on a novel image processing method that was able to precisely resolve the 3D structure of the cake layer on a micrometer scale. Fouling experiments were carried out with foulants having different physicochemical characteristics (silica nanoparticles and bentonite particles). The cake layers formed at a series of times were digitalized using the OCT-based characterization. The specific deposit (cake volume/membrane surface area) and surface coverage were evaluated as a function of time, which for the first time provided direct experimental evidence for the transition of various fouling mechanisms. Axial stripes were observed in the grayscale plots showing the deposit distribution in the scanned area; this interesting observation was in agreement with the instability analysis that correlated the polarized particle groups with the small disturbances in the boundary layer. This work confirms that the OCT-based characterization is able to provide deep insights into membrane fouling processes and offers a powerful tool for exploring membrane processes with enhanced performance.

A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.

PubMed

Isom, Daniel G; Marguet, Philippe R; Oas, Terrence G; Hellinga, Homme W

2011-04-01

Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics. Copyright © 2010 Wiley-Liss, Inc.

42 CFR 82.17 - What types of information could be used to supplement or substitute for individual monitoring data?

Code of Federal Regulations, 2014 CFR

2014-10-01

... SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED... environment; or, (b) A quantitative characterization of the radiation environment in which the covered... quantitative characterization of the radiation environment in which the employee worked, based on analysis of...

42 CFR 82.17 - What types of information could be used to supplement or substitute for individual monitoring data?

Code of Federal Regulations, 2011 CFR

2011-10-01

... SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED... environment; or, (b) A quantitative characterization of the radiation environment in which the covered... quantitative characterization of the radiation environment in which the employee worked, based on analysis of...

42 CFR 82.17 - What types of information could be used to supplement or substitute for individual monitoring data?

Code of Federal Regulations, 2012 CFR

2012-10-01

... SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED... environment; or, (b) A quantitative characterization of the radiation environment in which the covered... quantitative characterization of the radiation environment in which the employee worked, based on analysis of...

42 CFR 82.17 - What types of information could be used to supplement or substitute for individual monitoring data?

Code of Federal Regulations, 2013 CFR

2013-10-01

... SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED... environment; or, (b) A quantitative characterization of the radiation environment in which the covered... quantitative characterization of the radiation environment in which the employee worked, based on analysis of...

42 CFR 82.17 - What types of information could be used to supplement or substitute for individual monitoring data?

Code of Federal Regulations, 2010 CFR

2010-10-01

... SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES OCCUPATIONAL SAFETY AND HEALTH RESEARCH AND RELATED... environment; or, (b) A quantitative characterization of the radiation environment in which the covered... quantitative characterization of the radiation environment in which the employee worked, based on analysis of...

Quantitative comparison of bright field and annular bright field imaging modes for characterization of oxygen octahedral tilts

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

Kim, Young-Min; Pennycook, Stephen J.; Borisevich, Albina Y.

Octahedral tilt behavior is increasingly recognized as an important contributing factor to the physical behavior of perovskite oxide materials and especially their interfaces, necessitating the development of high-resolution methods of tilt mapping. There are currently two major approaches for quantitative imaging of tilts in scanning transmission electron microscopy (STEM), bright field (BF) and annular bright field (ABF). In this study, we show that BF STEM can be reliably used for measurements of oxygen octahedral tilts. While optimal conditions for BF imaging are more restricted with respect to sample thickness and defocus, we find that BF imaging with an aberration-corrected microscopemore » with the accelerating voltage of 300 kV gives us the most accurate quantitative measurement of the oxygen column positions. Using the tilted perovskite structure of BiFeO 3 (BFO) as our test sample, we simulate BF and ABF images in a wide range of conditions, identifying the optimal imaging conditions for each mode. Finally, we show that unlike ABF imaging, BF imaging remains directly quantitatively interpretable for a wide range of the specimen mistilt, suggesting that it should be preferable to the ABF STEM imaging for quantitative structure determination.« less

Quantitative comparison of bright field and annular bright field imaging modes for characterization of oxygen octahedral tilts

DOE PAGES

Kim, Young-Min; Pennycook, Stephen J.; Borisevich, Albina Y.

2017-04-29

Octahedral tilt behavior is increasingly recognized as an important contributing factor to the physical behavior of perovskite oxide materials and especially their interfaces, necessitating the development of high-resolution methods of tilt mapping. There are currently two major approaches for quantitative imaging of tilts in scanning transmission electron microscopy (STEM), bright field (BF) and annular bright field (ABF). In this study, we show that BF STEM can be reliably used for measurements of oxygen octahedral tilts. While optimal conditions for BF imaging are more restricted with respect to sample thickness and defocus, we find that BF imaging with an aberration-corrected microscopemore » with the accelerating voltage of 300 kV gives us the most accurate quantitative measurement of the oxygen column positions. Using the tilted perovskite structure of BiFeO 3 (BFO) as our test sample, we simulate BF and ABF images in a wide range of conditions, identifying the optimal imaging conditions for each mode. Finally, we show that unlike ABF imaging, BF imaging remains directly quantitatively interpretable for a wide range of the specimen mistilt, suggesting that it should be preferable to the ABF STEM imaging for quantitative structure determination.« less

Molecular rheology of branched polymers: decoding and exploring the role of architectural dispersity through a synergy of anionic synthesis, interaction chromatography, rheometry and modeling.

PubMed

van Ruymbeke, E; Lee, H; Chang, T; Nikopoulou, A; Hadjichristidis, N; Snijkers, F; Vlassopoulos, D

2014-07-21

An emerging challenge in polymer physics is the quantitative understanding of the influence of a macromolecular architecture (i.e., branching) on the rheological response of entangled complex polymers. Recent investigations of the rheology of well-defined architecturally complex polymers have determined the composition in the molecular structure and identified the role of side-products in the measured samples. The combination of different characterization techniques, experimental and/or theoretical, represents the current state-of-the-art. Here we review this interdisciplinary approach to molecular rheology of complex polymers, and show the importance of confronting these different tools for ensuring an accurate characterization of a given polymeric sample. We use statistical tools in order to relate the information available from the synthesis protocols of a sample and its experimental molar mass distribution (typically obtained from size exclusion chromatography), and hence obtain precise information about its structural composition, i.e. enhance the existing sensitivity limit. We critically discuss the use of linear rheology as a reliable quantitative characterization tool, along with the recently developed temperature gradient interaction chromatography. The latter, which has emerged as an indispensable characterization tool for branched architectures, offers unprecedented sensitivity in detecting the presence of different molecular structures in a sample. Combining these techniques is imperative in order to quantify the molecular composition of a polymer and its consequences on the macroscopic properties. We validate this approach by means of a new model asymmetric comb polymer which was synthesized anionically. It was thoroughly characterized and its rheology was carefully analyzed. The main result is that the rheological signal reveals fine molecular details, which must be taken into account to fully elucidate the viscoelastic response of entangled branched polymers. It is important to appreciate that, even optimal model systems, i.e., those synthesized with high-vacuum anionic methods, need thorough characterization via a combination of techniques. Besides helping to improve synthetic techniques, this methodology will be significant in fine-tuning mesoscopic tube-based models and addressing outstanding issues such as the quantitative description of the constraint release mechanism.

Laser-induced plasma characterization through self-absorption quantification

NASA Astrophysics Data System (ADS)

Hou, JiaJia; Zhang, Lei; Zhao, Yang; Yan, Xingyu; Ma, Weiguang; Dong, Lei; Yin, Wangbao; Xiao, Liantuan; Jia, Suotang

2018-07-01

A self-absorption quantification method is proposed to quantify the self-absorption degree of spectral lines, in which plasma characteristics including electron temperature, elemental concentration ratio, and absolute species number density can be deduced directly. Since there is no spectral intensity involved in the calculation, the analysis results are independent of the self-absorption effects and the additional spectral efficiency calibration is not required. In order to evaluate the practicality, the limitation for application and the precision of this method are also discussed. Experimental results of aluminum-lithium alloy prove that the proposed method is qualified to realize semi-quantitative measurements and fast plasma characteristics diagnostics.

Geometrical comparison of two protein structures using Wigner-D functions.

PubMed

Saberi Fathi, S M; White, Diana T; Tuszynski, Jack A

2014-10-01

In this article, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root-mean-square deviation characterization and employs a series expansion of the protein's shape function in terms of the Wigner-D functions to define a new criterion, which is called a "similarity value." We further demonstrate that the expansion coefficients for the shape function obtained with the help of the Wigner-D functions correspond to structure factors. Our method addresses the common problem of comparing two proteins with different numbers of atoms. We illustrate it with a worked example. © 2014 Wiley Periodicals, Inc.

Quantitative Examination of Corrosion Damage by Means of Thermal Response Measurements

NASA Technical Reports Server (NTRS)

Rajic, Nik

1998-01-01

Two computational methods are presented that enable a characterization of corrosion damage to be performed from thermal response measurements derived from a standard flash thermographic inspection. The first is based upon a one dimensional analytical solution to the heat diffusion equation and presumes the lateral extent of damage is large compared to the residual structural thickness, such that lateral heat diffusion effects can be considered insignificant. The second proposed method, based on a finite element optimization scheme, addresses the more general case where these conditions are not met. Results from an experimental application are given to illustrate the precision, robustness and practical efficacy of both methods.

Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors.

PubMed

Thakore, Pratiksha I; Gersbach, Charles A

2016-01-01

Transcription activator-like effectors (TALEs) are modular DNA-binding proteins that can be fused to a variety of effector domains to regulate the epigenome. Nucleotide recognition by TALE monomers follows a simple cipher, making this a powerful and versatile method to activate or repress gene expression. Described here are methods to design, assemble, and test TALE transcription factors (TALE-TFs) for control of endogenous gene expression. In this protocol, TALE arrays are constructed by Golden Gate cloning and tested for activity by transfection and quantitative RT-PCR. These methods for engineering TALE-TFs are useful for studies in reverse genetics and genomics, synthetic biology, and gene therapy.

Growth of group II-VI semiconductor quantum dots with strong quantum confinement and low size dispersion

NASA Astrophysics Data System (ADS)

Pandey, Praveen K.; Sharma, Kriti; Nagpal, Swati; Bhatnagar, P. K.; Mathur, P. C.

2003-11-01

CdTe quantum dots embedded in glass matrix are grown using two-step annealing method. The results for the optical transmission characterization are analysed and compared with the results obtained from CdTe quantum dots grown using conventional single-step annealing method. A theoretical model for the absorption spectra is used to quantitatively estimate the size dispersion in the two cases. In the present work, it is established that the quantum dots grown using two-step annealing method have stronger quantum confinement, reduced size dispersion and higher volume ratio as compared to the single-step annealed samples. (

In-injection port thermal desorption for explosives trace evidence analysis.

PubMed

Sigman, M E; Ma, C Y

1999-10-01

A gas chromatographic method utilizing thermal desorption of a dry surface wipe for the analysis of explosives trace chemical evidence has been developed and validated using electron capture and negative ion chemical ionization mass spectrometric detection. Thermal desorption was performed within a split/splitless injection port with minimal instrument modification. Surface-abraded Teflon tubing provided the solid support for sample collection and desorption. Performance was characterized by desorption efficiency, reproducibility, linearity of the calibration, and method detection and quantitation limits. Method validation was performed with a series of dinitrotoluenes, trinitrotoluene, two nitroester explosives, and one nitramine explosive. The method was applied to the sampling of a single piece of debris from an explosion containing trinitrotoluene.

Liquid chromatographic determination of benzocaine and N-acetylbenzocaine in the edible fillet tissue from rainbow trout

USGS Publications Warehouse

Meinertz, J.R.; Stehly, G.R.; Hubert, T.D.; Bernardy, J.A.

1999-01-01

A method was developed for determining benzocaine and N-acetylbenzocaine concentrations in fillet tissue of rainbow trout. The method involves extracting the analytes with acetonitrile, removing lipids or hydrophobic compounds from the extract with hexane, and providing additional clean-up with solid-phase extraction techniques. Analyte concentrations are determined using reversed-phase high-performance liquid chromatographic techniques with an isocratic mobile phase and UV detection. The accuracy (range, 92 to 121%), precision (R.S.D., <14%), and sensitivity (method quantitation limit, <24 ng/g) for each analyte indicate the usefulness of this method for studies characterizing the depletion of benzocaine residues from fish exposed to benzocaine. Copyright (C) 1999.

Quantitative evaluation of the matrix effect in bioanalytical methods based on LC-MS: A comparison of two approaches.

PubMed

Rudzki, Piotr J; Gniazdowska, Elżbieta; Buś-Kwaśnik, Katarzyna

2018-06-05

Liquid chromatography coupled to mass spectrometry (LC-MS) is a powerful tool for studying pharmacokinetics and toxicokinetics. Reliable bioanalysis requires the characterization of the matrix effect, i.e. influence of the endogenous or exogenous compounds on the analyte signal intensity. We have compared two methods for the quantitation of matrix effect. The CVs(%) of internal standard normalized matrix factors recommended by the European Medicines Agency were evaluated against internal standard normalized relative matrix effects derived from Matuszewski et al. (2003). Both methods use post-extraction spiked samples, but matrix factors require also neat solutions. We have tested both approaches using analytes of diverse chemical structures. The study did not reveal relevant differences in the results obtained with both calculation methods. After normalization with the internal standard, the CV(%) of the matrix factor was on average 0.5% higher than the corresponding relative matrix effect. The method adopted by the European Medicines Agency seems to be slightly more conservative in the analyzed datasets. Nine analytes of different structures enabled a general overview of the problem, still, further studies are encouraged to confirm our observations. Copyright © 2018 Elsevier B.V. All rights reserved.

Qualitative and quantitative analysis of an alkaloid fraction from Piper longum L. using ultra-high performance liquid chromatography-diode array detector-electrospray ionization mass spectrometry.

PubMed

Li, Kuiyong; Fan, Yunpeng; Wang, Hui; Fu, Qing; Jin, Yu; Liang, Xinmiao

2015-05-10

In a previous research, an alkaloid fraction and 18 alkaloid compounds were prepared from Piper longum L. by series of purification process. In this paper, a qualitative and quantitative analysis method using ultra-high performance liquid chromatography-diode array detector-mass spectrometry (UHPLC-DAD-MS) was developed to evaluate the alkaloid fraction. Qualitative analysis of the alkaloid fraction was firstly completed by UHPLC-DAD method and 18 amide alkaloid compounds were identified. A further qualitative analysis of the alkaloid fraction was accomplished by UHPLC-MS/MS method. Another 25 amide alkaloids were identified according to their characteristic ions and neutral losses. At last, a quantitative method for the alkaloid fraction was established using four marker compounds including piperine, pipernonatine, guineensine and N-isobutyl-2E,4E-octadecadienamide. After the validation of this method, the contents of above four marker compounds in the alkaloid fraction were 57.5mg/g, 65.6mg/g, 17.7mg/g and 23.9mg/g, respectively. Moreover, the relative response factors of other three compounds to piperine were calculated. A comparative study between external standard quantification and relative response factor quantification proved no remarkable difference. UHPLC-DAD-MS method was demonstrated to be a powerful tool for the characterization of the alkaloid fraction from P. longum L. and the result proved that the quality of alkaloid fraction was efficiently improved after appropriate purification. Copyright © 2015. Published by Elsevier B.V.

The local lymph node assay and skin sensitization testing.

PubMed

Kimber, Ian; Dearman, Rebecca J

2010-01-01

The mouse local lymph node assay (LLNA) is a method for the identification and characterization of skin sensitization hazards. In this context the method can be used both to identify contact allergens, and also determine the relative skin sensitizing potency as a basis for derivation of effective risk assessments.The assay is based on measurement of proliferative responses by draining lymph node cells induced following topical exposure of mice to test chemicals. Such responses are known to be causally and quantitatively associated with the acquisition of skin sensitization and therefore provide a relevant marker for characterization of contact allergic potential.The LLNA has been the subject of exhaustive evaluation and validation exercises and has been assigned Organization for Economic Cooperation and Development (OECD) test guideline 429. Herein we describe the conduct and interpretation of the LLNA.

A comparison of quantitative methods for clinical imaging with hyperpolarized (13)C-pyruvate.

PubMed

Daniels, Charlie J; McLean, Mary A; Schulte, Rolf F; Robb, Fraser J; Gill, Andrew B; McGlashan, Nicholas; Graves, Martin J; Schwaiger, Markus; Lomas, David J; Brindle, Kevin M; Gallagher, Ferdia A

2016-04-01

Dissolution dynamic nuclear polarization (DNP) enables the metabolism of hyperpolarized (13)C-labelled molecules, such as the conversion of [1-(13)C]pyruvate to [1-(13)C]lactate, to be dynamically and non-invasively imaged in tissue. Imaging of this exchange reaction in animal models has been shown to detect early treatment response and correlate with tumour grade. The first human DNP study has recently been completed, and, for widespread clinical translation, simple and reliable methods are necessary to accurately probe the reaction in patients. However, there is currently no consensus on the most appropriate method to quantify this exchange reaction. In this study, an in vitro system was used to compare several kinetic models, as well as simple model-free methods. Experiments were performed using a clinical hyperpolarizer, a human 3 T MR system, and spectroscopic imaging sequences. The quantitative methods were compared in vivo by using subcutaneous breast tumours in rats to examine the effect of pyruvate inflow. The two-way kinetic model was the most accurate method for characterizing the exchange reaction in vitro, and the incorporation of a Heaviside step inflow profile was best able to describe the in vivo data. The lactate time-to-peak and the lactate-to-pyruvate area under the curve ratio were simple model-free approaches that accurately represented the full reaction, with the time-to-peak method performing indistinguishably from the best kinetic model. Finally, extracting data from a single pixel was a robust and reliable surrogate of the whole region of interest. This work has identified appropriate quantitative methods for future work in the analysis of human hyperpolarized (13)C data. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

An optimized framework for quantitative magnetization transfer imaging of the cervical spinal cord in vivo

PubMed Central

Grussu, Francesco; Ianus, Andrada; Schneider, Torben; Prados, Ferran; Fairney, James; Ourselin, Sebastien; Alexander, Daniel C.; Cercignani, Mara; Gandini Wheeler‐Kingshott, Claudia A.M.; Samson, Rebecca S.

2017-01-01

Purpose To develop a framework to fully characterize quantitative magnetization transfer indices in the human cervical cord in vivo within a clinically feasible time. Methods A dedicated spinal cord imaging protocol for quantitative magnetization transfer was developed using a reduced field‐of‐view approach with echo planar imaging (EPI) readout. Sequence parameters were optimized based in the Cramer‐Rao‐lower bound. Quantitative model parameters (i.e., bound pool fraction, free and bound pool transverse relaxation times [ T2F, T2B], and forward exchange rate [k FB]) were estimated implementing a numerical model capable of dealing with the novelties of the sequence adopted. The framework was tested on five healthy subjects. Results Cramer‐Rao‐lower bound minimization produces optimal sampling schemes without requiring the establishment of a steady‐state MT effect. The proposed framework allows quantitative voxel‐wise estimation of model parameters at the resolution typically used for spinal cord imaging (i.e. 0.75 × 0.75 × 5 mm3), with a protocol duration of ∼35 min. Quantitative magnetization transfer parametric maps agree with literature values. Whole‐cord mean values are: bound pool fraction = 0.11(±0.01), T2F = 46.5(±1.6) ms, T2B = 11.0(±0.2) µs, and k FB = 1.95(±0.06) Hz. Protocol optimization has a beneficial effect on reproducibility, especially for T2B and k FB. Conclusion The framework developed enables robust characterization of spinal cord microstructure in vivo using qMT. Magn Reson Med 79:2576–2588, 2018. © 2017 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. PMID:28921614

Plot-scale soil loss estimation with laser scanning and photogrammetry methods

NASA Astrophysics Data System (ADS)

Szabó, Boglárka; Szabó, Judit; Jakab, Gergely; Centeri, Csaba; Szalai, Zoltán; Somogyi, Árpád; Barsi, Árpád

2017-04-01

Structure from Motion (SfM) is an automatic feature-matching algorithm, which nowadays is widely used tool in photogrammetry for geoscience applications. SfM method and parallel terrestrial laser scanning measurements are widespread and they can be well accomplished for quantitative soil erosion measurements as well. Therefore, our main scope was soil erosion characterization quantitatively and qualitatively, 3D visualization and morphological characterization of soil-erosion-dynamics. During the rainfall simulation, the surface had been measured and compared before and after the rainfall event by photogrammetry (SfM - Structure from Motion) and laser scanning (TLS - Terrestrial Laser Scanning) methods. The validation of the given results had been done by the caught runoff and the measured soil-loss value. During the laboratory experiment, the applied rainfall had 40 mm/h rainfall intensity. The size of the plot was 0.5 m2. The laser scanning had been implemented with Faro Focus 3D 120 S type equipment, while the SfM shooting had been carried out by 2 piece SJCAM SJ4000+ type, 12 MP resolution and 4K action cams. The photo-reconstruction had been made with Agisoft Photoscan software, while evaluation of the resulted point-cloud from laser scanning and photogrammetry had been implemented partly in CloudCompare and partly in ArcGIS. The resulted models and the calculated surface changes didn't prove to be suitable for estimating soil-loss, only for the detection of changes in the vertical surface. The laser scanning resulted a quite precise surface model, while the SfM method is affected by errors at the surface model due to other factors. The method needs more adequate technical laboratory preparation.

Analysis of automated quantification of motor activity in REM sleep behaviour disorder.

PubMed

Frandsen, Rune; Nikolic, Miki; Zoetmulder, Marielle; Kempfner, Lykke; Jennum, Poul

2015-10-01

Rapid eye movement (REM) sleep behaviour disorder (RBD) is characterized by dream enactment and REM sleep without atonia. Atonia is evaluated on the basis of visual criteria, but there is a need for more objective, quantitative measurements. We aimed to define and optimize a method for establishing baseline and all other parameters in automatic quantifying submental motor activity during REM sleep. We analysed the electromyographic activity of the submental muscle in polysomnographs of 29 patients with idiopathic RBD (iRBD), 29 controls and 43 Parkinson's (PD) patients. Six adjustable parameters for motor activity were defined. Motor activity was detected and quantified automatically. The optimal parameters for separating RBD patients from controls were investigated by identifying the greatest area under the receiver operating curve from a total of 648 possible combinations. The optimal parameters were validated on PD patients. Automatic baseline estimation improved characterization of atonia during REM sleep, as it eliminates inter/intra-observer variability and can be standardized across diagnostic centres. We found an optimized method for quantifying motor activity during REM sleep. The method was stable and can be used to differentiate RBD from controls and to quantify motor activity during REM sleep in patients with neurodegeneration. No control had more than 30% of REM sleep with increased motor activity; patients with known RBD had as low activity as 4.5%. We developed and applied a sensitive, quantitative, automatic algorithm to evaluate loss of atonia in RBD patients. © 2015 European Sleep Research Society.

Accurate phase measurements for thick spherical objects using optical quadrature microscopy

NASA Astrophysics Data System (ADS)

Warger, William C., II; DiMarzio, Charles A.

2009-02-01

In vitro fertilization (IVF) procedures have resulted in the birth of over three million babies since 1978. Yet the live birth rate in the United States was only 34% in 2005, with 32% of the successful pregnancies resulting in multiple births. These multiple pregnancies were directly attributed to the transfer of multiple embryos to increase the probability that a single, healthy embryo was included. Current viability markers used for IVF, such as the cell number, symmetry, size, and fragmentation, are analyzed qualitatively with differential interference contrast (DIC) microscopy. However, this method is not ideal for quantitative measures beyond the 8-cell stage of development because the cells overlap and obstruct the view within and below the cluster of cells. We have developed the phase-subtraction cell-counting method that uses the combination of DIC and optical quadrature microscopy (OQM) to count the number of cells accurately in live mouse embryos beyond the 8-cell stage. We have also created a preliminary analysis to measure the cell symmetry, size, and fragmentation quantitatively by analyzing the relative dry mass from the OQM image in conjunction with the phase-subtraction count. In this paper, we will discuss the characterization of OQM with respect to measuring the phase accurately for spherical samples that are much larger than the depth of field. Once fully characterized and verified with human embryos, this methodology could provide the means for a more accurate method to score embryo viability.

The Specificity of Observational Studies in Physical Activity and Sports Sciences: Moving Forward in Mixed Methods Research and Proposals for Achieving Quantitative and Qualitative Symmetry

PubMed Central

Anguera, M. Teresa; Camerino, Oleguer; Castañer, Marta; Sánchez-Algarra, Pedro; Onwuegbuzie, Anthony J.

2017-01-01

Mixed methods studies are been increasingly applied to a diversity of fields. In this paper, we discuss the growing use—and enormous potential—of mixed methods research in the field of sport and physical activity. A second aim is to contribute to strengthening the characteristics of mixed methods research by showing how systematic observation offers rigor within a flexible framework that can be applied to a wide range of situations. Observational methodology is characterized by high scientific rigor and flexibility throughout its different stages and allows the objective study of spontaneous behavior in natural settings, with no external influence. Mixed methods researchers need to take bold yet thoughtful decisions regarding both substantive and procedural issues. We present three fundamental and complementary ideas to guide researchers in this respect: we show why studies of sport and physical activity that use a mixed methods research approach should be included in the field of mixed methods research, we highlight the numerous possibilities offered by observational methodology in this field through the transformation of descriptive data into quantifiable code matrices, and we discuss possible solutions for achieving true integration of qualitative and quantitative findings. PMID:29312061

An integrative strategy for quantitative analysis of the N-glycoproteome in complex biological samples

PubMed Central

2014-01-01

Background The complexity of protein glycosylation makes it difficult to characterize glycosylation patterns on a proteomic scale. In this study, we developed an integrated strategy for comparatively analyzing N-glycosylation/glycoproteins quantitatively from complex biological samples in a high-throughput manner. This strategy entailed separating and enriching glycopeptides/glycoproteins using lectin affinity chromatography, and then tandem labeling them with 18O/16O to generate a mass shift of 6 Da between the paired glycopeptides, and finally analyzing them with liquid chromatography-mass spectrometry (LC-MS) and the automatic quantitative method we developed based on Mascot Distiller. Results The accuracy and repeatability of this strategy were first verified using standard glycoproteins; linearity was maintained within a range of 1:10–10:1. The peptide concentration ratios obtained by the self-build quantitative method were similar to both the manually calculated and theoretical values, with a standard deviation (SD) of 0.023–0.186 for glycopeptides. The feasibility of the strategy was further confirmed with serum from hepatocellular carcinoma (HCC) patients and healthy individuals; the expression of 44 glycopeptides and 30 glycoproteins were significantly different between HCC patient and control serum. Conclusions This strategy is accurate, repeatable, and efficient, and may be a useful tool for identification of disease-related N-glycosylation/glycoprotein changes. PMID:24428921

Quantitative electron density characterization of soft tissue substitute plastic materials using grating-based x-ray phase-contrast imaging

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

Sarapata, A.; Chabior, M.; Zanette, I.

2014-10-15

Many scientific research areas rely on accurate electron density characterization of various materials. For instance in X-ray optics and radiation therapy, there is a need for a fast and reliable technique to quantitatively characterize samples for electron density. We present how a precise measurement of electron density can be performed using an X-ray phase-contrast grating interferometer in a radiographic mode of a homogenous sample in a controlled geometry. A batch of various plastic materials was characterized quantitatively and compared with calculated results. We found that the measured electron densities closely match theoretical values. The technique yields comparable results between amore » monochromatic and a polychromatic X-ray source. Measured electron densities can be further used to design dedicated X-ray phase contrast phantoms and the additional information on small angle scattering should be taken into account in order to exclude unsuitable materials.« less

End of the chain? Rugosity and fine-scale bathymetry from existing underwater digital imagery using structure-from-motion (SfM) technology

USGS Publications Warehouse

Storlazzi, Curt; Dartnell, Peter; Hatcher, Gerry; Gibbs, Ann E.

2016-01-01

The rugosity or complexity of the seafloor has been shown to be an important ecological parameter for fish, algae, and corals. Historically, rugosity has been measured either using simple and subjective manual methods such as ‘chain-and-tape’ or complicated and expensive geophysical methods. Here, we demonstrate the application of structure-from-motion (SfM) photogrammetry to generate high-resolution, three-dimensional bathymetric models of a fringing reef from existing underwater video collected to characterize the seafloor. SfM techniques are capable of achieving spatial resolution that can be orders of magnitude greater than large-scale lidar and sonar mapping of coral reef ecosystems. The resulting data provide finer-scale measurements of bathymetry and rugosity that are more applicable to ecological studies of coral reefs than provided by the more expensive and time-consuming geophysical methods. Utilizing SfM techniques for characterizing the benthic habitat proved to be more effective and quantitatively powerful than conventional methods and thus might portend the end of the ‘chain-and-tape’ method for measuring benthic complexity.

Introducing anisotropic Minkowski functionals and quantitative anisotropy measures for local structure analysis in biomedical imaging

NASA Astrophysics Data System (ADS)

Wismüller, Axel; De, Titas; Lochmüller, Eva; Eckstein, Felix; Nagarajan, Mahesh B.

2013-03-01

The ability of Minkowski Functionals to characterize local structure in different biological tissue types has been demonstrated in a variety of medical image processing tasks. We introduce anisotropic Minkowski Functionals (AMFs) as a novel variant that captures the inherent anisotropy of the underlying gray-level structures. To quantify the anisotropy characterized by our approach, we further introduce a method to compute a quantitative measure motivated by a technique utilized in MR diffusion tensor imaging, namely fractional anisotropy. We showcase the applicability of our method in the research context of characterizing the local structure properties of trabecular bone micro-architecture in the proximal femur as visualized on multi-detector CT. To this end, AMFs were computed locally for each pixel of ROIs extracted from the head, neck and trochanter regions. Fractional anisotropy was then used to quantify the local anisotropy of the trabecular structures found in these ROIs and to compare its distribution in different anatomical regions. Our results suggest a significantly greater concentration of anisotropic trabecular structures in the head and neck regions when compared to the trochanter region (p < 10-4). We also evaluated the ability of such AMFs to predict bone strength in the femoral head of proximal femur specimens obtained from 50 donors. Our results suggest that such AMFs, when used in conjunction with multi-regression models, can outperform more conventional features such as BMD in predicting failure load. We conclude that such anisotropic Minkowski Functionals can capture valuable information regarding directional attributes of local structure, which may be useful in a wide scope of biomedical imaging applications.

Introducing Anisotropic Minkowski Functionals and Quantitative Anisotropy Measures for Local Structure Analysis in Biomedical Imaging

PubMed Central

Wismüller, Axel; De, Titas; Lochmüller, Eva; Eckstein, Felix; Nagarajan, Mahesh B.

2017-01-01

The ability of Minkowski Functionals to characterize local structure in different biological tissue types has been demonstrated in a variety of medical image processing tasks. We introduce anisotropic Minkowski Functionals (AMFs) as a novel variant that captures the inherent anisotropy of the underlying gray-level structures. To quantify the anisotropy characterized by our approach, we further introduce a method to compute a quantitative measure motivated by a technique utilized in MR diffusion tensor imaging, namely fractional anisotropy. We showcase the applicability of our method in the research context of characterizing the local structure properties of trabecular bone micro-architecture in the proximal femur as visualized on multi-detector CT. To this end, AMFs were computed locally for each pixel of ROIs extracted from the head, neck and trochanter regions. Fractional anisotropy was then used to quantify the local anisotropy of the trabecular structures found in these ROIs and to compare its distribution in different anatomical regions. Our results suggest a significantly greater concentration of anisotropic trabecular structures in the head and neck regions when compared to the trochanter region (p < 10−4). We also evaluated the ability of such AMFs to predict bone strength in the femoral head of proximal femur specimens obtained from 50 donors. Our results suggest that such AMFs, when used in conjunction with multi-regression models, can outperform more conventional features such as BMD in predicting failure load. We conclude that such anisotropic Minkowski Functionals can capture valuable information regarding directional attributes of local structure, which may be useful in a wide scope of biomedical imaging applications. PMID:29170580

Biophotonics of skin: method for correction of deep Raman spectra distorted by elastic scattering

NASA Astrophysics Data System (ADS)

Roig, Blandine; Koenig, Anne; Perraut, François; Piot, Olivier; Gobinet, Cyril; Manfait, Michel; Dinten, Jean-Marc

2015-03-01

Confocal Raman microspectroscopy allows in-depth molecular and conformational characterization of biological tissues non-invasively. Unfortunately, spectral distortions occur due to elastic scattering. Our objective is to correct the attenuation of in-depth Raman peaks intensity by considering this phenomenon, enabling thus quantitative diagnosis. In this purpose, we developed PDMS phantoms mimicking skin optical properties used as tools for instrument calibration and data processing method validation. An optical system based on a fibers bundle has been previously developed for in vivo skin characterization with Diffuse Reflectance Spectroscopy (DRS). Used on our phantoms, this technique allows checking their optical properties: the targeted ones were retrieved. Raman microspectroscopy was performed using a commercial confocal microscope. Depth profiles were constructed from integrated intensity of some specific PDMS Raman vibrations. Acquired on monolayer phantoms, they display a decline which is increasing with the scattering coefficient. Furthermore, when acquiring Raman spectra on multilayered phantoms, the signal attenuation through each single layer is directly dependent on its own scattering property. Therefore, determining the optical properties of any biological sample, obtained with DRS for example, is crucial to correct properly Raman depth profiles. A model, inspired from S.L. Jacques's expression for Confocal Reflectance Microscopy and modified at some points, is proposed and tested to fit the depth profiles obtained on the phantoms as function of the reduced scattering coefficient. Consequently, once the optical properties of a biological sample are known, the intensity of deep Raman spectra distorted by elastic scattering can be corrected with our reliable model, permitting thus to consider quantitative studies for purposes of characterization or diagnosis.

Lunar terrain mapping and relative-roughness analysis

NASA Technical Reports Server (NTRS)

Rowan, L. C.; Mccauley, J. F.; Holm, E. A.

1971-01-01

Terrain maps of the equatorial zone were prepared at scales of 1:2,000,000 and 1:1,000,000 to classify lunar terrain with respect to roughness and to provide a basis for selecting sites for Surveyor and Apollo landings, as well as for Ranger and Lunar Orbiter photographs. Lunar terrain was described by qualitative and quantitative methods and divided into four fundamental classes: maria, terrae, craters, and linear features. Some 35 subdivisions were defined and mapped throughout the equatorial zone, and, in addition, most of the map units were illustrated by photographs. The terrain types were analyzed quantitatively to characterize and order their relative roughness characteristics. For some morphologically homogeneous mare areas, relative roughness can be extrapolated to the large scales from measurements at small scales.

Rate Constants and Mechanisms of Protein–Ligand Binding

PubMed Central

Pang, Xiaodong; Zhou, Huan-Xiang

2017-01-01

Whereas protein–ligand binding affinities have long-established prominence, binding rate constants and binding mechanisms have gained increasing attention in recent years. Both new computational methods and new experimental techniques have been developed to characterize the latter properties. It is now realized that binding mechanisms, like binding rate constants, can and should be quantitatively determined. In this review, we summarize studies and synthesize ideas on several topics in the hope of providing a coherent picture of and physical insight into binding kinetics. The topics include microscopic formulation of the kinetic problem and its reduction to simple rate equations; computation of binding rate constants; quantitative determination of binding mechanisms; and elucidation of physical factors that control binding rate constants and mechanisms. PMID:28375732

Application of Analysis and Modeling for Surface Water-Ground Water System: Preliminary Study of Artificial Recharge in Jeju Island, Korea

NASA Astrophysics Data System (ADS)

Kim, Y.; Koo, M.; Lee, K.; Ko, K.; Barry, J. M.

2008-12-01

The primary goal of this study is to secure sustainable groundwater resources with application of the analysis and modeling of coupled surface water-groundwater system to Jeju Island in the form of artificial recharge. Artificial recharge technology is a feasible method to augment groundwater resources in Jeju Island, Korea. Jeju-friendly Aquifer Recharge Technology (J-ART) that will be developed in this study is a technology for securing sustainable water resources by capturing ephemeral stream water with no interference in the environment such as natural recharge or eco-system, capturing the water in the reservoirs, recharging it through designed borehole after appropriate treatment, and then making it to be used at down-gradient production wells. Precipitation pattern in the study area is shifting to more sparsely-distributed and heavier rain type in summer season which reduces infiltration and/or groundwater recharge but increases runoff and flash flood on stream. Stream water as a source for J-ART is available only a few times a year since the stream bed is highly feasible to be percolated. To characterize quantitatively stream water, automatic temporal data collection system for water level, water velocity, and water qualities of total 8 parameters including temperature, water depth, pH, EC, DO, turbidity, NO3-N and Cl-. Characterizing groundwater flow from recharge area to discharge area should be achieved to evaluate the efficiency of J-ART. Jeju volcanic island has very thick unsaturated zone which is approximately 50 percent of the elevation on which it is. This hydrogeological property is good to inject source water through unsaturated zone to increase transport time, to get main basal aquifer, and to naturally filter the injected water during the transport. However, characterizing groundwater flow through the thick unsaturated zone with repeatedly overlapping permeable/impermeable layers would be a challenge. Estimation method of the infiltration velocity of soil water, groundwater age dating, and evaluation method for groundwater flow/circulation using stable isotopes are developed to evaluate artificial recharge. Input parameters for groundwater flow model are collected and analyzed quantitatively to develop model for simulating groundwater flow and thermal transport during artificial recharge. Self-potential survey method is reviewed theoretically as a geophysical evaluation method to characterize unsaturated flow during artificial recharge.

Observational and Data Reduction Techniques to Optimize Mineralogical Characterizations of Asteroid Surface Materials

NASA Technical Reports Server (NTRS)

Gaffey, M. J.

2003-01-01

Mineralogy is the key to determining the compositional history of the asteroids and to determining the genetic relationships between the asteroids and meteorites. The most sophisticated remote mineralogical characterizations involve the quantitative extraction of specific diagnostic parameters from reflectance spectra and the use of quantitative interpretive calibrations to determine the presence, abundance and/or composition of mineral phases in a surface material. Although this approach is potentially subject to systematic errors, it provides the only consistent set of asteroid surface material characterizations.

NCI Launches Proteomics Assay Portal | Office of Cancer Clinical Proteomics Research

Cancer.gov

In a paper recently published by the journal Nature Methods, Investigators from the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (NCI-CPTAC) announced the launch of a proteomics Assay Portal for multiple reaction monitoring-mass spectrometry (MRM-MS) assays.  This community web-based repository for well-characterized quantitative proteomic assays currently consists of 456 unique peptide assays to 282 unique proteins and ser

Developing Xenopus Laevis as a Model to Screen Drugs for Fragile X Syndrome

DTIC Science & Technology

2014-06-01

demonstrated the capacity to rescue the decreased FMRP expression by gene delivery. We characterized an innate visually-guided avoidance behavior in tadpoles ... tadpole is a unique model system that allows easy access to the nervous system at early stages of development, is amenable to in vivo gene...established quantitative in vivo imaging methods to knockdown and assay synthesis of FMRP in Xenopus tadpole brains. We also established 2 behavioral

Toward computational crime prediction. Comment on "Statistical physics of crime: A review" by M.R. D'Orsogna and M. Perc

NASA Astrophysics Data System (ADS)

Ferrara, Emilio

2015-03-01

Containing the spreading of crime in modern society in an ongoing battle: our understanding of the dynamics underlying criminal events and the motifs behind individuals therein involved is crucial to design cost-effective prevention policies and intervention strategies. During recent years we witnessed various research fields joining forces, sharing models and methods, toward modeling and quantitatively characterizing crime and criminal behavior.

NMR Reconstructive Elasticity Imaging of Breast: Surrogate Remote Palpation Using Quantitative 3-D Displacement

DTIC Science & Technology

1998-09-01

breast tissues may provide unique information which could increase detection and/or characterization of potentially malignant masses not accessible... masses deep in the breast , or within relatively dense, stiff, or heterogeneous tissues, is poor. The principal objective of this project is to develop...or propagating shear wave is documented by imaging devices. In the original MRI method, spatial magnetization tagging was applied, but this had poor

QACD: A method for the quantitative assessment of compositional distribution in geologic materials

NASA Astrophysics Data System (ADS)

Loocke, M. P.; Lissenberg, J. C. J.; MacLeod, C. J.

2017-12-01

In order to fully understand the petrogenetic history of a rock, it is critical to obtain a thorough characterization of the chemical and textural relationships of its mineral constituents. Element mapping combines the microanalytical techniques that allow for the analysis of major- and minor elements at high spatial resolutions (e.g., electron microbeam analysis) with 2D mapping of samples in order to provide unprecedented detail regarding the growth histories and compositional distributions of minerals within a sample. We present a method for the acquisition and processing of large area X-ray element maps obtained by energy-dispersive X-ray spectrometer (EDS) to produce a quantitative assessment of compositional distribution (QACD) of mineral populations within geologic materials. By optimizing the conditions at which the EDS X-ray element maps are acquired, we are able to obtain full thin section quantitative element maps for most major elements in relatively short amounts of time. Such maps can be used to not only accurately identify all phases and calculate mineral modes for a sample (e.g., a petrographic thin section), but, critically, enable a complete quantitative assessment of their compositions. The QACD method has been incorporated into a python-based, easy-to-use graphical user interface (GUI) called Quack. The Quack software facilitates the generation of mineral modes, element and molar ratio maps and the quantification of full-sample compositional distributions. The open-source nature of the Quack software provides a versatile platform which can be easily adapted and modified to suit the needs of the user.

Measuring information transfer in a soft robotic arm.

PubMed

Nakajima, K; Schmidt, N; Pfeifer, R

2015-05-13

Soft robots can exhibit diverse behaviors with simple types of actuation by partially outsourcing control to the morphological and material properties of their soft bodies, which is made possible by the tight coupling between control, body, and environment. In this paper, we present a method that will quantitatively characterize these diverse spatiotemporal dynamics of a soft body based on the information-theoretic approach. In particular, soft bodies have the ability to propagate the effect of actuation through the entire body, with a certain time delay, due to their elasticity. Our goal is to capture this delayed interaction in a quantitative manner based on a measure called momentary information transfer. We extend this measure to soft robotic applications and demonstrate its power using a physical soft robotic platform inspired by the octopus. Our approach is illustrated in two ways. First, we statistically characterize the delayed actuation propagation through the body as a strength of information transfer. Second, we capture this information propagation directly as local information dynamics. As a result, we show that our approach can successfully characterize the spatiotemporal dynamics of the soft robotic platform, explicitly visualizing how information transfers through the entire body with delays. Further extension scenarios of our approach are discussed for soft robotic applications in general.

Towards precision medicine: from quantitative imaging to radiomics

PubMed Central

Acharya, U. Rajendra; Hagiwara, Yuki; Sudarshan, Vidya K.; Chan, Wai Yee; Ng, Kwan Hoong

2018-01-01

Radiology (imaging) and imaging-guided interventions, which provide multi-parametric morphologic and functional information, are playing an increasingly significant role in precision medicine. Radiologists are trained to understand the imaging phenotypes, transcribe those observations (phenotypes) to correlate with underlying diseases and to characterize the images. However, in order to understand and characterize the molecular phenotype (to obtain genomic information) of solid heterogeneous tumours, the advanced sequencing of those tissues using biopsy is required. Thus, radiologists image the tissues from various views and angles in order to have the complete image phenotypes, thereby acquiring a huge amount of data. Deriving meaningful details from all these radiological data becomes challenging and raises the big data issues. Therefore, interest in the application of radiomics has been growing in recent years as it has the potential to provide significant interpretive and predictive information for decision support. Radiomics is a combination of conventional computer-aided diagnosis, deep learning methods, and human skills, and thus can be used for quantitative characterization of tumour phenotypes. This paper discusses the overview of radiomics workflow, the results of various radiomics-based studies conducted using various radiological images such as computed tomography (CT), magnetic resonance imaging (MRI), and positron-emission tomography (PET), the challenges we are facing, and the potential contribution of radiomics towards precision medicine. PMID:29308604

Electro-optic holography method for determination of surface shape and deformation

NASA Astrophysics Data System (ADS)

Furlong, Cosme; Pryputniewicz, Ryszard J.

1998-06-01

Current demanding engineering analysis and design applications require effective experimental methodologies for characterization of surface shape and deformation. Such characterization is of primary importance in many applications, because these quantities are related to the functionality, performance, and integrity of the objects of interest, especially in view of advances relating to concurrent engineering. In this paper, a new approach to characterization of surface shape and deformation using a simple optical setup is described. The approach consists of a fiber optic based electro-optic holography (EOH) system based on an IR, temperature tuned laser diode, a single mode fiber optic directional coupler assembly, and a video processing computer. The EOH can be arranged in multiple configurations which include, the three-camera, three- illumination, and speckle correlation modes.In particular, the three-camera mode is described, as well as a brief description of the procedures for obtaining quantitative 3D shape and deformation information. A representative application of the three-camera EOH system demonstrates the viability of the approach as an effective engineering tool. A particular feature of this system and the procedure described in this paper is that the 3D quantitative data are written to data files which can be readily interfaced to commercial CAD/CAM environments.

Effects of spacer orientations on the cake formation during membrane fouling: Quantitative analysis based on 3D OCT imaging.

PubMed

Liu, Xin; Li, Weiyi; Chong, Tzyy Haur; Fane, Anthony G

2017-03-01

Spacer design plays an important role in improving the performance of membrane processes for water/wastewater treatment. This work focused on a fundamental issue of spacer design, i.e., investigating the effects of spacer orientations on the fouling behavior during a membrane process. A series of fouling experiments with different spacer orientation were carried out to in situ characterize the formation of a cake layer in a spacer unit cell via 3D optical coherence tomography (OCT) imaging. The cake layers formed at different times were digitalized for quantitatively analyzing the variation in the cake morphology as a function of time. In particular, the local deposition rates were evaluated to determine the active regions where the instantaneous changes in deposit thickness were significant. The characterization results indicate that varying the spacer orientation could substantially change the evolution of membrane fouling by particulate foulants and thereby result in a cake layer with various morphologies; the competition between growth and erosion at different locations would instantaneously respond to the micro-hydrodynamic environment that might change with time. This work confirms that the OCT-based characterization method is a powerful tool for exploring novel spacer design. Copyright © 2016 Elsevier Ltd. All rights reserved.

Eifel maars: Quantitative shape characterization of juvenile ash particles (Eifel Volcanic Field, Germany)

NASA Astrophysics Data System (ADS)

Rausch, Juanita; Grobéty, Bernard; Vonlanthen, Pierre

2015-01-01

The Eifel region in western central Germany is the type locality for maar volcanism, which is classically interpreted to be the result of explosive eruptions due to shallow interaction between magma and external water (i.e. phreatomagmatic eruptions). Sedimentary structures, deposit features and particle morphology found in many maar deposits of the West Eifel Volcanic Field (WEVF), in contrast to deposits in the East Eifel Volcanic Field (EEVF), lack the diagnostic criteria of typical phreatomagmatic deposits. The aim of this study was to determine quantitatively the shape of WEVF and EEVF maar ash particles in order to infer the governing eruption style in Eifel maar volcanoes. The quantitative shape characterization was done by analyzing fractal dimensions of particle contours (125-250 μm sieve fraction) obtained from Scanning electron microscopy (SEM) and SEM micro-computed tomography (SEM micro-CT) images. The fractal analysis (dilation method) and the fractal spectrum technique confirmed that the WEVF and EEVF maar particles have contrasting multifractal shapes. Whereas the low small-scale dimensions of EEVF particles (Eppelsberg Green Unit) coincide with previously published values for phreatomagmatic particles, the WEVF particles (Meerfelder Maar, Pulvermaar and Ulmener Maar) have larger values indicating more complex small-scale features, which are characteristic for magmatic particles. These quantitative results are strengthening the qualitative microscopic observations, that the studied WEVF maar eruptions are rather dominated by magmatic processes. The different eruption styles in the two volcanic fields can be explained by the different geological and hydrological settings found in both regions and the different chemical compositions of the magmas.

Standardization of chemical analytical techniques for pyrolysis bio-oil: history, challenges, and current status of methods

DOE PAGES

Ferrell, Jack R.; Olarte, Mariefel V.; Christensen, Earl D.; ...

2016-07-05

Here, we discuss the standardization of analytical techniques for pyrolysis bio-oils, including the current status of methods, and our opinions on future directions. First, the history of past standardization efforts is summarized, and both successful and unsuccessful validation of analytical techniques highlighted. The majority of analytical standardization studies to-date has tested only physical characterization techniques. In this paper, we present results from an international round robin on the validation of chemical characterization techniques for bio-oils. Techniques tested included acid number, carbonyl titrations using two different methods (one at room temperature and one at 80 °C), 31P NMR for determination ofmore » hydroxyl groups, and a quantitative gas chromatography–mass spectrometry (GC-MS) method. Both carbonyl titration and acid number methods have yielded acceptable inter-laboratory variabilities. 31P NMR produced acceptable results for aliphatic and phenolic hydroxyl groups, but not for carboxylic hydroxyl groups. As shown in previous round robins, GC-MS results were more variable. Reliable chemical characterization of bio-oils will enable upgrading research and allow for detailed comparisons of bio-oils produced at different facilities. Reliable analytics are also needed to enable an emerging bioenergy industry, as processing facilities often have different analytical needs and capabilities than research facilities. We feel that correlations in reliable characterizations of bio-oils will help strike a balance between research and industry, and will ultimately help to -determine metrics for bio-oil quality. Lastly, the standardization of additional analytical methods is needed, particularly for upgraded bio-oils.« less

Standardization of chemical analytical techniques for pyrolysis bio-oil: history, challenges, and current status of methods

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

Ferrell, Jack R.; Olarte, Mariefel V.; Christensen, Earl D.

Here, we discuss the standardization of analytical techniques for pyrolysis bio-oils, including the current status of methods, and our opinions on future directions. First, the history of past standardization efforts is summarized, and both successful and unsuccessful validation of analytical techniques highlighted. The majority of analytical standardization studies to-date has tested only physical characterization techniques. In this paper, we present results from an international round robin on the validation of chemical characterization techniques for bio-oils. Techniques tested included acid number, carbonyl titrations using two different methods (one at room temperature and one at 80 °C), 31P NMR for determination ofmore » hydroxyl groups, and a quantitative gas chromatography–mass spectrometry (GC-MS) method. Both carbonyl titration and acid number methods have yielded acceptable inter-laboratory variabilities. 31P NMR produced acceptable results for aliphatic and phenolic hydroxyl groups, but not for carboxylic hydroxyl groups. As shown in previous round robins, GC-MS results were more variable. Reliable chemical characterization of bio-oils will enable upgrading research and allow for detailed comparisons of bio-oils produced at different facilities. Reliable analytics are also needed to enable an emerging bioenergy industry, as processing facilities often have different analytical needs and capabilities than research facilities. We feel that correlations in reliable characterizations of bio-oils will help strike a balance between research and industry, and will ultimately help to -determine metrics for bio-oil quality. Lastly, the standardization of additional analytical methods is needed, particularly for upgraded bio-oils.« less

Quantitative Assessment of Transportation Network Vulnerability with Dynamic Traffic Simulation Methods

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

Shekar, Venkateswaran; Fiondella, Lance; Chatterjee, Samrat

Transportation networks are critical to the social and economic function of nations. Given the continuing increase in the populations of cities throughout the world, the criticality of transportation infrastructure is expected to increase. Thus, it is ever more important to mitigate congestion as well as to assess the impact disruptions would have on individuals who depend on transportation for their work and livelihood. Moreover, several government organizations are responsible for ensuring transportation networks are available despite the constant threat of natural disasters and terrorist activities. Most of the previous transportation network vulnerability research has been performed in the context ofmore » static traffic models, many of which are formulated as traditional optimization problems. However, transportation networks are dynamic because their usage varies over time. Thus, more appropriate methods to characterize the vulnerability of transportation networks should consider their dynamic properties. This paper presents a quantitative approach to assess the vulnerability of a transportation network to disruptions with methods from traffic simulation. Our approach can prioritize the critical links over time and is generalizable to the case where both link and node disruptions are of concern. We illustrate the approach through a series of examples. Our results demonstrate that the approach provides quantitative insight into the time varying criticality of links. Such an approach could be used as the objective function of less traditional optimization methods that use simulation and other techniques to evaluate the relative utility of a particular network defense to reduce vulnerability and increase resilience.« less

Orthoclinostatic test as one of the methods for evaluating the human functional state

NASA Technical Reports Server (NTRS)

Doskin, V. A.; Gissen, L. D.; Bomshteyn, O. Z.; Merkin, E. N.; Sarychev, S. B.

1980-01-01

The possible use of different methods to evaluate the autonomic regulation in hygienic studies were examined. The simplest and most objective tests were selected. It is shown that the use of the optimized standards not only makes it possible to detect earlier unfavorables shifts, but also permits a quantitative characterization of the degree of impairment in the state of the organism. Precise interpretation of the observed shifts is possible. Results indicate that the standards can serve as one of the criteria for evaluating the state and can be widely used in hygienic practice.

Quantitative characterization of the atomic-scale structure of oxyhydroxides in rusts formed on steel surfaces

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

Saito, M.; Suzuki, S.; Kimura, M.

Quantitative X-ray structural analysis coupled with anomalous X-ray scattering has been used for characterizing the atomic-scale structure of rust formed on steel surfaces. Samples were prepared from rust layers formed on the surfaces of two commercial steels. X-ray scattered intensity profiles of the two samples showed that the rusts consisted mainly of two types of ferric oxyhydroxide, {alpha}-FeOOH and {gamma}-FeOOH. The amounts of these rust components and the realistic atomic arrangements in the components were estimated by fitting both the ordinary and the environmental interference functions with a model structure calculated using the reverse Monte Carlo simulation technique. The twomore » rust components were found to be the network structure formed by FeO{sub 6} octahedral units, the network structure itself deviating from the ideal case. The present results also suggest that the structural analysis method using anomalous X-ray scattering and the reverse Monte Carlo technique is very successful in determining the atomic-scale structure of rusts formed on the steel surfaces.« less

Characterization of Colloidal Quantum Dot Ligand Exchange by X-ray Photoelectron Spectroscopy

NASA Astrophysics Data System (ADS)

Atewologun, Ayomide; Ge, Wangyao; Stiff-Roberts, Adrienne D.

2013-05-01

Colloidal quantum dots (CQDs) are chemically synthesized semiconductor nanoparticles with size-dependent wavelength tunability. Chemical synthesis of CQDs involves the attachment of long organic surface ligands to prevent aggregation; however, these ligands also impede charge transport. Therefore, it is beneficial to exchange longer surface ligands for shorter ones for optoelectronic devices. Typical characterization techniques used to analyze surface ligand exchange include Fourier-transform infrared spectroscopy, x-ray diffraction, transmission electron microscopy, and nuclear magnetic resonance spectroscopy, yet these techniques do not provide a simultaneously direct, quantitative, and sensitive method for evaluating surface ligands on CQDs. In contrast, x-ray photoelectron spectroscopy (XPS) can provide nanoscale sensitivity for quantitative analysis of CQD surface ligand exchange. A unique aspect of this work is that a fingerprint is identified for shorter surface ligands by resolving the regional XPS spectrum corresponding to different types of carbon bonds. In addition, a deposition technique known as resonant infrared matrix-assisted pulsed laser evaporation is used to improve the CQD film uniformity such that stronger XPS signals are obtained, enabling more accurate analysis of the ligand exchange process.

Quantitative Ultrasound for Nondestructive Characterization of Engineered Tissues and Biomaterials

PubMed Central

Dalecki, Diane; Mercado, Karla P.; Hocking, Denise C.

2015-01-01

Non-invasive, non-destructive technologies for imaging and quantitatively monitoring the development of artificial tissues are critical for the advancement of tissue engineering. Current standard techniques for evaluating engineered tissues, including histology, biochemical assays and mechanical testing, are destructive approaches. Ultrasound is emerging as a valuable tool for imaging and quantitatively monitoring the properties of engineered tissues and biomaterials longitudinally during fabrication and post-implantation. Ultrasound techniques are rapid, non-invasive, non-destructive and can be easily integrated into sterile environments necessary for tissue engineering. Furthermore, high-frequency quantitative ultrasound techniques can enable volumetric characterization of the structural, biological, and mechanical properties of engineered tissues during fabrication and post-implantation. This review provides an overview of ultrasound imaging, quantitative ultrasound techniques, and elastography, with representative examples of applications of these ultrasound-based techniques to the field of tissue engineering. PMID:26581347

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

PubMed Central

Kumawat, Giriraj; Gupta, Sanjay; Ratnaparkhe, Milind B.; Maranna, Shivakumar; Satpute, Gyanesh K.

2016-01-01

Food legumes play an important role in attaining both food and nutritional security along with sustainable agricultural production for the well-being of humans globally. The various traits of economic importance in legume crops are complex and quantitative in nature, which are governed by quantitative trait loci (QTLs). Mapping of quantitative traits is a tedious and costly process, however, a large number of QTLs has been mapped in soybean for various traits albeit their utilization in breeding programmes is poorly reported. For their effective use in breeding programme it is imperative to narrow down the confidence interval of QTLs, to identify the underlying genes, and most importantly allelic characterization of these genes for identifying superior variants. In the field of functional genomics, especially in the identification and characterization of gene responsible for quantitative traits, soybean is far ahead from other legume crops. The availability of genic information about quantitative traits is more significant because it is easy and effective to identify homologs than identifying shared syntenic regions in other crop species. In soybean, genes underlying QTLs have been identified and functionally characterized for phosphorous efficiency, flowering and maturity, pod dehiscence, hard-seededness, α-Tocopherol content, soybean cyst nematode, sudden death syndrome, and salt tolerance. Candidate genes have also been identified for many other quantitative traits for which functional validation is required. Using the sequence information of identified genes from soybean, comparative genomic analysis of homologs in other legume crops could discover novel structural variants and useful alleles for functional marker development. The functional markers may be very useful for molecular breeding in soybean and harnessing benefit of translational research from soybean to other leguminous crops. Thus, soybean crop can act as a model crop for translational genomics and breeding of quantitative traits in legume crops. In this review, we summarize current status of identification and characterization of genes underlying QTLs for various quantitative traits in soybean and their significance in translational genomics and breeding of other legume crops. PMID:28066449

High-throughput 3D whole-brain quantitative histopathology in rodents

PubMed Central

Vandenberghe, Michel E.; Hérard, Anne-Sophie; Souedet, Nicolas; Sadouni, Elmahdi; Santin, Mathieu D.; Briet, Dominique; Carré, Denis; Schulz, Jocelyne; Hantraye, Philippe; Chabrier, Pierre-Etienne; Rooney, Thomas; Debeir, Thomas; Blanchard, Véronique; Pradier, Laurent; Dhenain, Marc; Delzescaux, Thierry

2016-01-01

Histology is the gold standard to unveil microscopic brain structures and pathological alterations in humans and animal models of disease. However, due to tedious manual interventions, quantification of histopathological markers is classically performed on a few tissue sections, thus restricting measurements to limited portions of the brain. Recently developed 3D microscopic imaging techniques have allowed in-depth study of neuroanatomy. However, quantitative methods are still lacking for whole-brain analysis of cellular and pathological markers. Here, we propose a ready-to-use, automated, and scalable method to thoroughly quantify histopathological markers in 3D in rodent whole brains. It relies on block-face photography, serial histology and 3D-HAPi (Three Dimensional Histology Analysis Pipeline), an open source image analysis software. We illustrate our method in studies involving mouse models of Alzheimer’s disease and show that it can be broadly applied to characterize animal models of brain diseases, to evaluate therapeutic interventions, to anatomically correlate cellular and pathological markers throughout the entire brain and to validate in vivo imaging techniques. PMID:26876372

Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations

PubMed Central

Higgs, Richard E.; Butler, Jon P.; Han, Bomie; Knierman, Michael D.

2013-01-01

Recent improvements in the mass accuracy and resolution of mass spectrometers have led to renewed interest in label-free quantification using data from the primary mass spectrum (MS1) acquired from data-dependent proteomics experiments. The capacity for higher specificity quantification of peptides from samples enriched for proteins of biological interest offers distinct advantages for hypothesis generating experiments relative to immunoassay detection methods or prespecified peptide ions measured by multiple reaction monitoring (MRM) approaches. Here we describe an evaluation of different methods to post-process peptide level quantification information to support protein level inference. We characterize the methods by examining their ability to recover a known dilution of a standard protein in background matrices of varying complexity. Additionally, the MS1 quantification results are compared to a standard, targeted, MRM approach on the same samples under equivalent instrument conditions. We show the existence of multiple peptides with MS1 quantification sensitivity similar to the best MRM peptides for each of the background matrices studied. Based on these results we provide recommendations on preferred approaches to leveraging quantitative measurements of multiple peptides to improve protein level inference. PMID:23710359

Quantitative assessment of image motion blur in diffraction images of moving biological cells

NASA Astrophysics Data System (ADS)

Wang, He; Jin, Changrong; Feng, Yuanming; Qi, Dandan; Sa, Yu; Hu, Xin-Hua

2016-02-01

Motion blur (MB) presents a significant challenge for obtaining high-contrast image data from biological cells with a polarization diffraction imaging flow cytometry (p-DIFC) method. A new p-DIFC experimental system has been developed to evaluate the MB and its effect on image analysis using a time-delay-integration (TDI) CCD camera. Diffraction images of MCF-7 and K562 cells have been acquired with different speed-mismatch ratios and compared to characterize MB quantitatively. Frequency analysis of the diffraction images shows that the degree of MB can be quantified by bandwidth variations of the diffraction images along the motion direction. The analytical results were confirmed by the p-DIFC image data acquired at different speed-mismatch ratios and used to validate a method of numerical simulation of MB on blur-free diffraction images, which provides a useful tool to examine the blurring effect on diffraction images acquired from the same cell. These results provide insights on the dependence of diffraction image on MB and allow significant improvement on rapid biological cell assay with the p-DIFC method.

Electrochemical Quartz Crystal Microbalance with Dissipation Real-Time Hydrodynamic Spectroscopy of Porous Solids in Contact with Liquids.

PubMed

Sigalov, Sergey; Shpigel, Netanel; Levi, Mikhael D; Feldberg, Moshe; Daikhin, Leonid; Aurbach, Doron

2016-10-18

Using multiharmonic electrochemical quartz crystal microbalance with dissipation (EQCM-D) monitoring, a new method of characterization of porous solids in contact with liquids has been developed. The dynamic gravimetric information on the growing, dissolving, or stationary stored solid deposits is supplemented by their precise in-operando porous structure characterization on a mesoscopic scale. We present a very powerful method of quartz-crystal admittance modeling of hydrodynamic solid-liquid interactions in order to extract the porous structure parameters of solids during their formation in real time, using different deposition modes. The unique hydrodynamic spectroscopic characterization of electrolytic and rf-sputtered solid Cu coatings that we use for our "proof of concept" provides a new strategy for probing various electrochemically active thin and thick solid deposits, thereby offering inexpensive, noninvasive, and highly efficient quantitative control over their properties. A broad spectrum of applications of our method is proposed, from various metal electroplating and finishing technologies to deeper insight into dynamic build-up and subsequent development of solid-electrolyte interfaces in the operation of Li-battery electrodes, as well as monitoring hydrodynamic consequences of metal corrosion, and growth of biomass coatings (biofouling) on different solid surfaces in seawater.

Purity Determination by Capillary Electrophoresis Sodium Hexadecyl Sulfate (CE-SHS): A Novel Application For Therapeutic Protein Characterization.

PubMed

Beckman, Jeff; Song, Yuanli; Gu, Yan; Voronov, Sergey; Chennamsetty, Naresh; Krystek, Stanley; Mussa, Nesredin; Li, Zheng Jian

2018-02-20

Capillary gel electrophoresis using sodium dodecyl sulfate (CE-SDS) is used commercially to provide quantitative purity data for therapeutic protein characterization and release. In CE-SDS, proteins are denatured under reducing or nonreducing conditions in the presence of SDS and electrophoretically separated by molecular weight and hydrodynamic radius through a sieving polymer matrix. Acceptable performance of this method would yield protein peaks that are baseline resolved and symmetrical. Nominal CE-SDS conditions and parameters are not optimal for all therapeutic proteins, specifically for Recombinant Therapeutic Protein-1 (RTP-1), where acceptable resolution and peak symmetry were not achieved. The application of longer alkyl chain detergents in the running buffer matrix substantially improved assay performance. Matrix running buffer containing sodium hexadecyl sulfate (SHS) increased peak resolution and plate count 3- and 8-fold, respectively, compared to a traditional SDS-based running gel matrix. At Bristol-Myers Squibb (BMS), we developed and qualified a viable method for the characterization and release of RTP-1 using an SHS-containing running buffer matrix. This work underscores the potential of detergents other than SDS to enhance the resolution and separation power of CE-based separation methods.

Characterization of phenolic compounds and antinociceptive activity of Sempervivum tectorum L. leaf juice.

PubMed

Alberti, Ágnes; Béni, Szabolcs; Lackó, Erzsébet; Riba, Pál; Al-Khrasani, Mahmoud; Kéry, Ágnes

2012-11-01

Sempervivum tectorum L. (houseleek) leaf juice has been known as a traditional herbal remedy. The aim of the present study was the chemical characterization of its phenolic compounds and to develop quantitation methods for its main flavonol glycoside, as well as to evaluate its antinociceptive activity. Lyophilized houseleek leaf juice was studied by HPLC-DAD coupled to electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) to identify flavonol glycosides, hydroxy-benzoic and hydroxy-cinnamic acids. Ten flavonol glycosides and sixteen phenolic acid compounds were identified or tentatively characterized. Structure of the main flavonol compound was identified by nuclear magnetic resonance spectroscopy. Three characteristic kaempferol glycosides were isolated and determined by LC-ESI-MS/MS with external calibration method, using the isolated compounds as standard. The main flavonol glycoside was also determined by HPLC-DAD. Validated HPLC-DAD and LC-ESI-MS/MS methods were developed to quantify kaempferol-3-O-rhamnosyl-glucoside-7-O-rhamnoside and two other kaempferol glycosides. Antinociceptive activity of houseleek leaf juice was investigated by writhing test of mice. Sempervivum extract significantly reduced pain in the mouse writhing test. Copyright © 2012 Elsevier B.V. All rights reserved.

Identification and Quantitation of Flavanols and Proanthocyanidins in Foods: How Good are the Datas?

PubMed Central

Kelm, Mark A.; Hammerstone, John F.; Schmitz, Harold H.

2005-01-01

Evidence suggesting that dietary polyphenols, flavanols, and proanthocyanidins in particular offer significant cardiovascular health benefits is rapidly increasing. Accordingly, reliable and accurate methods are needed to provide qualitative and quantitative food composition data necessary for high quality epidemiological and clinical research. Measurements for flavonoids and proanthocyanidins have employed a range of analytical techniques, with various colorimetric assays still being popular for estimating total polyphenolic content in foods and other biological samples despite advances made with more sophisticated analyses. More crudely, estimations of polyphenol content as well as antioxidant activity are also reported with values relating to radical scavenging activity. High-performance liquid chromatography (HPLC) is the method of choice for quantitative analysis of individual polyphenols such as flavanols and proanthocyanidins. Qualitative information regarding proanthocyanidin structure has been determined by chemical methods such as thiolysis and by HPLC-mass spectrometry (MS) techniques at present. The lack of appropriate standards is the single most important factor that limits the aforementioned analyses. However, with ever expanding research in the arena of flavanols, proanthocyanidins, and health and the importance of their future inclusion in food composition databases, the need for standards becomes more critical. At present, sufficiently well-characterized standard material is available for selective flavanols and proanthocyanidins, and construction of at least a limited food composition database is feasible. PMID:15712597

Scaling Linguistic Characterization of Precipitation Variability

NASA Astrophysics Data System (ADS)

Primo, C.; Gutierrez, J. M.

2003-04-01

Rainfall variability is influenced by changes in the aggregation of daily rainfall. This problem is of great importance for hydrological, agricultural and ecological applications. Rainfall averages, or accumulations, are widely used as standard climatic parameters. However different aggregation schemes may lead to the same average or accumulated values. In this paper we present a fractal method to characterize different aggregation schemes. The method provides scaling exponents characterizing weekly or monthly rainfall patterns for a given station. To this aim, we establish an analogy with linguistic analysis, considering precipitation as a discrete variable (e.g., rain, no rain). Each weekly, or monthly, symbolic precipitation sequence of observed precipitation is then considered as a "word" (in this case, a binary word) which defines a specific weekly rainfall pattern. Thus, each site defines a "language" characterized by the words observed in that site during a period representative of the climatology. Then, the more variable the observed weekly precipitation sequences, the more complex the obtained language. To characterize these languages, we first applied the Zipf's method obtaining scaling histograms of rank ordered frequencies. However, to obtain significant exponents, the scaling must be maintained some orders of magnitude, requiring long sequences of daily precipitation which are not available at particular stations. Thus this analysis is not suitable for applications involving particular stations (such as regionalization). Then, we introduce an alternative fractal method applicable to data from local stations. The so-called Chaos-Game method uses Iterated Function Systems (IFS) for graphically representing rainfall languages, in a way that complex languages define complex graphical patterns. The box-counting dimension and the entropy of the resulting patterns are used as linguistic parameters to quantitatively characterize the complexity of the patterns. We illustrate the high climatological discrimination power of the linguistic parameters in the Iberian peninsula, when compared with other standard techniques (such as seasonal mean accumulated precipitation). As an example, standard and linguistic parameters are used as inputs for a clustering regionalization method, comparing the resulting clusters.

Methods for the physical characterization and quantification of extracellular vesicles in biological samples.

PubMed

Rupert, Déborah L M; Claudio, Virginia; Lässer, Cecilia; Bally, Marta

2017-01-01

Our body fluids contain a multitude of cell-derived vesicles, secreted by most cell types, commonly referred to as extracellular vesicles. They have attracted considerable attention for their function as intercellular communication vehicles in a broad range of physiological processes and pathological conditions. Extracellular vesicles and especially the smallest type, exosomes, have also generated a lot of excitement in view of their potential as disease biomarkers or as carriers for drug delivery. In this context, state-of-the-art techniques capable of comprehensively characterizing vesicles in biological fluids are urgently needed. This review presents the arsenal of techniques available for quantification and characterization of physical properties of extracellular vesicles, summarizes their working principles, discusses their advantages and limitations and further illustrates their implementation in extracellular vesicle research. The small size and physicochemical heterogeneity of extracellular vesicles make their physical characterization and quantification an extremely challenging task. Currently, structure, size, buoyant density, optical properties and zeta potential have most commonly been studied. The concentration of vesicles in suspension can be expressed in terms of biomolecular or particle content depending on the method at hand. In addition, common quantification methods may either provide a direct quantitative measurement of vesicle concentration or solely allow for relative comparison between samples. The combination of complementary methods capable of detecting, characterizing and quantifying extracellular vesicles at a single particle level promises to provide new exciting insights into their modes of action and to reveal the existence of vesicle subpopulations fulfilling key biological tasks. Copyright © 2016 Elsevier B.V. All rights reserved.

[Lithology feature extraction of CASI hyperspectral data based on fractal signal algorithm].

PubMed

Tang, Chao; Chen, Jian-Ping; Cui, Jing; Wen, Bo-Tao

2014-05-01

Hyperspectral data is characterized by combination of image and spectrum and large data volume dimension reduction is the main research direction. Band selection and feature extraction is the primary method used for this objective. In the present article, the authors tested methods applied for the lithology feature extraction from hyperspectral data. Based on the self-similarity of hyperspectral data, the authors explored the application of fractal algorithm to lithology feature extraction from CASI hyperspectral data. The "carpet method" was corrected and then applied to calculate the fractal value of every pixel in the hyperspectral data. The results show that fractal information highlights the exposed bedrock lithology better than the original hyperspectral data The fractal signal and characterized scale are influenced by the spectral curve shape, the initial scale selection and iteration step. At present, research on the fractal signal of spectral curve is rare, implying the necessity of further quantitative analysis and investigation of its physical implications.

Multipulse technique exploiting the intermodulation of ultrasound waves in a nonlinear medium.

PubMed

Biagi, Elena; Breschi, Luca; Vannacci, Enrico; Masotti, Leonardo

2009-03-01

In recent years, the nonlinear properties of materials have attracted much interest in nondestructive testing and in ultrasound diagnostic applications. Acoustic nonlinear parameters represent an opportunity to improve the information that can be extracted from a medium such as structural organization and pathologic status of tissue. In this paper, a method called pulse subtraction intermodulation (PSI), based on a multipulse technique, is presented and investigated both theoretically and experimentally. This method allows separation of the intermodulation products, which arise when 2 separate frequencies are transmitted in a nonlinear medium, from fundamental and second harmonic components, making them available for improved imaging techniques or signal processing algorithms devoted to tissue characterization. The theory of intermodulation product generation was developed according the Khokhlov-Zabolotskaya-Kuznetsov (KZK) nonlinear propagation equation, which is consistent with experimental results. The description of the proposed method, characterization of the intermodulation spectral contents, and quantitative results coming from in vitro experimentation are reported and discussed in this paper.

eSIP: A Novel Solution-Based Sectioned Image Property Approach for Microscope Calibration

PubMed Central

Butzlaff, Malte; Weigel, Arwed; Ponimaskin, Evgeni; Zeug, Andre

2015-01-01

Fluorescence confocal microscopy represents one of the central tools in modern sciences. Correspondingly, a growing amount of research relies on the development of novel microscopic methods. During the last decade numerous microscopic approaches were developed for the investigation of various scientific questions. Thereby, the former qualitative imaging methods became replaced by advanced quantitative methods to gain more and more information from a given sample. However, modern microscope systems being as complex as they are, require very precise and appropriate calibration routines, in particular when quantitative measurements should be compared over longer time scales or between different setups. Multispectral beads with sub-resolution size are often used to describe the point spread function and thus the optical properties of the microscope. More recently, a fluorescent layer was utilized to describe the axial profile for each pixel, which allows a spatially resolved characterization. However, fabrication of a thin fluorescent layer with matching refractive index is technically not solved yet. Therefore, we propose a novel type of calibration concept for sectioned image property (SIP) measurements which is based on fluorescent solution and makes the calibration concept available for a broader number of users. Compared to the previous approach, additional information can be obtained by application of this extended SIP chart approach, including penetration depth, detected number of photons, and illumination profile shape. Furthermore, due to the fit of the complete profile, our method is less susceptible to noise. Generally, the extended SIP approach represents a simple and highly reproducible method, allowing setup independent calibration and alignment procedures, which is mandatory for advanced quantitative microscopy. PMID:26244982

A novel orellanine containing mushroom Cortinarius armillatus.

PubMed

Shao, Dahai; Tang, Shusheng; Healy, Rosanne A; Imerman, Paula M; Schrunk, Dwayne E; Rumbeiha, Wilson K

2016-05-01

Orellanine (3,3',4,4'-tetrahydroxy-2,2'-bipyridine-1,1'-dioxide) is a tetrahydroxylated di-N-oxidized bipyridine compound. The toxin, present in certain species of Cortinarius mushrooms, is structurally similar to herbicides Paraquat and Diquat. Cortinarius orellanus and Cortinarius rubellus are the major orellanine-containing mushrooms. Cortinarius mushrooms are widely reported in Europe where they have caused human poisoning and deaths through accidental ingestion of the poisonous species mistaken for the edible ones. In North America, Cortinarius orellanosus mushroom poisoning was recently reported to cause renal failure in a Michigan patient. Cortinarius mushroom poisoning is characterized by delayed acute renal failure, with some cases progressing to end-stage kidney disease. There is debate whether other Cortinarius mushroom contain orellanine or not, especially in North America. Currently, there are no veterinary diagnostic laboratories in North America with established test methods for detection and quantitation of orellanine. We have developed two diagnostic test methods based on HPLC and LC-MSMS for identification and quantitation of orellanine in mushrooms. Using these methods, we have identified Cortinarius armillatus as a novel orellanine-containing mushroom in North America. The mean toxin concentration of 145 ug/g was <1% of that of the more toxic C. rubellus. The HPLC method can detect orellanine at 17 μg g(-1) while the LC-MSMS method is almost 2000 times more sensitive and can detect orellanine at 30 ng g(-1). Both tests are quantitative, selective and are now available for veterinary diagnostic applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Super-resolved calibration-free flow cytometric characterization of platelets and cell-derived microparticles in platelet-rich plasma.

PubMed

Konokhova, Anastasiya I; Chernova, Darya N; Moskalensky, Alexander E; Strokotov, Dmitry I; Yurkin, Maxim A; Chernyshev, Andrei V; Maltsev, Valeri P

2016-02-01

Importance of microparticles (MPs), also regarded as extracellular vesicles, in many physiological processes and clinical conditions motivates one to use the most informative and precise methods for their characterization. Methods based on individual particle analysis provide statistically reliable distributions of MP population over characteristics. Although flow cytometry is one of the most powerful technologies of this type, the standard forward-versus-side-scattering plots of MPs and platelets (PLTs) overlap considerably because of similarity of their morphological characteristics. Moreover, ordinary flow cytometry is not capable of measurement of size and refractive index (RI) of MPs. In this study, we 1) employed the potential of the scanning flow cytometer (SFC) for identification and characterization of MPs from light scattering; 2) suggested the reference method to characterize MP morphology (size and RI) with high precision; and 3) determined the lowest size of a MP that can be characterized from light scattering with the SFC. We equipped the SFC with 405 and 488 nm lasers to measure the light-scattering profiles and side scattering from MPs, respectively. The developed two-stage method allowed accurate separation of PLTs and MPs in platelet-rich plasma. We used two optical models for MPs, a sphere and a bisphere, in the solution of the inverse light-scattering problem. This solution provides unprecedented precision in determination of size and RI of individual spherical MPs-median uncertainties (standard deviations) were 6 nm and 0.003, respectively. The developed method provides instrument-independent quantitative information on MPs, which can be used in studies of various factors affecting MP population. © 2015 International Society for Advancement of Cytometry.

Characterization of organic matter of plants from lakes by thermal analysis in a N2 atmosphere

NASA Astrophysics Data System (ADS)

Guo, Fei; Wu, Fengchang; Mu, Yunsong; Hu, Yan; Zhao, Xiaoli; Meng, Wei; Giesy, John P.; Lin, Ying

2016-03-01

Organic matter (OM) has been characterized using thermal analysis in O2 atmospheres, but it is not clear if OM can be characterized using slow thermal degradation in N2 atmospheres (STDN). This article presents a new method to estimate the behavior of OM in anaerobic environment. Seventeen different plants from Tai Lake (Ch: Taihu), China were heated to 600 °C at a rate of 10 °C min-1 in a N2 atmosphere and characterized by use of differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA). DSC chromatograms were compared with 9 standard compounds. Seven peaks were observed in DSC chromatograms, 2 main peaks strongly correlated with biochemical indices, and one main peak was a transitional stage. Energy absorbed by a peak at approximately 200 °C and total organic carbon were well correlated, while energy absorbed at approximately 460 °C was negatively correlated with lignin content. Presence of peaks at approximately 350 and 420 °C varied among plant biomass sources, providing potential evidence for biomass identification. Methods of STDN reported here were rapid and accurate ways to quantitatively characterize OM, which may provide useful information for understanding anaerobic behaviors of natural organic matters.

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

PubMed Central

Shepard, Peter J.; Choi, Eun-A; Lu, Jente; Flanagan, Lisa A.; Hertel, Klemens J.; Shi, Yongsheng

2011-01-01

Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. PAS-Seq analyses of human and mouse transcriptomes showed that 40%–50% of all expressed genes produce alternatively polyadenylated mRNAs. Furthermore, our study detected evolutionarily conserved polyadenylation of histone mRNAs and revealed novel features of mitochondrial RNA polyadenylation. Finally, PAS-Seq analyses of mouse embryonic stem (ES) cells, neural stem/progenitor (NSP) cells, and neurons not only identified more poly(A) sites than what was found in the entire mouse EST database, but also detected significant changes in the global APA profile that lead to lengthening of 3′ untranslated regions (UTR) in many mRNAs during stem cell differentiation. Together, our PAS-Seq analyses revealed a complex landscape of RNA polyadenylation in mammalian cells and the dynamic regulation of APA during stem cell differentiation. PMID:21343387

Comparison of three‐dimensional analysis and stereological techniques for quantifying lithium‐ion battery electrode microstructures

PubMed Central

TAIWO, OLUWADAMILOLA O.; FINEGAN, DONAL P.; EASTWOOD, DAVID S.; FIFE, JULIE L.; BROWN, LEON D.; DARR, JAWWAD A.; LEE, PETER D.; BRETT, DANIEL J.L.

2016-01-01

Summary Lithium‐ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium‐ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3‐D imaging techniques, quantitative assessment of 3‐D microstructures from 2‐D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two‐dimensional (2‐D) data sets. In this study, stereological prediction and three‐dimensional (3‐D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium‐ion battery electrodes were imaged using synchrotron‐based X‐ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2‐D image sections generated from tomographic imaging, whereas direct 3‐D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2‐D image sections is bound to be associated with ambiguity and that volume‐based 3‐D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially‐dependent parameters, such as tortuosity and pore‐phase connectivity. PMID:26999804

Comparison of three-dimensional analysis and stereological techniques for quantifying lithium-ion battery electrode microstructures.

PubMed

Taiwo, Oluwadamilola O; Finegan, Donal P; Eastwood, David S; Fife, Julie L; Brown, Leon D; Darr, Jawwad A; Lee, Peter D; Brett, Daniel J L; Shearing, Paul R

2016-09-01

Lithium-ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium-ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3-D imaging techniques, quantitative assessment of 3-D microstructures from 2-D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two-dimensional (2-D) data sets. In this study, stereological prediction and three-dimensional (3-D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium-ion battery electrodes were imaged using synchrotron-based X-ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2-D image sections generated from tomographic imaging, whereas direct 3-D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2-D image sections is bound to be associated with ambiguity and that volume-based 3-D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially-dependent parameters, such as tortuosity and pore-phase connectivity. © 2016 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.

Analysis of Membrane Lipids of Airborne Micro-Organisms

NASA Technical Reports Server (NTRS)

MacNaughton, Sarah

2006-01-01

A method of characterization of airborne micro-organisms in a given location involves (1) large-volume filtration of air onto glass-fiber filters; (2) accelerated extraction of membrane lipids of the collected micro-organisms by use of pressurized hot liquid; and (3) identification and quantitation of the lipids by use of gas chromatography and mass spectrometry. This method is suitable for use in both outdoor and indoor environments; for example, it can be used to measure airborne microbial contamination in buildings ("sick-building syndrome"). The classical approach to analysis of airborne micro-organisms is based on the growth of cultureable micro-organisms and does not provide an account of viable but noncultureable micro-organisms, which typically amount to more than 90 percent of the micro-organisms present. In contrast, the present method provides an account of all micro-organisms, including cultureable, noncultureable, aerobic, and anaerobic ones. The analysis of lipids according to this method makes it possible to estimate the number of viable airborne micro-organisms present in the sampled air and to obtain a quantitative profile of the general types of micro-organisms present along with some information about their physiological statuses.

Comparison of Metabolomics Approaches for Evaluating the Variability of Complex Botanical Preparations: Green Tea (Camellia sinensis) as a Case Study.

PubMed

Kellogg, Joshua J; Graf, Tyler N; Paine, Mary F; McCune, Jeannine S; Kvalheim, Olav M; Oberlies, Nicholas H; Cech, Nadja B

2017-05-26

A challenge that must be addressed when conducting studies with complex natural products is how to evaluate their complexity and variability. Traditional methods of quantifying a single or a small range of metabolites may not capture the full chemical complexity of multiple samples. Different metabolomics approaches were evaluated to discern how they facilitated comparison of the chemical composition of commercial green tea [Camellia sinensis (L.) Kuntze] products, with the goal of capturing the variability of commercially used products and selecting representative products for in vitro or clinical evaluation. Three metabolomic-related methods-untargeted ultraperformance liquid chromatography-mass spectrometry (UPLC-MS), targeted UPLC-MS, and untargeted, quantitative 1 HNMR-were employed to characterize 34 commercially available green tea samples. Of these methods, untargeted UPLC-MS was most effective at discriminating between green tea, green tea supplement, and non-green-tea products. A method using reproduced correlation coefficients calculated from principal component analysis models was developed to quantitatively compare differences among samples. The obtained results demonstrated the utility of metabolomics employing UPLC-MS data for evaluating similarities and differences between complex botanical products.

Quantitative Method to Investigate the Balance between Metabolism and Proteome Biomass: Starting from Glycine.

PubMed

Gu, Haiwei; Carroll, Patrick A; Du, Jianhai; Zhu, Jiangjiang; Neto, Fausto Carnevale; Eisenman, Robert N; Raftery, Daniel

2016-12-12

The balance between metabolism and biomass is very important in biological systems; however, to date there has been no quantitative method to characterize the balance. In this methodological study, we propose to use the distribution of amino acids in different domains to investigate this balance. It is well known that endogenous or exogenous amino acids in a biological system are either metabolized or incorporated into free amino acids (FAAs) or proteome amino acids (PAAs). Using glycine (Gly) as an example, we demonstrate a novel method to accurately determine the amounts of amino acids in various domains using serum, urine, and cell samples. As expected, serum and urine had very different distributions of FAA- and PAA-Gly. Using Tet21N human neuroblastoma cells, we also found that Myc(oncogene)-induced metabolic reprogramming included a higher rate of metabolizing Gly, which provides additional evidence that the metabolism of proliferating cells is adapted to facilitate producing new cells. It is therefore anticipated that our method will be very valuable for further studies of the metabolism and biomass balance that will lead to a better understanding of human cancers. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative measurement of phosphoproteome response to osmotic stress in arabidopsis based on Library-Assisted eXtracted Ion Chromatogram (LAXIC).

PubMed

Xue, Liang; Wang, Pengcheng; Wang, Lianshui; Renzi, Emily; Radivojac, Predrag; Tang, Haixu; Arnold, Randy; Zhu, Jian-Kang; Tao, W Andy

2013-08-01

Global phosphorylation changes in plants in response to environmental stress have been relatively poorly characterized to date. Here we introduce a novel mass spectrometry-based label-free quantitation method that facilitates systematic profiling plant phosphoproteome changes with high efficiency and accuracy. This method employs synthetic peptide libraries tailored specifically as internal standards for complex phosphopeptide samples and accordingly, a local normalization algorithm, LAXIC, which calculates phosphopeptide abundance normalized locally with co-eluting library peptides. Normalization was achieved in a small time frame centered to each phosphopeptide to compensate for the diverse ion suppression effect across retention time. The label-free LAXIC method was further treated with a linear regression function to accurately measure phosphoproteome responses to osmotic stress in Arabidopsis. Among 2027 unique phosphopeptides identified and 1850 quantified phosphopeptides in Arabidopsis samples, 468 regulated phosphopeptides representing 497 phosphosites have shown significant changes. Several known and novel components in the abiotic stress pathway were identified, illustrating the capability of this method to identify critical signaling events among dynamic and complex phosphorylation. Further assessment of those regulated proteins may help shed light on phosphorylation response to osmotic stress in plants.

Identification, characterization and quantitation of pyrogenic polycylic aromatic hydrocarbons and other organic compounds in tire fire products.

PubMed

Wang, Zhendi; Li, K; Lambert, P; Yang, Chun

2007-01-12

On 15 August 2001, a tire fire took place at the Pneu Lavoie Facility in Gatineau, Quebec, in which 4000 to 6000 new and recycled tires were stored along with other potentially hazardous materials. Comprehensive gas chromatography-mass spectrometry (GC-MS) analyses were performed on the tire fire samples to facilitate detailed chemical composition characterization of toxic polycyclic aromatic hydrocarbons (PAHs) and other organic compounds in samples. It is found that significant amounts of PAHs, particularly the high-ring-number PAHs, were generated during the fire. In total, 165 PAH compounds including 13 isomers of molecular weight (MW) 302, 10 isomers of MW 278, 10 isomers of MW 276, 7 isomers of MW 252, 7 isomers of MW 228, and 8 isomers of MW 216 PAHs were positively identified in the tire fire wipe samples for the first time. Numerous S-, O-, and N-containing PAH compounds were also detected. The identification and characterization of the PAH isomers was mainly based on: (1) a positive match of mass spectral data of the PAH isomers with the NIST authentic mass spectra database; (2) a positive match of the GC retention indices (I) of PAHs with authentic standards and with those reported in the literature; (3) agreement of the PAH elution order with the NIST (US National Institute of Standards and Technology) Standard Reference Material 1597 for complex mixture of PAHs from coal tar; (4) a positive match of the distribution patterns of PAH isomers in the SIM mode between the tire fire samples and the NIST Standard Reference Materials and well-characterized reference oils. Quantitation of target PAHs was done on the GC-MS in the selected ion monitoring (SIM) mode using the internal standard method. The relative response factors (RRF) for target PAHs were obtained from analyses of authentic PAH standard compounds. Alkylated PAH homologues were quantitated using straight baseline integration of each level of alkylation.

Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics

PubMed Central

2012-01-01

Multiple reaction monitoring mass spectrometry (MRM-MS) with stable isotope dilution (SID) is increasingly becoming a widely accepted assay for the quantification of proteins and peptides. These assays have shown great promise in relatively high throughput verification of candidate biomarkers. While the use of MRM-MS assays is well established in the small molecule realm, their introduction and use in proteomics is relatively recent. As such, statistical and computational methods for the analysis of MRM-MS data from proteins and peptides are still being developed. Based on our extensive experience with analyzing a wide range of SID-MRM-MS data, we set forth a methodology for analysis that encompasses significant aspects ranging from data quality assessment, assay characterization including calibration curves, limits of detection (LOD) and quantification (LOQ), and measurement of intra- and interlaboratory precision. We draw upon publicly available seminal datasets to illustrate our methods and algorithms. PMID:23176545

Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.

PubMed

Mani, D R; Abbatiello, Susan E; Carr, Steven A

2012-01-01

Multiple reaction monitoring mass spectrometry (MRM-MS) with stable isotope dilution (SID) is increasingly becoming a widely accepted assay for the quantification of proteins and peptides. These assays have shown great promise in relatively high throughput verification of candidate biomarkers. While the use of MRM-MS assays is well established in the small molecule realm, their introduction and use in proteomics is relatively recent. As such, statistical and computational methods for the analysis of MRM-MS data from proteins and peptides are still being developed. Based on our extensive experience with analyzing a wide range of SID-MRM-MS data, we set forth a methodology for analysis that encompasses significant aspects ranging from data quality assessment, assay characterization including calibration curves, limits of detection (LOD) and quantification (LOQ), and measurement of intra- and interlaboratory precision. We draw upon publicly available seminal datasets to illustrate our methods and algorithms.

Multifractal Fluctuations of Jiuzhaigou Tourists Before and after Wenchuan Earthquake

NASA Astrophysics Data System (ADS)

Shi, Kai; Li, Wen-Yong; Liu, Chun-Qiong; Huang, Zheng-Wen

2013-03-01

In this work, multifractal methods have been successfully used to characterize the temporal fluctuations of daily Jiuzhai Valley domestic and foreign tourists before and after Wenchuan earthquake in China. We used multifractal detrending moving average method (MF-DMA). It showed that Jiuzhai Valley tourism markets are characterized by long-term memory and multifractal nature in. Moreover, the major sources of multifractality are studied. Based on the concept of sliding window, the time evolutions of the multifractal behavior of domestic and foreign tourists were analyzed and the influence of Wenchuan earthquake on Jiuzhai Valley tourism system dynamics were evaluated quantitatively. The study indicates that the inherent dynamical mechanism of Jiuzhai Valley tourism system has not been fundamentally changed from long views, although Jiuzhai Valley tourism system was seriously affected by the Wenchuan earthquake. Jiuzhai Valley tourism system has the ability to restore to its previous state in the short term.

Statistical Characterization of Environmental Error Sources Affecting Electronically Scanned Pressure Transducers

NASA Technical Reports Server (NTRS)

Green, Del L.; Walker, Eric L.; Everhart, Joel L.

2006-01-01

Minimization of uncertainty is essential to extend the usable range of the 15-psid Electronically Scanned Pressure [ESP) transducer measurements to the low free-stream static pressures found in hypersonic wind tunnels. Statistical characterization of environmental error sources inducing much of this uncertainty requires a well defined and controlled calibration method. Employing such a controlled calibration system, several studies were conducted that provide quantitative information detailing the required controls needed to minimize environmental and human induced error sources. Results of temperature, environmental pressure, over-pressurization, and set point randomization studies for the 15-psid transducers are presented along with a comparison of two regression methods using data acquired with both 0.36-psid and 15-psid transducers. Together these results provide insight into procedural and environmental controls required for long term high-accuracy pressure measurements near 0.01 psia in the hypersonic testing environment using 15-psid ESP transducers.

Statistical Characterization of Environmental Error Sources Affecting Electronically Scanned Pressure Transducers

NASA Technical Reports Server (NTRS)

Green, Del L.; Walker, Eric L.; Everhart, Joel L.

2006-01-01

Minimization of uncertainty is essential to extend the usable range of the 15-psid Electronically Scanned Pressure (ESP) transducer measurements to the low free-stream static pressures found in hypersonic wind tunnels. Statistical characterization of environmental error sources inducing much of this uncertainty requires a well defined and controlled calibration method. Employing such a controlled calibration system, several studies were conducted that provide quantitative information detailing the required controls needed to minimize environmental and human induced error sources. Results of temperature, environmental pressure, over-pressurization, and set point randomization studies for the 15-psid transducers are presented along with a comparison of two regression methods using data acquired with both 0.36-psid and 15-psid transducers. Together these results provide insight into procedural and environmental controls required for long term high-accuracy pressure measurements near 0.01 psia in the hypersonic testing environment using 15-psid ESP transducers.

Using Nano-mechanics and Surface Acoustic Wave (SAW) for Disease Monitoring and Diagnostics at a Cellular Level in Red Blood Cells

NASA Astrophysics Data System (ADS)

Sivanantha, Ninnuja; Ma, Charles; Collins, David J.; Sesen, Muhsincan; Brenker, Jason; Coppel, Ross L.; Neild, Adrian; Alan, Tuncay

A popular approach to monitoring diseases and their diagnosis is through biological, pathological or immunological characterization. However, at a cellular level progression of certain diseases manifests itself through mechanical effects as well. Here, we present a method which exploits localised flow; surface acoustic wave (SAW) induced acoustic streaming in a 9 μL droplet to characterize the adhesive properties of red blood cells (healthy, gluteraldehyde treated and malaria infected) in approximately 50 seconds. Our results show a 79% difference in cell mobilization between healthy malaria infected RBCs (and a 39% difference between healthy and treated ones), indicating that the method can serve as a platform for rapid clinical diagnosis; where separation of two or more different cell populations in a mixed solution is desirable. It can also act as a key biomarker for monitoring some diseases offering quantitative measures of disease progression and response to therapy.

Recombinant G protein-coupled receptor expression in Saccharomyces cerevisiae for protein characterization.

PubMed

Blocker, Kory M; Britton, Zachary T; Naranjo, Andrea N; McNeely, Patrick M; Young, Carissa L; Robinson, Anne S

2015-01-01

G protein-coupled receptors (GPCRs) are membrane proteins that mediate signaling across the cellular membrane and facilitate cellular responses to external stimuli. Due to the critical role that GPCRs play in signal transduction, therapeutics have been developed to influence GPCR function without an extensive understanding of the receptors themselves. Closing this knowledge gap is of paramount importance to improving therapeutic efficacy and specificity, where efforts to achieve this end have focused chiefly on improving our knowledge of the structure-function relationship. The purpose of this chapter is to review methods for the heterologous expression of GPCRs in Saccharomyces cerevisiae, including whole-cell assays that enable quantitation of expression, localization, and function in vivo. In addition, we describe methods for the micellular solubilization of the human adenosine A2a receptor and for reconstitution of the receptor in liposomes that have enabled its biophysical characterization. © 2015 Elsevier Inc. All rights reserved.

Nanoscale surface characterization using laser interference microscopy

NASA Astrophysics Data System (ADS)

Ignatyev, Pavel S.; Skrynnik, Andrey A.; Melnik, Yury A.

2018-03-01

Nanoscale surface characterization is one of the most significant parts of modern materials development and application. The modern microscopes are expensive and complicated tools, and its use for industrial tasks is limited due to laborious sample preparation, measurement procedures, and low operation speed. The laser modulation interference microscopy method (MIM) for real-time quantitative and qualitative analysis of glass, metals, ceramics, and various coatings has a spatial resolution of 0.1 nm for vertical and up to 100 nm for lateral. It is proposed as an alternative to traditional scanning electron microscopy (SEM) and atomic force microscopy (AFM) methods. It is demonstrated that in the cases of roughness metrology for super smooth (Ra >1 nm) surfaces the application of a laser interference microscopy techniques is more optimal than conventional SEM and AFM. The comparison of semiconductor test structure for lateral dimensions measurements obtained with SEM and AFM and white light interferometer also demonstrates the advantages of MIM technique.

Quantitative analysis of phosphoinositide 3-kinase (PI3K) signaling using live-cell total internal reflection fluorescence (TIRF) microscopy.

PubMed

Johnson, Heath E; Haugh, Jason M

2013-12-02

This unit focuses on the use of total internal reflection fluorescence (TIRF) microscopy and image analysis methods to study the dynamics of signal transduction mediated by class I phosphoinositide 3-kinases (PI3Ks) in mammalian cells. The first four protocols cover live-cell imaging experiments, image acquisition parameters, and basic image processing and segmentation. These methods are generally applicable to live-cell TIRF experiments. The remaining protocols outline more advanced image analysis methods, which were developed in our laboratory for the purpose of characterizing the spatiotemporal dynamics of PI3K signaling. These methods may be extended to analyze other cellular processes monitored using fluorescent biosensors. Copyright © 2013 John Wiley & Sons, Inc.

A Quadrupole Dalton-based multi-attribute method for product characterization, process development, and quality control of therapeutic proteins.

PubMed

Xu, Weichen; Jimenez, Rod Brian; Mowery, Rachel; Luo, Haibin; Cao, Mingyan; Agarwal, Nitin; Ramos, Irina; Wang, Xiangyang; Wang, Jihong

2017-10-01

During manufacturing and storage process, therapeutic proteins are subject to various post-translational modifications (PTMs), such as isomerization, deamidation, oxidation, disulfide bond modifications and glycosylation. Certain PTMs may affect bioactivity, stability or pharmacokinetics and pharmacodynamics profile and are therefore classified as potential critical quality attributes (pCQAs). Identifying, monitoring and controlling these PTMs are usually key elements of the Quality by Design (QbD) approach. Traditionally, multiple analytical methods are utilized for these purposes, which is time consuming and costly. In recent years, multi-attribute monitoring methods have been developed in the biopharmaceutical industry. However, these methods combine high-end mass spectrometry with complicated data analysis software, which could pose difficulty when implementing in a quality control (QC) environment. Here we report a multi-attribute method (MAM) using a Quadrupole Dalton (QDa) mass detector to selectively monitor and quantitate PTMs in a therapeutic monoclonal antibody. The result output from the QDa-based MAM is straightforward and automatic. Evaluation results indicate this method provides comparable results to the traditional assays. To ensure future application in the QC environment, this method was qualified according to the International Conference on Harmonization (ICH) guideline and applied in the characterization of drug substance and stability samples. The QDa-based MAM is shown to be an extremely useful tool for product and process characterization studies that facilitates facile understanding of process impact on multiple quality attributes, while being QC friendly and cost-effective.

Vectorial strain gauge method using single flexible orthogonal polydimethylsiloxane gratings

NASA Astrophysics Data System (ADS)

Guo, Hao; Tang, Jun; Qian, Kun; Tsoukalas, Dimitris; Zhao, Miaomiao; Yang, Jiangtao; Zhang, Binzhen; Chou, Xiujian; Liu, Jun; Xue, Chenyang; Zhang, Wendong

2016-03-01

A vectorial strain gauge method using a single sensing element is reported based on the double-sided polydimethylsiloxane (PDMS) Fraunhofer diffraction gratings structures. Using O2 plasma treatment steps, orthogonal wrinkled gratings were fabricated on both sides of a pre-strained PDMS film. Diffracted laser spots from this structure have been used to experimentally demonstrate, that any applied strain can be quantitatively characterized in both the x and y directions with an error of less than 0.6% and with a gauge factor of approximately 10. This simple and low cost technology which is completely different from the traditional vectorial strain gauge method, can be applied to surface vectorial strain measurement and multi-axis integrated mechanical sensors.

Microgravimetric Analysis Method for Activation-Energy Extraction from Trace-Amount Molecule Adsorption.

PubMed

Xu, Pengcheng; Yu, Haitao; Li, Xinxin

2016-05-03

Activation-energy (Ea) value for trace-amount adsorption of gas molecules on material is rapidly and inexpensively obtained, for the first time, from a microgravimetric analysis experiment. With the material loaded, a resonant microcantilever is used to record in real time the adsorption process at two temperatures. The kinetic parameter Ea is thereby extracted by solving the Arrhenius equation. As an example, two CO2 capture nanomaterials are examined by the Ea extracting method for evaluation/optimization and, thereby, demonstrating the applicability of the microgravimetric analysis method. The achievement helps to solve the absence in rapid quantitative characterization of sorption kinetics and opens a new route to investigate molecule adsorption processes and materials.

Program for plasma-sprayed self-lubricating coatings

NASA Technical Reports Server (NTRS)

Walther, G. C.

1979-01-01

A method for preparing composite powders of the three coating components was developed and a procedure that can be used in applying uniform coatings of the composite powders was demonstrated. Composite powders were prepared by adjusting particle sizes of the components and employing a small amount of monoaluminum phosphate as an inorganic binder. Quantitative microscopy (image analysis) was found to be a convenient method of characterizing the composition of the multiphase plasma-sprayed coatings. Area percentages and distribution of the components were readily obtained by this method. The adhesive strength of the coating to a nickel-chromium alloy substrate was increased by about 40 percent by a heat treatment of 20 hours at 650 C.

Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors

PubMed Central

Thakore, Pratiksha I.; Gersbach, Charles A.

2016-01-01

Transcription activator-like effectors (TALEs) are modular DNA-binding proteins that can be fused to a variety of effector domains to regulate the epigenome. Nucleotide recognition by TALE monomers follows a simple cipher, making this a powerful and versatile method to activate or repress gene expression. Described here are methods to design, assemble, and test TALE transcription factors (TALE-TFs) for control of endogenous gene expression. In this protocol, TALE arrays are constructed by Golden Gate cloning and tested for activity by transfection and quantitative RT-PCR. These methods for engineering TALE-TFs are useful for studies in reverse genetics and genomics, synthetic biology, and gene therapy. PMID:26443215

Determination of magneto-optical constant of Fe films with weak measurements

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

Qiu, Xiaodong; Hu, Dejiao; Du, Jinglei

2014-09-29

In this letter, a detecting method for the magneto-optical constant is presented by using weak measurements. The photonic spin Hall effect (PSHE), which manifests itself as spin-dependent splitting, is introduced to characterize the magneto-optical constant, and a propagation model to describe the quantitative relation between the magneto-optical constant and the PSHE is established. According to the amplified shift of the PSHE detected by weak measurements, we determinate the magneto-optical constant of the Fe film sample. The Kerr rotation is measured via the standard polarimetry method to verify the rationality and feasibility of our method. These findings may provide possible applicationsmore » in magnetic physics research.« less

MG63 cells behavior on rough polypyrrole scaffolds investigated by digital holographic microscopy

NASA Astrophysics Data System (ADS)

Mihailescu, M.; Matei, A.; Acasandrei, A.; Popescu, R. C.; Paun, I. A.; Dinescu, Maria

2014-07-01

The study of cells-substrate interaction became a stringent subject in the past decades, since an increasing variety of new materials and methods have been involved in tissue engineering or implants techniques. The investigation of this interaction using optical methods is a challenge, especially since these substrates are not optically polished. Due to their roughness in the micrometric or submicrometric range, the polymeric substrates offers good conditions for cells adhesion, but the characterization of cells properties can be hindered. In this study, we use Polypyrrole thin films, acting as substrates for cultured osteoblast-like MG63 cells having applications in tissue engineering for in vivo-like scaffolds. As characterization technique, we chose digital holographic microscopy, a single-shot technique, to obtain quantitative information about the sample features in a plane perpendicular to the substrate. Different parameters were tested in the experimental setup with the aim of finding the optimal conditions for details visualization. The reconstructed 3D images were filtered using a combination of analytical and implicit functions from MATLAB to exclude small/large objects, which correspond to Polypyrrole droplets to clearly identify the cells contour for quantitative measurements regarding their dimensions. These data were correlated with the effects on osteoblasts viability and differentiation. Also, the thickness and the refractive index of the substrate were determined using the decoupling procedure.

Characterization of the porosity of human dental enamel and shear bond strength in vitro after variable etch times: initial findings using the BET method.

PubMed

Nguyen, Trang T; Miller, Arthur; Orellana, Maria F

2011-07-01

(1) To quantitatively characterize human enamel porosity and surface area in vitro before and after etching for variable etching times; and (2) to evaluate shear bond strength after variable etching times. Specifically, our goal was to identify the presence of any correlation between enamel porosity and shear bond strength. Pore surface area, pore volume, and pore size of enamel from extracted human teeth were analyzed by Brunauer-Emmett-Teller (BET) gas adsorption before and after etching for 15, 30, and 60 seconds with 37% phosphoric acid. Orthodontic brackets were bonded with Transbond to the samples with variable etch times and were subsequently applied to a single-plane lap shear testing system. Pore volume and surface area increased after etching for 15 and 30 seconds. At 60 seconds, this increase was less pronounced. On the contrary, pore size appears to decrease after etching. No correlation was found between variable etching times and shear strength. Samples etched for 15, 30, and 60 seconds all demonstrated clinically viable shear strength values. The BET adsorption method could be a valuable tool in enhancing our understanding of enamel characteristics. Our findings indicate that distinct quantitative changes in enamel pore architecture are evident after etching. Further testing with a larger sample size would have to be carried out for more definitive conclusions to be made.

Quantitative determination of proteins at nanogram levels by the resonance light-scattering technique with macromolecules nanoparticles of PS-AA.

PubMed

Wang, Leyu; Chen, Hongqi; Li, Ling; Xia, Tingting; Dong, Ling; Wang, Lun

2004-03-01

The polystyrene-acrylic acid (PS-AA) nanoparticles have been prepared by ultrasonic polymerization, characterized by FT-IR and TEM. It is the first report on the determination of proteins with macromolecules nanoparticles of PS-AA by resonance light-scattering (RLS). At pH 6.9, the RLS of macromolecules nanoparticles of PS-AA can be enhanced by proteins. Based on this, a novel quantitative assay of proteins at the nanogram levels has been proposed. At pH 6.9, the RLS signals of PS-AA were greatly enhanced by proteins in the region of 250-700 nm characterized by the peak at 342 nm. Under optimal conditions, the linear ranges of the calibration curves were 0.02-11.0 microgml-1, 0.04-10.0 microgml-1 and 0.03-10.0 microgml-1 for gamma-globulin (gamma-IgG), bovine serum albumin (BSA) and human serum albumin (HSA), respectively. The detection limits were 16.0 ngml-1, 19.0 ngml-1, and 15.0 ngml-1 for gamma-IgG, BSA and HSA, respectively. The method has been applied to the analysis of total proteins in human serum samples collected from the hospital and the results were in good agreement with those reported by the hospital, which indicates that the method presented here is not only sensitive, simple, but also reliable and suitable for practical application.

Capillary Electrophoresis Chips for Fingerprinting Endotoxin Chemotypes and Subclasses.

PubMed

Kocsis, Béla; Makszin, Lilla; Kilár, Anikó; Péterfi, Zoltán; Kilár, Ferenc

2017-01-01

Endotoxins (lipopolysaccharides, LPS; lipooligosaccharides, LOS) are components of the envelope of Gram-negative bacteria. These molecules, responsible for both advantageous and harmful biological activity of these microorganisms, are highly immunogenic and directly involved in numerous bacterial diseases in humans, such as Gram-negative sepsis. The characterization of endotoxins is of importance, since their physiological and pathophysiological effects depend on their chemical structure. The differences among the LPS from different bacterial serotypes and their mutants include variations mainly within the composition and length or missing of their O-polysaccharide chains. Microchip electrophoretic methodology enables the structural characterization of LPS molecules from several bacteria and the quantitative evaluation of components of endotoxin extracts. The improved microchip electrophoretic method is based on the direct labeling of endotoxins by covalent binding of a fluorescent dye. The classification of the S-type LPSs can be done according to their electrophoretic profiles, which are characteristics of the respective bacterial strains. According to the number, distribution, and the relative amounts of components in an endotoxin extract, it is possible to differentiate between the S-type endotoxins from different Gram-negative bacterial strains. The microchip electrophoresis affords high-resolution separation of pure and partially purified (e.g., obtained from whole-cell lysate) S and R endotoxins. This microchip technique provides a new, standardizable, fast, and sensitive method for the detection of endotoxins and for the quantitative evaluation of components of an endotoxin extract.

Quantitative Interpretation of Multifrequency Multimode EPR Spectra of Metal Containing Proteins, Enzymes, and Biomimetic Complexes.

PubMed

Petasis, Doros T; Hendrich, Michael P

2015-01-01

Electron paramagnetic resonance (EPR) spectroscopy has long been a primary method for characterization of paramagnetic centers in materials and biological complexes. Transition metals in biological complexes have valence d-orbitals that largely define the chemistry of the metal centers. EPR spectra are distinctive for metal type, oxidation state, protein environment, substrates, and inhibitors. The study of many metal centers in proteins, enzymes, and biomimetic complexes has led to the development of a systematic methodology for quantitative interpretation of EPR spectra from a wide array of metal containing complexes. The methodology is now contained in the computer program SpinCount. SpinCount allows simulation of EPR spectra from any sample containing multiple species composed of one or two metals in any spin state. The simulations are quantitative, thus allowing determination of all species concentrations in a sample directly from spectra. This chapter will focus on applications to transition metals in biological systems using EPR spectra from multiple microwave frequencies and modes. © 2015 Elsevier Inc. All rights reserved.

Electro-mechanical properties of hydrogel composites with micro- and nano-cellulose fillers

NASA Astrophysics Data System (ADS)

N, Mohamed Shahid U.; Deshpande, Abhijit P.; Lakshmana Rao, C.

2015-09-01

Stimuli responsive cross-linked hydrogels are of great interest for applications in diverse fields such as sensors and biomaterials. In this study, we investigate polymer composites filled with cellulose fillers. The celluloses used in making the composites were a microcrystalline cellulose of commercial grade and cellulose nano-whiskers obtained through acid hydrolysis of microcrystalline cellulose. The filler concentration was varied and corresponding physical, mechanical and electro-mechanical characterization was carried out. The electro-mechanical properties were determined using a quasi-static method. The fillers not only enhance the mechanical properties of the composite by providing better reinforcement but also provide a quantitative electric potential in the composite. The measurements reveal that the polymer composites prepared from two different cellulose fillers possess a quantitative electric potential which can be utilized in biomedical applications. It is argued that the mechanism behind the quantitative electric potential in the composites is due to streaming potentials arising due to electrical double layer formation.

Novel cardiac magnetic resonance biomarkers: native T1 and extracellular volume myocardial mapping.

PubMed

Cannaò, Paola Maria; Altabella, Luisa; Petrini, Marcello; Alì, Marco; Secchi, Francesco; Sardanelli, Francesco

2016-04-28

Cardiac magnetic resonance (CMR) is a non-invasive diagnostic tool playing a key role in the assessment of cardiac morphology and function as well as in tissue characterization. Late gadolinium enhancement is a fundamental CMR technique for detecting focal or regional abnormalities such as scar tissue, replacement fibrosis, or inflammation using qualitative, semi-quantitative, or quantitative methods, but not allowing for evaluating the whole myocardium in the presence of diffuse disease. The novel T1 mapping approach permits a quantitative assessment of the entire myocardium providing a voxel-by-voxel map of native T1 relaxation time, obtained before the intravenous administration of gadolinium-based contrast material. Combining T1 data obtained before and after contrast injection, it is also possible to calculate the voxel-by-voxel extracellular volume (ECV), resulting in another myocardial parametric map. This article describes technical challenges and clinical perspectives of these two novel CMR biomarkers: myocardial native T1 and ECV mapping.

Quantitative adhesion characterization of antireflective coatings in multijunction photovoltaics

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

Brock, Ryan; Rewari, Raunaq; Novoa, Fernando D.

We discuss the development of a new composite dual cantilever beam (cDCB) thin-film adhesion testing method, which enables the quantitative measurement of adhesion on the thin and fragile substrates used in multijunction photovoltaics. In particular, we address the adhesion of several 2- and 3-layer antireflective coating systems on multijunction cells. By varying interface chemistry and morphology through processing, we demonstrate the marked effects on adhesion and help to develop an understanding of how high adhesion can be achieved, as adhesion values ranging from 0.5 J/m2 to 10 J/m2 were measured. Damp heat (85 degrees C/85% RH) was used to invokemore » degradation of interfacial adhesion. We demonstrate that even with germanium substrates that fracture relatively easily, quantitative measurements of adhesion can be made at high test yield. The cDCB test is discussed as an important new methodology, which can be broadly applied to any system that makes use of thin, brittle, or otherwise fragile substrates.« less

A quantitative telomeric chromatin isolation protocol identifies different telomeric states

NASA Astrophysics Data System (ADS)

Grolimund, Larissa; Aeby, Eric; Hamelin, Romain; Armand, Florence; Chiappe, Diego; Moniatte, Marc; Lingner, Joachim

2013-11-01

Telomere composition changes during tumourigenesis, aging and in telomere syndromes in a poorly defined manner. Here we develop a quantitative telomeric chromatin isolation protocol (QTIP) for human cells, in which chromatin is cross-linked, immunopurified and analysed by mass spectrometry. QTIP involves stable isotope labelling by amino acids in cell culture (SILAC) to compare and identify quantitative differences in telomere protein composition of cells from various states. With QTIP, we specifically enrich telomeric DNA and all shelterin components. We validate the method characterizing changes at dysfunctional telomeres, and identify and validate known, as well as novel telomere-associated polypeptides including all THO subunits, SMCHD1 and LRIF1. We apply QTIP to long and short telomeres and detect increased density of SMCHD1 and LRIF1 and increased association of the shelterins TRF1, TIN2, TPP1 and POT1 with long telomeres. Our results validate QTIP to study telomeric states during normal development and in disease.

Quantitative assessment of alkali-reactive aggregate mineral content through XRD using polished sections as a supplementary tool to RILEM AAR-1 (petrographic method)

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

Castro, Nelia, E-mail: nelia.castro@ntnu.no; Sorensen, Bjorn E.; Broekmans, Maarten A.T.M.

The mineral content of 5 aggregate samples from 4 different countries, including reactive and non-reactive aggregate types, was assessed quantitatively by X-ray diffraction (XRD) using polished sections. Additionally, electron probe microanalyzer (EPMA) mapping and cathodoluminescence (CL) were used to characterize the opal-CT identified in one of the aggregate samples. Critical review of results from polished sections against traditionally powdered specimen has demonstrated that for fine-grained rocks without preferred orientation the assessment of mineral content by XRD using polished sections may represent an advantage over traditional powder specimens. Comparison of data on mineral content and silica speciation with expansion data frommore » PARTNER project confirmed that the presence of opal-CT plays an important role in the reactivity of one of the studied aggregates. Used as a complementary tool to RILEM AAR-1, the methodology suggested in this paper has the potential to improve the strength of the petrographic method.« less

A Quantitative Measure of Handgrip Myotonia in Non-dystrophic Myotonia

PubMed Central

Statland, Jeffrey M; Bundy, Brian N; Wang, Yunxia; Trivedi, Jaya R; Rayan, Dipa Raja; Herbelin, Laura; Donlan, Merideth; McLin, Rhonda; Eichinger, Katy J; Findlater, Karen; Dewar, Liz; Pandya, Shree; Martens, William B; Venance, Shannon L; Matthews, Emma; Amato, Anthony A; Hanna, Michael G; Griggs, Robert C; Barohn, Richard J

2012-01-01

Introduction Non-dystrophic Myotonia (NDM) is characterized by myotonia without muscle wasting. A standardized quantitative myotonia assessment (QMA) is important for clinical trials. Methods Myotonia was assessed in 91 individuals enrolled in a natural history study using a commercially available computerized handgrip myometer and automated software. Average peak force and 90% to 5% relaxation times were compared to historical normal controls studied with identical methods. Results 30 subjects had chloride channel mutations, 31 sodium channel mutations, 6 DM2, and 24 no identified mutation. Chloride channel mutations were associated with prolonged 1st handgrip relaxation times, and warm up on subsequent handgrips. Sodium channel mutations were associated with prolonged 1st handgrip relaxation times and paradoxical myotonia or warm-up, depending on underlying mutations. DM2 subjects had normal relaxation times but decreased peak force. Sample size estimates are provided for clinical trial planning. Conclusion QMA is an automated, non-invasive technique for evaluating myotonia in NDM. PMID:22987687

Quantitative determination of amorphous cyclosporine in crystalline cyclosporine samples by Fourier transform infrared spectroscopy.

PubMed

Bertacche, Vittorio; Pini, Elena; Stradi, Riccardo; Stratta, Fabio

2006-01-01

The purpose of this study is the development of a quantification method to detect the amount of amorphous cyclosporine using Fourier transform infrared (FTIR) spectroscopy. The mixing of different percentages of crystalline cyclosporine with amorphous cyclosporine was used to obtain a set of standards, composed of cyclosporine samples characterized by different percentages of amorphous cyclosporine. Using a wavelength range of 450-4,000 cm(-1), FTIR spectra were obtained from samples in potassium bromide pellets and then a partial least squares (PLS) model was exploited to correlate the features of the FTIR spectra with the percentage of amorphous cyclosporine in the samples. This model gave a standard error of estimate (SEE) of 0.3562, with an r value of 0.9971 and a standard error of prediction (SEP) of 0.4168, which derives from the cross validation function used to check the precision of the model. Statistical values reveal the applicability of the method to the quantitative determination of amorphous cyclosporine in crystalline cyclosporine samples.

Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

PubMed Central

Maulucci, Giuseppe; Chiarpotto, Michela; Papi, Massimiliano; Samengo, Daniela; Pani, Giovambattista; De Spirito, Marco

2015-01-01

Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates. PMID:26506895

Rediscovery and Revival of Analytical Refractometry for Protein Determination: Recombining Simplicity With Accuracy in the Digital Era.

PubMed

Anderle, Heinz; Weber, Alfred

2016-03-01

Among "vintage" methods of protein determination, quantitative analytical refractometry has received far less attention than well-established pharmacopoeial techniques based on protein nitrogen content, such as Dumas combustion (1831) and Kjeldahl digestion (1883). Protein determination by quantitative refractometry dates back to 1903 and has been extensively investigated and characterized in the following 30 years, but has since vanished into a few niche applications that may not require the degree of accuracy and precision essential for pharmaceutical analysis. However, because high-resolution and precision digital refractometers have replaced manual instruments, reducing time and resource consumption, the method appears particularly attractive from an economic, ergonomic, and environmental viewpoint. The sample solution can be measured without dilution or other preparation procedures than the separation of the protein-free matrix by ultrafiltration, which might even be omitted for a constant matrix and excipient composition. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

The Use of 3D Telomere FISH for the Characterization of the Nuclear Architecture in EBV-Positive Hodgkin's Lymphoma.

PubMed

Knecht, Hans; Mai, Sabine

2017-01-01

The 3D nuclear architecture is closely related to cellular functions and chromosomes are organized in distinct territories. Quantitative 3D telomere FISH analysis (3D Q-FISH) and 3D super-resolution imaging (3D-SIM) at a resolution up to 80 nm as well as the recently developed combined quantitative 3D TRF2-telomere immune FISH technique (3D TRF2/Telo-Q-FISH) have substantially contributed to elucidate molecular pathogenic mechanisms of hematological diseases. Here we report the methods we applied to uncover major molecular steps involved in the pathogenesis of EBV-associated Hodgkin's lymphoma. These methods allowed us to identify the EBV-encoded oncoprotein LMP1 as a key element in the formation of Hodgkin (H-cell) and multinucleated Reed-Sternberg cells (RS-cell), the diagnostic tumor cell of classical Hodgkin's lymphoma (cHL). LMP1 mediates multinuclearity through downregulation of shelterin proteins, in particular telomere repeat binding factor 2 (TRF2).

Markov State Models of gene regulatory networks.

PubMed

Chu, Brian K; Tse, Margaret J; Sato, Royce R; Read, Elizabeth L

2017-02-06

Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have the potential to guide cell-reprogramming strategies. Networks are often modeled by the stochastic Chemical Master Equation, but methods for systematic identification of key properties of the global dynamics are currently lacking. The method identifies the number, phenotypes, and lifetimes of long-lived states for a set of common gene regulatory network models. Application of transition path theory to the constructed Markov State Model decomposes global dynamics into a set of dominant transition paths and associated relative probabilities for stochastic state-switching. In this proof-of-concept study, we found that the Markov State Model provides a general framework for analyzing and visualizing stochastic multistability and state-transitions in gene networks. Our results suggest that this framework-adopted from the field of atomistic Molecular Dynamics-can be a useful tool for quantitative Systems Biology at the network scale.

New Insights Toward Quantitative Relationships between Lignin Reactivity to Monomers and Their Structural Characteristics.

PubMed

Ma, Ruoshui; Zhang, Xiumei; Wang, Yi; Zhang, Xiao

2018-04-27

The heterogeneous and complex structural characteristics of lignin present a significant challenge to predict its processability (e.g. depolymerization, modifications etc) to valuable products. This study provides a detailed characterization and comparison of structural properties of seven representative biorefinery lignin samples derived from forest and agricultural residues, which were subjected to representative pretreatment methods. A range of wet chemistry and spectroscopy methods were applied to determine specific lignin structural characteristics such as functional groups, inter-unit linkages and peak molecular weight. In parallel, oxidative depolymerization of these lignin samples to either monomeric phenolic compounds or dicarboxylic acids were conducted, and the product yields were quantified. Based on these results (lignin structural characteristics and monomer yields), we demonstrated for the first time to apply multiple-variable linear estimations (MVLE) approach using R statistics to gain insight toward a quantitative correlation between lignin structural properties and their conversion reactivity toward oxidative depolymerization to monomers. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Robust and transferable quantification of NMR spectral quality using IROC analysis

NASA Astrophysics Data System (ADS)

Zambrello, Matthew A.; Maciejewski, Mark W.; Schuyler, Adam D.; Weatherby, Gerard; Hoch, Jeffrey C.

2017-12-01

Non-Fourier methods are increasingly utilized in NMR spectroscopy because of their ability to handle nonuniformly-sampled data. However, non-Fourier methods present unique challenges due to their nonlinearity, which can produce nonrandom noise and render conventional metrics for spectral quality such as signal-to-noise ratio unreliable. The lack of robust and transferable metrics (i.e. applicable to methods exhibiting different nonlinearities) has hampered comparison of non-Fourier methods and nonuniform sampling schemes, preventing the identification of best practices. We describe a novel method, in situ receiver operating characteristic analysis (IROC), for characterizing spectral quality based on the Receiver Operating Characteristic curve. IROC utilizes synthetic signals added to empirical data as "ground truth", and provides several robust scalar-valued metrics for spectral quality. This approach avoids problems posed by nonlinear spectral estimates, and provides a versatile quantitative means of characterizing many aspects of spectral quality. We demonstrate applications to parameter optimization in Fourier and non-Fourier spectral estimation, critical comparison of different methods for spectrum analysis, and optimization of nonuniform sampling schemes. The approach will accelerate the discovery of optimal approaches to nonuniform sampling experiment design and non-Fourier spectrum analysis for multidimensional NMR.

Combining land use information and small stream sampling with PCR-based methods for better characterization of diffuse sources of human fecal pollution.

PubMed

Peed, Lindsay A; Nietch, Christopher T; Kelty, Catherine A; Meckes, Mark; Mooney, Thomas; Sivaganesan, Mano; Shanks, Orin C

2011-07-01

Diffuse sources of human fecal pollution allow for the direct discharge of waste into receiving waters with minimal or no treatment. Traditional culture-based methods are commonly used to characterize fecal pollution in ambient waters, however these methods do not discern between human and other animal sources of fecal pollution making it difficult to identify diffuse pollution sources. Human-associated quantitative real-time PCR (qPCR) methods in combination with low-order headwatershed sampling, precipitation information, and high-resolution geographic information system land use data can be useful for identifying diffuse source of human fecal pollution in receiving waters. To test this assertion, this study monitored nine headwatersheds over a two-year period potentially impacted by faulty septic systems and leaky sanitary sewer lines. Human fecal pollution was measured using three different human-associated qPCR methods and a positive significant correlation was seen between abundance of human-associated genetic markers and septic systems following wet weather events. In contrast, a negative correlation was observed with sanitary sewer line densities suggesting septic systems are the predominant diffuse source of human fecal pollution in the study area. These results demonstrate the advantages of combining water sampling, climate information, land-use computer-based modeling, and molecular biology disciplines to better characterize diffuse sources of human fecal pollution in environmental waters.

Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

PubMed

Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

2014-04-04

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.