Methodology in Our Education Research Culture: Toward a Stronger Collective Quantitative Proficiency

ERIC Educational Resources Information Center

Henson, Robin K.; Hull, Darrell M.; Williams, Cynthia S.

2010-01-01

How doctoral programs train future researchers in quantitative methods has important implications for the quality of scientifically based research in education. The purpose of this article, therefore, is to examine how quantitative methods are used in the literature and taught in doctoral programs. Evidence points to deficiencies in quantitative…

Comparative evaluation of two quantitative test methods for determining the efficacy of liquid sporicides and sterilants on a hard surface: a precollaborative study.

PubMed

Tomasino, Stephen F; Hamilton, Martin A

2007-01-01

Two quantitative carrier-based test methods for determining the efficacy of liquid sporicides and sterilants on a hard surface, the Standard Quantitative Carrier Test Method-ASTM E 2111-00 and an adaptation of a quantitative micro-method as reported by Sagripanti and Bonifacino, were compared in this study. The methods were selected based on their desirable characteristics (e.g., well-developed protocol, previous use with spores, fully quantitative, and use of readily available equipment) for testing liquid sporicides and sterilants on a hard surface. In this paper, the Sagripanti-Bonifacino procedure is referred to as the Three Step Method (TSM). AOAC Official Method 966.04 was included in this study as a reference method. Three laboratories participated in the evaluation. Three chemical treatments were tested: (1) 3000 ppm sodium hypochlorite with pH adjusted to 7.0, (2) a hydrogen peroxide/peroxyacetic acid product, and (3) 3000 ppm sodium hypochlorite with pH unadjusted (pH of approximately 10.0). A fourth treatment, 6000 ppm sodium hypochlorite solution with pH adjusted to 7.0, was included only for Method 966.04 as a positive control (high level of efficacy). The contact time was 10 min for all chemical treatments except the 6000 ppm sodium hypochlorite treatment which was tested at 30 min. Each chemical treatment was tested 3 times using each of the methods. Only 2 of the laboratories performed the AOAC method. Method performance was assessed by the within-laboratory variance, between-laboratory variance, and total variance associated with the log reduction (LR) estimates generated by each quantitative method. The quantitative methods performed similarly, and the LR values generated by each method were not statistically different for the 3 treatments evaluated. Based on feedback from the participating laboratories, compared to the TSM, ASTM E 2111-00 was more resource demanding and required more set-up time. The logistical and resource concerns identified for ASTM E 2111-00 were largely associated with the filtration process and counting bacterial colonies on filters. Thus, the TSM was determined to be the most suitable method.

A new liquid chromatography-mass spectrometry-based method to quantitate exogenous recombinant transferrin in cerebrospinal fluid: a potential approach for pharmacokinetic studies of transferrin-based therapeutics in the central nervous systems.

PubMed

Wang, Shunhai; Bobst, Cedric E; Kaltashov, Igor A

2015-01-01

Transferrin (Tf) is an 80 kDa iron-binding protein that is viewed as a promising drug carrier to target the central nervous system as a result of its ability to penetrate the blood-brain barrier. Among the many challenges during the development of Tf-based therapeutics, the sensitive and accurate quantitation of the administered Tf in cerebrospinal fluid (CSF) remains particularly difficult because of the presence of abundant endogenous Tf. Herein, we describe the development of a new liquid chromatography-mass spectrometry-based method for the sensitive and accurate quantitation of exogenous recombinant human Tf in rat CSF. By taking advantage of a His-tag present in recombinant Tf and applying Ni affinity purification, the exogenous human serum Tf can be greatly enriched from rat CSF, despite the presence of the abundant endogenous protein. Additionally, we applied a newly developed (18)O-labeling technique that can generate internal standards at the protein level, which greatly improved the accuracy and robustness of quantitation. The developed method was investigated for linearity, accuracy, precision, and lower limit of quantitation, all of which met the commonly accepted criteria for bioanalytical method validation.

Revisiting the Quantitative-Qualitative Debate: Implications for Mixed-Methods Research

PubMed Central

SALE, JOANNA E. M.; LOHFELD, LYNNE H.; BRAZIL, KEVIN

2015-01-01

Health care research includes many studies that combine quantitative and qualitative methods. In this paper, we revisit the quantitative-qualitative debate and review the arguments for and against using mixed-methods. In addition, we discuss the implications stemming from our view, that the paradigms upon which the methods are based have a different view of reality and therefore a different view of the phenomenon under study. Because the two paradigms do not study the same phenomena, quantitative and qualitative methods cannot be combined for cross-validation or triangulation purposes. However, they can be combined for complementary purposes. Future standards for mixed-methods research should clearly reflect this recommendation. PMID:26523073

The absolute counting of red cell-derived microparticles with red cell bead by flow rate based assay.

PubMed

Nantakomol, Duangdao; Imwong, Malika; Soontarawirat, Ingfar; Kotjanya, Duangporn; Khakhai, Chulalak; Ohashi, Jun; Nuchnoi, Pornlada

2009-05-01

Activation of red blood cell is associated with the formation of red cell-derived microparticles (RMPs). Analysis of circulating RMPs is becoming more refined and clinically useful. A quantitative Trucount tube method is the conventional method uses for quantitating RMPs. In this study, we validated a quantitative method called "flow rate based assay using red cell bead (FCB)" to measure circulating RMPs in the peripheral blood of healthy subjects. Citrated blood samples collected from 30 cases of healthy subjects were determined the RMPs count by using double labeling of annexin V-FITC and anti-glycophorin A-PE. The absolute RMPs numbers were measured by FCB, and the results were compared with the Trucount or with flow rate based calibration (FR). Statistical correlation and agreement were analyzed using linear regression and Bland-Altman analysis. There was no significant difference in the absolute number of RMPs quantitated by FCB when compared with those two reference methods including the Trucount tube and FR method. The absolute RMPs count obtained from FCB method was highly correlated with those obtained from Trucount tube (r(2) = 0.98, mean bias 4 cell/microl, limit of agreement [LOA] -20.3 to 28.3 cell/microl), and FR method (r(2) = 1, mean bias 10.3 cell/microl, and LOA -5.5 to 26.2 cell/microl). This study demonstrates that FCB is suitable and more affordable for RMPs quantitation in the clinical samples. This method is a low cost and interchangeable to latex bead-based method for generating the absolute counts in the resource-limited areas. (c) 2008 Clinical Cytometry Society.

A review of state-of-the-art stereology for better quantitative 3D morphology in cardiac research.

PubMed

Mühlfeld, Christian; Nyengaard, Jens Randel; Mayhew, Terry M

2010-01-01

The aim of stereological methods in biomedical research is to obtain quantitative information about three-dimensional (3D) features of tissues, cells, or organelles from two-dimensional physical or optical sections. With immunogold labeling, stereology can even be used for the quantitative analysis of the distribution of molecules within tissues and cells. Nowadays, a large number of design-based stereological methods offer an efficient quantitative approach to intriguing questions in cardiac research, such as "Is there a significant loss of cardiomyocytes during progression from ventricular hypertrophy to heart failure?" or "Does a specific treatment reduce the degree of fibrosis in the heart?" Nevertheless, the use of stereological methods in cardiac research is rare. The present review article demonstrates how some of the potential pitfalls in quantitative microscopy may be avoided. To this end, we outline the concepts of design-based stereology and illustrate their practical applications to a wide range of biological questions in cardiac research. We hope that the present article will stimulate researchers in cardiac research to incorporate design-based stereology into their study designs, thus promoting an unbiased quantitative 3D microscopy.

40 CFR 93.123 - Procedures for determining localized CO, PM10, and PM2.5 concentrations (hot-spot analysis).

Code of Federal Regulations, 2011 CFR

2011-07-01

... (“Localized CO, PM10, and PM2.5 violations”) must be based on quantitative analysis using the applicable air... § 93.116 may be based on either: (i) Quantitative methods that represent reasonable and common... hot-spot analyses. (1) The hot-spot demonstration required by § 93.116 must be based on quantitative...

40 CFR 93.123 - Procedures for determining localized CO, PM10, and PM2.5 concentrations (hot-spot analysis).

Code of Federal Regulations, 2013 CFR

2013-07-01

... (“Localized CO, PM10, and PM2.5 violations”) must be based on quantitative analysis using the applicable air... § 93.116 may be based on either: (i) Quantitative methods that represent reasonable and common... hot-spot analyses. (1) The hot-spot demonstration required by § 93.116 must be based on quantitative...

40 CFR 93.123 - Procedures for determining localized CO, PM10, and PM2.5 concentrations (hot-spot analysis).

Code of Federal Regulations, 2012 CFR

2012-07-01

... (“Localized CO, PM10, and PM2.5 violations”) must be based on quantitative analysis using the applicable air... § 93.116 may be based on either: (i) Quantitative methods that represent reasonable and common... hot-spot analyses. (1) The hot-spot demonstration required by § 93.116 must be based on quantitative...

40 CFR 93.123 - Procedures for determining localized CO, PM10, and PM2.5 concentrations (hot-spot analysis).

Code of Federal Regulations, 2010 CFR

2010-07-01

... (“Localized CO, PM10, and PM2.5 violations”) must be based on quantitative analysis using the applicable air... § 93.116 may be based on either: (i) Quantitative methods that represent reasonable and common... hot-spot analyses. (1) The hot-spot demonstration required by § 93.116 must be based on quantitative...

NEW TARGET AND CONTROL ASSAYS FOR QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) ANALYSIS OF ENTEROCOCCI IN WATER

EPA Science Inventory

Enterococci are frequently monitored in water samples as indicators of fecal pollution. Attention is now shifting from culture based methods for enumerating these organisms to more rapid molecular methods such as QPCR. Accurate quantitative analyses by this method requires highly...

Quantitative Analysis of Qualitative Information from Interviews: A Systematic Literature Review

ERIC Educational Resources Information Center

Fakis, Apostolos; Hilliam, Rachel; Stoneley, Helen; Townend, Michael

2014-01-01

Background: A systematic literature review was conducted on mixed methods area. Objectives: The overall aim was to explore how qualitative information from interviews has been analyzed using quantitative methods. Methods: A contemporary review was undertaken and based on a predefined protocol. The references were identified using inclusion and…

Quantitative Methods in Psychology: Inevitable and Useless

PubMed Central

Toomela, Aaro

2010-01-01

Science begins with the question, what do I want to know? Science becomes science, however, only when this question is justified and the appropriate methodology is chosen for answering the research question. Research question should precede the other questions; methods should be chosen according to the research question and not vice versa. Modern quantitative psychology has accepted method as primary; research questions are adjusted to the methods. For understanding thinking in modern quantitative psychology, two epistemologies should be distinguished: structural-systemic that is based on Aristotelian thinking, and associative-quantitative that is based on Cartesian–Humean thinking. The first aims at understanding the structure that underlies the studied processes; the second looks for identification of cause–effect relationships between the events with no possible access to the understanding of the structures that underlie the processes. Quantitative methodology in particular as well as mathematical psychology in general, is useless for answering questions about structures and processes that underlie observed behaviors. Nevertheless, quantitative science is almost inevitable in a situation where the systemic-structural basis of behavior is not well understood; all sorts of applied decisions can be made on the basis of quantitative studies. In order to proceed, psychology should study structures; methodologically, constructive experiments should be added to observations and analytic experiments. PMID:21833199

Quantitative methods in psychology: inevitable and useless.

PubMed

Toomela, Aaro

2010-01-01

Science begins with the question, what do I want to know? Science becomes science, however, only when this question is justified and the appropriate methodology is chosen for answering the research question. Research question should precede the other questions; methods should be chosen according to the research question and not vice versa. Modern quantitative psychology has accepted method as primary; research questions are adjusted to the methods. For understanding thinking in modern quantitative psychology, two epistemologies should be distinguished: structural-systemic that is based on Aristotelian thinking, and associative-quantitative that is based on Cartesian-Humean thinking. The first aims at understanding the structure that underlies the studied processes; the second looks for identification of cause-effect relationships between the events with no possible access to the understanding of the structures that underlie the processes. Quantitative methodology in particular as well as mathematical psychology in general, is useless for answering questions about structures and processes that underlie observed behaviors. Nevertheless, quantitative science is almost inevitable in a situation where the systemic-structural basis of behavior is not well understood; all sorts of applied decisions can be made on the basis of quantitative studies. In order to proceed, psychology should study structures; methodologically, constructive experiments should be added to observations and analytic experiments.

Quantitative detection of bovine and porcine gelatin difference using surface plasmon resonance based biosensor

NASA Astrophysics Data System (ADS)

Wardani, Devy P.; Arifin, Muhammad; Suharyadi, Edi; Abraha, Kamsul

2015-05-01

Gelatin is a biopolymer derived from collagen that is widely used in food and pharmaceutical products. Due to some religion restrictions and health issues regarding the gelatin consumption which is extracted from certain species, it is necessary to establish a robust, reliable, sensitive and simple quantitative method to detect gelatin from different parent collagen species. To the best of our knowledge, there has not been a gelatin differentiation method based on optical sensor that could detect gelatin from different species quantitatively. Surface plasmon resonance (SPR) based biosensor is known to be a sensitive, simple and label free optical method for detecting biomaterials that is able to do quantitative detection. Therefore, we have utilized SPR-based biosensor to detect the differentiation between bovine and porcine gelatin in various concentration, from 0% to 10% (w/w). Here, we report the ability of SPR-based biosensor to detect difference between both gelatins, its sensitivity toward the gelatin concentration change, its reliability and limit of detection (LOD) and limit of quantification (LOQ) of the sensor. The sensor's LOD and LOQ towards bovine gelatin concentration are 0.38% and 1.26% (w/w), while towards porcine gelatin concentration are 0.66% and 2.20% (w/w), respectively. The results show that SPR-based biosensor is a promising tool for detecting gelatin from different raw materials quantitatively.

Laboratory Evaluations of the Enterococcus qPCR Method for Recreational Water Quality Testing: Method Performance and Sources of Uncertainty in Quantitative Measurements

EPA Science Inventory

The BEACH Act of 2000 directed the U.S. EPA to establish more expeditious methods for the detection of pathogen indicators in coastal waters, as well as new water quality criteria based on these methods. Progress has been made in developing a quantitative PCR (qPCR) method for en...

Quantitative analysis of drug distribution by ambient mass spectrometry imaging method with signal extinction normalization strategy and inkjet-printing technology.

PubMed

Luo, Zhigang; He, Jingjing; He, Jiuming; Huang, Lan; Song, Xiaowei; Li, Xin; Abliz, Zeper

2018-03-01

Quantitative mass spectrometry imaging (MSI) is a robust approach that provides both quantitative and spatial information for drug candidates' research. However, because of complicated signal suppression and interference, acquiring accurate quantitative information from MSI data remains a challenge, especially for whole-body tissue sample. Ambient MSI techniques using spray-based ionization appear to be ideal for pharmaceutical quantitative MSI analysis. However, it is more challenging, as it involves almost no sample preparation and is more susceptible to ion suppression/enhancement. Herein, based on our developed air flow-assisted desorption electrospray ionization (AFADESI)-MSI technology, an ambient quantitative MSI method was introduced by integrating inkjet-printing technology with normalization of the signal extinction coefficient (SEC) using the target compound itself. The method utilized a single calibration curve to quantify multiple tissue types. Basic blue 7 and an antitumor drug candidate (S-(+)-deoxytylophorinidine, CAT) were chosen to initially validate the feasibility and reliability of the quantitative MSI method. Rat tissue sections (heart, kidney, and brain) administered with CAT was then analyzed. The quantitative MSI analysis results were cross-validated by LC-MS/MS analysis data of the same tissues. The consistency suggests that the approach is able to fast obtain the quantitative MSI data without introducing interference into the in-situ environment of the tissue sample, and is potential to provide a high-throughput, economical and reliable approach for drug discovery and development. Copyright © 2017 Elsevier B.V. All rights reserved.

Levels of reconstruction as complementarity in mixed methods research: a social theory-based conceptual framework for integrating qualitative and quantitative research.

PubMed

Carroll, Linda J; Rothe, J Peter

2010-09-01

Like other areas of health research, there has been increasing use of qualitative methods to study public health problems such as injuries and injury prevention. Likewise, the integration of qualitative and quantitative research (mixed-methods) is beginning to assume a more prominent role in public health studies. Likewise, using mixed-methods has great potential for gaining a broad and comprehensive understanding of injuries and their prevention. However, qualitative and quantitative research methods are based on two inherently different paradigms, and their integration requires a conceptual framework that permits the unity of these two methods. We present a theory-driven framework for viewing qualitative and quantitative research, which enables us to integrate them in a conceptually sound and useful manner. This framework has its foundation within the philosophical concept of complementarity, as espoused in the physical and social sciences, and draws on Bergson's metaphysical work on the 'ways of knowing'. Through understanding how data are constructed and reconstructed, and the different levels of meaning that can be ascribed to qualitative and quantitative findings, we can use a mixed-methods approach to gain a conceptually sound, holistic knowledge about injury phenomena that will enhance our development of relevant and successful interventions.

Assessing covariate balance when using the generalized propensity score with quantitative or continuous exposures.

PubMed

Austin, Peter C

2018-01-01

Propensity score methods are increasingly being used to estimate the effects of treatments and exposures when using observational data. The propensity score was initially developed for use with binary exposures (e.g., active treatment vs. control). The generalized propensity score is an extension of the propensity score for use with quantitative exposures (e.g., dose or quantity of medication, income, years of education). A crucial component of any propensity score analysis is that of balance assessment. This entails assessing the degree to which conditioning on the propensity score (via matching, weighting, or stratification) has balanced measured baseline covariates between exposure groups. Methods for balance assessment have been well described and are frequently implemented when using the propensity score with binary exposures. However, there is a paucity of information on how to assess baseline covariate balance when using the generalized propensity score. We describe how methods based on the standardized difference can be adapted for use with quantitative exposures when using the generalized propensity score. We also describe a method based on assessing the correlation between the quantitative exposure and each covariate in the sample when weighted using generalized propensity score -based weights. We conducted a series of Monte Carlo simulations to evaluate the performance of these methods. We also compared two different methods of estimating the generalized propensity score: ordinary least squared regression and the covariate balancing propensity score method. We illustrate the application of these methods using data on patients hospitalized with a heart attack with the quantitative exposure being creatinine level.

Quantification of Microbial Phenotypes

PubMed Central

Martínez, Verónica S.; Krömer, Jens O.

2016-01-01

Metabolite profiling technologies have improved to generate close to quantitative metabolomics data, which can be employed to quantitatively describe the metabolic phenotype of an organism. Here, we review the current technologies available for quantitative metabolomics, present their advantages and drawbacks, and the current challenges to generate fully quantitative metabolomics data. Metabolomics data can be integrated into metabolic networks using thermodynamic principles to constrain the directionality of reactions. Here we explain how to estimate Gibbs energy under physiological conditions, including examples of the estimations, and the different methods for thermodynamics-based network analysis. The fundamentals of the methods and how to perform the analyses are described. Finally, an example applying quantitative metabolomics to a yeast model by 13C fluxomics and thermodynamics-based network analysis is presented. The example shows that (1) these two methods are complementary to each other; and (2) there is a need to take into account Gibbs energy errors. Better estimations of metabolic phenotypes will be obtained when further constraints are included in the analysis. PMID:27941694

An improved transmutation method for quantitative determination of the components in multicomponent overlapping chromatograms.

PubMed

Shao, Xueguang; Yu, Zhengliang; Ma, Chaoxiong

2004-06-01

An improved method is proposed for the quantitative determination of multicomponent overlapping chromatograms based on a known transmutation method. To overcome the main limitation of the transmutation method caused by the oscillation generated in the transmutation process, two techniques--wavelet transform smoothing and the cubic spline interpolation for reducing data points--were adopted, and a new criterion was also developed. By using the proposed algorithm, the oscillation can be suppressed effectively, and quantitative determination of the components in both the simulated and experimental overlapping chromatograms is successfully obtained.

Targeted, Site-specific quantitation of N- and O-glycopeptides using 18O-labeling and product ion based mass spectrometry.

PubMed

Srikanth, Jandhyam; Agalyadevi, Rathinasamy; Babu, Ponnusamy

2017-02-01

The site-specific quantitation of N- and O-glycosylation is vital to understanding the function(s) of different glycans expressed at a given site of a protein under physiological and disease conditions. Most commonly used precursor ion intensity based quantification method is less accurate and other labeled methods are expensive and require enrichment of glycopeptides. Here, we used glycopeptide product (y and Y0) ions and 18 O-labeling of C-terminal carboxyl group as a strategy to obtain quantitative information about fold-change and relative abundance of most of the glycoforms attached to the glycopeptides. As a proof of concept, the accuracy and robustness of this targeted, relative quantification LC-MS method was demonstrated using Rituximab. Furthermore, the N-glycopeptide quantification results were compared with a biosimilar of Rituximab and validated with quantitative data obtained from 2-AB-UHPLC-FL method. We further demonstrated the intensity fold-change and relative abundance of 46 unique N- and O-glycopeptides and aglycopeptides from innovator and biosimilar samples of Etanercept using both the normal-MS and product ion based quantitation. The results showed a very similar site-specific expression of N- and O-glycopeptides between the samples but with subtle differences. Interestingly, we have also been able to quantify macro-heterogeneity of all N- and O-glycopetides of Etanercept. In addition to applications in biotherapeutics, the developed method can also be used for site-specific quantitation of N- and O-glycopeptides and aglycopeptides of glycoproteins with known glycosylation pattern.

Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples.

PubMed

Zellner, Maria; Babeluk, Rita; Diestinger, Michael; Pirchegger, Petra; Skeledzic, Senada; Oehler, Rudolf

2008-09-01

Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.

High-resolution quantitative determination of dielectric function by using scattering scanning near-field optical microscopy

PubMed Central

Tranca, D. E.; Stanciu, S. G.; Hristu, R.; Stoichita, C.; Tofail, S. A. M.; Stanciu, G. A.

2015-01-01

A new method for high-resolution quantitative measurement of the dielectric function by using scattering scanning near-field optical microscopy (s-SNOM) is presented. The method is based on a calibration procedure that uses the s-SNOM oscillating dipole model of the probe-sample interaction and quantitative s-SNOM measurements. The nanoscale capabilities of the method have the potential to enable novel applications in various fields such as nano-electronics, nano-photonics, biology or medicine. PMID:26138665

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 evaluation methods of skin condition based on texture feature parameters.

PubMed

Pang, Hui; Chen, Tianhua; Wang, Xiaoyi; Chang, Zhineng; Shao, Siqi; Zhao, Jing

2017-03-01

In order to quantitatively evaluate the improvement of the skin condition after using skin care products and beauty, a quantitative evaluation method for skin surface state and texture is presented, which is convenient, fast and non-destructive. Human skin images were collected by image sensors. Firstly, the median filter of the 3 × 3 window is used and then the location of the hairy pixels on the skin is accurately detected according to the gray mean value and color information. The bilinear interpolation is used to modify the gray value of the hairy pixels in order to eliminate the negative effect of noise and tiny hairs on the texture. After the above pretreatment, the gray level co-occurrence matrix (GLCM) is calculated. On the basis of this, the four characteristic parameters, including the second moment, contrast, entropy and correlation, and their mean value are calculated at 45 ° intervals. The quantitative evaluation model of skin texture based on GLCM is established, which can calculate the comprehensive parameters of skin condition. Experiments show that using this method evaluates the skin condition, both based on biochemical indicators of skin evaluation methods in line, but also fully consistent with the human visual experience. This method overcomes the shortcomings of the biochemical evaluation method of skin damage and long waiting time, also the subjectivity and fuzziness of the visual evaluation, which achieves the non-destructive, rapid and quantitative evaluation of skin condition. It can be used for health assessment or classification of the skin condition, also can quantitatively evaluate the subtle improvement of skin condition after using skin care products or stage beauty.

Quantitative analysis of pork and chicken products by droplet digital PCR.

PubMed

Cai, Yicun; Li, Xiang; Lv, Rong; Yang, Jielin; Li, Jian; He, Yuping; Pan, Liangwen

2014-01-01

In this project, a highly precise quantitative method based on the digital polymerase chain reaction (dPCR) technique was developed to determine the weight of pork and chicken in meat products. Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of species-specific DNAs in meat products. However, it is limited in amplification efficiency and relies on standard curves based Ct values, detecting and quantifying low copy number target DNA, as in some complex mixture meat products. By using the dPCR method, we find the relationships between the raw meat weight and DNA weight and between the DNA weight and DNA copy number were both close to linear. This enabled us to establish formulae to calculate the raw meat weight based on the DNA copy number. The accuracy and applicability of this method were tested and verified using samples of pork and chicken powder mixed in known proportions. Quantitative analysis indicated that dPCR is highly precise in quantifying pork and chicken in meat products and therefore has the potential to be used in routine analysis by government regulators and quality control departments of commercial food and feed enterprises.

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

Multicomponent quantitative spectroscopic analysis without reference substances based on ICA modelling.

PubMed

Monakhova, Yulia B; Mushtakova, Svetlana P

2017-05-01

A fast and reliable spectroscopic method for multicomponent quantitative analysis of targeted compounds with overlapping signals in complex mixtures has been established. The innovative analytical approach is based on the preliminary chemometric extraction of qualitative and quantitative information from UV-vis and IR spectral profiles of a calibration system using independent component analysis (ICA). Using this quantitative model and ICA resolution results of spectral profiling of "unknown" model mixtures, the absolute analyte concentrations in multicomponent mixtures and authentic samples were then calculated without reference solutions. Good recoveries generally between 95% and 105% were obtained. The method can be applied to any spectroscopic data that obey the Beer-Lambert-Bouguer law. The proposed method was tested on analysis of vitamins and caffeine in energy drinks and aromatic hydrocarbons in motor fuel with 10% error. The results demonstrated that the proposed method is a promising tool for rapid simultaneous multicomponent analysis in the case of spectral overlap and the absence/inaccessibility of reference materials.

Retinal status analysis method based on feature extraction and quantitative grading in OCT images.

PubMed

Fu, Dongmei; Tong, Hejun; Zheng, Shuang; Luo, Ling; Gao, Fulin; Minar, Jiri

2016-07-22

Optical coherence tomography (OCT) is widely used in ophthalmology for viewing the morphology of the retina, which is important for disease detection and assessing therapeutic effect. The diagnosis of retinal diseases is based primarily on the subjective analysis of OCT images by trained ophthalmologists. This paper describes an OCT images automatic analysis method for computer-aided disease diagnosis and it is a critical part of the eye fundus diagnosis. This study analyzed 300 OCT images acquired by Optovue Avanti RTVue XR (Optovue Corp., Fremont, CA). Firstly, the normal retinal reference model based on retinal boundaries was presented. Subsequently, two kinds of quantitative methods based on geometric features and morphological features were proposed. This paper put forward a retinal abnormal grading decision-making method which was used in actual analysis and evaluation of multiple OCT images. This paper showed detailed analysis process by four retinal OCT images with different abnormal degrees. The final grading results verified that the analysis method can distinguish abnormal severity and lesion regions. This paper presented the simulation of the 150 test images, where the results of analysis of retinal status showed that the sensitivity was 0.94 and specificity was 0.92.The proposed method can speed up diagnostic process and objectively evaluate the retinal status. This paper aims on studies of retinal status automatic analysis method based on feature extraction and quantitative grading in OCT images. The proposed method can obtain the parameters and the features that are associated with retinal morphology. Quantitative analysis and evaluation of these features are combined with reference model which can realize the target image abnormal judgment and provide a reference for disease diagnosis.

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

Quantitative DIC microscopy using an off-axis self-interference approach.

PubMed

Fu, Dan; Oh, Seungeun; Choi, Wonshik; Yamauchi, Toyohiko; Dorn, August; Yaqoob, Zahid; Dasari, Ramachandra R; Feld, Michael S

2010-07-15

Traditional Normarski differential interference contrast (DIC) microscopy is a very powerful method for imaging nonstained biological samples. However, one of its major limitations is the nonquantitative nature of the imaging. To overcome this problem, we developed a quantitative DIC microscopy method based on off-axis sample self-interference. The digital holography algorithm is applied to obtain quantitative phase gradients in orthogonal directions, which leads to a quantitative phase image through a spiral integration of the phase gradients. This method is practically simple to implement on any standard microscope without stringent requirements on polarization optics. Optical sectioning can be obtained through enlarged illumination NA.

Structure-preserving interpolation of temporal and spatial image sequences using an optical flow-based method.

PubMed

Ehrhardt, J; Säring, D; Handels, H

2007-01-01

Modern tomographic imaging devices enable the acquisition of spatial and temporal image sequences. But, the spatial and temporal resolution of such devices is limited and therefore image interpolation techniques are needed to represent images at a desired level of discretization. This paper presents a method for structure-preserving interpolation between neighboring slices in temporal or spatial image sequences. In a first step, the spatiotemporal velocity field between image slices is determined using an optical flow-based registration method in order to establish spatial correspondence between adjacent slices. An iterative algorithm is applied using the spatial and temporal image derivatives and a spatiotemporal smoothing step. Afterwards, the calculated velocity field is used to generate an interpolated image at the desired time by averaging intensities between corresponding points. Three quantitative measures are defined to evaluate the performance of the interpolation method. The behavior and capability of the algorithm is demonstrated by synthetic images. A population of 17 temporal and spatial image sequences are utilized to compare the optical flow-based interpolation method to linear and shape-based interpolation. The quantitative results show that the optical flow-based method outperforms the linear and shape-based interpolation statistically significantly. The interpolation method presented is able to generate image sequences with appropriate spatial or temporal resolution needed for image comparison, analysis or visualization tasks. Quantitative and qualitative measures extracted from synthetic phantoms and medical image data show that the new method definitely has advantages over linear and shape-based interpolation.

Tendency for interlaboratory precision in the GMO analysis method based on real-time PCR.

PubMed

Kodama, Takashi; Kurosawa, Yasunori; Kitta, Kazumi; Naito, Shigehiro

2010-01-01

The Horwitz curve estimates interlaboratory precision as a function only of concentration, and is frequently used as a method performance criterion in food analysis with chemical methods. The quantitative biochemical methods based on real-time PCR require an analogous criterion to progressively promote method validation. We analyzed the tendency of precision using a simplex real-time PCR technique in 53 collaborative studies of seven genetically modified (GM) crops. Reproducibility standard deviation (SR) and repeatability standard deviation (Sr) of the genetically modified organism (GMO) amount (%) was more or less independent of GM crops (i.e., maize, soybean, cotton, oilseed rape, potato, sugar beet, and rice) and evaluation procedure steps. Some studies evaluated whole steps consisting of DNA extraction and PCR quantitation, whereas others focused only on the PCR quantitation step by using DNA extraction solutions. Therefore, SR and Sr for GMO amount (%) are functions only of concentration similar to the Horwitz curve. We proposed S(R) = 0.1971C 0.8685 and S(r) = 0.1478C 0.8424, where C is the GMO amount (%). We also proposed a method performance index in GMO quantitative methods that is analogous to the Horwitz Ratio.

Quantitative estimation of time-variable earthquake hazard by using fuzzy set theory

NASA Astrophysics Data System (ADS)

Deyi, Feng; Ichikawa, M.

1989-11-01

In this paper, the various methods of fuzzy set theory, called fuzzy mathematics, have been applied to the quantitative estimation of the time-variable earthquake hazard. The results obtained consist of the following. (1) Quantitative estimation of the earthquake hazard on the basis of seismicity data. By using some methods of fuzzy mathematics, seismicity patterns before large earthquakes can be studied more clearly and more quantitatively, highly active periods in a given region and quiet periods of seismic activity before large earthquakes can be recognized, similarities in temporal variation of seismic activity and seismic gaps can be examined and, on the other hand, the time-variable earthquake hazard can be assessed directly on the basis of a series of statistical indices of seismicity. Two methods of fuzzy clustering analysis, the method of fuzzy similarity, and the direct method of fuzzy pattern recognition, have been studied is particular. One method of fuzzy clustering analysis is based on fuzzy netting, and another is based on the fuzzy equivalent relation. (2) Quantitative estimation of the earthquake hazard on the basis of observational data for different precursors. The direct method of fuzzy pattern recognition has been applied to research on earthquake precursors of different kinds. On the basis of the temporal and spatial characteristics of recognized precursors, earthquake hazards in different terms can be estimated. This paper mainly deals with medium-short-term precursors observed in Japan and China.

Liquid Chromatography-Mass Spectrometry-based Quantitative Proteomics

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

Xie, Fang; Liu, Tao; Qian, Weijun

2011-07-22

Liquid chromatography-mass spectrometry (LC-MS)-based quantitative proteomics has become increasingly applied for a broad range of biological applications due to growing capabilities for broad proteome coverage and good accuracy in quantification. Herein, we review the current LC-MS-based quantification methods with respect to their advantages and limitations, and highlight their potential applications.

New Performance Metrics for Quantitative Polymerase Chain Reaction-Based Microbial Source Tracking Methods

EPA Science Inventory

Binary sensitivity and specificity metrics are not adequate to describe the performance of quantitative microbial source tracking methods because the estimates depend on the amount of material tested and limit of detection. We introduce a new framework to compare the performance ...

Quantitative prediction of drug side effects based on drug-related features.

PubMed

Niu, Yanqing; Zhang, Wen

2017-09-01

Unexpected side effects of drugs are great concern in the drug development, and the identification of side effects is an important task. Recently, machine learning methods are proposed to predict the presence or absence of interested side effects for drugs, but it is difficult to make the accurate prediction for all of them. In this paper, we transform side effect profiles of drugs as their quantitative scores, by summing up their side effects with weights. The quantitative scores may measure the dangers of drugs, and thus help to compare the risk of different drugs. Here, we attempt to predict quantitative scores of drugs, namely the quantitative prediction. Specifically, we explore a variety of drug-related features and evaluate their discriminative powers for the quantitative prediction. Then, we consider several feature combination strategies (direct combination, average scoring ensemble combination) to integrate three informative features: chemical substructures, targets, and treatment indications. Finally, the average scoring ensemble model which produces the better performances is used as the final quantitative prediction model. Since weights for side effects are empirical values, we randomly generate different weights in the simulation experiments. The experimental results show that the quantitative method is robust to different weights, and produces satisfying results. Although other state-of-the-art methods cannot make the quantitative prediction directly, the prediction results can be transformed as the quantitative scores. By indirect comparison, the proposed method produces much better results than benchmark methods in the quantitative prediction. In conclusion, the proposed method is promising for the quantitative prediction of side effects, which may work cooperatively with existing state-of-the-art methods to reveal dangers of drugs.

Behavioral Changes Based on a Course in Agroecology: A Mixed Methods Study

ERIC Educational Resources Information Center

Harms, Kristyn; King, James; Francis, Charles

2009-01-01

This study evaluated and described student perceptions of a course in agroecology to determine if participants experienced changed perceptions and behaviors resulting from the Agroecosystems Analysis course. A triangulation validating quantitative data mixed methods approach included a written survey comprised of both quantitative and open-ended…

On Measuring Quantitative Interpretations of Reasonable Doubt

ERIC Educational Resources Information Center

Dhami, Mandeep K.

2008-01-01

Beyond reasonable doubt represents a probability value that acts as the criterion for conviction in criminal trials. I introduce the membership function (MF) method as a new tool for measuring quantitative interpretations of reasonable doubt. Experiment 1 demonstrated that three different methods (i.e., direct rating, decision theory based, and…

Virtualising the Quantitative Research Methods Course: An Island-Based Approach

ERIC Educational Resources Information Center

Baglin, James; Reece, John; Baker, Jenalle

2015-01-01

Many recent improvements in pedagogical practice have been enabled by the rapid development of innovative technologies, particularly for teaching quantitative research methods and statistics. This study describes the design, implementation, and evaluation of a series of specialised computer laboratory sessions. The sessions combined the use of an…

76 FR 37620 - Risk-Based Capital Standards: Advanced Capital Adequacy Framework-Basel II; Establishment of a...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-28

... systems. E. Quantitative Methods for Comparing Capital Frameworks The NPR sought comment on how the... industry while assessing levels of capital. This commenter points out maintaining reliable comparative data over time could make quantitative methods for this purpose difficult. For example, evaluating asset...

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform

NASA Astrophysics Data System (ADS)

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-11-01

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05839b

Quantitative Detection of Cracks in Steel Using Eddy Current Pulsed Thermography.

PubMed

Shi, Zhanqun; Xu, Xiaoyu; Ma, Jiaojiao; Zhen, Dong; Zhang, Hao

2018-04-02

Small cracks are common defects in steel and often lead to catastrophic accidents in industrial applications. Various nondestructive testing methods have been investigated for crack detection; however, most current methods focus on qualitative crack identification and image processing. In this study, eddy current pulsed thermography (ECPT) was applied for quantitative crack detection based on derivative analysis of temperature variation. The effects of the incentive parameters on the temperature variation were analyzed in the simulation study. The crack profile and position are identified in the thermal image based on the Canny edge detection algorithm. Then, one or more trajectories are determined through the crack profile in order to determine the crack boundary through its temperature distribution. The slope curve along the trajectory is obtained. Finally, quantitative analysis of the crack sizes was performed by analyzing the features of the slope curves. The experimental verification showed that the crack sizes could be quantitatively detected with errors of less than 1%. Therefore, the proposed ECPT method was demonstrated to be a feasible and effective nondestructive approach for quantitative crack detection.

Linear Quantitative Profiling Method Fast Monitors Alkaloids of Sophora Flavescens That Was Verified by Tri-Marker Analyses.

PubMed

Hou, Zhifei; Sun, Guoxiang; Guo, Yong

2016-01-01

The present study demonstrated the use of the Linear Quantitative Profiling Method (LQPM) to evaluate the quality of Alkaloids of Sophora flavescens (ASF) based on chromatographic fingerprints in an accurate, economical and fast way. Both linear qualitative and quantitative similarities were calculated in order to monitor the consistency of the samples. The results indicate that the linear qualitative similarity (LQLS) is not sufficiently discriminating due to the predominant presence of three alkaloid compounds (matrine, sophoridine and oxymatrine) in the test samples; however, the linear quantitative similarity (LQTS) was shown to be able to obviously identify the samples based on the difference in the quantitative content of all the chemical components. In addition, the fingerprint analysis was also supported by the quantitative analysis of three marker compounds. The LQTS was found to be highly correlated to the contents of the marker compounds, indicating that quantitative analysis of the marker compounds may be substituted with the LQPM based on the chromatographic fingerprints for the purpose of quantifying all chemicals of a complex sample system. Furthermore, once reference fingerprint (RFP) developed from a standard preparation in an immediate detection way and the composition similarities calculated out, LQPM could employ the classical mathematical model to effectively quantify the multiple components of ASF samples without any chemical standard.

A Quantitative Study of Teacher Readiness to Teach School-Based HIV/AIDS Education in Kenyan Primary Schools

ERIC Educational Resources Information Center

Lang'at, Edwin K.

2014-01-01

Purpose and Method of Study: The purpose of this study was to investigate teachers' self-perceived readiness to teach school-based HIV/AIDS Awareness and Prevention education in Kenyan primary schools based on their knowledge, attitudes and instructional confidence. This research utilized a non-experimental quantitative approach with a…

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

NASA Astrophysics Data System (ADS)

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-01

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

PubMed

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-07

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Mass spectrometry based biomarker discovery, verification, and validation--quality assurance and control of protein biomarker assays.

PubMed

Parker, Carol E; Borchers, Christoph H

2014-06-01

In its early years, mass spectrometry (MS)-based proteomics focused on the cataloging of proteins found in different species or different tissues. By 2005, proteomics was being used for protein quantitation, typically based on "proteotypic" peptides which act as surrogates for the parent proteins. Biomarker discovery is usually done by non-targeted "shotgun" proteomics, using relative quantitation methods to determine protein expression changes that correlate with disease (output given as "up-or-down regulation" or "fold-increases"). MS-based techniques can also perform "absolute" quantitation which is required for clinical applications (output given as protein concentrations). Here we describe the differences between these methods, factors that affect the precision and accuracy of the results, and some examples of recent studies using MS-based proteomics to verify cancer-related biomarkers. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Sieve-based device for MALDI sample preparation. III. Its power for quantitative measurements.

PubMed

Molin, Laura; Cristoni, Simone; Seraglia, Roberta; Traldi, Pietro

2011-02-01

The solid sample inhomogeneity is a weak point of traditional MALDI deposition techniques that reflects negatively on quantitative analysis. The recently developed sieve-based device (SBD) sample deposition method, based on the electrospraying of matrix/analyte solutions through a grounded sieve, allows the homogeneous deposition of microcrystals with dimensions smaller than that of the laser spot. In each microcrystal the matrix/analyte molar ratio can be considered constant. Then, by irradiating different portions of the microcrystal distribution an identical response is obtained. This result suggests the employment of SBD in the development of quantitative procedures. For this aim, mixtures of different proteins of known molarity were analyzed, showing a good relationship between molarity and intensity ratios. This behaviour was also observed in the case of proteins with quite different ionic yields. The power of the developed method for quantitative evaluation was also tested by the measurement of the abundance of IGPP[Oxi]GPP[Oxi]GLMGPP (m/z 1219) present in the collagen-α-5(IV) chain precursor, differently expressed in urines from healthy subjects and diabetic-nephropathic patients, confirming its overexpression in the presence of nephropathy. The data obtained indicate that SBD is a particularly effective method for quantitative analysis also in biological fluids of interest. Copyright © 2011 John Wiley & Sons, Ltd.

Development of a rapid, robust, and universal picogreen-based method to titer adeno-associated vectors.

PubMed

Piedra, Jose; Ontiveros, Maria; Miravet, Susana; Penalva, Cristina; Monfar, Mercè; Chillon, Miguel

2015-02-01

Recombinant adeno-associated viruses (rAAVs) are promising vectors in preclinical and clinical assays for the treatment of diseases with gene therapy strategies. Recent technological advances in amplification and purification have allowed the production of highly purified rAAV vector preparations. Although quantitative polymerase chain reaction (qPCR) is the current method of choice for titrating rAAV genomes, it shows high variability. In this work, we report a rapid and robust rAAV titration method based on the quantitation of encapsidated DNA with the fluorescent dye PicoGreen®. This method allows detection from 3×10(10) viral genome/ml up to 2.4×10(13) viral genome/ml in a linear range. Contrasted with dot blot or qPCR, the PicoGreen-based assay has less intra- and interassay variability. Moreover, quantitation is rapid, does not require specific primers or probes, and is independent of the rAAV pseudotype analyzed. In summary, development of this universal rAAV-titering method may have substantive implications in rAAV technology.

[Adequate application of quantitative and qualitative statistic analytic methods in acupuncture clinical trials].

PubMed

Tan, Ming T; Liu, Jian-ping; Lao, Lixing

2012-08-01

Recently, proper use of the statistical methods in traditional Chinese medicine (TCM) randomized controlled trials (RCTs) has received increased attention. Statistical inference based on hypothesis testing is the foundation of clinical trials and evidence-based medicine. In this article, the authors described the methodological differences between literature published in Chinese and Western journals in the design and analysis of acupuncture RCTs and the application of basic statistical principles. In China, qualitative analysis method has been widely used in acupuncture and TCM clinical trials, while the between-group quantitative analysis methods on clinical symptom scores are commonly used in the West. The evidence for and against these analytical differences were discussed based on the data of RCTs assessing acupuncture for pain relief. The authors concluded that although both methods have their unique advantages, quantitative analysis should be used as the primary analysis while qualitative analysis can be a secondary criterion for analysis. The purpose of this paper is to inspire further discussion of such special issues in clinical research design and thus contribute to the increased scientific rigor of TCM research.

Quantitative data standardization of X-ray based densitometry methods

NASA Astrophysics Data System (ADS)

Sergunova, K. A.; Petraikin, A. V.; Petrjajkin, F. A.; Akhmad, K. S.; Semenov, D. S.; Potrakhov, N. N.

2018-02-01

In the present work is proposed the design of special liquid phantom for assessing the accuracy of quantitative densitometric data. Also are represented the dependencies between the measured bone mineral density values and the given values for different X-ray based densitometry techniques. Shown linear graphs make it possible to introduce correction factors to increase the accuracy of BMD measurement by QCT, DXA and DECT methods, and to use them for standardization and comparison of measurements.

Correlation between quantitative PCR and Culture-Based methods for measuring Enterococcus spp. over various temporal scales at three California marine beaches

EPA Science Inventory

Several studies have examined how fecal indicator bacteria (FIB) measurements compare between quantitative polymerase chain reaction (QPCR) and the culture methods it is intended to replace. Here we extend those studies by examining the stability of that relationship within a be...

Quantitative Infrared Spectroscopy in Challenging Environments: Applications to Passive Remote Sensing and Process Monitoring

DTIC Science & Technology

2012-12-01

IR remote sensing o ers a measurement method to detect gaseous species in the outdoor environment. Two major obstacles limit the application of this... method in quantitative analysis : (1) the e ect of both temperature and concentration on the measured spectral intensities and (2) the di culty and...crucial. In this research, particle swarm optimization, a population- based optimization method was applied. Digital ltering and wavelet processing methods

Visualizing dispersive features in 2D image via minimum gradient method

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

He, Yu; Wang, Yan; Shen, Zhi -Xun

Here, we developed a minimum gradient based method to track ridge features in a 2D image plot, which is a typical data representation in many momentum resolved spectroscopy experiments. Through both analytic formulation and numerical simulation, we compare this new method with existing DC (distribution curve) based and higher order derivative based analyses. We find that the new method has good noise resilience and enhanced contrast especially for weak intensity features and meanwhile preserves the quantitative local maxima information from the raw image. An algorithm is proposed to extract 1D ridge dispersion from the 2D image plot, whose quantitative applicationmore » to angle-resolved photoemission spectroscopy measurements on high temperature superconductors is demonstrated.« less

Visualizing dispersive features in 2D image via minimum gradient method

DOE PAGES

He, Yu; Wang, Yan; Shen, Zhi -Xun

2017-07-24

Here, we developed a minimum gradient based method to track ridge features in a 2D image plot, which is a typical data representation in many momentum resolved spectroscopy experiments. Through both analytic formulation and numerical simulation, we compare this new method with existing DC (distribution curve) based and higher order derivative based analyses. We find that the new method has good noise resilience and enhanced contrast especially for weak intensity features and meanwhile preserves the quantitative local maxima information from the raw image. An algorithm is proposed to extract 1D ridge dispersion from the 2D image plot, whose quantitative applicationmore » to angle-resolved photoemission spectroscopy measurements on high temperature superconductors is demonstrated.« less

Mapping Quantitative Traits in Unselected Families: Algorithms and Examples

PubMed Central

Dupuis, Josée; Shi, Jianxin; Manning, Alisa K.; Benjamin, Emelia J.; Meigs, James B.; Cupples, L. Adrienne; Siegmund, David

2009-01-01

Linkage analysis has been widely used to identify from family data genetic variants influencing quantitative traits. Common approaches have both strengths and limitations. Likelihood ratio tests typically computed in variance component analysis can accommodate large families but are highly sensitive to departure from normality assumptions. Regression-based approaches are more robust but their use has primarily been restricted to nuclear families. In this paper, we develop methods for mapping quantitative traits in moderately large pedigrees. Our methods are based on the score statistic which in contrast to the likelihood ratio statistic, can use nonparametric estimators of variability to achieve robustness of the false positive rate against departures from the hypothesized phenotypic model. Because the score statistic is easier to calculate than the likelihood ratio statistic, our basic mapping methods utilize relatively simple computer code that performs statistical analysis on output from any program that computes estimates of identity-by-descent. This simplicity also permits development and evaluation of methods to deal with multivariate and ordinal phenotypes, and with gene-gene and gene-environment interaction. We demonstrate our methods on simulated data and on fasting insulin, a quantitative trait measured in the Framingham Heart Study. PMID:19278016

Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis*

PubMed Central

León, Ileana R.; Schwämmle, Veit; Jensen, Ole N.; Sprenger, Richard R.

2013-01-01

The majority of mass spectrometry-based protein quantification studies uses peptide-centric analytical methods and thus strongly relies on efficient and unbiased protein digestion protocols for sample preparation. We present a novel objective approach to assess protein digestion efficiency using a combination of qualitative and quantitative liquid chromatography-tandem MS methods and statistical data analysis. In contrast to previous studies we employed both standard qualitative as well as data-independent quantitative workflows to systematically assess trypsin digestion efficiency and bias using mitochondrial protein fractions. We evaluated nine trypsin-based digestion protocols, based on standard in-solution or on spin filter-aided digestion, including new optimized protocols. We investigated various reagents for protein solubilization and denaturation (dodecyl sulfate, deoxycholate, urea), several trypsin digestion conditions (buffer, RapiGest, deoxycholate, urea), and two methods for removal of detergents before analysis of peptides (acid precipitation or phase separation with ethyl acetate). Our data-independent quantitative liquid chromatography-tandem MS workflow quantified over 3700 distinct peptides with 96% completeness between all protocols and replicates, with an average 40% protein sequence coverage and an average of 11 peptides identified per protein. Systematic quantitative and statistical analysis of physicochemical parameters demonstrated that deoxycholate-assisted in-solution digestion combined with phase transfer allows for efficient, unbiased generation and recovery of peptides from all protein classes, including membrane proteins. This deoxycholate-assisted protocol was also optimal for spin filter-aided digestions as compared with existing methods. PMID:23792921

Is quantitative PCR for the pneumolysin (ply) gene useful for detection of pneumococcal lower respiratory tract infection?

PubMed

Abdeldaim, G; Herrmann, B; Korsgaard, J; Olcén, P; Blomberg, J; Strålin, K

2009-06-01

The pneumolysin (ply) gene is widely used as a target in PCR assays for Streptococcus pneumoniae in respiratory secretions. However, false-positive results with conventional ply-based PCR have been reported. The aim here was to study the performance of a quantitative ply-based PCR for the identification of pneumococcal lower respiratory tract infection (LRTI). In a prospective study, fibreoptic bronchoscopy was performed in 156 hospitalized adult patients with LRTI and 31 controls who underwent bronchoscopy because of suspicion of malignancy. Among the LRTI patients and controls, the quantitative ply-based PCR applied to bronchoalveolar lavage (BAL) fluid was positive at >or=10(3) genome copies/mL in 61% and 71% of the subjects, at >or=10(5) genome copies/mL in 40% and 58% of the subjects, and at >or=10(7) genome copies/mL in 15% and 3.2% of the subjects, respectively. Using BAL fluid culture, blood culture, and/or a urinary antigen test, S. pneumoniae was identified in 19 LRTI patients. As compared with these diagnostic methods used in combination, quantitative ply-based PCR showed sensitivities and specificities of 89% and 43% at a cut-off of 10(3) genome copies/mL, of 84% and 66% at a cut-off of 10(5) genome copies/mL, and of 53% and 90% at a cut-off of 10(7) genome copies/mL, respectively. In conclusion, a high cut-off with the quantitative ply-based PCR was required to reach acceptable specificity. However, as a high cut-off resulted in low sensitivity, quantitative ply-based PCR does not appear to be clinically useful. Quantitative PCR methods for S. pneumoniae using alternative gene targets should be evaluated.

A Calibration-Free Laser-Induced Breakdown Spectroscopy (CF-LIBS) Quantitative Analysis Method Based on the Auto-Selection of an Internal Reference Line and Optimized Estimation of Plasma Temperature.

PubMed

Yang, Jianhong; Li, Xiaomeng; Xu, Jinwu; Ma, Xianghong

2018-01-01

The quantitative analysis accuracy of calibration-free laser-induced breakdown spectroscopy (CF-LIBS) is severely affected by the self-absorption effect and estimation of plasma temperature. Herein, a CF-LIBS quantitative analysis method based on the auto-selection of internal reference line and the optimized estimation of plasma temperature is proposed. The internal reference line of each species is automatically selected from analytical lines by a programmable procedure through easily accessible parameters. Furthermore, the self-absorption effect of the internal reference line is considered during the correction procedure. To improve the analysis accuracy of CF-LIBS, the particle swarm optimization (PSO) algorithm is introduced to estimate the plasma temperature based on the calculation results from the Boltzmann plot. Thereafter, the species concentrations of a sample can be calculated according to the classical CF-LIBS method. A total of 15 certified alloy steel standard samples of known compositions and elemental weight percentages were used in the experiment. Using the proposed method, the average relative errors of Cr, Ni, and Fe calculated concentrations were 4.40%, 6.81%, and 2.29%, respectively. The quantitative results demonstrated an improvement compared with the classical CF-LIBS method and the promising potential of in situ and real-time application.

Quantification of the methylation status of the PWS/AS imprinted region: comparison of two approaches based on bisulfite sequencing and methylation-sensitive MLPA.

PubMed

Dikow, Nicola; Nygren, Anders Oh; Schouten, Jan P; Hartmann, Carolin; Krämer, Nikola; Janssen, Bart; Zschocke, Johannes

2007-06-01

Standard methods used for genomic methylation analysis allow the detection of complete absence of either methylated or non-methylated alleles but are usually unable to detect changes in the proportion of methylated and unmethylated alleles. We compare two methods for quantitative methylation analysis, using the chromosome 15q11-q13 imprinted region as model. Absence of the non-methylated paternal allele in this region leads to Prader-Willi syndrome (PWS) whilst absence of the methylated maternal allele results in Angelman syndrome (AS). A proportion of AS is caused by mosaic imprinting defects which may be missed with standard methods and require quantitative analysis for their detection. Sequence-based quantitative methylation analysis (SeQMA) involves quantitative comparison of peaks generated through sequencing reactions after bisulfite treatment. It is simple, cost-effective and can be easily established for a large number of genes. However, our results support previous suggestions that methods based on bisulfite treatment may be problematic for exact quantification of methylation status. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) avoids bisulfite treatment. It detects changes in both CpG methylation as well as copy number of up to 40 chromosomal sequences in one simple reaction. Once established in a laboratory setting, the method is more accurate, reliable and less time consuming.

Comparison of blood flow models and acquisitions for quantitative myocardial perfusion estimation from dynamic CT

NASA Astrophysics Data System (ADS)

Bindschadler, Michael; Modgil, Dimple; Branch, Kelley R.; La Riviere, Patrick J.; Alessio, Adam M.

2014-04-01

Myocardial blood flow (MBF) can be estimated from dynamic contrast enhanced (DCE) cardiac CT acquisitions, leading to quantitative assessment of regional perfusion. The need for low radiation dose and the lack of consensus on MBF estimation methods motivates this study to refine the selection of acquisition protocols and models for CT-derived MBF. DCE cardiac CT acquisitions were simulated for a range of flow states (MBF = 0.5, 1, 2, 3 ml (min g)-1, cardiac output = 3, 5, 8 L min-1). Patient kinetics were generated by a mathematical model of iodine exchange incorporating numerous physiological features including heterogenenous microvascular flow, permeability and capillary contrast gradients. CT acquisitions were simulated for multiple realizations of realistic x-ray flux levels. CT acquisitions that reduce radiation exposure were implemented by varying both temporal sampling (1, 2, and 3 s sampling intervals) and tube currents (140, 70, and 25 mAs). For all acquisitions, we compared three quantitative MBF estimation methods (two-compartment model, an axially-distributed model, and the adiabatic approximation to the tissue homogeneous model) and a qualitative slope-based method. In total, over 11 000 time attenuation curves were used to evaluate MBF estimation in multiple patient and imaging scenarios. After iodine-based beam hardening correction, the slope method consistently underestimated flow by on average 47.5% and the quantitative models provided estimates with less than 6.5% average bias and increasing variance with increasing dose reductions. The three quantitative models performed equally well, offering estimates with essentially identical root mean squared error (RMSE) for matched acquisitions. MBF estimates using the qualitative slope method were inferior in terms of bias and RMSE compared to the quantitative methods. MBF estimate error was equal at matched dose reductions for all quantitative methods and range of techniques evaluated. This suggests that there is no particular advantage between quantitative estimation methods nor to performing dose reduction via tube current reduction compared to temporal sampling reduction. These data are important for optimizing implementation of cardiac dynamic CT in clinical practice and in prospective CT MBF trials.

Quantitative phase microscopy for cellular dynamics based on transport of intensity equation.

PubMed

Li, Ying; Di, Jianglei; Ma, Chaojie; Zhang, Jiwei; Zhong, Jinzhan; Wang, Kaiqiang; Xi, Teli; Zhao, Jianlin

2018-01-08

We demonstrate a simple method for quantitative phase imaging of tiny transparent objects such as living cells based on the transport of intensity equation. The experiments are performed using an inverted bright field microscope upgraded with a flipping imaging module, which enables to simultaneously create two laterally separated images with unequal defocus distances. This add-on module does not include any lenses or gratings and is cost-effective and easy-to-alignment. The validity of this method is confirmed by the measurement of microlens array and human osteoblastic cells in culture, indicating its potential in the applications of dynamically measuring living cells and other transparent specimens in a quantitative, non-invasive and label-free manner.

Quantitative analysis of single-molecule superresolution images

PubMed Central

Coltharp, Carla; Yang, Xinxing; Xiao, Jie

2014-01-01

This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10 – 50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images. PMID:25179006

A mass spectrometry-based method for comprehensive quantitative determination of post-transcriptional RNA modifications: the complete chemical structure of Schizosaccharomyces pombe ribosomal RNAs

PubMed Central

Taoka, Masato; Nobe, Yuko; Hori, Masayuki; Takeuchi, Aiko; Masaki, Shunpei; Yamauchi, Yoshio; Nakayama, Hiroshi; Takahashi, Nobuhiro; Isobe, Toshiaki

2015-01-01

We present a liquid chromatography–mass spectrometry (LC-MS)-based method for comprehensive quantitative identification of post-transcriptional modifications (PTMs) of RNA. We incorporated an in vitro-transcribed, heavy isotope-labeled reference RNA into a sample RNA solution, digested the mixture with a number of RNases and detected the post-transcriptionally modified oligonucleotides quantitatively based on shifts in retention time and the MS signal in subsequent LC-MS. This allowed the determination and quantitation of all PTMs in Schizosaccharomyces pombe ribosomal (r)RNAs and generated the first complete PTM maps of eukaryotic rRNAs at single-nucleotide resolution. There were 122 modified sites, most of which appear to locate at the interface of ribosomal subunits where translation takes place. We also identified PTMs at specific locations in rRNAs that were altered in response to growth conditions of yeast cells, suggesting that the cells coordinately regulate the modification levels of RNA. PMID:26013808

A Quantitative Comparative Study Measuring Consumer Satisfaction Based on Health Record Format

ERIC Educational Resources Information Center

Moore, Vivianne E.

2013-01-01

This research study used a quantitative comparative method to investigate the relationship between consumer satisfaction and communication based on the format of health record. The central problem investigated in this research study related to the format of health record used and consumer satisfaction with care provided and effect on communication…

Quantitative methods used in Australian health promotion research: a review of publications from 1992-2002.

PubMed

Smith, Ben J; Zehle, Katharina; Bauman, Adrian E; Chau, Josephine; Hawkshaw, Barbara; Frost, Steven; Thomas, Margaret

2006-04-01

This study examined the use of quantitative methods in Australian health promotion research in order to identify methodological trends and priorities for strengthening the evidence base for health promotion. Australian health promotion articles were identified by hand searching publications from 1992-2002 in six journals: Health Promotion Journal of Australia, Australian and New Zealand journal of Public Health, Health Promotion International, Health Education Research, Health Education and Behavior and the American Journal of Health Promotion. The study designs and statistical methods used in articles presenting quantitative research were recorded. 591 (57.7%) of the 1,025 articles used quantitative methods. Cross-sectional designs were used in the majority (54.3%) of studies with pre- and post-test (14.6%) and post-test only (9.5%) the next most common designs. Bivariate statistical methods were used in 45.9% of papers, multivariate methods in 27.1% and simple numbers and proportions in 25.4%. Few studies used higher-level statistical techniques. While most studies used quantitative methods, the majority were descriptive in nature. The study designs and statistical methods used provided limited scope for demonstrating intervention effects or understanding the determinants of change.

[Study on ethnic medicine quantitative reference herb,Tibetan medicine fruits of Capsicum frutescens as a case].

PubMed

Zan, Ke; Cui, Gan; Guo, Li-Nong; Ma, Shuang-Cheng; Zheng, Jian

2018-05-01

High price and difficult to get of reference substance have become obstacles to HPLC assay of ethnic medicine. A new method based on quantitative reference herb (QRH) was proposed. Specific chromatograms in fruits of Capsicum frutescens were employed to determine peak positions, and HPLC quantitative reference herb was prepared from fruits of C. frutescens. The content of capsaicin and dihydrocapsaicin in the quantitative control herb was determined by HPLC. Eleven batches of fruits of C. frutescens were analyzed with quantitative reference herb and reference substance respectively. The results showed no difference. The present method is feasible for quality control of ethnic medicines and quantitative reference herb is suitable to replace reference substances in assay. Copyright© by the Chinese Pharmaceutical Association.

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

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

Li, Zhou; Adams, Rachel M; Chourey, Karuna

2012-01-01

A variety of quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling using iTRAQ or TMT. Here, these methods were compared in terms of the depth of proteome coverage, quantification accuracy, precision, and reproducibility using a high-performance hybrid mass spectrometer, LTQ Orbitrap Velos. Our results show that (1) the spectral counting method provides the deepest proteome coverage for identification, but its quantification performance is worse than labeling-based approaches, especially the quantification reproducibility; (2) metabolic labeling and isobaric chemical labeling are capable of accurate, precise, and reproducible quantification and provide deep proteome coverage for quantification. Isobaricmore » chemical labeling surpasses metabolic labeling in terms of quantification precision and reproducibility; (3) iTRAQ and TMT perform similarly in all aspects compared in the current study using a CID-HCD dual scan configuration. Based on the unique advantages of each method, we provide guidance for selection of the appropriate method for a quantitative proteomics study.« less

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform.

PubMed

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-12-14

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.

Linear Quantitative Profiling Method Fast Monitors Alkaloids of Sophora Flavescens That Was Verified by Tri-Marker Analyses

PubMed Central

Hou, Zhifei; Sun, Guoxiang; Guo, Yong

2016-01-01

The present study demonstrated the use of the Linear Quantitative Profiling Method (LQPM) to evaluate the quality of Alkaloids of Sophora flavescens (ASF) based on chromatographic fingerprints in an accurate, economical and fast way. Both linear qualitative and quantitative similarities were calculated in order to monitor the consistency of the samples. The results indicate that the linear qualitative similarity (LQLS) is not sufficiently discriminating due to the predominant presence of three alkaloid compounds (matrine, sophoridine and oxymatrine) in the test samples; however, the linear quantitative similarity (LQTS) was shown to be able to obviously identify the samples based on the difference in the quantitative content of all the chemical components. In addition, the fingerprint analysis was also supported by the quantitative analysis of three marker compounds. The LQTS was found to be highly correlated to the contents of the marker compounds, indicating that quantitative analysis of the marker compounds may be substituted with the LQPM based on the chromatographic fingerprints for the purpose of quantifying all chemicals of a complex sample system. Furthermore, once reference fingerprint (RFP) developed from a standard preparation in an immediate detection way and the composition similarities calculated out, LQPM could employ the classical mathematical model to effectively quantify the multiple components of ASF samples without any chemical standard. PMID:27529425

Old wine in new bottles: decanting systemic family process research in the era of evidence-based practice.

PubMed

Rohrbaugh, Michael J

2014-09-01

Social cybernetic (systemic) ideas from the early Family Process era, though emanating from qualitative clinical observation, have underappreciated heuristic potential for guiding quantitative empirical research on problem maintenance and change. The old conceptual wines we have attempted to repackage in new, science-friendly bottles include ironic processes (when "solutions" maintain problems), symptom-system fit (when problems stabilize relationships), and communal coping (when we-ness helps people change). Both self-report and observational quantitative methods have been useful in tracking these phenomena, and together the three constructs inform a team-based family consultation approach to working with difficult health and behavior problems. In addition, a large-scale, quantitatively focused effectiveness trial of family therapy for adolescent drug abuse highlights the importance of treatment fidelity and qualitative approaches to examining it. In this sense, echoing the history of family therapy research, our experience with juxtaposing quantitative and qualitative methods has gone full circle-from qualitative to quantitative observation and back again. © 2014 FPI, Inc.

Old Wine in New Bottles: Decanting Systemic Family Process Research in the Era of Evidence-Based Practice†

PubMed Central

Rohrbaugh, Michael J.

2015-01-01

Social cybernetic (systemic) ideas from the early Family Process era, though emanating from qualitative clinical observation, have underappreciated heuristic potential for guiding quantitative empirical research on problem maintenance and change. The old conceptual wines we have attempted to repackage in new, science-friendly bottles include ironic processes (when “solutions” maintain problems), symptom-system fit (when problems stabilize relationships), and communal coping (when we-ness helps people change). Both self-report and observational quantitative methods have been useful in tracking these phenomena, and together the three constructs inform a team-based family consultation (FAMCON) approach to working with difficult health and behavior problems. In addition, a large-scale, quantitatively focused effectiveness trial of family therapy for adolescent drug abuse highlights the importance of treatment fidelity and qualitative approaches to examining it. In this sense, echoing the history of family therapy research, our experience with juxtaposing quantitative and qualitative methods has gone full circle – from qualitative to quantitative observation and back again. PMID:24905101

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.

Industrial ecology: Quantitative methods for exploring a lower carbon future

NASA Astrophysics Data System (ADS)

Thomas, Valerie M.

2015-03-01

Quantitative methods for environmental and cost analyses of energy, industrial, and infrastructure systems are briefly introduced and surveyed, with the aim of encouraging broader utilization and development of quantitative methods in sustainable energy research. Material and energy flow analyses can provide an overall system overview. The methods of engineering economics and cost benefit analysis, such as net present values, are the most straightforward approach for evaluating investment options, with the levelized cost of energy being a widely used metric in electricity analyses. Environmental lifecycle assessment has been extensively developed, with both detailed process-based and comprehensive input-output approaches available. Optimization methods provide an opportunity to go beyond engineering economics to develop detailed least-cost or least-impact combinations of many different choices.

Quantitation of Specific Barley, Rye, and Oat Marker Peptides by Targeted Liquid Chromatography-Mass Spectrometry To Determine Gluten Concentrations.

PubMed

Schalk, Kathrin; Koehler, Peter; Scherf, Katharina Anne

2018-04-04

Celiac disease is triggered by the ingestion of gluten from wheat, barley, rye, and possibly oats. Gluten is quantitated by DNA-based methods or enzyme-linked immunosorbent assays (ELISAs). ELISAs mostly detect the prolamin fraction and potentially over- or underestimate gluten contents. Therefore, a new independent method is required to comprehensively detect gluten. A targeted liquid chromatography-tandem mass spectrometry method was developed to quantitate seven barley, seven rye, and three oat marker peptides derived from each gluten protein fraction (prolamin and glutelin) and type (barley, B-, C-, D-, and γ-hordeins; rye, γ-75k-, γ-40k-, ω-, and HMW-secalins). The quantitation of each marker peptide in the chymotryptic digest of a defined amount of the respective reference gluten protein type resulted in peptide-specific yields, which enabled the conversion of peptide into protein concentrations. This method was applied to quantitate gluten in samples from the brewing process, in raw materials for sourdough fermentation, and in dried sourdoughs.

Mapping loci influencing blood pressure in the Framingham pedigrees using model-free LOD score analysis of a quantitative trait.

PubMed

Knight, Jo; North, Bernard V; Sham, Pak C; Curtis, David

2003-12-31

This paper presents a method of performing model-free LOD-score based linkage analysis on quantitative traits. It is implemented in the QMFLINK program. The method is used to perform a genome screen on the Framingham Heart Study data. A number of markers that show some support for linkage in our study coincide substantially with those implicated in other linkage studies of hypertension. Although the new method needs further testing on additional real and simulated data sets we can already say that it is straightforward to apply and may offer a useful complementary approach to previously available methods for the linkage analysis of quantitative traits.

Mapping loci influencing blood pressure in the Framingham pedigrees using model-free LOD score analysis of a quantitative trait

PubMed Central

Knight, Jo; North, Bernard V; Sham, Pak C; Curtis, David

2003-01-01

This paper presents a method of performing model-free LOD-score based linkage analysis on quantitative traits. It is implemented in the QMFLINK program. The method is used to perform a genome screen on the Framingham Heart Study data. A number of markers that show some support for linkage in our study coincide substantially with those implicated in other linkage studies of hypertension. Although the new method needs further testing on additional real and simulated data sets we can already say that it is straightforward to apply and may offer a useful complementary approach to previously available methods for the linkage analysis of quantitative traits. PMID:14975142

Improved Methods for Capture, Extraction, and Quantitative Assay of Environmental DNA from Asian Bigheaded Carp (Hypophthalmichthys spp.)

PubMed Central

Turner, Cameron R.; Miller, Derryl J.; Coyne, Kathryn J.; Corush, Joel

2014-01-01

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species. PMID:25474207

Improved methods for capture, extraction, and quantitative assay of environmental DNA from Asian bigheaded carp (Hypophthalmichthys spp.).

PubMed

Turner, Cameron R; Miller, Derryl J; Coyne, Kathryn J; Corush, Joel

2014-01-01

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. However, the standard eDNA methods of this program have not advanced since their development in 2010. We developed new, quantitative, and more cost-effective methods and tested them against the standard protocols. In laboratory testing, our new quantitative PCR (qPCR) assay for bigheaded carp eDNA was one to two orders of magnitude more sensitive than the existing endpoint PCR assays. When applied to eDNA samples from an experimental pond containing bigheaded carp, the qPCR assay produced a detection probability of 94.8% compared to 4.2% for the endpoint PCR assays. Also, the eDNA capture and extraction method we adapted from aquatic microbiology yielded five times more bigheaded carp eDNA from the experimental pond than the standard method, at a per sample cost over forty times lower. Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.

Solution identification and quantitative analysis of fiber-capacitive drop analyzer based on multivariate statistical methods

NASA Astrophysics Data System (ADS)

Chen, Zhe; Qiu, Zurong; Huo, Xinming; Fan, Yuming; Li, Xinghua

2017-03-01

A fiber-capacitive drop analyzer is an instrument which monitors a growing droplet to produce a capacitive opto-tensiotrace (COT). Each COT is an integration of fiber light intensity signals and capacitance signals and can reflect the unique physicochemical property of a liquid. In this study, we propose a solution analytical and concentration quantitative method based on multivariate statistical methods. Eight characteristic values are extracted from each COT. A series of COT characteristic values of training solutions at different concentrations compose a data library of this kind of solution. A two-stage linear discriminant analysis is applied to analyze different solution libraries and establish discriminant functions. Test solutions can be discriminated by these functions. After determining the variety of test solutions, Spearman correlation test and principal components analysis are used to filter and reduce dimensions of eight characteristic values, producing a new representative parameter. A cubic spline interpolation function is built between the parameters and concentrations, based on which we can calculate the concentration of the test solution. Methanol, ethanol, n-propanol, and saline solutions are taken as experimental subjects in this paper. For each solution, nine or ten different concentrations are chosen to be the standard library, and the other two concentrations compose the test group. By using the methods mentioned above, all eight test solutions are correctly identified and the average relative error of quantitative analysis is 1.11%. The method proposed is feasible which enlarges the applicable scope of recognizing liquids based on the COT and improves the concentration quantitative precision, as well.

Model-Based Linkage Analysis of a Quantitative Trait.

PubMed

Song, Yeunjoo E; Song, Sunah; Schnell, Audrey H

2017-01-01

Linkage Analysis is a family-based method of analysis to examine whether any typed genetic markers cosegregate with a given trait, in this case a quantitative trait. If linkage exists, this is taken as evidence in support of a genetic basis for the trait. Historically, linkage analysis was performed using a binary disease trait, but has been extended to include quantitative disease measures. Quantitative traits are desirable as they provide more information than binary traits. Linkage analysis can be performed using single-marker methods (one marker at a time) or multipoint (using multiple markers simultaneously). In model-based linkage analysis the genetic model for the trait of interest is specified. There are many software options for performing linkage analysis. Here, we use the program package Statistical Analysis for Genetic Epidemiology (S.A.G.E.). S.A.G.E. was chosen because it also includes programs to perform data cleaning procedures and to generate and test genetic models for a quantitative trait, in addition to performing linkage analysis. We demonstrate in detail the process of running the program LODLINK to perform single-marker analysis, and MLOD to perform multipoint analysis using output from SEGREG, where SEGREG was used to determine the best fitting statistical model for the trait.

NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs.

PubMed

Morisset, Dany; Dobnik, David; Hamels, Sandrine; Zel, Jana; Gruden, Kristina

2008-10-01

We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1-25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification.

NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs

PubMed Central

Morisset, Dany; Dobnik, David; Hamels, Sandrine; Žel, Jana; Gruden, Kristina

2008-01-01

We have developed a novel multiplex quantitative DNA-based target amplification method suitable for sensitive, specific and quantitative detection on microarray. This new method named NASBA Implemented Microarray Analysis (NAIMA) was applied to GMO detection in food and feed, but its application can be extended to all fields of biology requiring simultaneous detection of low copy number DNA targets. In a first step, the use of tailed primers allows the multiplex synthesis of template DNAs in a primer extension reaction. A second step of the procedure consists of transcription-based amplification using universal primers. The cRNA product is further on directly ligated to fluorescent dyes labelled 3DNA dendrimers allowing signal amplification and hybridized without further purification on an oligonucleotide probe-based microarray for multiplex detection. Two triplex systems have been applied to test maize samples containing several transgenic lines, and NAIMA has shown to be sensitive down to two target copies and to provide quantitative data on the transgenic contents in a range of 0.1–25%. Performances of NAIMA are comparable to singleplex quantitative real-time PCR. In addition, NAIMA amplification is faster since 20 min are sufficient to achieve full amplification. PMID:18710880

Efficient quantitative assessment of facial paralysis using iris segmentation and active contour-based key points detection with hybrid classifier.

PubMed

Barbosa, Jocelyn; Lee, Kyubum; Lee, Sunwon; Lodhi, Bilal; Cho, Jae-Gu; Seo, Woo-Keun; Kang, Jaewoo

2016-03-12

Facial palsy or paralysis (FP) is a symptom that loses voluntary muscles movement in one side of the human face, which could be very devastating in the part of the patients. Traditional methods are solely dependent to clinician's judgment and therefore time consuming and subjective in nature. Hence, a quantitative assessment system becomes apparently invaluable for physicians to begin the rehabilitation process; and to produce a reliable and robust method is challenging and still underway. We introduce a novel approach for a quantitative assessment of facial paralysis that tackles classification problem for FP type and degree of severity. Specifically, a novel method of quantitative assessment is presented: an algorithm that extracts the human iris and detects facial landmarks; and a hybrid approach combining the rule-based and machine learning algorithm to analyze and prognosticate facial paralysis using the captured images. A method combining the optimized Daugman's algorithm and Localized Active Contour (LAC) model is proposed to efficiently extract the iris and facial landmark or key points. To improve the performance of LAC, appropriate parameters of initial evolving curve for facial features' segmentation are automatically selected. The symmetry score is measured by the ratio between features extracted from the two sides of the face. Hybrid classifiers (i.e. rule-based with regularized logistic regression) were employed for discriminating healthy and unhealthy subjects, FP type classification, and for facial paralysis grading based on House-Brackmann (H-B) scale. Quantitative analysis was performed to evaluate the performance of the proposed approach. Experiments show that the proposed method demonstrates its efficiency. Facial movement feature extraction on facial images based on iris segmentation and LAC-based key point detection along with a hybrid classifier provides a more efficient way of addressing classification problem on facial palsy type and degree of severity. Combining iris segmentation and key point-based method has several merits that are essential for our real application. Aside from the facial key points, iris segmentation provides significant contribution as it describes the changes of the iris exposure while performing some facial expressions. It reveals the significant difference between the healthy side and the severe palsy side when raising eyebrows with both eyes directed upward, and can model the typical changes in the iris region.

A New Method to Comprehensively Diagnose Shock Waves in the Solar Atmosphere Based on Simultaneous Spectroscopic and Imaging Observations

NASA Astrophysics Data System (ADS)

Ruan, Wenzhi; Yan, Limei; He, Jiansen; Zhang, Lei; Wang, Linghua; Wei, Yong

2018-06-01

Shock waves are believed to play an important role in plasma heating. The shock-like temporal jumps in radiation intensity and Doppler shift have been identified in the solar atmosphere. However, a quantitative diagnosis of the shocks in the solar atmosphere is still lacking, seriously hindering the understanding of shock dissipative heating of the solar atmosphere. Here, we propose a new method to realize the goal of the shock quantitative diagnosis, based on Rankine–Hugoniot equations and taking the advantages of simultaneous imaging and spectroscopic observations from, e.g., IRIS (Interface Region Imaging Spectrograph). Because of this method, the key parameters of shock candidates can be derived, such as the bulk velocity and temperature of the plasma in the upstream and downstream, the propagation speed and direction. The method is applied to the shock candidates observed by IRIS, and the overall characteristics of the shocks are revealed quantitatively for the first time. This method is also tested with the help of forward modeling, i.e., virtual observations of simulated shocks. The parameters obtained from the method are consistent with the parameters of the shock formed in the model and are independent of the viewing direction. Therefore, the method we proposed here is applicable to the quantitative and comprehensive diagnosis of the observed shocks in the solar atmosphere.

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

USGS Publications Warehouse

Anderson, Ryan; Clegg, Samuel M.; Frydenvang, Jens; Wiens, Roger C.; McLennan, Scott M.; Morris, Richard V.; Ehlmann, Bethany L.; Dyar, M. Darby

2017-01-01

Accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response of an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “sub-model” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. The sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.

Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics

PubMed Central

Lavallée-Adam, Mathieu

2017-01-01

PSEA-Quant analyzes quantitative mass spectrometry-based proteomics datasets to identify enrichments of annotations contained in repositories such as the Gene Ontology and Molecular Signature databases. It allows users to identify the annotations that are significantly enriched for reproducibly quantified high abundance proteins. PSEA-Quant is available on the web and as a command-line tool. It is compatible with all label-free and isotopic labeling-based quantitative proteomics methods. This protocol describes how to use PSEA-Quant and interpret its output. The importance of each parameter as well as troubleshooting approaches are also discussed. PMID:27010334

A Statistical Framework for Protein Quantitation in Bottom-Up MS-Based Proteomics

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

Karpievitch, Yuliya; Stanley, Jeffrey R.; Taverner, Thomas

2009-08-15

Motivation: Quantitative mass spectrometry-based proteomics requires protein-level estimates and associated confidence measures. Challenges include the presence of low quality or incorrectly identified peptides and informative missingness. Furthermore, models are required for rolling peptide-level information up to the protein level. Results: We present a statistical model that carefully accounts for informative missingness in peak intensities and allows unbiased, model-based, protein-level estimation and inference. The model is applicable to both label-based and label-free quantitation experiments. We also provide automated, model-based, algorithms for filtering of proteins and peptides as well as imputation of missing values. Two LC/MS datasets are used to illustrate themore » methods. In simulation studies, our methods are shown to achieve substantially more discoveries than standard alternatives. Availability: The software has been made available in the opensource proteomics platform DAnTE (http://omics.pnl.gov/software/). Contact: adabney@stat.tamu.edu Supplementary information: Supplementary data are available at Bioinformatics online.« less

Comparing Online with Brick and Mortar Course Learning Outcomes: An Analysis of Quantitative Methods Curriculum in Public Administration

ERIC Educational Resources Information Center

Harris, Ronald A.; Nikitenko, Gleb O.

2014-01-01

Teaching graduate students in an intensive adult-learning format presents a special challenge for quantitative analytical competencies. Students often lack necessary background, skills and motivation to deal with quantitative-skill-based course work. This study compares learning outcomes for graduate students enrolled in three course sections…

Evaluation of a real-time quantitative PCR method with propidium monazide treatment for analyses of viable fecal indicator bacteria in wastewater samples

EPA Science Inventory

The U.S. EPA is currently evaluating rapid, real-time quantitative PCR (qPCR) methods for determining recreational water quality based on measurements of fecal indicator bacteria DNA sequences. In order to potentially use qPCR for other Clean Water Act needs, such as updating cri...

Accurate determination of reference materials and natural isolates by means of quantitative (1)h NMR spectroscopy.

PubMed

Frank, Oliver; Kreissl, Johanna Karoline; Daschner, Andreas; Hofmann, Thomas

2014-03-26

A fast and precise proton nuclear magnetic resonance (qHNMR) method for the quantitative determination of low molecular weight target molecules in reference materials and natural isolates has been validated using ERETIC 2 (Electronic REference To access In vivo Concentrations) based on the PULCON (PULse length based CONcentration determination) methodology and compared to the gravimetric results. Using an Avance III NMR spectrometer (400 MHz) equipped with a broad band observe (BBO) probe, the qHNMR method was validated by determining its linearity, range, precision, and accuracy as well as robustness and limit of quantitation. The linearity of the method was assessed by measuring samples of l-tyrosine, caffeine, or benzoic acid in a concentration range between 0.3 and 16.5 mmol/L (r(2) ≥ 0.99), whereas the interday and intraday precisions were found to be ≤2%. The recovery of a range of reference compounds was ≥98.5%, thus demonstrating the qHNMR method as a precise tool for the rapid quantitation (~15 min) of food-related target compounds in reference materials and natural isolates such as nucleotides, polyphenols, or cyclic peptides.

The application of time series models to cloud field morphology analysis

NASA Technical Reports Server (NTRS)

Chin, Roland T.; Jau, Jack Y. C.; Weinman, James A.

1987-01-01

A modeling method for the quantitative description of remotely sensed cloud field images is presented. A two-dimensional texture modeling scheme based on one-dimensional time series procedures is adopted for this purpose. The time series procedure used is the seasonal autoregressive, moving average (ARMA) process in Box and Jenkins. Cloud field properties such as directionality, clustering and cloud coverage can be retrieved by this method. It has been demonstrated that a cloud field image can be quantitatively defined by a small set of parameters and synthesized surrogates can be reconstructed from these model parameters. This method enables cloud climatology to be studied quantitatively.

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.

Caries Detection Methods Based on Changes in Optical Properties between Healthy and Carious Tissue

PubMed Central

Karlsson, Lena

2010-01-01

A conservative, noninvasive or minimally invasive approach to clinical management of dental caries requires diagnostic techniques capable of detecting and quantifying lesions at an early stage, when progression can be arrested or reversed. Objective evidence of initiation of the disease can be detected in the form of distinct changes in the optical properties of the affected tooth structure. Caries detection methods based on changes in a specific optical property are collectively referred to as optically based methods. This paper presents a simple overview of the feasibility of three such technologies for quantitative or semiquantitative assessment of caries lesions. Two of the techniques are well-established: quantitative light-induced fluorescence, which is used primarily in caries research, and laser-induced fluorescence, a commercially available method used in clinical dental practice. The third technique, based on near-infrared transillumination of dental enamel is in the developmental stages. PMID:20454579

Quantitative analysis of fatty-acid-based biofuels produced by wild-type and genetically engineered cyanobacteria by gas chromatography-mass spectrometry.

PubMed

Guan, Wenna; Zhao, Hui; Lu, Xuefeng; Wang, Cong; Yang, Menglong; Bai, Fali

2011-11-11

Simple and rapid quantitative determination of fatty-acid-based biofuels is greatly important for the study of genetic engineering progress for biofuels production by microalgae. Ideal biofuels produced from biological systems should be chemically similar to petroleum, like fatty-acid-based molecules including free fatty acids, fatty acid methyl esters, fatty acid ethyl esters, fatty alcohols and fatty alkanes. This study founded a gas chromatography-mass spectrometry (GC-MS) method for simultaneous quantification of seven free fatty acids, nine fatty acid methyl esters, five fatty acid ethyl esters, five fatty alcohols and three fatty alkanes produced by wild-type Synechocystis PCC 6803 and its genetically engineered strain. Data obtained from GC-MS analyses were quantified using internal standard peak area comparisons. The linearity, limit of detection (LOD) and precision (RSD) of the method were evaluated. The results demonstrated that fatty-acid-based biofuels can be directly determined by GC-MS without derivation. Therefore, rapid and reliable quantitative analysis of fatty-acid-based biofuels produced by wild-type and genetically engineered cyanobacteria can be achieved using the GC-MS method founded in this work. Copyright © 2011 Elsevier B.V. All rights reserved.

Preliminary research on quantitative methods of water resources carrying capacity based on water resources balance sheet

NASA Astrophysics Data System (ADS)

Wang, Yanqiu; Huang, Xiaorong; Gao, Linyun; Guo, Biying; Ma, Kai

2018-06-01

Water resources are not only basic natural resources, but also strategic economic resources and ecological control factors. Water resources carrying capacity constrains the sustainable development of regional economy and society. Studies of water resources carrying capacity can provide helpful information about how the socioeconomic system is both supported and restrained by the water resources system. Based on the research of different scholars, major problems in the study of water resources carrying capacity were summarized as follows: the definition of water resources carrying capacity is not yet unified; the methods of carrying capacity quantification based on the definition of inconsistency are poor in operability; the current quantitative research methods of water resources carrying capacity did not fully reflect the principles of sustainable development; it is difficult to quantify the relationship among the water resources, economic society and ecological environment. Therefore, it is necessary to develop a better quantitative evaluation method to determine the regional water resources carrying capacity. This paper proposes a new approach to quantifying water resources carrying capacity (that is, through the compilation of the water resources balance sheet) to get a grasp of the regional water resources depletion and water environmental degradation (as well as regional water resources stock assets and liabilities), figure out the squeeze of socioeconomic activities on the environment, and discuss the quantitative calculation methods and technical route of water resources carrying capacity which are able to embody the substance of sustainable development.

Sexing chick mRNA: A protocol based on quantitative real-time polymerase chain reaction.

PubMed

Wan, Z; Lu, Y; Rui, L; Yu, X; Li, Z

2017-03-01

The accurate identification of sex in birds is important for research on avian sex determination and differentiation. Polymerase chain reaction (PCR)-based methods have been widely applied for the molecular sexing of birds. However, these methods have used genomic DNA. Here, we present the first sexing protocol for chick mRNA based on real-time quantitative PCR. We demonstrate that this method can accurately determine sex using mRNA from chick gonads and other tissues, such as heart, liver, spleen, lung, and muscle. The strategy of this protocol also may be suitable for other species in which sex is determined by the inheritance of sex chromosomes (ZZ male and ZW female). © 2016 Poultry Science Association Inc.

Acoustics based assessment of respiratory diseases using GMM classification.

PubMed

Mayorga, P; Druzgalski, C; Morelos, R L; Gonzalez, O H; Vidales, J

2010-01-01

The focus of this paper is to present a method utilizing lung sounds for a quantitative assessment of patient health as it relates to respiratory disorders. In order to accomplish this, applicable traditional techniques within the speech processing domain were utilized to evaluate lung sounds obtained with a digital stethoscope. Traditional methods utilized in the evaluation of asthma involve auscultation and spirometry, but utilization of more sensitive electronic stethoscopes, which are currently available, and application of quantitative signal analysis methods offer opportunities of improved diagnosis. In particular we propose an acoustic evaluation methodology based on the Gaussian Mixed Models (GMM) which should assist in broader analysis, identification, and diagnosis of asthma based on the frequency domain analysis of wheezing and crackles.

Convergent and sequential synthesis designs: implications for conducting and reporting systematic reviews of qualitative and quantitative evidence.

PubMed

Hong, Quan Nha; Pluye, Pierre; Bujold, Mathieu; Wassef, Maggy

2017-03-23

Systematic reviews of qualitative and quantitative evidence can provide a rich understanding of complex phenomena. This type of review is increasingly popular, has been used to provide a landscape of existing knowledge, and addresses the types of questions not usually covered in reviews relying solely on either quantitative or qualitative evidence. Although several typologies of synthesis designs have been developed, none have been tested on a large sample of reviews. The aim of this review of reviews was to identify and develop a typology of synthesis designs and methods that have been used and to propose strategies for synthesizing qualitative and quantitative evidence. A review of systematic reviews combining qualitative and quantitative evidence was performed. Six databases were searched from inception to December 2014. Reviews were included if they were systematic reviews combining qualitative and quantitative evidence. The included reviews were analyzed according to three concepts of synthesis processes: (a) synthesis methods, (b) sequence of data synthesis, and (c) integration of data and synthesis results. A total of 459 reviews were included. The analysis of this literature highlighted a lack of transparency in reporting how evidence was synthesized and a lack of consistency in the terminology used. Two main types of synthesis designs were identified: convergent and sequential synthesis designs. Within the convergent synthesis design, three subtypes were found: (a) data-based convergent synthesis design, where qualitative and quantitative evidence is analyzed together using the same synthesis method, (b) results-based convergent synthesis design, where qualitative and quantitative evidence is analyzed separately using different synthesis methods and results of both syntheses are integrated during a final synthesis, and (c) parallel-results convergent synthesis design consisting of independent syntheses of qualitative and quantitative evidence and an interpretation of the results in the discussion. Performing systematic reviews of qualitative and quantitative evidence is challenging because of the multiple synthesis options. The findings provide guidance on how to combine qualitative and quantitative evidence. Also, recommendations are made to improve the conducting and reporting of this type of review.

SU-F-J-112: Clinical Feasibility Test of An RF Pulse-Based MRI Method for the Quantitative Fat-Water Segmentation

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

Yee, S; Wloch, J; Pirkola, M

Purpose: Quantitative fat-water segmentation is important not only because of the clinical utility of fat-suppressed MRI images in better detecting lesions of clinical significance (in the midst of bright fat signal) but also because of the possible physical need, in which CT-like images based on the materials’ photon attenuation properties may have to be generated from MR images; particularly, as in the case of MR-only radiation oncology environment to obtain radiation dose calculation or as in the case of hybrid PET/MR modality to obtain attenuation correction map for the quantitative PET reconstruction. The majority of such fat-water quantitative segmentations havemore » been performed by utilizing the Dixon’s method and its variations, which have to enforce the proper settings (often predefined) of echo time (TE) in the pulse sequences. Therefore, such methods have been unable to be directly combined with those ultrashort TE (UTE) sequences that, taking the advantage of very low TE values (∼ 10’s microsecond), might be beneficial to directly detect bones. Recently, an RF pulse-based method (http://dx.doi.org/10.1016/j.mri.2015.11.006), termed as PROD pulse method, was introduced as a method of quantitative fat-water segmentation that does not have to depend on predefined TE settings. Here, the clinical feasibility of this method is verified in brain tumor patients by combining the PROD pulse with several sequences. Methods: In a clinical 3T MRI, the PROD pulse was combined with turbo spin echo (e.g. TR=1500, TE=16 or 60, ETL=15) or turbo field echo (e.g. TR=5.6, TE=2.8, ETL=12) sequences without specifying TE values. Results: The fat-water segmentation was possible without having to set specific TE values. Conclusion: The PROD pulse method is clinically feasible. Although not yet combined with UTE sequences in our laboratory, the method is potentially compatible with UTE sequences, and thus, might be useful to directly segment fat, water, bone and air.« less

Quantitative and qualitative methods in medical education research: AMEE Guide No 90: Part II.

PubMed

Tavakol, Mohsen; Sandars, John

2014-10-01

Abstract Medical educators need to understand and conduct medical education research in order to make informed decisions based on the best evidence, rather than rely on their own hunches. The purpose of this Guide is to provide medical educators, especially those who are new to medical education research, with a basic understanding of how quantitative and qualitative methods contribute to the medical education evidence base through their different inquiry approaches and also how to select the most appropriate inquiry approach to answer their research questions.

Quantitative and qualitative methods in medical education research: AMEE Guide No 90: Part I.

PubMed

Tavakol, Mohsen; Sandars, John

2014-09-01

Medical educators need to understand and conduct medical education research in order to make informed decisions based on the best evidence, rather than rely on their own hunches. The purpose of this Guide is to provide medical educators, especially those who are new to medical education research, with a basic understanding of how quantitative and qualitative methods contribute to the medical education evidence base through their different inquiry approaches and also how to select the most appropriate inquiry approach to answer their research questions.

Quantitative Evaluation of Heavy Duty Machine Tools Remanufacturing Based on Modified Catastrophe Progression Method

NASA Astrophysics Data System (ADS)

shunhe, Li; jianhua, Rao; lin, Gui; weimin, Zhang; degang, Liu

2017-11-01

The result of remanufacturing evaluation is the basis for judging whether the heavy duty machine tool can remanufacture in the EOL stage of the machine tool lifecycle management.The objectivity and accuracy of evaluation is the key to the evaluation method.In this paper, the catastrophe progression method is introduced into the quantitative evaluation of heavy duty machine tools’ remanufacturing,and the results are modified by the comprehensive adjustment method,which makes the evaluation results accord with the standard of human conventional thinking.Using the catastrophe progression method to establish the heavy duty machine tools’ quantitative evaluation model,to evaluate the retired TK6916 type CNC floor milling-boring machine’s remanufacturing.The evaluation process is simple,high quantification,the result is objective.

Development of CD3 cell quantitation algorithms for renal allograft biopsy rejection assessment utilizing open source image analysis software.

PubMed

Moon, Andres; Smith, Geoffrey H; Kong, Jun; Rogers, Thomas E; Ellis, Carla L; Farris, Alton B Brad

2018-02-01

Renal allograft rejection diagnosis depends on assessment of parameters such as interstitial inflammation; however, studies have shown interobserver variability regarding interstitial inflammation assessment. Since automated image analysis quantitation can be reproducible, we devised customized analysis methods for CD3+ T-cell staining density as a measure of rejection severity and compared them with established commercial methods along with visual assessment. Renal biopsy CD3 immunohistochemistry slides (n = 45), including renal allografts with various degrees of acute cellular rejection (ACR) were scanned for whole slide images (WSIs). Inflammation was quantitated in the WSIs using pathologist visual assessment, commercial algorithms (Aperio nuclear algorithm for CD3+ cells/mm 2 and Aperio positive pixel count algorithm), and customized open source algorithms developed in ImageJ with thresholding/positive pixel counting (custom CD3+%) and identification of pixels fulfilling "maxima" criteria for CD3 expression (custom CD3+ cells/mm 2 ). Based on visual inspections of "markup" images, CD3 quantitation algorithms produced adequate accuracy. Additionally, CD3 quantitation algorithms correlated between each other and also with visual assessment in a statistically significant manner (r = 0.44 to 0.94, p = 0.003 to < 0.0001). Methods for assessing inflammation suggested a progression through the tubulointerstitial ACR grades, with statistically different results in borderline versus other ACR types, in all but the custom methods. Assessment of CD3-stained slides using various open source image analysis algorithms presents salient correlations with established methods of CD3 quantitation. These analysis techniques are promising and highly customizable, providing a form of on-slide "flow cytometry" that can facilitate additional diagnostic accuracy in tissue-based assessments.

Extraction efficiency and implications for absolute quantitation of propranolol in mouse brain, liver and kidney thin tissue sections using droplet-based liquid microjunction surface sampling-HPLC ESI-MS/MS

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

Kertesz, Vilmos; Weiskittel, Taylor M.; Vavek, Marissa

Currently, absolute quantitation aspects of droplet-based surface sampling for thin tissue analysis using a fully automated autosampler/HPLC-ESI-MS/MS system are not fully evaluated. Knowledge of extraction efficiency and its reproducibility is required to judge the potential of the method for absolute quantitation of analytes from thin tissue sections. Methods: Adjacent thin tissue sections of propranolol dosed mouse brain (10- μm-thick), kidney (10- μm-thick) and liver (8-, 10-, 16- and 24- μm-thick) were obtained. Absolute concentration of propranolol was determined in tissue punches from serial sections using standard bulk tissue extraction protocols and subsequent HPLC separations and tandem mass spectrometric analysis. Thesemore » values were used to determine propranolol extraction efficiency from the tissues with the droplet-based surface sampling approach. Results: Extraction efficiency of propranolol using 10- μm-thick brain, kidney and liver thin tissues using droplet-based surface sampling varied between ~45-63%. Extraction efficiency decreased from ~65% to ~36% with liver thickness increasing from 8 μm to 24 μm. Randomly selecting half of the samples as standards, precision and accuracy of propranolol concentrations obtained for the other half of samples as quality control metrics were determined. Resulting precision ( ±15%) and accuracy ( ±3%) values, respectively, were within acceptable limits. In conclusion, comparative quantitation of adjacent mouse thin tissue sections of different organs and of various thicknesses by droplet-based surface sampling and by bulk extraction of tissue punches showed that extraction efficiency was incomplete using the former method, and that it depended on the organ and tissue thickness. However, once extraction efficiency was determined and applied, the droplet-based approach provided the required quantitation accuracy and precision for assay validations. Furthermore, this means that once the extraction efficiency was calibrated for a given tissue type and drug, the droplet-based approach provides a non-labor intensive and high-throughput means to acquire spatially resolved quantitative analysis of multiple samples of the same type.« less

Extraction efficiency and implications for absolute quantitation of propranolol in mouse brain, liver and kidney thin tissue sections using droplet-based liquid microjunction surface sampling-HPLC ESI-MS/MS

DOE PAGES

Kertesz, Vilmos; Weiskittel, Taylor M.; Vavek, Marissa; ...

2016-06-22

Currently, absolute quantitation aspects of droplet-based surface sampling for thin tissue analysis using a fully automated autosampler/HPLC-ESI-MS/MS system are not fully evaluated. Knowledge of extraction efficiency and its reproducibility is required to judge the potential of the method for absolute quantitation of analytes from thin tissue sections. Methods: Adjacent thin tissue sections of propranolol dosed mouse brain (10- μm-thick), kidney (10- μm-thick) and liver (8-, 10-, 16- and 24- μm-thick) were obtained. Absolute concentration of propranolol was determined in tissue punches from serial sections using standard bulk tissue extraction protocols and subsequent HPLC separations and tandem mass spectrometric analysis. Thesemore » values were used to determine propranolol extraction efficiency from the tissues with the droplet-based surface sampling approach. Results: Extraction efficiency of propranolol using 10- μm-thick brain, kidney and liver thin tissues using droplet-based surface sampling varied between ~45-63%. Extraction efficiency decreased from ~65% to ~36% with liver thickness increasing from 8 μm to 24 μm. Randomly selecting half of the samples as standards, precision and accuracy of propranolol concentrations obtained for the other half of samples as quality control metrics were determined. Resulting precision ( ±15%) and accuracy ( ±3%) values, respectively, were within acceptable limits. In conclusion, comparative quantitation of adjacent mouse thin tissue sections of different organs and of various thicknesses by droplet-based surface sampling and by bulk extraction of tissue punches showed that extraction efficiency was incomplete using the former method, and that it depended on the organ and tissue thickness. However, once extraction efficiency was determined and applied, the droplet-based approach provided the required quantitation accuracy and precision for assay validations. Furthermore, this means that once the extraction efficiency was calibrated for a given tissue type and drug, the droplet-based approach provides a non-labor intensive and high-throughput means to acquire spatially resolved quantitative analysis of multiple samples of the same type.« less

Quantitation of peptides from non-invasive skin tapings using isotope dilution and tandem mass spectrometry.

PubMed

Reisdorph, Nichole; Armstrong, Michael; Powell, Roger; Quinn, Kevin; Legg, Kevin; Leung, Donald; Reisdorph, Rick

2018-05-01

Previous work from our laboratories utilized a novel skin taping method and mass spectrometry-based proteomics to discover clinical biomarkers of skin conditions; these included atopic dermatitis, Staphylococcus aureus colonization, and eczema herpeticum. While suitable for discovery purposes, semi-quantitative proteomics is generally time-consuming and expensive. Furthermore, depending on the method used, discovery-based proteomics can result in high variation and inadequate sensitivity to detect low abundant peptides. Therefore, we strove to develop a rapid, sensitive, and reproducible method to quantitate disease-related proteins from skin tapings. We utilized isotopically-labeled peptides and tandem mass spectrometry to obtain absolute quantitation values on 14 peptides from 7 proteins; these proteins had shown previous importance in skin disease. The method demonstrated good reproducibility, dynamic range, and linearity (R 2  > 0.993) when n = 3 standards were analyzed across 0.05-2.5 pmol. The method was used to determine if differences exist between skin proteins in a small group of atopic versus non-atopic individuals (n = 12). While only minimal differences were found, peptides were detected in all samples and exhibited good correlation between peptides for 5 of the 7 proteins (R 2  = 0.71-0.98). This method can be applied to larger cohorts to further establish the relationships of these proteins to skin disease. Copyright © 2017. Published by Elsevier B.V.

A mixed-methods investigation of successful aging among older women engaged in sports-based versus exercise-based leisure time physical activities.

PubMed

Berlin, Kathryn; Kruger, Tina; Klenosky, David B

2018-01-01

This mixed-methods study compares active older women in different physically based leisure activities and explores the difference in subjective ratings of successful aging and quantifiable predictors of success. A survey was administered to 256 women, 60-92 years of age, engaged in a sports- or exercise-based activity. Quantitative data were analyzed through ANOVA and multiple regression. Qualitative data (n = 79) was analyzed using the approach associated with means-end theory. While participants quantitatively appeared similar in terms of successful aging, qualitative interviews revealed differences in activity motivation. Women involved in sports highlighted social/psychological benefits, while those involved in exercise-based activities stressed fitness outcomes.

How Students Choose a College: Understanding the Role of Internet Based Resources in the College Choice Process

ERIC Educational Resources Information Center

Burdett, Kimberli R.

2013-01-01

The purpose of this study was to gain a better understanding of how current internet-based resources are affecting the college choice process. An explanatory mixed methods design was used, and the study involved collecting qualitative data after a quantitative phase to explain the quantitative data in greater depth. An additional study was…

Rapid Determination of Lymphogranuloma Venereum Serovars of Chlamydia trachomatis by Quantitative High-Resolution Melt Analysis (HRMA)

PubMed Central

Stevens, Matthew P.; Garland, Suzanne M.; Zaia, Angelo M.; Tabrizi, Sepehr N.

2012-01-01

A quantitative high-resolution melt analysis assay was developed to differentiate lymphogranuloma venereum-causing serovars of Chlamydia trachomatis (L1 to L3) from other C. trachomatis serovars (D to K). The detection limit of this assay is approximately 10 copies per reaction, comparable to the limits of other quantitative-PCR-based methods. PMID:22933594

The effects of AVIRIS atmospheric calibration methodology on identification and quantitative mapping of surface mineralogy, Drum Mountains, Utah

NASA Technical Reports Server (NTRS)

Kruse, Fred A.; Dwyer, John L.

1993-01-01

The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) measures reflected light in 224 contiguous spectra bands in the 0.4 to 2.45 micron region of the electromagnetic spectrum. Numerous studies have used these data for mineralogic identification and mapping based on the presence of diagnostic spectral features. Quantitative mapping requires conversion of the AVIRIS data to physical units (usually reflectance) so that analysis results can be compared and validated with field and laboratory measurements. This study evaluated two different AVIRIS calibration techniques to ground reflectance: an empirically-based method and an atmospheric model based method to determine their effects on quantitative scientific analyses. Expert system analysis and linear spectral unmixing were applied to both calibrated data sets to determine the effect of the calibration on the mineral identification and quantitative mapping results. Comparison of the image-map results and image reflectance spectra indicate that the model-based calibrated data can be used with automated mapping techniques to produce accurate maps showing the spatial distribution and abundance of surface mineralogy. This has positive implications for future operational mapping using AVIRIS or similar imaging spectrometer data sets without requiring a priori knowledge.

Fuzzy method of recognition of high molecular substances in evidence-based biology

NASA Astrophysics Data System (ADS)

Olevskyi, V. I.; Smetanin, V. T.; Olevska, Yu. B.

2017-10-01

Nowadays modern requirements to achieving reliable results along with high quality of researches put mathematical analysis methods of results at the forefront. Because of this, evidence-based methods of processing experimental data have become increasingly popular in the biological sciences and medicine. Their basis is meta-analysis, a method of quantitative generalization of a large number of randomized trails contributing to a same special problem, which are often contradictory and performed by different authors. It allows identifying the most important trends and quantitative indicators of the data, verification of advanced hypotheses and discovering new effects in the population genotype. The existing methods of recognizing high molecular substances by gel electrophoresis of proteins under denaturing conditions are based on approximate methods for comparing the contrast of electrophoregrams with a standard solution of known substances. We propose a fuzzy method for modeling experimental data to increase the accuracy and validity of the findings of the detection of new proteins.

Development and in-house validation of the event-specific qualitative and quantitative PCR detection methods for genetically modified cotton MON15985.

PubMed

Jiang, Lingxi; Yang, Litao; Rao, Jun; Guo, Jinchao; Wang, Shu; Liu, Jia; Lee, Seonghun; Zhang, Dabing

2010-02-01

To implement genetically modified organism (GMO) labeling regulations, an event-specific analysis method based on the junction sequence between exogenous integration and host genomic DNA has become the preferential approach for GMO identification and quantification. In this study, specific primers and TaqMan probes based on the revealed 5'-end junction sequence of GM cotton MON15985 were designed, and qualitative and quantitative polymerase chain reaction (PCR) assays were established employing the designed primers and probes. In the qualitative PCR assay, the limit of detection (LOD) was 0.5 g kg(-1) in 100 ng total cotton genomic DNA, corresponding to about 17 copies of haploid cotton genomic DNA, and the LOD and limit of quantification (LOQ) for quantitative PCR assay were 10 and 17 copies of haploid cotton genomic DNA, respectively. Furthermore, the developed quantitative PCR assays were validated in-house by five different researchers. Also, five practical samples with known GM contents were quantified using the developed PCR assay in in-house validation, and the bias between the true and quantification values ranged from 2.06% to 12.59%. This study shows that the developed qualitative and quantitative PCR methods are applicable for the identification and quantification of GM cotton MON15985 and its derivates.

Effective Heart Disease Detection Based on Quantitative Computerized Traditional Chinese Medicine Using Representation Based Classifiers.

PubMed

Shu, Ting; Zhang, Bob; Tang, Yuan Yan

2017-01-01

At present, heart disease is the number one cause of death worldwide. Traditionally, heart disease is commonly detected using blood tests, electrocardiogram, cardiac computerized tomography scan, cardiac magnetic resonance imaging, and so on. However, these traditional diagnostic methods are time consuming and/or invasive. In this paper, we propose an effective noninvasive computerized method based on facial images to quantitatively detect heart disease. Specifically, facial key block color features are extracted from facial images and analyzed using the Probabilistic Collaborative Representation Based Classifier. The idea of facial key block color analysis is founded in Traditional Chinese Medicine. A new dataset consisting of 581 heart disease and 581 healthy samples was experimented by the proposed method. In order to optimize the Probabilistic Collaborative Representation Based Classifier, an analysis of its parameters was performed. According to the experimental results, the proposed method obtains the highest accuracy compared with other classifiers and is proven to be effective at heart disease detection.

NNAlign: A Web-Based Prediction Method Allowing Non-Expert End-User Discovery of Sequence Motifs in Quantitative Peptide Data

PubMed Central

Andreatta, Massimo; Schafer-Nielsen, Claus; Lund, Ole; Buus, Søren; Nielsen, Morten

2011-01-01

Recent advances in high-throughput technologies have made it possible to generate both gene and protein sequence data at an unprecedented rate and scale thereby enabling entirely new “omics”-based approaches towards the analysis of complex biological processes. However, the amount and complexity of data that even a single experiment can produce seriously challenges researchers with limited bioinformatics expertise, who need to handle, analyze and interpret the data before it can be understood in a biological context. Thus, there is an unmet need for tools allowing non-bioinformatics users to interpret large data sets. We have recently developed a method, NNAlign, which is generally applicable to any biological problem where quantitative peptide data is available. This method efficiently identifies underlying sequence patterns by simultaneously aligning peptide sequences and identifying motifs associated with quantitative readouts. Here, we provide a web-based implementation of NNAlign allowing non-expert end-users to submit their data (optionally adjusting method parameters), and in return receive a trained method (including a visual representation of the identified motif) that subsequently can be used as prediction method and applied to unknown proteins/peptides. We have successfully applied this method to several different data sets including peptide microarray-derived sets containing more than 100,000 data points. NNAlign is available online at http://www.cbs.dtu.dk/services/NNAlign. PMID:22073191

NNAlign: a web-based prediction method allowing non-expert end-user discovery of sequence motifs in quantitative peptide data.

PubMed

Andreatta, Massimo; Schafer-Nielsen, Claus; Lund, Ole; Buus, Søren; Nielsen, Morten

2011-01-01

Recent advances in high-throughput technologies have made it possible to generate both gene and protein sequence data at an unprecedented rate and scale thereby enabling entirely new "omics"-based approaches towards the analysis of complex biological processes. However, the amount and complexity of data that even a single experiment can produce seriously challenges researchers with limited bioinformatics expertise, who need to handle, analyze and interpret the data before it can be understood in a biological context. Thus, there is an unmet need for tools allowing non-bioinformatics users to interpret large data sets. We have recently developed a method, NNAlign, which is generally applicable to any biological problem where quantitative peptide data is available. This method efficiently identifies underlying sequence patterns by simultaneously aligning peptide sequences and identifying motifs associated with quantitative readouts. Here, we provide a web-based implementation of NNAlign allowing non-expert end-users to submit their data (optionally adjusting method parameters), and in return receive a trained method (including a visual representation of the identified motif) that subsequently can be used as prediction method and applied to unknown proteins/peptides. We have successfully applied this method to several different data sets including peptide microarray-derived sets containing more than 100,000 data points. NNAlign is available online at http://www.cbs.dtu.dk/services/NNAlign.

Dissociative conceptual and quantitative problem solving outcomes across interactive engagement and traditional format introductory physics

NASA Astrophysics Data System (ADS)

McDaniel, Mark A.; Stoen, Siera M.; Frey, Regina F.; Markow, Zachary E.; Hynes, K. Mairin; Zhao, Jiuqing; Cahill, Michael J.

2016-12-01

The existing literature indicates that interactive-engagement (IE) based general physics classes improve conceptual learning relative to more traditional lecture-oriented classrooms. Very little research, however, has examined quantitative problem-solving outcomes from IE based relative to traditional lecture-based physics classes. The present study included both pre- and post-course conceptual-learning assessments and a new quantitative physics problem-solving assessment that included three representative conservation of energy problems from a first-semester calculus-based college physics course. Scores for problem translation, plan coherence, solution execution, and evaluation of solution plausibility were extracted for each problem. Over 450 students in three IE-based sections and two traditional lecture sections taught at the same university during the same semester participated. As expected, the IE-based course produced more robust gains on a Force Concept Inventory than did the lecture course. By contrast, when the full sample was considered, gains in quantitative problem solving were significantly greater for lecture than IE-based physics; when students were matched on pre-test scores, there was still no advantage for IE-based physics on gains in quantitative problem solving. Further, the association between performance on the concept inventory and quantitative problem solving was minimal. These results highlight that improved conceptual understanding does not necessarily support improved quantitative physics problem solving, and that the instructional method appears to have less bearing on gains in quantitative problem solving than does the kinds of problems emphasized in the courses and homework and the overlap of these problems to those on the assessment.

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

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

Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens

We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

DOE PAGES

Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens; ...

2016-12-15

We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

A method for operative quantitative interpretation of multispectral images of biological tissues

NASA Astrophysics Data System (ADS)

Lisenko, S. A.; Kugeiko, M. M.

2013-10-01

A method for operative retrieval of spatial distributions of biophysical parameters of a biological tissue by using a multispectral image of it has been developed. The method is based on multiple regressions between linearly independent components of the diffuse reflection spectrum of the tissue and unknown parameters. Possibilities of the method are illustrated by an example of determining biophysical parameters of the skin (concentrations of melanin, hemoglobin and bilirubin, blood oxygenation, and scattering coefficient of the tissue). Examples of quantitative interpretation of the experimental data are presented.

Precise Quantitation of MicroRNA in a Single Cell with Droplet Digital PCR Based on Ligation Reaction.

PubMed

Tian, Hui; Sun, Yuanyuan; Liu, Chenghui; Duan, Xinrui; Tang, Wei; Li, Zhengping

2016-12-06

MicroRNA (miRNA) analysis in a single cell is extremely important because it allows deep understanding of the exact correlation between the miRNAs and cell functions. Herein, we wish to report a highly sensitive and precisely quantitative assay for miRNA detection based on ligation-based droplet digital polymerase chain reaction (ddPCR), which permits the quantitation of miRNA in a single cell. In this ligation-based ddPCR assay, two target-specific oligonucleotide probes can be simply designed to be complementary to the half-sequence of the target miRNA, respectively, which avoids the sophisticated design of reverse transcription and provides high specificity to discriminate a single-base difference among miRNAs with simple operations. After the miRNA-templated ligation, the ddPCR partitions individual ligated products into a water-in-oil droplet and digitally counts the fluorescence-positive and negative droplets after PCR amplification for quantification of the target molecules, which possesses the power of precise quantitation and robustness to variation in PCR efficiency. By integrating the advantages of the precise quantification of ddPCR and the simplicity of the ligation-based PCR, the proposed method can sensitively measure let-7a miRNA with a detection limit of 20 aM (12 copies per microliter), and even a single-base difference can be discriminated in let-7 family members. More importantly, due to its high selectivity and sensitivity, the proposed method can achieve precise quantitation of miRNAs in single-cell lysate. Therefore, the ligation-based ddPCR assay may serve as a useful tool to exactly reveal the miRNAs' actions in a single cell, which is of great importance for the study of miRNAs' biofunction as well as for the related biomedical studies.

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.

Characterization and quantitation of polyolefin microplastics in personal-care products using high-temperature gel-permeation chromatography.

PubMed

Hintersteiner, Ingrid; Himmelsbach, Markus; Buchberger, Wolfgang W

2015-02-01

In recent years, the development of reliable methods for the quantitation of microplastics in different samples, including evaluating the particles' adverse effects in the marine environment, has become a great concern. Because polyolefins are the most prevalent type of polymer in personal-care products containing microplastics, this study presents a novel approach for their quantitation. The method is suitable for aqueous and hydrocarbon-based products, and includes a rapid sample clean-up involving twofold density separation and a subsequent quantitation with high-temperature gel-permeation chromatography. In contrast with previous procedures, both errors caused by weighing after insufficient separation of plastics and matrix and time-consuming visual sorting are avoided. In addition to reliable quantitative results, in this investigation a comprehensive characterization of the polymer particles isolated from the product matrix, covering size, shape, molecular weight distribution and stabilization, is provided. Results for seven different personal-care products are presented. Recoveries of this method were in the range of 92-96 %.

Methodological reporting in qualitative, quantitative, and mixed methods health services research articles.

PubMed

Wisdom, Jennifer P; Cavaleri, Mary A; Onwuegbuzie, Anthony J; Green, Carla A

2012-04-01

Methodologically sound mixed methods research can improve our understanding of health services by providing a more comprehensive picture of health services than either method can alone. This study describes the frequency of mixed methods in published health services research and compares the presence of methodological components indicative of rigorous approaches across mixed methods, qualitative, and quantitative articles. All empirical articles (n = 1,651) published between 2003 and 2007 from four top-ranked health services journals. All mixed methods articles (n = 47) and random samples of qualitative and quantitative articles were evaluated to identify reporting of key components indicating rigor for each method, based on accepted standards for evaluating the quality of research reports (e.g., use of p-values in quantitative reports, description of context in qualitative reports, and integration in mixed method reports). We used chi-square tests to evaluate differences between article types for each component. Mixed methods articles comprised 2.85 percent (n = 47) of empirical articles, quantitative articles 90.98 percent (n = 1,502), and qualitative articles 6.18 percent (n = 102). There was a statistically significant difference (χ(2) (1) = 12.20, p = .0005, Cramer's V = 0.09, odds ratio = 1.49 [95% confidence interval = 1,27, 1.74]) in the proportion of quantitative methodological components present in mixed methods compared to quantitative papers (21.94 versus 47.07 percent, respectively) but no statistically significant difference (χ(2) (1) = 0.02, p = .89, Cramer's V = 0.01) in the proportion of qualitative methodological components in mixed methods compared to qualitative papers (21.34 versus 25.47 percent, respectively). Few published health services research articles use mixed methods. The frequency of key methodological components is variable. Suggestions are provided to increase the transparency of mixed methods studies and the presence of key methodological components in published reports. © Health Research and Educational Trust.

Methodological Reporting in Qualitative, Quantitative, and Mixed Methods Health Services Research Articles

PubMed Central

Wisdom, Jennifer P; Cavaleri, Mary A; Onwuegbuzie, Anthony J; Green, Carla A

2012-01-01

Objectives Methodologically sound mixed methods research can improve our understanding of health services by providing a more comprehensive picture of health services than either method can alone. This study describes the frequency of mixed methods in published health services research and compares the presence of methodological components indicative of rigorous approaches across mixed methods, qualitative, and quantitative articles. Data Sources All empirical articles (n = 1,651) published between 2003 and 2007 from four top-ranked health services journals. Study Design All mixed methods articles (n = 47) and random samples of qualitative and quantitative articles were evaluated to identify reporting of key components indicating rigor for each method, based on accepted standards for evaluating the quality of research reports (e.g., use of p-values in quantitative reports, description of context in qualitative reports, and integration in mixed method reports). We used chi-square tests to evaluate differences between article types for each component. Principal Findings Mixed methods articles comprised 2.85 percent (n = 47) of empirical articles, quantitative articles 90.98 percent (n = 1,502), and qualitative articles 6.18 percent (n = 102). There was a statistically significant difference (χ2(1) = 12.20, p = .0005, Cramer's V = 0.09, odds ratio = 1.49 [95% confidence interval = 1,27, 1.74]) in the proportion of quantitative methodological components present in mixed methods compared to quantitative papers (21.94 versus 47.07 percent, respectively) but no statistically significant difference (χ2(1) = 0.02, p = .89, Cramer's V = 0.01) in the proportion of qualitative methodological components in mixed methods compared to qualitative papers (21.34 versus 25.47 percent, respectively). Conclusion Few published health services research articles use mixed methods. The frequency of key methodological components is variable. Suggestions are provided to increase the transparency of mixed methods studies and the presence of key methodological components in published reports. PMID:22092040

Iterative optimization method for design of quantitative magnetization transfer imaging experiments.

PubMed

Levesque, Ives R; Sled, John G; Pike, G Bruce

2011-09-01

Quantitative magnetization transfer imaging (QMTI) using spoiled gradient echo sequences with pulsed off-resonance saturation can be a time-consuming technique. A method is presented for selection of an optimum experimental design for quantitative magnetization transfer imaging based on the iterative reduction of a discrete sampling of the Z-spectrum. The applicability of the technique is demonstrated for human brain white matter imaging at 1.5 T and 3 T, and optimal designs are produced to target specific model parameters. The optimal number of measurements and the signal-to-noise ratio required for stable parameter estimation are also investigated. In vivo imaging results demonstrate that this optimal design approach substantially improves parameter map quality. The iterative method presented here provides an advantage over free form optimal design methods, in that pragmatic design constraints are readily incorporated. In particular, the presented method avoids clustering and repeated measures in the final experimental design, an attractive feature for the purpose of magnetization transfer model validation. The iterative optimal design technique is general and can be applied to any method of quantitative magnetization transfer imaging. Copyright © 2011 Wiley-Liss, Inc.

Analysis of Mammalian Sphingolipids by Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS) and Tissue Imaging Mass Spectrometry (TIMS)

PubMed Central

Sullards, M. Cameron; Liu, Ying; Chen, Yanfeng; Merrill, Alfred H.

2011-01-01

Sphingolipids are a highly diverse category of molecules that serve not only as components of biological structures but also as regulators of numerous cell functions. Because so many of the structural features of sphingolipids give rise to their biological activity, there is a need for comprehensive or “sphingolipidomic” methods for identification and quantitation of as many individual subspecies as possible. This review defines sphingolipids as a class, briefly discusses classical methods for their analysis, and focuses primarily on liquid chromatography tandem mass spectrometry (LC-MS/MS) and tissue imaging mass spectrometry (TIMS). Recently, a set of evolving and expanding methods have been developed and rigorously validated for the extraction, identification, separation, and quantitation of sphingolipids by LC-MS/MS. Quantitation of these biomolecules is made possible via the use of an internal standard cocktail. The compounds that can be readily analyzed are free long-chain (sphingoid) bases, sphingoid base 1-phosphates, and more complex species such as ceramides, ceramide 1-phosphates, sphingomyelins, mono- and di-hexosylceramides sulfatides, and novel compounds such as the 1-deoxy- and 1-(deoxymethyl)-sphingoid bases and their N-acyl-derivatives. These methods can be altered slightly to separate and quantitate isomeric species such as glucosyl/galactosylceramide. Because these techniques require the extraction of sphingolipids from their native environment, any information regarding their localization in histological slices is lost. Therefore, this review also describes methods for TIMS. This technique has been shown to be a powerful tool to determine the localization of individual molecular species of sphingolipids directly from tissue slices. PMID:21749933

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.

Constrained CVT meshes and a comparison of triangular mesh generators

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

Nguyen, Hoa; Burkardt, John; Gunzburger, Max

2009-01-01

Mesh generation in regions in Euclidean space is a central task in computational science, and especially for commonly used numerical methods for the solution of partial differential equations, e.g., finite element and finite volume methods. We focus on the uniform Delaunay triangulation of planar regions and, in particular, on how one selects the positions of the vertices of the triangulation. We discuss a recently developed method, based on the centroidal Voronoi tessellation (CVT) concept, for effecting such triangulations and present two algorithms, including one new one, for CVT-based grid generation. We also compare several methods, including CVT-based methods, for triangulatingmore » planar domains. To this end, we define several quantitative measures of the quality of uniform grids. We then generate triangulations of several planar regions, including some having complexities that are representative of what one may encounter in practice. We subject the resulting grids to visual and quantitative comparisons and conclude that all the methods considered produce high-quality uniform grids and that the CVT-based grids are at least as good as any of the others.« less

Boron concentration measurements by alpha spectrometry and quantitative neutron autoradiography in cells and tissues treated with different boronated formulations and administration protocols.

PubMed

Bortolussi, Silva; Ciani, Laura; Postuma, Ian; Protti, Nicoletta; Luca Reversi; Bruschi, Piero; Ferrari, Cinzia; Cansolino, Laura; Panza, Luigi; Ristori, Sandra; Altieri, Saverio

2014-06-01

The possibility to measure boron concentration with high precision in tissues that will be irradiated represents a fundamental step for a safe and effective BNCT treatment. In Pavia, two techniques have been used for this purpose, a quantitative method based on charged particles spectrometry and a boron biodistribution imaging based on neutron autoradiography. A quantitative method to determine boron concentration by neutron autoradiography has been recently set-up and calibrated for the measurement of biological samples, both solid and liquid, in the frame of the feasibility study of BNCT. This technique was calibrated and the obtained results were cross checked with those of α spectrometry, in order to validate them. The comparisons were performed using tissues taken form animals treated with different boron administration protocols. Subsequently the quantitative neutron autoradiography was employed to measure osteosarcoma cell samples treated with BPA and with new boronated formulations. © 2013 Published by Elsevier Ltd.

[Quantitative Analysis of Heavy Metals in Water with LIBS Based on Signal-to-Background Ratio].

PubMed

Hu, Li; Zhao, Nan-jing; Liu, Wen-qing; Fang, Li; Zhang, Da-hai; Wang, Yin; Meng, De Shuo; Yu, Yang; Ma, Ming-jun

2015-07-01

There are many influence factors in the precision and accuracy of the quantitative analysis with LIBS technology. According to approximately the same characteristics trend of background spectrum and characteristic spectrum along with the change of temperature through in-depth analysis, signal-to-background ratio (S/B) measurement and regression analysis could compensate the spectral line intensity changes caused by system parameters such as laser power, spectral efficiency of receiving. Because the measurement dates were limited and nonlinear, we used support vector machine (SVM) for regression algorithm. The experimental results showed that the method could improve the stability and the accuracy of quantitative analysis of LIBS, and the relative standard deviation and average relative error of test set respectively were 4.7% and 9.5%. Data fitting method based on signal-to-background ratio(S/B) is Less susceptible to matrix elements and background spectrum etc, and provides data processing reference for real-time online LIBS quantitative analysis technology.

Hepatitis C Virus RNA Real-Time Quantitative RT-PCR Method Based on a New Primer Design Strategy.

PubMed

Chen, Lida; Li, Wenli; Zhang, Kuo; Zhang, Rui; Lu, Tian; Hao, Mingju; Jia, Tingting; Sun, Yu; Lin, Guigao; Wang, Lunan; Li, Jinming

2016-01-01

Viral nucleic acids are unstable when improperly collected, handled, and stored, resulting in decreased sensitivity of currently available commercial quantitative nucleic acid testing kits. Using known unstable hepatitis C virus RNA, we developed a quantitative RT-PCR method based on a new primer design strategy to reduce the impact of nucleic acid instability on nucleic acid testing. The performance of the method was evaluated for linearity, limit of detection, precision, specificity, and agreement with commercial hepatitis C virus assays. Its clinical application was compared to that of two commercial kits--Cobas AmpliPrep/Cobas TaqMan (CAP/CTM) and Kehua. The quantitative RT-PCR method delivered a good performance, with a linearity of R(2) = 0.99, a total limit of detection (genotypes 1 to 6) of 42.6 IU/mL (95% CI, 32.84 to 67.76 IU/mL), a CV of 1.06% to 3.34%, a specificity of 100%, and a high concordance with the CAP/CTM assay (R(2) = 0.97), with a means ± SD value of -0.06 ± 1.96 log IU/mL (range, -0.38 to 0.25 log IU/mL). The method was superior to commercial assays in detecting unstable hepatitis C virus RNA (P < 0.05). This quantitative RT-PCR method can effectively eliminate the influence of RNA instability on nucleic acid testing. The principle of primer design strategy may be applied to the detection of other RNA or DNA viruses. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Development of quantitative analysis method for stereotactic brain image: assessment of reduced accumulation in extent and severity using anatomical segmentation.

PubMed

Mizumura, Sunao; Kumita, Shin-ichiro; Cho, Keiichi; Ishihara, Makiko; Nakajo, Hidenobu; Toba, Masahiro; Kumazaki, Tatsuo

2003-06-01

Through visual assessment by three-dimensional (3D) brain image analysis methods using stereotactic brain coordinates system, such as three-dimensional stereotactic surface projections and statistical parametric mapping, it is difficult to quantitatively assess anatomical information and the range of extent of an abnormal region. In this study, we devised a method to quantitatively assess local abnormal findings by segmenting a brain map according to anatomical structure. Through quantitative local abnormality assessment using this method, we studied the characteristics of distribution of reduced blood flow in cases with dementia of the Alzheimer type (DAT). Using twenty-five cases with DAT (mean age, 68.9 years old), all of whom were diagnosed as probable Alzheimer's disease based on NINCDS-ADRDA, we collected I-123 iodoamphetamine SPECT data. A 3D brain map using the 3D-SSP program was compared with the data of 20 cases in the control group, who age-matched the subject cases. To study local abnormalities on the 3D images, we divided the whole brain into 24 segments based on anatomical classification. We assessed the extent of an abnormal region in each segment (rate of the coordinates with a Z-value that exceeds the threshold value, in all coordinates within a segment), and severity (average Z-value of the coordinates with a Z-value that exceeds the threshold value). This method clarified orientation and expansion of reduced accumulation, through classifying stereotactic brain coordinates according to the anatomical structure. This method was considered useful for quantitatively grasping distribution abnormalities in the brain and changes in abnormality distribution.

A comparative proteomics method for multiple samples based on a 18O-reference strategy and a quantitation and identification-decoupled strategy.

PubMed

Wang, Hongbin; Zhang, Yongqian; Gui, Shuqi; Zhang, Yong; Lu, Fuping; Deng, Yulin

2017-08-15

Comparisons across large numbers of samples are frequently necessary in quantitative proteomics. Many quantitative methods used in proteomics are based on stable isotope labeling, but most of these are only useful for comparing two samples. For up to eight samples, the iTRAQ labeling technique can be used. For greater numbers of samples, the label-free method has been used, but this method was criticized for low reproducibility and accuracy. An ingenious strategy has been introduced, comparing each sample against a 18 O-labeled reference sample that was created by pooling equal amounts of all samples. However, it is necessary to use proportion-known protein mixtures to investigate and evaluate this new strategy. Another problem for comparative proteomics of multiple samples is the poor coincidence and reproducibility in protein identification results across samples. In present study, a method combining 18 O-reference strategy and a quantitation and identification-decoupled strategy was investigated with proportion-known protein mixtures. The results obviously demonstrated that the 18 O-reference strategy had greater accuracy and reliability than other previously used comparison methods based on transferring comparison or label-free strategies. By the decoupling strategy, the quantification data acquired by LC-MS and the identification data acquired by LC-MS/MS are matched and correlated to identify differential expressed proteins, according to retention time and accurate mass. This strategy made protein identification possible for all samples using a single pooled sample, and therefore gave a good reproducibility in protein identification across multiple samples, and allowed for optimizing peptide identification separately so as to identify more proteins. Copyright © 2017 Elsevier B.V. All rights reserved.

The need and approach for characterization - U.S. air force perspectives on materials state awareness

NASA Astrophysics Data System (ADS)

Aldrin, John C.; Lindgren, Eric A.

2018-04-01

This paper expands on the objective and motivation for NDE-based characterization and includes a discussion of the current approach using model-assisted inversion being pursued within the Air Force Research Laboratory (AFRL). This includes a discussion of the multiple model-based methods that can be used, including physics-based models, deep machine learning, and heuristic approaches. The benefits and drawbacks of each method is reviewed and the potential to integrate multiple methods is discussed. Initial successes are included to highlight the ability to obtain quantitative values of damage. Additional steps remaining to realize this capability with statistical metrics of accuracy are discussed, and how these results can be used to enable probabilistic life management are addressed. The outcome of this initiative will realize the long-term desired capability of NDE methods to provide quantitative characterization to accelerate certification of new materials and enhance life management of engineered systems.

Usefulness of a Dual Macro- and Micro-Energy-Dispersive X-Ray Fluorescence Spectrometer to Develop Quantitative Methodologies for Historic Mortar and Related Materials Characterization.

PubMed

García-Florentino, Cristina; Maguregui, Maite; Romera-Fernández, Miriam; Queralt, Ignasi; Margui, Eva; Madariaga, Juan Manuel

2018-05-01

Wavelength dispersive X-ray fluorescence (WD-XRF) spectrometry has been widely used for elemental quantification of mortars and cements. In this kind of instrument, samples are usually prepared as pellets or fused beads and the whole volume of sample is measured at once. In this work, the usefulness of a dual energy dispersive X-ray fluorescence spectrometer (ED-XRF), working at two lateral resolutions (1 mm and 25 μm) for macro and microanalysis respectively, to develop quantitative methods for the elemental characterization of mortars and concretes is demonstrated. A crucial step before developing any quantitative method with this kind of spectrometers is to verify the homogeneity of the standards at these two lateral resolutions. This new ED-XRF quantitative method also demonstrated the importance of matrix effects in the accuracy of the results being necessary to use Certified Reference Materials as standards. The results obtained with the ED-XRF quantitative method were compared with the ones obtained with two WD-XRF quantitative methods employing two different sample preparation strategies (pellets and fused beads). The selected ED-XRF and both WD-XRF quantitative methods were applied to the analysis of real mortars. The accuracy of the ED-XRF results turn out to be similar to the one achieved by WD-XRF, except for the lightest elements (Na and Mg). The results described in this work proved that μ-ED-XRF spectrometers can be used not only for acquiring high resolution elemental map distributions, but also to perform accurate quantitative studies avoiding the use of more sophisticated WD-XRF systems or the acid extraction/alkaline fusion required as destructive pretreatment in Inductively coupled plasma mass spectrometry based procedures.

Improvement of the analog forecasting method by using local thermodynamic data. Application to autumn precipitation in Catalonia

NASA Astrophysics Data System (ADS)

Gibergans-Báguena, J.; Llasat, M. C.

2007-12-01

The objective of this paper is to present the improvement of quantitative forecasting of daily rainfall in Catalonia (NE Spain) from an analogues technique, taking into account synoptic and local data. This method is based on an analogues sorting technique: meteorological situations similar to the current one, in terms of 700 and 1000 hPa geopotential fields at 00 UTC, complemented with the inclusion of some thermodynamic parameters extracted from an historical data file. Thermodynamic analysis acts as a highly discriminating feature for situations in which the synoptic situation fails to explain either atmospheric phenomena or rainfall distribution. This is the case in heavy rainfall situations, where the existence of instability and high water vapor content is essential. With the objective of including these vertical thermodynamic features, information provided by the Palma de Mallorca radiosounding (Spain) has been used. Previously, a selection of the most discriminating thermodynamic parameters for the daily rainfall was made, and then the analogues technique applied to them. Finally, three analog forecasting methods were applied for the quantitative daily rainfall forecasting in Catalonia. The first one is based on analogies from geopotential fields to synoptic scale; the second one is exclusively based on the search of similarity from local thermodynamic information and the third method combines the other two methods. The results show that this last method provides a substantial improvement of quantitative rainfall estimation.

ANTONIA perfusion and stroke. A software tool for the multi-purpose analysis of MR perfusion-weighted datasets and quantitative ischemic stroke assessment.

PubMed

Forkert, N D; Cheng, B; Kemmling, A; Thomalla, G; Fiehler, J

2014-01-01

The objective of this work is to present the software tool ANTONIA, which has been developed to facilitate a quantitative analysis of perfusion-weighted MRI (PWI) datasets in general as well as the subsequent multi-parametric analysis of additional datasets for the specific purpose of acute ischemic stroke patient dataset evaluation. Three different methods for the analysis of DSC or DCE PWI datasets are currently implemented in ANTONIA, which can be case-specifically selected based on the study protocol. These methods comprise a curve fitting method as well as a deconvolution-based and deconvolution-free method integrating a previously defined arterial input function. The perfusion analysis is extended for the purpose of acute ischemic stroke analysis by additional methods that enable an automatic atlas-based selection of the arterial input function, an analysis of the perfusion-diffusion and DWI-FLAIR mismatch as well as segmentation-based volumetric analyses. For reliability evaluation, the described software tool was used by two observers for quantitative analysis of 15 datasets from acute ischemic stroke patients to extract the acute lesion core volume, FLAIR ratio, perfusion-diffusion mismatch volume with manually as well as automatically selected arterial input functions, and follow-up lesion volume. The results of this evaluation revealed that the described software tool leads to highly reproducible results for all parameters if the automatic arterial input function selection method is used. Due to the broad selection of processing methods that are available in the software tool, ANTONIA is especially helpful to support image-based perfusion and acute ischemic stroke research projects.

The Functional Resonance Analysis Method for a systemic risk based environmental auditing in a sinter plant: A semi-quantitative approach

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

Patriarca, Riccardo, E-mail: riccardo.patriarca@uniroma1.it; Di Gravio, Giulio; Costantino, Francesco

Environmental auditing is a main issue for any production plant and assessing environmental performance is crucial to identify risks factors. The complexity of current plants arises from interactions among technological, human and organizational system components, which are often transient and not easily detectable. The auditing thus requires a systemic perspective, rather than focusing on individual behaviors, as emerged in recent research in the safety domain for socio-technical systems. We explore the significance of modeling the interactions of system components in everyday work, by the application of a recent systemic method, i.e. the Functional Resonance Analysis Method (FRAM), in order tomore » define dynamically the system structure. We present also an innovative evolution of traditional FRAM following a semi-quantitative approach based on Monte Carlo simulation. This paper represents the first contribution related to the application of FRAM in the environmental context, moreover considering a consistent evolution based on Monte Carlo simulation. The case study of an environmental risk auditing in a sinter plant validates the research, showing the benefits in terms of identifying potential critical activities, related mitigating actions and comprehensive environmental monitoring indicators. - Highlights: • We discuss the relevance of a systemic risk based environmental audit. • We present FRAM to represent functional interactions of the system. • We develop a semi-quantitative FRAM framework to assess environmental risks. • We apply the semi-quantitative FRAM framework to build a model for a sinter plant.« less

Quantitative characterization of genetic parts and circuits for plant synthetic biology.

PubMed

Schaumberg, Katherine A; Antunes, Mauricio S; Kassaw, Tessema K; Xu, Wenlong; Zalewski, Christopher S; Medford, June I; Prasad, Ashok

2016-01-01

Plant synthetic biology promises immense technological benefits, including the potential development of a sustainable bio-based economy through the predictive design of synthetic gene circuits. Such circuits are built from quantitatively characterized genetic parts; however, this characterization is a significant obstacle in work with plants because of the time required for stable transformation. We describe a method for rapid quantitative characterization of genetic plant parts using transient expression in protoplasts and dual luciferase outputs. We observed experimental variability in transient-expression assays and developed a mathematical model to describe, as well as statistical normalization methods to account for, this variability, which allowed us to extract quantitative parameters. We characterized >120 synthetic parts in Arabidopsis and validated our method by comparing transient expression with expression in stably transformed plants. We also tested >100 synthetic parts in sorghum (Sorghum bicolor) protoplasts, and the results showed that our method works in diverse plant groups. Our approach enables the construction of tunable gene circuits in complex eukaryotic organisms.

Probing myocardium biomechanics using quantitative optical coherence elastography

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

We present a quantitative optical coherence elastographic method for noncontact assessment of the myocardium elasticity. The method is based on shear wave imaging optical coherence tomography (SWI-OCT), where a focused air-puff system is used to induce localized tissue deformation through a low-pressure short-duration air stream and a phase-sensitive OCT system is utilized to monitor the propagation of the induced tissue displacement with nanoscale sensitivity. The 1-D scanning of M-mode OCT imaging and the application of optical phase retrieval and mapping techniques enable the reconstruction and visualization of 2-D depth-resolved shear wave propagation in tissue with ultra-high frame rate. The feasibility of this method in quantitative elasticity measurement is demonstrated on tissue-mimicking phantoms with the estimated Young's modulus compared with uniaxial compression tests. We also performed pilot experiments on ex vivo mouse cardiac muscle tissues with normal and genetically altered cardiomyocytes. Our results indicate this noncontact quantitative optical coherence elastographic method can be a useful tool for the cardiac muscle research and studies.

Grid workflow validation using ontology-based tacit knowledge: A case study for quantitative remote sensing applications

NASA Astrophysics Data System (ADS)

Liu, Jia; Liu, Longli; Xue, Yong; Dong, Jing; Hu, Yingcui; Hill, Richard; Guang, Jie; Li, Chi

2017-01-01

Workflow for remote sensing quantitative retrieval is the ;bridge; between Grid services and Grid-enabled application of remote sensing quantitative retrieval. Workflow averts low-level implementation details of the Grid and hence enables users to focus on higher levels of application. The workflow for remote sensing quantitative retrieval plays an important role in remote sensing Grid and Cloud computing services, which can support the modelling, construction and implementation of large-scale complicated applications of remote sensing science. The validation of workflow is important in order to support the large-scale sophisticated scientific computation processes with enhanced performance and to minimize potential waste of time and resources. To research the semantic correctness of user-defined workflows, in this paper, we propose a workflow validation method based on tacit knowledge research in the remote sensing domain. We first discuss the remote sensing model and metadata. Through detailed analysis, we then discuss the method of extracting the domain tacit knowledge and expressing the knowledge with ontology. Additionally, we construct the domain ontology with Protégé. Through our experimental study, we verify the validity of this method in two ways, namely data source consistency error validation and parameters matching error validation.

Mixed methods for implementation research: application to evidence-based practice implementation and staff turnover in community-based organizations providing child welfare services.

PubMed

Aarons, Gregory A; Fettes, Danielle L; Sommerfeld, David H; Palinkas, Lawrence A

2012-02-01

Many public sector service systems and provider organizations are in some phase of learning about or implementing evidence-based interventions. Child welfare service systems represent a context where implementation spans system, management, and organizational concerns. Research utilizing mixed methods that combine qualitative and quantitative design, data collection, and analytic approaches are particularly well suited to understanding both the process and outcomes of dissemination and implementation efforts in child welfare systems. This article describes the process of using mixed methods in implementation research and provides an applied example of an examination of factors impacting staff retention during an evidence-based intervention implementation in a statewide child welfare system. The authors integrate qualitative data with previously published quantitative analyses of job autonomy and staff turnover during this statewide implementation project in order to illustrate the utility of mixed method approaches in providing a more comprehensive understanding of opportunities and challenges in implementation research.

Mixed Methods for Implementation Research: Application to Evidence-Based Practice Implementation and Staff Turnover in Community Based Organizations Providing Child Welfare Services

PubMed Central

Aarons, Gregory A.; Fettes, Danielle L.; Sommerfeld, David H.; Palinkas, Lawrence

2013-01-01

Many public sector services systems and provider organizations are in some phase of learning about or implementing evidence-based interventions. Child welfare service systems represent a context where implementation spans system, management, and organizational concerns. Research utilizing mixed methods that combine qualitative and quantitative design, data collection, and analytic approaches are particularly well-suited to understanding both the process and outcomes of dissemination and implementation efforts in child welfare systems. This paper describes the process of using mixed methods in implementation research and provides an applied example of an examination of factors impacting staff retention during an evidence-based intervention implementation in a statewide child welfare system. We integrate qualitative data with previously published quantitative analyses of job autonomy and staff turnover during this statewide implementation project in order to illustrate the utility of mixed method approaches in providing a more comprehensive understanding of opportunities and challenges in implementation research. PMID:22146861

Ultratrace level determination and quantitative analysis of kidney injury biomarkers in patient samples attained by zinc oxide nanorods

NASA Astrophysics Data System (ADS)

Singh, Manpreet; Alabanza, Anginelle; Gonzalez, Lorelis E.; Wang, Weiwei; Reeves, W. Brian; Hahm, Jong-In

2016-02-01

Determining ultratrace amounts of protein biomarkers in patient samples in a straightforward and quantitative manner is extremely important for early disease diagnosis and treatment. Here, we successfully demonstrate the novel use of zinc oxide nanorods (ZnO NRs) in the ultrasensitive and quantitative detection of two acute kidney injury (AKI)-related protein biomarkers, tumor necrosis factor (TNF)-α and interleukin (IL)-8, directly from patient samples. We first validate the ZnO NRs-based IL-8 results via comparison with those obtained from using a conventional enzyme-linked immunosorbent method in samples from 38 individuals. We further assess the full detection capability of the ZnO NRs-based technique by quantifying TNF-α, whose levels in human urine are often below the detection limits of conventional methods. Using the ZnO NR platforms, we determine the TNF-α concentrations of all 46 patient samples tested, down to the fg per mL level. Subsequently, we screen for TNF-α levels in approximately 50 additional samples collected from different patient groups in order to demonstrate a potential use of the ZnO NRs-based assay in assessing cytokine levels useful for further clinical monitoring. Our research efforts demonstrate that ZnO NRs can be straightforwardly employed in the rapid, ultrasensitive, quantitative, and simultaneous detection of multiple AKI-related biomarkers directly in patient urine samples, providing an unparalleled detection capability beyond those of conventional analysis methods. Additional key advantages of the ZnO NRs-based approach include a fast detection speed, low-volume assay condition, multiplexing ability, and easy automation/integration capability to existing fluorescence instrumentation. Therefore, we anticipate that our ZnO NRs-based detection method will be highly beneficial for overcoming the frequent challenges in early biomarker development and treatment assessment, pertaining to the facile and ultrasensitive quantification of hard-to-trace biomolecules.Determining ultratrace amounts of protein biomarkers in patient samples in a straightforward and quantitative manner is extremely important for early disease diagnosis and treatment. Here, we successfully demonstrate the novel use of zinc oxide nanorods (ZnO NRs) in the ultrasensitive and quantitative detection of two acute kidney injury (AKI)-related protein biomarkers, tumor necrosis factor (TNF)-α and interleukin (IL)-8, directly from patient samples. We first validate the ZnO NRs-based IL-8 results via comparison with those obtained from using a conventional enzyme-linked immunosorbent method in samples from 38 individuals. We further assess the full detection capability of the ZnO NRs-based technique by quantifying TNF-α, whose levels in human urine are often below the detection limits of conventional methods. Using the ZnO NR platforms, we determine the TNF-α concentrations of all 46 patient samples tested, down to the fg per mL level. Subsequently, we screen for TNF-α levels in approximately 50 additional samples collected from different patient groups in order to demonstrate a potential use of the ZnO NRs-based assay in assessing cytokine levels useful for further clinical monitoring. Our research efforts demonstrate that ZnO NRs can be straightforwardly employed in the rapid, ultrasensitive, quantitative, and simultaneous detection of multiple AKI-related biomarkers directly in patient urine samples, providing an unparalleled detection capability beyond those of conventional analysis methods. Additional key advantages of the ZnO NRs-based approach include a fast detection speed, low-volume assay condition, multiplexing ability, and easy automation/integration capability to existing fluorescence instrumentation. Therefore, we anticipate that our ZnO NRs-based detection method will be highly beneficial for overcoming the frequent challenges in early biomarker development and treatment assessment, pertaining to the facile and ultrasensitive quantification of hard-to-trace biomolecules. Electronic supplementary information (ESI) available: Typical SEM images of the ZnO NRs used in the biomarker assays are provided in Fig. S1. See DOI: 10.1039/c5nr08706f

[The water content reference material of water saturated octanol].

PubMed

Wang, Haifeng; Ma, Kang; Zhang, Wei; Li, Zhanyuan

2011-03-01

The national standards of biofuels specify the technique specification and analytical methods. A water content certified reference material based on the water saturated octanol was developed in order to satisfy the needs of the instrument calibration and the methods validation, assure the accuracy and consistency of results in water content measurements of biofuels. Three analytical methods based on different theories were employed to certify the water content of the reference material, including Karl Fischer coulometric titration, Karl Fischer volumetric titration and quantitative nuclear magnetic resonance. The consistency of coulometric and volumetric titration was achieved through the improvement of methods. The accuracy of the certified result was improved by the introduction of the new method of quantitative nuclear magnetic resonance. Finally, the certified value of reference material is 4.76% with an expanded uncertainty of 0.09%.

A novel multi-walled carbon nanotube-based antibody conjugate for quantitative and semi-quantitative lateral flow assays.

PubMed

Sun, Wenjuan; Hu, Xiaolong; Liu, Jia; Zhang, Yurong; Lu, Jianzhong; Zeng, Libo

2017-10-01

In this study, the multi-walled carbon nanotubes (MWCNTs) were applied in lateral flow strips (LFS) for semi-quantitative and quantitative assays. Firstly, the solubility of MWCNTs was improved using various surfactants to enhance their biocompatibility for practical application. The dispersed MWCNTs were conjugated with the methamphetamine (MET) antibody in a non-covalent manner and then manufactured into the LFS for the quantitative detection of MET. The MWCNTs-based lateral flow assay (MWCNTs-LFA) exhibited an excellent linear relationship between the values of test line and MET when its concentration ranges from 62.5 to 1500 ng/mL. The sensitivity of the LFS was evaluated by conjugating MWCNTs with HCG antibody and the MWCNTs conjugated method is 10 times more sensitive than the one conjugated with classical colloidal gold nanoparticles. Taken together, our data demonstrate that MWCNTs-LFA is a more sensitive and reliable assay for semi-quantitative and quantitative detection which can be used in forensic analysis.

[Study of Cervical Exfoliated Cell's DNA Quantitative Analysis Based on Multi-Spectral Imaging Technology].

PubMed

Wu, Zheng; Zeng, Li-bo; Wu, Qiong-shui

2016-02-01

The conventional cervical cancer screening methods mainly include TBS (the bethesda system) classification method and cellular DNA quantitative analysis, however, by using multiple staining method in one cell slide, which is staining the cytoplasm with Papanicolaou reagent and the nucleus with Feulgen reagent, the study of achieving both two methods in the cervical cancer screening at the same time is still blank. Because the difficulty of this multiple staining method is that the absorbance of the non-DNA material may interfere with the absorbance of DNA, so that this paper has set up a multi-spectral imaging system, and established an absorbance unmixing model by using multiple linear regression method based on absorbance's linear superposition character, and successfully stripped out the absorbance of DNA to run the DNA quantitative analysis, and achieved the perfect combination of those two kinds of conventional screening method. Through a series of experiment we have proved that between the absorbance of DNA which is calculated by the absorbance unmixxing model and the absorbance of DNA which is measured there is no significant difference in statistics when the test level is 1%, also the result of actual application has shown that there is no intersection between the confidence interval of the DNA index of the tetraploid cells which are screened by using this paper's analysis method when the confidence level is 99% and the DNA index's judging interval of cancer cells, so that the accuracy and feasibility of the quantitative DNA analysis with multiple staining method expounded by this paper have been verified, therefore this analytical method has a broad application prospect and considerable market potential in early diagnosis of cervical cancer and other cancers.

Bibliometrics for Social Validation.

PubMed

Hicks, Daniel J

2016-01-01

This paper introduces a bibliometric, citation network-based method for assessing the social validation of novel research, and applies this method to the development of high-throughput toxicology research at the US Environmental Protection Agency. Social validation refers to the acceptance of novel research methods by a relevant scientific community; it is formally independent of the technical validation of methods, and is frequently studied in history, philosophy, and social studies of science using qualitative methods. The quantitative methods introduced here find that high-throughput toxicology methods are spread throughout a large and well-connected research community, which suggests high social validation. Further assessment of social validation involving mixed qualitative and quantitative methods are discussed in the conclusion.

Bibliometrics for Social Validation

PubMed Central

2016-01-01

This paper introduces a bibliometric, citation network-based method for assessing the social validation of novel research, and applies this method to the development of high-throughput toxicology research at the US Environmental Protection Agency. Social validation refers to the acceptance of novel research methods by a relevant scientific community; it is formally independent of the technical validation of methods, and is frequently studied in history, philosophy, and social studies of science using qualitative methods. The quantitative methods introduced here find that high-throughput toxicology methods are spread throughout a large and well-connected research community, which suggests high social validation. Further assessment of social validation involving mixed qualitative and quantitative methods are discussed in the conclusion. PMID:28005974

The qualitative-quantitative debate: moving from positivism and confrontation to post-positivism and reconciliation.

PubMed

Clark, A M

1998-06-01

Critiques of logical positivism form the foundation for a significant number of nursing research papers, with the philosophy being inappropriately deemed synonymous with empirical method. Frequently, proposing an alternative method to those identified with the quantitative paradigm, these critiques are based on a poor foundation. This paper highlights an alternative philosophy to positivism which can also underpin empirical inquiry, that of post-positivism. Post-positivism is contrasted with positivism, which is presented as an outmoded and rejected philosophy which should cease to significantly shape inquiry. Though some acknowledgement of post-positivism has occurred in the nursing literature, this has yet to permeate into mainstream nursing research. Many still base their arguments on a positivistic view of science. Through achievement of a better understanding of post-positivism and greater focus on explicating the philosophical assumptions underpinning all research methods, the distinctions that have long been perceived to exist between qualitative and quantitative methodologies can be confined to the past. Rather methods will be selected solely on the nature of research questions.

Fatigue crack identification method based on strain amplitude changing

NASA Astrophysics Data System (ADS)

Guo, Tiancai; Gao, Jun; Wang, Yonghong; Xu, Youliang

2017-09-01

Aiming at the difficulties in identifying the location and time of crack initiation in the castings of helicopter transmission system during fatigue tests, by introducing the classification diagnostic criteria of similar failure mode to find out the similarity of fatigue crack initiation among castings, an engineering method and quantitative criterion for detecting fatigue cracks based on strain amplitude changing is proposed. This method is applied on the fatigue test of a gearbox housing, whose results indicates: during the fatigue test, the system alarms when SC strain meter reaches the quantitative criterion. The afterwards check shows that a fatigue crack less than 5mm is found at the corresponding location of SC strain meter. The test result proves that the method can provide accurate test data for strength life analysis.

Quantitative phase imaging method based on an analytical nonparaxial partially coherent phase optical transfer function.

PubMed

Bao, Yijun; Gaylord, Thomas K

2016-11-01

Multifilter phase imaging with partially coherent light (MFPI-PC) is a promising new quantitative phase imaging method. However, the existing MFPI-PC method is based on the paraxial approximation. In the present work, an analytical nonparaxial partially coherent phase optical transfer function is derived. This enables the MFPI-PC to be extended to the realistic nonparaxial case. Simulations over a wide range of test phase objects as well as experimental measurements on a microlens array verify higher levels of imaging accuracy compared to the paraxial method. Unlike the paraxial version, the nonparaxial MFPI-PC with obliquity factor correction exhibits no systematic error. In addition, due to its analytical expression, the increase in computation time compared to the paraxial version is negligible.

A quantitative analysis of qualitative studies in clinical journals for the 2000 publishing year

PubMed Central

McKibbon, Kathleen Ann; Gadd, Cynthia S

2004-01-01

Background Quantitative studies are becoming more recognized as important to understanding health care with all of its richness and complexities. The purpose of this descriptive survey was to provide a quantitative evaluation of the qualitative studies published in 170 core clinical journals for 2000. Methods All identified studies that used qualitative methods were reviewed to ascertain which clinical journals publish qualitative studies and to extract research methods, content (persons and health care issues studied), and whether mixed methods (quantitative and qualitative methods) were used. Results 60 330 articles were reviewed. 355 reports of original qualitative studies and 12 systematic review articles were identified in 48 journals. Most of the journals were in the discipline of nursing. Only 4 of the most highly cited health care journals, based on ISI Science Citation Index (SCI) Impact Factors, published qualitative studies. 37 of the 355 original reports used both qualitative and quantitative (mixed) methods. Patients and non-health care settings were the most common groups of people studied. Diseases and conditions were cancer, mental health, pregnancy and childbirth, and cerebrovascular disease with many other diseases and conditions represented. Phenomenology and grounded theory were commonly used; substantial ethnography was also present. No substantial differences were noted for content or methods when articles published in all disciplines were compared with articles published in nursing titles or when studies with mixed methods were compared with studies that included only qualitative methods. Conclusions The clinical literature includes many qualitative studies although they are often published in nursing journals or journals with low SCI Impact Factor journals. Many qualitative studies incorporate both qualitative and quantitative methods. PMID:15271221

A globotetraosylceramide (Gb₄) receptor-based ELISA for quantitative detection of Shiga toxin 2e.

PubMed

Togashi, Katsuhiro; Sasaki, Shiho; Sato, Wataru

2015-08-01

Currently, no simple assays are available for routine quantitative detection of Escherichia coli-produced Shiga toxin 2e (Stx2e) that causes porcine edema disease. Here, we present a novel quantitative detection method for Stx2e based on the measurement of Stx2e binding to the specific globotetraosylceramide (Gb4) receptor by ELISA (Gb4-ELISA). No cross-reactivity was found with the other Shiga toxins Stx1 and Stx2, indicating high specificity. When the recombinant Stx2e B subunit (Stx2eB) was used, the absorbance measured by Gb4-ELISA increased linearly with Stx2eB concentration in the range of 20-2,500 ng/ml. The Gb4-ELISA method can be easily performed, suggesting that it would be a useful diagnostic tool for porcine edema disease.

Evaluation of Quantitative Performance of Sequential Immobilized Metal Affinity Chromatographic Enrichment for Phosphopeptides

PubMed Central

Sun, Zeyu; Hamilton, Karyn L.; Reardon, Kenneth F.

2014-01-01

We evaluated a sequential elution protocol from immobilized metal affinity chromatography (SIMAC) employing gallium-based immobilized metal affinity chromatography (IMAC) in conjunction with titanium-dioxide-based metal oxide affinity chromatography (MOAC). The quantitative performance of this SIMAC enrichment approach, assessed in terms of repeatability, dynamic range, and linearity, was evaluated using a mixture composed of tryptic peptides from caseins, bovine serum albumin, and phosphopeptide standards. While our data demonstrate the overall consistent performance of the SIMAC approach under various loading conditions, the results also revealed that the method had limited repeatability and linearity for most phosphopeptides tested, and different phosphopeptides were found to have different linear ranges. These data suggest that, unless additional strategies are used, SIMAC should be regarded as a semi-quantitative method when used in large-scale phosphoproteomics studies in complex backgrounds. PMID:24096195

Advanced quantitative measurement methodology in physics education research

NASA Astrophysics Data System (ADS)

Wang, Jing

The ultimate goal of physics education research (PER) is to develop a theoretical framework to understand and improve the learning process. In this journey of discovery, assessment serves as our headlamp and alpenstock. It sometimes detects signals in student mental structures, and sometimes presents the difference between expert understanding and novice understanding. Quantitative assessment is an important area in PER. Developing research-based effective assessment instruments and making meaningful inferences based on these instruments have always been important goals of the PER community. Quantitative studies are often conducted to provide bases for test development and result interpretation. Statistics are frequently used in quantitative studies. The selection of statistical methods and interpretation of the results obtained by these methods shall be connected to the education background. In this connecting process, the issues of educational models are often raised. Many widely used statistical methods do not make assumptions on the mental structure of subjects, nor do they provide explanations tailored to the educational audience. There are also other methods that consider the mental structure and are tailored to provide strong connections between statistics and education. These methods often involve model assumption and parameter estimation, and are complicated mathematically. The dissertation provides a practical view of some advanced quantitative assessment methods. The common feature of these methods is that they all make educational/psychological model assumptions beyond the minimum mathematical model. The purpose of the study is to provide a comparison between these advanced methods and the pure mathematical methods. The comparison is based on the performance of the two types of methods under physics education settings. In particular, the comparison uses both physics content assessments and scientific ability assessments. The dissertation includes three parts. The first part involves the comparison between item response theory (IRT) and classical test theory (CTT). The two theories both provide test item statistics for educational inferences and decisions. The two theories are both applied to Force Concept Inventory data obtained from students enrolled in The Ohio State University. Effort was made to examine the similarity and difference between the two theories, and the possible explanation to the difference. The study suggests that item response theory is more sensitive to the context and conceptual features of the test items than classical test theory. The IRT parameters provide a better measure than CTT parameters for the educational audience to investigate item features. The second part of the dissertation is on the measure of association for binary data. In quantitative assessment, binary data is often encountered because of its simplicity. The current popular measures of association fail under some extremely unbalanced conditions. However, the occurrence of these conditions is not rare in educational data. Two popular association measures, the Pearson's correlation and the tetrachoric correlation are examined. A new method, model based association is introduced, and an educational testing constraint is discussed. The existing popular methods are compared with the model based association measure with and without the constraint. Connections between the value of association and the context and conceptual features of questions are discussed in detail. Results show that all the methods have their advantages and disadvantages. Special attention to the test and data conditions is necessary. The last part of the dissertation is focused on exploratory factor analysis (EFA). The theoretical advantages of EFA are discussed. Typical misunderstanding and misusage of EFA are explored. The EFA is performed on Lawson's Classroom Test of Scientific Reasoning (LCTSR), a widely used assessment on scientific reasoning skills. The reasoning ability structures for U.S. and Chinese students at different educational levels are given by the analysis. A final discussion on the advanced quantitative assessment methodology and the pure mathematical methodology is presented at the end.

Using PSEA-Quant for Protein Set Enrichment Analysis of Quantitative Mass Spectrometry-Based Proteomics.

PubMed

Lavallée-Adam, Mathieu; Yates, John R

2016-03-24

PSEA-Quant analyzes quantitative mass spectrometry-based proteomics datasets to identify enrichments of annotations contained in repositories such as the Gene Ontology and Molecular Signature databases. It allows users to identify the annotations that are significantly enriched for reproducibly quantified high abundance proteins. PSEA-Quant is available on the Web and as a command-line tool. It is compatible with all label-free and isotopic labeling-based quantitative proteomics methods. This protocol describes how to use PSEA-Quant and interpret its output. The importance of each parameter as well as troubleshooting approaches are also discussed. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Qualification of a Quantitative Method for Monitoring Aspartate Isomerization of a Monoclonal Antibody by Focused Peptide Mapping.

PubMed

Cao, Mingyan; Mo, Wenjun David; Shannon, Anthony; Wei, Ziping; Washabaugh, Michael; Cash, Patricia

Aspartate (Asp) isomerization is a common post-translational modification of recombinant therapeutic proteins that can occur during manufacturing, storage, or administration. Asp isomerization in the complementarity-determining regions of a monoclonal antibody may affect the target binding and thus a sufficiently robust quality control method for routine monitoring is desirable. In this work, we utilized a liquid chromatography-mass spectrometry (LC/MS)-based approach to identify the Asp isomerization in the complementarity-determining regions of a therapeutic monoclonal antibody. To quantitate the site-specific Asp isomerization of the monoclonal antibody, a UV detection-based quantitation assay utilizing the same LC platform was developed. The assay was qualified and implemented for routine monitoring of this product-specific modification. Compared with existing methods, this analytical paradigm is applicable to identify Asp isomerization (or other modifications) and subsequently develop a rapid, sufficiently robust quality control method for routine site-specific monitoring and quantitation to ensure product quality. This approach first identifies and locates a product-related impurity (a critical quality attribute) caused by isomerization, deamidation, oxidation, or other post-translational modifications, and then utilizes synthetic peptides and MS to assist the development of a LC-UV-based chromatographic method that separates and quantifies the product-related impurities by UV peaks. The established LC-UV method has acceptable peak specificity, precision, linearity, and accuracy; it can be validated and used in a good manufacturing practice environment for lot release and stability testing. Aspartate isomerization is a common post-translational modification of recombinant proteins during manufacture process and storage. Isomerization in the complementarity-determining regions (CDRs) of a monoclonal antibody A (mAb-A) has been detected and has been shown to have impact on the binding affinity to the antigen. In this work, we utilized a mass spectrometry-based peptide mapping approach to detect and quantitate the Asp isomerization in the CDRs of mAb-A. To routinely monitor the CDR isomerization of mAb-A, a focused peptide mapping method utilizing reversed phase chromatographic separation and UV detection has been developed and qualified. This approach is generally applicable to monitor isomerization and other post-translational modifications of proteins in a specific and high-throughput mode to ensure product quality. © PDA, Inc. 2016.

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.

Improving Student Understanding of Qualitative and Quantitative Analysis via GC/MS Using a Rapid SPME-Based Method for Determination of Trihalomethanes in Drinking Water

ERIC Educational Resources Information Center

Huang, Shu Rong; Palmer, Peter T.

2017-01-01

This paper describes a method for determination of trihalomethanes (THMs) in drinking water via solid-phase microextraction (SPME) GC/MS as a means to develop and improve student understanding of the use of GC/MS for qualitative and quantitative analysis. In the classroom, students are introduced to SPME, GC/MS instrumentation, and the use of MS…

A simple approach to quantitative analysis using three-dimensional spectra based on selected Zernike moments.

PubMed

Zhai, Hong Lin; Zhai, Yue Yuan; Li, Pei Zhen; Tian, Yue Li

2013-01-21

A very simple approach to quantitative analysis is proposed based on the technology of digital image processing using three-dimensional (3D) spectra obtained by high-performance liquid chromatography coupled with a diode array detector (HPLC-DAD). As the region-based shape features of a grayscale image, Zernike moments with inherently invariance property were employed to establish the linear quantitative models. This approach was applied to the quantitative analysis of three compounds in mixed samples using 3D HPLC-DAD spectra, and three linear models were obtained, respectively. The correlation coefficients (R(2)) for training and test sets were more than 0.999, and the statistical parameters and strict validation supported the reliability of established models. The analytical results suggest that the Zernike moment selected by stepwise regression can be used in the quantitative analysis of target compounds. Our study provides a new idea for quantitative analysis using 3D spectra, which can be extended to the analysis of other 3D spectra obtained by different methods or instruments.

Translational value of liquid chromatography coupled with tandem mass spectrometry-based quantitative proteomics for in vitro-in vivo extrapolation of drug metabolism and transport and considerations in selecting appropriate techniques.

PubMed

Al Feteisi, Hajar; Achour, Brahim; Rostami-Hodjegan, Amin; Barber, Jill

2015-01-01

Drug-metabolizing enzymes and transporters play an important role in drug absorption, distribution, metabolism and excretion and, consequently, they influence drug efficacy and toxicity. Quantification of drug-metabolizing enzymes and transporters in various tissues is therefore essential for comprehensive elucidation of drug absorption, distribution, metabolism and excretion. Recent advances in liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) have improved the quantification of pharmacologically relevant proteins. This report presents an overview of mass spectrometry-based methods currently used for the quantification of drug-metabolizing enzymes and drug transporters, mainly focusing on applications and cost associated with various quantitative strategies based on stable isotope-labeled standards (absolute quantification peptide standards, quantification concatemers, protein standards for absolute quantification) and label-free analysis. In mass spectrometry, there is no simple relationship between signal intensity and analyte concentration. Proteomic strategies are therefore complex and several factors need to be considered when selecting the most appropriate method for an intended application, including the number of proteins and samples. Quantitative strategies require appropriate mass spectrometry platforms, yet choice is often limited by the availability of appropriate instrumentation. Quantitative proteomics research requires specialist practical skills and there is a pressing need to dedicate more effort and investment to training personnel in this area. Large-scale multicenter collaborations are also needed to standardize quantitative strategies in order to improve physiologically based pharmacokinetic models.

Stable Isotope Quantitative N-Glycan Analysis by Liquid Separation Techniques and Mass Spectrometry.

PubMed

Mittermayr, Stefan; Albrecht, Simone; Váradi, Csaba; Millán-Martín, Silvia; Bones, Jonathan

2017-01-01

Liquid phase separation analysis and subsequent quantitation remains a challenging task for protein-derived oligosaccharides due to their inherent structural complexity and diversity. Incomplete resolution or co-detection of multiple glycan species complicates peak area-based quantitation and associated statistical analysis when optical detection methods are used. The approach outlined herein describes the utilization of stable isotope variants of commonly used fluorescent tags that allow for mass-based glycan identification and relative quantitation following separation by liquid chromatography (LC) or capillary electrophoresis (CE). Comparability assessment of glycoprotein-derived oligosaccharides is performed by derivatization with commercially available isotope variants of 2-aminobenzoic acid or aniline and analysis by LC- and CE-mass spectrometry. Quantitative information is attained from the extracted ion chromatogram/electropherogram ratios generated from the light and heavy isotope clusters.

The efficacy of semi-quantitative urine protein-to-creatinine (P/C) ratio for the detection of significant proteinuria in urine specimens in health screening settings.

PubMed

Chang, Chih-Chun; Su, Ming-Jang; Ho, Jung-Li; Tsai, Yu-Hui; Tsai, Wei-Ting; Lee, Shu-Jene; Yen, Tzung-Hai; Chu, Fang-Yeh

2016-01-01

Urine protein detection could be underestimated using the conventional dipstick method because of variations in urine aliquots. This study aimed to assess the efficacy of the semi-quantitative urine protein-to-creatinine (P/C) ratio compared with other laboratory methods. Random urine samples were requested from patients undergoing chronic kidney disease screening. Significant proteinuria was determined by the quantitative P/C ratio of at least 150 mg protein/g creatinine. The semi-quantitative P/C ratio, dipstick protein and quantitative protein concentrations were compared and analyzed. In the 2932 urine aliquots, 156 (5.3 %) urine samples were considered as diluted and 60 (39.2 %) were found as significant proteinuria. The semi-quantitative P/C ratio testing had the best sensitivity (70.0 %) and specificity (95.9 %) as well as the lowest underestimation rate (0.37 %) when compared to other laboratory methods in the study. In the semi-quantitative P/C ratio test, 19 (12.2 %) had positive, 52 (33.3 %) had diluted, and 85 (54.5 %) had negative results. Of those with positive results, 7 (36.8 %) were positive detected by traditional dipstick urine protein test, and 9 (47.4 %) were positive detected by quantitative urine protein test. Additionally, of those with diluted results, 25 (48.1 %) had significant proteinuria, and all were assigned as no significant proteinuria by both tests. The semi-quantitative urine P/C ratio is clinically applicable based on its better sensitivity and screening ability for significant proteinuria than other laboratory methods, particularly in diluted urine samples. To establish an effective strategy for CKD prevention, urine protein screening with semi-quantitative P/C ratio could be considered.

Recombinant plasmid-based quantitative Real-Time PCR analysis of Salmonella enterica serotypes and its application to milk samples.

PubMed

Gokduman, Kurtulus; Avsaroglu, M Dilek; Cakiris, Aris; Ustek, Duran; Gurakan, G Candan

2016-03-01

The aim of the current study was to develop, a new, rapid, sensitive and quantitative Salmonella detection method using a Real-Time PCR technique based on an inexpensive, easy to produce, convenient and standardized recombinant plasmid positive control. To achieve this, two recombinant plasmids were constructed as reference molecules by cloning the two most commonly used Salmonella-specific target gene regions, invA and ttrRSBC. The more rapid detection enabled by the developed method (21 h) compared to the traditional culture method (90 h) allows the quantitative evaluation of Salmonella (quantification limits of 10(1)CFU/ml and 10(0)CFU/ml for the invA target and the ttrRSBC target, respectively), as illustrated using milk samples. Three advantages illustrated by the current study demonstrate the potential of the newly developed method to be used in routine analyses in the medical, veterinary, food and water/environmental sectors: I--The method provides fast analyses including the simultaneous detection and determination of correct pathogen counts; II--The method is applicable to challenging samples, such as milk; III--The method's positive controls (recombinant plasmids) are reproducible in large quantities without the need to construct new calibration curves. Copyright © 2016 Elsevier B.V. All rights reserved.

Linkage disequilibrium interval mapping of quantitative trait loci.

PubMed

Boitard, Simon; Abdallah, Jihad; de Rochambeau, Hubert; Cierco-Ayrolles, Christine; Mangin, Brigitte

2006-03-16

For many years gene mapping studies have been performed through linkage analyses based on pedigree data. Recently, linkage disequilibrium methods based on unrelated individuals have been advocated as powerful tools to refine estimates of gene location. Many strategies have been proposed to deal with simply inherited disease traits. However, locating quantitative trait loci is statistically more challenging and considerable research is needed to provide robust and computationally efficient methods. Under a three-locus Wright-Fisher model, we derived approximate expressions for the expected haplotype frequencies in a population. We considered haplotypes comprising one trait locus and two flanking markers. Using these theoretical expressions, we built a likelihood-maximization method, called HAPim, for estimating the location of a quantitative trait locus. For each postulated position, the method only requires information from the two flanking markers. Over a wide range of simulation scenarios it was found to be more accurate than a two-marker composite likelihood method. It also performed as well as identity by descent methods, whilst being valuable in a wider range of populations. Our method makes efficient use of marker information, and can be valuable for fine mapping purposes. Its performance is increased if multiallelic markers are available. Several improvements can be developed to account for more complex evolution scenarios or provide robust confidence intervals for the location estimates.

Technology-based self-care methods of improving antiretroviral adherence: a systematic review.

PubMed

Saberi, Parya; Johnson, Mallory O

2011-01-01

As HIV infection has shifted to a chronic condition, self-care practices have emerged as an important topic for HIV-positive individuals in maintaining an optimal level of health. Self-care refers to activities that patients undertake to maintain and improve health, such as strategies to achieve and maintain high levels of antiretroviral adherence. Technology-based methods are increasingly used to enhance antiretroviral adherence; therefore, we systematically reviewed the literature to examine technology-based self-care methods that HIV-positive individuals utilize to improve adherence. Seven electronic databases were searched from 1/1/1980 through 12/31/2010. We included quantitative and qualitative studies. Among quantitative studies, the primary outcomes included ARV adherence, viral load, and CD4+ cell count and secondary outcomes consisted of quality of life, adverse effects, and feasibility/acceptability data. For qualitative/descriptive studies, interview themes, reports of use, and perceptions of use were summarized. Thirty-six publications were included (24 quantitative and 12 qualitative/descriptive). Studies with exclusive utilization of medication reminder devices demonstrated less evidence of enhancing adherence in comparison to multi-component methods. This systematic review offers support for self-care technology-based approaches that may result in improved antiretroviral adherence. There was a clear pattern of results that favored individually-tailored, multi-function technologies, which allowed for periodic communication with health care providers rather than sole reliance on electronic reminder devices.

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study

USGS Publications Warehouse

Layton, Blythe A.; Cao, Yiping; Ebentier, Darcy L.; Hanley, Kaitlyn; Ballesté, Elisenda; Brandão, João; Byappanahalli, Muruleedhara N.; Converse, Reagan; Farnleitner, Andreas H.; Gentry-Shields, Jennifer; Gourmelon, Michèle; Lee, Chang Soo; Lee, Jiyoung; Lozach, Solen; Madi, Tania; Meijer, Wim G.; Noble, Rachel; Peed, Lindsay; Reischer, Georg H.; Rodrigues, Raquel; Rose, Joan B.; Schriewer, Alexander; Sinigalliano, Chris; Srinivasan, Sangeetha; Stewart, Jill; ,; Laurie, C.; Wang, Dan; Whitman, Richard; Wuertz, Stefan; Jay, Jenny; Holden, Patricia A.; Boehm, Alexandria B.; Shanks, Orin; Griffith, John F.

2013-01-01

A number of PCR-based methods for detecting human fecal material in environmental waters have been developed over the past decade, but these methods have rarely received independent comparative testing in large multi-laboratory studies. Here, we evaluated ten of these methods (BacH, BacHum-UCD, Bacteroides thetaiotaomicron (BtH), BsteriF1, gyrB, HF183 endpoint, HF183 SYBR, HF183 Taqman®, HumM2, and Methanobrevibacter smithii nifH (Mnif)) using 64 blind samples prepared in one laboratory. The blind samples contained either one or two fecal sources from human, wastewater or non-human sources. The assay results were assessed for presence/absence of the human markers and also quantitatively while varying the following: 1) classification of samples that were detected but not quantifiable (DNQ) as positive or negative; 2) reference fecal sample concentration unit of measure (such as culturable indicator bacteria, wet mass, total DNA, etc); and 3) human fecal source type (stool, sewage or septage). Assay performance using presence/absence metrics was found to depend on the classification of DNQ samples. The assays that performed best quantitatively varied based on the fecal concentration unit of measure and laboratory protocol. All methods were consistently more sensitive to human stools compared to sewage or septage in both the presence/absence and quantitative analysis. Overall, HF183 Taqman® was found to be the most effective marker of human fecal contamination in this California-based study.

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.

Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data

PubMed Central

2015-01-01

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 (R2 > 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. PMID:24635752

Multicomplex-based pharmacophore-guided 3D-QSAR studies of N-substituted 2'-(aminoaryl)benzothiazoles as Aurora-A inhibitors.

PubMed

He, Gu; Qiu, Minghua; Li, Rui; Ouyang, Liang; Wu, Fengbo; Song, Xiangrong; Cheng, Li; Xiang, Mingli; Yu, Luoting

2012-06-01

Aurora-A has been known as one of the most important targets for cancer therapy, and some Aurora-A inhibitors have entered clinical trails. In this study, combination of the ligand-based and structure-based methods is used to clarify the essential quantitative structure-activity relationship of known Aurora-A inhibitors, and multicomplex-based pharmacophore-guided method has been suggested to generate a comprehensive pharmacophore of Aurora-A kinase based on a collection of crystal structures of Aurora-A-inhibitor complex. This model has been successfully used to identify the bioactive conformation and align 37 structurally diverse N-substituted 2'-(aminoaryl)benzothiazoles derivatives. The quantitative structure-activity relationship analyses have been performed on these Aurora-A inhibitors based on multicomplex-based pharmacophore-guided alignment. These results may provide important information for further design and virtual screening of novel Aurora-A inhibitors. © 2012 John Wiley & Sons A/S.

Design-based and model-based inference in surveys of freshwater mollusks

USGS Publications Warehouse

Dorazio, R.M.

1999-01-01

Well-known concepts in statistical inference and sampling theory are used to develop recommendations for planning and analyzing the results of quantitative surveys of freshwater mollusks. Two methods of inference commonly used in survey sampling (design-based and model-based) are described and illustrated using examples relevant in surveys of freshwater mollusks. The particular objectives of a survey and the type of information observed in each unit of sampling can be used to help select the sampling design and the method of inference. For example, the mean density of a sparsely distributed population of mollusks can be estimated with higher precision by using model-based inference or by using design-based inference with adaptive cluster sampling than by using design-based inference with conventional sampling. More experience with quantitative surveys of natural assemblages of freshwater mollusks is needed to determine the actual benefits of different sampling designs and inferential procedures.

Quantitative imaging of glutathione in live cells using a reversible reaction-based ratiometric fluorescent probe

USDA-ARS?s Scientific Manuscript database

Glutathione (GSH) plays an important role in maintaining redox homeostasis inside cells. Currently, there are no methods available to quantitatively assess the GSH concentration in live cells. Live cell fluorescence imaging revolutionized the understanding of cell biology and has become an indispens...

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...

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.

Audiovisual quality estimation of mobile phone video cameras with interpretation-based quality approach

NASA Astrophysics Data System (ADS)

Radun, Jenni E.; Virtanen, Toni; Olives, Jean-Luc; Vaahteranoksa, Mikko; Vuori, Tero; Nyman, Göte

2007-01-01

We present an effective method for comparing subjective audiovisual quality and the features related to the quality changes of different video cameras. Both quantitative estimation of overall quality and qualitative description of critical quality features are achieved by the method. The aim was to combine two image quality evaluation methods, the quantitative Absolute Category Rating (ACR) method with hidden reference removal and the qualitative Interpretation- Based Quality (IBQ) method in order to see how they complement each other in audiovisual quality estimation tasks. 26 observers estimated the audiovisual quality of six different cameras, mainly mobile phone video cameras. In order to achieve an efficient subjective estimation of audiovisual quality, only two contents with different quality requirements were recorded with each camera. The results show that the subjectively important quality features were more related to the overall estimations of cameras' visual video quality than to the features related to sound. The data demonstrated two significant quality dimensions related to visual quality: darkness and sharpness. We conclude that the qualitative methodology can complement quantitative quality estimations also with audiovisual material. The IBQ approach is valuable especially, when the induced quality changes are multidimensional.

An Improved Method for Measuring Quantitative Resistance to the Wheat Pathogen Zymoseptoria tritici Using High-Throughput Automated Image Analysis.

PubMed

Stewart, Ethan L; Hagerty, Christina H; Mikaberidze, Alexey; Mundt, Christopher C; Zhong, Ziming; McDonald, Bruce A

2016-07-01

Zymoseptoria tritici causes Septoria tritici blotch (STB) on wheat. An improved method of quantifying STB symptoms was developed based on automated analysis of diseased leaf images made using a flatbed scanner. Naturally infected leaves (n = 949) sampled from fungicide-treated field plots comprising 39 wheat cultivars grown in Switzerland and 9 recombinant inbred lines (RIL) grown in Oregon were included in these analyses. Measures of quantitative resistance were percent leaf area covered by lesions, pycnidia size and gray value, and pycnidia density per leaf and lesion. These measures were obtained automatically with a batch-processing macro utilizing the image-processing software ImageJ. All phenotypes in both locations showed a continuous distribution, as expected for a quantitative trait. The trait distributions at both sites were largely overlapping even though the field and host environments were quite different. Cultivars and RILs could be assigned to two or more statistically different groups for each measured phenotype. Traditional visual assessments of field resistance were highly correlated with quantitative resistance measures based on image analysis for the Oregon RILs. These results show that automated image analysis provides a promising tool for assessing quantitative resistance to Z. tritici under field conditions.

Lunar-base construction equipment and methods evaluation

NASA Technical Reports Server (NTRS)

Boles, Walter W.; Ashley, David B.; Tucker, Richard L.

1993-01-01

A process for evaluating lunar-base construction equipment and methods concepts is presented. The process is driven by the need for more quantitative, systematic, and logical methods for assessing further research and development requirements in an area where uncertainties are high, dependence upon terrestrial heuristics is questionable, and quantitative methods are seldom applied. Decision theory concepts are used in determining the value of accurate information and the process is structured as a construction-equipment-and-methods selection methodology. Total construction-related, earth-launch mass is the measure of merit chosen for mathematical modeling purposes. The work is based upon the scope of the lunar base as described in the National Aeronautics and Space Administration's Office of Exploration's 'Exploration Studies Technical Report, FY 1989 Status'. Nine sets of conceptually designed construction equipment are selected as alternative concepts. It is concluded that the evaluation process is well suited for assisting in the establishment of research agendas in an approach that is first broad, with a low level of detail, followed by more-detailed investigations into areas that are identified as critical due to high degrees of uncertainty and sensitivity.

Smartphone based hand-held quantitative phase microscope using the transport of intensity equation method.

PubMed

Meng, Xin; Huang, Huachuan; Yan, Keding; Tian, Xiaolin; Yu, Wei; Cui, Haoyang; Kong, Yan; Xue, Liang; Liu, Cheng; Wang, Shouyu

2016-12-20

In order to realize high contrast imaging with portable devices for potential mobile healthcare, we demonstrate a hand-held smartphone based quantitative phase microscope using the transport of intensity equation method. With a cost-effective illumination source and compact microscope system, multi-focal images of samples can be captured by the smartphone's camera via manual focusing. Phase retrieval is performed using a self-developed Android application, which calculates sample phases from multi-plane intensities via solving the Poisson equation. We test the portable microscope using a random phase plate with known phases, and to further demonstrate its performance, a red blood cell smear, a Pap smear and monocot root and broad bean epidermis sections are also successfully imaged. Considering its advantages as an accurate, high-contrast, cost-effective and field-portable device, the smartphone based hand-held quantitative phase microscope is a promising tool which can be adopted in the future in remote healthcare and medical diagnosis.

A novel approach for evaluating the performance of real time quantitative loop-mediated isothermal amplification-based methods.

PubMed

Nixon, Gavin J; Svenstrup, Helle F; Donald, Carol E; Carder, Caroline; Stephenson, Judith M; Morris-Jones, Stephen; Huggett, Jim F; Foy, Carole A

2014-12-01

Molecular diagnostic measurements are currently underpinned by the polymerase chain reaction (PCR). There are also a number of alternative nucleic acid amplification technologies, which unlike PCR, work at a single temperature. These 'isothermal' methods, reportedly offer potential advantages over PCR such as simplicity, speed and resistance to inhibitors and could also be used for quantitative molecular analysis. However there are currently limited mechanisms to evaluate their quantitative performance, which would assist assay development and study comparisons. This study uses a sexually transmitted infection diagnostic model in combination with an adapted metric termed isothermal doubling time (IDT), akin to PCR efficiency, to compare quantitative PCR and quantitative loop-mediated isothermal amplification (qLAMP) assays, and to quantify the impact of matrix interference. The performance metric described here facilitates the comparison of qLAMP assays that could assist assay development and validation activities.

Nontargeted quantitation of lipid classes using hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry with single internal standard and response factor approach.

PubMed

Cífková, Eva; Holčapek, Michal; Lísa, Miroslav; Ovčačíková, Magdaléna; Lyčka, Antonín; Lynen, Frédéric; Sandra, Pat

2012-11-20

The identification and quantitation of a wide range of lipids in complex biological samples is an essential requirement for the lipidomic studies. High-performance liquid chromatography-mass spectrometry (HPLC/MS) has the highest potential to obtain detailed information on the whole lipidome, but the reliable quantitation of multiple lipid classes is still a challenging task. In this work, we describe a new method for the nontargeted quantitation of polar lipid classes separated by hydrophilic interaction liquid chromatography (HILIC) followed by positive-ion electrospray ionization mass spectrometry (ESI-MS) using a single internal lipid standard to which all class specific response factors (RFs) are related to. The developed method enables the nontargeted quantitation of lipid classes and molecules inside these classes in contrast to the conventional targeted quantitation, which is based on predefined selected reaction monitoring (SRM) transitions for selected lipids only. In the nontargeted quantitation method described here, concentrations of lipid classes are obtained by the peak integration in HILIC chromatograms multiplied by their RFs related to the single internal standard (i.e., sphingosyl PE, d17:1/12:0) used as common reference for all polar lipid classes. The accuracy, reproducibility and robustness of the method have been checked by various means: (1) the comparison with conventional lipidomic quantitation using SRM scans on a triple quadrupole (QqQ) mass analyzer, (2) (31)P nuclear magnetic resonance (NMR) quantitation of the total lipid extract, (3) method robustness test using subsequent measurements by three different persons, (4) method transfer to different HPLC/MS systems using different chromatographic conditions, and (5) comparison with previously published results for identical samples, especially human reference plasma from the National Institute of Standards and Technology (NIST human plasma). Results on human plasma, egg yolk and porcine liver extracts are presented and discussed.

Semi-quantitative methods yield greater inter- and intraobserver agreement than subjective methods for interpreting 99m technetium-hydroxymethylene-diphosphonate uptake in equine thoracic processi spinosi.

PubMed

van Zadelhoff, Claudia; Ehrle, Anna; Merle, Roswitha; Jahn, Werner; Lischer, Christoph

2018-05-09

Scintigraphy is a standard diagnostic method for evaluating horses with back pain due to suspected thoracic processus spinosus pathology. Lesion detection is based on subjective or semi-quantitative assessments of increased uptake. This retrospective, analytical study is aimed to compare semi-quantitative and subjective methods in the evaluation of scintigraphic images of the processi spinosi in the equine thoracic spine. Scintigraphic images of 20 Warmblood horses, presented for assessment of orthopedic conditions between 2014 and 2016, were included in the study. Randomized, blinded image evaluation was performed by 11 veterinarians using subjective and semi-quantitative methods. Subjective grading was performed for the analysis of red-green-blue and grayscale scintigraphic images, which were presented in full-size or as masked images. For the semi-quantitative assessment, observers placed regions of interest over each processus spinosus. The uptake ratio of each processus spinosus in comparison to a reference region of interest was determined. Subsequently, a modified semi-quantitative calculation was developed whereby only the highest counts-per-pixel for a specified number of pixels was processed. Inter- and intraobserver agreement was calculated using intraclass correlation coefficients. Inter- and intraobserver intraclass correlation coefficients were 41.65% and 71.39%, respectively, for the subjective image assessment. Additionally, a correlation between intraobserver agreement, experience, and grayscale images was identified. The inter- and intraobserver agreement was significantly increased when using semi-quantitative analysis (97.35% and 98.36%, respectively) or the modified semi-quantitative calculation (98.61% and 98.82%, respectively). The proposed modified semi-quantitative technique showed a higher inter- and intraobserver agreement when compared to other methods, which makes it a useful tool for the analysis of scintigraphic images. The association of the findings from this study with clinical and radiological examinations requires further investigation. © 2018 American College of Veterinary Radiology.

Protocol for a systematic review of quantitative burn wound microbiology in the management of burns patients.

PubMed

Kwei, Johnny; Halstead, Fenella D; Dretzke, Janine; Oppenheim, Beryl A; Moiemen, Naiem S

2015-11-06

Sepsis from burn injuries can result from colonisation of burn wounds, especially in large surface area burns. Reducing bacterial infection will reduce morbidity and mortality, and mortality for severe burns can be as high as 15 %. There are various quantitative and semi-quantitative techniques to monitor bacterial load on wounds. In the UK, burn wounds are typically monitored for the presence or absence of bacteria through the collection and culture of swabs, but no absolute count is obtained. Quantitative burn wound culture provides a measure of bacterial count and is gaining increased popularity in some countries. It is however more resource intensive, and evidence for its utility appears to be inconsistent. This systematic review therefore aims to assess the evidence on the utility and reliability of different quantitative microbiology techniques in terms of diagnosing or predicting clinical outcomes. Standard systematic review methods aimed at minimising bias will be employed for study identification, selection and data extraction. Bibliographic databases and ongoing trial registers will be searched and conference abstracts screened. Studies will be eligible if they are prospective studies or systematic reviews of burn patients (any age) for whom quantitative microbiology has been performed, whether it is compared to another method. Quality assessment will be based on quality assessment tools for diagnostic and prognostic studies and tailored to the review as necessary. Synthesis is likely to be primarily narrative, but meta-analysis may be considered where clinical and methodological homogeneity exists. Given the increasing use of quantitative methods, this is a timely systematic review, which will attempt to clarify the evidence base. As far as the authors are aware, it will be the first to address this topic. PROSPERO, CRD42015023903.

Reverse Transcription Quantitative Polymerase Chain Reaction for Detection of and Differentiation Between RNA and DNA of HIV-1-Based Lentiviral Vectors.

PubMed

Pavlovic, Melanie; Koehler, Nina; Anton, Martina; Dinkelmeier, Anna; Haase, Maren; Stellberger, Thorsten; Busch, Ulrich; Baiker, Armin E

2017-08-01

The purpose of the described method is the detection of and differentiation between RNA and DNA of human immunodeficiency virus (HIV)-derived lentiviral vectors (LV) in cell culture supernatants and swab samples. For the analytical surveillance of genetic engineering, operations methods for the detection of the HIV-1-based LV generations are required. Furthermore, for research issues, it is important to prove the absence of LV particles for downgrading experimental settings in terms of the biosafety level. Here, a quantitative polymerase chain reaction method targeting the long terminal repeat U5 subunit and the start sequence of the packaging signal ψ is described. Numerous controls are included in order to monitor the technical procedure.

Quantitative estimation of minimum offset for multichannel surface-wave survey with actively exciting source

USGS Publications Warehouse

Xu, Y.; Xia, J.; Miller, R.D.

2006-01-01

Multichannel analysis of surface waves is a developing method widely used in shallow subsurface investigations. The field procedures and related parameters are very important for successful applications. Among these parameters, the source-receiver offset range is seldom discussed in theory and normally determined by empirical or semi-quantitative methods in current practice. This paper discusses the problem from a theoretical perspective. A formula for quantitatively evaluating a layered homogenous elastic model was developed. The analytical results based on simple models and experimental data demonstrate that the formula is correct for surface wave surveys for near-surface applications. ?? 2005 Elsevier B.V. All rights reserved.

Quantitative model analysis with diverse biological data: applications in developmental pattern formation.

PubMed

Pargett, Michael; Umulis, David M

2013-07-15

Mathematical modeling of transcription factor and signaling networks is widely used to understand if and how a mechanism works, and to infer regulatory interactions that produce a model consistent with the observed data. Both of these approaches to modeling are informed by experimental data, however, much of the data available or even acquirable are not quantitative. Data that is not strictly quantitative cannot be used by classical, quantitative, model-based analyses that measure a difference between the measured observation and the model prediction for that observation. To bridge the model-to-data gap, a variety of techniques have been developed to measure model "fitness" and provide numerical values that can subsequently be used in model optimization or model inference studies. Here, we discuss a selection of traditional and novel techniques to transform data of varied quality and enable quantitative comparison with mathematical models. This review is intended to both inform the use of these model analysis methods, focused on parameter estimation, and to help guide the choice of method to use for a given study based on the type of data available. Applying techniques such as normalization or optimal scaling may significantly improve the utility of current biological data in model-based study and allow greater integration between disparate types of data. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

Methods for Quantitative Creatinine Determination.

PubMed

Moore, John F; Sharer, J Daniel

2017-04-06

Reliable measurement of creatinine is necessary to assess kidney function, and also to quantitate drug levels and diagnostic compounds in urine samples. The most commonly used methods are based on the Jaffe principal of alkaline creatinine-picric acid complex color formation. However, other compounds commonly found in serum and urine may interfere with Jaffe creatinine measurements. Therefore, many laboratories have made modifications to the basic method to remove or account for these interfering substances. This appendix will summarize the basic Jaffe method, as well as a modified, automated version. Also described is a high performance liquid chromatography (HPLC) method that separates creatinine from contaminants prior to direct quantification by UV absorption. Lastly, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method is described that uses stable isotope dilution to reliably quantify creatinine in any sample. This last approach has been recommended by experts in the field as a means to standardize all quantitative creatinine methods against an accepted reference. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Multiple internal standard normalization for improving HS-SPME-GC-MS quantitation in virgin olive oil volatile organic compounds (VOO-VOCs) profile.

PubMed

Fortini, Martina; Migliorini, Marzia; Cherubini, Chiara; Cecchi, Lorenzo; Calamai, Luca

2017-04-01

The commercial value of virgin olive oils (VOOs) strongly depends on their classification, also based on the aroma of the oils, usually evaluated by a panel test. Nowadays, a reliable analytical method is still needed to evaluate the volatile organic compounds (VOCs) and support the standard panel test method. To date, the use of HS-SPME sampling coupled to GC-MS is generally accepted for the analysis of VOCs in VOOs. However, VOO is a challenging matrix due to the simultaneous presence of: i) compounds at ppm and ppb concentrations; ii) molecules belonging to different chemical classes and iii) analytes with a wide range of molecular mass. Therefore, HS-SPME-GC-MS quantitation based upon the use of external standard method or of only a single internal standard (ISTD) for data normalization in an internal standard method, may be troublesome. In this work a multiple internal standard normalization is proposed to overcome these problems and improving quantitation of VOO-VOCs. As many as 11 ISTDs were used for quantitation of 71 VOCs. For each of them the most suitable ISTD was selected and a good linearity in a wide range of calibration was obtained. Except for E-2-hexenal, without ISTD or with an unsuitable ISTD, the linear range of calibration was narrower with respect to that obtained by a suitable ISTD, confirming the usefulness of multiple internal standard normalization for the correct quantitation of VOCs profile in VOOs. The method was validated for 71 VOCs, and then applied to a series of lampante virgin olive oils and extra virgin olive oils. In light of our results, we propose the application of this analytical approach for routine quantitative analyses and to support sensorial analysis for the evaluation of positive and negative VOOs attributes. Copyright © 2017 Elsevier B.V. All rights reserved.

Teachers' Reactions towards Performance-Based Language Assessment

ERIC Educational Resources Information Center

Chinda, Bordin

2014-01-01

This research aims at examining the reactions of tertiary EFL teachers towards the use of performance-based language assessment. The study employed a mixed-method research methodology. For the quantitative method, 36 teachers responded to a questionnaire survey. In addition, four teachers participated in the in-depth interviews which were…

Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models

PubMed Central

Hamilton, Joshua J.; Dwivedi, Vivek; Reed, Jennifer L.

2013-01-01

Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. PMID:23870272

A scoring system for appraising mixed methods research, and concomitantly appraising qualitative, quantitative and mixed methods primary studies in Mixed Studies Reviews.

PubMed

Pluye, Pierre; Gagnon, Marie-Pierre; Griffiths, Frances; Johnson-Lafleur, Janique

2009-04-01

A new form of literature review has emerged, Mixed Studies Review (MSR). These reviews include qualitative, quantitative and mixed methods studies. In the present paper, we examine MSRs in health sciences, and provide guidance on processes that should be included and reported. However, there are no valid and usable criteria for concomitantly appraising the methodological quality of the qualitative, quantitative and mixed methods studies. To propose criteria for concomitantly appraising the methodological quality of qualitative, quantitative and mixed methods studies or study components. A three-step critical review was conducted. 2322 references were identified in MEDLINE, and their titles and abstracts were screened; 149 potentially relevant references were selected and the full-text papers were examined; 59 MSRs were retained and scrutinized using a deductive-inductive qualitative thematic data analysis. This revealed three types of MSR: convenience, reproducible, and systematic. Guided by a proposal, we conducted a qualitative thematic data analysis of the quality appraisal procedures used in the 17 systematic MSRs (SMSRs). Of 17 SMSRs, 12 showed clear quality appraisal procedures with explicit criteria but no SMSR used valid checklists to concomitantly appraise qualitative, quantitative and mixed methods studies. In two SMSRs, criteria were developed following a specific procedure. Checklists usually contained more criteria than needed. In four SMSRs, a reliability assessment was described or mentioned. While criteria for quality appraisal were usually based on descriptors that require specific methodological expertise (e.g., appropriateness), no SMSR described the fit between reviewers' expertise and appraised studies. Quality appraisal usually resulted in studies being ranked by methodological quality. A scoring system is proposed for concomitantly appraising the methodological quality of qualitative, quantitative and mixed methods studies for SMSRs. This scoring system may also be used to appraise the methodological quality of qualitative, quantitative and mixed methods components of mixed methods research.

A Label-Free, Quantitative Fecal Hemoglobin Detection Platform for Colorectal Cancer Screening

PubMed Central

Soraya, Gita V.; Nguyen, Thanh C.; Abeyrathne, Chathurika D.; Huynh, Duc H.; Chan, Jianxiong; Nguyen, Phuong D.; Nasr, Babak; Chana, Gursharan; Kwan, Patrick; Skafidas, Efstratios

2017-01-01

The early detection of colorectal cancer is vital for disease management and patient survival. Fecal hemoglobin detection is a widely-adopted method for screening and early diagnosis. Fecal Immunochemical Test (FIT) is favored over the older generation chemical based Fecal Occult Blood Test (FOBT) as it does not require dietary or drug restrictions, and is specific to human blood from the lower digestive tract. To date, no quantitative FIT platforms are available for use in the point-of-care setting. Here, we report proof of principle data of a novel low cost quantitative fecal immunochemical-based biosensor platform that may be further developed into a point-of-care test in low-resource settings. The label-free prototype has a lower limit of detection (LOD) of 10 µg hemoglobin per gram (Hb/g) of feces, comparable to that of conventional laboratory based quantitative FIT diagnostic systems. PMID:28475117

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.

Qualitative Methods in Mental Health Services Research

PubMed Central

Palinkas, Lawrence A.

2014-01-01

Qualitative and mixed methods play a prominent role in mental health services research. However, the standards for their use are not always evident, especially for those not trained in such methods. This paper reviews the rationale and common approaches to using qualitative and mixed methods in mental health services and implementation research based on a review of the papers included in this special series along with representative examples from the literature. Qualitative methods are used to provide a “thick description” or depth of understanding to complement breadth of understanding afforded by quantitative methods, elicit the perspective of those being studied, explore issues that have not been well studied, develop conceptual theories or test hypotheses, or evaluate the process of a phenomenon or intervention. Qualitative methods adhere to many of the same principles of scientific rigor as quantitative methods, but often differ with respect to study design, data collection and data analysis strategies. For instance, participants for qualitative studies are usually sampled purposefully rather than at random and the design usually reflects an iterative process alternating between data collection and analysis. The most common techniques for data collection are individual semi-structured interviews, focus groups, document reviews, and participant observation. Strategies for analysis are usually inductive, based on principles of grounded theory or phenomenology. Qualitative methods are also used in combination with quantitative methods in mixed method designs for convergence, complementarity, expansion, development, and sampling. Rigorously applied qualitative methods offer great potential in contributing to the scientific foundation of mental health services research. PMID:25350675

Qualitative and mixed methods in mental health services and implementation research.

PubMed

Palinkas, Lawrence A

2014-01-01

Qualitative and mixed methods play a prominent role in mental health services research. However, the standards for their use are not always evident, especially for those not trained in such methods. This article reviews the rationale and common approaches to using qualitative and mixed methods in mental health services and implementation research based on a review of the articles included in this special series along with representative examples from the literature. Qualitative methods are used to provide a "thick description" or depth of understanding to complement breadth of understanding afforded by quantitative methods, elicit the perspective of those being studied, explore issues that have not been well studied, develop conceptual theories or test hypotheses, or evaluate the process of a phenomenon or intervention. Qualitative methods adhere to many of the same principles of scientific rigor as quantitative methods but often differ with respect to study design, data collection, and data analysis strategies. For instance, participants for qualitative studies are usually sampled purposefully rather than at random and the design usually reflects an iterative process alternating between data collection and analysis. The most common techniques for data collection are individual semistructured interviews, focus groups, document reviews, and participant observation. Strategies for analysis are usually inductive, based on principles of grounded theory or phenomenology. Qualitative methods are also used in combination with quantitative methods in mixed-method designs for convergence, complementarity, expansion, development, and sampling. Rigorously applied qualitative methods offer great potential in contributing to the scientific foundation of mental health services research.

Widely-targeted quantitative lipidomics methodology by supercritical fluid chromatography coupled with fast-scanning triple quadrupole mass spectrometry.

PubMed

Takeda, Hiroaki; Izumi, Yoshihiro; Takahashi, Masatomo; Paxton, Thanai; Tamura, Shohei; Koike, Tomonari; Yu, Ying; Kato, Noriko; Nagase, Katsutoshi; Shiomi, Masashi; Bamba, Takeshi

2018-05-03

Lipidomics, the mass spectrometry-based comprehensive analysis of lipids, has attracted attention as an analytical approach to provide novel insight into lipid metabolism and to search for biomarkers. However, an ideal method for both comprehensive and quantitative analysis of lipids has not been fully developed. Herein, we have proposed a practical methodology for widely-targeted quantitative lipidome analysis using supercritical fluid chromatography fast-scanning triple-quadrupole mass spectrometry (SFC/QqQMS) and theoretically calculated a comprehensive lipid multiple reaction monitoring (MRM) library. Lipid classes can be separated by SFC with a normal phase diethylamine-bonded silica column with high-resolution, high-throughput, and good repeatability. Structural isomers of phospholipids can be monitored by mass spectrometric separation with fatty acyl-based MRM transitions. SFC/QqQMS analysis with an internal standard-dilution method offers quantitative information for both lipid class and individual lipid molecular species in the same lipid class. Additionally, data acquired using this method has advantages including reduction of misidentification and acceleration of data analysis. Using the SFC/QqQMS system, alteration of plasma lipid levels in myocardial infarction-prone rabbits to the supplementation of eicosapentaenoic acid was first observed. Our developed SFC/QqQMS method represents a potentially useful tool for in-depth studies focused on complex lipid metabolism and biomarker discovery. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

An iterative method for near-field Fresnel region polychromatic phase contrast imaging

NASA Astrophysics Data System (ADS)

Carroll, Aidan J.; van Riessen, Grant A.; Balaur, Eugeniu; Dolbnya, Igor P.; Tran, Giang N.; Peele, Andrew G.

2017-07-01

We present an iterative method for polychromatic phase contrast imaging that is suitable for broadband illumination and which allows for the quantitative determination of the thickness of an object given the refractive index of the sample material. Experimental and simulation results suggest the iterative method provides comparable image quality and quantitative object thickness determination when compared to the analytical polychromatic transport of intensity and contrast transfer function methods. The ability of the iterative method to work over a wider range of experimental conditions means the iterative method is a suitable candidate for use with polychromatic illumination and may deliver more utility for laboratory-based x-ray sources, which typically have a broad spectrum.

Quantitative real-time in vivo detection of magnetic nanoparticles by their nonlinear magnetization

NASA Astrophysics Data System (ADS)

Nikitin, M. P.; Torno, M.; Chen, H.; Rosengart, A.; Nikitin, P. I.

2008-04-01

A novel method of highly sensitive quantitative detection of magnetic nanoparticles (MP) in biological tissues and blood system has been realized and tested in real time in vivo experiments. The detection method is based on nonlinear magnetic properties of MP and the related device can record a very small relative variation of nonlinear magnetic susceptibility up to 10-8 at room temperature, providing sensitivity of several nanograms of MP in 0.1ml volume. Real-time quantitative in vivo measurements of dynamics of MP concentration in blood flow have been performed. A catheter that carried the blood flow of a rat passed through the measuring device. After an MP injection, the quantity of MP in the circulating blood was continuously recorded. The method has also been used to evaluate the MP distribution between rat's organs. Its sensitivity was compared with detection of the radioactive MP based on isotope of Fe59. The comparison of magnetic and radioactive signals in the rat's blood and organ samples demonstrated similar sensitivity for both methods. However, the proposed magnetic method is much more convenient as it is safe, less expensive, and provides real-time measurements in vivo. Moreover, the sensitivity of the method can be further improved by optimization of the device geometry.

Determination of total dietary fiber (CODEX definition) by enzymatic-gravimetric method and liquid chromatography: collaborative study.

PubMed

McCleary, Barry V; DeVries, Jonathan W; Rader, Jeanne I; Cohen, Gerald; Prosky, Leon; Mugford, David C; Champ, Martine; Okuma, Kazuhiro

2010-01-01

A method for the determination of total dietary fiber (TDF), as defined by the CODEX Alimentarius, was validated in foods. Based upon the principles of AOAC Official Methods 985.29, 991.43, 2001.03, and 2002.02, the method quantitates high- and low-molecular-weight dietary fiber (HMWDF and LMWDF, respectively). In 2007, McCleary described a method of extended enzymatic digestion at 37 degrees C to simulate human intestinal digestion followed by gravimetric isolation and quantitation of HMWDF and the use of LC to quantitate low-molecular-weight soluble dietary fiber (LMWSDF). The method thus quantitates the complete range of dietary fiber components from resistant starch (by utilizing the digestion conditions of AOAC Method 2002.02) to digestion resistant oligosaccharides (by incorporating the deionization and LC procedures of AOAC Method 2001.03). The method was evaluated through an AOAC collaborative study. Eighteen laboratories participated with 16 laboratories returning valid assay data for 16 test portions (eight blind duplicates) consisting of samples with a range of traditional dietary fiber, resistant starch, and nondigestible oligosaccharides. The dietary fiber content of the eight test pairs ranged from 11.57 to 47.83%. Digestion of samples under the conditions of AOAC Method 2002.02 followed by the isolation and gravimetric procedures of AOAC Methods 985.29 and 991.43 results in quantitation of HMWDF. The filtrate from the quantitation of HMWDF is concentrated, deionized, concentrated again, and analyzed by LC to determine the LMWSDF, i.e., all nondigestible oligosaccharides of degree of polymerization > or =3. TDF is calculated as the sum of HMWDF and LMWSDF. Repeatability standard deviations (Sr) ranged from 0.41 to 1.43, and reproducibility standard deviations (S(R)) ranged from 1.18 to 5.44. These results are comparable to other official dietary fiber methods, and the method is recommended for adoption as Official First Action.

COREPA-M: NEW MULTI-DIMENSIONAL FUNCTIONALITY OF THE COREPA METHOD

EPA Science Inventory

The COmmon REactivity PAttern (COREPA) method is a recently developed pattern recognition technique accounting for conformational flexibility of chemicals in 3-D quantitative structure-activity relationships (QSARs). The method is based on the assumption that non-congeneric chemi...

EPA Scientists Develop Research Methods for Studying Mold Fact Sheet

EPA Pesticide Factsheets

In 2002, U.S. Environmental Protection Agency researchers developed a DNA-based Mold Specific Quantitative Polymerase Chain Reaction method (MSQPCR) for identifying and quantifying over 100 common molds and fungi.

A qualitative and quantitative assessment for a bone marrow harvest simulator.

PubMed

Machado, Liliane S; Moraes, Ronei M

2009-01-01

Several approaches to perform assessment in training simulators based on virtual reality have been proposed. There are two kinds of assessment methods: offline and online. The main requirements related to online training assessment methodologies applied to virtual reality systems are the low computational complexity and the high accuracy. In the literature it can be found several approaches for general cases which can satisfy such requirements. An inconvenient about those approaches is related to an unsatisfactory solution for specific cases, as in some medical procedures, where there are quantitative and qualitative information available to perform the assessment. In this paper, we present an approach to online training assessment based on a Modified Naive Bayes which can manipulate qualitative and quantitative variables simultaneously. A special medical case was simulated in a bone marrow harvest simulator. The results obtained were satisfactory and evidenced the applicability of the method.

Real-Time PCR-Based Quantitation Method for the Genetically Modified Soybean Line GTS 40-3-2.

PubMed

Kitta, Kazumi; Takabatake, Reona; Mano, Junichi

2016-01-01

This chapter describes a real-time PCR-based method for quantitation of the relative amount of genetically modified (GM) soybean line GTS 40-3-2 [Roundup Ready(®) soybean (RRS)] contained in a batch. The method targets a taxon-specific soybean gene (lectin gene, Le1) and the specific DNA construct junction region between the Petunia hybrida chloroplast transit peptide sequence and the Agrobacterium 5-enolpyruvylshikimate-3-phosphate synthase gene (epsps) sequence present in GTS 40-3-2. The method employs plasmid pMulSL2 as a reference material in order to quantify the relative amount of GTS 40-3-2 in soybean samples using a conversion factor (Cf) equal to the ratio of the RRS-specific DNA to the taxon-specific DNA in representative genuine GTS 40-3-2 seeds.

Marker-based quantitative genetics in the wild?: the heritability and genetic correlation of chemical defenses in eucalyptus.

PubMed

Andrew, R L; Peakall, R; Wallis, I R; Wood, J T; Knight, E J; Foley, W J

2005-12-01

Marker-based methods for estimating heritability and genetic correlation in the wild have attracted interest because traditional methods may be impractical or introduce bias via G x E effects, mating system variation, and sampling effects. However, they have not been widely used, especially in plants. A regression-based approach, which uses a continuous measure of genetic relatedness, promises to be particularly appropriate for use in plants with mixed-mating systems and overlapping generations. Using this method, we found significant narrow-sense heritability of foliar defense chemicals in a natural population of Eucalyptus melliodora. We also demonstrated a genetic basis for the phenotypic correlation underlying an ecological example of conditioned flavor aversion involving different biosynthetic pathways. Our results revealed that heritability estimates depend on the spatial scale of the analysis in a way that offers insight into the distribution of genetic and environmental variance. This study is the first to successfully use a marker-based method to measure quantitative genetic parameters in a tree. We suggest that this method will prove to be a useful tool in other studies and offer some recommendations for future applications of the method.

Risk analysis for veterinary biologicals released into the environment.

PubMed

Silva, S V; Samagh, B S; Morley, R S

1995-12-01

All veterinary biologicals licensed in Canada must be shown to be pure, potent, safe and effective. A risk-based approach is used to evaluate the safety of all biologicals, whether produced by conventional methods or by molecular biological techniques. Traditionally, qualitative risk assessment methods have been used for this purpose. More recently, quantitative risk assessment has become available for complex issues. The quantitative risk assessment method uses "scenario tree analysis' to predict the likelihood of various outcomes and their respective impacts. The authors describe the quantitative risk assessment approach which is used within the broader context of risk analysis (i.e. risk assessment, risk management and risk communication) to develop recommendations for the field release of veterinary biologicals. The general regulatory framework for the licensing of veterinary biologicals in Canada is also presented.

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.

Conflicts Management Model in School: A Mixed Design Study

ERIC Educational Resources Information Center

Dogan, Soner

2016-01-01

The object of this study is to evaluate the reasons for conflicts occurring in school according to perceptions and views of teachers and resolution strategies used for conflicts and to build a model based on the results obtained. In the research, explanatory design including quantitative and qualitative methods has been used. The quantitative part…

The applicability of TaqMan-based quantitative real-time PCR assays for detecting and enumeratIng Cryptosporidium spp. oocysts in the environment

EPA Science Inventory

Molecular detection methods such as PCR have been extensively used to type Cryptosporidium oocysts detected in the environment. More recently, studies have developed quantitative real-time PCR assays for detection and quantification of microbial contaminants in water as well as ...

Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters

EPA Science Inventory

Modern techniques for tracking fecal pollution in environmental waters require investing in DNA-based methods to determine the presence of specific fecal sources. To help water quality managers decide whether to employ routine polymerase chain reaction (PCR) or quantitative PC...

Rapid and Quantitative Detection of Vibrio parahemolyticus by the Mixed-Dye-Based Loop-Mediated Isothermal Amplification Assay on a Self-Priming Compartmentalization Microfluidic Chip.

PubMed

Pang, Bo; Ding, Xiong; Wang, Guoping; Zhao, Chao; Xu, Yanan; Fu, Kaiyue; Sun, Jingjing; Song, Xiuling; Wu, Wenshuai; Liu, Yushen; Song, Qi; Hu, Jiumei; Li, Juan; Mu, Ying

2017-12-27

Vibrio parahemolyticus (VP) mostly isolated from aquatic products is one of the major causes of bacterial food-poisoning events worldwide, which could be reduced using a promising on-site detection method. Herein, a rapid and quantitative method for VP detection was developed by applying a mixed-dye-loaded loop-mediated isothermal amplification (LAMP) assay on a self-priming compartmentalization (SPC) microfluidic chip, termed on-chip mixed-dye-based LAMP (CMD-LAMP). In comparison to conventional approaches, CMD-LAMP was advantageous on the limit of detection, which reached down to 1 × 10 3 CFU/mL in food-contaminated samples without the pre-enrichment of bacteria. Additionally, as a result of the use of a mixed dye and SPC chip, the quantitative result could be easily acquired, avoiding the requirement of sophisticated instruments and tedious operation. Also, CMD-LAMP was rapid and cost-effective. Conclusively, CMD-LAMP has great potential in realizing the on-site quantitative analysis of VP for food safety.

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry.

PubMed

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J; Kertesz, Vilmos; Gan, Jinping

2016-03-25

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites were studied. Major organs (brain, lung, liver, kidney and muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed the same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. In addition, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

DOE PAGES

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J.; ...

2015-11-03

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites was studied. Major organs (brain, lung, liver, kidney, muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed themore » same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. Furthermore, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement.« less

Quantitation of repaglinide and metabolites in mouse whole-body thin tissue sections using droplet-based liquid microjunction surface sampling-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry

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

Chen, Weiqi; Wang, Lifei; Van Berkel, Gary J.

Herein, quantitation aspects of a fully automated autosampler/HPLC-MS/MS system applied for unattended droplet-based surface sampling of repaglinide dosed thin tissue sections with subsequent HPLC separation and mass spectrometric analysis of parent drug and various drug metabolites was studied. Major organs (brain, lung, liver, kidney, muscle) from whole-body thin tissue sections and corresponding organ homogenates prepared from repaglinide dosed mice were sampled by surface sampling and by bulk extraction, respectively, and analyzed by HPLC-MS/MS. A semi-quantitative agreement between data obtained by surface sampling and that by employing organ homogenate extraction was observed. Drug concentrations obtained by the two methods followed themore » same patterns for post-dose time points (0.25, 0.5, 1 and 2 h). Drug amounts determined in the specific tissues was typically higher when analyzing extracts from the organ homogenates. Furthermore, relative comparison of the levels of individual metabolites between the two analytical methods also revealed good semi-quantitative agreement.« less

Composite Interval Mapping Based on Lattice Design for Error Control May Increase Power of Quantitative Trait Locus Detection.

PubMed

He, Jianbo; Li, Jijie; Huang, Zhongwen; Zhao, Tuanjie; Xing, Guangnan; Gai, Junyi; Guan, Rongzhan

2015-01-01

Experimental error control is very important in quantitative trait locus (QTL) mapping. Although numerous statistical methods have been developed for QTL mapping, a QTL detection model based on an appropriate experimental design that emphasizes error control has not been developed. Lattice design is very suitable for experiments with large sample sizes, which is usually required for accurate mapping of quantitative traits. However, the lack of a QTL mapping method based on lattice design dictates that the arithmetic mean or adjusted mean of each line of observations in the lattice design had to be used as a response variable, resulting in low QTL detection power. As an improvement, we developed a QTL mapping method termed composite interval mapping based on lattice design (CIMLD). In the lattice design, experimental errors are decomposed into random errors and block-within-replication errors. Four levels of block-within-replication errors were simulated to show the power of QTL detection under different error controls. The simulation results showed that the arithmetic mean method, which is equivalent to a method under random complete block design (RCBD), was very sensitive to the size of the block variance and with the increase of block variance, the power of QTL detection decreased from 51.3% to 9.4%. In contrast to the RCBD method, the power of CIMLD and the adjusted mean method did not change for different block variances. The CIMLD method showed 1.2- to 7.6-fold higher power of QTL detection than the arithmetic or adjusted mean methods. Our proposed method was applied to real soybean (Glycine max) data as an example and 10 QTLs for biomass were identified that explained 65.87% of the phenotypic variation, while only three and two QTLs were identified by arithmetic and adjusted mean methods, respectively.

Advanced body composition assessment: from body mass index to body composition profiling.

PubMed

Borga, Magnus; West, Janne; Bell, Jimmy D; Harvey, Nicholas C; Romu, Thobias; Heymsfield, Steven B; Dahlqvist Leinhard, Olof

2018-06-01

This paper gives a brief overview of common non-invasive techniques for body composition analysis and a more in-depth review of a body composition assessment method based on fat-referenced quantitative MRI. Earlier published studies of this method are summarized, and a previously unpublished validation study, based on 4753 subjects from the UK Biobank imaging cohort, comparing the quantitative MRI method with dual-energy X-ray absorptiometry (DXA) is presented. For whole-body measurements of adipose tissue (AT) or fat and lean tissue (LT), DXA and quantitative MRIs show excellent agreement with linear correlation of 0.99 and 0.97, and coefficient of variation (CV) of 4.5 and 4.6 per cent for fat (computed from AT) and LT, respectively, but the agreement was found significantly lower for visceral adipose tissue, with a CV of >20 per cent. The additional ability of MRI to also measure muscle volumes, muscle AT infiltration and ectopic fat, in combination with rapid scanning protocols and efficient image analysis tools, makes quantitative MRI a powerful tool for advanced body composition assessment. © American Federation for Medical Research (unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Soldier Quality of Life (Operational) and Readiness at Contingency Base Camps: Insights From Qualitative Interviews

DTIC Science & Technology

2017-03-13

camps and Soldier/small unit readiness to guide the development of a quantitative readiness survey . • During structured interviews, 31 Soldiers...camps and Soldier/small unit readiness to guide the development of a quantitative readiness survey . 11UNCLASSIFIED Click to hear quote Methods...We were rock stars.” 60UNCLASSIFIED • These data are driving the selection of attributes for a future quantitative survey of the link between QoL

AUTOMATED ANALYSIS OF QUANTITATIVE IMAGE DATA USING ISOMORPHIC FUNCTIONAL MIXED MODELS, WITH APPLICATION TO PROTEOMICS DATA.

PubMed

Morris, Jeffrey S; Baladandayuthapani, Veerabhadran; Herrick, Richard C; Sanna, Pietro; Gutstein, Howard

2011-01-01

Image data are increasingly encountered and are of growing importance in many areas of science. Much of these data are quantitative image data, which are characterized by intensities that represent some measurement of interest in the scanned images. The data typically consist of multiple images on the same domain and the goal of the research is to combine the quantitative information across images to make inference about populations or interventions. In this paper, we present a unified analysis framework for the analysis of quantitative image data using a Bayesian functional mixed model approach. This framework is flexible enough to handle complex, irregular images with many local features, and can model the simultaneous effects of multiple factors on the image intensities and account for the correlation between images induced by the design. We introduce a general isomorphic modeling approach to fitting the functional mixed model, of which the wavelet-based functional mixed model is one special case. With suitable modeling choices, this approach leads to efficient calculations and can result in flexible modeling and adaptive smoothing of the salient features in the data. The proposed method has the following advantages: it can be run automatically, it produces inferential plots indicating which regions of the image are associated with each factor, it simultaneously considers the practical and statistical significance of findings, and it controls the false discovery rate. Although the method we present is general and can be applied to quantitative image data from any application, in this paper we focus on image-based proteomic data. We apply our method to an animal study investigating the effects of opiate addiction on the brain proteome. Our image-based functional mixed model approach finds results that are missed with conventional spot-based analysis approaches. In particular, we find that the significant regions of the image identified by the proposed method frequently correspond to subregions of visible spots that may represent post-translational modifications or co-migrating proteins that cannot be visually resolved from adjacent, more abundant proteins on the gel image. Thus, it is possible that this image-based approach may actually improve the realized resolution of the gel, revealing differentially expressed proteins that would not have even been detected as spots by modern spot-based analyses.

Accuracy and precision of pseudo-continuous arterial spin labeling perfusion during baseline and hypercapnia: a head-to-head comparison with ¹⁵O H₂O positron emission tomography.

PubMed

Heijtel, D F R; Mutsaerts, H J M M; Bakker, E; Schober, P; Stevens, M F; Petersen, E T; van Berckel, B N M; Majoie, C B L M; Booij, J; van Osch, M J P; Vanbavel, E; Boellaard, R; Lammertsma, A A; Nederveen, A J

2014-05-15

Measurements of the cerebral blood flow (CBF) and cerebrovascular reactivity (CVR) provide useful information about cerebrovascular condition and regional metabolism. Pseudo-continuous arterial spin labeling (pCASL) is a promising non-invasive MRI technique to quantitatively measure the CBF, whereas additional hypercapnic pCASL measurements are currently showing great promise to quantitatively assess the CVR. However, the introduction of pCASL at a larger scale awaits further evaluation of the exact accuracy and precision compared to the gold standard. (15)O H₂O positron emission tomography (PET) is currently regarded as the most accurate and precise method to quantitatively measure both CBF and CVR, though it is one of the more invasive methods as well. In this study we therefore assessed the accuracy and precision of quantitative pCASL-based CBF and CVR measurements by performing a head-to-head comparison with (15)O H₂O PET, based on quantitative CBF measurements during baseline and hypercapnia. We demonstrate that pCASL CBF imaging is accurate during both baseline and hypercapnia with respect to (15)O H₂O PET with a comparable precision. These results pave the way for quantitative usage of pCASL MRI in both clinical and research settings. Copyright © 2014 Elsevier Inc. All rights reserved.

Development of a screening method for genetically modified soybean by plasmid-based quantitative competitive polymerase chain reaction.

PubMed

Shimizu, Eri; Kato, Hisashi; Nakagawa, Yuki; Kodama, Takashi; Futo, Satoshi; Minegishi, Yasutaka; Watanabe, Takahiro; Akiyama, Hiroshi; Teshima, Reiko; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

2008-07-23

A novel type of quantitative competitive polymerase chain reaction (QC-PCR) system for the detection and quantification of the Roundup Ready soybean (RRS) was developed. This system was designed based on the advantage of a fully validated real-time PCR method used for the quantification of RRS in Japan. A plasmid was constructed as a competitor plasmid for the detection and quantification of genetically modified soy, RRS. The plasmid contained the construct-specific sequence of RRS and the taxon-specific sequence of lectin1 (Le1), and both had 21 bp oligonucleotide insertion in the sequences. The plasmid DNA was used as a reference molecule instead of ground seeds, which enabled us to precisely and stably adjust the copy number of targets. The present study demonstrated that the novel plasmid-based QC-PCR method could be a simple and feasible alternative to the real-time PCR method used for the quantification of genetically modified organism contents.

FT-IR imaging for quantitative determination of liver fat content in non-alcoholic fatty liver.

PubMed

Kochan, K; Maslak, E; Chlopicki, S; Baranska, M

2015-08-07

In this work we apply FT-IR imaging of large areas of liver tissue cross-section samples (∼5 cm × 5 cm) for quantitative assessment of steatosis in murine model of Non-Alcoholic Fatty Liver (NAFLD). We quantified the area of liver tissue occupied by lipid droplets (LDs) by FT-IR imaging and Oil Red O (ORO) staining for comparison. Two alternative FT-IR based approaches are presented. The first, straightforward method, was based on average spectra from tissues and provided values of the fat content by using a PLS regression model and the reference method. The second one – the chemometric-based method – enabled us to determine the values of the fat content, independently of the reference method by means of k-means cluster (KMC) analysis. In summary, FT-IR images of large size liver sections may prove to be useful for quantifying liver steatosis without the need of tissue staining.

New horizons in mouse immunoinformatics: reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity.

PubMed

Hattotuwagama, Channa K; Guan, Pingping; Doytchinova, Irini A; Flower, Darren R

2004-11-21

Quantitative structure-activity relationship (QSAR) analysis is a main cornerstone of modern informatic disciplines. Predictive computational models, based on QSAR technology, of peptide-major histocompatibility complex (MHC) binding affinity have now become a vital component of modern day computational immunovaccinology. Historically, such approaches have been built around semi-qualitative, classification methods, but these are now giving way to quantitative regression methods. The additive method, an established immunoinformatics technique for the quantitative prediction of peptide-protein affinity, was used here to identify the sequence dependence of peptide binding specificity for three mouse class I MHC alleles: H2-D(b), H2-K(b) and H2-K(k). As we show, in terms of reliability the resulting models represent a significant advance on existing methods. They can be used for the accurate prediction of T-cell epitopes and are freely available online ( http://www.jenner.ac.uk/MHCPred).

The detection of large deletions or duplications in genomic DNA.

PubMed

Armour, J A L; Barton, D E; Cockburn, D J; Taylor, G R

2002-11-01

While methods for the detection of point mutations and small insertions or deletions in genomic DNA are well established, the detection of larger (>100 bp) genomic duplications or deletions can be more difficult. Most mutation scanning methods use PCR as a first step, but the subsequent analyses are usually qualitative rather than quantitative. Gene dosage methods based on PCR need to be quantitative (i.e., they should report molar quantities of starting material) or semi-quantitative (i.e., they should report gene dosage relative to an internal standard). Without some sort of quantitation, heterozygous deletions and duplications may be overlooked and therefore be under-ascertained. Gene dosage methods provide the additional benefit of reporting allele drop-out in the PCR. This could impact on SNP surveys, where large-scale genotyping may miss null alleles. Here we review recent developments in techniques for the detection of this type of mutation and compare their relative strengths and weaknesses. We emphasize that comprehensive mutation analysis should include scanning for large insertions and deletions and duplications. Copyright 2002 Wiley-Liss, Inc.

Comparison of EPA Method 1615 RT-qPCR Assays in Standard and Kit Format

EPA Science Inventory

EPA Method 1615 contains protocols for measuring enterovirus and norovirus by reverse transcription quantitative polymerase chain reaction. A commercial kit based upon these protocols was designed and compared to the method's standard approach. Reagent grade, secondary effluent, ...

ICP-MS as a novel detection system for quantitative element-tagged immunoassay of hidden peanut allergens in foods.

PubMed

Careri, Maria; Elviri, Lisa; Mangia, Alessandro; Mucchino, Claudio

2007-03-01

A novel ICP-MS-based ELISA immunoassay via element-tagged determination was devised for quantitative analysis of hidden allergens in food. The method was able to detect low amounts of peanuts (down to approximately 2 mg peanuts kg(-1) cereal-based matrix) by using a europium-tagged antibody. Selectivity was proved by the lack of detectable cross-reaction with a number of protein-rich raw materials.

Classification-based quantitative analysis of stable isotope labeling by amino acids in cell culture (SILAC) data.

PubMed

Kim, Seongho; Carruthers, Nicholas; Lee, Joohyoung; Chinni, Sreenivasa; Stemmer, Paul

2016-12-01

Stable isotope labeling by amino acids in cell culture (SILAC) is a practical and powerful approach for quantitative proteomic analysis. A key advantage of SILAC is the ability to simultaneously detect the isotopically labeled peptides in a single instrument run and so guarantee relative quantitation for a large number of peptides without introducing any variation caused by separate experiment. However, there are a few approaches available to assessing protein ratios and none of the existing algorithms pays considerable attention to the proteins having only one peptide hit. We introduce new quantitative approaches to dealing with SILAC protein-level summary using classification-based methodologies, such as Gaussian mixture models with EM algorithms and its Bayesian approach as well as K-means clustering. In addition, a new approach is developed using Gaussian mixture model and a stochastic, metaheuristic global optimization algorithm, particle swarm optimization (PSO), to avoid either a premature convergence or being stuck in a local optimum. Our simulation studies show that the newly developed PSO-based method performs the best among others in terms of F1 score and the proposed methods further demonstrate the ability of detecting potential markers through real SILAC experimental data. No matter how many peptide hits the protein has, the developed approach can be applicable, rescuing many proteins doomed to removal. Furthermore, no additional correction for multiple comparisons is necessary for the developed methods, enabling direct interpretation of the analysis outcomes. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

ELEGANT ENVIRONMENTAL IMMUNOASSAYS

EPA Science Inventory

Immunochemical methods are based on selective antibodies directed to a particular target analyte. The specific binding between antibody and analyte can be used for detection and quantitation. Methods such as the enzyme-linked immunosorbent assay (ELISA) can provide a sensitiv...

Quantitative methods for compensation of matrix effects and self-absorption in Laser Induced Breakdown Spectroscopy signals of solids

NASA Astrophysics Data System (ADS)

Takahashi, Tomoko; Thornton, Blair

2017-12-01

This paper reviews methods to compensate for matrix effects and self-absorption during quantitative analysis of compositions of solids measured using Laser Induced Breakdown Spectroscopy (LIBS) and their applications to in-situ analysis. Methods to reduce matrix and self-absorption effects on calibration curves are first introduced. The conditions where calibration curves are applicable to quantification of compositions of solid samples and their limitations are discussed. While calibration-free LIBS (CF-LIBS), which corrects matrix effects theoretically based on the Boltzmann distribution law and Saha equation, has been applied in a number of studies, requirements need to be satisfied for the calculation of chemical compositions to be valid. Also, peaks of all elements contained in the target need to be detected, which is a bottleneck for in-situ analysis of unknown materials. Multivariate analysis techniques are gaining momentum in LIBS analysis. Among the available techniques, principal component regression (PCR) analysis and partial least squares (PLS) regression analysis, which can extract related information to compositions from all spectral data, are widely established methods and have been applied to various fields including in-situ applications in air and for planetary explorations. Artificial neural networks (ANNs), where non-linear effects can be modelled, have also been investigated as a quantitative method and their applications are introduced. The ability to make quantitative estimates based on LIBS signals is seen as a key element for the technique to gain wider acceptance as an analytical method, especially in in-situ applications. In order to accelerate this process, it is recommended that the accuracy should be described using common figures of merit which express the overall normalised accuracy, such as the normalised root mean square errors (NRMSEs), when comparing the accuracy obtained from different setups and analytical methods.

Detecting Genetic Interactions for Quantitative Traits Using m-Spacing Entropy Measure

PubMed Central

Yee, Jaeyong; Kwon, Min-Seok; Park, Taesung; Park, Mira

2015-01-01

A number of statistical methods for detecting gene-gene interactions have been developed in genetic association studies with binary traits. However, many phenotype measures are intrinsically quantitative and categorizing continuous traits may not always be straightforward and meaningful. Association of gene-gene interactions with an observed distribution of such phenotypes needs to be investigated directly without categorization. Information gain based on entropy measure has previously been successful in identifying genetic associations with binary traits. We extend the usefulness of this information gain by proposing a nonparametric evaluation method of conditional entropy of a quantitative phenotype associated with a given genotype. Hence, the information gain can be obtained for any phenotype distribution. Because any functional form, such as Gaussian, is not assumed for the entire distribution of a trait or a given genotype, this method is expected to be robust enough to be applied to any phenotypic association data. Here, we show its use to successfully identify the main effect, as well as the genetic interactions, associated with a quantitative trait. PMID:26339620

Quantitative x-ray phase-contrast imaging using a single grating of comparable pitch to sample feature size.

PubMed

Morgan, Kaye S; Paganin, David M; Siu, Karen K W

2011-01-01

The ability to quantitatively retrieve transverse phase maps during imaging by using coherent x rays often requires a precise grating or analyzer-crystal-based setup. Imaging of live animals presents further challenges when these methods require multiple exposures for image reconstruction. We present a simple method of single-exposure, single-grating quantitative phase contrast for a regime in which the grating period is much greater than the effective pixel size. A grating is used to create a high-visibility reference pattern incident on the sample, which is distorted according to the complex refractive index and thickness of the sample. The resolution, along a line parallel to the grating, is not restricted by the grating spacing, and the detector resolution becomes the primary determinant of the spatial resolution. We present a method of analysis that maps the displacement of interrogation windows in order to retrieve a quantitative phase map. Application of this analysis to the imaging of known phantoms shows excellent correspondence.

[Quantitative determination of 7-phenoxyacetamidodesacetoxycephalosporanic acid].

PubMed

Dzegilenko, N B; Riabova, N M; Zinchenko, E Ia; Korchagin, V B

1976-11-01

7-Phenoxyacetamidodesacetoxycephalosporanic acid, an intermediate product in synthesis of cephalexin, was prepared by oxydation of phenoxymethylpenicillin into the respective sulphoxide and transformation of the latter. The UV-spectra of the reaction products were studied. A quantitative method is proposed for determination of 7-phenoxyacetamidodesacetoxycephalosporanic acid in the finished products based on estimation os the coefficient of specific extinction of the ethanol solutions at a wave length of 268 um in the UV-spectrum region in combination with semiquantitative estimation of the admixtures with the method of thin-layer chromatography.

Quantitative analysis of regional myocardial performance in coronary artery disease

NASA Technical Reports Server (NTRS)

Stewart, D. K.; Dodge, H. T.; Frimer, M.

1975-01-01

Findings from a group of subjects with significant coronary artery stenosis are given. A group of controls determined by use of a quantitative method for the study of regional myocardial performance based on the frame-by-frame analysis of biplane left ventricular angiograms are presented. Particular emphasis was placed upon the analysis of wall motion in terms of normalized segment dimensions, timing and velocity of contraction. The results were compared with the method of subjective assessment used clinically.

Germicidal Activity against Carbapenem/Colistin-Resistant Enterobacteriaceae Using a Quantitative Carrier Test Method.

PubMed

Kanamori, Hajime; Rutala, William A; Gergen, Maria F; Sickbert-Bennett, Emily E; Weber, David J

2018-05-07

Susceptibility to germicides for carbapenem/colistin-resistant Enterobacteriaceae is poorly described. We investigated the efficacy of multiple germicides against these emerging antibiotic-resistant pathogens using the disc-based quantitative carrier test method that can produce results more similar to those encountered in healthcare settings than a suspension test. Our study results demonstrated that germicides commonly used in healthcare facilities likely will be effective against carbapenem/colistin-resistant Enterobacteriaceae when used appropriately in healthcare facilities. Copyright © 2018 American Society for Microbiology.

Analysis of Ergot Alkaloids

PubMed Central

Crews, Colin

2015-01-01

The principles and application of established and newer methods for the quantitative and semi-quantitative determination of ergot alkaloids in food, feed, plant materials and animal tissues are reviewed. The techniques of sampling, extraction, clean-up, detection, quantification and validation are described. The major procedures for ergot alkaloid analysis comprise liquid chromatography with tandem mass spectrometry (LC-MS/MS) and liquid chromatography with fluorescence detection (LC-FLD). Other methods based on immunoassays are under development and variations of these and minor techniques are available for specific purposes. PMID:26046699

Development of a Computer-Based Visualised Quantitative Learning System for Playing Violin Vibrato

ERIC Educational Resources Information Center

Ho, Tracy Kwei-Liang; Lin, Huann-shyang; Chen, Ching-Kong; Tsai, Jih-Long

2015-01-01

Traditional methods of teaching music are largely subjective, with the lack of objectivity being particularly challenging for violin students learning vibrato because of the existence of conflicting theories. By using a computer-based analysis method, this study found that maintaining temporal coincidence between the intensity peak and the target…

Using Inquiry-Based Strategies for Enhancing Students' STEM Education Learning

ERIC Educational Resources Information Center

Lai, Ching-San

2018-01-01

The major purpose of this study was to investigate whether or not the inquiry-based method is effective in improving students' learning in STEM (Science, Technology, Engineering, and Mathematics) education. Both quantitative and qualitative methods were used. A total of 73 college students studying Information Technology (IT) were chosen as…

Development of quantitative radioactive methodologies on paper to determine important lateral-flow immunoassay parameters.

PubMed

Mosley, Garrett L; Nguyen, Phuong; Wu, Benjamin M; Kamei, Daniel T

2016-08-07

The lateral-flow immunoassay (LFA) is a well-established diagnostic technology that has recently seen significant advancements due in part to the rapidly expanding fields of paper diagnostics and paper-fluidics. As LFA-based diagnostics become more complex, it becomes increasingly important to quantitatively determine important parameters during the design and evaluation process. However, current experimental methods for determining these parameters have certain limitations when applied to LFA systems. In this work, we describe our novel methods of combining paper and radioactive measurements to determine nanoprobe molarity, the number of antibodies per nanoprobe, and the forward and reverse rate constants for nanoprobe binding to immobilized target on the LFA test line. Using a model LFA system that detects for the presence of the protein transferrin (Tf), we demonstrate the application of our methods, which involve quantitative experimentation and mathematical modeling. We also compare the results of our rate constant experiments with traditional experiments to demonstrate how our methods more appropriately capture the influence of the LFA environment on the binding interaction. Our novel experimental approaches can therefore more efficiently guide the research process for LFA design, leading to more rapid advancement of the field of paper-based diagnostics.

Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy

NASA Astrophysics Data System (ADS)

Cao, Binghua; Fan, Mengbao

2010-10-01

Terahertz wave is the electromagnetic spectrum situated between microwave and infrared wave. Quantitative analysis based on terahertz spectroscopy is very important for the application of terahertz techniques. But how to realize it is still under study. L-tartaric acid is widely used as acidulant in beverage, and other food, such as soft drinks, wine, candy, bread and some colloidal sweetmeats. In this paper, terahertz time-domain spectroscopy is applied to quantify the tartaric acid. Two methods are employed to process the terahertz spectra of different samples with different content of tartaric acid. The first one is linear regression combining correlation analysis. The second is partial least square (PLS), in which the absorption spectra in the 0.8-1.4THz region are used to quantify the tartaric acid. To compare the performance of these two principles, the relative error of the two methods is analyzed. For this experiment, the first method does better than the second one. But the first method is suitable for the quantitative analysis of materials which has obvious terahertz absorption peaks, while for material which has no obvious terahertz absorption peaks, the second one is more appropriate.

Improvements to direct quantitative analysis of multiple microRNAs facilitating faster analysis.

PubMed

Ghasemi, Farhad; Wegman, David W; Kanoatov, Mirzo; Yang, Burton B; Liu, Stanley K; Yousef, George M; Krylov, Sergey N

2013-11-05

Studies suggest that patterns of deregulation in sets of microRNA (miRNA) can be used as cancer diagnostic and prognostic biomarkers. Establishing a "miRNA fingerprint"-based diagnostic technique requires a suitable miRNA quantitation method. The appropriate method must be direct, sensitive, capable of simultaneous analysis of multiple miRNAs, rapid, and robust. Direct quantitative analysis of multiple microRNAs (DQAMmiR) is a recently introduced capillary electrophoresis-based hybridization assay that satisfies most of these criteria. Previous implementations of the method suffered, however, from slow analysis time and required lengthy and stringent purification of hybridization probes. Here, we introduce a set of critical improvements to DQAMmiR that address these technical limitations. First, we have devised an efficient purification procedure that achieves the required purity of the hybridization probe in a fast and simple fashion. Second, we have optimized the concentrations of the DNA probe to decrease the hybridization time to 10 min. Lastly, we have demonstrated that the increased probe concentrations and decreased incubation time removed the need for masking DNA, further simplifying the method and increasing its robustness. The presented improvements bring DQAMmiR closer to use in a clinical setting.

Quantitative estimation of α-PVP metabolites in urine by GC-APCI-QTOFMS with nitrogen chemiluminescence detection based on parent drug calibration.

PubMed

Mesihää, Samuel; Rasanen, Ilpo; Ojanperä, Ilkka

2018-05-01

Gas chromatography (GC) hyphenated with nitrogen chemiluminescence detection (NCD) and quadrupole time-of-flight mass spectrometry (QTOFMS) was applied for the first time to the quantitative analysis of new psychoactive substances (NPS) in urine, based on the N-equimolar response of NCD. A method was developed and validated to estimate the concentrations of three metabolites of the common stimulant NPS α-pyrrolidinovalerophenone (α-PVP) in spiked urine samples, simulating an analysis having no authentic reference standards for the metabolites and using the parent drug instead for quantitative calibration. The metabolites studied were OH-α-PVP (M1), 2″-oxo-α-PVP (M3), and N,N-bis-dealkyl-PVP (2-amino-1-phenylpentan-1-one; M5). Sample preparation involved liquid-liquid extraction with a mixture of ethyl acetate and butyl chloride at a basic pH and subsequent silylation of the sec-hydroxyl and prim-amino groups of M1 and M5, respectively. Simultaneous compound identification was based on the accurate masses of the protonated molecules for each compound by QTOFMS following atmospheric pressure chemical ionization. The accuracy of quantification of the parent-calibrated NCD method was compared with that of the corresponding parent-calibrated QTOFMS method, as well as with a reference QTOFMS method calibrated with the authentic reference standards. The NCD method produced an equally good accuracy to the reference method for α-PVP, M3 and M5, while a higher negative bias (25%) was obtained for M1, best explainable by recovery and stability issues. The performance of the parent-calibrated QTOFMS method was inferior to the reference method with an especially high negative bias (60%) for M1. The NCD method enabled better quantitative precision than the QTOFMS methods To evaluate the novel approach in casework, twenty post- mortem urine samples previously found positive for α-PVP were analyzed by the parent calibrated NCD method and the reference QTOFMS method. The highest difference in the quantitative results between the two methods was only 33%, and the NCD method's precision as the coefficient of variation was better than 13%. The limit of quantification for the NCD method was approximately 0.25μg/mL in urine, which generally allowed the analysis of α-PVP and the main metabolite M1. However, the sensitivity was not sufficient for the low concentrations of M3 and M5. Consequently, while having potential for instant analysis of NPS and metabolites in moderate concentrations without reference standards, the NCD method should be further developed for improved sensitivity to be more generally applicable. Copyright © 2018 Elsevier B.V. All rights reserved.

Evaluation of empirical rule of linearly correlated peptide selection (ERLPS) for proteotypic peptide-based quantitative proteomics.

PubMed

Liu, Kehui; Zhang, Jiyang; Fu, Bin; Xie, Hongwei; Wang, Yingchun; Qian, Xiaohong

2014-07-01

Precise protein quantification is essential in comparative proteomics. Currently, quantification bias is inevitable when using proteotypic peptide-based quantitative proteomics strategy for the differences in peptides measurability. To improve quantification accuracy, we proposed an "empirical rule for linearly correlated peptide selection (ERLPS)" in quantitative proteomics in our previous work. However, a systematic evaluation on general application of ERLPS in quantitative proteomics under diverse experimental conditions needs to be conducted. In this study, the practice workflow of ERLPS was explicitly illustrated; different experimental variables, such as, different MS systems, sample complexities, sample preparations, elution gradients, matrix effects, loading amounts, and other factors were comprehensively investigated to evaluate the applicability, reproducibility, and transferability of ERPLS. The results demonstrated that ERLPS was highly reproducible and transferable within appropriate loading amounts and linearly correlated response peptides should be selected for each specific experiment. ERLPS was used to proteome samples from yeast to mouse and human, and in quantitative methods from label-free to O18/O16-labeled and SILAC analysis, and enabled accurate measurements for all proteotypic peptide-based quantitative proteomics over a large dynamic range. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Allocation of Load-Loss Cost Caused by Voltage Sag

NASA Astrophysics Data System (ADS)

Gao, X.

2017-10-01

This paper focuses on the allocation of load-loss cost caused by voltage sag in the environment of electricity market. To compensate the loss of loads due to voltage sags, the load-loss cost is allocated to both sources and power consumers. On the basis of Load Drop Cost (LDC), a quantitative evaluation index of load-loss cost caused by voltage sag is identified. The load-loss cost to be allocated to power consumers themselves is calculated according to load classification. Based on the theory of power component the quantitative relation between sources and loads is established, thereby a quantitative calculation method for load-loss cost allocated to each source is deduced and the quantitative compensation from individual source to load is proposed. A simple five-bus system illustrates the main features of the proposed method.

Quantitative angle-insensitive flow measurement using relative standard deviation OCT.

PubMed

Zhu, Jiang; Zhang, Buyun; Qi, Li; Wang, Ling; Yang, Qiang; Zhu, Zhuqing; Huo, Tiancheng; Chen, Zhongping

2017-10-30

Incorporating different data processing methods, optical coherence tomography (OCT) has the ability for high-resolution angiography and quantitative flow velocity measurements. However, OCT angiography cannot provide quantitative information of flow velocities, and the velocity measurement based on Doppler OCT requires the determination of Doppler angles, which is a challenge in a complex vascular network. In this study, we report on a relative standard deviation OCT (RSD-OCT) method which provides both vascular network mapping and quantitative information for flow velocities within a wide range of Doppler angles. The RSD values are angle-insensitive within a wide range of angles, and a nearly linear relationship was found between the RSD values and the flow velocities. The RSD-OCT measurement in a rat cortex shows that it can quantify the blood flow velocities as well as map the vascular network in vivo .

Quantitative angle-insensitive flow measurement using relative standard deviation OCT

NASA Astrophysics Data System (ADS)

Zhu, Jiang; Zhang, Buyun; Qi, Li; Wang, Ling; Yang, Qiang; Zhu, Zhuqing; Huo, Tiancheng; Chen, Zhongping

2017-10-01

Incorporating different data processing methods, optical coherence tomography (OCT) has the ability for high-resolution angiography and quantitative flow velocity measurements. However, OCT angiography cannot provide quantitative information of flow velocities, and the velocity measurement based on Doppler OCT requires the determination of Doppler angles, which is a challenge in a complex vascular network. In this study, we report on a relative standard deviation OCT (RSD-OCT) method which provides both vascular network mapping and quantitative information for flow velocities within a wide range of Doppler angles. The RSD values are angle-insensitive within a wide range of angles, and a nearly linear relationship was found between the RSD values and the flow velocities. The RSD-OCT measurement in a rat cortex shows that it can quantify the blood flow velocities as well as map the vascular network in vivo.

Facile and quantitative electrochemical detection of yeast cell apoptosis

NASA Astrophysics Data System (ADS)

Yue, Qiulin; Xiong, Shiquan; Cai, Dongqing; Wu, Zhengyan; Zhang, Xin

2014-03-01

An electrochemical method based on square wave anodic stripping voltammetry (SWASV) was developed to detect the apoptosis of yeast cells conveniently and quantitatively through the high affinity between Cu2+ and phosphatidylserine (PS) translocated from the inner to the outer plasma membrane of the apoptotic cells. The combination of negatively charged PS and Cu2+ could decrease the electrochemical response of Cu2+ on the electrode. The results showed that the apoptotic rates of cells could be detected quantitatively through the variations of peak currents of Cu2+ by SWASV, and agreed well with those obtained through traditional flow cytometry detection. This work thus may provide a novel, simple, immediate and accurate detection method for cell apoptosis.

Toward quantitative estimation of material properties with dynamic mode atomic force microscopy: a comparative study.

PubMed

Ghosal, Sayan; Gannepalli, Anil; Salapaka, Murti

2017-08-11

In this article, we explore methods that enable estimation of material properties with the dynamic mode atomic force microscopy suitable for soft matter investigation. The article presents the viewpoint of casting the system, comprising of a flexure probe interacting with the sample, as an equivalent cantilever system and compares a steady-state analysis based method with a recursive estimation technique for determining the parameters of the equivalent cantilever system in real time. The steady-state analysis of the equivalent cantilever model, which has been implicitly assumed in studies on material property determination, is validated analytically and experimentally. We show that the steady-state based technique yields results that quantitatively agree with the recursive method in the domain of its validity. The steady-state technique is considerably simpler to implement, however, slower compared to the recursive technique. The parameters of the equivalent system are utilized to interpret storage and dissipative properties of the sample. Finally, the article identifies key pitfalls that need to be avoided toward the quantitative estimation of material properties.

Examination of a Method to Determine the Reference Region for Calculating the Specific Binding Ratio in Dopamine Transporter Imaging.

PubMed

Watanabe, Ayumi; Inoue, Yusuke; Asano, Yuji; Kikuchi, Kei; Miyatake, Hiroki; Tokushige, Takanobu

2017-01-01

The specific binding ratio (SBR) was first reported by Tossici-Bolt et al. for quantitative indicators for dopamine transporter (DAT) imaging. It is defined as the ratio of the specific binding concentration of the striatum to the non-specific binding concentration of the whole brain other than the striatum. The non-specific binding concentration is calculated based on the region of interest (ROI), which is set 20 mm inside the outer contour, defined by a threshold technique. Tossici-Bolt et al. used a 50% threshold, but sometimes we couldn't define the ROI of non-specific binding concentration (reference region) and calculate SBR appropriately with a 50% threshold. Therefore, we sought a new method for determining the reference region when calculating SBR. We used data from 20 patients who had undergone DAT imaging in our hospital, to calculate the non-specific binding concentration by the following methods, the threshold to define a reference region was fixed at some specific values (the fixing method) and reference region was visually optimized by an examiner at every examination (the visual optimization method). First, we assessed the reference region of each method visually, and afterward, we quantitatively compared SBR calculated based on each method. In the visual assessment, the scores of the fixing method at 30% and visual optimization method were higher than the scores of the fixing method at other values, with or without scatter correction. In the quantitative assessment, the SBR obtained by visual optimization of the reference region, based on consensus of three radiological technologists, was used as a baseline (the standard method). The values of SBR showed good agreement between the standard method and both the fixing method at 30% and the visual optimization method, with or without scatter correction. Therefore, the fixing method at 30% and the visual optimization method were equally suitable for determining the reference region.

Enhanced sensitivity and multiplexing with 2D LC/MRM-MS and labeled standards for deeper and more comprehensive protein quantitation.

PubMed

Percy, Andrew J; Simon, Romain; Chambers, Andrew G; Borchers, Christoph H

2014-06-25

Mass spectrometry (MS)-based protein quantitation is increasingly being employed to verify candidate protein biomarkers. Multiple or selected reaction monitoring-mass spectrometry (MRM-MS or SRM-MS) with isotopically labeled internal standards has proven to be a successful approach in that regard, but has yet to reach its full potential in terms of multiplexing and sensitivity. Here, we report the development of a new MRM method for the quantitation of 253 disease-associated proteins (represented by 625 interference-free peptides) in 13 LC fractions. This 2D RPLC/MRM-MS approach extends the depth and breadth of the assay by 2 orders of magnitude over pre-fractionation-free assays, with 31 proteins below 10 ng/mL and 41 proteins above 10 ng/mL now quantifiable. Standard flow rates are used in both chromatographic dimensions, and up-front depletion or antibody-based enrichment is not required. The LC separations utilize high and low pH conditions, with the former employing an ammonium hydroxide-based eluent, instead of the conventional ammonium formate, resulting in improved LC column lifetime and performance. The high sensitivity (determined concentration range: 15 mg/mL to 452 pg/mL) and robustness afforded by this method makes the full MRM panel, or subsets thereof, useful for the verification of disease-associated plasma protein biomarkers in patient samples. The described research extends the breadth and depth of protein quantitation in undepleted and non-enriched human plasma by employing standard-flow 2D RPLC/MRM-MS in conjunction with a complex mixture of isotopically labeled peptide standards. The proteins quantified are mainly putative biomarkers of non-communicable (i.e., non-infectious) disease (e.g., cardiovascular or cancer), which require pre-clinical verification and validation before clinical implementation. Based on the enhanced sensitivity and multiplexing, this quantitative plasma proteomic method should prove useful in future candidate biomarker verification studies. Copyright © 2014 Elsevier B.V. All rights reserved.

Developing Environmentally Responsible Behaviours Through the Implementation of Argumentation- and Problem-Based Learning Models

NASA Astrophysics Data System (ADS)

Fettahlıoğlu, Pınar; Aydoğdu, Mustafa

2018-04-01

The purpose of this research is to investigate the effect of using argumentation and problem-based learning approaches on the development of environmentally responsible behaviours among pre-service science teachers. Experimental activities were implemented for 14 weeks for 52 class hours in an environmental education class within a science teaching department. A mixed method was used as a research design; particularly, a special type of Concurrent Nested Strategy was applied. The quantitative portion was based on the one-group pre-test and post-test models, and the qualitative portion was based on the holistic multiple-case study method. The quantitative portion of the research was conducted with 34 third-year pre-service science teachers studying at a state university. The qualitative portion of the study was conducted with six pre-service science teachers selected among the 34 pre-service science teachers based on the pre-test results obtained from an environmentally responsible behaviour scale. t tests for dependent groups were used to analyse quantitative data. Both descriptive and content analyses of the qualitative data were performed. The results of the study showed that the use of the argumentation and problem-based learning approaches significantly contributed to the development of environmentally responsible behaviours among pre-service science teachers.

Quantitative validation of a nonlinear histology-MRI coregistration method using Generalized Q-sampling Imaging in complex human cortical white matter

PubMed Central

Gangolli, Mihika; Holleran, Laurena; Kim, Joong Hee; Stein, Thor D.; Alvarez, Victor; McKee, Ann C.; Brody, David L.

2017-01-01

Advanced diffusion MRI methods have recently been proposed for detection of pathologies such as traumatic axonal injury and chronic traumatic encephalopathy which commonly affect complex cortical brain regions. However, radiological-pathological correlations in human brain tissue that detail the relationship between the multi-component diffusion signal and underlying pathology are lacking. We present a nonlinear voxel based two dimensional coregistration method that is useful for matching diffusion signals to quantitative metrics of high resolution histological images. When validated in ex vivo human cortical tissue at a 250 × 250 × 500 micron spatial resolution, the method proved robust in correlations between generalized q-sampling imaging and histologically based white matter fiber orientations, with r = 0.94 for the primary fiber direction and r = 0.88 for secondary fiber direction in each voxel. Importantly, however, the correlation was substantially worse with reduced spatial resolution or with fiber orientations derived using a diffusion tensor model. Furthermore, we have detailed a quantitative histological metric of white matter fiber integrity termed power coherence capable of distinguishing between architecturally complex but intact white matter from disrupted white matter regions. These methods may allow for more sensitive and specific radiological-pathological correlations of neurodegenerative diseases affecting complex gray and white matter. PMID:28365421

A quantitative method for residues of macrolide antibiotics in porcine kidney by liquid chromatography/tandem mass spectrometry.

PubMed

Dickson, Leslie C; O'Byrne, Collin; Chan, Wayne

2012-01-01

An LC/MS/MS-based multiresidue quantitative method was developed for the macrolides erythromycin A, neospiramycin I, oleandomycin, spiramycin I, tilmicosin, and tylosin A in porcine kidney tissues. The Canadian Food Inspection Agency (CFIA) had as part of its analytical scope an LC/UV method for quantification of residues of two macrolide antibiotics, tilmicosin and tylosin A, in the kidney, liver, and muscle of cattle, swine, and poultry. The method could not reliably detect concentrations below 10 microg/kg. To increase the scope of the CFIA's analytical capabilities, a sensitive multiresidue quantitative method for macrolide residues in food animal tissues was required. Porcine kidney samples were extracted with acetonitrile and alkaline buffer and cleaned-up using silica-based C18 SPE cartridges. Sample extracts were analyzed using LC/MS/MS with positive electrospray ionization. Fitness for purpose was verified in a single-laboratory validation study using a second analyst. The working analytical range was 5 to 50 microg/kg. LOD and LOQ were 0.5 to 0.6 microg/kg and 1.5 to 3.0 microg/kg, respectively. Limits of identification were 0.5 to 2.0 microg/kg. Relative intermediate precisions were 8 to 17%. Average absolute recoveries were 68 to 76%.

To label or not to label: applications of quantitative proteomics in neuroscience research.

PubMed

Filiou, Michaela D; Martins-de-Souza, Daniel; Guest, Paul C; Bahn, Sabine; Turck, Christoph W

2012-02-01

Proteomics has provided researchers with a sophisticated toolbox of labeling-based and label-free quantitative methods. These are now being applied in neuroscience research where they have already contributed to the elucidation of fundamental mechanisms and the discovery of candidate biomarkers. In this review, we evaluate and compare labeling-based and label-free quantitative proteomic techniques for applications in neuroscience research. We discuss the considerations required for the analysis of brain and central nervous system specimens, the experimental design of quantitative proteomic workflows as well as the feasibility, advantages, and disadvantages of the available techniques for neuroscience-oriented questions. Furthermore, we assess the use of labeled standards as internal controls for comparative studies in humans and review applications of labeling-based and label-free mass spectrometry approaches in relevant model organisms and human subjects. Providing a comprehensive guide of feasible and meaningful quantitative proteomic methodologies for neuroscience research is crucial not only for overcoming current limitations but also for gaining useful insights into brain function and translating proteomics from bench to bedside. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Targeted liquid chromatography tandem mass spectrometry to quantitate wheat gluten using well-defined reference proteins.

PubMed

Schalk, Kathrin; Koehler, Peter; Scherf, Katharina Anne

2018-01-01

Celiac disease (CD) is an inflammatory disorder of the upper small intestine caused by the ingestion of storage proteins (prolamins and glutelins) from wheat, barley, rye, and, in rare cases, oats. CD patients need to follow a gluten-free diet by consuming gluten-free products with gluten contents of less than 20 mg/kg. Currently, the recommended method for the quantitative determination of gluten is an enzyme-linked immunosorbent assay (ELISA) based on the R5 monoclonal antibody. Because the R5 ELISA mostly detects the prolamin fraction of gluten, a new independent method is required to detect prolamins as well as glutelins. This paper presents the development of a method to quantitate 16 wheat marker peptides derived from all wheat gluten protein types by liquid chromatography tandem mass spectrometry (LC-MS/MS) in the multiple reaction monitoring mode. The quantitation of each marker peptide in the chymotryptic digest of a defined amount of the respective reference wheat protein type resulted in peptide-specific yields. This enabled the conversion of peptide into protein type concentrations. Gluten contents were expressed as sum of all determined protein type concentrations. This new method was applied to quantitate gluten in wheat starches and compared to R5 ELISA and gel-permeation high-performance liquid chromatography with fluorescence detection (GP-HPLC-FLD), which resulted in a strong correlation between LC-MS/MS and the other two methods.

Comparison of Gavage, Water Bottle, and a High-Moisture Diet Bolus as Dosing Methods for Quantitative D-xylose Administration to B6D2F1 (Mus musculus) Mice

NASA Technical Reports Server (NTRS)

Zimmer, J. Paul; Lewis, Sherry M.; Moyer, Jerry L.

1993-01-01

Gavage, water bottle, and diet incorporation are 3 dosing methods used orally to administer test compounds to rodents. These 3 methods were compared in mice to determine which represented the most quantitative delivery system. For dietary incorporation, a high-moisture bolus form of NIH-31 rodent meal was developed using hydroxypropyl methylcellulose as an autoclave-stable binding agent. A high-moisture bolus were selected to increase the acceptability of the dosed diet and to promote quantitative consumption through reduced wastage. The test compound used was D-xylose, a pentose sugar that may be quantitatively detected, colorimetrically, in urine following oral dosing. Six male and 6 female B6D2FI mice were placed in metabolism cages and dosed with a known quantity of D-xylose by each of the 3 methods. Urine was collected before and after each method of administration and analysed for total D-xylose; the per cent recovery was based upon the amount of D-xylose consumed. Quantitative consumption was apparently greatest for water bottle dosing with an average recovery of 56.0% of the original D-xylose dose. High-moisture bolus incorporation ranked second with 50.0% D-xylose recovery, and gavage was third with 41.0% D-xylose recovery.

Automated compromised right lung segmentation method using a robust atlas-based active volume model with sparse shape composition prior in CT.

PubMed

Zhou, Jinghao; Yan, Zhennan; Lasio, Giovanni; Huang, Junzhou; Zhang, Baoshe; Sharma, Navesh; Prado, Karl; D'Souza, Warren

2015-12-01

To resolve challenges in image segmentation in oncologic patients with severely compromised lung, we propose an automated right lung segmentation framework that uses a robust, atlas-based active volume model with a sparse shape composition prior. The robust atlas is achieved by combining the atlas with the output of sparse shape composition. Thoracic computed tomography images (n=38) from patients with lung tumors were collected. The right lung in each scan was manually segmented to build a reference training dataset against which the performance of the automated segmentation method was assessed. The quantitative results of this proposed segmentation method with sparse shape composition achieved mean Dice similarity coefficient (DSC) of (0.72, 0.81) with 95% CI, mean accuracy (ACC) of (0.97, 0.98) with 95% CI, and mean relative error (RE) of (0.46, 0.74) with 95% CI. Both qualitative and quantitative comparisons suggest that this proposed method can achieve better segmentation accuracy with less variance than other atlas-based segmentation methods in the compromised lung segmentation. Published by Elsevier Ltd.

Development and evaluation of a model-based downscatter compensation method for quantitative I-131 SPECT

PubMed Central

Song, Na; Du, Yong; He, Bin; Frey, Eric C.

2011-01-01

Purpose: The radionuclide 131I has found widespread use in targeted radionuclide therapy (TRT), partly due to the fact that it emits photons that can be imaged to perform treatment planning or posttherapy dose verification as well as beta rays that are suitable for therapy. In both the treatment planning and dose verification applications, it is necessary to estimate the activity distribution in organs or tumors at several time points. In vivo estimates of the 131I activity distribution at each time point can be obtained from quantitative single-photon emission computed tomography (QSPECT) images and organ activity estimates can be obtained either from QSPECT images or quantification of planar projection data. However, in addition to the photon used for imaging, 131I decay results in emission of a number of other higher-energy photons with significant abundances. These higher-energy photons can scatter in the body, collimator, or detector and be counted in the 364 keV photopeak energy window, resulting in reduced image contrast and degraded quantitative accuracy; these photons are referred to as downscatter. The goal of this study was to develop and evaluate a model-based downscatter compensation method specifically designed for the compensation of high-energy photons emitted by 131I and detected in the imaging energy window. Methods: In the evaluation study, we used a Monte Carlo simulation (MCS) code that had previously been validated for other radionuclides. Thus, in preparation for the evaluation study, we first validated the code for 131I imaging simulation by comparison with experimental data. Next, we assessed the accuracy of the downscatter model by comparing downscatter estimates with MCS results. Finally, we combined the downscatter model with iterative reconstruction-based compensation for attenuation (A) and scatter (S) and the full (D) collimator-detector response of the 364 keV photons to form a comprehensive compensation method. We evaluated this combined method in terms of quantitative accuracy using the realistic 3D NCAT phantom and an activity distribution obtained from patient studies. We compared the accuracy of organ activity estimates in images reconstructed with and without addition of downscatter compensation from projections with and without downscatter contamination. Results: We observed that the proposed method provided substantial improvements in accuracy compared to no downscatter compensation and had accuracies comparable to reconstructions from projections without downscatter contamination. Conclusions: The results demonstrate that the proposed model-based downscatter compensation method is effective and may have a role in quantitative 131I imaging. PMID:21815394

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

PubMed

Choi, Hyungwon; Kim, Sinae; Fermin, Damian; Tsou, Chih-Chiang; Nesvizhskii, Alexey I

2015-11-03

We introduce QPROT, a statistical framework and computational tool for differential protein expression analysis using protein intensity data. QPROT is an extension of the QSPEC suite, originally developed for spectral count data, adapted for the analysis using continuously measured protein-level intensity data. QPROT offers a new intensity normalization procedure and model-based differential expression analysis, both of which account for missing data. Determination of differential expression of each protein is based on the standardized Z-statistic based on the posterior distribution of the log fold change parameter, guided by the false discovery rate estimated by a well-known Empirical Bayes method. We evaluated the classification performance of QPROT using the quantification calibration data from the clinical proteomic technology assessment for cancer (CPTAC) study and a recently published Escherichia coli benchmark dataset, with evaluation of FDR accuracy in the latter. QPROT is a statistical framework with computational software tool for comparative quantitative proteomics analysis. It features various extensions of QSPEC method originally built for spectral count data analysis, including probabilistic treatment of missing values in protein intensity data. With the increasing popularity of label-free quantitative proteomics data, the proposed method and accompanying software suite will be immediately useful for many proteomics laboratories. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigation on microfluidic particles manipulation by holographic 3D tracking strategies

NASA Astrophysics Data System (ADS)

Cacace, Teresa; Paturzo, Melania; Memmolo, Pasquale; Vassalli, Massimo; Fraldi, Massimiliano; Mensitieri, Giuseppe; Ferraro, Pietro

2017-06-01

We demonstrate a 3D holographic tracking method to investigate particles motion in a microfluidic channel while unperturbed while inducing their migration through microfluidic manipulation. Digital holography (DH) in microscopy is a full-field, label-free imaging technique able to provide quantitative phase-contrast. The employed 3D tracking method is articulated in steps. First, the displacements along the optical axis are assessed by numerical refocusing criteria. In particular, an automatic refocusing method to recover the particles axial position is implemented employing a contrast-based refocusing criterion. Then, the transverse position of the in-focus object is evaluated through quantitative phase map segmentation methods and centroid-based 2D tracking strategy. The introduction of DH is thus suggested as a powerful approach for control of particles and biological samples manipulation, as well as a possible aid to precise design and implementation of advanced lab-on-chip microfluidic devices.

Institutional Gender Equity Salary Analysis and Recursive Impact of Career and Life Choices

ERIC Educational Resources Information Center

Peterson, Teri S.

2013-01-01

This study employed mixed methods, engaging both quantitative and qualitative inquiries. In terms of the quantitative inquiry, the purpose of this study was to explore and assess gender-based salary inequities at a Carnegie Classified Research High university in the Intermountain West. Qualitative inquiry was used to follow up and contextually…

COMPARISON OF ENTEROCOCCUS MEASUREMENTS IN FRESHWATER AT TWO RECREATIONAL BEACHES BY QUANTITATIVE POLYMERASE CHAIN REACTION AND MEMBRANE FILER CULTURE ANALYSIS

EPA Science Inventory

Cell densities of the fecal pollution indicator genus, Enterococcus, were determined by a rapid (2-3 hr) quantitative PCR (QPCR) analysis based method in 100 ml water samples collected from recreational beaches on Lake Michigan and Lake Erie during the summer of 2003. Enumeration...

In situ flash x-ray high-speed computed tomography for the quantitative analysis of highly dynamic processes

NASA Astrophysics Data System (ADS)

Moser, Stefan; Nau, Siegfried; Salk, Manfred; Thoma, Klaus

2014-02-01

The in situ investigation of dynamic events, ranging from car crash to ballistics, often is key to the understanding of dynamic material behavior. In many cases the important processes and interactions happen on the scale of milli- to microseconds at speeds of 1000 m s-1 or more. Often, 3D information is necessary to fully capture and analyze all relevant effects. High-speed 3D-visualization techniques are thus required for the in situ analysis. 3D-capable optical high-speed methods often are impaired by luminous effects and dust, while flash x-ray based methods usually deliver only 2D data. In this paper, a novel 3D-capable flash x-ray based method, in situ flash x-ray high-speed computed tomography is presented. The method is capable of producing 3D reconstructions of high-speed processes based on an undersampled dataset consisting of only a few (typically 3 to 6) x-ray projections. The major challenges are identified, discussed and the chosen solution outlined. The application is illustrated with an exemplary application of a 1000 m s-1 high-speed impact event on the scale of microseconds. A quantitative analysis of the in situ measurement of the material fragments with a 3D reconstruction with 1 mm voxel size is presented and the results are discussed. The results show that the HSCT method allows gaining valuable visual and quantitative mechanical information for the understanding and interpretation of high-speed events.

Assessing the performance of the generalized propensity score for estimating the effect of quantitative or continuous exposures on survival or time-to-event outcomes.

PubMed

Austin, Peter C

2018-01-01

Propensity score methods are frequently used to estimate the effects of interventions using observational data. The propensity score was originally developed for use with binary exposures. The generalized propensity score (GPS) is an extension of the propensity score for use with quantitative or continuous exposures (e.g. pack-years of cigarettes smoked, dose of medication, or years of education). We describe how the GPS can be used to estimate the effect of continuous exposures on survival or time-to-event outcomes. To do so we modified the concept of the dose-response function for use with time-to-event outcomes. We used Monte Carlo simulations to examine the performance of different methods of using the GPS to estimate the effect of quantitative exposures on survival or time-to-event outcomes. We examined covariate adjustment using the GPS and weighting using weights based on the inverse of the GPS. The use of methods based on the GPS was compared with the use of conventional G-computation and weighted G-computation. Conventional G-computation resulted in estimates of the dose-response function that displayed the lowest bias and the lowest variability. Amongst the two GPS-based methods, covariate adjustment using the GPS tended to have the better performance. We illustrate the application of these methods by estimating the effect of average neighbourhood income on the probability of survival following hospitalization for an acute myocardial infarction.

Impact of reconstruction parameters on quantitative I-131 SPECT

NASA Astrophysics Data System (ADS)

van Gils, C. A. J.; Beijst, C.; van Rooij, R.; de Jong, H. W. A. M.

2016-07-01

Radioiodine therapy using I-131 is widely used for treatment of thyroid disease or neuroendocrine tumors. Monitoring treatment by accurate dosimetry requires quantitative imaging. The high energy photons however render quantitative SPECT reconstruction challenging, potentially requiring accurate correction for scatter and collimator effects. The goal of this work is to assess the effectiveness of various correction methods on these effects using phantom studies. A SPECT/CT acquisition of the NEMA IEC body phantom was performed. Images were reconstructed using the following parameters: (1) without scatter correction, (2) with triple energy window (TEW) scatter correction and (3) with Monte Carlo-based scatter correction. For modelling the collimator-detector response (CDR), both (a) geometric Gaussian CDRs as well as (b) Monte Carlo simulated CDRs were compared. Quantitative accuracy, contrast to noise ratios and recovery coefficients were calculated, as well as the background variability and the residual count error in the lung insert. The Monte Carlo scatter corrected reconstruction method was shown to be intrinsically quantitative, requiring no experimentally acquired calibration factor. It resulted in a more accurate quantification of the background compartment activity density compared with TEW or no scatter correction. The quantification error relative to a dose calibrator derived measurement was found to be  <1%,-26% and 33%, respectively. The adverse effects of partial volume were significantly smaller with the Monte Carlo simulated CDR correction compared with geometric Gaussian or no CDR modelling. Scatter correction showed a small effect on quantification of small volumes. When using a weighting factor, TEW correction was comparable to Monte Carlo reconstruction in all measured parameters, although this approach is clinically impractical since this factor may be patient dependent. Monte Carlo based scatter correction including accurately simulated CDR modelling is the most robust and reliable method to reconstruct accurate quantitative iodine-131 SPECT images.

Quantitative secondary electron detection

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

Agrawal, Jyoti; Joy, David C.; Nayak, Subuhadarshi

Quantitative Secondary Electron Detection (QSED) using the array of solid state devices (SSD) based electron-counters enable critical dimension metrology measurements in materials such as semiconductors, nanomaterials, and biological samples (FIG. 3). Methods and devices effect a quantitative detection of secondary electrons with the array of solid state detectors comprising a number of solid state detectors. An array senses the number of secondary electrons with a plurality of solid state detectors, counting the number of secondary electrons with a time to digital converter circuit in counter mode.

Assessment of acute myocarditis by cardiac magnetic resonance imaging: Comparison of qualitative and quantitative analysis methods.

PubMed

Imbriaco, Massimo; Nappi, Carmela; Puglia, Marta; De Giorgi, Marco; Dell'Aversana, Serena; Cuocolo, Renato; Ponsiglione, Andrea; De Giorgi, Igino; Polito, Maria Vincenza; Klain, Michele; Piscione, Federico; Pace, Leonardo; Cuocolo, Alberto

2017-10-26

To compare cardiac magnetic resonance (CMR) qualitative and quantitative analysis methods for the noninvasive assessment of myocardial inflammation in patients with suspected acute myocarditis (AM). A total of 61 patients with suspected AM underwent coronary angiography and CMR. Qualitative analysis was performed applying Lake-Louise Criteria (LLC), followed by quantitative analysis based on the evaluation of edema ratio (ER) and global relative enhancement (RE). Diagnostic performance was assessed for each method by measuring the area under the curves (AUC) of the receiver operating characteristic analyses. The final diagnosis of AM was based on symptoms and signs suggestive of cardiac disease, evidence of myocardial injury as defined by electrocardiogram changes, elevated troponin I, exclusion of coronary artery disease by coronary angiography, and clinical and echocardiographic follow-up at 3 months after admission to the chest pain unit. In all patients, coronary angiography did not show significant coronary artery stenosis. Troponin I levels and creatine kinase were higher in patients with AM compared to those without (both P < .001). There were no significant differences among LLC, T2-weighted short inversion time inversion recovery (STIR) sequences, early (EGE), and late (LGE) gadolinium-enhancement sequences for diagnosis of AM. The AUC for qualitative (T2-weighted STIR 0.92, EGE 0.87 and LGE 0.88) and quantitative (ER 0.89 and global RE 0.80) analyses were also similar. Qualitative and quantitative CMR analysis methods show similar diagnostic accuracy for the diagnosis of AM. These findings suggest that a simplified approach using a shortened CMR protocol including only T2-weighted STIR sequences might be useful to rule out AM in patients with acute coronary syndrome and normal coronary angiography.

Quantitative imaging methods in osteoporosis.

PubMed

Oei, Ling; Koromani, Fjorda; Rivadeneira, Fernando; Zillikens, M Carola; Oei, Edwin H G

2016-12-01

Osteoporosis is characterized by a decreased bone mass and quality resulting in an increased fracture risk. Quantitative imaging methods are critical in the diagnosis and follow-up of treatment effects in osteoporosis. Prior radiographic vertebral fractures and bone mineral density (BMD) as a quantitative parameter derived from dual-energy X-ray absorptiometry (DXA) are among the strongest known predictors of future osteoporotic fractures. Therefore, current clinical decision making relies heavily on accurate assessment of these imaging features. Further, novel quantitative techniques are being developed to appraise additional characteristics of osteoporosis including three-dimensional bone architecture with quantitative computed tomography (QCT). Dedicated high-resolution (HR) CT equipment is available to enhance image quality. At the other end of the spectrum, by utilizing post-processing techniques such as the trabecular bone score (TBS) information on three-dimensional architecture can be derived from DXA images. Further developments in magnetic resonance imaging (MRI) seem promising to not only capture bone micro-architecture but also characterize processes at the molecular level. This review provides an overview of various quantitative imaging techniques based on different radiological modalities utilized in clinical osteoporosis care and research.

A standardized kit for automated quantitative assessment of candidate protein biomarkers in human plasma.

PubMed

Percy, Andrew J; Mohammed, Yassene; Yang, Juncong; Borchers, Christoph H

2015-12-01

An increasingly popular mass spectrometry-based quantitative approach for health-related research in the biomedical field involves the use of stable isotope-labeled standards (SIS) and multiple/selected reaction monitoring (MRM/SRM). To improve inter-laboratory precision and enable more widespread use of this 'absolute' quantitative technique in disease-biomarker assessment studies, methods must be standardized. Results/methodology: Using this MRM-with-SIS-peptide approach, we developed an automated method (encompassing sample preparation, processing and analysis) for quantifying 76 candidate protein markers (spanning >4 orders of magnitude in concentration) in neat human plasma. The assembled biomarker assessment kit - the 'BAK-76' - contains the essential materials (SIS mixes), methods (for acquisition and analysis), and tools (Qualis-SIS software) for performing biomarker discovery or verification studies in a rapid and standardized manner.

Analysis of swimming performance: perceptions and practices of US-based swimming coaches.

PubMed

Mooney, Robert; Corley, Gavin; Godfrey, Alan; Osborough, Conor; Newell, John; Quinlan, Leo Richard; ÓLaighin, Gearóid

2016-01-01

In elite swimming, a broad range of methods are used to assess performance, inform coaching practices and monitor athletic progression. The aim of this paper was to examine the performance analysis practices of swimming coaches and to explore the reasons behind the decisions that coaches take when analysing performance. Survey data were analysed from 298 Level 3 competitive swimming coaches (245 male, 53 female) based in the United States. Results were compiled to provide a generalised picture of practices and perceptions and to examine key emerging themes. It was found that a disparity exists between the importance swim coaches place on biomechanical analysis of swimming performance and the types of analyses that are actually conducted. Video-based methods are most frequently employed, with over 70% of coaches using these methods at least monthly, with analyses being mainly qualitative in nature rather than quantitative. Barriers to the more widespread use of quantitative biomechanical analysis in elite swimming environments were explored. Constraints include time, cost and availability of resources, but other factors such as sources of information on swimming performance and analysis and control over service provision are also discussed, with particular emphasis on video-based methods and emerging sensor-based technologies.

Analysis of airborne MAIS imaging spectrometric data for mineral exploration

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

Wang Jinnian; Zheng Lanfen; Tong Qingxi

1996-11-01

The high spectral resolution imaging spectrometric system made quantitative analysis and mapping of surface composition possible. The key issue will be the quantitative approach for analysis of surface parameters for imaging spectrometer data. This paper describes the methods and the stages of quantitative analysis. (1) Extracting surface reflectance from imaging spectrometer image. Lab. and inflight field measurements are conducted for calibration of imaging spectrometer data, and the atmospheric correction has also been used to obtain ground reflectance by using empirical line method and radiation transfer modeling. (2) Determining quantitative relationship between absorption band parameters from the imaging spectrometer data andmore » chemical composition of minerals. (3) Spectral comparison between the spectra of spectral library and the spectra derived from the imagery. The wavelet analysis-based spectrum-matching techniques for quantitative analysis of imaging spectrometer data has beer, developed. Airborne MAIS imaging spectrometer data were used for analysis and the analysis results have been applied to the mineral and petroleum exploration in Tarim Basin area china. 8 refs., 8 figs.« less

Quantitative electrophysiological monitoring of anti-histamine drug effects on live cells via reusable sensor platforms.

PubMed

Pham Ba, Viet Anh; Cho, Dong-Guk; Kim, Daesan; Yoo, Haneul; Ta, Van-Thao; Hong, Seunghun

2017-08-15

We demonstrated the quantitative electrophysiological monitoring of histamine and anti-histamine drug effects on live cells via reusable sensor platforms based on carbon nanotube transistors. This method enabled us to monitor the real-time electrophysiological responses of a single HeLa cell to histamine with different concentrations. The measured electrophysiological responses were attributed to the activity of histamine type 1 receptors on a HeLa cell membrane by histamine. Furthermore, the effects of anti-histamine drugs such as cetirizine or chlorphenamine on the electrophysiological activities of HeLa cells were also evaluated quantitatively. Significantly, we utilized only a single device to monitor the responses of multiple HeLa cells to each drug, which allowed us to quantitatively analyze the antihistamine drug effects on live cells without errors from the device-to-device variation in device characteristics. Such quantitative evaluation capability of our method would promise versatile applications such as drug screening and nanoscale bio sensor researches. Copyright © 2017 Elsevier B.V. All rights reserved.

Designing a mixed methods study in primary care.

PubMed

Creswell, John W; Fetters, Michael D; Ivankova, Nataliya V

2004-01-01

Mixed methods or multimethod research holds potential for rigorous, methodologically sound investigations in primary care. The objective of this study was to use criteria from the literature to evaluate 5 mixed methods studies in primary care and to advance 3 models useful for designing such investigations. We first identified criteria from the social and behavioral sciences to analyze mixed methods studies in primary care research. We then used the criteria to evaluate 5 mixed methods investigations published in primary care research journals. Of the 5 studies analyzed, 3 included a rationale for mixing based on the need to develop a quantitative instrument from qualitative data or to converge information to best understand the research topic. Quantitative data collection involved structured interviews, observational checklists, and chart audits that were analyzed using descriptive and inferential statistical procedures. Qualitative data consisted of semistructured interviews and field observations that were analyzed using coding to develop themes and categories. The studies showed diverse forms of priority: equal priority, qualitative priority, and quantitative priority. Data collection involved quantitative and qualitative data gathered both concurrently and sequentially. The integration of the quantitative and qualitative data in these studies occurred between data analysis from one phase and data collection from a subsequent phase, while analyzing the data, and when reporting the results. We recommend instrument-building, triangulation, and data transformation models for mixed methods designs as useful frameworks to add rigor to investigations in primary care. We also discuss the limitations of our study and the need for future research.

An Illustration of Determining Quantitatively the Rock Mass Quality Parameters of the Hoek-Brown Failure Criterion

NASA Astrophysics Data System (ADS)

Wu, Li; Adoko, Amoussou Coffi; Li, Bo

2018-04-01

In tunneling, determining quantitatively the rock mass strength parameters of the Hoek-Brown (HB) failure criterion is useful since it can improve the reliability of the design of tunnel support systems. In this study, a quantitative method is proposed to determine the rock mass quality parameters of the HB failure criterion, namely the Geological Strength Index (GSI) and the disturbance factor ( D) based on the structure of drilling core and weathering condition of rock mass combined with acoustic wave test to calculate the strength of rock mass. The Rock Mass Structure Index and the Rock Mass Weathering Index are used to quantify the GSI while the longitudinal wave velocity ( V p) is employed to derive the value of D. The DK383+338 tunnel face of Yaojia tunnel of Shanghai-Kunming passenger dedicated line served as illustration of how the methodology is implemented. The values of the GSI and D are obtained using the HB criterion and then using the proposed method. The measured in situ stress is used to evaluate their accuracy. To this end, the major and minor principal stresses are calculated based on the GSI and D given by HB criterion and the proposed method. The results indicated that both methods were close to the field observation which suggests that the proposed method can be used for determining quantitatively the rock quality parameters, as well. However, these results remain valid only for rock mass quality and rock type similar to those of the DK383+338 tunnel face of Yaojia tunnel.

Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.

PubMed

Hamilton, Joshua J; Dwivedi, Vivek; Reed, Jennifer L

2013-07-16

Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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.

Multiplicative effects model with internal standard in mobile phase for quantitative liquid chromatography-mass spectrometry.

PubMed

Song, Mi; Chen, Zeng-Ping; Chen, Yao; Jin, Jing-Wen

2014-07-01

Liquid chromatography-mass spectrometry assays suffer from signal instability caused by the gradual fouling of the ion source, vacuum instability, aging of the ion multiplier, etc. To address this issue, in this contribution, an internal standard was added into the mobile phase. The internal standard was therefore ionized and detected together with the analytes of interest by the mass spectrometer to ensure that variations in measurement conditions and/or instrument have similar effects on the signal contributions of both the analytes of interest and the internal standard. Subsequently, based on the unique strategy of adding internal standard in mobile phase, a multiplicative effects model was developed for quantitative LC-MS assays and tested on a proof of concept model system: the determination of amino acids in water by LC-MS. The experimental results demonstrated that the proposed method could efficiently mitigate the detrimental effects of continuous signal variation, and achieved quantitative results with average relative predictive error values in the range of 8.0-15.0%, which were much more accurate than the corresponding results of conventional internal standard method based on the peak height ratio and partial least squares method (their average relative predictive error values were as high as 66.3% and 64.8%, respectively). Therefore, it is expected that the proposed method can be developed and extended in quantitative LC-MS analysis of more complex systems. Copyright © 2014 Elsevier B.V. All rights reserved.

Ultra-fast quantitative imaging using ptychographic iterative engine based digital micro-mirror device

NASA Astrophysics Data System (ADS)

Sun, Aihui; Tian, Xiaolin; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Wang, Shouyu; Liu, Cheng

2018-01-01

As a lensfree imaging technique, ptychographic iterative engine (PIE) method can provide both quantitative sample amplitude and phase distributions avoiding aberration. However, it requires field of view (FoV) scanning often relying on mechanical translation, which not only slows down measuring speed, but also introduces mechanical errors decreasing both resolution and accuracy in retrieved information. In order to achieve high-accurate quantitative imaging with fast speed, digital micromirror device (DMD) is adopted in PIE for large FoV scanning controlled by on/off state coding by DMD. Measurements were implemented using biological samples as well as USAF resolution target, proving high resolution in quantitative imaging using the proposed system. Considering its fast and accurate imaging capability, it is believed the DMD based PIE technique provides a potential solution for medical observation and measurements.

Sub-band denoising and spline curve fitting method for hemodynamic measurement in perfusion MRI

NASA Astrophysics Data System (ADS)

Lin, Hong-Dun; Huang, Hsiao-Ling; Hsu, Yuan-Yu; Chen, Chi-Chen; Chen, Ing-Yi; Wu, Liang-Chi; Liu, Ren-Shyan; Lin, Kang-Ping

2003-05-01

In clinical research, non-invasive MR perfusion imaging is capable of investigating brain perfusion phenomenon via various hemodynamic measurements, such as cerebral blood volume (CBV), cerebral blood flow (CBF), and mean trasnit time (MTT). These hemodynamic parameters are useful in diagnosing brain disorders such as stroke, infarction and periinfarct ischemia by further semi-quantitative analysis. However, the accuracy of quantitative analysis is usually affected by poor signal-to-noise ratio image quality. In this paper, we propose a hemodynamic measurement method based upon sub-band denoising and spline curve fitting processes to improve image quality for better hemodynamic quantitative analysis results. Ten sets of perfusion MRI data and corresponding PET images were used to validate the performance. For quantitative comparison, we evaluate gray/white matter CBF ratio. As a result, the hemodynamic semi-quantitative analysis result of mean gray to white matter CBF ratio is 2.10 +/- 0.34. The evaluated ratio of brain tissues in perfusion MRI is comparable to PET technique is less than 1-% difference in average. Furthermore, the method features excellent noise reduction and boundary preserving in image processing, and short hemodynamic measurement time.

Improving statistical inference on pathogen densities estimated by quantitative molecular methods: malaria gametocytaemia as a case study.

PubMed

Walker, Martin; Basáñez, María-Gloria; Ouédraogo, André Lin; Hermsen, Cornelus; Bousema, Teun; Churcher, Thomas S

2015-01-16

Quantitative molecular methods (QMMs) such as quantitative real-time polymerase chain reaction (q-PCR), reverse-transcriptase PCR (qRT-PCR) and quantitative nucleic acid sequence-based amplification (QT-NASBA) are increasingly used to estimate pathogen density in a variety of clinical and epidemiological contexts. These methods are often classified as semi-quantitative, yet estimates of reliability or sensitivity are seldom reported. Here, a statistical framework is developed for assessing the reliability (uncertainty) of pathogen densities estimated using QMMs and the associated diagnostic sensitivity. The method is illustrated with quantification of Plasmodium falciparum gametocytaemia by QT-NASBA. The reliability of pathogen (e.g. gametocyte) densities, and the accompanying diagnostic sensitivity, estimated by two contrasting statistical calibration techniques, are compared; a traditional method and a mixed model Bayesian approach. The latter accounts for statistical dependence of QMM assays run under identical laboratory protocols and permits structural modelling of experimental measurements, allowing precision to vary with pathogen density. Traditional calibration cannot account for inter-assay variability arising from imperfect QMMs and generates estimates of pathogen density that have poor reliability, are variable among assays and inaccurately reflect diagnostic sensitivity. The Bayesian mixed model approach assimilates information from replica QMM assays, improving reliability and inter-assay homogeneity, providing an accurate appraisal of quantitative and diagnostic performance. Bayesian mixed model statistical calibration supersedes traditional techniques in the context of QMM-derived estimates of pathogen density, offering the potential to improve substantially the depth and quality of clinical and epidemiological inference for a wide variety of pathogens.

Species Identification of Fox-, Mink-, Dog-, and Rabbit-Derived Ingredients by Multiplex PCR and Real-Time PCR Assay.

PubMed

Wu, Qingqing; Xiang, Shengnan; Wang, Wenjun; Zhao, Jinyan; Xia, Jinhua; Zhen, Yueran; Liu, Bang

2018-05-01

Various detection methods have been developed to date for identification of animal species. New techniques based on PCR approach have raised the hope of developing better identification methods, which can overcome the limitations of the existing methods. PCR-based methods used the mitochondrial DNA (mtDNA) as well as nuclear DNA sequences. In this study, by targeting nuclear DNA, multiplex PCR and real-time PCR methods were developed to assist with qualitative and quantitative analysis. The multiplex PCR was found to simultaneously and effectively distinguish four species (fox, dog, mink, and rabbit) ingredients by the different sizes of electrophoretic bands: 480, 317, 220, and 209 bp. Real-time fluorescent PCR's amplification profiles and standard curves showed good quantitative measurement responses and linearity, as indicated by good repeatability and coefficient of determination R 2  > 0.99. The quantitative results of quaternary DNA mixtures including mink, fox, dog, and rabbit DNA are in line with our expectations: R.D. (relative deviation) varied between 1.98 and 12.23% and R.S.D. (relative standard deviation) varied between 3.06 and 11.51%, both of which are well within the acceptance criterion of ≤ 25%. Combining the two methods is suitable for the rapid identification and accurate quantification of fox-, dog-, mink-, and rabbit-derived ingredients in the animal products.

Dynamic and quantitative method of analyzing service consistency evolution based on extended hierarchical finite state automata.

PubMed

Fan, Linjun; Tang, Jun; Ling, Yunxiang; Li, Benxian

2014-01-01

This paper is concerned with the dynamic evolution analysis and quantitative measurement of primary factors that cause service inconsistency in service-oriented distributed simulation applications (SODSA). Traditional methods are mostly qualitative and empirical, and they do not consider the dynamic disturbances among factors in service's evolution behaviors such as producing, publishing, calling, and maintenance. Moreover, SODSA are rapidly evolving in terms of large-scale, reusable, compositional, pervasive, and flexible features, which presents difficulties in the usage of traditional analysis methods. To resolve these problems, a novel dynamic evolution model extended hierarchical service-finite state automata (EHS-FSA) is constructed based on finite state automata (FSA), which formally depict overall changing processes of service consistency states. And also the service consistency evolution algorithms (SCEAs) based on EHS-FSA are developed to quantitatively assess these impact factors. Experimental results show that the bad reusability (17.93% on average) is the biggest influential factor, the noncomposition of atomic services (13.12%) is the second biggest one, and the service version's confusion (1.2%) is the smallest one. Compared with previous qualitative analysis, SCEAs present good effectiveness and feasibility. This research can guide the engineers of service consistency technologies toward obtaining a higher level of consistency in SODSA.

Dynamic and Quantitative Method of Analyzing Service Consistency Evolution Based on Extended Hierarchical Finite State Automata

PubMed Central

Fan, Linjun; Tang, Jun; Ling, Yunxiang; Li, Benxian

2014-01-01

This paper is concerned with the dynamic evolution analysis and quantitative measurement of primary factors that cause service inconsistency in service-oriented distributed simulation applications (SODSA). Traditional methods are mostly qualitative and empirical, and they do not consider the dynamic disturbances among factors in service's evolution behaviors such as producing, publishing, calling, and maintenance. Moreover, SODSA are rapidly evolving in terms of large-scale, reusable, compositional, pervasive, and flexible features, which presents difficulties in the usage of traditional analysis methods. To resolve these problems, a novel dynamic evolution model extended hierarchical service-finite state automata (EHS-FSA) is constructed based on finite state automata (FSA), which formally depict overall changing processes of service consistency states. And also the service consistency evolution algorithms (SCEAs) based on EHS-FSA are developed to quantitatively assess these impact factors. Experimental results show that the bad reusability (17.93% on average) is the biggest influential factor, the noncomposition of atomic services (13.12%) is the second biggest one, and the service version's confusion (1.2%) is the smallest one. Compared with previous qualitative analysis, SCEAs present good effectiveness and feasibility. This research can guide the engineers of service consistency technologies toward obtaining a higher level of consistency in SODSA. PMID:24772033

Event-specific qualitative and quantitative PCR detection of the GMO carnation (Dianthus caryophyllus) variety Moonlite based upon the 5'-transgene integration sequence.

PubMed

Li, P; Jia, J W; Jiang, L X; Zhu, H; Bai, L; Wang, J B; Tang, X M; Pan, A H

2012-04-27

To ensure the implementation of genetically modified organism (GMO)-labeling regulations, an event-specific detection method was developed based on the junction sequence of an exogenous integrant in the transgenic carnation variety Moonlite. The 5'-transgene integration sequence was isolated by thermal asymmetric interlaced PCR. Based upon the 5'-transgene integration sequence, the event-specific primers and TaqMan probe were designed to amplify the fragments, which spanned the exogenous DNA and carnation genomic DNA. Qualitative and quantitative PCR assays were developed employing the designed primers and probe. The detection limit of the qualitative PCR assay was 0.05% for Moonlite in 100 ng total carnation genomic DNA, corresponding to about 79 copies of the carnation haploid genome; the limit of detection and quantification of the quantitative PCR assay were estimated to be 38 and 190 copies of haploid carnation genomic DNA, respectively. Carnation samples with different contents of genetically modified components were quantified and the bias between the observed and true values of three samples were lower than the acceptance criterion (<25%) of the GMO detection method. These results indicated that these event-specific methods would be useful for the identification and quantification of the GMO carnation Moonlite.

A Comparison of Protein Extraction Methods Suitable for Gel-Based Proteomic Studies of Aphid Proteins

PubMed Central

Cilia, M.; Fish, T.; Yang, X.; Mclaughlin, M.; Thannhauser, T. W.

2009-01-01

Protein extraction methods can vary widely in reproducibility and in representation of the total proteome, yet there are limited data comparing protein isolation methods. The methodical comparison of protein isolation methods is the first critical step for proteomic studies. To address this, we compared three methods for isolation, purification, and solubilization of insect proteins. The aphid Schizaphis graminum, an agricultural pest, was the source of insect tissue. Proteins were extracted using TCA in acetone (TCA-acetone), phenol, or multi-detergents in a chaotrope solution. Extracted proteins were solubilized in a multiple chaotrope solution and examined using 1-D and 2-D electrophoresis and compared directly using 2-D Difference Gel Electrophoresis (2-D DIGE). Mass spectrometry was used to identify proteins from each extraction type. We were unable to ascribe the differences in the proteins extracted to particular physical characteristics, cell location, or biological function. The TCA-acetone extraction yielded the greatest amount of protein from aphid tissues. Each extraction method isolated a unique subset of the aphid proteome. The TCA-acetone method was explored further for its quantitative reliability using 2-D DIGE. Principal component analysis showed that little of the variation in the data was a result of technical issues, thus demonstrating that the TCA-acetone extraction is a reliable method for preparing aphid proteins for a quantitative proteomics experiment. These data suggest that although the TCA-acetone method is a suitable method for quantitative aphid proteomics, a combination of extraction approaches is recommended for increasing proteome coverage when using gel-based separation techniques. PMID:19721822

Reflections on Mixing Methods in Applied Linguistics Research

ERIC Educational Resources Information Center

Hashemi, Mohammad R.

2012-01-01

This commentary advocates the use of mixed methods research--that is the integration of qualitative and quantitative methods in a single study--in applied linguistics. Based on preliminary findings from a research project in progress, some reflections on the current practice of mixing methods as a new trend in applied linguistics are put forward.…

Detection and correction of laser induced breakdown spectroscopy spectral background based on spline interpolation method

NASA Astrophysics Data System (ADS)

Tan, Bing; Huang, Min; Zhu, Qibing; Guo, Ya; Qin, Jianwei

2017-12-01

Laser-induced breakdown spectroscopy (LIBS) is an analytical technique that has gained increasing attention because of many applications. The production of continuous background in LIBS is inevitable because of factors associated with laser energy, gate width, time delay, and experimental environment. The continuous background significantly influences the analysis of the spectrum. Researchers have proposed several background correction methods, such as polynomial fitting, Lorenz fitting and model-free methods. However, less of them apply these methods in the field of LIBS Technology, particularly in qualitative and quantitative analyses. This study proposes a method based on spline interpolation for detecting and estimating the continuous background spectrum according to its smooth property characteristic. Experiment on the background correction simulation indicated that, the spline interpolation method acquired the largest signal-to-background ratio (SBR) over polynomial fitting, Lorenz fitting and model-free method after background correction. These background correction methods all acquire larger SBR values than that acquired before background correction (The SBR value before background correction is 10.0992, whereas the SBR values after background correction by spline interpolation, polynomial fitting, Lorentz fitting, and model-free methods are 26.9576, 24.6828, 18.9770, and 25.6273 respectively). After adding random noise with different kinds of signal-to-noise ratio to the spectrum, spline interpolation method acquires large SBR value, whereas polynomial fitting and model-free method obtain low SBR values. All of the background correction methods exhibit improved quantitative results of Cu than those acquired before background correction (The linear correlation coefficient value before background correction is 0.9776. Moreover, the linear correlation coefficient values after background correction using spline interpolation, polynomial fitting, Lorentz fitting, and model-free methods are 0.9998, 0.9915, 0.9895, and 0.9940 respectively). The proposed spline interpolation method exhibits better linear correlation and smaller error in the results of the quantitative analysis of Cu compared with polynomial fitting, Lorentz fitting and model-free methods, The simulation and quantitative experimental results show that the spline interpolation method can effectively detect and correct the continuous background.

DNA microsatellite region for a reliable quantification of soft wheat adulteration in durum wheat-based foodstuffs by real-time PCR.

PubMed

Sonnante, Gabriella; Montemurro, Cinzia; Morgese, Anita; Sabetta, Wilma; Blanco, Antonio; Pasqualone, Antonella

2009-11-11

Italian industrial pasta and durum wheat typical breads must be prepared using exclusively durum wheat semolina. Previously, a microsatellite sequence specific of the wheat D-genome had been chosen for traceability of soft wheat in semolina and bread samples, using qualitative and quantitative Sybr green-based real-time experiments. In this work, we describe an improved method based on the same soft wheat genomic region by means of a quantitative real-time PCR using a dual-labeled probe. Standard curves based on dilutions of 100% soft wheat flour, pasta, or bread were constructed. Durum wheat semolina, pasta, and bread samples were prepared with increasing amounts of soft wheat to verify the accuracy of the method. Results show that reliable quantifications were obtained especially for the samples containing a lower amount of soft wheat DNA, fulfilling the need to verify labeling of pasta and typical durum wheat breads.

Quantitative Assessment of Parkinsonian Tremor Based on an Inertial Measurement Unit

PubMed Central

Dai, Houde; Zhang, Pengyue; Lueth, Tim C.

2015-01-01

Quantitative assessment of parkinsonian tremor based on inertial sensors can provide reliable feedback on the effect of medication. In this regard, the features of parkinsonian tremor and its unique properties such as motor fluctuations and dyskinesia are taken into account. Least-square-estimation models are used to assess the severities of rest, postural, and action tremors. In addition, a time-frequency signal analysis algorithm for tremor state detection was also included in the tremor assessment method. This inertial sensor-based method was verified through comparison with an electromagnetic motion tracking system. Seven Parkinson’s disease (PD) patients were tested using this tremor assessment system. The measured tremor amplitudes correlated well with the judgments of a neurologist (r = 0.98). The systematic analysis of sensor-based tremor quantification and the corresponding experiments could be of great help in monitoring the severity of parkinsonian tremor. PMID:26426020

Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics.

PubMed

Shen, Xiaomeng; Hu, Qiang; Li, Jun; Wang, Jianmin; Qu, Jun

2015-10-02

Comprehensive and accurate evaluation of data quality and false-positive biomarker discovery is critical to direct the method development/optimization for quantitative proteomics, which nonetheless remains challenging largely due to the high complexity and unique features of proteomic data. Here we describe an experimental null (EN) method to address this need. Because the method experimentally measures the null distribution (either technical or biological replicates) using the same proteomic samples, the same procedures and the same batch as the case-vs-contol experiment, it correctly reflects the collective effects of technical variability (e.g., variation/bias in sample preparation, LC-MS analysis, and data processing) and project-specific features (e.g., characteristics of the proteome and biological variation) on the performances of quantitative analysis. To show a proof of concept, we employed the EN method to assess the quantitative accuracy and precision and the ability to quantify subtle ratio changes between groups using different experimental and data-processing approaches and in various cellular and tissue proteomes. It was found that choices of quantitative features, sample size, experimental design, data-processing strategies, and quality of chromatographic separation can profoundly affect quantitative precision and accuracy of label-free quantification. The EN method was also demonstrated as a practical tool to determine the optimal experimental parameters and rational ratio cutoff for reliable protein quantification in specific proteomic experiments, for example, to identify the necessary number of technical/biological replicates per group that affords sufficient power for discovery. Furthermore, we assessed the ability of EN method to estimate levels of false-positives in the discovery of altered proteins, using two concocted sample sets mimicking proteomic profiling using technical and biological replicates, respectively, where the true-positives/negatives are known and span a wide concentration range. It was observed that the EN method correctly reflects the null distribution in a proteomic system and accurately measures false altered proteins discovery rate (FADR). In summary, the EN method provides a straightforward, practical, and accurate alternative to statistics-based approaches for the development and evaluation of proteomic experiments and can be universally adapted to various types of quantitative techniques.

Designing A Mixed Methods Study In Primary Care

PubMed Central

Creswell, John W.; Fetters, Michael D.; Ivankova, Nataliya V.

2004-01-01

BACKGROUND Mixed methods or multimethod research holds potential for rigorous, methodologically sound investigations in primary care. The objective of this study was to use criteria from the literature to evaluate 5 mixed methods studies in primary care and to advance 3 models useful for designing such investigations. METHODS We first identified criteria from the social and behavioral sciences to analyze mixed methods studies in primary care research. We then used the criteria to evaluate 5 mixed methods investigations published in primary care research journals. RESULTS Of the 5 studies analyzed, 3 included a rationale for mixing based on the need to develop a quantitative instrument from qualitative data or to converge information to best understand the research topic. Quantitative data collection involved structured interviews, observational checklists, and chart audits that were analyzed using descriptive and inferential statistical procedures. Qualitative data consisted of semistructured interviews and field observations that were analyzed using coding to develop themes and categories. The studies showed diverse forms of priority: equal priority, qualitative priority, and quantitative priority. Data collection involved quantitative and qualitative data gathered both concurrently and sequentially. The integration of the quantitative and qualitative data in these studies occurred between data analysis from one phase and data collection from a subsequent phase, while analyzing the data, and when reporting the results. DISCUSSION We recommend instrument-building, triangulation, and data transformation models for mixed methods designs as useful frameworks to add rigor to investigations in primary care. We also discuss the limitations of our study and the need for future research. PMID:15053277

Development of quantitative screen for 1550 chemicals with GC-MS.

PubMed

Bergmann, Alan J; Points, Gary L; Scott, Richard P; Wilson, Glenn; Anderson, Kim A

2018-05-01

With hundreds of thousands of chemicals in the environment, effective monitoring requires high-throughput analytical techniques. This paper presents a quantitative screening method for 1550 chemicals based on statistical modeling of responses with identification and integration performed using deconvolution reporting software. The method was evaluated with representative environmental samples. We tested biological extracts, low-density polyethylene, and silicone passive sampling devices spiked with known concentrations of 196 representative chemicals. A multiple linear regression (R 2  = 0.80) was developed with molecular weight, logP, polar surface area, and fractional ion abundance to predict chemical responses within a factor of 2.5. Linearity beyond the calibration had R 2  > 0.97 for three orders of magnitude. Median limits of quantitation were estimated to be 201 pg/μL (1.9× standard deviation). The number of detected chemicals and the accuracy of quantitation were similar for environmental samples and standard solutions. To our knowledge, this is the most precise method for the largest number of semi-volatile organic chemicals lacking authentic standards. Accessible instrumentation and software make this method cost effective in quantifying a large, customizable list of chemicals. When paired with silicone wristband passive samplers, this quantitative screen will be very useful for epidemiology where binning of concentrations is common. Graphical abstract A multiple linear regression of chemical responses measured with GC-MS allowed quantitation of 1550 chemicals in samples such as silicone wristbands.

A quantitative framework for the forward design of synthetic miRNA circuits.

PubMed

Bloom, Ryan J; Winkler, Sally M; Smolke, Christina D

2014-11-01

Synthetic genetic circuits incorporating regulatory components based on RNA interference (RNAi) have been used in a variety of systems. A comprehensive understanding of the parameters that determine the relationship between microRNA (miRNA) and target expression levels is lacking. We describe a quantitative framework supporting the forward engineering of gene circuits that incorporate RNAi-based regulatory components in mammalian cells. We developed a model that captures the quantitative relationship between miRNA and target gene expression levels as a function of parameters, including mRNA half-life and miRNA target-site number. We extended the model to synthetic circuits that incorporate protein-responsive miRNA switches and designed an optimized miRNA-based protein concentration detector circuit that noninvasively measures small changes in the nuclear concentration of β-catenin owing to induction of the Wnt signaling pathway. Our results highlight the importance of methods for guiding the quantitative design of genetic circuits to achieve robust, reliable and predictable behaviors in mammalian cells.

Quantitative phase imaging using four interferograms with special phase shifts by dual-wavelength in-line phase-shifting interferometry

NASA Astrophysics Data System (ADS)

Xu, Xiaoqing; Wang, Yawei; Ji, Ying; Xu, Yuanyuan; Xie, Ming; Han, Hao

2018-05-01

A new approach of quantitative phase imaging using four interferograms with special phase shifts in dual-wavelength in-line phase-shifting interferometry is presented. In this method, positive negative 2π phase shifts are employed to easily separate the incoherent addition of two single-wavelength interferograms by combining the phase-shifting technique with the subtraction procedure, then the quantitative phase at one of both wavelengths can be achieved based on two intensities without the corresponding dc terms by the use of the character of the trigonometric function. The quantitative phase of the other wavelength can be retrieved from two dc-term suppressed intensities obtained by employing the two-step phase-shifting technique or the filtering technique in the frequency domain. The proposed method is illustrated with theory, and its effectiveness is demonstrated by simulation experiments of the spherical cap and the HeLa cell, respectively.

Building quantitative, three-dimensional atlases of gene expression and morphology at cellular resolution.

PubMed

Knowles, David W; Biggin, Mark D

2013-01-01

Animals comprise dynamic three-dimensional arrays of cells that express gene products in intricate spatial and temporal patterns that determine cellular differentiation and morphogenesis. A rigorous understanding of these developmental processes requires automated methods that quantitatively record and analyze complex morphologies and their associated patterns of gene expression at cellular resolution. Here we summarize light microscopy-based approaches to establish permanent, quantitative datasets-atlases-that record this information. We focus on experiments that capture data for whole embryos or large areas of tissue in three dimensions, often at multiple time points. We compare and contrast the advantages and limitations of different methods and highlight some of the discoveries made. We emphasize the need for interdisciplinary collaborations and integrated experimental pipelines that link sample preparation, image acquisition, image analysis, database design, visualization, and quantitative analysis. Copyright © 2013 Wiley Periodicals, Inc.

Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

PubMed Central

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

2011-01-01

Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

Method and platform standardization in MRM-based quantitative plasma proteomics.

PubMed

Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Jackson, Angela M; Domanski, Dominik; Burkhart, Julia; Sickmann, Albert; Borchers, Christoph H

2013-12-16

There exists a growing demand in the proteomics community to standardize experimental methods and liquid chromatography-mass spectrometry (LC/MS) platforms in order to enable the acquisition of more precise and accurate quantitative data. This necessity is heightened by the evolving trend of verifying and validating candidate disease biomarkers in complex biofluids, such as blood plasma, through targeted multiple reaction monitoring (MRM)-based approaches with stable isotope-labeled standards (SIS). Considering the lack of performance standards for quantitative plasma proteomics, we previously developed two reference kits to evaluate the MRM with SIS peptide approach using undepleted and non-enriched human plasma. The first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). Here, these kits have been refined for practical use and then evaluated through intra- and inter-laboratory testing on 6 common LC/MS platforms. For an identical panel of 22 plasma proteins, similar concentrations were determined, regardless of the kit, instrument platform, and laboratory of analysis. These results demonstrate the value of the kit and reinforce the utility of standardized methods and protocols. The proteomics community needs standardized experimental protocols and quality control methods in order to improve the reproducibility of MS-based quantitative data. This need is heightened by the evolving trend for MRM-based validation of proposed disease biomarkers in complex biofluids such as blood plasma. We have developed two kits to assist in the inter- and intra-laboratory quality control of MRM experiments: the first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). In this paper, we report the use of these kits in intra- and inter-laboratory testing on 6 common LC/MS platforms. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics. © 2013.

Guidance for using mixed methods design in nursing practice research.

PubMed

Chiang-Hanisko, Lenny; Newman, David; Dyess, Susan; Piyakong, Duangporn; Liehr, Patricia

2016-08-01

The mixed methods approach purposefully combines both quantitative and qualitative techniques, enabling a multi-faceted understanding of nursing phenomena. The purpose of this article is to introduce three mixed methods designs (parallel; sequential; conversion) and highlight interpretive processes that occur with the synthesis of qualitative and quantitative findings. Real world examples of research studies conducted by the authors will demonstrate the processes leading to the merger of data. The examples include: research questions; data collection procedures and analysis with a focus on synthesizing findings. Based on experience with mixed methods studied, the authors introduce two synthesis patterns (complementary; contrasting), considering application for practice and implications for research. Copyright © 2015 Elsevier Inc. All rights reserved.

Some selected quantitative methods of thermal image analysis in Matlab.

PubMed

Koprowski, Robert

2016-05-01

The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Localization-based super-resolution imaging meets high-content screening.

PubMed

Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

2017-12-01

Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

Geographical classification of Epimedium based on HPLC fingerprint analysis combined with multi-ingredients quantitative analysis.

PubMed

Xu, Ning; Zhou, Guofu; Li, Xiaojuan; Lu, Heng; Meng, Fanyun; Zhai, Huaqiang

2017-05-01

A reliable and comprehensive method for identifying the origin and assessing the quality of Epimedium has been developed. The method is based on analysis of HPLC fingerprints, combined with similarity analysis, hierarchical cluster analysis (HCA), principal component analysis (PCA) and multi-ingredient quantitative analysis. Nineteen batches of Epimedium, collected from different areas in the western regions of China, were used to establish the fingerprints and 18 peaks were selected for the analysis. Similarity analysis, HCA and PCA all classified the 19 areas into three groups. Simultaneous quantification of the five major bioactive ingredients in the Epimedium samples was also carried out to confirm the consistency of the quality tests. These methods were successfully used to identify the geographical origin of the Epimedium samples and to evaluate their quality. Copyright © 2016 John Wiley & Sons, Ltd.

Ultrasensitive Hybridization-Based ELISA Method for the Determination of Phosphorodiamidate Morpholino Oligonucleotides in Biological samples.

PubMed

Burki, Umar; Straub, Volker

2017-01-01

Determining the concentration of oligonucleotide in biological samples such as tissue lysate and serum is essential for determining the biodistribution and pharmacokinetic profile, respectively. ELISA-based assays have shown far greater sensitivities compared to other methods such as HPLC and LC/MS. Here, we describe a novel ultrasensitive hybridization-based ELISA method for quantitating morpholino oligonucleotides in mouse tissue lysate and serum samples. The assay has a linear detection range of 5-250 pM (R2 > 0.99).

Fully automatic multi-atlas segmentation of CTA for partial volume correction in cardiac SPECT/CT

NASA Astrophysics Data System (ADS)

Liu, Qingyi; Mohy-ud-Din, Hassan; Boutagy, Nabil E.; Jiang, Mingyan; Ren, Silin; Stendahl, John C.; Sinusas, Albert J.; Liu, Chi

2017-05-01

Anatomical-based partial volume correction (PVC) has been shown to improve image quality and quantitative accuracy in cardiac SPECT/CT. However, this method requires manual segmentation of various organs from contrast-enhanced computed tomography angiography (CTA) data. In order to achieve fully automatic CTA segmentation for clinical translation, we investigated the most common multi-atlas segmentation methods. We also modified the multi-atlas segmentation method by introducing a novel label fusion algorithm for multiple organ segmentation to eliminate overlap and gap voxels. To evaluate our proposed automatic segmentation, eight canine 99mTc-labeled red blood cell SPECT/CT datasets that incorporated PVC were analyzed, using the leave-one-out approach. The Dice similarity coefficient of each organ was computed. Compared to the conventional label fusion method, our proposed label fusion method effectively eliminated gaps and overlaps and improved the CTA segmentation accuracy. The anatomical-based PVC of cardiac SPECT images with automatic multi-atlas segmentation provided consistent image quality and quantitative estimation of intramyocardial blood volume, as compared to those derived using manual segmentation. In conclusion, our proposed automatic multi-atlas segmentation method of CTAs is feasible, practical, and facilitates anatomical-based PVC of cardiac SPECT/CT images.

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).

A 96-well-plate-based optical method for the quantitative and qualitative evaluation of Pseudomonas aeruginosa biofilm formation and its application to susceptibility testing.

PubMed

Müsken, Mathias; Di Fiore, Stefano; Römling, Ute; Häussler, Susanne

2010-08-01

A major reason for bacterial persistence during chronic infections is the survival of bacteria within biofilm structures, which protect cells from environmental stresses, host immune responses and antimicrobial therapy. Thus, there is concern that laboratory methods developed to measure the antibiotic susceptibility of planktonic bacteria may not be relevant to chronic biofilm infections, and it has been suggested that alternative methods should test antibiotic susceptibility within a biofilm. In this paper, we describe a fast and reliable protocol for using 96-well microtiter plates for the formation of Pseudomonas aeruginosa biofilms; the method is easily adaptable for antimicrobial susceptibility testing. This method is based on bacterial viability staining in combination with automated confocal laser scanning microscopy. The procedure simplifies qualitative and quantitative evaluation of biofilms and has proven to be effective for standardized determination of antibiotic efficiency on P. aeruginosa biofilms. The protocol can be performed within approximately 60 h.

The Quantitative Evaluation of the Clinical and Translational Science Awards (CTSA) Program Based on Science Mapping and Scientometric Analysis

PubMed Central

Zhang, Yin; Wang, Lei

2013-01-01

Abstract The Clinical and Translational Science Awards (CTSA) program is one of the most important initiatives in translational medical funding. The quantitative evaluation of the efficiency and performance of the CTSA program has a significant referential meaning for the decision making of global translational medical funding. Using science mapping and scientometric analytic tools, this study quantitatively analyzed the scientific articles funded by the CTSA program. The results of the study showed that the quantitative productivities of the CTSA program had a stable increase since 2008. In addition, the emerging trends of the research funded by the CTSA program covered clinical and basic medical research fields. The academic benefits from the CTSA program were assisting its members to build a robust academic home for the Clinical and Translational Science and to attract other financial support. This study provided a quantitative evaluation of the CTSA program based on science mapping and scientometric analysis. Further research is required to compare and optimize other quantitative methods and to integrate various research results. PMID:24330689

Comprehensive evaluation of direct injection mass spectrometry for the quantitative profiling of volatiles in food samples

PubMed Central

2016-01-01

Although qualitative strategies based on direct injection mass spectrometry (DIMS) have recently emerged as an alternative for the rapid classification of food samples, the potential of these approaches in quantitative tasks has scarcely been addressed to date. In this paper, the applicability of different multivariate regression procedures to data collected by DIMS from simulated mixtures has been evaluated. The most relevant factors affecting quantitation, such as random noise, the number of calibration samples, type of validation, mixture complexity and similarity of mass spectra, were also considered and comprehensively discussed. Based on the conclusions drawn from simulated data, and as an example of application, experimental mass spectral fingerprints collected by direct thermal desorption coupled to mass spectrometry were used for the quantitation of major volatiles in Thymus zygis subsp. zygis chemotypes. The results obtained, validated with the direct thermal desorption coupled to gas chromatography–mass spectrometry method here used as a reference, show the potential of DIMS approaches for the fast and precise quantitative profiling of volatiles in foods. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644978

The quantitative evaluation of the Clinical and Translational Science Awards (CTSA) program based on science mapping and scientometric analysis.

PubMed

Zhang, Yin; Wang, Lei; Diao, Tianxi

2013-12-01

The Clinical and Translational Science Awards (CTSA) program is one of the most important initiatives in translational medical funding. The quantitative evaluation of the efficiency and performance of the CTSA program has a significant referential meaning for the decision making of global translational medical funding. Using science mapping and scientometric analytic tools, this study quantitatively analyzed the scientific articles funded by the CTSA program. The results of the study showed that the quantitative productivities of the CTSA program had a stable increase since 2008. In addition, the emerging trends of the research funded by the CTSA program covered clinical and basic medical research fields. The academic benefits from the CTSA program were assisting its members to build a robust academic home for the Clinical and Translational Science and to attract other financial support. This study provided a quantitative evaluation of the CTSA program based on science mapping and scientometric analysis. Further research is required to compare and optimize other quantitative methods and to integrate various research results. © 2013 Wiley Periodicals, Inc.

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.

[Quantitative classification-based occupational health management for electroplating enterprises in Baoan District of Shenzhen, China].

PubMed

Zhang, Sheng; Huang, Jinsheng; Yang, Baigbing; Lin, Binjie; Xu, Xinyun; Chen, Jinru; Zhao, Zhuandi; Tu, Xiaozhi; Bin, Haihua

2014-04-01

To improve the occupational health management levels in electroplating enterprises with quantitative classification measures and to provide a scientific basis for the prevention and control of occupational hazards in electroplating enterprises and the protection of workers' health. A quantitative classification table was created for the occupational health management in electroplating enterprises. The evaluation indicators included 6 items and 27 sub-items, with a total score of 100 points. Forty electroplating enterprises were selected and scored according to the quantitative classification table. These electroplating enterprises were classified into grades A, B, and C based on the scores. Among 40 electroplating enterprises, 11 (27.5%) had scores of >85 points (grade A), 23 (57.5%) had scores of 60∼85 points (grade B), and 6 (15.0%) had scores of <60 points (grade C). Quantitative classification management for electroplating enterprises is a valuable attempt, which is helpful for the supervision and management by the health department and provides an effective method for the self-management of enterprises.

Variations in definition and method of retrieval of complications influence outcomes statistics after pancreatoduodenectomy: comparison of NSQIP with non-NSQIP methods.

PubMed

Sanford, Dominic E; Woolsey, Cheryl A; Hall, Bruce L; Linehan, David C; Hawkins, William G; Fields, Ryan C; Strasberg, Steven M

2014-09-01

NSQIP and the Accordion Severity Grading System have recently been used to develop quantitative methods for measuring the burden of postoperative complications. However, other audit methods such as chart reviews and prospective institutional databases are commonly used to gather postoperative complications. The purpose of this study was to evaluate discordance between different audit methods in pancreatoduodenectomy--a common major surgical procedure. The chief aim was to determine how these different methods could affect quantitative evaluations of postoperative complications. Three common audit methods were compared with NSQIP in 84 patients who underwent pancreatoduodenectomy. The methods were use of a prospective database, a chart review based on discharge summaries only, and a detailed retrospective chart review. The methods were evaluated for discordance with NSQIP and among themselves. Severity grading was performed using the Modified Accordion System. Fifty-three complications were listed by NSQIP and 31 complications were identified that were not listed by NSQIP. There was poor agreement for NSQIP-type complications between NSQIP and the other audit methods for mild and moderate complications (kappa 0.381 to 0.744), but excellent agreement for severe complications (kappa 0.953 to 1.00). Discordance was usually due to variations in definition of the complications in non-NSQIP methods. There was good agreement among non-NSQIP methods for non-NSQIP complications for moderate and severe complications, but not for mild complications. There are important differences in perceived surgical outcomes based on the method of complication retrieval. The non-NSQIP methods used in this study could not be substituted for NSQIP in a quantitative analysis unless that analysis was limited to severe complications. Copyright © 2014 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

A simultaneous screening and quantitative method for the multiresidue analysis of pesticides in spices using ultra-high performance liquid chromatography-high resolution (Orbitrap) mass spectrometry.

PubMed

Goon, Arnab; Khan, Zareen; Oulkar, Dasharath; Shinde, Raviraj; Gaikwad, Suresh; Banerjee, Kaushik

2018-01-12

A novel screening and quantitation method is reported for non-target multiresidue analysis of pesticides using ultra-HPLC-quadrupole-Orbitrap mass spectrometry in spice matrices, including black pepper, cardamom, chili, coriander, cumin, and turmeric. The method involved sequential full-scan (resolution = 70,000), and variable data independent acquisition (vDIA) with nine consecutive fragmentation events (resolution = 17,500). Samples were extracted by the QuEChERS method. The introduction of an SPE-based clean-up step through hydrophilic-lipophilic-balance (HLB) cartridges proved advantageous in minimizing the false negatives. For coriander, cumin, chili, and cardamom, the screening detection limit was largely at 2 ng/g, while it was 5 ng/g for black pepper, and turmeric. When the method was quantitatively validated for 199 pesticides, the limit of quantification (LOQ) was mostly at 10 ng/g (excluding black pepper, and turmeric with LOQ = 20 ng/g) with recoveries within 70-120%, and precision-RSDs <20%. Furthermore, the method allowed the identification of suspected non-target analytes through retrospective search of the accurate mass of the compound-specific precursor and product ions. Compared to LC-MS/MS, the quantitative performance of this Orbitrap-MS method had agreements in residue values between 78-100%. Copyright © 2017 Elsevier B.V. All rights reserved.

Clinical applications of a quantitative analysis of regional lift ventricular wall motion

NASA Technical Reports Server (NTRS)

Leighton, R. F.; Rich, J. M.; Pollack, M. E.; Altieri, P. I.

1975-01-01

Observations were summarized which may have clinical application. These were obtained from a quantitative analysis of wall motion that was used to detect both hypokinesis and tardokinesis in left ventricular cineangiograms. The method was based on statistical comparisons with normal values for regional wall motion derived from the cineangiograms of patients who were found not to have heart disease.

IWGT report on quantitative approaches to genotoxicity risk assessment I. Methods and metrics for defining exposure-response relationships and points of departure (PoDs)

EPA Science Inventory

This report summarizes the discussion, conclusions, and points of consensus of the IWGT Working Group on Quantitative Approaches to Genetic Toxicology Risk Assessment (QWG) based on a meeting in Foz do Iguaçu, Brazil October 31–November 2, 2013. Topics addressed incl...

QUANTITATION OF PERCHLORATE ION BY ELECTROSPRAY IONIZATION MASS SPECTROMETRY (ESI-MS) USING STABLE ASSOCIATION COMPLEXES WITH ORGANIC CATIONS AND BASES TO ENHANCE SELECTIVITY

EPA Science Inventory

Quantitation of trace levels of perchlorate ion in water has become a key issue since this species was discovered in water supplies around the United States. Although ion chromatographic methods presently offer the lowest limit of detection, =40 nm (4ngm1-1), chromatographic ret...

New insight in quantitative analysis of vascular permeability during immune reaction (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kalchenko, Vyacheslav; Molodij, Guillaume; Kuznetsov, Yuri; Smolyakov, Yuri; Israeli, David; Meglinski, Igor; Harmelin, Alon

2016-03-01

The use of fluorescence imaging of vascular permeability becomes a golden standard for assessing the inflammation process during experimental immune response in vivo. The use of the optical fluorescence imaging provides a very useful and simple tool to reach this purpose. The motivation comes from the necessity of a robust and simple quantification and data presentation of inflammation based on a vascular permeability. Changes of the fluorescent intensity, as a function of time is a widely accepted method to assess the vascular permeability during inflammation related to the immune response. In the present study we propose to bring a new dimension by applying a more sophisticated approach to the analysis of vascular reaction by using a quantitative analysis based on methods derived from astronomical observations, in particular by using a space-time Fourier filtering analysis followed by a polynomial orthogonal modes decomposition. We demonstrate that temporal evolution of the fluorescent intensity observed at certain pixels correlates quantitatively to the blood flow circulation at normal conditions. The approach allows to determine the regions of permeability and monitor both the fast kinetics related to the contrast material distribution in the circulatory system and slow kinetics associated with extravasation of the contrast material. Thus, we introduce a simple and convenient method for fast quantitative visualization of the leakage related to the inflammatory (immune) reaction in vivo.

Quantitative evaluation of dual-flip-angle T1 mapping on DCE-MRI kinetic parameter estimation in head and neck

PubMed Central

Chow, Steven Kwok Keung; Yeung, David Ka Wai; Ahuja, Anil T; King, Ann D

2012-01-01

Purpose To quantitatively evaluate the kinetic parameter estimation for head and neck (HN) dynamic contrast-enhanced (DCE) MRI with dual-flip-angle (DFA) T1 mapping. Materials and methods Clinical DCE-MRI datasets of 23 patients with HN tumors were included in this study. T1 maps were generated based on multiple-flip-angle (MFA) method and different DFA combinations. Tofts model parameter maps of kep, Ktrans and vp based on MFA and DFAs were calculated and compared. Fitted parameter by MFA and DFAs were quantitatively evaluated in primary tumor, salivary gland and muscle. Results T1 mapping deviations by DFAs produced remarkable kinetic parameter estimation deviations in head and neck tissues. In particular, the DFA of [2º, 7º] overestimated, while [7º, 12º] and [7º, 15º] underestimated Ktrans and vp, significantly (P<0.01). [2º, 15º] achieved the smallest but still statistically significant overestimation for Ktrans and vp in primary tumors, 32.1% and 16.2% respectively. kep fitting results by DFAs were relatively close to the MFA reference compared to Ktrans and vp. Conclusions T1 deviations induced by DFA could result in significant errors in kinetic parameter estimation, particularly Ktrans and vp, through Tofts model fitting. MFA method should be more reliable and robust for accurate quantitative pharmacokinetic analysis in head and neck. PMID:23289084

Quality evaluation of LC-MS/MS-based E. coli H antigen typing (MS-H) through label-free quantitative data analysis in a clinical sample setup.

PubMed

Cheng, Keding; Sloan, Angela; McCorrister, Stuart; Peterson, Lorea; Chui, Huixia; Drebot, Mike; Nadon, Celine; Knox, J David; Wang, Gehua

2014-12-01

The need for rapid and accurate H typing is evident during Escherichia coli outbreak situations. This study explores the transition of MS-H, a method originally developed for rapid H antigen typing of E. coli using LC-MS/MS of flagella digest of reference strains and some clinical strains, to E. coli isolates in clinical scenario through quantitative analysis and method validation. Motile and nonmotile strains were examined in batches to simulate clinical sample scenario. Various LC-MS/MS batch run procedures and MS-H typing rules were compared and summarized through quantitative analysis of MS-H data output for a standard method development. Label-free quantitative data analysis of MS-H typing was proven very useful for examining the quality of MS-H result and the effects of some sample carryovers from motile E. coli isolates. Based on this, a refined procedure and protein identification rule specific for clinical MS-H typing was established and validated. With LC-MS/MS batch run procedure and database search parameter unique for E. coli MS-H typing, the standard procedure maintained high accuracy and specificity in clinical situations, and its potential to be used in a clinical setting was clearly established. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Maximum entropy estimation of a Benzene contaminated plume using ecotoxicological assays.

PubMed

Wahyudi, Agung; Bartzke, Mariana; Küster, Eberhard; Bogaert, Patrick

2013-01-01

Ecotoxicological bioassays, e.g. based on Danio rerio teratogenicity (DarT) or the acute luminescence inhibition with Vibrio fischeri, could potentially lead to significant benefits for detecting on site contaminations on qualitative or semi-quantitative bases. The aim was to use the observed effects of two ecotoxicological assays for estimating the extent of a Benzene groundwater contamination plume. We used a Maximum Entropy (MaxEnt) method to rebuild a bivariate probability table that links the observed toxicity from the bioassays with Benzene concentrations. Compared with direct mapping of the contamination plume as obtained from groundwater samples, the MaxEnt concentration map exhibits on average slightly higher concentrations though the global pattern is close to it. This suggest MaxEnt is a valuable method to build a relationship between quantitative data, e.g. contaminant concentrations, and more qualitative or indirect measurements, in a spatial mapping framework, which is especially useful when clear quantitative relation is not at hand. Copyright © 2012 Elsevier Ltd. All rights reserved.

Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

PubMed

Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

2015-01-01

Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.

Pansharpening on the Narrow Vnir and SWIR Spectral Bands of SENTINEL-2

NASA Astrophysics Data System (ADS)

Vaiopoulos, A. D.; Karantzalos, K.

2016-06-01

In this paper results from the evaluation of several state-of-the-art pansharpening techniques are presented for the VNIR and SWIR bands of Sentinel-2. A procedure for the pansharpening is also proposed which aims at respecting the closest spectral similarities between the higher and lower resolution bands. The evaluation included 21 different fusion algorithms and three evaluation frameworks based both on standard quantitative image similarity indexes and qualitative evaluation from remote sensing experts. The overall analysis of the evaluation results indicated that remote sensing experts disagreed with the outcomes and method ranking from the quantitative assessment. The employed image quality similarity indexes and quantitative evaluation framework based on both high and reduced resolution data from the literature didn't manage to highlight/evaluate mainly the spatial information that was injected to the lower resolution images. Regarding the SWIR bands none of the methods managed to deliver significantly better results than a standard bicubic interpolation on the original low resolution bands.

Detection of blur artifacts in histopathological whole-slide images of endomyocardial biopsies.

PubMed

Hang Wu; Phan, John H; Bhatia, Ajay K; Cundiff, Caitlin A; Shehata, Bahig M; Wang, May D

2015-01-01

Histopathological whole-slide images (WSIs) have emerged as an objective and quantitative means for image-based disease diagnosis. However, WSIs may contain acquisition artifacts that affect downstream image feature extraction and quantitative disease diagnosis. We develop a method for detecting blur artifacts in WSIs using distributions of local blur metrics. As features, these distributions enable accurate classification of WSI regions as sharp or blurry. We evaluate our method using over 1000 portions of an endomyocardial biopsy (EMB) WSI. Results indicate that local blur metrics accurately detect blurry image regions.

Collaborating to improve the use of free-energy and other quantitative methods in drug discovery

NASA Astrophysics Data System (ADS)

Sherborne, Bradley; Shanmugasundaram, Veerabahu; Cheng, Alan C.; Christ, Clara D.; DesJarlais, Renee L.; Duca, Jose S.; Lewis, Richard A.; Loughney, Deborah A.; Manas, Eric S.; McGaughey, Georgia B.; Peishoff, Catherine E.; van Vlijmen, Herman

2016-12-01

In May and August, 2016, several pharmaceutical companies convened to discuss and compare experiences with Free Energy Perturbation (FEP). This unusual synchronization of interest was prompted by Schrödinger's FEP+ implementation and offered the opportunity to share fresh studies with FEP and enable broader discussions on the topic. This article summarizes key conclusions of the meetings, including a path forward of actions for this group to aid the accelerated evaluation, application and development of free energy and related quantitative, structure-based design methods.

A no-gold-standard technique for objective assessment of quantitative nuclear-medicine imaging methods

PubMed Central

Jha, Abhinav K; Caffo, Brian; Frey, Eric C

2016-01-01

The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest. Results showed that the proposed technique provided accurate ranking of the reconstruction methods for 97.5% of the 50 noise realizations. Further, the technique was robust to the choice of evaluated reconstruction methods. The simulation study pointed to possible violations of the assumptions made in the NGS technique under clinical scenarios. However, numerical experiments indicated that the NGS technique was robust in ranking methods even when there was some degree of such violation. PMID:26982626

A no-gold-standard technique for objective assessment of quantitative nuclear-medicine imaging methods.

PubMed

Jha, Abhinav K; Caffo, Brian; Frey, Eric C

2016-04-07

The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest. Results showed that the proposed technique provided accurate ranking of the reconstruction methods for 97.5% of the 50 noise realizations. Further, the technique was robust to the choice of evaluated reconstruction methods. The simulation study pointed to possible violations of the assumptions made in the NGS technique under clinical scenarios. However, numerical experiments indicated that the NGS technique was robust in ranking methods even when there was some degree of such violation.

X-ray Topographic Methods and Application to Analysis of Electronic Materials

NASA Technical Reports Server (NTRS)

Mayo, W. E.; Liu, H. Y.; Chaudhuri, J.

1984-01-01

Three supplementary X-ray techniques new to semiconductor applications are discussed. These are the Computer Aided Rocking Curve Analyzer, the Divergent Beam Method and a new method based on enhanced X-ray flourescence. The first method is used for quantitative mapping of an elastic or plastic strain field while the other two methods are used only to measure elastic strains. The divergent beam method is used for measuring the full strain tensor while the microfluorescence method is useful for monitoring strain uniformity. These methods are discussed in detail and examples of their application is presented. Among these are determination of the full strain ellipsoid in state-of-the-art liquid phase epitaxy deposited III-V epitaxial films; mapping of the plastic strain concentrations in tensile deformed Si; and quantitative determination of damage in V3Si due to ion implantation.

Variable selection based near infrared spectroscopy quantitative and qualitative analysis on wheat wet gluten

NASA Astrophysics Data System (ADS)

Lü, Chengxu; Jiang, Xunpeng; Zhou, Xingfan; Zhang, Yinqiao; Zhang, Naiqian; Wei, Chongfeng; Mao, Wenhua

2017-10-01

Wet gluten is a useful quality indicator for wheat, and short wave near infrared spectroscopy (NIRS) is a high performance technique with the advantage of economic rapid and nondestructive test. To study the feasibility of short wave NIRS analyzing wet gluten directly from wheat seed, 54 representative wheat seed samples were collected and scanned by spectrometer. 8 spectral pretreatment method and genetic algorithm (GA) variable selection method were used to optimize analysis. Both quantitative and qualitative model of wet gluten were built by partial least squares regression and discriminate analysis. For quantitative analysis, normalization is the optimized pretreatment method, 17 wet gluten sensitive variables are selected by GA, and GA model performs a better result than that of all variable model, with R2V=0.88, and RMSEV=1.47. For qualitative analysis, automatic weighted least squares baseline is the optimized pretreatment method, all variable models perform better results than those of GA models. The correct classification rates of 3 class of <24%, 24-30%, >30% wet gluten content are 95.45, 84.52, and 90.00%, respectively. The short wave NIRS technique shows potential for both quantitative and qualitative analysis of wet gluten for wheat seed.

A method for evaluating the murine pulmonary vasculature using micro-computed tomography.

PubMed

Phillips, Michael R; Moore, Scott M; Shah, Mansi; Lee, Clara; Lee, Yueh Z; Faber, James E; McLean, Sean E

2017-01-01

Significant mortality and morbidity are associated with alterations in the pulmonary vasculature. While techniques have been described for quantitative morphometry of whole-lung arterial trees in larger animals, no methods have been described in mice. We report a method for the quantitative assessment of murine pulmonary arterial vasculature using high-resolution computed tomography scanning. Mice were harvested at 2 weeks, 4 weeks, and 3 months of age. The pulmonary artery vascular tree was pressure perfused to maximal dilation with a radio-opaque casting material with viscosity and pressure set to prevent capillary transit and venous filling. The lungs were fixed and scanned on a specimen computed tomography scanner at 8-μm resolution, and the vessels were segmented. Vessels were grouped into categories based on lumen diameter and branch generation. Robust high-resolution segmentation was achieved, permitting detailed quantitation of pulmonary vascular morphometrics. As expected, postnatal lung development was associated with progressive increase in small-vessel number and arterial branching complexity. These methods for quantitative analysis of the pulmonary vasculature in postnatal and adult mice provide a useful tool for the evaluation of mouse models of disease that affect the pulmonary vasculature. Copyright © 2016 Elsevier Inc. All rights reserved.

Three-dimensional quantitative structure-activity relationship studies on c-Src inhibitors based on different docking methods.

PubMed

Bairy, Santhosh Kumar; Suneel Kumar, B V S; Bhalla, Joseph Uday Tej; Pramod, A B; Ravikumar, Muttineni

2009-04-01

c-Src kinase play an important role in cell growth and differentiation and its inhibitors can be useful for the treatment of various diseases, including cancer, osteoporosis, and metastatic bone disease. Three dimensional quantitative structure-activity relationship (3D-QSAR) studies were carried out on quinazolin derivatives inhibiting c-Src kinase. Molecular field analysis (MFA) models with four different alignment techniques, namely, GLIDE, GOLD, LIGANDFIT and Least squares based methods were developed. glide based MFA model showed better results (Leave one out cross validation correlation coefficient r(2)(cv) = 0.923 and non-cross validation correlation coefficient r(2)= 0.958) when compared with other models. These results help us to understand the nature of descriptors required for activity of these compounds and thereby provide guidelines to design novel and potent c-Src kinase inhibitors.

The priority group index: a proposed new method incorporating high risk and population burden to identify target populations for public health interventions.

PubMed

Zhang, Bo; Cohen, Joanna E; OʼConnor, Shawn

2014-01-01

Selection of priority groups is important for health interventions. However, no quantitative method has been developed. To develop a quantitative method to support the process of selecting priority groups for public health interventions based on both high risk and population health burden. Secondary data analysis of the 2010 Canadian Community Health Survey. Canadian population. Survey respondents. We identified priority groups for 3 diseases: heart disease, stroke, and chronic lower respiratory diseases. Three measures--prevalence, population counts, and adjusted odds ratios (OR)--were calculated for subpopulations (sociodemographic characteristics and other risk factors). A Priority Group Index (PGI) was calculated by summing the rank scores of these 3 measures. Of the 30 priority groups identified by the PGI (10 for each of the 3 disease outcomes), 7 were identified on the basis of high prevalence only, 5 based on population count only, 3 based on high OR only, and the remainder based on combinations of these. The identified priority groups were all in line with the literature as risk factors for the 3 diseases, such as elderly people for heart disease and stroke and those with low income for chronic lower respiratory diseases. The PGI was thus able to balance both high risk and population burden approaches in selecting priority groups, and thus it would address health inequities as well as disease burden in the overall population. The PGI is a quantitative method to select priority groups for public health interventions; it has the potential to enhance the effective use of limited public resources.

The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis.

PubMed

Devonshire, Alison S; O'Sullivan, Denise M; Honeyborne, Isobella; Jones, Gerwyn; Karczmarczyk, Maria; Pavšič, Jernej; Gutteridge, Alice; Milavec, Mojca; Mendoza, Pablo; Schimmel, Heinz; Van Heuverswyn, Fran; Gorton, Rebecca; Cirillo, Daniela Maria; Borroni, Emanuele; Harris, Kathryn; Barnard, Marinus; Heydenrych, Anthenette; Ndusilo, Norah; Wallis, Carole L; Pillay, Keshree; Barry, Thomas; Reddington, Kate; Richter, Elvira; Mozioğlu, Erkan; Akyürek, Sema; Yalçınkaya, Burhanettin; Akgoz, Muslum; Žel, Jana; Foy, Carole A; McHugh, Timothy D; Huggett, Jim F

2016-08-03

Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB patients requires quantitative methods currently performed using smear microscopy. The potential use of quantitative molecular measurements for therapeutic monitoring has been investigated but findings have been variable and inconclusive. The lack of an adequate reference method and reference materials is a barrier to understanding the source of such disagreement. Digital PCR (dPCR) offers the potential for an accurate method for quantification of specific DNA sequences in reference materials which can be used to evaluate quantitative molecular methods for TB treatment monitoring. To assess a novel approach for the development of quality assurance materials we used dPCR to quantify specific DNA sequences in a range of prototype reference materials and evaluated accuracy between different laboratories and instruments. The materials were then also used to evaluate the quantitative performance of qPCR and Xpert MTB/RIF in eight clinical testing laboratories. dPCR was found to provide results in good agreement with the other methods tested and to be highly reproducible between laboratories without calibration even when using different instruments. When the reference materials were analysed with qPCR and Xpert MTB/RIF by clinical laboratories, all laboratories were able to correctly rank the reference materials according to concentration, however there was a marked difference in the measured magnitude. TB is a disease where the quantification of the pathogen could lead to better patient management and qPCR methods offer the potential to rapidly perform such analysis. However, our findings suggest that when precisely characterised materials are used to evaluate qPCR methods, the measurement result variation is too high to determine whether molecular quantification of Mycobacterium tuberculosis would provide a clinically useful readout. The methods described in this study provide a means by which the technical performance of quantitative molecular methods can be evaluated independently of clinical variability to improve accuracy of measurement results. These will assist in ultimately increasing the likelihood that such approaches could be used to improve patient management of TB.

Comparing the MRI-based Goutallier Classification to an experimental quantitative MR spectroscopic fat measurement of the supraspinatus muscle.

PubMed

Gilbert, Fabian; Böhm, Dirk; Eden, Lars; Schmalzl, Jonas; Meffert, Rainer H; Köstler, Herbert; Weng, Andreas M; Ziegler, Dirk

2016-08-22

The Goutallier Classification is a semi quantitative classification system to determine the amount of fatty degeneration in rotator cuff muscles. Although initially proposed for axial computer tomography scans it is currently applied to magnet-resonance-imaging-scans. The role for its clinical use is controversial, as the reliability of the classification has been shown to be inconsistent. The purpose of this study was to compare the semi quantitative MRI-based Goutallier Classification applied by 5 different raters to experimental MR spectroscopic quantitative fat measurement in order to determine the correlation between this classification system and the true extent of fatty degeneration shown by spectroscopy. MRI-scans of 42 patients with rotator cuff tears were examined by 5 shoulder surgeons and were graduated according to the MRI-based Goutallier Classification proposed by Fuchs et al. Additionally the fat/water ratio was measured with MR spectroscopy using the experimental SPLASH technique. The semi quantitative grading according to the Goutallier Classification was statistically correlated with the quantitative measured fat/water ratio using Spearman's rank correlation. Statistical analysis of the data revealed only fair correlation of the Goutallier Classification system and the quantitative fat/water ratio with R = 0.35 (p < 0.05). By dichotomizing the scale the correlation was 0.72. The interobserver and intraobserver reliabilities were substantial with R = 0.62 and R = 0.74 (p < 0.01). The correlation between the semi quantitative MRI based Goutallier Classification system and MR spectroscopic fat measurement is weak. As an adequate estimation of fatty degeneration based on standard MRI may not be possible, quantitative methods need to be considered in order to increase diagnostic safety and thus provide patients with ideal care in regard to the amount of fatty degeneration. Spectroscopic MR measurement may increase the accuracy of the Goutallier classification and thus improve the prediction of clinical results after rotator cuff repair. However, these techniques are currently only available in an experimental setting.

ASPECTS: an automation-assisted SPE method development system.

PubMed

Li, Ming; Chou, Judy; King, Kristopher W; Yang, Liyu

2013-07-01

A typical conventional SPE method development (MD) process usually involves deciding the chemistry of the sorbent and eluent based on information about the analyte; experimentally preparing and trying out various combinations of adsorption chemistry and elution conditions; quantitatively evaluating the various conditions; and comparing quantitative results from all combination of conditions to select the best condition for method qualification. The second and fourth steps have mostly been performed manually until now. We developed an automation-assisted system that expedites the conventional SPE MD process by automating 99% of the second step, and expedites the fourth step by automatically processing the results data and presenting it to the analyst in a user-friendly format. The automation-assisted SPE MD system greatly saves the manual labor in SPE MD work, prevents analyst errors from causing misinterpretation of quantitative results, and shortens data analysis and interpretation time.

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.

Microstencils to generate defined, multi-species patterns of bacteria

DOE PAGES

Timm, Collin M.; Hansen, Ryan R.; Doktycz, Mitchel J.; ...

2015-11-12

Microbial communities are complex heterogeneous systems that are influenced by physical and chemical interactions with their environment, host, and community members. Techniques that facilitate the quantitative evaluation of how microscale organization influences the morphogenesis of multispecies communities could provide valuable insights into the dynamic behavior and organization of natural communities, the design of synthetic environments for multispecies culture, and the engineering of artificial consortia. In this work, we demonstrate a method for patterning microbes into simple arrangements that allow the quantitative measurement of growth dynamics as a function of their proximity to one another. The method combines parylene-based liftoff techniquesmore » with microfluidic delivery to simultaneously pattern multiple bacterial species with high viability using low-cost, customizable methods. Furthermore, quantitative measurements of bacterial growth for two competing isolates demonstrate that spatial coordination can play a critical role in multispecies growth and structure.« less

Mass Spectral Characterization and UPLC Quantitation of 3-Deoxyanthocyanidins in Sorghum bicolor Varietals.

PubMed

Stern, Nathan P; Rana, Jatinder; Chandra, Amitabh; Balles, John

2018-01-01

A quantitative ultra-performance LC (UPLC) method was developed and validated to successfully separate, identify, and quantitate the major polyphenolic compounds present in different varieties of sorghum (Sorghum bicolor) feedstock. The method was linear from 3.2 to 320 ppm, with an r2 of 0.99999 when using luteolinidin chloride as the external standard. Method accuracy was determined to be 99.5%, and precision of replicate preparations was less than 1% RSD. Characterization by UPLC-MS determined that the predominant polyphenolic components of the sorghum varietals were 3-deoxyanthocyanidins (3-DXAs). High-throughput screening for 3-DXA identified four unique classes within the sorghum varieties. Certain feedstock varieties have been found to have a high potential to not only be plant-based colorants, but also provide significant amounts of bioactive 3-DXAs, making them of unique interest to the dietary supplement industry.

Quantitative Image Restoration in Bright Field Optical Microscopy.

PubMed

Gutiérrez-Medina, Braulio; Sánchez Miranda, Manuel de Jesús

2017-11-07

Bright field (BF) optical microscopy is regarded as a poor method to observe unstained biological samples due to intrinsic low image contrast. We introduce quantitative image restoration in bright field (QRBF), a digital image processing method that restores out-of-focus BF images of unstained cells. Our procedure is based on deconvolution, using a point spread function modeled from theory. By comparing with reference images of bacteria observed in fluorescence, we show that QRBF faithfully recovers shape and enables quantify size of individual cells, even from a single input image. We applied QRBF in a high-throughput image cytometer to assess shape changes in Escherichia coli during hyperosmotic shock, finding size heterogeneity. We demonstrate that QRBF is also applicable to eukaryotic cells (yeast). Altogether, digital restoration emerges as a straightforward alternative to methods designed to generate contrast in BF imaging for quantitative analysis. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Microstencils to generate defined, multi-species patterns of bacteria

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

Timm, Collin M.; Hansen, Ryan R.; Doktycz, Mitchel J.

Microbial communities are complex heterogeneous systems that are influenced by physical and chemical interactions with their environment, host, and community members. Techniques that facilitate the quantitative evaluation of how microscale organization influences the morphogenesis of multispecies communities could provide valuable insights into the dynamic behavior and organization of natural communities, the design of synthetic environments for multispecies culture, and the engineering of artificial consortia. In this work, we demonstrate a method for patterning microbes into simple arrangements that allow the quantitative measurement of growth dynamics as a function of their proximity to one another. The method combines parylene-based liftoff techniquesmore » with microfluidic delivery to simultaneously pattern multiple bacterial species with high viability using low-cost, customizable methods. Furthermore, quantitative measurements of bacterial growth for two competing isolates demonstrate that spatial coordination can play a critical role in multispecies growth and structure.« less

[Analysis and Control of in Vivo Kinetics of Exosomes for the Development of Exosome-based DDS].

PubMed

Takahashi, Yuki; Nishikawa, Makiya; Takakura, Yoshinobu

2016-01-01

  Exosomes are secretory membrane vesicles containing lipids, proteins, and nucleic acids. They act as intercellular transporters by delivering their components to exosome recipient cells. Based on their endogenous delivery system properties, exosomes are expected to become drug delivery systems (DDS) for various molecules such as nucleic acid-based drugs. Important factors such as drug loading to exosomes, production, and pharmacokinetics of exosomes need to be considered for the development of exosome-based DDS. Of these, the pharmacokinetics of exosomes have rarely been studied, probably because of the lack of quantitative evaluation methods of in vivo exosomal pharmacokinetics. We selected lactadherin as an exosome tropic protein and developed it as a fusion protein with Gaussia luciferase to label exosomes for in vivo imaging. In addition, a fusion protein of lactadherin and streptavidin was developed, and the tissue distribution of exosomes was quantitatively evaluated by radiolabeling the exosomes using (125)I-labeled biotin. Using labeled exosomes, we found that intravenously injected exosomes were rapidly cleared from the systemic circulation by macrophages. In addition, the exosomes were mainly distributed to the liver, lung, and spleen. We also examined the effect of exosome isolation methods on their physicochemical and pharmacokinetic properties. We found that exosomes collected by the ultracentrifugation-based density-gradient method were more dispersed than exosomes collected by other methods, including the ultracentrifugation-based pelleting method. The gradient method is more time-consuming than others; therefore the development of a more efficient method for exosome isolation will advance the development of exosome-based DDS.

Evaluation of viral removal by nanofiltration using real-time quantitative polymerase chain reaction.

PubMed

Zhao, Xiaowen; Bailey, Mark R; Emery, Warren R; Lambooy, Peter K; Chen, Dayue

2007-06-01

Nanofiltration is commonly introduced into purification processes of biologics produced in mammalian cells to serve as a designated step for removal of potential exogenous viral contaminants and endogenous retrovirus-like particles. The LRV (log reduction value) achieved by nanofiltration is often determined by cell-based infectivity assay, which is time-consuming and labour-intensive. We have explored the possibility of employing QPCR (quantitative PCR) to evaluate LRV achieved by nanofiltration in scaled-down studies using two model viruses, namely xenotropic murine leukemia virus and murine minute virus. We report here the successful development of a QPCR-based method suitable for quantification of virus removal by nanofiltration. The method includes a nuclease treatment step to remove free viral nucleic acids, while viral genome associated with intact virus particles is shielded from the nuclease. In addition, HIV Armored RNA was included as an internal control to ensure the accuracy and reliability of the method. The QPCRbased method described here provides several advantages such as better sensitivity, faster turnaround time, reduced cost and higher throughput over the traditional cell-based infectivity assays.

Molecule kernels: a descriptor- and alignment-free quantitative structure-activity relationship approach.

PubMed

Mohr, Johannes A; Jain, Brijnesh J; Obermayer, Klaus

2008-09-01

Quantitative structure activity relationship (QSAR) analysis is traditionally based on extracting a set of molecular descriptors and using them to build a predictive model. In this work, we propose a QSAR approach based directly on the similarity between the 3D structures of a set of molecules measured by a so-called molecule kernel, which is independent of the spatial prealignment of the compounds. Predictors can be build using the molecule kernel in conjunction with the potential support vector machine (P-SVM), a recently proposed machine learning method for dyadic data. The resulting models make direct use of the structural similarities between the compounds in the test set and a subset of the training set and do not require an explicit descriptor construction. We evaluated the predictive performance of the proposed method on one classification and four regression QSAR datasets and compared its results to the results reported in the literature for several state-of-the-art descriptor-based and 3D QSAR approaches. In this comparison, the proposed molecule kernel method performed better than the other QSAR methods.

Targeted liquid chromatography tandem mass spectrometry to quantitate wheat gluten using well-defined reference proteins

PubMed Central

Schalk, Kathrin; Koehler, Peter

2018-01-01

Celiac disease (CD) is an inflammatory disorder of the upper small intestine caused by the ingestion of storage proteins (prolamins and glutelins) from wheat, barley, rye, and, in rare cases, oats. CD patients need to follow a gluten-free diet by consuming gluten-free products with gluten contents of less than 20 mg/kg. Currently, the recommended method for the quantitative determination of gluten is an enzyme-linked immunosorbent assay (ELISA) based on the R5 monoclonal antibody. Because the R5 ELISA mostly detects the prolamin fraction of gluten, a new independent method is required to detect prolamins as well as glutelins. This paper presents the development of a method to quantitate 16 wheat marker peptides derived from all wheat gluten protein types by liquid chromatography tandem mass spectrometry (LC-MS/MS) in the multiple reaction monitoring mode. The quantitation of each marker peptide in the chymotryptic digest of a defined amount of the respective reference wheat protein type resulted in peptide-specific yields. This enabled the conversion of peptide into protein type concentrations. Gluten contents were expressed as sum of all determined protein type concentrations. This new method was applied to quantitate gluten in wheat starches and compared to R5 ELISA and gel-permeation high-performance liquid chromatography with fluorescence detection (GP-HPLC-FLD), which resulted in a strong correlation between LC-MS/MS and the other two methods. PMID:29425234

Quantitative diagnostic method for biceps long head tendinitis by using ultrasound.

PubMed

Huang, Shih-Wei; Wang, Wei-Te

2013-01-01

To investigate the feasibility of grayscale quantitative diagnostic method for biceps tendinitis and determine the cut-off points of a quantitative biceps ultrasound (US) method to diagnose biceps tendinitis. Design. Prospective cross-sectional case controlled study. Outpatient rehabilitation service. A total of 336 shoulder pain patients with suspected biceps tendinitis were recruited in this prospective observational study. The grayscale pixel data of the range of interest (ROI) were obtained for both the transverse and longitudinal views of the biceps US. A total of 136 patients were classified with biceps tendinitis, and 200 patients were classified as not having biceps tendinitis based on the diagnostic criteria. Based on the Youden index, the cut-off points were determined as 26.85 for the transverse view and 21.25 for the longitudinal view of the standard deviation (StdDev) of the ROI values, respectively. When the ROI evaluation of the US surpassed the cut-off point, the sensitivity was 68% and the specificity was 90% in the StdDev of the transverse view, and the sensitivity was 81% and the specificity was 73% in the StdDev of the longitudinal view to diagnose biceps tendinitis. For equivocal cases or inexperienced sonographers, our study provides a more objective method for diagnosing biceps tendinitis in shoulder pain patients.

Changes in monosaccharides, organic acids and amino acids during Cabernet Sauvignon wine ageing based on a simultaneous analysis using gas chromatography-mass spectrometry.

PubMed

Zhang, Xin-Ke; Lan, Yi-Bin; Zhu, Bao-Qing; Xiang, Xiao-Feng; Duan, Chang-Qing; Shi, Ying

2018-01-01

Monosaccharides, organic acids and amino acids are the important flavour-related components in wines. The aim of this article is to develop and validate a method that could simultaneously analyse these compounds in wine based on silylation derivatisation and gas chromatography-mass spectrometry (GC-MS), and apply this method to the investigation of the changes of these compounds and speculate upon their related influences on Cabernet Sauvignon wine flavour during wine ageing. This work presented a new approach for wine analysis and provided more information concerning red wine ageing. This method could simultaneously quantitatively analyse 2 monosaccharides, 8 organic acids and 13 amino acids in wine. A validation experiment showed good linearity, sensitivity, reproducibility and recovery. Multiple derivatives of five amino acids have been found but their effects on quantitative analysis were negligible, except for methionine. The evolution pattern of each category was different, and we speculated that the corresponding mechanisms involving microorganism activities, physical interactions and chemical reactions had a great correlation with red wine flavours during ageing. Simultaneously quantitative analysis of monosaccharides, organic acids and amino acids in wine was feasible and reliable and this method has extensive application prospects. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Automated quantitative gait analysis during overground locomotion in the rat: its application to spinal cord contusion and transection injuries.

PubMed

Hamers, F P; Lankhorst, A J; van Laar, T J; Veldhuis, W B; Gispen, W H

2001-02-01

Analysis of locomotion is an important tool in the study of peripheral and central nervous system damage. Most locomotor scoring systems in rodents are based either upon open field locomotion assessment, for example, the BBB score or upon foot print analysis. The former yields a semiquantitative description of locomotion as a whole, whereas the latter generates quantitative data on several selected gait parameters. In this paper, we describe the use of a newly developed gait analysis method that allows easy quantitation of a large number of locomotion parameters during walkway crossing. We were able to extract data on interlimb coordination, swing duration, paw print areas (total over stance, and at 20-msec time resolution), stride length, and base of support: Similar data can not be gathered by any single previously described method. We compare changes in gait parameters induced by two different models of spinal cord injury in rats, transection of the dorsal half of the spinal cord and spinal cord contusion injury induced by the NYU or MASCIS device. Although we applied this method to rats with spinal cord injury, the usefulness of this method is not limited to rats or to the investigation of spinal cord injuries alone.

Assay Development for the Determination of Phosphorylation Stoichiometry using MRM methods with and without Phosphatase Treatment: Application to Breast Cancer Signaling Pathways

PubMed Central

Domanski, Dominik; Murphy, Leigh C.; Borchers, Christoph H.

2010-01-01

We have developed a phosphatase-based phosphopeptide quantitation (PPQ) method for determining phosphorylation stoichiometry in complex biological samples. This PPQ method is based on enzymatic dephosphorylation, combined with specific and accurate peptide identification and quantification by multiple reaction monitoring (MRM) detection with stable-isotope-labeled standard peptides. In contrast with the classical MRM methods for the quantitation of phosphorylation stoichiometry, the PPQ-MRM method needs only one non-phosphorylated SIS (stable isotope-coded standard) and two analyses (one for the untreated and one for the phosphatase-treated sample), from which the expression and modification levels can accurately be determined. From these analyses, the % phosphorylation can be determined. In this manuscript, we compare the PPQ-MRM method with an MRM method without phosphatase, and demonstrate the application of these methods to the detection and quantitation of phosphorylation of the classic phosphorylated breast cancer biomarkers (ERα and HER2), and for phosphorylated RAF and ERK1, which also contain phosphorylation sites with important biological implications. Using synthetic peptides spiked into a complex protein digest, we were able to use our PPQ-MRM method to accurately determine the total phosphorylation stoichiometry on specific peptides, as well as the absolute amount of the peptide and phosphopeptide present. Analyses of samples containing ERα protein revealed that the PPQ-MRM is capable of determining phosphorylation stoichiometry in proteins from cell lines, and is in good agreement with determinations obtained using the direct MRM approach in terms of phosphorylation and total protein amount. PMID:20524616

Mixed-methods research in pharmacy practice: basics and beyond (part 1).

PubMed

Hadi, Muhammad Abdul; Alldred, David Phillip; Closs, S José; Briggs, Michelle

2013-10-01

This is the first of two papers which explore the use of mixed-methods research in pharmacy practice. In an era of evidence-based medicine and policy, high-quality research evidence is essential for the development of effective pharmacist-led services. Over the past decade, the use of mixed-methods research has become increasingly common in healthcare, although to date its use has been relatively limited in pharmacy practice research. In this article, the basic concepts of mixed-methods research including its definition, typologies and advantages in relation to pharmacy practice research are discussed. Mixed-methods research brings together qualitative and quantitative methodologies within a single study to answer or understand a research problem. There are a number of mixed-methods designs available, but the selection of an appropriate design must always be dictated by the research question. Importantly, mixed-methods research should not be seen as a 'tool' to collect qualitative and quantitative data, rather there should be some degree of 'integration' between the two data sets. If conducted appropriately, mixed-methods research has the potential to generate quality research evidence by combining strengths and overcoming the respective limitations of qualitative and quantitative methodologies. © 2012 Royal Pharmaceutical Society.

Qualitative PCR method for Roundup Ready soybean: interlaboratory study.

PubMed

Kodama, Takashi; Kasahara, Masaki; Minegishi, Yasutaka; Futo, Satoshi; Sawada, Chihiro; Watai, Masatoshi; Akiyama, Hiroshi; Teshima, Reiko; Kurosawa, Yasunori; Furui, Satoshi; Hino, Akihiro; Kitta, Kazumi

2011-01-01

Quantitative and qualitative methods based on PCR have been developed for genetically modified organisms (GMO). Interlaboratory studies were previously conducted for GMO quantitative methods; in this study, an interlaboratory study was conducted for a qualitative method for a GM soybean, Roundup Ready soy (RR soy), with primer pairs designed for the quantitative method of RR soy studied previously. Fourteen laboratories in Japan participated. Each participant extracted DNA from 1.0 g each of the soy samples containing 0, 0.05, and 0.10% of RR soy, and performed PCR with primer pairs for an internal control gene (Le1) and RR soy followed by agarose gel electrophoresis. The PCR product amplified in this PCR system for Le1 was detected from all samples. The sensitivity, specificity, and false-negative and false-positive rates of the method were obtained from the results of RR soy detection. False-negative rates at the level of 0.05 and 0.10% of the RR soy samples were 6.0 and 2.3%, respectively, revealing that the LOD of the method was somewhat below 0.10%. The current study demonstrated that the qualitative method would be practical for monitoring the labeling system of GM soy in kernel lots.

Single Fluorescence Channel-based Multiplex Detection of Avian Influenza Virus by Quantitative PCR with Intercalating Dye

PubMed Central

Ahberg, Christian D.; Manz, Andreas; Neuzil, Pavel

2015-01-01

Since its invention in 1985 the polymerase chain reaction (PCR) has become a well-established method for amplification and detection of segments of double-stranded DNA. Incorporation of fluorogenic probe or DNA intercalating dyes (such as SYBR Green) into the PCR mixture allowed real-time reaction monitoring and extraction of quantitative information (qPCR). Probes with different excitation spectra enable multiplex qPCR of several DNA segments using multi-channel optical detection systems. Here we show multiplex qPCR using an economical EvaGreen-based system with single optical channel detection. Previously reported non quantitative multiplex real-time PCR techniques based on intercalating dyes were conducted once the PCR is completed by performing melting curve analysis (MCA). The technique presented in this paper is both qualitative and quantitative as it provides information about the presence of multiple DNA strands as well as the number of starting copies in the tested sample. Besides important internal control, multiplex qPCR also allows detecting concentrations of more than one DNA strand within the same sample. Detection of the avian influenza virus H7N9 by PCR is a well established method. Multiplex qPCR greatly enhances its specificity as it is capable of distinguishing both haemagglutinin (HA) and neuraminidase (NA) genes as well as their ratio. PMID:26088868

Automatic identification of the reference system based on the fourth ventricular landmarks in T1-weighted MR images.

PubMed

Fu, Yili; Gao, Wenpeng; Chen, Xiaoguang; Zhu, Minwei; Shen, Weigao; Wang, Shuguo

2010-01-01

The reference system based on the fourth ventricular landmarks (including the fastigial point and ventricular floor plane) is used in medical image analysis of the brain stem. The objective of this study was to develop a rapid, robust, and accurate method for the automatic identification of this reference system on T1-weighted magnetic resonance images. The fully automated method developed in this study consisted of four stages: preprocessing of the data set, expectation-maximization algorithm-based extraction of the fourth ventricle in the region of interest, a coarse-to-fine strategy for identifying the fastigial point, and localization of the base point. The method was evaluated on 27 Brain Web data sets qualitatively and 18 Internet Brain Segmentation Repository data sets and 30 clinical scans quantitatively. The results of qualitative evaluation indicated that the method was robust to rotation, landmark variation, noise, and inhomogeneity. The results of quantitative evaluation indicated that the method was able to identify the reference system with an accuracy of 0.7 +/- 0.2 mm for the fastigial point and 1.1 +/- 0.3 mm for the base point. It took <6 seconds for the method to identify the related landmarks on a personal computer with an Intel Core 2 6300 processor and 2 GB of random-access memory. The proposed method for the automatic identification of the reference system based on the fourth ventricular landmarks was shown to be rapid, robust, and accurate. The method has potentially utility in image registration and computer-aided surgery.

Signal Amplification by Glyco-qPCR for Ultrasensitive Detection of Carbohydrates: Applications in Glycobiology**

PubMed Central

Kwon, Seok Joon; Lee, Kyung Bok; Solakyildirim, Kemal; Masuko, Sayaka; Ly, Mellisa; Zhang, Fuming; Li, Lingyun; Dordick, Jonathan S.; Linhardt, Robert J.

2012-01-01

Tiny amounts of carbohydrates (ca. 1 zmol) can be detected quantitatively by a real-time method based on the conjugation of carbohydrates with DNA markers (see picture). The proposed method (glyco-qPCR) provides uniform, ultrasensitive detection of carbohydrates, which can be applied to glycobiology, as well as carbohydrate-based drug discovery. PMID:23073897

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

Determination of alkylphenol and alkylphenolethoxylates in biota by liquid chromatography with detection by tandem mass spectrometry and fluorescence spectroscopy

USGS Publications Warehouse

Schmitz-Afonso, I.; Loyo-Rosales, J.E.; de la Paz Aviles, M.; Rattner, B.A.; Rice, C.P.

2003-01-01

A quantitative method for the simultaneous determination of octylphenol, nonylphenol and the corresponding ethoxylates (1 to 5) in biota is presented. Extraction methods were developed for egg and fish matrices based on accelerated solvent extraction followed by a solid-phase extraction cleanup, using octadecylsilica or aminopropyl cartridges. Identification and quantitation were accomplished by liquid chromatography-electrospray tandem mass spectrometry (LC-MS-MS) and compared to the traditional liquid chromatography with fluorescence spectroscopy detection. LC-MS-MS provides high sensitivity and specificity required for these complex matrices and an accurate quantitation with the use of 13C-labeled internal standards. Quantitation limits by LC-MS-MS ranged from 4 to 12 ng/g in eggs, and from 6 to 22 ng/g in fish samples. These methods were successfully applied to osprey eggs from the Chesapeake Bay and fish from the Great Lakes area. Total levels found in osprey egg samples were up to 18 ng/g wet mass and as high as 8.2 ug/g wet mass in the fish samples.

A method for three-dimensional quantitative observation of the microstructure of biological samples

NASA Astrophysics Data System (ADS)

Wang, Pengfei; Chen, Dieyan; Ma, Wanyun; Wu, Hongxin; Ji, Liang; Sun, Jialin; Lv, Danyu; Zhang, Lu; Li, Ying; Tian, Ning; Zheng, Jinggao; Zhao, Fengying

2009-07-01

Contemporary biology has developed into the era of cell biology and molecular biology, and people try to study the mechanism of all kinds of biological phenomena at the microcosmic level now. Accurate description of the microstructure of biological samples is exigent need from many biomedical experiments. This paper introduces a method for 3-dimensional quantitative observation on the microstructure of vital biological samples based on two photon laser scanning microscopy (TPLSM). TPLSM is a novel kind of fluorescence microscopy, which has excellence in its low optical damage, high resolution, deep penetration depth and suitability for 3-dimensional (3D) imaging. Fluorescent stained samples were observed by TPLSM, and afterward the original shapes of them were obtained through 3D image reconstruction. The spatial distribution of all objects in samples as well as their volumes could be derived by image segmentation and mathematic calculation. Thus the 3-dimensionally and quantitatively depicted microstructure of the samples was finally derived. We applied this method to quantitative analysis of the spatial distribution of chromosomes in meiotic mouse oocytes at metaphase, and wonderful results came out last.

Stable isotope labelling methods in mass spectrometry-based quantitative proteomics.

PubMed

Chahrour, Osama; Cobice, Diego; Malone, John

2015-09-10

Mass-spectrometry based proteomics has evolved as a promising technology over the last decade and is undergoing a dramatic development in a number of different areas, such as; mass spectrometric instrumentation, peptide identification algorithms and bioinformatic computational data analysis. The improved methodology allows quantitative measurement of relative or absolute protein amounts, which is essential for gaining insights into their functions and dynamics in biological systems. Several different strategies involving stable isotopes label (ICAT, ICPL, IDBEST, iTRAQ, TMT, IPTL, SILAC), label-free statistical assessment approaches (MRM, SWATH) and absolute quantification methods (AQUA) are possible, each having specific strengths and weaknesses. Inductively coupled plasma mass spectrometry (ICP-MS), which is still widely recognised as elemental detector, has recently emerged as a complementary technique to the previous methods. The new application area for ICP-MS is targeting the fast growing field of proteomics related research, allowing absolute protein quantification using suitable elemental based tags. This document describes the different stable isotope labelling methods which incorporate metabolic labelling in live cells, ICP-MS based detection and post-harvest chemical label tagging for protein quantification, in addition to summarising their pros and cons. Copyright © 2015 Elsevier B.V. All rights reserved.

Diagnosis of breast cancer biopsies using quantitative phase imaging

NASA Astrophysics Data System (ADS)

Majeed, Hassaan; Kandel, Mikhail E.; Han, Kevin; Luo, Zelun; Macias, Virgilia; Tangella, Krishnarao; Balla, Andre; Popescu, Gabriel

2015-03-01

The standard practice in the histopathology of breast cancers is to examine a hematoxylin and eosin (H&E) stained tissue biopsy under a microscope. The pathologist looks at certain morphological features, visible under the stain, to diagnose whether a tumor is benign or malignant. This determination is made based on qualitative inspection making it subject to investigator bias. Furthermore, since this method requires a microscopic examination by the pathologist it suffers from low throughput. A quantitative, label-free and high throughput method for detection of these morphological features from images of tissue biopsies is, hence, highly desirable as it would assist the pathologist in making a quicker and more accurate diagnosis of cancers. We present here preliminary results showing the potential of using quantitative phase imaging for breast cancer screening and help with differential diagnosis. We generated optical path length maps of unstained breast tissue biopsies using Spatial Light Interference Microscopy (SLIM). As a first step towards diagnosis based on quantitative phase imaging, we carried out a qualitative evaluation of the imaging resolution and contrast of our label-free phase images. These images were shown to two pathologists who marked the tumors present in tissue as either benign or malignant. This diagnosis was then compared against the diagnosis of the two pathologists on H&E stained tissue images and the number of agreements were counted. In our experiment, the agreement between SLIM and H&E based diagnosis was measured to be 88%. Our preliminary results demonstrate the potential and promise of SLIM for a push in the future towards quantitative, label-free and high throughput diagnosis.

Application of quantitative real-time PCR compared to filtration methods for the enumeration of Escherichia coli in surface waters within Vietnam.

PubMed

Vital, Pierangeli G; Van Ha, Nguyen Thi; Tuyet, Le Thi Hong; Widmer, Kenneth W

2017-02-01

Surface water samples in Vietnam were collected from the Saigon River, rural and suburban canals, and urban runoff canals in Ho Chi Minh City, Vietnam, and were processed to enumerate Escherichia coli. Quantification was done through membrane filtration and quantitative real-time polymerase chain reaction (PCR). Mean log colony-forming unit (CFU)/100 ml E. coli counts in the dry season for river/suburban canals and urban canals were log 2.8 and 3.7, respectively, using a membrane filtration method, while using Taqman quantitative real-time PCR they were log 2.4 and 2.8 for river/suburban canals and urban canals, respectively. For the wet season, data determined by the membrane filtration method in river/suburban canals and urban canals samples had mean counts of log 3.7 and 4.1, respectively. While mean log CFU/100 ml counts in the wet season using quantitative PCR were log 3 and 2, respectively. Additionally, the urban canal samples were significantly lower than those determined by conventional culture methods for the wet season. These results show that while quantitative real-time PCR can be used to determine levels of fecal indicator bacteria in surface waters, there are some limitations to its application and it may be impacted by sources of runoff based on surveyed samples.

Allelic-based gene-gene interaction associated with quantitative traits.

PubMed

Jung, Jeesun; Sun, Bin; Kwon, Deukwoo; Koller, Daniel L; Foroud, Tatiana M

2009-05-01

Recent studies have shown that quantitative phenotypes may be influenced not only by multiple single nucleotide polymorphisms (SNPs) within a gene but also by the interaction between SNPs at unlinked genes. We propose a new statistical approach that can detect gene-gene interactions at the allelic level which contribute to the phenotypic variation in a quantitative trait. By testing for the association of allelic combinations at multiple unlinked loci with a quantitative trait, we can detect the SNP allelic interaction whether or not it can be detected as a main effect. Our proposed method assigns a score to unrelated subjects according to their allelic combination inferred from observed genotypes at two or more unlinked SNPs, and then tests for the association of the allelic score with a quantitative trait. To investigate the statistical properties of the proposed method, we performed a simulation study to estimate type I error rates and power and demonstrated that this allelic approach achieves greater power than the more commonly used genotypic approach to test for gene-gene interaction. As an example, the proposed method was applied to data obtained as part of a candidate gene study of sodium retention by the kidney. We found that this method detects an interaction between the calcium-sensing receptor gene (CaSR), the chloride channel gene (CLCNKB) and the Na, K, 2Cl cotransporter gene (CLC12A1) that contributes to variation in diastolic blood pressure.

Identification of common coexpression modules based on quantitative network comparison.

PubMed

Jo, Yousang; Kim, Sanghyeon; Lee, Doheon

2018-06-13

Finding common molecular interactions from different samples is essential work to understanding diseases and other biological processes. Coexpression networks and their modules directly reflect sample-specific interactions among genes. Therefore, identification of common coexpression network or modules may reveal the molecular mechanism of complex disease or the relationship between biological processes. However, there has been no quantitative network comparison method for coexpression networks and we examined previous methods for other networks that cannot be applied to coexpression network. Therefore, we aimed to propose quantitative comparison methods for coexpression networks and to find common biological mechanisms between Huntington's disease and brain aging by the new method. We proposed two similarity measures for quantitative comparison of coexpression networks. Then, we performed experiments using known coexpression networks. We showed the validity of two measures and evaluated threshold values for similar coexpression network pairs from experiments. Using these similarity measures and thresholds, we quantitatively measured the similarity between disease-specific and aging-related coexpression modules and found similar Huntington's disease-aging coexpression module pairs. We identified similar Huntington's disease-aging coexpression module pairs and found that these modules are related to brain development, cell death, and immune response. It suggests that up-regulated cell signalling related cell death and immune/ inflammation response may be the common molecular mechanisms in the pathophysiology of HD and normal brain aging in the frontal cortex.

Semi-quantitative estimation of cellular SiO2 nanoparticles using flow cytometry combined with X-ray fluorescence measurements.

PubMed

Choi, Seo Yeon; Yang, Nuri; Jeon, Soo Kyung; Yoon, Tae Hyun

2014-09-01

In this study, we have demonstrated feasibility of a semi-quantitative approach for the estimation of cellular SiO2 nanoparticles (NPs), which is based on the flow cytometry measurements of their normalized side scattering intensity. In order to improve our understanding on the quantitative aspects of cell-nanoparticle interactions, flow cytometry, transmission electron microscopy, and X-ray fluorescence experiments were carefully performed for the HeLa cells exposed to SiO2 NPs with different core diameters, hydrodynamic sizes, and surface charges. Based on the observed relationships among the experimental data, a semi-quantitative cellular SiO2 NPs estimation method from their normalized side scattering and core diameters was proposed, which can be applied for the determination of cellular SiO2 NPs within their size-dependent linear ranges. © 2014 International Society for Advancement of Cytometry.

Mapping Mixed Methods Research: Methods, Measures, and Meaning

ERIC Educational Resources Information Center

Wheeldon, J.

2010-01-01

This article explores how concept maps and mind maps can be used as data collection tools in mixed methods research to combine the clarity of quantitative counts with the nuance of qualitative reflections. Based on more traditional mixed methods approaches, this article details how the use of pre/post concept maps can be used to design qualitative…

Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

NASA Astrophysics Data System (ADS)

Lazariev, A.; Allouche, A.-R.; Aubert-Frécon, M.; Fauvelle, F.; Piotto, M.; Elbayed, K.; Namer, I.-J.; van Ormondt, D.; Graveron-Demilly, D.

2011-11-01

High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed.

Simultaneous determination of hydrocarbon renewable diesel, biodiesel and petroleum diesel contents in diesel fuel blends using near infrared (NIR) spectroscopy and chemometrics.

PubMed

Alves, Julio Cesar Laurentino; Poppi, Ronei Jesus

2013-11-07

Highly polluting fuels based on non-renewable resources such as fossil fuels need to be replaced with potentially less polluting renewable fuels derived from vegetable or animal biomass, these so-called biofuels, are a reality nowadays and many countries have started the challenge of increasing the use of different types of biofuels, such as ethanol and biodiesel (fatty acid alkyl esters), often mixed with petroleum derivatives, such as gasoline and diesel, respectively. The quantitative determination of these fuel blends using simple, fast and low cost methods based on near infrared (NIR) spectroscopy combined with chemometric methods has been reported. However, advanced biofuels based on a mixture of hydrocarbons or a single hydrocarbon molecule, such as farnesane (2,6,10-trimethyldodecane), a hydrocarbon renewable diesel, can also be used in mixtures with biodiesel and petroleum diesel fuel and the use of NIR spectroscopy for the quantitative determination of a ternary fuel blend of these two hydrocarbon-based fuels and biodiesel can be a useful tool for quality control. This work presents a development of an analytical method for the quantitative determination of hydrocarbon renewable diesel (farnesane), biodiesel and petroleum diesel fuel blends using NIR spectroscopy combined with chemometric methods, such as partial least squares (PLS) and support vector machines (SVM). This development leads to a more accurate, simpler, faster and cheaper method when compared to the standard reference method ASTM D6866 and with the main advantage of providing the individual quantification of two different biofuels in a mixture with petroleum diesel fuel. Using the developed PLS model the three fuel blend components were determined simultaneously with values of root mean square error of prediction (RMSEP) of 0.25%, 0.19% and 0.38% for hydrocarbon renewable diesel, biodiesel and petroleum diesel, respectively, the values obtained were in agreement with those suggested by reference methods for the determination of renewable fuels.

Practical no-gold-standard evaluation framework for quantitative imaging methods: application to lesion segmentation in positron emission tomography

PubMed Central

Jha, Abhinav K.; Mena, Esther; Caffo, Brian; Ashrafinia, Saeed; Rahmim, Arman; Frey, Eric; Subramaniam, Rathan M.

2017-01-01

Abstract. Recently, a class of no-gold-standard (NGS) techniques have been proposed to evaluate quantitative imaging methods using patient data. These techniques provide figures of merit (FoMs) quantifying the precision of the estimated quantitative value without requiring repeated measurements and without requiring a gold standard. However, applying these techniques to patient data presents several practical difficulties including assessing the underlying assumptions, accounting for patient-sampling-related uncertainty, and assessing the reliability of the estimated FoMs. To address these issues, we propose statistical tests that provide confidence in the underlying assumptions and in the reliability of the estimated FoMs. Furthermore, the NGS technique is integrated within a bootstrap-based methodology to account for patient-sampling-related uncertainty. The developed NGS framework was applied to evaluate four methods for segmenting lesions from F-Fluoro-2-deoxyglucose positron emission tomography images of patients with head-and-neck cancer on the task of precisely measuring the metabolic tumor volume. The NGS technique consistently predicted the same segmentation method as the most precise method. The proposed framework provided confidence in these results, even when gold-standard data were not available. The bootstrap-based methodology indicated improved performance of the NGS technique with larger numbers of patient studies, as was expected, and yielded consistent results as long as data from more than 80 lesions were available for the analysis. PMID:28331883

A New Kinetic Spectrophotometric Method for the Quantitation of Amorolfine.

PubMed

Soto, César; Poza, Cristian; Contreras, David; Yáñez, Jorge; Nacaratte, Fallon; Toral, M Inés

2017-01-01

Amorolfine (AOF) is a compound with fungicide activity based on the dual inhibition of growth of the fungal cell membrane, the biosynthesis and accumulation of sterols, and the reduction of ergosterol. In this work a sensitive kinetic and spectrophotometric method for the AOF quantitation based on the AOF oxidation by means of KMnO 4 at 30 min (fixed time), pH alkaline, and ionic strength controlled was developed. Measurements of changes in absorbance at 610 nm were used as criterion of the oxidation progress. In order to maximize the sensitivity, different experimental reaction parameters were carefully studied via factorial screening and optimized by multivariate method. The linearity, intraday, and interday assay precision and accuracy were determined. The absorbance-concentration plot corresponding to tap water spiked samples was rectilinear, over the range of 7.56 × 10 -6 -3.22 × 10 -5  mol L -1 , with detection and quantitation limits of 2.49 × 10 -6  mol L -1 and 7.56 × 10 -6  mol L -1 , respectively. The proposed method was successfully validated for the application of the determination of the drug in the spiked tap water samples and the percentage recoveries were 94.0-105.0%. The method is simple and does not require expensive instruments or complicated extraction steps of the reaction product.

A qualitative and quantitative laser-based computer-aided flow visualization method. M.S. Thesis, 1992 Final Report

NASA Technical Reports Server (NTRS)

Canacci, Victor A.; Braun, M. Jack

1994-01-01

The experimental approach presented here offers a nonintrusive, qualitative and quantitative evaluation of full field flow patterns applicable in various geometries in a variety of fluids. This Full Flow Field Tracking (FFFT) Particle Image Velocimetry (PIV) technique, by means of particle tracers illuminated by a laser light sheet, offers an alternative to Laser Doppler Velocimetry (LDV), and intrusive systems such as Hot Wire/Film Anemometry. The method makes obtainable the flow patterns, and allows quantitative determination of the velocities, accelerations, and mass flows of an entire flow field. The method uses a computer based digitizing system attached through an imaging board to a low luminosity camera. A customized optical train allows the system to become a long distance microscope (LDM), allowing magnifications of areas of interest ranging up to 100 times. Presented in addition to the method itself, are studies in which the flow patterns and velocities were observed and evaluated in three distinct geometries, with three different working fluids. The first study involved pressure and flow analysis of a brush seal in oil. The next application involved studying the velocity and flow patterns in a cowl lip cooling passage of an air breathing aircraft engine using water as the working fluid. Finally, the method was extended to a study in air to examine the flows in a staggered pin arrangement located on one side of a branched duct.

Influence analysis in quantitative trait loci detection.

PubMed

Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

2014-07-01

This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. © 2014 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid quantitative analysis of individual anthocyanin content based on high-performance liquid chromatography with diode array detection with the pH differential method.

PubMed

Wang, Huayin

2014-09-01

A new quantitative technique for the simultaneous quantification of the individual anthocyanins based on the pH differential method and high-performance liquid chromatography with diode array detection is proposed in this paper. The six individual anthocyanins (cyanidin 3-glucoside, cyanidin 3-rutinoside, petunidin 3-glucoside, petunidin 3-rutinoside, and malvidin 3-rutinoside) from mulberry (Morus rubra) and Liriope platyphylla were used for demonstration and validation. The elution of anthocyanins was performed using a C18 column with stepwise gradient elution and individual anthocyanins were identified by high-performance liquid chromatography with tandem mass spectrometry. Based on the pH differential method, the high-performance liquid chromatography peak areas of maximum and reference absorption wavelengths of anthocyanin extracts were conducted to quantify individual anthocyanins. The calibration curves for these anthocyanins were linear within the range of 10-5500 mg/L. The correlation coefficients (r(2)) all exceeded 0.9972, and the limits of detection were in the range of 1-4 mg/L at a signal-to-noise ratio ≥5 for these anthocyanins. The proposed quantitative analysis was reproducible with good accuracy of all individual anthocyanins ranging from 96.3 to 104.2% and relative recoveries were in the range 98.4-103.2%. The proposed technique is performed without anthocyanin standards and is a simple, rapid, accurate, and economical method to determine individual anthocyanin contents. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automated classification of cell morphology by coherence-controlled holographic microscopy

NASA Astrophysics Data System (ADS)

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity.

Time-Gated Raman Spectroscopy for Quantitative Determination of Solid-State Forms of Fluorescent Pharmaceuticals.

PubMed

Lipiäinen, Tiina; Pessi, Jenni; Movahedi, Parisa; Koivistoinen, Juha; Kurki, Lauri; Tenhunen, Mari; Yliruusi, Jouko; Juppo, Anne M; Heikkonen, Jukka; Pahikkala, Tapio; Strachan, Clare J

2018-04-03

Raman spectroscopy is widely used for quantitative pharmaceutical analysis, but a common obstacle to its use is sample fluorescence masking the Raman signal. Time-gating provides an instrument-based method for rejecting fluorescence through temporal resolution of the spectral signal and allows Raman spectra of fluorescent materials to be obtained. An additional practical advantage is that analysis is possible in ambient lighting. This study assesses the efficacy of time-gated Raman spectroscopy for the quantitative measurement of fluorescent pharmaceuticals. Time-gated Raman spectroscopy with a 128 × (2) × 4 CMOS SPAD detector was applied for quantitative analysis of ternary mixtures of solid-state forms of the model drug, piroxicam (PRX). Partial least-squares (PLS) regression allowed quantification, with Raman-active time domain selection (based on visual inspection) improving performance. Model performance was further improved by using kernel-based regularized least-squares (RLS) regression with greedy feature selection in which the data use in both the Raman shift and time dimensions was statistically optimized. Overall, time-gated Raman spectroscopy, especially with optimized data analysis in both the spectral and time dimensions, shows potential for sensitive and relatively routine quantitative analysis of photoluminescent pharmaceuticals during drug development and manufacturing.

Automated classification of cell morphology by coherence-controlled holographic microscopy.

PubMed

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Applications of mixed-methods methodology in clinical pharmacy research.

PubMed

Hadi, Muhammad Abdul; Closs, S José

2016-06-01

Introduction Mixed-methods methodology, as the name suggests refers to mixing of elements of both qualitative and quantitative methodologies in a single study. In the past decade, mixed-methods methodology has gained popularity among healthcare researchers as it promises to bring together the strengths of both qualitative and quantitative approaches. Methodology A number of mixed-methods designs are available in the literature and the four most commonly used designs in healthcare research are: the convergent parallel design, the embedded design, the exploratory design, and the explanatory design. Each has its own unique advantages, challenges and procedures and selection of a particular design should be guided by the research question. Guidance on designing, conducting and reporting mixed-methods research is available in the literature, so it is advisable to adhere to this to ensure methodological rigour. When to use it is best suited when the research questions require: triangulating findings from different methodologies to explain a single phenomenon; clarifying the results of one method using another method; informing the design of one method based on the findings of another method, development of a scale/questionnaire and answering different research questions within a single study. Two case studies have been presented to illustrate possible applications of mixed-methods methodology. Limitations Possessing the necessary knowledge and skills to undertake qualitative and quantitative data collection, analysis, interpretation and integration remains the biggest challenge for researchers conducting mixed-methods studies. Sequential study designs are often time consuming, being in two (or more) phases whereas concurrent study designs may require more than one data collector to collect both qualitative and quantitative data at the same time.

Systems Biology, Neuroimaging, Neuropsychology, Neuroconnectivity and Traumatic Brain Injury

PubMed Central

Bigler, Erin D.

2016-01-01

The patient who sustains a traumatic brain injury (TBI) typically undergoes neuroimaging studies, usually in the form of computed tomography (CT) and magnetic resonance imaging (MRI). In most cases the neuroimaging findings are clinically assessed with descriptive statements that provide qualitative information about the presence/absence of visually identifiable abnormalities; though little if any of the potential information in a scan is analyzed in any quantitative manner, except in research settings. Fortunately, major advances have been made, especially during the last decade, in regards to image quantification techniques, especially those that involve automated image analysis methods. This review argues that a systems biology approach to understanding quantitative neuroimaging findings in TBI provides an appropriate framework for better utilizing the information derived from quantitative neuroimaging and its relation with neuropsychological outcome. Different image analysis methods are reviewed in an attempt to integrate quantitative neuroimaging methods with neuropsychological outcome measures and to illustrate how different neuroimaging techniques tap different aspects of TBI-related neuropathology. Likewise, how different neuropathologies may relate to neuropsychological outcome is explored by examining how damage influences brain connectivity and neural networks. Emphasis is placed on the dynamic changes that occur following TBI and how best to capture those pathologies via different neuroimaging methods. However, traditional clinical neuropsychological techniques are not well suited for interpretation based on contemporary and advanced neuroimaging methods and network analyses. Significant improvements need to be made in the cognitive and behavioral assessment of the brain injured individual to better interface with advances in neuroimaging-based network analyses. By viewing both neuroimaging and neuropsychological processes within a systems biology perspective could represent a significant advancement for the field. PMID:27555810

Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud.

PubMed

Burns, Malcolm; Wiseman, Gordon; Knight, Angus; Bramley, Peter; Foster, Lucy; Rollinson, Sophie; Damant, Andrew; Primrose, Sandy

2016-01-07

Following a report on a significant amount of horse DNA being detected in a beef burger product on sale to the public at a UK supermarket in early 2013, the Elliott report was published in 2014 and contained a list of recommendations for helping ensure food integrity. One of the recommendations included improving laboratory testing capacity and capability to ensure a harmonised approach for testing for food authenticity. Molecular biologists have developed exquisitely sensitive methods based on the polymerase chain reaction (PCR) or mass spectrometry for detecting the presence of particular nucleic acid or peptide/protein sequences. These methods have been shown to be specific and sensitive in terms of lower limits of applicability, but they are largely qualitative in nature. Historically, the conversion of these qualitative techniques into reliable quantitative methods has been beset with problems even when used on relatively simple sample matrices. When the methods are applied to complex sample matrices, as found in many foods, the problems are magnified resulting in a high measurement uncertainty associated with the result which may mean that the assay is not fit for purpose. However, recent advances in the technology and the understanding of molecular biology approaches have further given rise to the re-assessment of these methods for their quantitative potential. This review focuses on important issues for consideration when validating a molecular biology assay and the various factors that can impact on the measurement uncertainty of a result associated with molecular biology approaches used in detection of food fraud, with a particular focus on quantitative PCR-based and proteomics assays.

Comparative evaluation of two Rickettsia typhi-specific quantitative real-time PCRs for research and diagnostic purposes.

PubMed

Papp, Stefanie; Rauch, Jessica; Kuehl, Svenja; Richardt, Ulricke; Keller, Christian; Osterloh, Anke

2017-02-01

Rickettsioses are caused by intracellular bacteria of the family of Rickettsiaceae. Rickettsia (R.) typhi is the causative agent of endemic typhus. The disease occurs worldwide and is one of the most prevalent rickettsioses. Rickettsial diseases, however, are generally underdiagnosed which is mainly due to the lack of sensitive and specific methods. In addition, methods for quantitative detection of the bacteria for research purposes are rare. We established two qPCRs for the detection of R. typhi by amplification of the outer membrane protein B (ompB) and parvulin-type PPIase (prsA) genes. Both qPCRs are specific and exclusively recognize R. typhi but no other rickettsiae including the closest relative, R. prowazekii. The prsA-based qPCR revealed to be much more sensitive than the amplification of ompB and provided highly reproducible results in the detection of R. typhi in organs of infected mice. Furthermore, as a nested PCR the prsA qPCR was applicable for the detection of R. typhi in human blood samples. Collectively, the prsA-based qPCR represents a reliable method for the quantitative detection of R. typhi for research purposes and is a promising candidate for differential diagnosis.

Rapid determination of environmentally persistent free radicals (EPFRs) in atmospheric particles with a quartz sheet-based approach using electron paramagnetic resonance (EPR) spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Qingcai; Wang, Mamin; Wang, Yuqin; Zhang, Lixin; Xue, Jian; Sun, Haoyao; Mu, Zhen

2018-07-01

Environmentally persistent free radicals (EPFRs) are present within atmospheric fine particles, and they are assumed to be a potential factor responsible for human pneumonia and lung cancer. This study presents a new method for the rapid quantification of EPFRs in atmospheric particles with a quartz sheet-based approach using electron paramagnetic resonance (EPR) spectroscopy. The three-dimensional distributions of the relative response factors in a cavity resonator were simulated and utilized for an accurate quantitative determination of EPFRs in samples. Comparisons between the proposed method and conventional quantitative methods were also performed to illustrate the advantages of the proposed method. The results suggest that the reproducibility and accuracy of the proposed method are superior to those of the quartz tube-based method. Although the solvent extraction method is capable of extracting specific EPFR species, the developed method can be used to determine the total EPFR content; moreover, the analysis process of the proposed approach is substantially quicker than that of the solvent extraction method. The proposed method has been applied in this study to determine the EPFRs in ambient PM2.5 samples collected over Xi'an, the results of which will be useful for extensive research on the sources, concentrations, and physical-chemical characteristics of EPFRs in the atmosphere.

High School Students' Concepts of Acids and Bases.

ERIC Educational Resources Information Center

Ross, Bertram H. B.

An investigation of Ontario high school students' understanding of acids and bases with quantitative and qualitative methods revealed misconceptions. A concept map, based on the objectives of the Chemistry Curriculum Guideline, generated multiple-choice items and interview questions. The multiple-choice test was administered to 34 grade 12…

A Universally Applicable and Rapid Method for Measuring the Growth of Streptomyces and Other Filamentous Microorganisms by Methylene Blue Adsorption-Desorption

PubMed Central

Fischer, Marco

2013-01-01

Quantitative assessment of growth of filamentous microorganisms, such as streptomycetes, is generally restricted to determination of dry weight. Here, we describe a straightforward methylene blue-based sorption assay to monitor microbial growth quantitatively, simply, and rapidly. The assay is equally applicable to unicellular and filamentous bacterial and eukaryotic microorganisms. PMID:23666340

On the Development and Use of Large Chemical Similarity Networks, Informatics Best Practices and Novel Chemical Descriptors towards Materials Quantitative Structure Property Relationships

ERIC Educational Resources Information Center

Krein, Michael

2011-01-01

After decades of development and use in a variety of application areas, Quantitative Structure Property Relationships (QSPRs) and related descriptor-based statistical learning methods have achieved a level of infamy due to their misuse. The field is rife with past examples of overtrained models, overoptimistic performance assessment, and outright…

A brief update on physical and optical disector applications and sectioning-staining methods in neuroscience.

PubMed

Yurt, Kıymet Kübra; Kivrak, Elfide Gizem; Altun, Gamze; Mohamed, Hamza; Ali, Fathelrahman; Gasmalla, Hosam Eldeen; Kaplan, Suleyman

2018-02-26

A quantitative description of a three-dimensional (3D) object based on two-dimensional images can be made using stereological methods These methods involve unbiased approaches and provide reliable results with quantitative data. The quantitative morphology of the nervous system has been thoroughly researched in this context. In particular, various novel methods such as design-based stereological approaches have been applied in neuoromorphological studies. The main foundations of these methods are systematic random sampling and a 3D approach to structures such as tissues and organs. One key point in these methods is that selected samples should represent the entire structure. Quantification of neurons, i.e. particles, is important for revealing degrees of neurodegeneration and regeneration in an organ or system. One of the most crucial morphometric parameters in biological studies is thus the "number". The disector counting method introduced by Sterio in 1984 is an efficient and reliable solution for particle number estimation. In order to obtain precise results by means of stereological analysis, counting items should be seen clearly in the tissue. If an item in the tissue cannot be seen, these cannot be analyzed even using unbiased stereological techniques. Staining and sectioning processes therefore play a critical role in stereological analysis. The purpose of this review is to evaluate current neuroscientific studies using optical and physical disector counting methods and to discuss their definitions and methodological characteristics. Although the efficiency of the optical disector method in light microscopic studies has been revealed in recent years, the physical disector method is more easily performed in electron microscopic studies. Also, we offered to readers summaries of some common basic staining and sectioning methods, which can be used for stereological techniques in this review. Copyright © 2018 Elsevier B.V. All rights reserved.

Recommendations for Using the Case Study Method in International Business Research

ERIC Educational Resources Information Center

Vissak, Tiia

2010-01-01

The case study method has not been as frequently used in international business (IB) research as quantitative methods. Moreover, it has been sometimes misused and quite often criticized. Still, it can be very useful for understanding such complex phenomena as the internationalization process or the management of multinational enterprises. Based on…

Comparison of English Language Rhythm and Kalhori Kurdish Language Rhythm

ERIC Educational Resources Information Center

Taghva, Nafiseh; Zadeh, Vahideh Abolhasani

2016-01-01

Interval-based method is a method of studying the rhythmic quantitative features of languages. This method use Pairwise Variability Index (PVI) to consider the variability of vocalic duration and inter-vocalic duration of sentences which leads to classification of languages rhythm into stress-timed languages and syllable-timed ones. This study…

A GIS-BASED METHOD FOR MULTI-OBJECTIVE EVALUATION OF PARK VEGETATION. (R824766)

EPA Science Inventory

Abstract

In this paper we describe a method for evaluating the concordance between a set of mapped landscape attributes and a set of quantitatively expressed management priorities. The method has proved to be useful in planning urban green areas, allowing objectively d...

Quantitative SIMS Imaging of Agar-Based Microbial Communities.

PubMed

Dunham, Sage J B; Ellis, Joseph F; Baig, Nameera F; Morales-Soto, Nydia; Cao, Tianyuan; Shrout, Joshua D; Bohn, Paul W; Sweedler, Jonathan V

2018-05-01

After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

Quantification of measles, mumps and rubella viruses using real-time quantitative TaqMan-based RT-PCR assay.

PubMed

Ammour, Y; Faizuloev, E; Borisova, T; Nikonova, A; Dmitriev, G; Lobodanov, S; Zverev, V

2013-01-01

In this study, a rapid quantitative method using TaqMan-based real-time reverse transcription-polymerase chain reaction (qPCR-RT) has been developed for estimating the titers of measles, mumps and rubella (MMR) viruses in infected cell culture supernatants. The qPCR-RT assay was demonstrated to be a specific, sensitive, efficient and reproducible method. For MMR viral samples obtained during MMR viral propagations in Vero cells at a different multiplicity of infection, titers determined by the qPCR-RT assay have been compared with estimates of infectious virus obtained by a traditional commonly used method for MMR viruses - 50% cell culture infective dose (CCID(50)) assay, in paired samples. Pearson analysis evidenced a significant correlation between both methods for a certain period after viral inoculation. Furthermore, the established qPCR-RT assay was faster and less-laborious. The developed method could be used as an alternative method or a supplementary tool for the routine titer estimation during MMR vaccine production. Copyright © 2012 Elsevier B.V. All rights reserved.

[Progress in stable isotope labeled quantitative proteomics methods].

PubMed

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2013-06-01

Quantitative proteomics is an important research field in post-genomics era. There are two strategies for proteome quantification: label-free methods and stable isotope labeling methods which have become the most important strategy for quantitative proteomics at present. In the past few years, a number of quantitative methods have been developed, which support the fast development in biology research. In this work, we discuss the progress in the stable isotope labeling methods for quantitative proteomics including relative and absolute quantitative proteomics, and then give our opinions on the outlook of proteome quantification methods.

Two schemes for quantitative photoacoustic tomography based on Monte Carlo simulation

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

Liu, Yubin; Yuan, Zhen, E-mail: zhenyuan@umac.mo

Purpose: The aim of this study was to develop novel methods for photoacoustically determining the optical absorption coefficient of biological tissues using Monte Carlo (MC) simulation. Methods: In this study, the authors propose two quantitative photoacoustic tomography (PAT) methods for mapping the optical absorption coefficient. The reconstruction methods combine conventional PAT with MC simulation in a novel way to determine the optical absorption coefficient of biological tissues or organs. Specifically, the authors’ two schemes were theoretically and experimentally examined using simulations, tissue-mimicking phantoms, ex vivo, and in vivo tests. In particular, the authors explored these methods using several objects withmore » different absorption contrasts embedded in turbid media and by using high-absorption media when the diffusion approximation was not effective at describing the photon transport. Results: The simulations and experimental tests showed that the reconstructions were quantitatively accurate in terms of the locations, sizes, and optical properties of the targets. The positions of the recovered targets were accessed by the property profiles, where the authors discovered that the off center error was less than 0.1 mm for the circular target. Meanwhile, the sizes and quantitative optical properties of the targets were quantified by estimating the full width half maximum of the optical absorption property. Interestingly, for the reconstructed sizes, the authors discovered that the errors ranged from 0 for relatively small-size targets to 26% for relatively large-size targets whereas for the recovered optical properties, the errors ranged from 0% to 12.5% for different cases. Conclusions: The authors found that their methods can quantitatively reconstruct absorbing objects of different sizes and optical contrasts even when the diffusion approximation is unable to accurately describe the photon propagation in biological tissues. In particular, their methods are able to resolve the intrinsic difficulties that occur when quantitative PAT is conducted by combining conventional PAT with the diffusion approximation or with radiation transport modeling.« less

[Development and application of morphological analysis method in Aspergillus niger fermentation].

PubMed

Tang, Wenjun; Xia, Jianye; Chu, Ju; Zhuang, Yingping; Zhang, Siliang

2015-02-01

Filamentous fungi are widely used in industrial fermentation. Particular fungal morphology acts as a critical index for a successful fermentation. To break the bottleneck of morphological analysis, we have developed a reliable method for fungal morphological analysis. By this method, we can prepare hundreds of pellet samples simultaneously and obtain quantitative morphological information at large scale quickly. This method can largely increase the accuracy and reliability of morphological analysis result. Based on that, the studies of Aspergillus niger morphology under different oxygen supply conditions and shear rate conditions were carried out. As a result, the morphological responding patterns of A. niger morphology to these conditions were quantitatively demonstrated, which laid a solid foundation for the further scale-up.

Ecological content validation of the Information Assessment Method for parents (IAM-parent): A mixed methods study.

PubMed

Bujold, M; El Sherif, R; Bush, P L; Johnson-Lafleur, J; Doray, G; Pluye, P

2018-02-01

This mixed methods study content validated the Information Assessment Method for parents (IAM-parent) that allows users to systematically rate and comment on online parenting information. Quantitative data and results: 22,407 IAM ratings were collected; of the initial 32 items, descriptive statistics showed that 10 had low relevance. Qualitative data and results: IAM-based comments were collected, and 20 IAM users were interviewed (maximum variation sample); the qualitative data analysis assessed the representativeness of IAM items, and identified items with problematic wording. Researchers, the program director, and Web editors integrated quantitative and qualitative results, which led to a shorter and clearer IAM-parent. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

A novel quantitative analysis method of three-dimensional fluorescence spectra for vegetable oils contents in edible blend oil

NASA Astrophysics Data System (ADS)

Xu, Jing; Wang, Yu-Tian; Liu, Xiao-Fei

2015-04-01

Edible blend oil is a mixture of vegetable oils. Eligible blend oil can meet the daily need of two essential fatty acids for human to achieve the balanced nutrition. Each vegetable oil has its different composition, so vegetable oils contents in edible blend oil determine nutritional components in blend oil. A high-precision quantitative analysis method to detect the vegetable oils contents in blend oil is necessary to ensure balanced nutrition for human being. Three-dimensional fluorescence technique is high selectivity, high sensitivity, and high-efficiency. Efficiency extraction and full use of information in tree-dimensional fluorescence spectra will improve the accuracy of the measurement. A novel quantitative analysis is proposed based on Quasi-Monte-Carlo integral to improve the measurement sensitivity and reduce the random error. Partial least squares method is used to solve nonlinear equations to avoid the effect of multicollinearity. The recovery rates of blend oil mixed by peanut oil, soybean oil and sunflower are calculated to verify the accuracy of the method, which are increased, compared the linear method used commonly for component concentration measurement.

Quantitative measurement of intact alpha-synuclein proteoforms from post-mortem control and Parkinson's disease brain tissue by intact protein mass spectrometry.

PubMed

Kellie, John F; Higgs, Richard E; Ryder, John W; Major, Anthony; Beach, Thomas G; Adler, Charles H; Merchant, Kalpana; Knierman, Michael D

2014-07-23

A robust top down proteomics method is presented for profiling alpha-synuclein species from autopsied human frontal cortex brain tissue from Parkinson's cases and controls. The method was used to test the hypothesis that pathology associated brain tissue will have a different profile of post-translationally modified alpha-synuclein than the control samples. Validation of the sample processing steps, mass spectrometry based measurements, and data processing steps were performed. The intact protein quantitation method features extraction and integration of m/z data from each charge state of a detected alpha-synuclein species and fitting of the data to a simple linear model which accounts for concentration and charge state variability. The quantitation method was validated with serial dilutions of intact protein standards. Using the method on the human brain samples, several previously unreported modifications in alpha-synuclein were identified. Low levels of phosphorylated alpha synuclein were detected in brain tissue fractions enriched for Lewy body pathology and were marginally significant between PD cases and controls (p = 0.03).

Bridging the qualitative-quantitative divide: Experiences from conducting a mixed methods evaluation in the RUCAS programme.

PubMed

Makrakis, Vassilios; Kostoulas-Makrakis, Nelly

2016-02-01

Quantitative and qualitative approaches to planning and evaluation in education for sustainable development have often been treated by practitioners from a single research paradigm. This paper discusses the utility of mixed method evaluation designs which integrate qualitative and quantitative data through a sequential transformative process. Sequential mixed method data collection strategies involve collecting data in an iterative process whereby data collected in one phase contribute to data collected in the next. This is done through examples from a programme addressing the 'Reorientation of University Curricula to Address Sustainability (RUCAS): A European Commission Tempus-funded Programme'. It is argued that the two approaches are complementary and that there are significant gains from combining both. Using methods from both research paradigms does not, however, mean that the inherent differences among epistemologies and methodologies should be neglected. Based on this experience, it is recommended that using a sequential transformative mixed method evaluation can produce more robust results than could be accomplished using a single approach in programme planning and evaluation focussed on education for sustainable development. Copyright © 2015 Elsevier Ltd. All rights reserved.

An augmented classical least squares method for quantitative Raman spectral analysis against component information loss.

PubMed

Zhou, Yan; Cao, Hui

2013-01-01

We propose an augmented classical least squares (ACLS) calibration method for quantitative Raman spectral analysis against component information loss. The Raman spectral signals with low analyte concentration correlations were selected and used as the substitutes for unknown quantitative component information during the CLS calibration procedure. The number of selected signals was determined by using the leave-one-out root-mean-square error of cross-validation (RMSECV) curve. An ACLS model was built based on the augmented concentration matrix and the reference spectral signal matrix. The proposed method was compared with partial least squares (PLS) and principal component regression (PCR) using one example: a data set recorded from an experiment of analyte concentration determination using Raman spectroscopy. A 2-fold cross-validation with Venetian blinds strategy was exploited to evaluate the predictive power of the proposed method. The one-way variance analysis (ANOVA) was used to access the predictive power difference between the proposed method and existing methods. Results indicated that the proposed method is effective at increasing the robust predictive power of traditional CLS model against component information loss and its predictive power is comparable to that of PLS or PCR.

Mixing it but not mixed-up: mixed methods research in medical education (a critical narrative review).

PubMed

Maudsley, Gillian

2011-01-01

Some important research questions in medical education and health services research need 'mixed methods research' (particularly synthesizing quantitative and qualitative findings). The approach is not new, but should be more explicitly reported. The broad search question here, of a disjointed literature, was thus: What is mixed methods research - how should it relate to medical education research?, focused on explicit acknowledgement of 'mixing'. Literature searching focused on Web of Knowledge supplemented by other databases across disciplines. Five main messages emerged: - Thinking quantitative and qualitative, not quantitative versus qualitative - Appreciating that mixed methods research blends different knowledge claims, enquiry strategies, and methods - Using a 'horses for courses' [whatever works] approach to the question, and clarifying the mix - Appreciating how medical education research competes with the 'evidence-based' movement, health services research, and the 'RCT' - Being more explicit about the role of mixed methods in medical education research, and the required expertise Mixed methods research is valuable, yet the literature relevant to medical education is fragmented and poorly indexed. The required time, effort, expertise, and techniques deserve better recognition. More write-ups should explicitly discuss the 'mixing' (particularly of findings), rather than report separate components.

Computational Methods in Drug Discovery

PubMed Central

Sliwoski, Gregory; Kothiwale, Sandeepkumar; Meiler, Jens

2014-01-01

Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades. These methods are broadly classified as either structure-based or ligand-based methods. Structure-based methods are in principle analogous to high-throughput screening in that both target and ligand structure information is imperative. Structure-based approaches include ligand docking, pharmacophore, and ligand design methods. The article discusses theory behind the most important methods and recent successful applications. Ligand-based methods use only ligand information for predicting activity depending on its similarity/dissimilarity to previously known active ligands. We review widely used ligand-based methods such as ligand-based pharmacophores, molecular descriptors, and quantitative structure-activity relationships. In addition, important tools such as target/ligand data bases, homology modeling, ligand fingerprint methods, etc., necessary for successful implementation of various computer-aided drug discovery/design methods in a drug discovery campaign are discussed. Finally, computational methods for toxicity prediction and optimization for favorable physiologic properties are discussed with successful examples from literature. PMID:24381236

A general way for quantitative magnetic measurement by transmitted electrons

NASA Astrophysics Data System (ADS)

Song, Dongsheng; Li, Gen; Cai, Jianwang; Zhu, Jing

2016-01-01

EMCD (electron magnetic circular dichroism) technique opens a new door to explore magnetic properties by transmitted electrons. The recently developed site-specific EMCD technique makes it possible to obtain rich magnetic information from the Fe atoms sited at nonequivalent crystallographic planes in NiFe2O4, however it is based on a critical demand for the crystallographic structure of the testing sample. Here, we have further improved and tested the method for quantitative site-specific magnetic measurement applicable for more complex crystallographic structure by using the effective dynamical diffraction effects (general routine for selecting proper diffraction conditions, making use of the asymmetry of dynamical diffraction for design of experimental geometry and quantitative measurement, etc), and taken yttrium iron garnet (Y3Fe5O12, YIG) with more complex crystallographic structure as an example to demonstrate its applicability. As a result, the intrinsic magnetic circular dichroism signals, spin and orbital magnetic moment of iron with site-specific are quantitatively determined. The method will further promote the development of quantitative magnetic measurement with high spatial resolution by transmitted electrons.

Quantitative analysis of amygdalin and prunasin in Prunus serotina Ehrh. using (1) H-NMR spectroscopy.

PubMed

Santos Pimenta, Lúcia P; Schilthuizen, Menno; Verpoorte, Robert; Choi, Young Hae

2014-01-01

Prunus serotina is native to North America but has been invasively introduced in Europe since the seventeenth century. This plant contains cyanogenic glycosides that are believed to be related to its success as an invasive plant. For these compounds, chromatographic- or spectrometric-based (targeting on HCN hydrolysis) methods of analysis have been employed so far. However, the conventional methods require tedious preparation steps and a long measuring time. To develop a fast and simple method to quantify the cyanogenic glycosides, amygdalin and prunasin in dried Prunus serotina leaves without any pre-purification steps using (1) H-NMR spectroscopy. Extracts of Prunus serotina leaves using CH3 OH-d4 and KH2 PO4 buffer in D2 O (1:1) were quantitatively analysed for amygdalin and prunasin using (1) H-NMR spectroscopy. Different internal standards were evaluated for accuracy and stability. The purity of quantitated (1) H-NMR signals was evaluated using several two-dimensional NMR experiments. Trimethylsilylpropionic acid sodium salt-d4 proved most suitable as the internal standard for quantitative (1) H-NMR analysis. Two-dimensional J-resolved NMR was shown to be a useful tool to confirm the structures and to check for possible signal overlapping with the target signals for the quantitation. Twenty-two samples of P. serotina were subsequently quantitatively analysed for the cyanogenic glycosides prunasin and amygdalin. The NMR method offers a fast, high-throughput analysis of cyanogenic glycosides in dried leaves permitting simultaneous quantification and identification of prunasin and amygdalin in Prunus serotina. Copyright © 2013 John Wiley & Sons, Ltd.

Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design.

PubMed

Du, Qi-Shi; Huang, Ri-Bo; Wei, Yu-Tuo; Pang, Zong-Wen; Du, Li-Qin; Chou, Kuo-Chen

2009-01-30

In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" (FB-QSAR) is proposed. The essence of the new method is that the molecular framework in a family of drug candidates are divided into several fragments according to their substitutes being investigated. The bioactivities of molecules are correlated with the physicochemical properties of the molecular fragments through two sets of coefficients in the linear free energy equations. One coefficient set is for the physicochemical properties and the other for the weight factors of the molecular fragments. Meanwhile, an iterative double least square (IDLS) technique is developed to solve the two sets of coefficients in a training data set alternately and iteratively. The IDLS technique is a feedback procedure with machine learning ability. The standard Two-dimensional quantitative structure-activity relationship (2D-QSAR) is a special case, in the FB-QSAR, when the whole molecule is treated as one entity. The FB-QSAR approach can remarkably enhance the predictive power and provide more structural insights into rational drug design. As an example, the FB-QSAR is applied to build a predictive model of neuraminidase inhibitors for drug development against H5N1 influenza virus. (c) 2008 Wiley Periodicals, Inc.

Training of lay health educators to implement an evidence-based behavioral weight loss intervention in rural senior centers.

PubMed

Krukowski, Rebecca A; Lensing, Shelly; Love, Sharhonda; Prewitt, T Elaine; Adams, Becky; Cornell, Carol E; Felix, Holly C; West, Delia

2013-02-01

Lay health educators (LHEs) offer great promise for facilitating the translation of evidence-based health promotion programs to underserved areas; yet, there is little guidance on how to train LHEs to implement these programs, particularly in the crucial area of empirically validated obesity interventions. This article describes experiences in recruiting, training, and retaining 20 LHEs who delivered a 12-month evidence-based behavioral lifestyle intervention (based on the Diabetes Prevention Program) in senior centers across a rural state. A mixed method approach was used which incorporated collecting the folllowing: quantitative data on sociodemographic characteristics of LHEs; process data related to training, recruitment, intervention implementation, and retention of LHEs; and a quantitative program evaluation questionnaire, which was supplemented by a qualitative program evaluation questionnaire. Descriptive statistics were calculated for quantitative data, and qualitative data were analyzed using content analysis. The training program was well received, and the LHEs effectively recruited participants and implemented the lifestyle intervention in senior centers following a structured protocol. The methods used in this study produced excellent long-term retention of LHEs and good adherence to intervention protocol, and as such may provide a model that could be effective for others seeking to implement LHE-delivered health promotion programs.

Real-time quantitative PCR of Staphylococcus aureus and application in restaurant meals.

PubMed

Berrada, H; Soriano, J M; Mañes, J; Picó, Y

2006-01-01

Staphylococcus aureus is considered the second most common pathogen to cause outbreaks of food poisoning, exceeded only by Campylobacter. Consumption of foods containing this microorganism is often identified as the cause of illness. In this study, a rapid, reliable, and sensitive real-time quantitative PCR was developed and compared with conventional culture methods. Real-time quantitative PCR was carried out by purifying DNA extracts of S. aureus with a Staphylococcus sample preparation kit and quantifying it in the LightCycler system with hybridization probes. The assay was linear from a range of 10 to 10(6) S. aureus cells (r2 > 0.997). The PCR reaction presented an efficiency of >85%. Accuracy of the PCR-based assay, expressed as percent bias, was around 13%, and the precision, expressed as a percentage of the coefficient of variation, was 7 to 10%. Intraday and interday variability were studied at 10(2) CFU/g and was 12 and 14%, respectively. The proposed method was applied to the analysis of 77 samples of restaurant meals in Valencia (Spain). In 11.6% of samples S. aureus was detected by real-time quantitative PCR, as well as by the conventional microbiological method. An excellent correspondence between real-time quantitative PCR and microbiological numbers (CFU/g) was observed with deviations of < 28%.

Three-dimensional label-free imaging and quantification of lipid droplets in live hepatocytes

NASA Astrophysics Data System (ADS)

Kim, Kyoohyun; Lee, Seoeun; Yoon, Jonghee; Heo, Jihan; Choi, Chulhee; Park, Yongkeun

2016-11-01

Lipid droplets (LDs) are subcellular organelles with important roles in lipid storage and metabolism and involved in various diseases including cancer, obesity, and diabetes. Conventional methods, however, have limited ability to provide quantitative information on individual LDs and have limited capability for three-dimensional (3-D) imaging of LDs in live cells especially for fast acquisition of 3-D dynamics. Here, we present an optical method based on 3-D quantitative phase imaging to measure the 3-D structural distribution and biochemical parameters (concentration and dry mass) of individual LDs in live cells without using exogenous labelling agents. The biochemical change of LDs under oleic acid treatment was quantitatively investigated, and 4-D tracking of the fast dynamics of LDs revealed the intracellular transport of LDs in live cells.

A sampling framework for incorporating quantitative mass spectrometry data in protein interaction analysis.

PubMed

Tucker, George; Loh, Po-Ru; Berger, Bonnie

2013-10-04

Comprehensive protein-protein interaction (PPI) maps are a powerful resource for uncovering the molecular basis of genetic interactions and providing mechanistic insights. Over the past decade, high-throughput experimental techniques have been developed to generate PPI maps at proteome scale, first using yeast two-hybrid approaches and more recently via affinity purification combined with mass spectrometry (AP-MS). Unfortunately, data from both protocols are prone to both high false positive and false negative rates. To address these issues, many methods have been developed to post-process raw PPI data. However, with few exceptions, these methods only analyze binary experimental data (in which each potential interaction tested is deemed either observed or unobserved), neglecting quantitative information available from AP-MS such as spectral counts. We propose a novel method for incorporating quantitative information from AP-MS data into existing PPI inference methods that analyze binary interaction data. Our approach introduces a probabilistic framework that models the statistical noise inherent in observations of co-purifications. Using a sampling-based approach, we model the uncertainty of interactions with low spectral counts by generating an ensemble of possible alternative experimental outcomes. We then apply the existing method of choice to each alternative outcome and aggregate results over the ensemble. We validate our approach on three recent AP-MS data sets and demonstrate performance comparable to or better than state-of-the-art methods. Additionally, we provide an in-depth discussion comparing the theoretical bases of existing approaches and identify common aspects that may be key to their performance. Our sampling framework extends the existing body of work on PPI analysis using binary interaction data to apply to the richer quantitative data now commonly available through AP-MS assays. This framework is quite general, and many enhancements are likely possible. Fruitful future directions may include investigating more sophisticated schemes for converting spectral counts to probabilities and applying the framework to direct protein complex prediction methods.

*A FASTER METHOD OF MEASURING RECREATIONAL WATER QUALITY FOR BETTER PROTECTION OF SWIMMER'S HEALTH

EPA Science Inventory

We previously reported that a faster method (< 2 hours) of measuring fecal indicator bacteria (FIB), based on Quantitative Polymerase Chain Reaction (QPCR), was predictive of swimming associated gastrointestinal illness. Using data from two additional beaches, we examined the re...

Separation and reconstruction of BCG and EEG signals during continuous EEG and fMRI recordings

PubMed Central

Xia, Hongjing; Ruan, Dan; Cohen, Mark S.

2014-01-01

Despite considerable effort to remove it, the ballistocardiogram (BCG) remains a major artifact in electroencephalographic data (EEG) acquired inside magnetic resonance imaging (MRI) scanners, particularly in continuous (as opposed to event-related) recordings. In this study, we have developed a new Direct Recording Prior Encoding (DRPE) method to extract and separate the BCG and EEG components from contaminated signals, and have demonstrated its performance by comparing it quantitatively to the popular Optimal Basis Set (OBS) method. Our modified recording configuration allows us to obtain representative bases of the BCG- and EEG-only signals. Further, we have developed an optimization-based reconstruction approach to maximally incorporate prior knowledge of the BCG/EEG subspaces, and of the signal characteristics within them. Both OBS and DRPE methods were tested with experimental data, and compared quantitatively using cross-validation. In the challenging continuous EEG studies, DRPE outperforms the OBS method by nearly sevenfold in separating the continuous BCG and EEG signals. PMID:25002836

Portable and sensitive quantitative detection of DNA based on personal glucose meters and isothermal circular strand-displacement polymerization reaction.

PubMed

Xu, Xue-tao; Liang, Kai-yi; Zeng, Jia-ying

2015-02-15

A portable and sensitive quantitative DNA detection method based on personal glucose meters and isothermal circular strand-displacement polymerization reaction was developed. The target DNA triggered target recycling process, which opened capture DNA. The released target then found another capture DNA to trigger another polymerization cycle, which was repeated for many rounds, resulting in the multiplication of the DNA-invertase conjugation on the surface of Streptavidin-MNBs. The DNA-invertase was used to catalyze the hydrolysis of sucrose into glucose for PGM readout. There was a liner relationship between the signal of PGM and the concentration of target DNA in the range of 5.0 to 1000 fM, which is lower than some DNA detection method. In addition, the method exhibited excellent sequence selectivity and there was almost no effect of biological complex to the detection performance, which suggested our method can be successfully applied to DNA detection in real biological samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Computational method for multi-modal microscopy based on transport of intensity equation

NASA Astrophysics Data System (ADS)

Li, Jiaji; Chen, Qian; Sun, Jiasong; Zhang, Jialin; Zuo, Chao

2017-02-01

In this paper, we develop the requisite theory to describe a hybrid virtual-physical multi-modal imaging system which yields quantitative phase, Zernike phase contrast, differential interference contrast (DIC), and light field moment imaging simultaneously based on transport of intensity equation(TIE). We then give the experimental demonstration of these ideas by time-lapse imaging of live HeLa cell mitosis. Experimental results verify that a tunable lens based TIE system, combined with the appropriate post-processing algorithm, can achieve a variety of promising imaging modalities in parallel with the quantitative phase images for the dynamic study of cellular processes.

Qualitative and Quantitative Detection of Botulinum Neurotoxins from Complex Matrices: Results of the First International Proficiency Test

PubMed Central

Worbs, Sylvia; Fiebig, Uwe; Zeleny, Reinhard; Schimmel, Heinz; Rummel, Andreas; Luginbühl, Werner; Dorner, Brigitte G.

2015-01-01

In the framework of the EU project EQuATox, a first international proficiency test (PT) on the detection and quantification of botulinum neurotoxins (BoNT) was conducted. Sample materials included BoNT serotypes A, B and E spiked into buffer, milk, meat extract and serum. Different methods were applied by the participants combining different principles of detection, identification and quantification. Based on qualitative assays, 95% of all results reported were correct. Successful strategies for BoNT detection were based on a combination of complementary immunological, MS-based and functional methods or on suitable functional in vivo/in vitro approaches (mouse bioassay, hemidiaphragm assay and Endopep-MS assay). Quantification of BoNT/A, BoNT/B and BoNT/E was performed by 48% of participating laboratories. It turned out that precise quantification of BoNT was difficult, resulting in a substantial scatter of quantitative data. This was especially true for results obtained by the mouse bioassay which is currently considered as “gold standard” for BoNT detection. The results clearly demonstrate the urgent need for certified BoNT reference materials and the development of methods replacing animal testing. In this context, the BoNT PT provided the valuable information that both the Endopep-MS assay and the hemidiaphragm assay delivered quantitative results superior to the mouse bioassay. PMID:26703724

Kernel-based whole-genome prediction of complex traits: a review.

PubMed

Morota, Gota; Gianola, Daniel

2014-01-01

Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright's models to confront new challenges. In particular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways), thus generating interactions. Motivated by this view, a growing number of statistical approaches based on kernels attempt to capture non-additive effects, either parametrically or non-parametrically. This review centers on whole-genome regression using kernel methods applied to a wide range of quantitative traits of agricultural importance in animals and plants. We discuss various kernel-based approaches tailored to capturing total genetic variation, with the aim of arriving at an enhanced predictive performance in the light of available genome annotation information. Connections between prediction machines born in animal breeding, statistics, and machine learning are revisited, and their empirical prediction performance is discussed. Overall, while some encouraging results have been obtained with non-parametric kernels, recovering non-additive genetic variation in a validation dataset remains a challenge in quantitative genetics.

Analysis of Biomass Sugars Using a Novel HPLC Method

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

Agblevor, F. A.; Hames, B. R.; Schell, D.

The precise quantitative analysis of biomass sugars is a very important step in the conversion of biomass feedstocks to fuels and chemicals. However, the most accurate method of biomass sugar analysis is based on the gas chromatography analysis of derivatized sugars either as alditol acetates or trimethylsilanes. The derivatization method is time consuming but the alternative high-performance liquid chromatography (HPLC) method cannot resolve most sugars found in biomass hydrolysates. We have demonstrated for the first time that by careful manipulation of the HPLC mobile phase, biomass monomeric sugars (arabinose, xylose, fructose, glucose, mannose, and galactose) can be analyzed quantitatively andmore » there is excellent baseline resolution of all the sugars. This method was demonstrated for standard sugars, pretreated corn stover liquid and solid fractions. Our method can also be used to analyze dimeric sugars (cellobiose and sucrose).« less

Provider imposed restrictions to clients’ access to family planning in urban Uttar Pradesh, India: a mixed methods study

PubMed Central

2013-01-01

Background Medical barriers refer to unnecessary policies or procedures imposed by health care providers that are not necessarily medically advised; these restrictions impede clients’ access to family planning (FP). This mixed methods study investigates provider imposed barriers to provision of FP using recent quantitative and qualitative data from urban Uttar Pradesh, India. Methods Baseline quantitative data were collected in six cities in Uttar Pradesh, India from service delivery points (SDP), using facility audits, exit interviews, and provider surveys; for this study, the focus is on the provider surveys. More than 250 providers were surveyed in each city. Providers were asked about the FP methods they provide, and if they restrict clients’ access to each method based on age, parity, partner consent, or marital status. For the qualitative research, we conducted one-on-one interviews with 21 service providers in four of the six cities in Uttar Pradesh. Each interview lasted approximately 45 minutes. Results The quantitative findings show that providers restrict clients’ access to spacing and long-acting and permanent methods of FP based on age, parity, partner consent and marital status. Qualitative findings reinforce that providers, at times, make judgments about their clients’ education, FP needs and ability to understand FP options thereby imposing unnecessary barriers to FP methods. Conclusions Provider restrictions on FP methods are common in these urban Uttar Pradesh sites. This means that women who are young, unmarried, have few or no children, do not have the support of their partner, or are less educated may not be able to access or use FP or their preferred method. These findings highlight the need for in-service training for staff, with a focus on reviewing current guidelines and eligibility criteria for provision of methods. PMID:24365015

Quantitative analysis of crystalline pharmaceuticals in powders and tablets by a pattern-fitting procedure using X-ray powder diffraction data.

PubMed

Yamamura, S; Momose, Y

2001-01-16

A pattern-fitting procedure for quantitative analysis of crystalline pharmaceuticals in solid dosage forms using X-ray powder diffraction data is described. This method is based on a procedure for pattern-fitting in crystal structure refinement, and observed X-ray scattering intensities were fitted to analytical expressions including some fitting parameters, i.e. scale factor, peak positions, peak widths and degree of preferred orientation of the crystallites. All fitting parameters were optimized by the non-linear least-squares procedure. Then the weight fraction of each component was determined from the optimized scale factors. In the present study, well-crystallized binary systems, zinc oxide-zinc sulfide (ZnO-ZnS) and salicylic acid-benzoic acid (SA-BA), were used as the samples. In analysis of the ZnO-ZnS system, the weight fraction of ZnO or ZnS could be determined quantitatively in the range of 5-95% in the case of both powders and tablets. In analysis of the SA-BA systems, the weight fraction of SA or BA could be determined quantitatively in the range of 20-80% in the case of both powders and tablets. Quantitative analysis applying this pattern-fitting procedure showed better reproducibility than other X-ray methods based on the linear or integral intensities of particular diffraction peaks. Analysis using this pattern-fitting procedure also has the advantage that the preferred orientation of the crystallites in solid dosage forms can be also determined in the course of quantitative analysis.

Photon-counting-based diffraction phase microscopy combined with single-pixel imaging

NASA Astrophysics Data System (ADS)

Shibuya, Kyuki; Araki, Hiroyuki; Iwata, Tetsuo

2018-04-01

We propose a photon-counting (PC)-based quantitative-phase imaging (QPI) method for use in diffraction phase microscopy (DPM) that is combined with a single-pixel imaging (SPI) scheme (PC-SPI-DPM). This combination of DPM with the SPI scheme overcomes a low optical throughput problem that has occasionally prevented us from obtaining quantitative-phase images in DPM through use of a high-sensitivity single-channel photodetector such as a photomultiplier tube (PMT). The introduction of a PMT allowed us to perform PC with ease and thus solved a dynamic range problem that was inherent to SPI. As a proof-of-principle experiment, we performed a comparison study of analogue-based SPI-DPM and PC-SPI-DPM for a 125-nm-thick indium tin oxide (ITO) layer coated on a silica glass substrate. We discuss the basic performance of the method and potential future modifications of the proposed system.

Development of a Moodle Course for Schoolchildren's Table Tennis Learning Based on Competence Motivation Theory: Its Effectiveness in Comparison to Traditional Training Method

ERIC Educational Resources Information Center

Zou, Junhua; Liu, Qingtang; Yang, Zongkai

2012-01-01

Based on Competence Motivation Theory (CMT), a Moodle course for schoolchildren's table tennis learning was developed (The URL is http://www.bssepp.com, and this course allows guest access). The effects of the course on students' knowledge, perceived competence and interest were evaluated through quantitative methods. The sample of the study…

Fuzzy pulmonary vessel segmentation in contrast enhanced CT data

NASA Astrophysics Data System (ADS)

Kaftan, Jens N.; Kiraly, Atilla P.; Bakai, Annemarie; Das, Marco; Novak, Carol L.; Aach, Til

2008-03-01

Pulmonary vascular tree segmentation has numerous applications in medical imaging and computer-aided diagnosis (CAD), including detection and visualization of pulmonary emboli (PE), improved lung nodule detection, and quantitative vessel analysis. We present a novel approach to pulmonary vessel segmentation based on a fuzzy segmentation concept, combining the strengths of both threshold and seed point based methods. The lungs of the original image are first segmented and a threshold-based approach identifies core vessel components with a high specificity. These components are then used to automatically identify reliable seed points for a fuzzy seed point based segmentation method, namely fuzzy connectedness. The output of the method consists of the probability of each voxel belonging to the vascular tree. Hence, our method provides the possibility to adjust the sensitivity/specificity of the segmentation result a posteriori according to application-specific requirements, through definition of a minimum vessel-probability required to classify a voxel as belonging to the vascular tree. The method has been evaluated on contrast-enhanced thoracic CT scans from clinical PE cases and demonstrates overall promising results. For quantitative validation we compare the segmentation results to randomly selected, semi-automatically segmented sub-volumes and present the resulting receiver operating characteristic (ROC) curves. Although we focus on contrast enhanced chest CT data, the method can be generalized to other regions of the body as well as to different imaging modalities.

Modeling of Continuum Manipulators Using Pythagorean Hodograph Curves.

PubMed

Singh, Inderjeet; Amara, Yacine; Melingui, Achille; Mani Pathak, Pushparaj; Merzouki, Rochdi

2018-05-10

Research on continuum manipulators is increasingly developing in the context of bionic robotics because of their many advantages over conventional rigid manipulators. Due to their soft structure, they have inherent flexibility, which makes it a huge challenge to control them with high performances. Before elaborating a control strategy of such robots, it is essential to reconstruct first the behavior of the robot through development of an approximate behavioral model. This can be kinematic or dynamic depending on the conditions of operation of the robot itself. Kinematically, two types of modeling methods exist to describe the robot behavior; quantitative methods describe a model-based method, and qualitative methods describe a learning-based method. In kinematic modeling of continuum manipulator, the assumption of constant curvature is often considered to simplify the model formulation. In this work, a quantitative modeling method is proposed, based on the Pythagorean hodograph (PH) curves. The aim is to obtain a three-dimensional reconstruction of the shape of the continuum manipulator with variable curvature, allowing the calculation of its inverse kinematic model (IKM). It is noticed that the performances of the PH-based kinematic modeling of continuum manipulators are considerable regarding position accuracy, shape reconstruction, and time/cost of the model calculation, than other kinematic modeling methods, for two cases: free load manipulation and variable load manipulation. This modeling method is applied to the compact bionic handling assistant (CBHA) manipulator for validation. The results are compared with other IKMs developed in case of CBHA manipulator.

Development of the local magnification method for quantitative evaluation of endoscope geometric distortion

NASA Astrophysics Data System (ADS)

Wang, Quanzeng; Cheng, Wei-Chung; Suresh, Nitin; Hua, Hong

2016-05-01

With improved diagnostic capabilities and complex optical designs, endoscopic technologies are advancing. As one of the several important optical performance characteristics, geometric distortion can negatively affect size estimation and feature identification related diagnosis. Therefore, a quantitative and simple distortion evaluation method is imperative for both the endoscopic industry and the medical device regulatory agent. However, no such method is available yet. While the image correction techniques are rather mature, they heavily depend on computational power to process multidimensional image data based on complex mathematical model, i.e., difficult to understand. Some commonly used distortion evaluation methods, such as the picture height distortion (DPH) or radial distortion (DRAD), are either too simple to accurately describe the distortion or subject to the error of deriving a reference image. We developed the basic local magnification (ML) method to evaluate endoscope distortion. Based on the method, we also developed ways to calculate DPH and DRAD. The method overcomes the aforementioned limitations, has clear physical meaning in the whole field of view, and can facilitate lesion size estimation during diagnosis. Most importantly, the method can facilitate endoscopic technology to market and potentially be adopted in an international endoscope standard.

A statistical framework for protein quantitation in bottom-up MS-based proteomics

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

Karpievitch, Yuliya; Stanley, Jeffrey R.; Taverner, Thomas

2009-08-15

ABSTRACT Motivation: Quantitative mass spectrometry-based proteomics requires protein-level estimates and confidence measures. Challenges include the presence of low-quality or incorrectly identified peptides and widespread, informative, missing data. Furthermore, models are required for rolling peptide-level information up to the protein level. Results: We present a statistical model for protein abundance in terms of peptide peak intensities, applicable to both label-based and label-free quantitation experiments. The model allows for both random and censoring missingness mechanisms and provides naturally for protein-level estimates and confidence measures. The model is also used to derive automated filtering and imputation routines. Three LC-MS datasets are used tomore » illustrate the methods. Availability: The software has been made available in the open-source proteomics platform DAnTE (Polpitiya et al. (2008)) (http://omics.pnl.gov/software/). Contact: adabney@stat.tamu.edu« less

Portable smartphone based quantitative phase microscope

NASA Astrophysics Data System (ADS)

Meng, Xin; Tian, Xiaolin; Yu, Wei; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Liu, Cheng; Wang, Shouyu

2018-01-01

To realize portable device with high contrast imaging capability, we designed a quantitative phase microscope using transport of intensity equation method based on a smartphone. The whole system employs an objective and an eyepiece as imaging system and a cost-effective LED as illumination source. A 3-D printed cradle is used to align these components. Images of different focal planes are captured by manual focusing, followed by calculation of sample phase via a self-developed Android application. To validate its accuracy, we first tested the device by measuring a random phase plate with known phases, and then red blood cell smear, Pap smear, broad bean epidermis sections and monocot root were also measured to show its performance. Owing to its advantages as accuracy, high-contrast, cost-effective and portability, the portable smartphone based quantitative phase microscope is a promising tool which can be future adopted in remote healthcare and medical diagnosis.

Nonlocal means-based speckle filtering for ultrasound images

PubMed Central

Coupé, Pierrick; Hellier, Pierre; Kervrann, Charles; Barillot, Christian

2009-01-01

In image processing, restoration is expected to improve the qualitative inspection of the image and the performance of quantitative image analysis techniques. In this paper, an adaptation of the Non Local (NL-) means filter is proposed for speckle reduction in ultrasound (US) images. Originally developed for additive white Gaussian noise, we propose to use a Bayesian framework to derive a NL-means filter adapted to a relevant ultrasound noise model. Quantitative results on synthetic data show the performances of the proposed method compared to well-established and state-of-the-art methods. Results on real images demonstrate that the proposed method is able to preserve accurately edges and structural details of the image. PMID:19482578

Simultaneous extraction and quantitation of several bioactive amines in cheese and chocolate.

PubMed

Baker, G B; Wong, J T; Coutts, R T; Pasutto, F M

1987-04-17

A method is described for simultaneous extraction and quantitation of the amines 2-phenylethylamine, tele-methylhistamine, histamine, tryptamine, m- and p-tyramine, 3-methoxytyramine, 5-hydroxytryptamine, cadaverine, putrescine, spermidine and spermine. This method is based on extractive derivatization of the amines with a perfluoroacylating agent, pentafluorobenzoyl chloride, under basic aqueous conditions. Analysis was done on a gas chromatograph equipped with an electron-capture detector and a capillary column system. The procedure is relatively rapid and provides derivatives with good chromatographic properties. Its application to analysis of the above amines in cheese and chocolate products is described.

QUANTITATIVE RADIO-CHEMICAL ANALYSIS-SOLVENT EXTRACTION OF MOLYBDENUM-99

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

Wish, L.

1961-09-12

A method was developed for the rapid quantitative separation of Mo/sup 99/ from fission product mixtures. It is based on the extraction of Mo into a solution of alpha -benzoin oxime in chloroform. The main contaminants are Zr, Nb, and 1. The first two are eliminated by couple with fluoride and the third by volatilization or solvent extraction. About 5% of the Te/sup 99/ daughter is extracted with its parent, and it is necessary to wait 48 hrs for equilibrium of fission product mixtures by this method and a standard radiochemical gravimetric procedure showed agreement within 1 to 2%. (auth)

Investigation of β-lactam antibacterial drugs, β-lactamases, and penicillin-binding proteins with fluorescence polarization and anisotropy: a review

NASA Astrophysics Data System (ADS)

Shapiro, Adam B.

2016-06-01

This review covers the uses of fluorescence polarization and anisotropy for the investigation of bacterial penicillin binding proteins (PBPs), which are the targets of β-lactam antibacterial drugs (penicillins, cephalosporins, carbapenems, and monobactams), and of the β-lactamase enzymes that destroy these drugs and help to render bacterial pathogens resistant to them. Fluorescence polarization and anisotropy-based methods for quantitation of β-lactam drugs are also reviewed. A particular emphasis is on methods for quantitative measurement of the interactions of β-lactams and other inhibitors with PBPs and β-lactamases.

HPLC method for determination of SN-38 content and SN-38 entrapment efficiency in a novel liposome-based formulation, LE-SN38.

PubMed

Xuan, Tong; Zhang, J Allen; Ahmad, Imran

2006-05-03

A simple HPLC method was developed for quantification of SN-38, 7-ethyl-10-hydroxycamptothecin, in a novel liposome-based formulation (LE-SN38). The chromatographic separation was achieved on an Agilent Zorbax SB-C18 (4.6 mmx250 mm, 5 microm) analytical column using a mobile phase consisting of a mixture of NaH2PO4 (pH 3.1, 25 mM) and acetonitrile (50:50, v/v). SN-38 was detected at UV wavelength of 265 nm and quantitatively determined using an external calibration method. The limit of detection (LOD) and limit of quantitation (LOQ) were found to be 0.05 and 0.25 microg/mL, respectively. The individual spike recovery of SN-38 ranged from 100 to 101%. The percent of relative standard deviation (%R.S.D.) of intra-day and inter-day analyses were less than 1.6%. The method validation results confirmed that the method is specific, linear, accurate, precise, robust and sensitive for its intended use. The current method was successfully applied to the determination of SN-38 content and drug entrapment efficiency in liposome-based formulation, LE-SN38 during early stage formulation development.

[A new method of processing quantitative PCR data].

PubMed

Ke, Bing-Shen; Li, Guang-Yun; Chen, Shi-Min; Huang, Xiang-Yan; Chen, Ying-Jian; Xu, Jun

2003-05-01

Today standard PCR can't satisfy the need of biotechnique development and clinical research any more. After numerous dynamic research, PE company found there is a linear relation between initial template number and cycling time when the accumulating fluorescent product is detectable.Therefore,they developed a quantitative PCR technique to be used in PE7700 and PE5700. But the error of this technique is too great to satisfy the need of biotechnique development and clinical research. A better quantitative PCR technique is needed. The mathematical model submitted here is combined with the achievement of relative science,and based on the PCR principle and careful analysis of molecular relationship of main members in PCR reaction system. This model describes the function relation between product quantity or fluorescence intensity and initial template number and other reaction conditions, and can reflect the accumulating rule of PCR product molecule accurately. Accurate quantitative PCR analysis can be made use this function relation. Accumulated PCR product quantity can be obtained from initial template number. Using this model to do quantitative PCR analysis,result error is only related to the accuracy of fluorescence intensity or the instrument used. For an example, when the fluorescence intensity is accurate to 6 digits and the template size is between 100 to 1,000,000, the quantitative result accuracy will be more than 99%. The difference of result error is distinct using same condition,same instrument but different analysis method. Moreover,if the PCR quantitative analysis system is used to process data, it will get result 80 times of accuracy than using CT method.

Validation of Greyscale-Based Quantitative Ultrasound in Manual Wheelchair Users

PubMed Central

Collinger, Jennifer L.; Fullerton, Bradley; Impink, Bradley G.; Koontz, Alicia M.; Boninger, Michael L.

2010-01-01

Objective The primary aim of this study is to establish the validity of greyscale-based quantitative ultrasound (QUS) measures of the biceps and supraspinatus tendons. Design Nine QUS measures of the biceps and supraspinatus tendons were computed from ultrasound images collected from sixty-seven manual wheelchair users. Shoulder pathology was measured using questionnaires, physical examination maneuvers, and a clinical ultrasound grading scale. Results Increased age, duration of wheelchair use, and body mass correlated with a darker, more homogenous tendon appearance. Subjects with pain during physical examination tests for biceps tenderness and acromioclavicular joint tenderness exhibited significantly different supraspinatus QUS values. Even when controlling for tendon depth, QUS measures of the biceps tendon differed significantly between subjects with healthy tendons, mild tendinosis, and severe tendinosis. Clinical grading of supraspinatus tendon health was correlated with QUS measures of the supraspinatus tendon. Conclusions Quantitative ultrasound is valid method to quantify tendinopathy and may allow for early detection of tendinosis. Manual wheelchair users are at a high risk for developing shoulder tendon pathology and may benefit from quantitative ultrasound-based research that focuses on identifying interventions designed to reduce this risk. PMID:20407304

Combining Phage and Yeast Cell Surface Antibody Display to Identify Novel Cell Type-Selective Internalizing Human Monoclonal Antibodies.

PubMed

Bidlingmaier, Scott; Su, Yang; Liu, Bin

2015-01-01

Using phage antibody display, large libraries can be generated and screened to identify monoclonal antibodies with affinity for target antigens. However, while library size and diversity is an advantage of the phage display method, there is limited ability to quantitatively enrich for specific binding properties such as affinity. One way of overcoming this limitation is to combine the scale of phage display selections with the flexibility and quantitativeness of FACS-based yeast surface display selections. In this chapter we describe protocols for generating yeast surface antibody display libraries using phage antibody display selection outputs as starting material and FACS-based enrichment of target antigen-binding clones from these libraries. These methods should be widely applicable for the identification of monoclonal antibodies with specific binding properties.

Sub-aperture switching based ptychographic iterative engine (sasPIE) method for quantitative imaging

NASA Astrophysics Data System (ADS)

Sun, Aihui; Kong, Yan; Jiang, Zhilong; Yu, Wei; Liu, Fei; Xue, Liang; Wang, Shouyu; Liu, Cheng

2018-03-01

Though ptychographic iterative engine (PIE) has been widely adopted in the quantitative micro-imaging with various illuminations as visible light, X-ray and electron beam, the mechanical inaccuracy in the raster scanning of the sample relative to the illumination always degrades the reconstruction quality seriously and makes the resolution reached much lower than that determined by the numerical aperture of the optical system. To overcome this disadvantage, the sub-aperture switching based PIE method is proposed: the mechanical scanning in the common PIE is replaced by the sub-aperture switching, and the reconstruction error related to the positioning inaccuracy is completely avoided. The proposed technique remarkably improves the reconstruction quality, reduces the complexity of the experimental setup and fundamentally accelerates the data acquisition and reconstruction.

Methods for assessing geodiversity

NASA Astrophysics Data System (ADS)

Zwoliński, Zbigniew; Najwer, Alicja; Giardino, Marco

2017-04-01

The accepted systematics of geodiversity assessment methods will be presented in three categories: qualitative, quantitative and qualitative-quantitative. Qualitative methods are usually descriptive methods that are suited to nominal and ordinal data. Quantitative methods use a different set of parameters and indicators to determine the characteristics of geodiversity in the area being researched. Qualitative-quantitative methods are a good combination of the collection of quantitative data (i.e. digital) and cause-effect data (i.e. relational and explanatory). It seems that at the current stage of the development of geodiversity research methods, qualitative-quantitative methods are the most advanced and best assess the geodiversity of the study area. Their particular advantage is the integration of data from different sources and with different substantive content. Among the distinguishing features of the quantitative and qualitative-quantitative methods for assessing geodiversity are their wide use within geographic information systems, both at the stage of data collection and data integration, as well as numerical processing and their presentation. The unresolved problem for these methods, however, is the possibility of their validation. It seems that currently the best method of validation is direct filed confrontation. Looking to the next few years, the development of qualitative-quantitative methods connected with cognitive issues should be expected, oriented towards ontology and the Semantic Web.

PCA-based groupwise image registration for quantitative MRI.

PubMed

Huizinga, W; Poot, D H J; Guyader, J-M; Klaassen, R; Coolen, B F; van Kranenburg, M; van Geuns, R J M; Uitterdijk, A; Polfliet, M; Vandemeulebroucke, J; Leemans, A; Niessen, W J; Klein, S

2016-04-01

Quantitative magnetic resonance imaging (qMRI) is a technique for estimating quantitative tissue properties, such as the T1 and T2 relaxation times, apparent diffusion coefficient (ADC), and various perfusion measures. This estimation is achieved by acquiring multiple images with different acquisition parameters (or at multiple time points after injection of a contrast agent) and by fitting a qMRI signal model to the image intensities. Image registration is often necessary to compensate for misalignments due to subject motion and/or geometric distortions caused by the acquisition. However, large differences in image appearance make accurate image registration challenging. In this work, we propose a groupwise image registration method for compensating misalignment in qMRI. The groupwise formulation of the method eliminates the requirement of choosing a reference image, thus avoiding a registration bias. The method minimizes a cost function that is based on principal component analysis (PCA), exploiting the fact that intensity changes in qMRI can be described by a low-dimensional signal model, but not requiring knowledge on the specific acquisition model. The method was evaluated on 4D CT data of the lungs, and both real and synthetic images of five different qMRI applications: T1 mapping in a porcine heart, combined T1 and T2 mapping in carotid arteries, ADC mapping in the abdomen, diffusion tensor mapping in the brain, and dynamic contrast-enhanced mapping in the abdomen. Each application is based on a different acquisition model. The method is compared to a mutual information-based pairwise registration method and four other state-of-the-art groupwise registration methods. Registration accuracy is evaluated in terms of the precision of the estimated qMRI parameters, overlap of segmented structures, distance between corresponding landmarks, and smoothness of the deformation. In all qMRI applications the proposed method performed better than or equally well as competing methods, while avoiding the need to choose a reference image. It is also shown that the results of the conventional pairwise approach do depend on the choice of this reference image. We therefore conclude that our groupwise registration method with a similarity measure based on PCA is the preferred technique for compensating misalignments in qMRI. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of vulnerability curves to typhoon hazards based on insurance policy and claim dataset

NASA Astrophysics Data System (ADS)

Mo, Wanmei; Fang, Weihua; li, Xinze; Wu, Peng; Tong, Xingwei

2016-04-01

Vulnerability refers to the characteristics and circumstances of an exposure that make it vulnerable to the effects of some certain hazards. It can be divided into physical vulnerability, social vulnerability, economic vulnerabilities and environmental vulnerability. Physical vulnerability indicates the potential physical damage of exposure caused by natural hazards. Vulnerability curves, quantifying the loss ratio against hazard intensity with a horizontal axis for the intensity and a vertical axis for the Mean Damage Ratio (MDR), is essential to the vulnerability assessment and quantitative evaluation of disasters. Fragility refers to the probability of diverse damage states under different hazard intensity, revealing a kind of characteristic of the exposure. Fragility curves are often used to quantify the probability of a given set of exposure at or exceeding a certain damage state. The development of quantitative fragility and vulnerability curves is the basis of catastrophe modeling. Generally, methods for quantitative fragility and vulnerability assessment can be categorized into empirical, analytical and expert opinion or judgment-based ones. Empirical method is one of the most popular methods and it relies heavily on the availability and quality of historical hazard and loss dataset, which has always been a great challenge. Analytical method is usually based on the engineering experiments and it is time-consuming and lacks built-in validation, so its credibility is also sometimes criticized widely. Expert opinion or judgment-based method is quite effective in the absence of data but the results could be too subjective so that the uncertainty is likely to be underestimated. In this study, we will present the fragility and vulnerability curves developed with empirical method based on simulated historical typhoon wind, rainfall and induced flood, and insurance policy and claim datasets of more than 100 historical typhoon events. Firstly, an insurance exposure classification system is built according to structure type, occupation type and insurance coverage. Then MDR estimation method based on considering insurance policy structure and claim information is proposed and validated. Following that, fragility and vulnerability curves of the major exposure types for construction, homeowner insurance and enterprise property insurance are fitted with empirical function based on the historical dataset. The results of this study can not only help understand catastrophe risk and mange insured disaster risks, but can also be applied in other disaster risk reduction efforts.

Synthesising quantitative and qualitative research in evidence‐based patient information

PubMed Central

Goldsmith, Megan R; Bankhead, Clare R; Austoker, Joan

2007-01-01

Background Systematic reviews have, in the past, focused on quantitative studies and clinical effectiveness, while excluding qualitative evidence. Qualitative research can inform evidence‐based practice independently of other research methodologies but methods for the synthesis of such data are currently evolving. Synthesising quantitative and qualitative research in a single review is an important methodological challenge. Aims This paper describes the review methods developed and the difficulties encountered during the process of updating a systematic review of evidence to inform guidelines for the content of patient information related to cervical screening. Methods Systematic searches of 12 electronic databases (January 1996 to July 2004) were conducted. Studies that evaluated the content of information provided to women about cervical screening or that addressed women's information needs were assessed for inclusion. A data extraction form and quality assessment criteria were developed from published resources. A non‐quantitative synthesis was conducted and a tabular evidence profile for each important outcome (eg “explain what the test involves”) was prepared. The overall quality of evidence for each outcome was then assessed using an approach published by the GRADE working group, which was adapted to suit the review questions and modified to include qualitative research evidence. Quantitative and qualitative studies were considered separately for every outcome. Results 32 papers were included in the systematic review following data extraction and assessment of methodological quality. The review questions were best answered by evidence from a range of data sources. The inclusion of qualitative research, which was often highly relevant and specific to many components of the screening information materials, enabled the production of a set of recommendations that will directly affect policy within the NHS Cervical Screening Programme. Conclusions A practical example is provided of how quantitative and qualitative data sources might successfully be brought together and considered in one review. PMID:17325406

On iterative algorithms for quantitative photoacoustic tomography in the radiative transport regime

NASA Astrophysics Data System (ADS)

Wang, Chao; Zhou, Tie

2017-11-01

In this paper, we present a numerical reconstruction method for quantitative photoacoustic tomography (QPAT), based on the radiative transfer equation (RTE), which models light propagation more accurately than diffusion approximation (DA). We investigate the reconstruction of absorption coefficient and scattering coefficient of biological tissues. An improved fixed-point iterative method to retrieve the absorption coefficient, given the scattering coefficient, is proposed for its cheap computational cost; the convergence of this method is also proved. The Barzilai-Borwein (BB) method is applied to retrieve two coefficients simultaneously. Since the reconstruction of optical coefficients involves the solutions of original and adjoint RTEs in the framework of optimization, an efficient solver with high accuracy is developed from Gao and Zhao (2009 Transp. Theory Stat. Phys. 38 149-92). Simulation experiments illustrate that the improved fixed-point iterative method and the BB method are competitive methods for QPAT in the relevant cases.

Isoperms: An Environmental Management Tool.

ERIC Educational Resources Information Center

Sebera, Donald K.

A quantitative tool, the isoperm method, is described; it quantifies the effect of environmental factors of temperature (T) and percent relative humidity (%RH) on the anticipated useful life expectancy of paper-based collections. The isoperm method provides answers to questions of the expected lifetime of the collection under various temperature…

The Analysis of Seawater: A Laboratory-Centered Learning Project in General Chemistry.

ERIC Educational Resources Information Center

Selco, Jodye I.; Roberts, Julian L., Jr.; Wacks, Daniel B.

2003-01-01

Describes a sea-water analysis project that introduces qualitative and quantitative analysis methods and laboratory methods such as gravimetric analysis, potentiometric titration, ion-selective electrodes, and the use of calibration curves. Uses a problem-based cooperative teaching approach. (Contains 24 references.) (YDS)

Quantitative analysis of MRI-guided attenuation correction techniques in time-of-flight brain PET/MRI.

PubMed

Mehranian, Abolfazl; Arabi, Hossein; Zaidi, Habib

2016-04-15

In quantitative PET/MR imaging, attenuation correction (AC) of PET data is markedly challenged by the need of deriving accurate attenuation maps from MR images. A number of strategies have been developed for MRI-guided attenuation correction with different degrees of success. In this work, we compare the quantitative performance of three generic AC methods, including standard 3-class MR segmentation-based, advanced atlas-registration-based and emission-based approaches in the context of brain time-of-flight (TOF) PET/MRI. Fourteen patients referred for diagnostic MRI and (18)F-FDG PET/CT brain scans were included in this comparative study. For each study, PET images were reconstructed using four different attenuation maps derived from CT-based AC (CTAC) serving as reference, standard 3-class MR-segmentation, atlas-registration and emission-based AC methods. To generate 3-class attenuation maps, T1-weighted MRI images were segmented into background air, fat and soft-tissue classes followed by assignment of constant linear attenuation coefficients of 0, 0.0864 and 0.0975 cm(-1) to each class, respectively. A robust atlas-registration based AC method was developed for pseudo-CT generation using local weighted fusion of atlases based on their morphological similarity to target MR images. Our recently proposed MRI-guided maximum likelihood reconstruction of activity and attenuation (MLAA) algorithm was employed to estimate the attenuation map from TOF emission data. The performance of the different AC algorithms in terms of prediction of bones and quantification of PET tracer uptake was objectively evaluated with respect to reference CTAC maps and CTAC-PET images. Qualitative evaluation showed that the MLAA-AC method could sparsely estimate bones and accurately differentiate them from air cavities. It was found that the atlas-AC method can accurately predict bones with variable errors in defining air cavities. Quantitative assessment of bone extraction accuracy based on Dice similarity coefficient (DSC) showed that MLAA-AC and atlas-AC resulted in DSC mean values of 0.79 and 0.92, respectively, in all patients. The MLAA-AC and atlas-AC methods predicted mean linear attenuation coefficients of 0.107 and 0.134 cm(-1), respectively, for the skull compared to reference CTAC mean value of 0.138cm(-1). The evaluation of the relative change in tracer uptake within 32 distinct regions of the brain with respect to CTAC PET images showed that the 3-class MRAC, MLAA-AC and atlas-AC methods resulted in quantification errors of -16.2 ± 3.6%, -13.3 ± 3.3% and 1.0 ± 3.4%, respectively. Linear regression and Bland-Altman concordance plots showed that both 3-class MRAC and MLAA-AC methods result in a significant systematic bias in PET tracer uptake, while the atlas-AC method results in a negligible bias. The standard 3-class MRAC method significantly underestimated cerebral PET tracer uptake. While current state-of-the-art MLAA-AC methods look promising, they were unable to noticeably reduce quantification errors in the context of brain imaging. Conversely, the proposed atlas-AC method provided the most accurate attenuation maps, and thus the lowest quantification bias. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantitative analysis of voids in percolating structures in two-dimensional N-body simulations

NASA Technical Reports Server (NTRS)

Harrington, Patrick M.; Melott, Adrian L.; Shandarin, Sergei F.

1993-01-01

We present in this paper a quantitative method for defining void size in large-scale structure based on percolation threshold density. Beginning with two-dimensional gravitational clustering simulations smoothed to the threshold of nonlinearity, we perform percolation analysis to determine the large scale structure. The resulting objective definition of voids has a natural scaling property, is topologically interesting, and can be applied immediately to redshift surveys.

Quantitative interaction proteomics using mass spectrometry.

PubMed

Wepf, Alexander; Glatter, Timo; Schmidt, Alexander; Aebersold, Ruedi; Gstaiger, Matthias

2009-03-01

We present a mass spectrometry-based strategy for the absolute quantification of protein complex components isolated through affinity purification. We quantified bait proteins via isotope-labeled reference peptides corresponding to an affinity tag sequence and prey proteins by label-free correlational quantification using the precursor ion signal intensities of proteotypic peptides generated in reciprocal purifications. We used this method to quantitatively analyze interaction stoichiometries in the human protein phosphatase 2A network.

Automated Tumor Volumetry Using Computer-Aided Image Segmentation

PubMed Central

Bilello, Michel; Sadaghiani, Mohammed Salehi; Akbari, Hamed; Atthiah, Mark A.; Ali, Zarina S.; Da, Xiao; Zhan, Yiqang; O'Rourke, Donald; Grady, Sean M.; Davatzikos, Christos

2015-01-01

Rationale and Objectives Accurate segmentation of brain tumors, and quantification of tumor volume, is important for diagnosis, monitoring, and planning therapeutic intervention. Manual segmentation is not widely used because of time constraints. Previous efforts have mainly produced methods that are tailored to a particular type of tumor or acquisition protocol and have mostly failed to produce a method that functions on different tumor types and is robust to changes in scanning parameters, resolution, and image quality, thereby limiting their clinical value. Herein, we present a semiautomatic method for tumor segmentation that is fast, accurate, and robust to a wide variation in image quality and resolution. Materials and Methods A semiautomatic segmentation method based on the geodesic distance transform was developed and validated by using it to segment 54 brain tumors. Glioblastomas, meningiomas, and brain metastases were segmented. Qualitative validation was based on physician ratings provided by three clinical experts. Quantitative validation was based on comparing semiautomatic and manual segmentations. Results Tumor segmentations obtained using manual and automatic methods were compared quantitatively using the Dice measure of overlap. Subjective evaluation was performed by having human experts rate the computerized segmentations on a 0–5 rating scale where 5 indicated perfect segmentation. Conclusions The proposed method addresses a significant, unmet need in the field of neuro-oncology. Specifically, this method enables clinicians to obtain accurate and reproducible tumor volumes without the need for manual segmentation. PMID:25770633

Development and evaluation of thin-layer chromatography-digital image-based analysis for the quantitation of the botanical pesticide azadirachtin in agricultural matrixes and commercial formulations: comparison with ELISA.

PubMed

Tanuja, Penmatsa; Venugopal, Namburi; Sashidhar, Rao Beedu

2007-01-01

A simple thin-layer chromatography-digital image-based analytical method has been developed for the quantitation of the botanical pesticide, azadirachtin. The method was validated by analyzing azadirachtin in the spiked food matrixes and processed commercial pesticide formulations, using acidified vanillin reagent as a postchromatographic derivatizing agent. The separated azadirachtin was clearly identified as a green spot. The Rf value was found to be 0.55, which was similar to that of a reference standard. A standard calibration plot was established using a reference standard, based on the linear regression analysis [r2 = 0.996; y = 371.43 + (634.82)x]. The sensitivity of the method was found to be 0.875 microg azadirachtin. Spiking studies conducted at the 1 ppm (microg/g) level in various agricultural matrixes, such as brinjal, tomato, coffee, and cotton seeds, revealed the recoveries of azadirachtin in the range of 67-92%. Azadirachtin content of commercial neem formulations analyzed by the method was in the range of 190-1825 ppm (microg/mL). Further, the present method was compared with an immunoanalytical method enzyme-linked immonosorbent assay developed earlier in our laboratory. Statistical comparison of the 2 methods, using Fischer's F-test, indicated no significant difference in variance, suggesting that both methods are comparable.

Analysis of mathematical literacy ability based on self-efficacy in model eliciting activities using metaphorical thinking approach

NASA Astrophysics Data System (ADS)

Setiani, C.; Waluya, S. B.; Wardono

2018-03-01

The purposes of this research are: (1) to identify learning quality in Model Eliciting Activities (MEAs) using a Metaphorical Thinking (MT) approach regarding qualitative and quantitative; (2) to analyze mathematical literacy of students based on Self-Efficacy (SE). This research is mixed method concurrent embedded design with qualitative research as the primary method. The quantitative research used quasi-experimental with non-equivalent control group design. The population is VIII grade students of SMP Negeri 3 Semarang Indonesia. Quantitative data is examined by conducting completeness mean test, standard completeness test, mean differentiation test and proportional differentiation test. Qualitative data is analyzed descriptively. The result of this research shows that MEAs learning using MT approach accomplishes good criteria both quantitatively and qualitatively. Students with low self-efficacy can identify problems, but they are lack ability to arrange problem-solving strategy on mathematical literacy questions. Students with medium self-efficacy can identify information provided in issues, but they find difficulties to use math symbols in making a representation. Students with high self-efficacy are excellent to represent problems into mathematical models as well as figures by using appropriate symbols and tools, so they can arrange strategy easily to solve mathematical literacy questions.

Detection of propofol concentrations in blood by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Wróbel, M. S.; Gnyba, M.; UrniaŻ, R.; Myllylä, T. S.; Jedrzejewska-Szczerska, M.

2015-07-01

In this paper we present a proof-of-concept of a Raman spectroscopy-based approach for measuring the content of propofol, a common anesthesia drug, in whole human blood, and plasma, which is intended for use during clinical procedures. This method utilizes the Raman spectroscopy as a chemically-sensitive method for qualitative detection of the presence of a drug and a quantitative determination of its concentration. A number of samples from different patients with added various concentrations of propofol IV solution were measured. This is most equivalent to a real in-vivo situation. Subsequent analysis of a set of spectra was carried out to extract qualitative and quantitative information. We conclude, that the changes in the spectra of blood with propofol, overlap with the most prominent lines of the propofol solution, especially at spectral regions: 1450 cm-1, 1250- 1260 cm-1, 1050 cm-1, 875-910 cm-1, 640 cm-1. Later, we have introduced a quantitative analysis program based on correlation matrix closest fit, and a LOO cross-validation. We have achieved 36.67% and 60% model precision when considering full spectra, or specified bands, respectively. These results prove the possibility of using Raman spectroscopy for quantitative detection of propofol concentrations in whole human blood.

Mathematics of quantitative kinetic PCR and the application of standard curves.

PubMed

Rutledge, R G; Côté, C

2003-08-15

Fluorescent monitoring of DNA amplification is the basis of real-time PCR, from which target DNA concentration can be determined from the fractional cycle at which a threshold amount of amplicon DNA is produced. Absolute quantification can be achieved using a standard curve constructed by amplifying known amounts of target DNA. In this study, the mathematics of quantitative PCR are examined in detail, from which several fundamental aspects of the threshold method and the application of standard curves are illustrated. The construction of five replicate standard curves for two pairs of nested primers was used to examine the reproducibility and degree of quantitative variation using SYBER Green I fluorescence. Based upon this analysis the application of a single, well- constructed standard curve could provide an estimated precision of +/-6-21%, depending on the number of cycles required to reach threshold. A simplified method for absolute quantification is also proposed, in which quantitative scale is determined by DNA mass at threshold.

Data from quantitative label free proteomics analysis of rat spleen.

PubMed

Dudekula, Khadar; Le Bihan, Thierry

2016-09-01

The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

Desirability-based methods of multiobjective optimization and ranking for global QSAR studies. Filtering safe and potent drug candidates from combinatorial libraries.

PubMed

Cruz-Monteagudo, Maykel; Borges, Fernanda; Cordeiro, M Natália D S; Cagide Fajin, J Luis; Morell, Carlos; Ruiz, Reinaldo Molina; Cañizares-Carmenate, Yudith; Dominguez, Elena Rosa

2008-01-01

Up to now, very few applications of multiobjective optimization (MOOP) techniques to quantitative structure-activity relationship (QSAR) studies have been reported in the literature. However, none of them report the optimization of objectives related directly to the final pharmaceutical profile of a drug. In this paper, a MOOP method based on Derringer's desirability function that allows conducting global QSAR studies, simultaneously considering the potency, bioavailability, and safety of a set of drug candidates, is introduced. The results of the desirability-based MOOP (the levels of the predictor variables concurrently producing the best possible compromise between the properties determining an optimal drug candidate) are used for the implementation of a ranking method that is also based on the application of desirability functions. This method allows ranking drug candidates with unknown pharmaceutical properties from combinatorial libraries according to the degree of similarity with the previously determined optimal candidate. Application of this method will make it possible to filter the most promising drug candidates of a library (the best-ranked candidates), which should have the best pharmaceutical profile (the best compromise between potency, safety and bioavailability). In addition, a validation method of the ranking process, as well as a quantitative measure of the quality of a ranking, the ranking quality index (Psi), is proposed. The usefulness of the desirability-based methods of MOOP and ranking is demonstrated by its application to a library of 95 fluoroquinolones, reporting their gram-negative antibacterial activity and mammalian cell cytotoxicity. Finally, the combined use of the desirability-based methods of MOOP and ranking proposed here seems to be a valuable tool for rational drug discovery and development.

Hypersensitive Detection and Quantitation of BoNT/A by IgY Antibody against Substrate Linear-Peptide

PubMed Central

Li, Tao; Liu, Hao; Cai, Kun; Tian, Maoren; Wang, Qin; Shi, Jing; Gao, Xiang; Wang, Hui

2013-01-01

Botulinum neurotoxin A (BoNT/A), the most acutely poisonous substance to humans known, cleave its SNAP-25 substrate with high specificity. Based on the endopeptidase activity, different methods have been developed to detect BoNT/A, but most lack ideal reproducibility or sensitivity, or suffer from long-term or unwanted interferences. In this study, we developed a simple method to detect and quantitate trace amounts of botulinum neurotoxin A using the IgY antibody against a linear-peptide substrate. The effects of reaction buffer, time, and temperature were analyzed and optimized. When the optimized assay was used to detect BoNT/A, the limit of detection of the assay was 0.01 mouse LD50 (0.04 pg), and the limit of quantitation was 0.12 mouse LD50/ml (0.48 pg). The findings also showed favorable specificity of detecting BoNT/A. When used to detect BoNT/A in milk or human serum, the proposed assay exhibited good quantitative accuracy (88% < recovery < 111%; inter- and intra-assay CVs < 18%). This method of detection took less than 3 h to complete, indicating that it can be a valuable method of detecting BoNT/A in food or clinical diagnosis. PMID:23555605

Hypersensitive detection and quantitation of BoNT/A by IgY antibody against substrate linear-peptide.

PubMed

Li, Tao; Liu, Hao; Cai, Kun; Tian, Maoren; Wang, Qin; Shi, Jing; Gao, Xiang; Wang, Hui

2013-01-01

Botulinum neurotoxin A (BoNT/A), the most acutely poisonous substance to humans known, cleave its SNAP-25 substrate with high specificity. Based on the endopeptidase activity, different methods have been developed to detect BoNT/A, but most lack ideal reproducibility or sensitivity, or suffer from long-term or unwanted interferences. In this study, we developed a simple method to detect and quantitate trace amounts of botulinum neurotoxin A using the IgY antibody against a linear-peptide substrate. The effects of reaction buffer, time, and temperature were analyzed and optimized. When the optimized assay was used to detect BoNT/A, the limit of detection of the assay was 0.01 mouse LD50 (0.04 pg), and the limit of quantitation was 0.12 mouse LD50/ml (0.48 pg). The findings also showed favorable specificity of detecting BoNT/A. When used to detect BoNT/A in milk or human serum, the proposed assay exhibited good quantitative accuracy (88% < recovery < 111%; inter- and intra-assay CVs < 18%). This method of detection took less than 3 h to complete, indicating that it can be a valuable method of detecting BoNT/A in food or clinical diagnosis.

A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

PubMed Central

Lawless, Craig; Hubbard, Simon J.; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R.

2012-01-01

Abstract New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616

Portable paper-based device for quantitative colorimetric assays relying on light reflectance principle.

PubMed

Li, Bowei; Fu, Longwen; Zhang, Wei; Feng, Weiwei; Chen, Lingxin

2014-04-01

This paper presents a novel paper-based analytical device based on the colorimetric paper assays through its light reflectance. The device is portable, low cost (<20 dollars), and lightweight (only 176 g) that is available to assess the cost-effectiveness and appropriateness of the original health care or on-site detection information. Based on the light reflectance principle, the signal can be obtained directly, stably and user-friendly in our device. We demonstrated the utility and broad applicability of this technique with measurements of different biological and pollution target samples (BSA, glucose, Fe, and nitrite). Moreover, the real samples of Fe (II) and nitrite in the local tap water were successfully analyzed, and compared with the standard UV absorption method, the quantitative results showed good performance, reproducibility, and reliability. This device could provide quantitative information very conveniently and show great potential to broad fields of resource-limited analysis, medical diagnostics, and on-site environmental detection. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Asynchronous adaptive time step in quantitative cellular automata modeling

PubMed Central

Zhu, Hao; Pang, Peter YH; Sun, Yan; Dhar, Pawan

2004-01-01

Background The behaviors of cells in metazoans are context dependent, thus large-scale multi-cellular modeling is often necessary, for which cellular automata are natural candidates. Two related issues are involved in cellular automata based multi-cellular modeling: how to introduce differential equation based quantitative computing to precisely describe cellular activity, and upon it, how to solve the heavy time consumption issue in simulation. Results Based on a modified, language based cellular automata system we extended that allows ordinary differential equations in models, we introduce a method implementing asynchronous adaptive time step in simulation that can considerably improve efficiency yet without a significant sacrifice of accuracy. An average speedup rate of 4–5 is achieved in the given example. Conclusions Strategies for reducing time consumption in simulation are indispensable for large-scale, quantitative multi-cellular models, because even a small 100 × 100 × 100 tissue slab contains one million cells. Distributed and adaptive time step is a practical solution in cellular automata environment. PMID:15222901

Quantitative O-glycomics based on improvement of the one-pot method for nonreductive O-glycan release and simultaneous stable isotope labeling with 1-(d0/d5)phenyl-3-methyl-5-pyrazolone followed by mass spectrometric analysis.

PubMed

Wang, Chengjian; Zhang, Ping; Jin, Wanjun; Li, Lingmei; Qiang, Shan; Zhang, Ying; Huang, Linjuan; Wang, Zhongfu

2017-01-06

Rapid, simple and versatile methods for quantitative analysis of glycoprotein O-glycans are urgently required for current studies on protein O-glycosylation patterns and the search for disease O-glycan biomarkers. Relative quantitation of O-glycans using stable isotope labeling followed by mass spectrometric analysis represents an ideal and promising technique. However, it is hindered by the shortage of reliable nonreductive O-glycan release methods as well as the too large or too small inconstant mass difference between the light and heavy isotope form derivatives of O-glycans, which results in difficulties during the recognition and quantitative analysis of O-glycans by mass spectrometry. Herein we report a facile and versatile O-glycan relative quantification strategy, based on an improved one-pot method that can quantitatively achieve nonreductive release and in situ chromophoric labeling of intact mucin-type O-glycans in one step. In this study, the one-pot method is optimized and applied for quantitative O-glycan release and tagging with either non-deuterated (d 0 -) or deuterated (d 5 -) 1-phenyl-3-methyl-5-pyrazolone (PMP). The obtained O-glycan derivatives feature a permanent 10-Da mass difference between the d 0 - and d 5 -PMP forms, allowing complete discrimination and comparative quantification of these isotopically labeled O-glycans by mass spectrometric techniques. Moreover, the d 0 - and d 5 -PMP derivatives of O-glycans also have a relatively high hydrophobicity as well as a strong UV adsorption, especially suitable for high-resolution separation and high-sensitivity detection by RP-HPLC-UV. We have refined the conditions for the one-pot reaction as well as the corresponding sample purification approach. The good quantitation feasibility, reliability and linearity of this strategy have been verified using bovine fetuin and porcine stomach mucin as model O-glycoproteins. Additionally, we have also successfully applied this method to the quantitative O-glycomic comparison between perch and salmon eggs by ESI-MS, MS/MS and online RP-HPLC-UV-ESI-MS/MS, demonstrating its excellent applicability to various complex biological samples. O-Linked glycoproteins, generated via a widely existing glycosylation modification process on serine (Ser) or threonine (Thr) residues of nascent proteins, play essential roles in a series of biological processes. As a type of informational molecule, the O-glycans of these glycoproteins participate directly in these biological mechanisms. Thus, the characteristic differences or changes of O-glycans in expression level usually relate to pathologies of many diseases and represent an important opportunity to uncover the functional mechanisms of various glycoprotein O-glycans. The novel strategy introduced here provides a simple and versatile analytical method for the precise quantitation of glycoprotein O-glycans by mass spectrometry, enabling rapid evaluation of the differences or changes of O-glycans in expression level. It is attractive for the field of quantitative/comparative O-glycomics, which has great significance for exploring the complex structure-function relationship of O-glycans, as well as for the search of O-glycan biomarkers of some major diseases and O-glycan related targets of some drugs. Copyright © 2016 Elsevier B.V. All rights reserved.

Determinants of fruit and vegetable consumption among children and adolescents: a review of the literature. Part II: qualitative studies

PubMed Central

2011-01-01

Background Large proportions of children do not fulfil the World Health Organization recommendation of eating at least 400 grams of fruit and vegetables (FV) per day. To promote an increased FV intake among children it is important to identify factors which influence their consumption. Both qualitative and quantitative studies are needed. Earlier reviews have analysed evidence from quantitative studies. The aim of this paper is to present a systematic review of qualitative studies of determinants of children's FV intake. Methods Relevant studies were identified by searching Anthropology Plus, Cinahl, CSA illumine, Embase, International Bibliography of the Social Sciences, Medline, PsycINFO, and Web of Science using combinations of synonyms for FV intake, children/adolescents and qualitative methods as search terms. The literature search was completed by December 1st 2010. Papers were included if they applied qualitative methods to investigate 6-18-year-olds' perceptions of factors influencing their FV consumption. Quantitative studies, review studies, studies reported in other languages than English, and non-peer reviewed or unpublished manuscripts were excluded. The papers were reviewed systematically using standardised templates for summary of papers, quality assessment, and synthesis of findings across papers. Results The review included 31 studies, mostly based on US populations and focus group discussions. The synthesis identified the following potential determinants for FV intake which supplement the quantitative knowledge base: Time costs; lack of taste guarantee; satiety value; appropriate time/occasions/settings for eating FV; sensory and physical aspects; variety, visibility, methods of preparation; access to unhealthy food; the symbolic value of food for image, gender identity and social interaction with peers; short term outcome expectancies. Conclusions The review highlights numerous potential determinants which have not been investigated thoroughly in quantitative studies. Future large scale quantitative studies should attempt to quantify the importance of these factors. Further, mechanisms behind gender, age and socioeconomic differences in FV consumption are proposed which should be tested quantitatively in order to better tailor interventions to vulnerable groups. Finally, the review provides input to the conceptualisation and measurements of concepts (i.e. peer influence, availability in schools) which may refine survey instruments and theoretical frameworks concerning eating behaviours. PMID:21999291

Quantitative Information Differences Between Object-Person Presentation Methods

ERIC Educational Resources Information Center

Boyd, J. Edwin; Perry, Raymond P.

1972-01-01

Subjects used significantly more adjectives, on an adjective checklist (ACL), in giving their impressions of an object-person; based on written and audiovisual presentations, more than audio presentations. (SD)

Improving membrane based multiplex immunoassays for semi-quantitative detection of multiple cytokines in a single sample

PubMed Central

2014-01-01

Background Inflammatory mediators can serve as biomarkers for the monitoring of the disease progression or prognosis in many conditions. In the present study we introduce an adaptation of a membrane-based technique in which the level of up to 40 cytokines and chemokines can be determined in both human and rodent blood in a semi-quantitative way. The planar assay was modified using the LI-COR (R) detection system (fluorescence based) rather than chemiluminescence and semi-quantitative outcomes were achieved by normalizing the outcomes using the automated exposure settings of the Odyssey readout device. The results were compared to the gold standard assay, namely ELISA. Results The improved planar assay allowed the detection of a considerably higher number of analytes (n = 30 and n = 5 for fluorescent and chemiluminescent detection, respectively). The improved planar method showed high sensitivity up to 17 pg/ml and a linear correlation of the normalized fluorescence intensity with the results from the ELISA (r = 0.91). Conclusions The results show that the membrane-based technique is a semi-quantitative assay that correlates satisfactorily to the gold standard when enhanced by the use of fluorescence and subsequent semi-quantitative analysis. This promising technique can be used to investigate inflammatory profiles in multiple conditions, particularly in studies with constraints in sample sizes and/or budget. PMID:25022797

Visual and Quantitative Analysis Methods of Respiratory Patterns for Respiratory Gated PET/CT.

PubMed

Son, Hye Joo; Jeong, Young Jin; Yoon, Hyun Jin; Park, Jong-Hwan; Kang, Do-Young

2016-01-01

We integrated visual and quantitative methods for analyzing the stability of respiration using four methods: phase space diagrams, Fourier spectra, Poincaré maps, and Lyapunov exponents. Respiratory patterns of 139 patients were grouped based on the combination of the regularity of amplitude, period, and baseline positions. Visual grading was done by inspecting the shape of diagram and classified into two states: regular and irregular. Quantitation was done by measuring standard deviation of x and v coordinates of Poincaré map (SD x , SD v ) or the height of the fundamental peak ( A 1 ) in Fourier spectrum or calculating the difference between maximal upward and downward drift. Each group showed characteristic pattern on visual analysis. There was difference of quantitative parameters (SD x , SD v , A 1 , and MUD-MDD) among four groups (one way ANOVA, p = 0.0001 for MUD-MDD, SD x , and SD v , p = 0.0002 for A 1 ). In ROC analysis, the cutoff values were 0.11 for SD x (AUC: 0.982, p < 0.0001), 0.062 for SD v (AUC: 0.847, p < 0.0001), 0.117 for A 1 (AUC: 0.876, p < 0.0001), and 0.349 for MUD-MDD (AUC: 0.948, p < 0.0001). This is the first study to analyze multiple aspects of respiration using various mathematical constructs and provides quantitative indices of respiratory stability and determining quantitative cutoff value for differentiating regular and irregular respiration.

Searching for rigour in the reporting of mixed methods population health research: a methodological review.

PubMed

Brown, K M; Elliott, S J; Leatherdale, S T; Robertson-Wilson, J

2015-12-01

The environments in which population health interventions occur shape both their implementation and outcomes. Hence, when evaluating these interventions, we must explore both intervention content and context. Mixed methods (integrating quantitative and qualitative methods) provide this opportunity. However, although criteria exist for establishing rigour in quantitative and qualitative research, there is poor consensus regarding rigour in mixed methods. Using the empirical example of school-based obesity interventions, this methodological review examined how mixed methods have been used and reported, and how rigour has been addressed. Twenty-three peer-reviewed mixed methods studies were identified through a systematic search of five databases and appraised using the guidelines for Good Reporting of a Mixed Methods Study. In general, more detailed description of data collection and analysis, integration, inferences and justifying the use of mixed methods is needed. Additionally, improved reporting of methodological rigour is required. This review calls for increased discussion of practical techniques for establishing rigour in mixed methods research, beyond those for quantitative and qualitative criteria individually. A guide for reporting mixed methods research in population health should be developed to improve the reporting quality of mixed methods studies. Through improved reporting, mixed methods can provide strong evidence to inform policy and practice. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Towards standardized assessment of endoscope optical performance: geometric distortion

NASA Astrophysics Data System (ADS)

Wang, Quanzeng; Desai, Viraj N.; Ngo, Ying Z.; Cheng, Wei-Chung; Pfefer, Joshua

2013-12-01

Technological advances in endoscopes, such as capsule, ultrathin and disposable devices, promise significant improvements in safety, clinical effectiveness and patient acceptance. Unfortunately, the industry lacks test methods for preclinical evaluation of key optical performance characteristics (OPCs) of endoscopic devices that are quantitative, objective and well-validated. As a result, it is difficult for researchers and developers to compare image quality and evaluate equivalence to, or improvement upon, prior technologies. While endoscope OPCs include resolution, field of view, and depth of field, among others, our focus in this paper is geometric image distortion. We reviewed specific test methods for distortion and then developed an objective, quantitative test method based on well-defined experimental and data processing steps to evaluate radial distortion in the full field of view of an endoscopic imaging system. Our measurements and analyses showed that a second-degree polynomial equation could well describe the radial distortion curve of a traditional endoscope. The distortion evaluation method was effective for correcting the image and can be used to explain other widely accepted evaluation methods such as picture height distortion. Development of consensus standards based on promising test methods for image quality assessment, such as the method studied here, will facilitate clinical implementation of innovative endoscopic devices.

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.

Distance-Based Tear Lactoferrin Assay on Microfluidic Paper Device Using Interfacial Interactions on Surface-Modified Cellulose.

PubMed

Yamada, Kentaro; Henares, Terence G; Suzuki, Koji; Citterio, Daniel

2015-11-11

"Distance-based" detection motifs on microfluidic paper-based analytical devices (μPADs) allow quantitative analysis without using signal readout instruments in a similar manner to classical analogue thermometers. To realize a cost-effective and calibration-free distance-based assay of lactoferrin in human tear fluid on a μPAD not relying on antibodies or enzymes, we investigated the fluidic mobilities of the target protein and Tb(3+) cations used as the fluorescent detection reagent on surface-modified cellulosic filter papers. Chromatographic elution experiments in a tear-like sample matrix containing electrolytes and proteins revealed a collapse of attractive electrostatic interactions between lactoferrin or Tb(3+) and the cellulosic substrate, which was overcome by the modification of the paper surface with the sulfated polysaccharide ι-carrageenan. The resulting μPAD based on the fluorescence emission distance successfully analyzed 0-4 mg mL(-1) of lactoferrin in complex human tear matrix with a lower limit of detection of 0.1 mg mL(-1) by simple visual inspection. Assay results of 18 human tear samples including ocular disease patients and healthy volunteers showed good correlation to the reference ELISA method with a slope of 0.997 and a regression coefficient of 0.948. The distance-based quantitative signal and the good batch-to-batch fabrication reproducibility relying on printing methods enable quantitative analysis by simply reading out "concentration scale marks" printed on the μPAD without performing any calibration and using any signal readout instrument.

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.

A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes.

PubMed

Uchii, Kimiko; Doi, Hideyuki; Minamoto, Toshifumi

2016-03-01

The invasion of non-native species that are closely related to native species can lead to competitive elimination of the native species and/or genomic extinction through hybridization. Such invasions often become serious before they are detected, posing unprecedented threats to biodiversity. A Japanese native strain of common carp (Cyprinus carpio) has become endangered owing to the invasion of non-native strains introduced from the Eurasian continent. Here, we propose a rapid environmental DNA-based approach to quantitatively monitor the invasion of non-native genotypes. Using this system, we developed a method to quantify the relative proportion of native and non-native DNA based on a single-nucleotide polymorphism using cycling probe technology in real-time PCR. The efficiency of this method was confirmed in aquarium experiments, where the quantified proportion of native and non-native DNA in the water was well correlated to the biomass ratio of native and non-native genotypes. This method provided quantitative estimates for the proportion of native and non-native DNA in natural rivers and reservoirs, which allowed us to estimate the degree of invasion of non-native genotypes without catching and analysing individual fish. Our approach would dramatically facilitate the process of quantitatively monitoring the invasion of non-native conspecifics in aquatic ecosystems, thus revealing a promising method for risk assessment and management in biodiversity conservation. © 2015 John Wiley & Sons Ltd.

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

QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

PubMed Central

Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

2015-01-01

Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

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

[Modeling continuous scaling of NDVI based on fractal theory].

PubMed

Luan, Hai-Jun; Tian, Qing-Jiu; Yu, Tao; Hu, Xin-Li; Huang, Yan; Du, Ling-Tong; Zhao, Li-Min; Wei, Xi; Han, Jie; Zhang, Zhou-Wei; Li, Shao-Peng

2013-07-01

Scale effect was one of the very important scientific problems of remote sensing. The scale effect of quantitative remote sensing can be used to study retrievals' relationship between different-resolution images, and its research became an effective way to confront the challenges, such as validation of quantitative remote sensing products et al. Traditional up-scaling methods cannot describe scale changing features of retrievals on entire series of scales; meanwhile, they are faced with serious parameters correction issues because of imaging parameters' variation of different sensors, such as geometrical correction, spectral correction, etc. Utilizing single sensor image, fractal methodology was utilized to solve these problems. Taking NDVI (computed by land surface radiance) as example and based on Enhanced Thematic Mapper Plus (ETM+) image, a scheme was proposed to model continuous scaling of retrievals. Then the experimental results indicated that: (a) For NDVI, scale effect existed, and it could be described by fractal model of continuous scaling; (2) The fractal method was suitable for validation of NDVI. All of these proved that fractal was an effective methodology of studying scaling of quantitative remote sensing.

Quantitative tomographic imaging of intermolecular FRET in small animals

PubMed Central

Venugopal, Vivek; Chen, Jin; Barroso, Margarida; Intes, Xavier

2012-01-01

Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule. PMID:23243567

Human judgment vs. quantitative models for the management of ecological resources.

PubMed

Holden, Matthew H; Ellner, Stephen P

2016-07-01

Despite major advances in quantitative approaches to natural resource management, there has been resistance to using these tools in the actual practice of managing ecological populations. Given a managed system and a set of assumptions, translated into a model, optimization methods can be used to solve for the most cost-effective management actions. However, when the underlying assumptions are not met, such methods can potentially lead to decisions that harm the environment and economy. Managers who develop decisions based on past experience and judgment, without the aid of mathematical models, can potentially learn about the system and develop flexible management strategies. However, these strategies are often based on subjective criteria and equally invalid and often unstated assumptions. Given the drawbacks of both methods, it is unclear whether simple quantitative models improve environmental decision making over expert opinion. In this study, we explore how well students, using their experience and judgment, manage simulated fishery populations in an online computer game and compare their management outcomes to the performance of model-based decisions. We consider harvest decisions generated using four different quantitative models: (1) the model used to produce the simulated population dynamics observed in the game, with the values of all parameters known (as a control), (2) the same model, but with unknown parameter values that must be estimated during the game from observed data, (3) models that are structurally different from those used to simulate the population dynamics, and (4) a model that ignores age structure. Humans on average performed much worse than the models in cases 1-3, but in a small minority of scenarios, models produced worse outcomes than those resulting from students making decisions based on experience and judgment. When the models ignored age structure, they generated poorly performing management decisions, but still outperformed students using experience and judgment 66% of the time. © 2016 by the Ecological Society of America.

Development and Application of Quantitative Detection Method for Viral Hemorrhagic Septicemia Virus (VHSV) Genogroup IVa

PubMed Central

Kim, Jong-Oh; Kim, Wi-Sik; Kim, Si-Woo; Han, Hyun-Ja; Kim, Jin Woo; Park, Myoung Ae; Oh, Myung-Joo

2014-01-01

Viral hemorrhagic septicemia virus (VHSV) is a problematic pathogen in olive flounder (Paralichthys olivaceus) aquaculture farms in Korea. Thus, it is necessary to develop a rapid and accurate diagnostic method to detect this virus. We developed a quantitative RT-PCR (qRT-PCR) method based on the nucleocapsid (N) gene sequence of Korean VHSV isolate (Genogroup IVa). The slope and R2 values of the primer set developed in this study were −0.2928 (96% efficiency) and 0.9979, respectively. Its comparison with viral infectivity calculated by traditional quantifying method (TCID50) showed a similar pattern of kinetic changes in vitro and in vivo. The qRT-PCR method reduced detection time compared to that of TCID50, making it a very useful tool for VHSV diagnosis. PMID:24859343

Development of a quantitative diagnostic method of estrogen receptor expression levels by immunohistochemistry using organic fluorescent material-assembled nanoparticles

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

Gonda, Kohsuke, E-mail: gonda@med.tohoku.ac.jp; Miyashita, Minoru; Watanabe, Mika

2012-09-28

Highlights: Black-Right-Pointing-Pointer Organic fluorescent material-assembled nanoparticles for IHC were prepared. Black-Right-Pointing-Pointer New nanoparticle fluorescent intensity was 10.2-fold greater than Qdot655. Black-Right-Pointing-Pointer Nanoparticle staining analyzed a wide range of ER expression levels in tissue. Black-Right-Pointing-Pointer Nanoparticle staining enhanced the quantitative sensitivity for ER diagnosis. -- Abstract: The detection of estrogen receptors (ERs) by immunohistochemistry (IHC) using 3,3 Prime -diaminobenzidine (DAB) is slightly weak as a prognostic marker, but it is essential to the application of endocrine therapy, such as antiestrogen tamoxifen-based therapy. IHC using DAB is a poor quantitative method because horseradish peroxidase (HRP) activity depends on reaction time, temperature andmore » substrate concentration. However, IHC using fluorescent material provides an effective method to quantitatively use IHC because the signal intensity is proportional to the intensity of the photon excitation energy. However, the high level of autofluorescence has impeded the development of quantitative IHC using fluorescence. We developed organic fluorescent material (tetramethylrhodamine)-assembled nanoparticles for IHC. Tissue autofluorescence is comparable to the fluorescence intensity of quantum dots, which are the most representative fluorescent nanoparticles. The fluorescent intensity of our novel nanoparticles was 10.2-fold greater than quantum dots, and they did not bind non-specifically to breast cancer tissues due to the polyethylene glycol chain that coated their surfaces. Therefore, the fluorescent intensity of our nanoparticles significantly exceeded autofluorescence, which produced a significantly higher signal-to-noise ratio on IHC-imaged cancer tissues than previous methods. Moreover, immunostaining data from our nanoparticle fluorescent IHC and IHC with DAB were compared in the same region of adjacent tissues sections to quantitatively examine the two methods. The results demonstrated that our nanoparticle staining analyzed a wide range of ER expression levels with higher accuracy and quantitative sensitivity than DAB staining. This enhancement in the diagnostic accuracy and sensitivity for ERs using our immunostaining method will improve the prediction of responses to therapies that target ERs and progesterone receptors that are induced by a downstream ER signal.« less

Determinants of fruit and vegetable consumption among children and adolescents: a review of the literature. Part II: qualitative studies.

PubMed

Krølner, Rikke; Rasmussen, Mette; Brug, Johannes; Klepp, Knut-Inge; Wind, Marianne; Due, Pernille

2011-10-14

Large proportions of children do not fulfil the World Health Organization recommendation of eating at least 400 grams of fruit and vegetables (FV) per day. To promote an increased FV intake among children it is important to identify factors which influence their consumption. Both qualitative and quantitative studies are needed. Earlier reviews have analysed evidence from quantitative studies. The aim of this paper is to present a systematic review of qualitative studies of determinants of children's FV intake. Relevant studies were identified by searching Anthropology Plus, Cinahl, CSA illumine, Embase, International Bibliography of the Social Sciences, Medline, PsycINFO, and Web of Science using combinations of synonyms for FV intake, children/adolescents and qualitative methods as search terms. The literature search was completed by December 1st 2010. Papers were included if they applied qualitative methods to investigate 6-18-year-olds' perceptions of factors influencing their FV consumption. Quantitative studies, review studies, studies reported in other languages than English, and non-peer reviewed or unpublished manuscripts were excluded. The papers were reviewed systematically using standardised templates for summary of papers, quality assessment, and synthesis of findings across papers. The review included 31 studies, mostly based on US populations and focus group discussions. The synthesis identified the following potential determinants for FV intake which supplement the quantitative knowledge base: Time costs; lack of taste guarantee; satiety value; appropriate time/occasions/settings for eating FV; sensory and physical aspects; variety, visibility, methods of preparation; access to unhealthy food; the symbolic value of food for image, gender identity and social interaction with peers; short term outcome expectancies. The review highlights numerous potential determinants which have not been investigated thoroughly in quantitative studies. Future large scale quantitative studies should attempt to quantify the importance of these factors. Further, mechanisms behind gender, age and socioeconomic differences in FV consumption are proposed which should be tested quantitatively in order to better tailor interventions to vulnerable groups. Finally, the review provides input to the conceptualisation and measurements of concepts (i.e. peer influence, availability in schools) which may refine survey instruments and theoretical frameworks concerning eating behaviours.

Diffusion properties of conventional and calcium-sensitive MRI contrast agents in the rat cerebral cortex.

PubMed

Hagberg, Gisela E; Mamedov, Ilgar; Power, Anthony; Beyerlein, Michael; Merkle, Hellmut; Kiselev, Valerij G; Dhingra, Kirti; Kubìček, Vojtĕch; Angelovski, Goran; Logothetis, Nikos K

2014-01-01

Calcium-sensitive MRI contrast agents can only yield quantitative results if the agent concentration in the tissue is known. The agent concentration could be determined by diffusion modeling, if relevant parameters were available. We have established an MRI-based method capable of determining diffusion properties of conventional and calcium-sensitive agents. Simulations and experiments demonstrate that the method is applicable both for conventional contrast agents with a fixed relaxivity value and for calcium-sensitive contrast agents. The full pharmacokinetic time-course of gadolinium concentration estimates was observed by MRI before, during and after intracerebral administration of the agent, and the effective diffusion coefficient D* was determined by voxel-wise fitting of the solution to the diffusion equation. The method yielded whole brain coverage with a high spatial and temporal sampling. The use of two types of MRI sequences for sampling of the diffusion time courses was investigated: Look-Locker-based quantitative T(1) mapping, and T(1) -weighted MRI. The observation times of the proposed MRI method is long (up to 20 h) and consequently the diffusion distances covered are also long (2-4 mm). Despite this difference, the D* values in vivo were in agreement with previous findings using optical measurement techniques, based on observation times of a few minutes. The effective diffusion coefficient determined for the calcium-sensitive contrast agents may be used to determine local tissue concentrations and to design infusion protocols that maintain the agent concentration at a steady state, thereby enabling quantitative sensing of the local calcium concentration. Copyright © 2014 John Wiley & Sons, Ltd.

Validation of a stability-indicating hydrophilic interaction liquid chromatographic method for the quantitative determination of vitamin k3 (menadione sodium bisulfite) in injectable solution formulation.

PubMed

Ghanem, Mashhour M; Abu-Lafi, Saleh A; Hallak, Hussein O

2013-01-01

A simple, specific, accurate, and stability-indicating method was developed and validated for the quantitative determination of menadione sodium bisulfite in the injectable solution formulation. The method is based on zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) coupled with a photodiode array detector. The desired separation was achieved on the ZIC-HILIC column (250 mm × 4.6 mm, 5 μm) at 25°C temperature. The optimized mobile phase consisted of an isocratic solvent mixture of 200mM ammonium acetate (NH4AC) solution and acetonitrile (ACN) (20:80; v/v) pH-adjusted to 5.7 by glacial acetic acid. The mobile phase was fixed at 0.5 ml/min and the analytes were monitored at 261 nm using a photodiode array detector. The effects of the chromatographic conditions on the peak retention, peak USP tailing factor, and column efficiency were systematically optimized. Forced degradation experiments were carried out by exposing menadione sodium bisulfite standard and the injectable solution formulation to thermal, photolytic, oxidative, and acid-base hydrolytic stress conditions. The degradation products were well-resolved from the main peak and the excipients, thus proving that the method is a reliable, stability-indicating tool. The method was validated as per ICH and USP guidelines (USP34/NF29) and found to be adequate for the routine quantitative estimation of menadione sodium bisulfite in commercially available menadione sodium bisulfite injectable solution dosage forms.

Use of machine learning methods to classify Universities based on the income structure

NASA Astrophysics Data System (ADS)

Terlyga, Alexandra; Balk, Igor

2017-10-01

In this paper we discuss use of machine learning methods such as self organizing maps, k-means and Ward’s clustering to perform classification of universities based on their income. This classification will allow us to quantitate classification of universities as teaching, research, entrepreneur, etc. which is important tool for government, corporations and general public alike in setting expectation and selecting universities to achieve different goals.

Improving efficacy of metastatic tumor segmentation to facilitate early prediction of ovarian cancer patients' response to chemotherapy

NASA Astrophysics Data System (ADS)

Danala, Gopichandh; Wang, Yunzhi; Thai, Theresa; Gunderson, Camille C.; Moxley, Katherine M.; Moore, Kathleen; Mannel, Robert S.; Cheng, Samuel; Liu, Hong; Zheng, Bin; Qiu, Yuchen

2017-02-01

Accurate tumor segmentation is a critical step in the development of the computer-aided detection (CAD) based quantitative image analysis scheme for early stage prognostic evaluation of ovarian cancer patients. The purpose of this investigation is to assess the efficacy of several different methods to segment the metastatic tumors occurred in different organs of ovarian cancer patients. In this study, we developed a segmentation scheme consisting of eight different algorithms, which can be divided into three groups: 1) Region growth based methods; 2) Canny operator based methods; and 3) Partial differential equation (PDE) based methods. A number of 138 tumors acquired from 30 ovarian cancer patients were used to test the performance of these eight segmentation algorithms. The results demonstrate each of the tested tumors can be successfully segmented by at least one of the eight algorithms without the manual boundary correction. Furthermore, modified region growth, classical Canny detector, and fast marching, and threshold level set algorithms are suggested in the future development of the ovarian cancer related CAD schemes. This study may provide meaningful reference for developing novel quantitative image feature analysis scheme to more accurately predict the response of ovarian cancer patients to the chemotherapy at early stage.

Automated Video Based Facial Expression Analysis of Neuropsychiatric Disorders

PubMed Central

Wang, Peng; Barrett, Frederick; Martin, Elizabeth; Milanova, Marina; Gur, Raquel E.; Gur, Ruben C.; Kohler, Christian; Verma, Ragini

2008-01-01

Deficits in emotional expression are prominent in several neuropsychiatric disorders, including schizophrenia. Available clinical facial expression evaluations provide subjective and qualitative measurements, which are based on static 2D images that do not capture the temporal dynamics and subtleties of expression changes. Therefore, there is a need for automated, objective and quantitative measurements of facial expressions captured using videos. This paper presents a computational framework that creates probabilistic expression profiles for video data and can potentially help to automatically quantify emotional expression differences between patients with neuropsychiatric disorders and healthy controls. Our method automatically detects and tracks facial landmarks in videos, and then extracts geometric features to characterize facial expression changes. To analyze temporal facial expression changes, we employ probabilistic classifiers that analyze facial expressions in individual frames, and then propagate the probabilities throughout the video to capture the temporal characteristics of facial expressions. The applications of our method to healthy controls and case studies of patients with schizophrenia and Asperger’s syndrome demonstrate the capability of the video-based expression analysis method in capturing subtleties of facial expression. Such results can pave the way for a video based method for quantitative analysis of facial expressions in clinical research of disorders that cause affective deficits. PMID:18045693

Leaf epidermis images for robust identification of plants

PubMed Central

da Silva, Núbia Rosa; Oliveira, Marcos William da Silva; Filho, Humberto Antunes de Almeida; Pinheiro, Luiz Felipe Souza; Rossatto, Davi Rodrigo; Kolb, Rosana Marta; Bruno, Odemir Martinez

2016-01-01

This paper proposes a methodology for plant analysis and identification based on extracting texture features from microscopic images of leaf epidermis. All the experiments were carried out using 32 plant species with 309 epidermal samples captured by an optical microscope coupled to a digital camera. The results of the computational methods using texture features were compared to the conventional approach, where quantitative measurements of stomatal traits (density, length and width) were manually obtained. Epidermis image classification using texture has achieved a success rate of over 96%, while success rate was around 60% for quantitative measurements taken manually. Furthermore, we verified the robustness of our method accounting for natural phenotypic plasticity of stomata, analysing samples from the same species grown in different environments. Texture methods were robust even when considering phenotypic plasticity of stomatal traits with a decrease of 20% in the success rate, as quantitative measurements proved to be fully sensitive with a decrease of 77%. Results from the comparison between the computational approach and the conventional quantitative measurements lead us to discover how computational systems are advantageous and promising in terms of solving problems related to Botany, such as species identification. PMID:27217018

Dynamic phase differences based on quantitative phase imaging for the objective evaluation of cell behavior.

PubMed

Krizova, Aneta; Collakova, Jana; Dostal, Zbynek; Kvasnica, Lukas; Uhlirova, Hana; Zikmund, Tomas; Vesely, Pavel; Chmelik, Radim

2015-01-01

Quantitative phase imaging (QPI) brought innovation to noninvasive observation of live cell dynamics seen as cell behavior. Unlike the Zernike phase contrast or differential interference contrast, QPI provides quantitative information about cell dry mass distribution. We used such data for objective evaluation of live cell behavioral dynamics by the advanced method of dynamic phase differences (DPDs). The DPDs method is considered a rational instrument offered by QPI. By subtracting the antecedent from the subsequent image in a time-lapse series, only the changes in mass distribution in the cell are detected. The result is either visualized as a two dimensional color-coded projection of these two states of the cell or as a time dependence of changes quantified in picograms. Then in a series of time-lapse recordings, the chain of cell mass distribution changes that would otherwise escape attention is revealed. Consequently, new salient features of live cell behavior should emerge. Construction of the DPDs method and results exhibiting the approach are presented. Advantage of the DPDs application is demonstrated on cells exposed to an osmotic challenge. For time-lapse acquisition of quantitative phase images, the recently developed coherence-controlled holographic microscope was employed.

Dynamic phase differences based on quantitative phase imaging for the objective evaluation of cell behavior

NASA Astrophysics Data System (ADS)

Krizova, Aneta; Collakova, Jana; Dostal, Zbynek; Kvasnica, Lukas; Uhlirova, Hana; Zikmund, Tomas; Vesely, Pavel; Chmelik, Radim

2015-11-01

Quantitative phase imaging (QPI) brought innovation to noninvasive observation of live cell dynamics seen as cell behavior. Unlike the Zernike phase contrast or differential interference contrast, QPI provides quantitative information about cell dry mass distribution. We used such data for objective evaluation of live cell behavioral dynamics by the advanced method of dynamic phase differences (DPDs). The DPDs method is considered a rational instrument offered by QPI. By subtracting the antecedent from the subsequent image in a time-lapse series, only the changes in mass distribution in the cell are detected. The result is either visualized as a two-dimensional color-coded projection of these two states of the cell or as a time dependence of changes quantified in picograms. Then in a series of time-lapse recordings, the chain of cell mass distribution changes that would otherwise escape attention is revealed. Consequently, new salient features of live cell behavior should emerge. Construction of the DPDs method and results exhibiting the approach are presented. Advantage of the DPDs application is demonstrated on cells exposed to an osmotic challenge. For time-lapse acquisition of quantitative phase images, the recently developed coherence-controlled holographic microscope was employed.

Relationship and Variation of qPCR and Culturable Enterococci Estimates in Ambient Surface Waters Are Predictable

EPA Science Inventory

The quantitative polymerase chain reaction (qPCR) method provides rapid estimates of fecal indicator bacteria densities that have been indicated to be useful in the assessment of water quality. Primarily because this method provides faster results than standard culture-based meth...

Research in Education: Evidence-Based Inquiry, 7th Edition. MyEducationLab Series

ERIC Educational Resources Information Center

McMillan, James H.; Schumacher, Sally

2010-01-01

This substantially revised text provides a comprehensive, highly accessible, and student friendly introduction to the principles, concepts, and methods currently used in educational research. This text provides a balanced combination of quantitative and qualitative methods and enables students to master skills in reading, understanding,…