An Ibm PC/AT-Based Image Acquisition And Processing System For Quantitative Image Analysis

NASA Astrophysics Data System (ADS)

Kim, Yongmin; Alexander, Thomas

1986-06-01

In recent years, a large number of applications have been developed for image processing systems in the area of biological imaging. We have already finished the development of a dedicated microcomputer-based image processing and analysis system for quantitative microscopy. The system's primary function has been to facilitate and ultimately automate quantitative image analysis tasks such as the measurement of cellular DNA contents. We have recognized from this development experience, and interaction with system users, biologists and technicians, that the increasingly widespread use of image processing systems, and the development and application of new techniques for utilizing the capabilities of such systems, would generate a need for some kind of inexpensive general purpose image acquisition and processing system specially tailored for the needs of the medical community. We are currently engaged in the development and testing of hardware and software for a fairly high-performance image processing computer system based on a popular personal computer. In this paper, we describe the design and development of this system. Biological image processing computer systems have now reached a level of hardware and software refinement where they could become convenient image analysis tools for biologists. The development of a general purpose image processing system for quantitative image analysis that is inexpensive, flexible, and easy-to-use represents a significant step towards making the microscopic digital image processing techniques more widely applicable not only in a research environment as a biologist's workstation, but also in clinical environments as a diagnostic tool.

Quantitative Data Analysis--In the Graduate Curriculum

ERIC Educational Resources Information Center

Albers, Michael J.

2017-01-01

A quantitative research study collects numerical data that must be analyzed to help draw the study's conclusions. Teaching quantitative data analysis is not teaching number crunching, but teaching a way of critical thinking for how to analyze the data. The goal of data analysis is to reveal the underlying patterns, trends, and relationships of a…

A semi-quantitative approach to GMO risk-benefit analysis.

PubMed

Morris, E Jane

2011-10-01

In many countries there are increasing calls for the benefits of genetically modified organisms (GMOs) to be considered as well as the risks, and for a risk-benefit analysis to form an integral part of GMO regulatory frameworks. This trend represents a shift away from the strict emphasis on risks, which is encapsulated in the Precautionary Principle that forms the basis for the Cartagena Protocol on Biosafety, and which is reflected in the national legislation of many countries. The introduction of risk-benefit analysis of GMOs would be facilitated if clear methodologies were available to support the analysis. Up to now, methodologies for risk-benefit analysis that would be applicable to the introduction of GMOs have not been well defined. This paper describes a relatively simple semi-quantitative methodology that could be easily applied as a decision support tool, giving particular consideration to the needs of regulators in developing countries where there are limited resources and experience. The application of the methodology is demonstrated using the release of an insect resistant maize variety in South Africa as a case study. The applicability of the method in the South African regulatory system is also discussed, as an example of what might be involved in introducing changes into an existing regulatory process.

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

PubMed

Sreedharan, Vipin T; Schultheiss, Sebastian J; Jean, Géraldine; Kahles, André; Bohnert, Regina; Drewe, Philipp; Mudrakarta, Pramod; Görnitz, Nico; Zeller, Georg; Rätsch, Gunnar

2014-05-01

We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that is integrated in Galaxy. Its distinguishing features include customizable computational workflows and a modular pipeline architecture that facilitates comparative assessment of tool and data quality. Oqtans integrates an assortment of machine learning-powered tools into Galaxy, which show superior or equal performance to state-of-the-art tools. Implemented tools comprise a complete transcriptome analysis workflow: short-read alignment, transcript identification/quantification and differential expression analysis. Oqtans and Galaxy facilitate persistent storage, data exchange and documentation of intermediate results and analysis workflows. We illustrate how Oqtans aids the interpretation of data from different experiments in easy to understand use cases. Users can easily create their own workflows and extend Oqtans by integrating specific tools. Oqtans is available as (i) a cloud machine image with a demo instance at cloud.oqtans.org, (ii) a public Galaxy instance at galaxy.cbio.mskcc.org, (iii) a git repository containing all installed software (oqtans.org/git); most of which is also available from (iv) the Galaxy Toolshed and (v) a share string to use along with Galaxy CloudMan.

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.

Using learning theory, interprofessional facilitation competencies, and behavioral indicators to evaluate facilitator training.

PubMed

LeGros, Theresa A; Amerongen, Helen M; Cooley, Janet H; Schloss, Ernest P

2015-01-01

Despite the increasing need for faculty and preceptors skilled in interprofessional facilitation (IPF), the relative novelty of the field poses a challenge to the development and evaluation of IPF programs. We use learning theory and IPF competencies with associated behavioral indicators to develop and evaluate six key messages in IPF training and experience. Our mixed methods approach included two phases: quantitative data collection with embedded qualitative data, followed by qualitative data collection in explanatory sequential fashion. This enabled triangulated analyses of both data types and of facilitation behaviors from facilitator and student perspectives. Results indicate the competency-based training was effective. Facilitators felt comfortable performing behaviors associated with IPF competencies; student observations of those behaviors supported facilitator self-reported performance. Overall, students perceived more facilitation opportunities than facilitators. Findings corroborate the importance of recruiting seasoned facilitators and establishing IPF guidelines that acknowledge variable team dynamics and help facilitators recognize teachable moments.

Facilitator control as automatic behavior: A verbal behavior analysis

PubMed Central

Hall, Genae A.

1993-01-01

Several studies of facilitated communication have demonstrated that the facilitators were controlling and directing the typing, although they appeared to be unaware of doing so. Such results shift the focus of analysis to the facilitator's behavior and raise questions regarding the controlling variables for that behavior. This paper analyzes facilitator behavior as an instance of automatic verbal behavior, from the perspective of Skinner's (1957) book Verbal Behavior. Verbal behavior is automatic when the speaker or writer is not stimulated by the behavior at the time of emission, the behavior is not edited, the products of behavior differ from what the person would produce normally, and the behavior is attributed to an outside source. All of these characteristics appear to be present in facilitator behavior. Other variables seem to account for the thematic content of the typed messages. These variables also are discussed. PMID:22477083

Quantitative molecular analysis in mantle cell lymphoma.

PubMed

Brízová, H; Hilská, I; Mrhalová, M; Kodet, R

2011-07-01

A molecular analysis has three major roles in modern oncopathology--as an aid in the differential diagnosis, in molecular monitoring of diseases, and in estimation of the potential prognosis. In this report we review the application of the molecular analysis in a group of patients with mantle cell lymphoma (MCL). We demonstrate that detection of the cyclin D1 mRNA level is a molecular marker in 98% of patients with MCL. Cyclin D1 quantitative monitoring is specific and sensitive for the differential diagnosis and for the molecular monitoring of the disease in the bone marrow. Moreover, the dynamics of cyclin D1 in bone marrow reflects the disease development and it predicts the clinical course. We employed the molecular analysis for a precise quantitative detection of proliferation markers, Ki-67, topoisomerase IIalpha, and TPX2, that are described as effective prognostic factors. Using the molecular approach it is possible to measure the proliferation rate in a reproducible, standard way which is an essential prerequisite for using the proliferation activity as a routine clinical tool. Comparing with immunophenotyping we may conclude that the quantitative PCR-based analysis is a useful, reliable, rapid, reproducible, sensitive and specific method broadening our diagnostic tools in hematopathology. In comparison to interphase FISH in paraffin sections quantitative PCR is less technically demanding and less time-consuming and furthermore it is more sensitive in detecting small changes in the mRNA level. Moreover, quantitative PCR is the only technology which provides precise and reproducible quantitative information about the expression level. Therefore it may be used to demonstrate the decrease or increase of a tumor-specific marker in bone marrow in comparison with a previously aspirated specimen. Thus, it has a powerful potential to monitor the course of the disease in correlation with clinical data.

Quantitative analysis of naphthenic acids in water by liquid chromatography-accurate mass time-of-flight mass spectrometry.

PubMed

Hindle, Ralph; Noestheden, Matthew; Peru, Kerry; Headley, John

2013-04-19

This study details the development of a routine method for quantitative analysis of oil sands naphthenic acids, which are a complex class of compounds found naturally and as contaminants in oil sands process waters from Alberta's Athabasca region. Expanding beyond classical naphthenic acids (CnH2n-zO2), those compounds conforming to the formula CnH2n-zOx (where 2≥x≤4) were examined in commercial naphthenic acid and environmental water samples. HPLC facilitated a five-fold reduction in ion suppression when compared to the more commonly used flow injection analysis. A comparison of 39 model naphthenic acids revealed significant variability in response factors, demonstrating the necessity of using naphthenic acid mixtures for quantitation, rather than model compounds. It was also demonstrated that naphthenic acidic heterogeneity (commercial and environmental) necessitates establishing a single NA mix as the standard against which all quantitation is performed. The authors present the first ISO17025 accredited method for the analysis of naphthenic acids in water using HPLC high resolution accurate mass time-of-flight mass spectrometry. The method detection limit was 1mg/L total oxy-naphthenic acids (Sigma technical mix). Copyright © 2013 Elsevier B.V. All rights reserved.

Accurate ECG diagnosis of atrial tachyarrhythmias using quantitative analysis: a prospective diagnostic and cost-effectiveness study.

PubMed

Krummen, David E; Patel, Mitul; Nguyen, Hong; Ho, Gordon; Kazi, Dhruv S; Clopton, Paul; Holland, Marian C; Greenberg, Scott L; Feld, Gregory K; Faddis, Mitchell N; Narayan, Sanjiv M

2010-11-01

Quantitative ECG Analysis. Optimal atrial tachyarrhythmia management is facilitated by accurate electrocardiogram interpretation, yet typical atrial flutter (AFl) may present without sawtooth F-waves or RR regularity, and atrial fibrillation (AF) may be difficult to separate from atypical AFl or rapid focal atrial tachycardia (AT). We analyzed whether improved diagnostic accuracy using a validated analysis tool significantly impacts costs and patient care. We performed a prospective, blinded, multicenter study using a novel quantitative computerized algorithm to identify atrial tachyarrhythmia mechanism from the surface ECG in patients referred for electrophysiology study (EPS). In 122 consecutive patients (age 60 ± 12 years) referred for EPS, 91 sustained atrial tachyarrhythmias were studied. ECGs were also interpreted by 9 physicians from 3 specialties for comparison and to allow healthcare system modeling. Diagnostic accuracy was compared to the diagnosis at EPS. A Markov model was used to estimate the impact of improved arrhythmia diagnosis. We found 13% of typical AFl ECGs had neither sawtooth flutter waves nor RR regularity, and were misdiagnosed by the majority of clinicians (0/6 correctly diagnosed by consensus visual interpretation) but correctly by quantitative analysis in 83% (5/6, P = 0.03). AF diagnosis was also improved through use of the algorithm (92%) versus visual interpretation (primary care: 76%, P < 0.01). Economically, we found that these improvements in diagnostic accuracy resulted in an average cost-savings of $1,303 and 0.007 quality-adjusted-life-years per patient. Typical AFl and AF are frequently misdiagnosed using visual criteria. Quantitative analysis improves diagnostic accuracy and results in improved healthcare costs and patient outcomes. © 2010 Wiley Periodicals, Inc.

[Quantitative data analysis for live imaging of bone.

PubMed

Seno, Shigeto

Bone tissue is a hard tissue, it was difficult to observe the interior of the bone tissue alive. With the progress of microscopic technology and fluorescent probe technology in recent years, it becomes possible to observe various activities of various cells forming bone society. On the other hand, the quantitative increase in data and the diversification and complexity of the images makes it difficult to perform quantitative analysis by visual inspection. It has been expected to develop a methodology for processing microscopic images and data analysis. In this article, we introduce the research field of bioimage informatics which is the boundary area of biology and information science, and then outline the basic image processing technology for quantitative analysis of live imaging data of bone.

Quantitative analysis of CMV DNA in children the first year after liver transplantation.

PubMed

Kullberg-Lindh, Carola; Ascher, Henry; Krantz, Marie; Lindh, Magnus

2003-08-01

CMV infection is a major problem after solid organ transplantation especially in children where primary infection is more common than in adults. Early diagnosis is critical and might be facilitated by quantitative analysis of CMV DNA in blood. In this retrospective study of 18 children who had a liver transplantation 1995-2000, serum samples were analysed by Cobas Amplicor Monitor (Roche). Four patients developed symptomatic CMV infection at a mean time of 4 wk after transplantation. They showed maximum CMV DNA levels in serum of 26 400, 1900, 1300 and 970 copies/mL, respectively. In comparison, CA Monitor was positive, at a low level (415 copies/mL), in one of 11 patients with asymptomatic (4) or latent (7) infection. CMV IgM was detected at significant levels (> or =1/80) in all four patients with symptomatic, and in one with asymptomatic CMV infection. Eight patients were given one or several courses of ganciclovir. Five of these lacked symptoms of CMV disease, and had low (415 copies/mL) or undetectable CMV DNA in serum. The data suggest that quantitative analysis of CMV DNA may be of value in early identification of CMV disease and for avoiding unnecessary antiviral treatment.

Quantitative trait nucleotide analysis using Bayesian model selection.

PubMed

Blangero, John; Goring, Harald H H; Kent, Jack W; Williams, Jeff T; Peterson, Charles P; Almasy, Laura; Dyer, Thomas D

2005-10-01

Although much attention has been given to statistical genetic methods for the initial localization and fine mapping of quantitative trait loci (QTLs), little methodological work has been done to date on the problem of statistically identifying the most likely functional polymorphisms using sequence data. In this paper we provide a general statistical genetic framework, called Bayesian quantitative trait nucleotide (BQTN) analysis, for assessing the likely functional status of genetic variants. The approach requires the initial enumeration of all genetic variants in a set of resequenced individuals. These polymorphisms are then typed in a large number of individuals (potentially in families), and marker variation is related to quantitative phenotypic variation using Bayesian model selection and averaging. For each sequence variant a posterior probability of effect is obtained and can be used to prioritize additional molecular functional experiments. An example of this quantitative nucleotide analysis is provided using the GAW12 simulated data. The results show that the BQTN method may be useful for choosing the most likely functional variants within a gene (or set of genes). We also include instructions on how to use our computer program, SOLAR, for association analysis and BQTN analysis.

Development of an interprofessional lean facilitator assessment scale.

PubMed

Bravo-Sanchez, Cindy; Dorazio, Vincent; Denmark, Robert; Heuer, Albert J; Parrott, J Scott

2018-05-01

High reliability is important for optimising quality and safety in healthcare organisations. Reliability efforts include interprofessional collaborative practice (IPCP) and Lean quality/process improvement strategies, which require skilful facilitation. Currently, no validated Lean facilitator assessment tool for interprofessional collaboration exists. This article describes the development and pilot evaluation of such a tool; the Interprofessional Lean Facilitator Assessment Scale (ILFAS), which measures both technical and 'soft' skills, which have not been measured in other instruments. The ILFAS was developed using methodologies and principles from Lean/Shingo, IPCP, metacognition research and Bloom's Taxonomy of Learning Domains. A panel of experts confirmed the initial face validity of the instrument. Researchers independently assessed five facilitators, during six Lean sessions. Analysis included quantitative evaluation of rater agreement. Overall inter-rater agreement of the assessment of facilitator performance was high (92%), and discrepancies in the agreement statistics were analysed. Face and content validity were further established, and usability was evaluated, through primary stakeholder post-pilot feedback, uncovering minor concerns, leading to tool revision. The ILFAS appears comprehensive in the assessment of facilitator knowledge, skills, abilities, and may be useful in the discrimination between facilitators of different skill levels. Further study is needed to explore instrument performance and validity.

A Quantitative Approach to Scar Analysis

PubMed Central

Khorasani, Hooman; Zheng, Zhong; Nguyen, Calvin; Zara, Janette; Zhang, Xinli; Wang, Joyce; Ting, Kang; Soo, Chia

2011-01-01

Analysis of collagen architecture is essential to wound healing research. However, to date no consistent methodologies exist for quantitatively assessing dermal collagen architecture in scars. In this study, we developed a standardized approach for quantitative analysis of scar collagen morphology by confocal microscopy using fractal dimension and lacunarity analysis. Full-thickness wounds were created on adult mice, closed by primary intention, and harvested at 14 days after wounding for morphometrics and standard Fourier transform-based scar analysis as well as fractal dimension and lacunarity analysis. In addition, transmission electron microscopy was used to evaluate collagen ultrastructure. We demonstrated that fractal dimension and lacunarity analysis were superior to Fourier transform analysis in discriminating scar versus unwounded tissue in a wild-type mouse model. To fully test the robustness of this scar analysis approach, a fibromodulin-null mouse model that heals with increased scar was also used. Fractal dimension and lacunarity analysis effectively discriminated unwounded fibromodulin-null versus wild-type skin as well as healing fibromodulin-null versus wild-type wounds, whereas Fourier transform analysis failed to do so. Furthermore, fractal dimension and lacunarity data also correlated well with transmission electron microscopy collagen ultrastructure analysis, adding to their validity. These results demonstrate that fractal dimension and lacunarity are more sensitive than Fourier transform analysis for quantification of scar morphology. PMID:21281794

Coupling of oceanic carbon and nitrogen facilitates spatially resolved quantitative reconstruction of nitrate inventories.

PubMed

Glock, Nicolaas; Erdem, Zeynep; Wallmann, Klaus; Somes, Christopher J; Liebetrau, Volker; Schönfeld, Joachim; Gorb, Stanislav; Eisenhauer, Anton

2018-03-23

Anthropogenic impacts are perturbing the global nitrogen cycle via warming effects and pollutant sources such as chemical fertilizers and burning of fossil fuels. Understanding controls on past nitrogen inventories might improve predictions for future global biogeochemical cycling. Here we show the quantitative reconstruction of deglacial bottom water nitrate concentrations from intermediate depths of the Peruvian upwelling region, using foraminiferal pore density. Deglacial nitrate concentrations correlate strongly with downcore δ 13 C, consistent with modern water column observations in the intermediate Pacific, facilitating the use of δ 13 C records as a paleo-nitrate-proxy at intermediate depths and suggesting that the carbon and nitrogen cycles were closely coupled throughout the last deglaciation in the Peruvian upwelling region. Combining the pore density and intermediate Pacific δ 13 C records shows an elevated nitrate inventory of >10% during the Last Glacial Maximum relative to the Holocene, consistent with a δ 13 C-based and δ 15 N-based 3D ocean biogeochemical model and previous box modeling studies.

Acquiring Teacher Commitment to 1:1 Initiatives: The Role of the Technology Facilitator

ERIC Educational Resources Information Center

Stanhope, Daniel S.; Corn, Jenifer O.

2014-01-01

Using mixed methods, we examined the impact of technology facilitators (TFs) on teacher commitment to 1:1 initiatives. Findings from quantitative analysis complemented by qualitative analyses suggest teachers benefitted from having TFs assist with the technological integration. Teachers from schools with a TF endorsed attitudes that were…

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.

Design and analysis issues in quantitative proteomics studies.

PubMed

Karp, Natasha A; Lilley, Kathryn S

2007-09-01

Quantitative proteomics is the comparison of distinct proteomes which enables the identification of protein species which exhibit changes in expression or post-translational state in response to a given stimulus. Many different quantitative techniques are being utilized and generate large datasets. Independent of the technique used, these large datasets need robust data analysis to ensure valid conclusions are drawn from such studies. Approaches to address the problems that arise with large datasets are discussed to give insight into the types of statistical analyses of data appropriate for the various experimental strategies that can be employed by quantitative proteomic studies. This review also highlights the importance of employing a robust experimental design and highlights various issues surrounding the design of experiments. The concepts and examples discussed within will show how robust design and analysis will lead to confident results that will ensure quantitative proteomics delivers.

3D Slicer as an Image Computing Platform for the Quantitative Imaging Network

PubMed Central

Fedorov, Andriy; Beichel, Reinhard; Kalpathy-Cramer, Jayashree; Finet, Julien; Fillion-Robin, Jean-Christophe; Pujol, Sonia; Bauer, Christian; Jennings, Dominique; Fennessy, Fiona; Sonka, Milan; Buatti, John; Aylward, Stephen; Miller, James V.; Pieper, Steve; Kikinis, Ron

2012-01-01

Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm, and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions. In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams, and we elaborate on the future

An interactive graphics system to facilitate finite element structural analysis

NASA Technical Reports Server (NTRS)

Burk, R. C.; Held, F. H.

1973-01-01

The characteristics of an interactive graphics systems to facilitate the finite element method of structural analysis are described. The finite element model analysis consists of three phases: (1) preprocessing (model generation), (2) problem solution, and (3) postprocessing (interpretation of results). The advantages of interactive graphics to finite element structural analysis are defined.

An Quantitative Analysis Method Of Trabecular Pattern In A Bone

NASA Astrophysics Data System (ADS)

Idesawa, Masanor; Yatagai, Toyohiko

1982-11-01

Orientation and density of trabecular pattern observed in a bone is closely related to its mechanical properties and deseases of a bone are appeared as changes of orientation and/or density distrbution of its trabecular patterns. They have been treated from a qualitative point of view so far because quantitative analysis method has not be established. In this paper, the authors proposed and investigated some quantitative analysis methods of density and orientation of trabecular patterns observed in a bone. These methods can give an index for evaluating orientation of trabecular pattern quantitatively and have been applied to analyze trabecular pattern observed in a head of femur and their availabilities are confirmed. Key Words: Index of pattern orientation, Trabecular pattern, Pattern density, Quantitative analysis

Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

PubMed

Gunar, O V; Sakhno, N G

2015-12-30

The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods. Copyright © 2015 Elsevier B.V. All rights reserved.

Screening for diverse PDGFRA or PDGFRB fusion genes is facilitated by generic quantitative reverse transcriptase polymerase chain reaction analysis

PubMed Central

Erben, Philipp; Gosenca, Darko; Müller, Martin C.; Reinhard, Jelena; Score, Joannah; del Valle, Francesco; Walz, Christoph; Mix, Jürgen; Metzgeroth, Georgia; Ernst, Thomas; Haferlach, Claudia; Cross, Nicholas C.P.; Hochhaus, Andreas; Reiter, Andreas

2010-01-01

Background Rapid identification of diverse fusion genes with involvement of PDGFRA or PDGFRB in eosinophilia-associated myeloproliferative neoplasms is essential for adequate clinical management but is complicated by the multitude and heterogeneity of partner genes and breakpoints. Design and Methods We established a generic quantitative reverse transcriptase polymerase chain reaction to detect overexpression of the 3′-regions of PDGFRA or PDGFRB as a possible indicator of an underlying fusion. Results At diagnosis, all patients with known fusion genes involving PDGFRA (n=5; 51 patients) or PDGFRB (n=5; 7 patients) showed significantly increased normalized expression levels compared to 191 patients with fusion gene-negative eosinophilia or healthy individuals (PDGFRA/ABL: 0.73 versus 0.0066 versus 0.0064, P<0.0001; PDGFRB/ABL: 196 versus 3.8 versus 5.85, P<0.0001). The sensitivity and specificity of the activation screening test were, respectively, 100% and 88.4% for PDGFRA and 100% and 94% for PDGFRB. Furthermore, significant overexpression of PDGFRB was found in a patient with an eosinophilia-associated myeloproliferative neoplasm with uninformative cytogenetics and an excellent response to imatinib. Subsequently, a new SART3-PDGFRB fusion gene was identified by 5′-rapid amplification of cDNA ends polymerase chain reaction (5′-RACE-PCR). Conclusions Quantitative reverse transcriptase polymerase chain reaction analysis is a simple and useful adjunct to standard diagnostic assays to detect clinically significant overexpression of PDGFRA and PDGFRB in eosinophilia-associated myeloproliferative neoplasms or related disorders. PMID:20107158

Good practices for quantitative bias analysis.

PubMed

Lash, Timothy L; Fox, Matthew P; MacLehose, Richard F; Maldonado, George; McCandless, Lawrence C; Greenland, Sander

2014-12-01

Quantitative bias analysis serves several objectives in epidemiological research. First, it provides a quantitative estimate of the direction, magnitude and uncertainty arising from systematic errors. Second, the acts of identifying sources of systematic error, writing down models to quantify them, assigning values to the bias parameters and interpreting the results combat the human tendency towards overconfidence in research results, syntheses and critiques and the inferences that rest upon them. Finally, by suggesting aspects that dominate uncertainty in a particular research result or topic area, bias analysis can guide efficient allocation of sparse research resources. The fundamental methods of bias analyses have been known for decades, and there have been calls for more widespread use for nearly as long. There was a time when some believed that bias analyses were rarely undertaken because the methods were not widely known and because automated computing tools were not readily available to implement the methods. These shortcomings have been largely resolved. We must, therefore, contemplate other barriers to implementation. One possibility is that practitioners avoid the analyses because they lack confidence in the practice of bias analysis. The purpose of this paper is therefore to describe what we view as good practices for applying quantitative bias analysis to epidemiological data, directed towards those familiar with the methods. We focus on answering questions often posed to those of us who advocate incorporation of bias analysis methods into teaching and research. These include the following. When is bias analysis practical and productive? How does one select the biases that ought to be addressed? How does one select a method to model biases? How does one assign values to the parameters of a bias model? How does one present and interpret a bias analysis?. We hope that our guide to good practices for conducting and presenting bias analyses will encourage

High-Throughput Quantitative Lipidomics Analysis of Nonesterified Fatty Acids in Plasma by LC-MS.

PubMed

Christinat, Nicolas; Morin-Rivron, Delphine; Masoodi, Mojgan

2017-01-01

Nonesterified fatty acids are important biological molecules which have multiple functions such as energy storage, gene regulation, or cell signaling. Comprehensive profiling of nonesterified fatty acids in biofluids can facilitate studying and understanding their roles in biological systems. For these reasons, we have developed and validated a high-throughput, nontargeted lipidomics method coupling liquid chromatography to high-resolution mass spectrometry for quantitative analysis of nonesterified fatty acids. Sufficient chromatographic separation is achieved to separate positional isomers such as polyunsaturated and branched-chain species and quantify a wide range of nonesterified fatty acids in human plasma samples. However, this method is not limited only to these fatty acid species and offers the possibility to perform untargeted screening of additional nonesterified fatty acid species.

Perceived barriers and facilitators to mental health help-seeking in young people: a systematic review

PubMed Central

2010-01-01

Background Adolescents and young adults frequently experience mental disorders, yet tend not to seek help. This systematic review aims to summarise reported barriers and facilitators of help-seeking in young people using both qualitative research from surveys, focus groups, and interviews and quantitative data from published surveys. It extends previous reviews through its systematic research methodology and by the inclusion of published studies describing what young people themselves perceive are the barriers and facilitators to help-seeking for common mental health problems. Methods Twenty two published studies of perceived barriers or facilitators in adolescents or young adults were identified through searches of PubMed, PsycInfo, and the Cochrane database. A thematic analysis was undertaken on the results reported in the qualitative literature and quantitative literature. Results Fifteen qualitative and seven quantitative studies were identified. Young people perceived stigma and embarrassment, problems recognising symptoms (poor mental health literacy), and a preference for self-reliance as the most important barriers to help-seeking. Facilitators were comparatively under-researched. However, there was evidence that young people perceived positive past experiences, and social support and encouragement from others as aids to the help-seeking process. Conclusions Strategies for improving help-seeking by adolescents and young adults should focus on improving mental health literacy, reducing stigma, and taking into account the desire of young people for self-reliance. PMID:21192795

Perceived barriers and facilitators to mental health help-seeking in young people: a systematic review.

PubMed

Gulliver, Amelia; Griffiths, Kathleen M; Christensen, Helen

2010-12-30

Adolescents and young adults frequently experience mental disorders, yet tend not to seek help. This systematic review aims to summarise reported barriers and facilitators of help-seeking in young people using both qualitative research from surveys, focus groups, and interviews and quantitative data from published surveys. It extends previous reviews through its systematic research methodology and by the inclusion of published studies describing what young people themselves perceive are the barriers and facilitators to help-seeking for common mental health problems. Twenty two published studies of perceived barriers or facilitators in adolescents or young adults were identified through searches of PubMed, PsycInfo, and the Cochrane database. A thematic analysis was undertaken on the results reported in the qualitative literature and quantitative literature. Fifteen qualitative and seven quantitative studies were identified. Young people perceived stigma and embarrassment, problems recognising symptoms (poor mental health literacy), and a preference for self-reliance as the most important barriers to help-seeking. Facilitators were comparatively under-researched. However, there was evidence that young people perceived positive past experiences, and social support and encouragement from others as aids to the help-seeking process. Strategies for improving help-seeking by adolescents and young adults should focus on improving mental health literacy, reducing stigma, and taking into account the desire of young people for self-reliance.

Facilitation and Teacher Behaviors: An Analysis of Literacy Teachers' Video-Case Discussions

ERIC Educational Resources Information Center

Arya, Poonam; Christ, Tanya; Chiu, Ming Ming

2014-01-01

This study explored how peer and professor facilitations are related to teachers' behaviors during video-case discussions. Fourteen inservice teachers produced 1,787 turns of conversation during 12 video-case discussions that were video-recorded, transcribed, coded, and analyzed with statistical discourse analysis. Professor facilitations (sharing…

Quantitative mass spectrometry methods for pharmaceutical analysis

PubMed Central

Loos, Glenn; Van Schepdael, Ann

2016-01-01

Quantitative pharmaceutical analysis is nowadays frequently executed using mass spectrometry. Electrospray ionization coupled to a (hybrid) triple quadrupole mass spectrometer is generally used in combination with solid-phase extraction and liquid chromatography. Furthermore, isotopically labelled standards are often used to correct for ion suppression. The challenges in producing sensitive but reliable quantitative data depend on the instrumentation, sample preparation and hyphenated techniques. In this contribution, different approaches to enhance the ionization efficiencies using modified source geometries and improved ion guidance are provided. Furthermore, possibilities to minimize, assess and correct for matrix interferences caused by co-eluting substances are described. With the focus on pharmaceuticals in the environment and bioanalysis, different separation techniques, trends in liquid chromatography and sample preparation methods to minimize matrix effects and increase sensitivity are discussed. Although highly sensitive methods are generally aimed for to provide automated multi-residue analysis, (less sensitive) miniaturized set-ups have a great potential due to their ability for in-field usage. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644982

Children's drawings as facilitators of communication: a meta-analysis.

PubMed

Driessnack, Martha

2005-12-01

In an attempt to explore new methods for accessing children's voices, this meta-analysis explores the facilitative effects of offering children the opportunity to draw as an interview strategy as compared with a traditional directed interview. Based on this analysis, introducing the opportunity to draw appears to be a relatively robust interview strategy with a large overall effect size (d = .95). Both research and clinical implications are discussed.

Quantitative twoplex glycan analysis using 12C6 and 13C6 stable isotope 2-aminobenzoic acid labelling and capillary electrophoresis mass spectrometry.

PubMed

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

2016-12-01

Capillary electrophoresis (CE) offers excellent efficiency and orthogonality to liquid chromatographic (LC) separations for oligosaccharide structural analysis. Combination of CE with high resolution mass spectrometry (MS) for glycan analysis remains a challenging task due to the MS incompatibility of background electrolyte buffers and additives commonly used in offline CE separations. Here, a novel method is presented for the analysis of 2-aminobenzoic acid (2-AA) labelled glycans by capillary electrophoresis coupled to mass spectrometry (CE-MS). To ensure maximum resolution and excellent precision without the requirement for excessive analysis times, CE separation conditions including the concentration and pH of the background electrolyte, the effect of applied pressure on the capillary inlet and the capillary length were evaluated. Using readily available 12/13 C 6 stable isotopologues of 2-AA, the developed method can be applied for quantitative glycan profiling in a twoplex manner based on the generation of extracted ion electropherograms (EIE) for 12 C 6 'light' and 13 C 6 'heavy' 2-AA labelled glycan isotope clusters. The twoplex quantitative CE-MS glycan analysis platform is ideally suited for comparability assessment of biopharmaceuticals, such as monoclonal antibodies, for differential glycomic analysis of clinical material for potential biomarker discovery or for quantitative microheterogeneity analysis of different glycosylation sites within a glycoprotein. Additionally, due to the low injection volume requirements of CE, subsequent LC-MS analysis of the same sample can be performed facilitating the use of orthogonal separation techniques for structural elucidation or verification of quantitative performance.

Project FAST: [Functional Analysis Systems Training]: Adopter/Facilitator Information.

ERIC Educational Resources Information Center

Essexville-Hampton Public Schools, MI.

Presented is adopter/facilitator information of Project FAST (Functional Analysis Systems Training) to provide educational and support services to learning disordered children and their regular elementary teachers. Briefly described are the three schools in the Essexville-Hampton (Michigan) school district; objectives of the program; program…

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

Quantitative Detection and Biological Propagation of Scrapie Seeding Activity In Vitro Facilitate Use of Prions as Model Pathogens for Disinfection

PubMed Central

Pritzkow, Sandra; Wagenführ, Katja; Daus, Martin L.; Boerner, Susann; Lemmer, Karin; Thomzig, Achim; Mielke, Martin; Beekes, Michael

2011-01-01

Prions are pathogens with an unusually high tolerance to inactivation and constitute a complex challenge to the re-processing of surgical instruments. On the other hand, however, they provide an informative paradigm which has been exploited successfully for the development of novel broad-range disinfectants simultaneously active also against bacteria, viruses and fungi. Here we report on the development of a methodological platform that further facilitates the use of scrapie prions as model pathogens for disinfection. We used specifically adapted serial protein misfolding cyclic amplification (PMCA) for the quantitative detection, on steel wires providing model carriers for decontamination, of 263K scrapie seeding activity converting normal protease-sensitive into abnormal protease-resistant prion protein. Reference steel wires carrying defined amounts of scrapie infectivity were used for assay calibration, while scrapie-contaminated test steel wires were subjected to fifteen different procedures for disinfection that yielded scrapie titre reductions of ≤101- to ≥105.5-fold. As confirmed by titration in hamsters the residual scrapie infectivity on test wires could be reliably deduced for all examined disinfection procedures, from our quantitative seeding activity assay. Furthermore, we found that scrapie seeding activity present in 263K hamster brain homogenate or multiplied by PMCA of scrapie-contaminated steel wires both triggered accumulation of protease-resistant prion protein and was further propagated in a novel cell assay for 263K scrapie prions, i.e., cerebral glial cell cultures from hamsters. The findings from our PMCA- and glial cell culture assays revealed scrapie seeding activity as a biochemically and biologically replicative principle in vitro, with the former being quantitatively linked to prion infectivity detected on steel wires in vivo. When combined, our in vitro assays provide an alternative to titrations of biological scrapie infectivity

Why Do Women Not Use Preconception Care? A Systematic Review On Barriers And Facilitators.

PubMed

Poels, Marjolein; Koster, Maria P H; Boeije, Hennie R; Franx, Arie; van Stel, Henk F

2016-10-01

Preconception care (PCC) has the potential to optimize pregnancy outcomes. However, awareness of PCC among the target population is generally limited, and the use of PCC remains low. The objective of this study was to review the literature on women's perceptions regarding barriers and facilitators for the use of PCC. A systematic search was conducted in MEDLINE, Embase, CINAHL, and PsycINFO for published studies until February 2015. Original qualitative and quantitative peer-reviewed studies from Western countries in English, holding women's perceptions regarding barriers and facilitators for the use of PCC. Data extraction and analysis were performed using NVivo version 10 software. A coding frame was derived from the findings and applied by 2 authors. Thematic analysis was used to identify key topics and themes. Twenty-one good-quality articles were included, of which 10 qualitative and 11 quantitative studies. Seven main themes were identified: preconditions, emotions and beliefs, perceived need, knowledge and experience, social structure, accessibility, and provider characteristics. "Not (fully) planning pregnancy", "perceived absence of risks", "lack of awareness", and "pregnancy experiences" were the most frequently identified barriers and "believing in the benefits" and "availability of PCC" the most frequently identified facilitators for PCC use. Women perceive more barriers than facilitators related to PCC uptake, which explains why the use of PCC remains low. Our results provide a starting point to refocus interventions and strategies, aiming on enlarging the awareness, perceived importance, and accessibility of PCC to improve its uptake.

A gold nanoparticle-based semi-quantitative and quantitative ultrasensitive paper sensor for the detection of twenty mycotoxins

NASA Astrophysics Data System (ADS)

Kong, Dezhao; Liu, Liqiang; Song, Shanshan; Suryoprabowo, Steven; Li, Aike; Kuang, Hua; Wang, Libing; Xu, Chuanlai

2016-02-01

A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan reader, with the calculated limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.04-0.17, 0.06-49, 0.15-0.22, 0.056-0.49 and 0.53-1.05 μg kg-1, respectively. The analytical results of spiked samples were in accordance with the accurate content in the simultaneous detection analysis. This newly developed ICA strip assay is suitable for the on-site detection and rapid initial screening of mycotoxins in cereal samples, facilitating both semi-quantitative and quantitative determination.A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan

Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.

ERIC Educational Resources Information Center

Anderson, James L.; And Others

1980-01-01

Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)

Quantitative analysis of arm movement smoothness

NASA Astrophysics Data System (ADS)

Szczesna, Agnieszka; Błaszczyszyn, Monika

2017-07-01

The paper deals with the problem of motion data quantitative smoothness analysis. We investigated values of movement unit, fluidity and jerk for healthy and paralyzed arm of patients with hemiparesis after stroke. Patients were performing drinking task. To validate the approach, movement of 24 patients were captured using optical motion capture system.

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena

PubMed Central

Tohsato, Yukako; Ho, Kenneth H. L.; Kyoda, Koji; Onami, Shuichi

2016-01-01

Motivation: Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis. Results: We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus. The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis. Availability and Implementation: SSBD is accessible at http://ssbd.qbic.riken.jp. Contact: sonami@riken.jp PMID:27412095

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena.

PubMed

Tohsato, Yukako; Ho, Kenneth H L; Kyoda, Koji; Onami, Shuichi

2016-11-15

Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis. We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis. SSBD is accessible at http://ssbd.qbic.riken.jp CONTACT: sonami@riken.jp. © The Author 2016. Published by Oxford University Press.

Quantitative Proteomic Analysis of the Hfq-Regulon in Sinorhizobium meliloti 2011

PubMed Central

Sobrero, Patricio; Schlüter, Jan-Philip; Lanner, Ulrike; Schlosser, Andreas; Becker, Anke; Valverde, Claudio

2012-01-01

Riboregulation stands for RNA-based control of gene expression. In bacteria, small non-coding RNAs (sRNAs) are a major class of riboregulatory elements, most of which act at the post-transcriptional level by base-pairing target mRNA genes. The RNA chaperone Hfq facilitates antisense interactions between target mRNAs and regulatory sRNAs, thus influencing mRNA stability and/or translation rate. In the α-proteobacterium Sinorhizobium meliloti strain 2011, the identification and detection of multiple sRNAs genes and the broadly pleitropic phenotype associated to the absence of a functional Hfq protein both support the existence of riboregulatory circuits controlling gene expression to ensure the fitness of this bacterium in both free living and symbiotic conditions. In order to identify target mRNAs subject to Hfq-dependent riboregulation, we have compared the proteome of an hfq mutant and the wild type S. meliloti by quantitative proteomics following protein labelling with 15N. Among 2139 univocally identified proteins, a total of 195 proteins showed a differential abundance between the Hfq mutant and the wild type strain; 65 proteins accumulated ≥2-fold whereas 130 were downregulated (≤0.5-fold) in the absence of Hfq. This profound proteomic impact implies a major role for Hfq on regulation of diverse physiological processes in S. meliloti, from transport of small molecules to homeostasis of iron and nitrogen. Changes in the cellular levels of proteins involved in transport of nucleotides, peptides and amino acids, and in iron homeostasis, were confirmed with phenotypic assays. These results represent the first quantitative proteomic analysis in S. meliloti. The comparative analysis of the hfq mutant proteome allowed identification of novel strongly Hfq-regulated genes in S. meliloti. PMID:23119037

Quantitative proteomic analysis of the Hfq-regulon in Sinorhizobium meliloti 2011.

PubMed

Sobrero, Patricio; Schlüter, Jan-Philip; Lanner, Ulrike; Schlosser, Andreas; Becker, Anke; Valverde, Claudio

2012-01-01

Riboregulation stands for RNA-based control of gene expression. In bacteria, small non-coding RNAs (sRNAs) are a major class of riboregulatory elements, most of which act at the post-transcriptional level by base-pairing target mRNA genes. The RNA chaperone Hfq facilitates antisense interactions between target mRNAs and regulatory sRNAs, thus influencing mRNA stability and/or translation rate. In the α-proteobacterium Sinorhizobium meliloti strain 2011, the identification and detection of multiple sRNAs genes and the broadly pleitropic phenotype associated to the absence of a functional Hfq protein both support the existence of riboregulatory circuits controlling gene expression to ensure the fitness of this bacterium in both free living and symbiotic conditions. In order to identify target mRNAs subject to Hfq-dependent riboregulation, we have compared the proteome of an hfq mutant and the wild type S. meliloti by quantitative proteomics following protein labelling with (15)N. Among 2139 univocally identified proteins, a total of 195 proteins showed a differential abundance between the Hfq mutant and the wild type strain; 65 proteins accumulated ≥2-fold whereas 130 were downregulated (≤0.5-fold) in the absence of Hfq. This profound proteomic impact implies a major role for Hfq on regulation of diverse physiological processes in S. meliloti, from transport of small molecules to homeostasis of iron and nitrogen. Changes in the cellular levels of proteins involved in transport of nucleotides, peptides and amino acids, and in iron homeostasis, were confirmed with phenotypic assays. These results represent the first quantitative proteomic analysis in S. meliloti. The comparative analysis of the hfq mutant proteome allowed identification of novel strongly Hfq-regulated genes in S. meliloti.

Extraction and quantitative analysis of iodine in solid and solution matrixes.

PubMed

Brown, Christopher F; Geiszler, Keith N; Vickerman, Tanya S

2005-11-01

129I is a contaminant of interest in the vadose zone and groundwater at numerous federal and privately owned facilities. Several techniques have been utilized to extract iodine from solid matrixes; however, all of them rely on two fundamental approaches: liquid extraction or chemical/heat-facilitated volatilization. While these methods are typically chosen for their ease of implementation, they do not totally dissolve the solid. We defined a method that produces complete solid dissolution and conducted laboratory tests to assess its efficacy to extract iodine from solid matrixes. Testing consisted of potassium nitrate/potassium hydroxide fusion of the sample, followed by sample dissolution in a mixture of sulfuric acid and sodium bisulfite. The fusion extraction method resulted in complete sample dissolution of all solid matrixes tested. Quantitative analysis of 127I and 129I via inductively coupled plasma mass spectrometry showed better than +/-10% accuracy for certified reference standards, with the linear operating range extending more than 3 orders of magnitude (0.005-5 microg/L). Extraction and analysis of four replicates of standard reference material containing 5 microg/g 127I resulted in an average recovery of 98% with a relative deviation of 6%. This simple and cost-effective technique can be applied to solid samples of varying matrixes with little or no adaptation.

Control of separation and quantitative analysis by GC-FTIR

NASA Astrophysics Data System (ADS)

Semmoud, A.; Huvenne, Jean P.; Legrand, P.

1992-03-01

Software for 3-D representations of the 'Absorbance-Wavenumber-Retention time' is used to control the quality of the GC separation. Spectral information given by the FTIR detection allows the user to be sure that a chromatographic peak is 'pure.' The analysis of peppermint essential oil is presented as an example. This assurance is absolutely required for quantitative applications. In these conditions, we have worked out a quantitative analysis of caffeine. Correlation coefficients between integrated absorbance measurements and concentration of caffeine are discussed at two steps of the data treatment.

Quantitative Analysis of the Efficiency of OLEDs.

PubMed

Sim, Bomi; Moon, Chang-Ki; Kim, Kwon-Hyeon; Kim, Jang-Joo

2016-12-07

We present a comprehensive model for the quantitative analysis of factors influencing the efficiency of organic light-emitting diodes (OLEDs) as a function of the current density. The model takes into account the contribution made by the charge carrier imbalance, quenching processes, and optical design loss of the device arising from various optical effects including the cavity structure, location and profile of the excitons, effective radiative quantum efficiency, and out-coupling efficiency. Quantitative analysis of the efficiency can be performed with an optical simulation using material parameters and experimental measurements of the exciton profile in the emission layer and the lifetime of the exciton as a function of the current density. This method was applied to three phosphorescent OLEDs based on a single host, mixed host, and exciplex-forming cohost. The three factors (charge carrier imbalance, quenching processes, and optical design loss) were influential in different ways, depending on the device. The proposed model can potentially be used to optimize OLED configurations on the basis of an analysis of the underlying physical processes.

Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method.

PubMed

Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

2014-02-01

To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil.

Quantitative analysis of γ-oryzanol content in cold pressed rice bran oil by TLC-image analysis method

PubMed Central

Sakunpak, Apirak; Suksaeree, Jirapornchai; Monton, Chaowalit; Pathompak, Pathamaporn; Kraisintu, Krisana

2014-01-01

Objective To develop and validate an image analysis method for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. Methods TLC-densitometric and TLC-image analysis methods were developed, validated, and used for quantitative analysis of γ-oryzanol in cold pressed rice bran oil. The results obtained by these two different quantification methods were compared by paired t-test. Results Both assays provided good linearity, accuracy, reproducibility and selectivity for determination of γ-oryzanol. Conclusions The TLC-densitometric and TLC-image analysis methods provided a similar reproducibility, accuracy and selectivity for the quantitative determination of γ-oryzanol in cold pressed rice bran oil. A statistical comparison of the quantitative determinations of γ-oryzanol in samples did not show any statistically significant difference between TLC-densitometric and TLC-image analysis methods. As both methods were found to be equal, they therefore can be used for the determination of γ-oryzanol in cold pressed rice bran oil. PMID:25182282

Applying Qualitative Hazard Analysis to Support Quantitative Safety Analysis for Proposed Reduced Wake Separation Conops

NASA Technical Reports Server (NTRS)

Shortle, John F.; Allocco, Michael

2005-01-01

This paper describes a scenario-driven hazard analysis process to identify, eliminate, and control safety-related risks. Within this process, we develop selective criteria to determine the applicability of applying engineering modeling to hypothesized hazard scenarios. This provides a basis for evaluating and prioritizing the scenarios as candidates for further quantitative analysis. We have applied this methodology to proposed concepts of operations for reduced wake separation for closely spaced parallel runways. For arrivals, the process identified 43 core hazard scenarios. Of these, we classified 12 as appropriate for further quantitative modeling, 24 that should be mitigated through controls, recommendations, and / or procedures (that is, scenarios not appropriate for quantitative modeling), and 7 that have the lowest priority for further analysis.

A quantitative analysis of the F18 flight control system

NASA Technical Reports Server (NTRS)

Doyle, Stacy A.; Dugan, Joanne B.; Patterson-Hine, Ann

1993-01-01

This paper presents an informal quantitative analysis of the F18 flight control system (FCS). The analysis technique combines a coverage model with a fault tree model. To demonstrate the method's extensive capabilities, we replace the fault tree with a digraph model of the F18 FCS, the only model available to us. The substitution shows that while digraphs have primarily been used for qualitative analysis, they can also be used for quantitative analysis. Based on our assumptions and the particular failure rates assigned to the F18 FCS components, we show that coverage does have a significant effect on the system's reliability and thus it is important to include coverage in the reliability analysis.

Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH

PubMed Central

Komosa, Martin; Root, Heather; Meyn, M. Stephen

2015-01-01

Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain <5 ECTR DNA molecules/nucleus. ECTR DNA in ALT cells exhibit striking cell-to-cell variations in number (<20 to >300), range widely in length (<1 to >200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but <4% in U2OS cells. In addition to its use in ALT cell analysis, Halo-FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells. PMID:25662602

A strategy to apply quantitative epistasis analysis on developmental traits.

PubMed

Labocha, Marta K; Yuan, Wang; Aleman-Meza, Boanerges; Zhong, Weiwei

2017-05-15

Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement. Using two different C. elegans developmental phenotypes, body length and sex ratio, as examples, we showed that this method could accommodate various metazoan phenotypes with performances comparable to those methods in single cell growth studies. Comparing with qualitative observations, this method of quantitative epistasis enabled detection of new interactions involving subtle phenotypes. For example, several sex-ratio genes were found to interact with brc-1 and brd-1, the orthologs of the human breast cancer genes BRCA1 and BARD1, respectively. We confirmed the brc-1 interactions with the following genes in DNA damage response: C34F6.1, him-3 (ortholog of HORMAD1, HORMAD2), sdc-1, and set-2 (ortholog of SETD1A, SETD1B, KMT2C, KMT2D), validating the effectiveness of our method in detecting genetic interactions. We developed a reliable, high-throughput method for quantitative epistasis analysis of developmental phenotypes.

Strategies facilitating practice change in pediatric cancer: a systematic review.

PubMed

Robinson, Paula D; Dupuis, Lee L; Tomlinson, George; Phillips, Bob; Greenberg, Mark; Sung, Lillian

2016-09-01

By conducting a systematic review, we describe strategies to actively disseminate knowledge or facilitate practice change among healthcare providers caring for children with cancer and we evaluate the effectiveness of these strategies. We searched Ovid Medline, EMBASE and PsychINFO. Fully published primary studies were included if they evaluated one or more professional intervention strategies to actively disseminate knowledge or facilitate practice change in pediatric cancer or hematopoietic stem cell transplantation. Data extracted included study characteristics and strategies evaluated. In studies with a quantitative analysis of patient outcomes, the relationship between study-level characteristics and statistically significant primary analyses was evaluated. Of 20 644 titles and abstracts screened, 146 studies were retrieved in full and 60 were included. In 20 studies, quantitative evaluation of patient outcomes was examined and a primary outcome was stated. Eighteen studies were 'before and after' design; there were no randomized studies. All studies were at risk for bias. Interrupted time series was never the primary analytic approach. No specific strategy type was successful at improving patient outcomes. Literature describing strategies to facilitate practice change in pediatric cancer is emerging. However, major methodological limitations exist. Studies with robust designs are required to identify effective strategies to effect practice change. © The Author 2016. Published by Oxford University Press in association with the International Society for Quality in Health Care. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Quantiprot - a Python package for quantitative analysis of protein sequences.

PubMed

Konopka, Bogumił M; Marciniak, Marta; Dyrka, Witold

2017-07-17

The field of protein sequence analysis is dominated by tools rooted in substitution matrices and alignments. A complementary approach is provided by methods of quantitative characterization. A major advantage of the approach is that quantitative properties defines a multidimensional solution space, where sequences can be related to each other and differences can be meaningfully interpreted. Quantiprot is a software package in Python, which provides a simple and consistent interface to multiple methods for quantitative characterization of protein sequences. The package can be used to calculate dozens of characteristics directly from sequences or using physico-chemical properties of amino acids. Besides basic measures, Quantiprot performs quantitative analysis of recurrence and determinism in the sequence, calculates distribution of n-grams and computes the Zipf's law coefficient. We propose three main fields of application of the Quantiprot package. First, quantitative characteristics can be used in alignment-free similarity searches, and in clustering of large and/or divergent sequence sets. Second, a feature space defined by quantitative properties can be used in comparative studies of protein families and organisms. Third, the feature space can be used for evaluating generative models, where large number of sequences generated by the model can be compared to actually observed sequences.

What Really Happens in Quantitative Group Research? Results of a Content Analysis of Recent Quantitative Research in "JSGW"

ERIC Educational Resources Information Center

Boyle, Lauren H.; Whittaker, Tiffany A.; Eyal, Maytal; McCarthy, Christopher J.

2017-01-01

The authors conducted a content analysis on quantitative studies published in "The Journal for Specialists in Group Work" ("JSGW") between 2012 and 2015. This brief report provides a general overview of the current practices of quantitative group research in counseling. The following study characteristics are reported and…

Method and apparatus for chromatographic quantitative analysis

DOEpatents

Fritz, James S.; Gjerde, Douglas T.; Schmuckler, Gabriella

1981-06-09

An improved apparatus and method for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single eluent and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.

Quantitative Analysis of High-Quality Officer Selection by Commandants Career-Level Education Board

DTIC Science & Technology

2017-03-01

due to Marines being evaluated before the end of their initial service commitment. Our research utilizes quantitative variables to analyze the...not provide detailed information why. B. LIMITATIONS The photograph analysis in this research is strictly limited to a quantitative analysis in...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. QUANTITATIVE

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.

Comprehensive Quantitative Analysis on Privacy Leak Behavior

PubMed Central

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

Comprehensive quantitative analysis on privacy leak behavior.

PubMed

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects.

Automated image analysis for quantitative fluorescence in situ hybridization with environmental samples.

PubMed

Zhou, Zhi; Pons, Marie Noëlle; Raskin, Lutgarde; Zilles, Julie L

2007-05-01

When fluorescence in situ hybridization (FISH) analyses are performed with complex environmental samples, difficulties related to the presence of microbial cell aggregates and nonuniform background fluorescence are often encountered. The objective of this study was to develop a robust and automated quantitative FISH method for complex environmental samples, such as manure and soil. The method and duration of sample dispersion were optimized to reduce the interference of cell aggregates. An automated image analysis program that detects cells from 4',6'-diamidino-2-phenylindole (DAPI) micrographs and extracts the maximum and mean fluorescence intensities for each cell from corresponding FISH images was developed with the software Visilog. Intensity thresholds were not consistent even for duplicate analyses, so alternative ways of classifying signals were investigated. In the resulting method, the intensity data were divided into clusters using fuzzy c-means clustering, and the resulting clusters were classified as target (positive) or nontarget (negative). A manual quality control confirmed this classification. With this method, 50.4, 72.1, and 64.9% of the cells in two swine manure samples and one soil sample, respectively, were positive as determined with a 16S rRNA-targeted bacterial probe (S-D-Bact-0338-a-A-18). Manual counting resulted in corresponding values of 52.3, 70.6, and 61.5%, respectively. In two swine manure samples and one soil sample 21.6, 12.3, and 2.5% of the cells were positive with an archaeal probe (S-D-Arch-0915-a-A-20), respectively. Manual counting resulted in corresponding values of 22.4, 14.0, and 2.9%, respectively. This automated method should facilitate quantitative analysis of FISH images for a variety of complex environmental samples.

Global scaling for semi-quantitative analysis in FP-CIT SPECT.

PubMed

Kupitz, D; Apostolova, I; Lange, C; Ulrich, G; Amthauer, H; Brenner, W; Buchert, R

2014-01-01

Semi-quantitative characterization of dopamine transporter availability from single photon emission computed tomography (SPECT) with 123I-ioflupane (FP-CIT) is based on uptake ratios relative to a reference region. The aim of this study was to evaluate the whole brain as reference region for semi-quantitative analysis of FP-CIT SPECT. The rationale was that this might reduce statistical noise associated with the estimation of non-displaceable FP-CIT uptake. 150 FP-CIT SPECTs were categorized as neurodegenerative or non-neurodegenerative by an expert. Semi-quantitative analysis of specific binding ratios (SBR) was performed with a custom-made tool based on the Statistical Parametric Mapping software package using predefined regions of interest (ROIs) in the anatomical space of the Montreal Neurological Institute. The following reference regions were compared: predefined ROIs for frontal and occipital lobe and whole brain (without striata, thalamus and brainstem). Tracer uptake in the reference region was characterized by the mean, median or 75th percentile of its voxel intensities. The area (AUC) under the receiver operating characteristic curve was used as performance measure. The highest AUC of 0.973 was achieved by the SBR of the putamen with the 75th percentile in the whole brain as reference. The lowest AUC for the putamen SBR of 0.937 was obtained with the mean in the frontal lobe as reference. We recommend the 75th percentile in the whole brain as reference for semi-quantitative analysis in FP-CIT SPECT. This combination provided the best agreement of the semi-quantitative analysis with visual evaluation of the SPECT images by an expert and, therefore, is appropriate to support less experienced physicians.

Fabrication of type I collagen microcarrier using a microfluidic 3D T-junction device and its application for the quantitative analysis of cell-ECM interactions.

PubMed

Yoon, Junghyo; Kim, Jaehoon; Jeong, Hyo Eun; Sudo, Ryo; Park, Myung-Jin; Chung, Seok

2016-08-26

We presented a new quantitative analysis for cell and extracellular matrix (ECM) interactions, using cell-coated ECM hydrogel microbeads (hydrobeads) made of type I collagen. The hydrobeads can carry cells as three-dimensional spheroidal forms with an ECM inside, facilitating a direct interaction between the cells and ECM. The cells on hydrobeads do not have a hypoxic core, which opens the possibility for using as a cell microcarrier for bottom-up tissue reconstitution. This technique can utilize various types of cells, even MDA-MB-231 cells, which have weak cell-cell interactions and do not form spheroids in conventional spheroid culture methods. Morphological indices of the cell-coated hydrobead visually present cell-ECM interactions in a quantitative manner.

Public and patient involvement in quantitative health research: A statistical perspective.

PubMed

Hannigan, Ailish

2018-06-19

The majority of studies included in recent reviews of impact for public and patient involvement (PPI) in health research had a qualitative design. PPI in solely quantitative designs is underexplored, particularly its impact on statistical analysis. Statisticians in practice have a long history of working in both consultative (indirect) and collaborative (direct) roles in health research, yet their perspective on PPI in quantitative health research has never been explicitly examined. To explore the potential and challenges of PPI from a statistical perspective at distinct stages of quantitative research, that is sampling, measurement and statistical analysis, distinguishing between indirect and direct PPI. Statistical analysis is underpinned by having a representative sample, and a collaborative or direct approach to PPI may help achieve that by supporting access to and increasing participation of under-represented groups in the population. Acknowledging and valuing the role of lay knowledge of the context in statistical analysis and in deciding what variables to measure may support collective learning and advance scientific understanding, as evidenced by the use of participatory modelling in other disciplines. A recurring issue for quantitative researchers, which reflects quantitative sampling methods, is the selection and required number of PPI contributors, and this requires further methodological development. Direct approaches to PPI in quantitative health research may potentially increase its impact, but the facilitation and partnership skills required may require further training for all stakeholders, including statisticians. © 2018 The Authors Health Expectations published by John Wiley & Sons Ltd.

Seniors' Online Communities: A Quantitative Content Analysis

ERIC Educational Resources Information Center

Nimrod, Galit

2010-01-01

Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was…

Targeted methods for quantitative analysis of protein glycosylation

PubMed Central

Goldman, Radoslav; Sanda, Miloslav

2018-01-01

Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated. PMID:25522218

Software for quantitative analysis of radiotherapy: overview, requirement analysis and design solutions.

PubMed

Zhang, Lanlan; Hub, Martina; Mang, Sarah; Thieke, Christian; Nix, Oliver; Karger, Christian P; Floca, Ralf O

2013-06-01

Radiotherapy is a fast-developing discipline which plays a major role in cancer care. Quantitative analysis of radiotherapy data can improve the success of the treatment and support the prediction of outcome. In this paper, we first identify functional, conceptional and general requirements on a software system for quantitative analysis of radiotherapy. Further we present an overview of existing radiotherapy analysis software tools and check them against the stated requirements. As none of them could meet all of the demands presented herein, we analyzed possible conceptional problems and present software design solutions and recommendations to meet the stated requirements (e.g. algorithmic decoupling via dose iterator pattern; analysis database design). As a proof of concept we developed a software library "RTToolbox" following the presented design principles. The RTToolbox is available as open source library and has already been tested in a larger-scale software system for different use cases. These examples demonstrate the benefit of the presented design principles. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

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.

ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

NASA Astrophysics Data System (ADS)

Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

Understanding Facilitation: Theory and Principles.

ERIC Educational Resources Information Center

Hogan, Christine

This book introduces newcomers to the concept of facilitation, and it presents a critical analysis of established and current theory on facilitation for existing practitioners. The following are among the topics discussed: (1) emergence of the field of facilitation; (2) development of facilitation in management; (3) development of facilitation in…

Trans individuals' facilitative coping: An analysis of internal and external processes.

PubMed

Budge, Stephanie L; Chin, Mun Yuk; Minero, Laura P

2017-01-01

Existing research on trans individuals has primarily focused on their negative experiences and has disproportionately examined coming-out processes and identity development stages. Using a grounded theory approach, this qualitative study sought to examine facilitative coping processes among trans-identified individuals. Facilitative coping was operationalized as processes whereby individuals seek social support, learn new skills, change behaviors to positively adapt, and find alternative means to seek personal growth and acceptance. The sample included 15 participants who self-identified with a gender identity that was different from their assigned sex at birth. Results yielded a total of nine overarching themes: Accepting Support from Others, Actions to Increase Protection, Active Engagement Throughout the Transition Process, Actively Seeking Social Interactions, Engaging in Exploration, Internal Processes Leading to Self-Acceptance, Self-Efficacy, Shifts Leading to Embracing Change and Flexibility, and Utilization of Agency. Based on the analysis, a theoretical model emerged that highlighted the importance of internal and external coping processes in facilitating gender identity development and navigating stressors among trans individuals. Clinical implications focusing on how to implement facilitative coping processes are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues.

PubMed

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health.Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper,we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameter scan provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

Mueller matrix microscope: a quantitative tool to facilitate detections and fibrosis scorings of liver cirrhosis and cancer tissues

NASA Astrophysics Data System (ADS)

Wang, Ye; He, Honghui; Chang, Jintao; He, Chao; Liu, Shaoxiong; Li, Migao; Zeng, Nan; Wu, Jian; Ma, Hui

2016-07-01

Today the increasing cancer incidence rate is becoming one of the biggest threats to human health. Among all types of cancers, liver cancer ranks in the top five in both frequency and mortality rate all over the world. During the development of liver cancer, fibrosis often evolves as part of a healing process in response to liver damage, resulting in cirrhosis of liver tissues. In a previous study, we applied the Mueller matrix microscope to pathological liver tissue samples and found that both the Mueller matrix polar decomposition (MMPD) and Mueller matrix transformation (MMT) parameters are closely related to the fibrous microstructures. In this paper, we take this one step further to quantitatively facilitate the fibrosis detections and scorings of pathological liver tissue samples in different stages from cirrhosis to cancer using the Mueller matrix microscope. The experimental results of MMPD and MMT parameters for the fibrotic liver tissue samples in different stages are measured and analyzed. We also conduct Monte Carlo simulations based on the sphere birefringence model to examine in detail the influence of structural changes in different fibrosis stages on the imaging parameters. Both the experimental and simulated results indicate that the polarized light microscope and transformed Mueller matrix parameters can provide additional quantitative information helpful for fibrosis detections and scorings of liver cirrhosis and cancers. Therefore, the polarized light microscope and transformed Mueller matrix parameters have a good application prospect in liver cancer diagnosis.

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.

Computerized image analysis for quantitative neuronal phenotyping in zebrafish.

PubMed

Liu, Tianming; Lu, Jianfeng; Wang, Ye; Campbell, William A; Huang, Ling; Zhu, Jinmin; Xia, Weiming; Wong, Stephen T C

2006-06-15

An integrated microscope image analysis pipeline is developed for automatic analysis and quantification of phenotypes in zebrafish with altered expression of Alzheimer's disease (AD)-linked genes. We hypothesize that a slight impairment of neuronal integrity in a large number of zebrafish carrying the mutant genotype can be detected through the computerized image analysis method. Key functionalities of our zebrafish image processing pipeline include quantification of neuron loss in zebrafish embryos due to knockdown of AD-linked genes, automatic detection of defective somites, and quantitative measurement of gene expression levels in zebrafish with altered expression of AD-linked genes or treatment with a chemical compound. These quantitative measurements enable the archival of analyzed results and relevant meta-data. The structured database is organized for statistical analysis and data modeling to better understand neuronal integrity and phenotypic changes of zebrafish under different perturbations. Our results show that the computerized analysis is comparable to manual counting with equivalent accuracy and improved efficacy and consistency. Development of such an automated data analysis pipeline represents a significant step forward to achieve accurate and reproducible quantification of neuronal phenotypes in large scale or high-throughput zebrafish imaging studies.

ImatraNMR: novel software for batch integration and analysis of quantitative NMR spectra.

PubMed

Mäkelä, A V; Heikkilä, O; Kilpeläinen, I; Heikkinen, S

2011-08-01

Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D (1)H and (13)C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request. Copyright © 2011 Elsevier Inc. All rights reserved.

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis.

PubMed

Larimer, Curtis; Winder, Eric; Jeters, Robert; Prowant, Matthew; Nettleship, Ian; Addleman, Raymond Shane; Bonheyo, George T

2016-01-01

The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms.

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.

[Quantitative surface analysis of Pt-Co, Cu-Au and Cu-Ag alloy films by XPS and AES].

PubMed

Li, Lian-Zhong; Zhuo, Shang-Jun; Shen, Ru-Xiang; Qian, Rong; Gao, Jie

2013-11-01

In order to improve the quantitative analysis accuracy of AES, We associated XPS with AES and studied the method to reduce the error of AES quantitative analysis, selected Pt-Co, Cu-Au and Cu-Ag binary alloy thin-films as the samples, used XPS to correct AES quantitative analysis results by changing the auger sensitivity factors to make their quantitative analysis results more similar. Then we verified the accuracy of the quantitative analysis of AES when using the revised sensitivity factors by other samples with different composition ratio, and the results showed that the corrected relative sensitivity factors can reduce the error in quantitative analysis of AES to less than 10%. Peak defining is difficult in the form of the integral spectrum of AES analysis since choosing the starting point and ending point when determining the characteristic auger peak intensity area with great uncertainty, and to make analysis easier, we also processed data in the form of the differential spectrum, made quantitative analysis on the basis of peak to peak height instead of peak area, corrected the relative sensitivity factors, and verified the accuracy of quantitative analysis by the other samples with different composition ratio. The result showed that the analytical error in quantitative analysis of AES reduced to less than 9%. It showed that the accuracy of AES quantitative analysis can be highly improved by the way of associating XPS with AES to correct the auger sensitivity factors since the matrix effects are taken into account. Good consistency was presented, proving the feasibility of this method.

Genetic toxicology at the crossroads-from qualitative hazard evaluation to quantitative risk assessment.

PubMed

White, Paul A; Johnson, George E

2016-05-01

Applied genetic toxicology is undergoing a transition from qualitative hazard identification to quantitative dose-response analysis and risk assessment. To facilitate this change, the Health and Environmental Sciences Institute (HESI) Genetic Toxicology Technical Committee (GTTC) sponsored a workshop held in Lancaster, UK on July 10-11, 2014. The event included invited speakers from several institutions and the contents was divided into three themes-1: Point-of-departure Metrics for Quantitative Dose-Response Analysis in Genetic Toxicology; 2: Measurement and Estimation of Exposures for Better Extrapolation to Humans and 3: The Use of Quantitative Approaches in Genetic Toxicology for human health risk assessment (HHRA). A host of pertinent issues were discussed relating to the use of in vitro and in vivo dose-response data, the development of methods for in vitro to in vivo extrapolation and approaches to use in vivo dose-response data to determine human exposure limits for regulatory evaluations and decision-making. This Special Issue, which was inspired by the workshop, contains a series of papers that collectively address topics related to the aforementioned themes. The Issue includes contributions that collectively evaluate, describe and discuss in silico, in vitro, in vivo and statistical approaches that are facilitating the shift from qualitative hazard evaluation to quantitative risk assessment. The use and application of the benchmark dose approach was a central theme in many of the workshop presentations and discussions, and the Special Issue includes several contributions that outline novel applications for the analysis and interpretation of genetic toxicity data. Although the contents of the Special Issue constitutes an important step towards the adoption of quantitative methods for regulatory assessment of genetic toxicity, formal acceptance of quantitative methods for HHRA and regulatory decision-making will require consensus regarding the

Metabolomics relative quantitation with mass spectrometry using chemical derivatization and isotope labeling

DOE PAGES

O'Maille, Grace; Go, Eden P.; Hoang, Linh; ...

2008-01-01

Comprehensive detection and quantitation of metabolites from a biological source constitute the major challenges of current metabolomics research. Two chemical derivatization methodologies, butylation and amination, were applied to human serum for ionization enhancement of a broad spectrum of metabolite classes, including steroids and amino acids. LC-ESI-MS analysis of the derivatized serum samples provided a significant signal elevation across the total ion chromatogram to over a 100-fold increase in ionization efficiency. It was also demonstrated that derivatization combined with isotopically labeled reagents facilitated the relative quantitation of derivatized metabolites from individual as well as pooled samples.

Improved method and apparatus for chromatographic quantitative analysis

DOEpatents

Fritz, J.S.; Gjerde, D.T.; Schmuckler, G.

An improved apparatus and method are described for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single element and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.

Spotsizer: High-throughput quantitative analysis of microbial growth.

PubMed

Bischof, Leanne; Převorovský, Martin; Rallis, Charalampos; Jeffares, Daniel C; Arzhaeva, Yulia; Bähler, Jürg

2016-10-01

Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.

Issues in Quantitative Analysis of Ultraviolet Imager (UV) Data: Airglow

NASA Technical Reports Server (NTRS)

Germany, G. A.; Richards, P. G.; Spann, J. F.; Brittnacher, M. J.; Parks, G. K.

1999-01-01

The GGS Ultraviolet Imager (UVI) has proven to be especially valuable in correlative substorm, auroral morphology, and extended statistical studies of the auroral regions. Such studies are based on knowledge of the location, spatial, and temporal behavior of auroral emissions. More quantitative studies, based on absolute radiometric intensities from UVI images, require a more intimate knowledge of the instrument behavior and data processing requirements and are inherently more difficult than studies based on relative knowledge of the oval location. In this study, UVI airglow observations are analyzed and compared with model predictions to illustrate issues that arise in quantitative analysis of UVI images. These issues include instrument calibration, long term changes in sensitivity, and imager flat field response as well as proper background correction. Airglow emissions are chosen for this study because of their relatively straightforward modeling requirements and because of their implications for thermospheric compositional studies. The analysis issues discussed here, however, are identical to those faced in quantitative auroral studies.

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.

Quantitative High-Resolution Genomic Analysis of Single Cancer Cells

PubMed Central

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A.; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics. PMID:22140428

Quantitative high-resolution genomic analysis of single cancer cells.

PubMed

Hannemann, Juliane; Meyer-Staeckling, Sönke; Kemming, Dirk; Alpers, Iris; Joosse, Simon A; Pospisil, Heike; Kurtz, Stefan; Görndt, Jennifer; Püschel, Klaus; Riethdorf, Sabine; Pantel, Klaus; Brandt, Burkhard

2011-01-01

During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics.

Benefit-risk analysis : a brief review and proposed quantitative approaches.

PubMed

Holden, William L

2003-01-01

Given the current status of benefit-risk analysis as a largely qualitative method, two techniques for a quantitative synthesis of a drug's benefit and risk are proposed to allow a more objective approach. The recommended methods, relative-value adjusted number-needed-to-treat (RV-NNT) and its extension, minimum clinical efficacy (MCE) analysis, rely upon efficacy or effectiveness data, adverse event data and utility data from patients, describing their preferences for an outcome given potential risks. These methods, using hypothetical data for rheumatoid arthritis drugs, demonstrate that quantitative distinctions can be made between drugs which would better inform clinicians, drug regulators and patients about a drug's benefit-risk profile. If the number of patients needed to treat is less than the relative-value adjusted number-needed-to-harm in an RV-NNT analysis, patients are willing to undergo treatment with the experimental drug to derive a certain benefit knowing that they may be at risk for any of a series of potential adverse events. Similarly, the results of an MCE analysis allow for determining the worth of a new treatment relative to an older one, given not only the potential risks of adverse events and benefits that may be gained, but also by taking into account the risk of disease without any treatment. Quantitative methods of benefit-risk analysis have a place in the evaluative armamentarium of pharmacovigilance, especially those that incorporate patients' perspectives.

Quantitative risk analysis of oil storage facilities in seismic areas.

PubMed

Fabbrocino, Giovanni; Iervolino, Iunio; Orlando, Francesca; Salzano, Ernesto

2005-08-31

Quantitative risk analysis (QRA) of industrial facilities has to take into account multiple hazards threatening critical equipment. Nevertheless, engineering procedures able to evaluate quantitatively the effect of seismic action are not well established. Indeed, relevant industrial accidents may be triggered by loss of containment following ground shaking or other relevant natural hazards, either directly or through cascade effects ('domino effects'). The issue of integrating structural seismic risk into quantitative probabilistic seismic risk analysis (QpsRA) is addressed in this paper by a representative study case regarding an oil storage plant with a number of atmospheric steel tanks containing flammable substances. Empirical seismic fragility curves and probit functions, properly defined both for building-like and non building-like industrial components, have been crossed with outcomes of probabilistic seismic hazard analysis (PSHA) for a test site located in south Italy. Once the seismic failure probabilities have been quantified, consequence analysis has been performed for those events which may be triggered by the loss of containment following seismic action. Results are combined by means of a specific developed code in terms of local risk contour plots, i.e. the contour line for the probability of fatal injures at any point (x, y) in the analysed area. Finally, a comparison with QRA obtained by considering only process-related top events is reported for reference.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes*

PubMed Central

Mosley, Amber L.; Sardiu, Mihaela E.; Pattenden, Samantha G.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

2011-01-01

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports. PMID

Chemical Fingerprint Analysis and Quantitative Analysis of Rosa rugosa by UPLC-DAD.

PubMed

Mansur, Sanawar; Abdulla, Rahima; Ayupbec, Amatjan; Aisa, Haji Akbar

2016-12-21

A method based on ultra performance liquid chromatography with a diode array detector (UPLC-DAD) was developed for quantitative analysis of five active compounds and chemical fingerprint analysis of Rosa rugosa . Ten batches of R. rugosa collected from different plantations in the Xinjiang region of China were used to establish the fingerprint. The feasibility and advantages of the used UPLC fingerprint were verified for its similarity evaluation by systematically comparing chromatograms with professional analytical software recommended by State Food and Drug Administration (SFDA) of China. In quantitative analysis, the five compounds showed good regression (R² = 0.9995) within the test ranges, and the recovery of the method was in the range of 94.2%-103.8%. The similarities of liquid chromatography fingerprints of 10 batches of R. rugosa were more than 0.981. The developed UPLC fingerprint method is simple, reliable, and validated for the quality control and identification of R. rugosa . Additionally, simultaneous quantification of five major bioactive ingredients in the R. rugosa samples was conducted to interpret the consistency of the quality test. The results indicated that the UPLC fingerprint, as a characteristic distinguishing method combining similarity evaluation and quantification analysis, can be successfully used to assess the quality and to identify the authenticity of R. rugosa .

Comparative study of standard space and real space analysis of quantitative MR brain data.

PubMed

Aribisala, Benjamin S; He, Jiabao; Blamire, Andrew M

2011-06-01

To compare the robustness of region of interest (ROI) analysis of magnetic resonance imaging (MRI) brain data in real space with analysis in standard space and to test the hypothesis that standard space image analysis introduces more partial volume effect errors compared to analysis of the same dataset in real space. Twenty healthy adults with no history or evidence of neurological diseases were recruited; high-resolution T(1)-weighted, quantitative T(1), and B(0) field-map measurements were collected. Algorithms were implemented to perform analysis in real and standard space and used to apply a simple standard ROI template to quantitative T(1) datasets. Regional relaxation values and histograms for both gray and white matter tissues classes were then extracted and compared. Regional mean T(1) values for both gray and white matter were significantly lower using real space compared to standard space analysis. Additionally, regional T(1) histograms were more compact in real space, with smaller right-sided tails indicating lower partial volume errors compared to standard space analysis. Standard space analysis of quantitative MRI brain data introduces more partial volume effect errors biasing the analysis of quantitative data compared to analysis of the same dataset in real space. Copyright © 2011 Wiley-Liss, Inc.

Statistical shape analysis using 3D Poisson equation--A quantitatively validated approach.

PubMed

Gao, Yi; Bouix, Sylvain

2016-05-01

Statistical shape analysis has been an important area of research with applications in biology, anatomy, neuroscience, agriculture, paleontology, etc. Unfortunately, the proposed methods are rarely quantitatively evaluated, and as shown in recent studies, when they are evaluated, significant discrepancies exist in their outputs. In this work, we concentrate on the problem of finding the consistent location of deformation between two population of shapes. We propose a new shape analysis algorithm along with a framework to perform a quantitative evaluation of its performance. Specifically, the algorithm constructs a Signed Poisson Map (SPoM) by solving two Poisson equations on the volumetric shapes of arbitrary topology, and statistical analysis is then carried out on the SPoMs. The method is quantitatively evaluated on synthetic shapes and applied on real shape data sets in brain structures. Copyright © 2016 Elsevier B.V. All rights reserved.

[The Role of Segmental Analysis of Clonazepam in Hair in Drug Facilitated Cases].

PubMed

Chen, H; Xiang, P; Shen, M

2017-06-01

To infer the frequency of dosage and medication history investigate of the victims in drug facilitated cases by the segmental analysis of clonazepam in hair. Freezing milling under liquid nitrogen environment combined with ultrasonic bath was used as sample pretreatment in this study, and liquid chromatography-tandem mass spectrometry was used for the segmental analysis of the hair samples collected from 6 victims in different cases. The concentrations of clonazepam and 7-aminoclonazepam were detected in each hair section. Clonazepam and its metabolite 7-aminoclonazepam were detected in parts of hair sections from the 6 victims. The occurrence time of drug peak concentration was consistent with the intake timing provided by victims. Segmental analysis of hair can provide the information of frequency of dosage and intake timing, which shows an unique evidential value in drug facilitated crimes. Copyright© by the Editorial Department of Journal of Forensic Medicine

Development of a task analysis tool to facilitate user interface design

NASA Technical Reports Server (NTRS)

Scholtz, Jean C.

1992-01-01

A good user interface is one that facilitates the user in carrying out his task. Such interfaces are difficult and costly to produce. The most important aspect in producing a good interface is the ability to communicate to the software designers what the user's task is. The Task Analysis Tool is a system for cooperative task analysis and specification of the user interface requirements. This tool is intended to serve as a guide to development of initial prototypes for user feedback.

iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress

PubMed Central

Li, Qingye; Chang, Rong; Sun, Yijun; Li, Bosheng

2016-01-01

Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT. A total of 3,782 proteins were identified, of which 1,062 showed differential expression. Bioinformatics analysis indicated that differentially expressed proteins that were enriched in photosynthesis, carbohydrate metabolism, amino acid biosynthesis, and translation are important for the maintenance of cellular homeostasis and metabolic balance in Spirulina when subjected to LT stress. The up-regulation of proteins involved in gluconeogenesis, starch and sucrose metabolism, and amino acid biosynthesis served as coping mechanisms of Spirulina in response to LT stress. Moreover, the down-regulated expression of proteins involved in glycolysis, TCA cycle, pentose phosphate pathway, photosynthesis, and translation were associated with reduced energy consumption. The findings of the present study allow a better understanding of the response of Spirulina to LT stress and may facilitate in the elucidation of mechanisms underlying LT tolerance. PMID:27902743

iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress.

PubMed

Li, Qingye; Chang, Rong; Sun, Yijun; Li, Bosheng

2016-01-01

Low temperature (LT) is one of the most important abiotic stresses that can significantly reduce crop yield. To gain insight into how Spirulina responds to LT stress, comprehensive physiological and proteomic analyses were conducted in this study. Significant decreases in growth and pigment levels as well as excessive accumulation of compatible osmolytes were observed in response to LT stress. An isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomics approach was used to identify changes in protein abundance in Spirulina under LT. A total of 3,782 proteins were identified, of which 1,062 showed differential expression. Bioinformatics analysis indicated that differentially expressed proteins that were enriched in photosynthesis, carbohydrate metabolism, amino acid biosynthesis, and translation are important for the maintenance of cellular homeostasis and metabolic balance in Spirulina when subjected to LT stress. The up-regulation of proteins involved in gluconeogenesis, starch and sucrose metabolism, and amino acid biosynthesis served as coping mechanisms of Spirulina in response to LT stress. Moreover, the down-regulated expression of proteins involved in glycolysis, TCA cycle, pentose phosphate pathway, photosynthesis, and translation were associated with reduced energy consumption. The findings of the present study allow a better understanding of the response of Spirulina to LT stress and may facilitate in the elucidation of mechanisms underlying LT tolerance.

Role Of Social Networks In Resilience Of Naval Recruits: A Quantitative Analysis

DTIC Science & Technology

2016-06-01

comprises 1,297 total surveys from a total of eight divisions of recruits at two different time periods. Quantitative analyses using surveys and network... surveys from a total of eight divisions of recruits at two different time periods. Quantitative analyses using surveys and network data examine the effects...NETWORKS IN RESILIENCE OF NAVAL RECRUITS: A QUANTITATIVE ANALYSIS by Andrea M. Watling June 2016 Thesis Advisor: Edward H. Powley Co

Quantitative Analysis of Mutant Subclones in Chronic Myeloid Leukemia: Comparison of Different Methodological Approaches

PubMed Central

Preuner, Sandra; Barna, Agnes; Frommlet, Florian; Czurda, Stefan; Konstantin, Byrgazov; Alikian, Mary; Machova Polakova, Katerina; Sacha, Tomasz; Richter, Johan; Lion, Thomas; Gabriel, Christian

2016-01-01

Identification and quantitative monitoring of mutant BCR-ABL1 subclones displaying resistance to tyrosine kinase inhibitors (TKIs) have become important tasks in patients with Ph-positive leukemias. Different technologies have been established for patient screening. Various next-generation sequencing (NGS) platforms facilitating sensitive detection and quantitative monitoring of mutations in the ABL1-kinase domain (KD) have been introduced recently, and are expected to become the preferred technology in the future. However, broad clinical implementation of NGS methods has been hampered by the limited accessibility at different centers and the current costs of analysis which may not be regarded as readily affordable for routine diagnostic monitoring. It is therefore of interest to determine whether NGS platforms can be adequately substituted by other methodological approaches. We have tested three different techniques including pyrosequencing, LD (ligation-dependent)-PCR and NGS in a series of peripheral blood specimens from chronic myeloid leukemia (CML) patients carrying single or multiple mutations in the BCR-ABL1 KD. The proliferation kinetics of mutant subclones in serial specimens obtained during the course of TKI-treatment revealed similar profiles via all technical approaches, but individual specimens showed statistically significant differences between NGS and the other methods tested. The observations indicate that different approaches to detection and quantification of mutant subclones may be applicable for the monitoring of clonal kinetics, but careful calibration of each method is required for accurate size assessment of mutant subclones at individual time points. PMID:27136541

Quantitative Analysis of Mutant Subclones in Chronic Myeloid Leukemia: Comparison of Different Methodological Approaches.

PubMed

Preuner, Sandra; Barna, Agnes; Frommlet, Florian; Czurda, Stefan; Konstantin, Byrgazov; Alikian, Mary; Machova Polakova, Katerina; Sacha, Tomasz; Richter, Johan; Lion, Thomas; Gabriel, Christian

2016-04-29

Identification and quantitative monitoring of mutant BCR-ABL1 subclones displaying resistance to tyrosine kinase inhibitors (TKIs) have become important tasks in patients with Ph-positive leukemias. Different technologies have been established for patient screening. Various next-generation sequencing (NGS) platforms facilitating sensitive detection and quantitative monitoring of mutations in the ABL1-kinase domain (KD) have been introduced recently, and are expected to become the preferred technology in the future. However, broad clinical implementation of NGS methods has been hampered by the limited accessibility at different centers and the current costs of analysis which may not be regarded as readily affordable for routine diagnostic monitoring. It is therefore of interest to determine whether NGS platforms can be adequately substituted by other methodological approaches. We have tested three different techniques including pyrosequencing, LD (ligation-dependent)-PCR and NGS in a series of peripheral blood specimens from chronic myeloid leukemia (CML) patients carrying single or multiple mutations in the BCR-ABL1 KD. The proliferation kinetics of mutant subclones in serial specimens obtained during the course of TKI-treatment revealed similar profiles via all technical approaches, but individual specimens showed statistically significant differences between NGS and the other methods tested. The observations indicate that different approaches to detection and quantification of mutant subclones may be applicable for the monitoring of clonal kinetics, but careful calibration of each method is required for accurate size assessment of mutant subclones at individual time points.

A Strategy for Identifying Quantitative Trait Genes Using Gene Expression Analysis and Causal Analysis.

PubMed

Ishikawa, Akira

2017-11-27

Large numbers of quantitative trait loci (QTL) affecting complex diseases and other quantitative traits have been reported in humans and model animals. However, the genetic architecture of these traits remains elusive due to the difficulty in identifying causal quantitative trait genes (QTGs) for common QTL with relatively small phenotypic effects. A traditional strategy based on techniques such as positional cloning does not always enable identification of a single candidate gene for a QTL of interest because it is difficult to narrow down a target genomic interval of the QTL to a very small interval harboring only one gene. A combination of gene expression analysis and statistical causal analysis can greatly reduce the number of candidate genes. This integrated approach provides causal evidence that one of the candidate genes is a putative QTG for the QTL. Using this approach, I have recently succeeded in identifying a single putative QTG for resistance to obesity in mice. Here, I outline the integration approach and discuss its usefulness using my studies as an example.

Quantitative analysis of diffusion tensor orientation: theoretical framework.

PubMed

Wu, Yu-Chien; Field, Aaron S; Chung, Moo K; Badie, Benham; Alexander, Andrew L

2004-11-01

Diffusion-tensor MRI (DT-MRI) yields information about the magnitude, anisotropy, and orientation of water diffusion of brain tissues. Although white matter tractography and eigenvector color maps provide visually appealing displays of white matter tract organization, they do not easily lend themselves to quantitative and statistical analysis. In this study, a set of visual and quantitative tools for the investigation of tensor orientations in the human brain was developed. Visual tools included rose diagrams, which are spherical coordinate histograms of the major eigenvector directions, and 3D scatterplots of the major eigenvector angles. A scatter matrix of major eigenvector directions was used to describe the distribution of major eigenvectors in a defined anatomic region. A measure of eigenvector dispersion was developed to describe the degree of eigenvector coherence in the selected region. These tools were used to evaluate directional organization and the interhemispheric symmetry of DT-MRI data in five healthy human brains and two patients with infiltrative diseases of the white matter tracts. In normal anatomical white matter tracts, a high degree of directional coherence and interhemispheric symmetry was observed. The infiltrative diseases appeared to alter the eigenvector properties of affected white matter tracts, showing decreased eigenvector coherence and interhemispheric symmetry. This novel approach distills the rich, 3D information available from the diffusion tensor into a form that lends itself to quantitative analysis and statistical hypothesis testing. (c) 2004 Wiley-Liss, Inc.

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.

A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

ERIC Educational Resources Information Center

Katharaki, Maria; Katharakis, George

2010-01-01

In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

From the voices of women: facilitating survivor access to IPV services.

PubMed

Simmons, Catherine A; Farrar, Melissa; Frazer, Kitty; Thompson, Mary Jane

2011-10-01

This mixed-method study investigated perceptions women domestic violence survivors/victims have about why women do not seek help from formal support structures and actions domestic helping agencies can take to facilitate survivor access to services. Congruent with previous research, quantitative analysis identified 17 reasons women do not seek help from formal support structures. Expanding current knowledge, concept mapping revealed six ways family violence programs can better reach women in abusive relationships, including (1) remove barriers to services, (2) improve comfort with services, (3) "talk about it," (4) improve community awareness, (5) victim-targeted marketing, and (6) "I honestly don't know."

Food Consumption and Handling Survey for Quantitative Microbiological Consumer Phase Risk Assessments.

PubMed

Chardon, Jurgen; Swart, Arno

2016-07-01

In the consumer phase of a typical quantitative microbiological risk assessment (QMRA), mathematical equations identify data gaps. To acquire useful data we designed a food consumption and food handling survey (2,226 respondents) for QMRA applications that is especially aimed at obtaining quantitative data. For a broad spectrum of food products, the survey covered the following topics: processing status at retail, consumer storage, preparation, and consumption. Questions were designed to facilitate distribution fitting. In the statistical analysis, special attention was given to the selection of the most adequate distribution to describe the data. Bootstrap procedures were used to describe uncertainty. The final result was a coherent quantitative consumer phase food survey and parameter estimates for food handling and consumption practices in The Netherlands, including variation over individuals and uncertainty estimates.

[Correspondence analysis between traditional commercial specifications and quantitative quality indices of Notopterygii Rhizoma et Radix].

PubMed

Jiang, Shun-Yuan; Sun, Hong-Bing; Sun, Hui; Ma, Yu-Ying; Chen, Hong-Yu; Zhu, Wen-Tao; Zhou, Yi

2016-03-01

This paper aims to explore a comprehensive assessment method combined traditional Chinese medicinal material specifications with quantitative quality indicators. Seventy-six samples of Notopterygii Rhizoma et Radix were collected on market and at producing areas. Traditional commercial specifications were described and assigned, and 10 chemical components and volatile oils were determined for each sample. Cluster analysis, Fisher discriminant analysis and correspondence analysis were used to establish the relationship between the traditional qualitative commercial specifications and quantitative chemical indices for comprehensive evaluating quality of medicinal materials, and quantitative classification of commercial grade and quality grade. A herb quality index (HQI) including traditional commercial specifications and chemical components for quantitative grade classification were established, and corresponding discriminant function were figured out for precise determination of quality grade and sub-grade of Notopterygii Rhizoma et Radix. The result showed that notopterol, isoimperatorin and volatile oil were the major components for determination of chemical quality, and their dividing values were specified for every grade and sub-grade of the commercial materials of Notopterygii Rhizoma et Radix. According to the result, essential relationship between traditional medicinal indicators, qualitative commercial specifications, and quantitative chemical composition indicators can be examined by K-mean cluster, Fisher discriminant analysis and correspondence analysis, which provide a new method for comprehensive quantitative evaluation of traditional Chinese medicine quality integrated traditional commodity specifications and quantitative modern chemical index. Copyright© by the Chinese Pharmaceutical Association.

Use of MRI in Differentiation of Papillary Renal Cell Carcinoma Subtypes: Qualitative and Quantitative Analysis.

PubMed

Doshi, Ankur M; Ream, Justin M; Kierans, Andrea S; Bilbily, Matthew; Rusinek, Henry; Huang, William C; Chandarana, Hersh

2016-03-01

The purpose of this study was to determine whether qualitative and quantitative MRI feature analysis is useful for differentiating type 1 from type 2 papillary renal cell carcinoma (PRCC). This retrospective study included 21 type 1 and 17 type 2 PRCCs evaluated with preoperative MRI. Two radiologists independently evaluated various qualitative features, including signal intensity, heterogeneity, and margin. For the quantitative analysis, a radiology fellow and a medical student independently drew 3D volumes of interest over the entire tumor on T2-weighted HASTE images, apparent diffusion coefficient parametric maps, and nephrographic phase contrast-enhanced MR images to derive first-order texture metrics. Qualitative and quantitative features were compared between the groups. For both readers, qualitative features with greater frequency in type 2 PRCC included heterogeneous enhancement, indistinct margin, and T2 heterogeneity (all, p < 0.035). Indistinct margins and heterogeneous enhancement were independent predictors (AUC, 0.822). Quantitative analysis revealed that apparent diffusion coefficient, HASTE, and contrast-enhanced entropy were greater in type 2 PRCC (p < 0.05; AUC, 0.682-0.716). A combined quantitative and qualitative model had an AUC of 0.859. Qualitative features within the model had interreader concordance of 84-95%, and the quantitative data had intraclass coefficients of 0.873-0.961. Qualitative and quantitative features can help discriminate between type 1 and type 2 PRCC. Quantitative analysis may capture useful information that complements the qualitative appearance while benefiting from high interobserver agreement.

Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

DTIC Science & Technology

2017-05-10

repertoire-wide properties. Finally, through 75 the use of appropriate statistical analyses, the repertoire profiles can be quantitatively compared and 76...cell response to eVLP and 503 quantitatively compare GC B-cell repertoires from immunization conditions. We partitioned the 504 resulting clonotype... Quantitative analysis of repertoire-scale immunoglobulin properties in vaccine-induced B-cell responses Ilja V. Khavrutskii1, Sidhartha Chaudhury*1

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.

PubMed

Blattmann, Peter; Heusel, Moritz; Aebersold, Ruedi

2016-01-01

SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.

CUMULATIVE RISK ASSESSMENT: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS

EPA Science Inventory

INTRODUCTION: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS FOR CUMULATIVE RISK

Hugh A. Barton1 and Carey N. Pope2
1US EPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC
2Department of...

Evaluation of shear wave elastography for differential diagnosis of breast lesions: A new qualitative analysis versus conventional quantitative analysis.

PubMed

Ren, Wei-Wei; Li, Xiao-Long; Wang, Dan; Liu, Bo-Ji; Zhao, Chong-Ke; Xu, Hui-Xiong

2018-04-13

To evaluate a special kind of ultrasound (US) shear wave elastography for differential diagnosis of breast lesions, using a new qualitative analysis (i.e. the elasticity score in the travel time map) compared with conventional quantitative analysis. From June 2014 to July 2015, 266 pathologically proven breast lesions were enrolled in this study. The maximum, mean, median, minimum, and standard deviation of shear wave speed (SWS) values (m/s) were assessed. The elasticity score, a new qualitative feature, was evaluated in the travel time map. The area under the receiver operating characteristic (AUROC) curves were plotted to evaluate the diagnostic performance of both qualitative and quantitative analyses for differentiation of breast lesions. Among all quantitative parameters, SWS-max showed the highest AUROC (0.805; 95% CI: 0.752, 0.851) compared with SWS-mean (0.786; 95% CI:0.732, 0.834; P = 0.094), SWS-median (0.775; 95% CI:0.720, 0.824; P = 0.046), SWS-min (0.675; 95% CI:0.615, 0.731; P = 0.000), and SWS-SD (0.768; 95% CI:0.712, 0.817; P = 0.074). The AUROC of qualitative analysis in this study obtained the best diagnostic performance (0.871; 95% CI: 0.825, 0.909, compared with the best parameter of SWS-max in quantitative analysis, P = 0.011). The new qualitative analysis of shear wave travel time showed the superior diagnostic performance in the differentiation of breast lesions in comparison with conventional quantitative analysis.

Quantitation of glycerophosphorylcholine by flow injection analysis using immobilized enzymes.

PubMed

Mancini, A; Del Rosso, F; Roberti, R; Caligiana, P; Vecchini, A; Binaglia, L

1996-09-20

A method for quantitating glycerophosphorylcholine by flow injection analysis is reported in the present paper. Glycerophosphorylcholine phosphodiesterase and choline oxidase, immobilized on controlled porosity glass beads, are packed in a small reactor inserted in a flow injection manifold. When samples containing glycerophosphorylcholine are injected, glycerophosphorylcholine is hydrolyzed into choline and sn-glycerol-3-phosphate. The free choline produced in this reaction is oxidized to betain and hydrogen peroxide. Hydrogen peroxide is detected amperometrically. Quantitation of glycerophosphorylcholine in samples containing choline and phosphorylcholine is obtained inserting ahead of the reactor a small column packed with a mixed bed ion exchange resin. The time needed for each determination does not exceed one minute. The present method, applied to quantitate glycerophosphorylcholine in samples of seminal plasma, gave results comparable with those obtained using the standard enzymatic-spectrophotometric procedure. An alternative procedure, making use of co-immobilized glycerophosphorylcholine phosphodiesterase and glycerol-3-phosphate oxidase for quantitating glycerophosphorylcholine, glycerophosphorylethanolamine and glycerophosphorylserine is also described.

Quantitative analysis to guide orphan drug development.

PubMed

Lesko, L J

2012-08-01

The development of orphan drugs for rare diseases has made impressive strides in the past 10 years. There has been a surge in orphan drug designations, but new drug approvals have not kept up. This article presents a three-pronged hierarchical strategy for quantitative analysis of data at the descriptive, mechanistic, and systems levels of the biological system that could represent a standardized and rational approach to orphan drug development. Examples are provided to illustrate the concept.

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

Practice change in community pharmacy: quantification of facilitators.

PubMed

Roberts, Alison S; Benrimoj, Shalom I; Chen, Timothy F; Williams, Kylie A; Aslani, Parisa

2008-06-01

There has been an increasing international trend toward the delivery of cognitive pharmaceutical services (CPS) in community pharmacy. CPS have been developed and disseminated individually, without a framework underpinning their implementation and with limited knowledge of factors that might assist practice change. The implementation process is complex, involving a range of internal and external factors. To quantify facilitators of practice change in Australian community pharmacies. We employed a literature review and qualitative study to facilitate the design of a 43-item "facilitators of practice change" scale as part of a quantitative survey instrument, using a framework of organizational theory. The questionnaire was pilot-tested (n = 100), then mailed to a random sample of 2000 community pharmacies, with a copy each for the pharmacy owner, employed pharmacist, and pharmacy assistant. The construct validity and reliability of the scale were established using exploratory factor analysis and Cronbach's alpha, respectively. A total of 735 (37%) pharmacies responded, with 1303 individual questionnaires. Factor analysis of the scale yielded 7 factors, explaining 48.8% of the total variance. The factors were: relationship with physicians (item loading range 0.59-0.85; Cronbach's alpha 0.90), remuneration (0.52-0.74; 0.82), pharmacy layout (0.52-0.79; 0.81), patient expectation (0.52-0.85; 0.82), manpower/staff (0.49-0.66; 0.80), communication and teamwork (0.37-0.65; 0.77), and external support/assistance (0.47-0.69; 0.74). All of the factors demonstrated good reliability and construct validity and explained approximately half of the variance. Implementing CPS requires support not only with the clinical aspects of service delivery, but also for the process of implementation itself, and remuneration models must reflect this. The identified facilitators should be used in a multilevel strategy to integrate professional services into the community pharmacy business

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.

MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis

PubMed Central

Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

2016-01-01

ABSTRACT Introduction/Background: Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. Material and Methods: n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Results: Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Conclusion: Both Ki-67 and MCM-2 are

MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis.

PubMed

Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

2016-01-01

Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Both Ki-67 and MCM-2 are markers of proliferation which are closely linked to grade. Therefore, they

Quantitative Myocardial Perfusion Imaging Versus Visual Analysis in Diagnosing Myocardial Ischemia: A CE-MARC Substudy.

PubMed

Biglands, John D; Ibraheem, Montasir; Magee, Derek R; Radjenovic, Aleksandra; Plein, Sven; Greenwood, John P

2018-05-01

This study sought to compare the diagnostic accuracy of visual and quantitative analyses of myocardial perfusion cardiovascular magnetic resonance against a reference standard of quantitative coronary angiography. Visual analysis of perfusion cardiovascular magnetic resonance studies for assessing myocardial perfusion has been shown to have high diagnostic accuracy for coronary artery disease. However, only a few small studies have assessed the diagnostic accuracy of quantitative myocardial perfusion. This retrospective study included 128 patients randomly selected from the CE-MARC (Clinical Evaluation of Magnetic Resonance Imaging in Coronary Heart Disease) study population such that the distribution of risk factors and disease status was proportionate to the full population. Visual analysis results of cardiovascular magnetic resonance perfusion images, by consensus of 2 expert readers, were taken from the original study reports. Quantitative myocardial blood flow estimates were obtained using Fermi-constrained deconvolution. The reference standard for myocardial ischemia was a quantitative coronary x-ray angiogram stenosis severity of ≥70% diameter in any coronary artery of >2 mm diameter, or ≥50% in the left main stem. Diagnostic performance was calculated using receiver-operating characteristic curve analysis. The area under the curve for visual analysis was 0.88 (95% confidence interval: 0.81 to 0.95) with a sensitivity of 81.0% (95% confidence interval: 69.1% to 92.8%) and specificity of 86.0% (95% confidence interval: 78.7% to 93.4%). For quantitative stress myocardial blood flow the area under the curve was 0.89 (95% confidence interval: 0.83 to 0.96) with a sensitivity of 87.5% (95% confidence interval: 77.3% to 97.7%) and specificity of 84.5% (95% confidence interval: 76.8% to 92.3%). There was no statistically significant difference between the diagnostic performance of quantitative and visual analyses (p = 0.72). Incorporating rest myocardial

Quantitative Analysis of the Cervical Texture by Ultrasound and Correlation with Gestational Age.

PubMed

Baños, Núria; Perez-Moreno, Alvaro; Migliorelli, Federico; Triginer, Laura; Cobo, Teresa; Bonet-Carne, Elisenda; Gratacos, Eduard; Palacio, Montse

2017-01-01

Quantitative texture analysis has been proposed to extract robust features from the ultrasound image to detect subtle changes in the textures of the images. The aim of this study was to evaluate the feasibility of quantitative cervical texture analysis to assess cervical tissue changes throughout pregnancy. This was a cross-sectional study including singleton pregnancies between 20.0 and 41.6 weeks of gestation from women who delivered at term. Cervical length was measured, and a selected region of interest in the cervix was delineated. A model to predict gestational age based on features extracted from cervical images was developed following three steps: data splitting, feature transformation, and regression model computation. Seven hundred images, 30 per gestational week, were included for analysis. There was a strong correlation between the gestational age at which the images were obtained and the estimated gestational age by quantitative analysis of the cervical texture (R = 0.88). This study provides evidence that quantitative analysis of cervical texture can extract features from cervical ultrasound images which correlate with gestational age. Further research is needed to evaluate its applicability as a biomarker of the risk of spontaneous preterm birth, as well as its role in cervical assessment in other clinical situations in which cervical evaluation might be relevant. © 2016 S. Karger AG, Basel.

Quantitative analysis of culture using millions of digitized books

PubMed Central

Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva P.; Veres, Adrian; Gray, Matthew K.; Pickett, Joseph P.; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A.; Aiden, Erez Lieberman

2011-01-01

We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics’, focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. ‘Culturomics’ extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities. PMID:21163965

Quantitative analysis of culture using millions of digitized books.

PubMed

Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva Presser; Veres, Adrian; Gray, Matthew K; Pickett, Joseph P; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A; Aiden, Erez Lieberman

2011-01-14

We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of 'culturomics,' focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.

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.

Appraising Quantitative Research in Health Education: Guidelines for Public Health Educators

PubMed Central

Hayes, Sandra C.; Scharalda, Jeanfreau G.; Stetson, Barbara; Jones-Jack, Nkenge H.; Valliere, Matthew; Kirchain, William R.; Fagen, Michael; LeBlanc, Cris

2010-01-01

Many practicing health educators do not feel they possess the skills necessary to critically appraise quantitative research. This publication is designed to help provide practicing health educators with basic tools helpful to facilitate a better understanding of quantitative research. This article describes the major components—title, introduction, methods, analyses, results and discussion sections—of quantitative research. Readers will be introduced to information on the various types of study designs and seven key questions health educators can use to facilitate the appraisal process. Upon reading, health educators will be in a better position to determine whether research studies are well designed and executed. PMID:20400654

Facilitating Video Analysis for Teacher Development: A Systematic Review of the Research

ERIC Educational Resources Information Center

Baecher, Laura; Kung, Shiao-Chuan; Ward, Sarah Laleman; Kern, Kimberly

2018-01-01

Video analysis of classroom practice as a tool in teacher professional learning has become ever more widely used, with hundreds of articles published on the topic over the past decade. When designing effective professional development for teachers using video, facilitators turn to the literature to identify promising approaches. This article…

Practice Facilitators' and Leaders' Perspectives on a Facilitated Quality Improvement Program.

PubMed

McHugh, Megan; Brown, Tiffany; Liss, David T; Walunas, Theresa L; Persell, Stephen D

2018-04-01

Practice facilitation is a promising approach to helping practices implement quality improvements. Our purpose was to describe practice facilitators' and practice leaders' perspectives on implementation of a practice facilitator-supported quality improvement program and describe where their perspectives aligned and diverged. We conducted interviews with practice leaders and practice facilitators who participated in a program that included 35 improvement strategies aimed at the ABCS of heart health (aspirin use in high-risk individuals, blood pressure control, cholesterol management, and smoking cessation). Rapid qualitative analysis was used to collect, organize, and analyze the data. We interviewed 17 of the 33 eligible practice leaders, and the 10 practice facilitators assigned to those practices. Practice leaders and practice facilitators both reported value in the program's ability to bring needed, high-quality resources to practices. Practice leaders appreciated being able to set the schedule for facilitation and select among the 35 interventions. According to practice facilitators, however, relying on practice leaders to set the pace of the intervention resulted in a lower level of program intensity than intended. Practice leaders preferred targeted assistance, particularly electronic health record documentation guidance and linkages to state smoking cessation programs. Practice facilitators reported that the easiest interventions were those that did not alter care practices. The dual perspectives of practice leaders and practice facilitators provide a more holistic picture of enablers and barriers to program implementation. There may be greater opportunities to assist small practices through simple, targeted practice facilitator-supported efforts rather than larger, comprehensive quality improvement projects. © 2018 Annals of Family Medicine, Inc.

Quantitative Doppler Analysis Using Conventional Color Flow Imaging Acquisitions.

PubMed

Karabiyik, Yucel; Ekroll, Ingvild Kinn; Eik-Nes, Sturla H; Lovstakken, Lasse

2018-05-01

Interleaved acquisitions used in conventional triplex mode result in a tradeoff between the frame rate and the quality of velocity estimates. On the other hand, workflow becomes inefficient when the user has to switch between different modes, and measurement variability is increased. This paper investigates the use of power spectral Capon estimator in quantitative Doppler analysis using data acquired with conventional color flow imaging (CFI) schemes. To preserve the number of samples used for velocity estimation, only spatial averaging was utilized, and clutter rejection was performed after spectral estimation. The resulting velocity spectra were evaluated in terms of spectral width using a recently proposed spectral envelope estimator. The spectral envelopes were also used for Doppler index calculations using in vivo and string phantom acquisitions. In vivo results demonstrated that the Capon estimator can provide spectral estimates with sufficient quality for quantitative analysis using packet-based CFI acquisitions. The calculated Doppler indices were similar to the values calculated using spectrograms estimated on a commercial ultrasound scanner.

High-throughput quantitative analysis by desorption electrospray ionization mass spectrometry.

PubMed

Manicke, Nicholas E; Kistler, Thomas; Ifa, Demian R; Cooks, R Graham; Ouyang, Zheng

2009-02-01

A newly developed high-throughput desorption electrospray ionization (DESI) source was characterized in terms of its performance in quantitative analysis. A 96-sample array, containing pharmaceuticals in various matrices, was analyzed in a single run with a total analysis time of 3 min. These solution-phase samples were examined from a hydrophobic PTFE ink printed on glass. The quantitative accuracy, precision, and limit of detection (LOD) were characterized. Chemical background-free samples of propranolol (PRN) with PRN-d(7) as internal standard (IS) and carbamazepine (CBZ) with CBZ-d(10) as IS were examined. So were two other sample sets consisting of PRN/PRN-d(7) at varying concentration in a biological milieu of 10% urine or porcine brain total lipid extract, total lipid concentration 250 ng/microL. The background-free samples, examined in a total analysis time of 1.5 s/sample, showed good quantitative accuracy and precision, with a relative error (RE) and relative standard deviation (RSD) generally less than 3% and 5%, respectively. The samples in urine and the lipid extract required a longer analysis time (2.5 s/sample) and showed RSD values of around 10% for the samples in urine and 4% for the lipid extract samples and RE values of less than 3% for both sets. The LOD for PRN and CBZ when analyzed without chemical background was 10 and 30 fmol, respectively. The LOD of PRN increased to 400 fmol analyzed in 10% urine, and 200 fmol when analyzed in the brain lipid extract.

On the Need for Quantitative Bias Analysis in the Peer-Review Process.

PubMed

Fox, Matthew P; Lash, Timothy L

2017-05-15

Peer review is central to the process through which epidemiologists generate evidence to inform public health and medical interventions. Reviewers thereby act as critical gatekeepers to high-quality research. They are asked to carefully consider the validity of the proposed work or research findings by paying careful attention to the methodology and critiquing the importance of the insight gained. However, although many have noted problems with the peer-review system for both manuscripts and grant submissions, few solutions have been proposed to improve the process. Quantitative bias analysis encompasses all methods used to quantify the impact of systematic error on estimates of effect in epidemiologic research. Reviewers who insist that quantitative bias analysis be incorporated into the design, conduct, presentation, and interpretation of epidemiologic research could substantially strengthen the process. In the present commentary, we demonstrate how quantitative bias analysis can be used by investigators and authors, reviewers, funding agencies, and editors. By utilizing quantitative bias analysis in the peer-review process, editors can potentially avoid unnecessary rejections, identify key areas for improvement, and improve discussion sections by shifting from speculation on the impact of sources of error to quantification of the impact those sources of bias may have had. © The Author 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Quantitative analysis of professionally trained versus untrained voices.

PubMed

Siupsinskiene, Nora

2003-01-01

The aim of this study was to compare healthy trained and untrained voices as well as healthy and dysphonic trained voices in adults using combined voice range profile and aerodynamic tests, to define the normal range limiting values of quantitative voice parameters and to select the most informative quantitative voice parameters for separation between healthy and dysphonic trained voices. Three groups of persons were evaluated. One hundred eighty six healthy volunteers were divided into two groups according to voice training: non-professional speakers group consisted of 106 untrained voices persons (36 males and 70 females) and professional speakers group--of 80 trained voices persons (21 males and 59 females). Clinical group consisted of 103 dysphonic professional speakers (23 males and 80 females) with various voice disorders. Eighteen quantitative voice parameters from combined voice range profile (VRP) test were analyzed: 8 of voice range profile, 8 of speaking voice, overall vocal dysfunction degree and coefficient of sound, and aerodynamic maximum phonation time. Analysis showed that healthy professional speakers demonstrated expanded vocal abilities in comparison to healthy non-professional speakers. Quantitative voice range profile parameters- pitch range, high frequency limit, area of high frequencies and coefficient of sound differed significantly between healthy professional and non-professional voices, and were more informative than speaking voice or aerodynamic parameters in showing the voice training. Logistic stepwise regression revealed that VRP area in high frequencies was sufficient to discriminate between healthy and dysphonic professional speakers for male subjects (overall discrimination accuracy--81.8%) and combination of three quantitative parameters (VRP high frequency limit, maximum voice intensity and slope of speaking curve) for female subjects (overall model discrimination accuracy--75.4%). We concluded that quantitative voice assessment

Quantitative Determination of Aluminum in Deodorant Brands: A Guided Inquiry Learning Experience in Quantitative Analysis Laboratory

ERIC Educational Resources Information Center

Sedwick, Victoria; Leal, Anne; Turner, Dea; Kanu, A. Bakarr

2018-01-01

The monitoring of metals in commercial products is essential for protecting public health against the hazards of metal toxicity. This article presents a guided inquiry (GI) experimental lab approach in a quantitative analysis lab class that enabled students' to determine the levels of aluminum in deodorant brands. The utility of a GI experimental…

Quantitative Analysis of Critical Factors for the Climate Impact of Landfill Mining.

PubMed

Laner, David; Cencic, Oliver; Svensson, Niclas; Krook, Joakim

2016-07-05

Landfill mining has been proposed as an innovative strategy to mitigate environmental risks associated with landfills, to recover secondary raw materials and energy from the deposited waste, and to enable high-valued land uses at the site. The present study quantitatively assesses the importance of specific factors and conditions for the net contribution of landfill mining to global warming using a novel, set-based modeling approach and provides policy recommendations for facilitating the development of projects contributing to global warming mitigation. Building on life-cycle assessment, scenario modeling and sensitivity analysis methods are used to identify critical factors for the climate impact of landfill mining. The net contributions to global warming of the scenarios range from -1550 (saving) to 640 (burden) kg CO2e per Mg of excavated waste. Nearly 90% of the results' total variation can be explained by changes in four factors, namely the landfill gas management in the reference case (i.e., alternative to mining the landfill), the background energy system, the composition of the excavated waste, and the applied waste-to-energy technology. Based on the analyses, circumstances under which landfill mining should be prioritized or not are identified and sensitive parameters for the climate impact assessment of landfill mining are highlighted.

Quantitative genetics

USDA-ARS?s Scientific Manuscript database

The majority of economically important traits targeted for cotton improvement are quantitatively inherited. In this chapter, the current state of cotton quantitative genetics is described and separated into four components. These components include: 1) traditional quantitative inheritance analysis, ...

Quantitative analysis on electrooculography (EOG) for neurodegenerative disease

NASA Astrophysics Data System (ADS)

Liu, Chang-Chia; Chaovalitwongse, W. Art; Pardalos, Panos M.; Seref, Onur; Xanthopoulos, Petros; Sackellares, J. C.; Skidmore, Frank M.

2007-11-01

Many studies have documented abnormal horizontal and vertical eye movements in human neurodegenerative disease as well as during altered states of consciousness (including drowsiness and intoxication) in healthy adults. Eye movement measurement may play an important role measuring the progress of neurodegenerative diseases and state of alertness in healthy individuals. There are several techniques for measuring eye movement, Infrared detection technique (IR). Video-oculography (VOG), Scleral eye coil and EOG. Among those available recording techniques, EOG is a major source for monitoring the abnormal eye movement. In this real-time quantitative analysis study, the methods which can capture the characteristic of the eye movement were proposed to accurately categorize the state of neurodegenerative subjects. The EOG recordings were taken while 5 tested subjects were watching a short (>120 s) animation clip. In response to the animated clip the participants executed a number of eye movements, including vertical smooth pursued (SVP), horizontal smooth pursued (HVP) and random saccades (RS). Detection of abnormalities in ocular movement may improve our diagnosis and understanding a neurodegenerative disease and altered states of consciousness. A standard real-time quantitative analysis will improve detection and provide a better understanding of pathology in these disorders.

Electroencephalography reactivity for prognostication of post-anoxic coma after cardiopulmonary resuscitation: A comparison of quantitative analysis and visual analysis.

PubMed

Liu, Gang; Su, Yingying; Jiang, Mengdi; Chen, Weibi; Zhang, Yan; Zhang, Yunzhou; Gao, Daiquan

2016-07-28

Electroencephalogram reactivity (EEG-R) is a positive predictive factor for assessing outcomes in comatose patients. Most studies assess the prognostic value of EEG-R utilizing visual analysis; however, this method is prone to subjectivity. We sought to categorize EEG-R with a quantitative approach. We retrospectively studied consecutive comatose patients who had an EEG-R recording performed 1-3 days after cardiopulmonary resuscitation (CPR) or during normothermia after therapeutic hypothermia. EEG-R was assessed via visual analysis and quantitative analysis separately. Clinical outcomes were followed-up at 3-month and dichotomized as recovery of awareness or no recovery of awareness. A total of 96 patients met the inclusion criteria, and 38 (40%) patients recovered awareness at 3-month followed-up. Of 27 patients with EEG-R measured with visual analysis, 22 patients recovered awareness; and of the 69 patients who did not demonstrated EEG-R, 16 patients recovered awareness. The sensitivity and specificity of visually measured EEG-R were 58% and 91%, respectively. The area under the receiver operating characteristic curve for the quantitative analysis was 0.92 (95% confidence interval, 0.87-0.97), with the best cut-off value of 0.10. EEG-R through quantitative analysis might be a good method in predicting the recovery of awareness in patients with post-anoxic coma after CPR. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Quantitative Proteomic Analysis of Mosquito C6/36 Cells Reveals Host Proteins Involved in Zika Virus Infection.

PubMed

Xin, Qi-Lin; Deng, Cheng-Lin; Chen, Xi; Wang, Jun; Wang, Shao-Bo; Wang, Wei; Deng, Fei; Zhang, Bo; Xiao, Gengfu; Zhang, Lei-Ke

2017-06-15

Zika virus (ZIKV) is an emerging arbovirus belonging to the genus Flavivirus of the family Flaviviridae During replication processes, flavivirus manipulates host cell systems to facilitate its replication, while the host cells activate antiviral responses. Identification of host proteins involved in the flavivirus replication process may lead to the discovery of antiviral targets. The mosquitoes Aedes aegypti and Aedes albopictus are epidemiologically important vectors for ZIKV, and effective restrictions of ZIKV replication in mosquitoes will be vital in controlling the spread of virus. In this study, an iTRAQ-based quantitative proteomic analysis of ZIKV-infected Aedes albopictus C6/36 cells was performed to investigate host proteins involved in the ZIKV infection process. A total of 3,544 host proteins were quantified, with 200 being differentially regulated, among which CHCHD2 can be upregulated by ZIKV infection in both mosquito C6/36 and human HeLa cells. Our further study indicated that CHCHD2 can promote ZIKV replication and inhibit beta interferon (IFN-β) production in HeLa cells, suggesting that ZIKV infection may upregulate CHCHD2 to inhibit IFN-I production and thus promote virus replication. Bioinformatics analysis of regulated host proteins highlighted several ZIKV infection-regulated biological processes. Further study indicated that the ubiquitin proteasome system (UPS) plays roles in the ZIKV entry process and that an FDA-approved inhibitor of the 20S proteasome, bortezomib, can inhibit ZIKV infection in vivo Our study illustrated how host cells respond to ZIKV infection and also provided a candidate drug for the control of ZIKV infection in mosquitoes and treatment of ZIKV infection in patients. IMPORTANCE ZIKV infection poses great threats to human health, and there is no FDA-approved drug available for the treatment of ZIKV infection. During replication, ZIKV manipulates host cell systems to facilitate its replication, while host cells activate

Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis.

PubMed

Neilson, Julia W; Jordan, Fiona L; Maier, Raina M

2013-03-01

PCR-denaturing gradient gel electrophoresis (PCR-DGGE) is widely used in microbial ecology for the analysis of comparative community structure. However, artifacts generated during PCR-DGGE of mixed template communities impede the application of this technique to quantitative analysis of community diversity. The objective of the current study was to employ an artificial bacterial community to document and analyze artifacts associated with multiband signatures and preferential template amplification and to highlight their impacts on the use of this technique for quantitative diversity analysis. Six bacterial species (three Betaproteobacteria, two Alphaproteobacteria, and one Firmicutes) were amplified individually and in combinations with primers targeting the V7/V8 region of the 16S rRNA gene. Two of the six isolates produced multiband profiles demonstrating that band number does not correlate directly with α-diversity. Analysis of the multiple bands from one of these isolates confirmed that both bands had identical sequences which lead to the hypothesis that the multiband pattern resulted from two distinct structural conformations of the same amplicon. In addition, consistent preferential amplification was demonstrated following pairwise amplifications of the six isolates. DGGE and real time PCR analysis identified primer mismatch and PCR inhibition due to 16S rDNA secondary structure as the most probable causes of preferential amplification patterns. Reproducible DGGE community profiles generated in this study confirm that PCR-DGGE provides an excellent high-throughput tool for comparative community structure analysis, but that method-specific artifacts preclude its use for accurate comparative diversity analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantitative kinetic analysis of lung nodules by temporal subtraction technique in dynamic chest radiography with a flat panel detector

NASA Astrophysics Data System (ADS)

Tsuchiya, Yuichiro; Kodera, Yoshie; Tanaka, Rie; Sanada, Shigeru

2007-03-01

Early detection and treatment of lung cancer is one of the most effective means to reduce cancer mortality; chest X-ray radiography has been widely used as a screening examination or health checkup. The new examination method and the development of computer analysis system allow obtaining respiratory kinetics by the use of flat panel detector (FPD), which is the expanded method of chest X-ray radiography. Through such changes functional evaluation of respiratory kinetics in chest has become available. Its introduction into clinical practice is expected in the future. In this study, we developed the computer analysis algorithm for the purpose of detecting lung nodules and evaluating quantitative kinetics. Breathing chest radiograph obtained by modified FPD was converted into 4 static images drawing the feature, by sequential temporal subtraction processing, morphologic enhancement processing, kinetic visualization processing, and lung region detection processing, after the breath synchronization process utilizing the diaphragmatic analysis of the vector movement. The artificial neural network used to analyze the density patterns detected the true nodules by analyzing these static images, and drew their kinetic tracks. For the algorithm performance and the evaluation of clinical effectiveness with 7 normal patients and simulated nodules, both showed sufficient detecting capability and kinetic imaging function without statistically significant difference. Our technique can quantitatively evaluate the kinetic range of nodules, and is effective in detecting a nodule on a breathing chest radiograph. Moreover, the application of this technique is expected to extend computer-aided diagnosis systems and facilitate the development of an automatic planning system for radiation therapy.

Database for Simulation of Electron Spectra for Surface Analysis (SESSA)Database for Simulation of Electron Spectra for Surface Analysis (SESSA)

National Institute of Standards and Technology Data Gateway

SRD 100 Database for Simulation of Electron Spectra for Surface Analysis (SESSA)Database for Simulation of Electron Spectra for Surface Analysis (SESSA) (PC database for purchase)   This database has been designed to facilitate quantitative interpretation of Auger-electron and X-ray photoelectron spectra and to improve the accuracy of quantitation in routine analysis. The database contains all physical data needed to perform quantitative interpretation of an electron spectrum for a thin-film specimen of given composition. A simulation module provides an estimate of peak intensities as well as the energy and angular distributions of the emitted electron flux.

A three-component system incorporating Ppd-D1, copy number variation at Ppd-B1, and numerous small-effect quantitative trait loci facilitates adaptation of heading time in winter wheat cultivars of worldwide origin.

PubMed

Würschum, Tobias; Langer, Simon M; Longin, C Friedrich H; Tucker, Matthew R; Leiser, Willmar L

2018-06-01

The broad adaptability of heading time has contributed to the global success of wheat in a diverse array of climatic conditions. Here, we investigated the genetic architecture underlying heading time in a large panel of 1,110 winter wheat cultivars of worldwide origin. Genome-wide association mapping, in combination with the analysis of major phenology loci, revealed a three-component system that facilitates the adaptation of heading time in winter wheat. The photoperiod sensitivity locus Ppd-D1 was found to account for almost half of the genotypic variance in this panel and can advance or delay heading by many days. In addition, copy number variation at Ppd-B1 was the second most important source of variation in heading, explaining 8.3% of the genotypic variance. Results from association mapping and genomic prediction indicated that the remaining variation is attributed to numerous small-effect quantitative trait loci that facilitate fine-tuning of heading to the local climatic conditions. Collectively, our results underpin the importance of the two Ppd-1 loci for the adaptation of heading time in winter wheat and illustrate how the three components have been exploited for wheat breeding globally. © 2018 John Wiley & Sons Ltd.

Quantitative analysis of eyes and other optical systems in linear optics.

PubMed

Harris, William F; Evans, Tanya; van Gool, Radboud D

2017-05-01

To show that 14-dimensional spaces of augmented point P and angle Q characteristics, matrices obtained from the ray transference, are suitable for quantitative analysis although only the latter define an inner-product space and only on it can one define distances and angles. The paper examines the nature of the spaces and their relationships to other spaces including symmetric dioptric power space. The paper makes use of linear optics, a three-dimensional generalization of Gaussian optics. Symmetric 2 × 2 dioptric power matrices F define a three-dimensional inner-product space which provides a sound basis for quantitative analysis (calculation of changes, arithmetic means, etc.) of refractive errors and thin systems. For general systems the optical character is defined by the dimensionally-heterogeneous 4 × 4 symplectic matrix S, the transference, or if explicit allowance is made for heterocentricity, the 5 × 5 augmented symplectic matrix T. Ordinary quantitative analysis cannot be performed on them because matrices of neither of these types constitute vector spaces. Suitable transformations have been proposed but because the transforms are dimensionally heterogeneous the spaces are not naturally inner-product spaces. The paper obtains 14-dimensional spaces of augmented point P and angle Q characteristics. The 14-dimensional space defined by the augmented angle characteristics Q is dimensionally homogenous and an inner-product space. A 10-dimensional subspace of the space of augmented point characteristics P is also an inner-product space. The spaces are suitable for quantitative analysis of the optical character of eyes and many other systems. Distances and angles can be defined in the inner-product spaces. The optical systems may have multiple separated astigmatic and decentred refracting elements. © 2017 The Authors Ophthalmic & Physiological Optics © 2017 The College of Optometrists.

Biotin Switch Assays for Quantitation of Reversible Cysteine Oxidation.

PubMed

Li, R; Kast, J

2017-01-01

Thiol groups in protein cysteine residues can be subjected to different oxidative modifications by reactive oxygen/nitrogen species. Reversible cysteine oxidation, including S-nitrosylation, S-sulfenylation, S-glutathionylation, and disulfide formation, modulate multiple biological functions, such as enzyme catalysis, antioxidant, and other signaling pathways. However, the biological relevance of reversible cysteine oxidation is typically underestimated, in part due to the low abundance and high reactivity of some of these modifications, and the lack of methods to enrich and quantify them. To facilitate future research efforts, this chapter describes detailed procedures to target the different modifications using mass spectrometry-based biotin switch assays. By switching the modification of interest to a biotin moiety, these assays leverage the high affinity between biotin and avidin to enrich the modification. The use of stable isotope labeling and a range of selective reducing agents facilitate the quantitation of individual as well as total reversible cysteine oxidation. The biotin switch assay has been widely applied to the quantitative analysis of S-nitrosylation in different disease models and is now also emerging as a valuable research tool for other oxidative cysteine modifications, highlighting its relevance as a versatile, robust strategy for carrying out in-depth studies in redox proteomics. © 2017 Elsevier Inc. All rights reserved.

Quantitative proteomic analysis of intact plastids.

PubMed

Shiraya, Takeshi; Kaneko, Kentaro; Mitsui, Toshiaki

2014-01-01

Plastids are specialized cell organelles in plant cells that are differentiated into various forms including chloroplasts, chromoplasts, and amyloplasts, and fulfill important functions in maintaining the overall cell metabolism and sensing environmental factors such as sunlight. It is therefore important to grasp the mechanisms of differentiation and functional changes of plastids in order to enhance the understanding of vegetality. In this chapter, details of a method for the extraction of intact plastids that makes analysis possible while maintaining the plastid functions are provided; in addition, a quantitative shotgun method for analyzing the composition and changes in the content of proteins in plastids as a result of environmental impacts is described.

Renal geology (quantitative renal stone analysis) by 'Fourier transform infrared spectroscopy'.

PubMed

Singh, Iqbal

2008-01-01

To prospectively determine the precise stone composition (quantitative analysis) by using infrared spectroscopy in patients with urinary stone disease presenting to our clinic. To determine an ideal method for stone analysis suitable for use in a clinical setting. After routine and a detailed metabolic workup of all patients of urolithiasis, stone samples of 50 patients of urolithiasis satisfying the entry criteria were subjected to the Fourier transform infrared spectroscopic analysis after adequate sample homogenization at a single testing center. Calcium oxalate monohydrate and dihydrate stone mixture was most commonly encountered in 35 (71%) followed by calcium phosphate, carbonate apatite, magnesium ammonium hexahydrate and xanthine stones. Fourier transform infrared spectroscopy allows an accurate, reliable quantitative method of stone analysis. It also helps in maintaining a computerized large reference library. Knowledge of precise stone composition may allow the institution of appropriate prophylactic therapy despite the absence of any detectable metabolic abnormalities. This may prevent and or delay stone recurrence.

Quantitative Oxygenation Venography from MRI Phase

PubMed Central

Fan, Audrey P.; Bilgic, Berkin; Gagnon, Louis; Witzel, Thomas; Bhat, Himanshu; Rosen, Bruce R.; Adalsteinsson, Elfar

2014-01-01

Purpose To demonstrate acquisition and processing methods for quantitative oxygenation venograms that map in vivo oxygen saturation (SvO2) along cerebral venous vasculature. Methods Regularized quantitative susceptibility mapping (QSM) is used to reconstruct susceptibility values and estimate SvO2 in veins. QSM with ℓ1 and ℓ2 regularization are compared in numerical simulations of vessel structures with known magnetic susceptibility. Dual-echo, flow-compensated phase images are collected in three healthy volunteers to create QSM images. Bright veins in the susceptibility maps are vectorized and used to form a three-dimensional vascular mesh, or venogram, along which to display SvO2 values from QSM. Results Quantitative oxygenation venograms that map SvO2 along brain vessels of arbitrary orientation and geometry are shown in vivo. SvO2 values in major cerebral veins lie within the normal physiological range reported by 15O positron emission tomography. SvO2 from QSM is consistent with previous MR susceptometry methods for vessel segments oriented parallel to the main magnetic field. In vessel simulations, ℓ1 regularization results in less than 10% SvO2 absolute error across all vessel tilt orientations and provides more accurate SvO2 estimation than ℓ2 regularization. Conclusion The proposed analysis of susceptibility images enables reliable mapping of quantitative SvO2 along venograms and may facilitate clinical use of venous oxygenation imaging. PMID:24006229

Quantitative Analysis of Filament Branch Orientation in Listeria Actin Comet Tails.

PubMed

Jasnin, Marion; Crevenna, Alvaro H

2016-02-23

Several bacterial and viral pathogens hijack the host actin cytoskeleton machinery to facilitate spread and infection. In particular, Listeria uses Arp2/3-mediated actin filament nucleation at the bacterial surface to generate a branched network that will help propel the bacteria. However, the mechanism of force generation remains elusive due to the lack of high-resolution three-dimensional structural data on the spatial organization of the actin mother and daughter (i.e., branch) filaments within this network. Here, we have explored the three-dimensional structure of Listeria actin tails in Xenopus laevis egg extracts using cryo-electron tomography. We found that the architecture of Listeria actin tails is shared between those formed in cells and in cell extracts. Both contained nanoscopic bundles along the plane of the substrate, where the bacterium lies, and upright filaments (also called Z filaments), both oriented tangentially to the bacterial cell wall. Here, we were able to identify actin filament intersections, which likely correspond to branches, within the tails. A quantitative analysis of putative Arp2/3-mediated branches in the actin network showed that mother filaments lie on the plane of the substrate, whereas daughter filaments have random deviations out of this plane. Moreover, the analysis revealed that branches are randomly oriented with respect to the bacterial surface. Therefore, the actin filament network does not push directly toward the surface but rather accumulates, building up stress around the Listeria surface. Our results favor a mechanism of force generation for Listeria movement where the stress is released into propulsive motion. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Brief report: the smiles of a child with autism spectrum disorder during an animal-assisted activity may facilitate social positive behaviors--quantitative analysis with smile-detecting interface.

PubMed

Funahashi, Atsushi; Gruebler, Anna; Aoki, Takeshi; Kadone, Hideki; Suzuki, Kenji

2014-03-01

We quantitatively measured the smiles of a child with autism spectrum disorder (ASD-C) using a wearable interface device during animal-assisted activities (AAA) for 7 months, and compared the results with a control of the same age. The participant was a 10-year-old boy with ASD, and a normal healthy boy of the same age was the control. They voluntarily participated in this study. Neither child had difficulty putting on the wearable device. They kept putting on the device comfortably through the entire experiment (duration of a session was about 30-40 min). This study was approved by the Ethical Committee based on the rules established by the Institute for Developmental Research, Aichi Human Service Center. The behavior of the participants during AAA was video-recorded and coded by the medical examiner (ME). In both groups, the smiles recognized by the ME corresponded with the computer-detected smiles. In both groups, positive social behaviors increased when the smiles increased. Also, negative social behaviors decreased when the smiles increased in the (ASD-C). It is suggested that by leading the (ASD-C) into a social environment that may cause smiling, the child's social positive behaviors may be facilitated and his social negative behaviors may be decreased.

Patient-specific coronary blood supply territories for quantitative perfusion analysis

PubMed Central

Zakkaroff, Constantine; Biglands, John D.; Greenwood, John P.; Plein, Sven; Boyle, Roger D.; Radjenovic, Aleksandra; Magee, Derek R.

2018-01-01

Abstract Myocardial perfusion imaging, coupled with quantitative perfusion analysis, provides an important diagnostic tool for the identification of ischaemic heart disease caused by coronary stenoses. The accurate mapping between coronary anatomy and under-perfused areas of the myocardium is important for diagnosis and treatment. However, in the absence of the actual coronary anatomy during the reporting of perfusion images, areas of ischaemia are allocated to a coronary territory based on a population-derived 17-segment (American Heart Association) AHA model of coronary blood supply. This work presents a solution for the fusion of 2D Magnetic Resonance (MR) myocardial perfusion images and 3D MR angiography data with the aim to improve the detection of ischaemic heart disease. The key contribution of this work is a novel method for the mediated spatiotemporal registration of perfusion and angiography data and a novel method for the calculation of patient-specific coronary supply territories. The registration method uses 4D cardiac MR cine series spanning the complete cardiac cycle in order to overcome the under-constrained nature of non-rigid slice-to-volume perfusion-to-angiography registration. This is achieved by separating out the deformable registration problem and solving it through phase-to-phase registration of the cine series. The use of patient-specific blood supply territories in quantitative perfusion analysis (instead of the population-based model of coronary blood supply) has the potential of increasing the accuracy of perfusion analysis. Quantitative perfusion analysis diagnostic accuracy evaluation with patient-specific territories against the AHA model demonstrates the value of the mediated spatiotemporal registration in the context of ischaemic heart disease diagnosis. PMID:29392098

An Inexpensive Electrodeposition Device and Its Use in a Quantitative Analysis Laboratory Exercise

ERIC Educational Resources Information Center

Parker, Richard H.

2011-01-01

An experimental procedure, using an apparatus that is easy to construct, was developed to incorporate a quantitative electrogravimetric determination of the solution nickel content into an undergraduate or advanced high school quantitative analysis laboratory. This procedure produces results comparable to the procedure used for the gravimetric…

Quantitative analysis of cardiovascular MR images.

PubMed

van der Geest, R J; de Roos, A; van der Wall, E E; Reiber, J H

1997-06-01

The diagnosis of cardiovascular disease requires the precise assessment of both morphology and function. Nearly all aspects of cardiovascular function and flow can be quantified nowadays with fast magnetic resonance (MR) imaging techniques. Conventional and breath-hold cine MR imaging allow the precise and highly reproducible assessment of global and regional left ventricular function. During the same examination, velocity encoded cine (VEC) MR imaging provides measurements of blood flow in the heart and great vessels. Quantitative image analysis often still relies on manual tracing of contours in the images. Reliable automated or semi-automated image analysis software would be very helpful to overcome the limitations associated with the manual and tedious processing of the images. Recent progress in MR imaging of the coronary arteries and myocardial perfusion imaging with contrast media, along with the further development of faster imaging sequences, suggest that MR imaging could evolve into a single technique ('one stop shop') for the evaluation of many aspects of heart disease. As a result, it is very likely that the need for automated image segmentation and analysis software algorithms will further increase. In this paper the developments directed towards the automated image analysis and semi-automated contour detection for cardiovascular MR imaging are presented.

Segmentation of fluorescence microscopy images for quantitative analysis of cell nuclear architecture.

PubMed

Russell, Richard A; Adams, Niall M; Stephens, David A; Batty, Elizabeth; Jensen, Kirsten; Freemont, Paul S

2009-04-22

Considerable advances in microscopy, biophysics, and cell biology have provided a wealth of imaging data describing the functional organization of the cell nucleus. Until recently, cell nuclear architecture has largely been assessed by subjective visual inspection of fluorescently labeled components imaged by the optical microscope. This approach is inadequate to fully quantify spatial associations, especially when the patterns are indistinct, irregular, or highly punctate. Accurate image processing techniques as well as statistical and computational tools are thus necessary to interpret this data if meaningful spatial-function relationships are to be established. Here, we have developed a thresholding algorithm, stable count thresholding (SCT), to segment nuclear compartments in confocal laser scanning microscopy image stacks to facilitate objective and quantitative analysis of the three-dimensional organization of these objects using formal statistical methods. We validate the efficacy and performance of the SCT algorithm using real images of immunofluorescently stained nuclear compartments and fluorescent beads as well as simulated images. In all three cases, the SCT algorithm delivers a segmentation that is far better than standard thresholding methods, and more importantly, is comparable to manual thresholding results. By applying the SCT algorithm and statistical analysis, we quantify the spatial configuration of promyelocytic leukemia nuclear bodies with respect to irregular-shaped SC35 domains. We show that the compartments are closer than expected under a null model for their spatial point distribution, and furthermore that their spatial association varies according to cell state. The methods reported are general and can readily be applied to quantify the spatial interactions of other nuclear compartments.

Segmentation of Fluorescence Microscopy Images for Quantitative Analysis of Cell Nuclear Architecture

PubMed Central

Russell, Richard A.; Adams, Niall M.; Stephens, David A.; Batty, Elizabeth; Jensen, Kirsten; Freemont, Paul S.

2009-01-01

Abstract Considerable advances in microscopy, biophysics, and cell biology have provided a wealth of imaging data describing the functional organization of the cell nucleus. Until recently, cell nuclear architecture has largely been assessed by subjective visual inspection of fluorescently labeled components imaged by the optical microscope. This approach is inadequate to fully quantify spatial associations, especially when the patterns are indistinct, irregular, or highly punctate. Accurate image processing techniques as well as statistical and computational tools are thus necessary to interpret this data if meaningful spatial-function relationships are to be established. Here, we have developed a thresholding algorithm, stable count thresholding (SCT), to segment nuclear compartments in confocal laser scanning microscopy image stacks to facilitate objective and quantitative analysis of the three-dimensional organization of these objects using formal statistical methods. We validate the efficacy and performance of the SCT algorithm using real images of immunofluorescently stained nuclear compartments and fluorescent beads as well as simulated images. In all three cases, the SCT algorithm delivers a segmentation that is far better than standard thresholding methods, and more importantly, is comparable to manual thresholding results. By applying the SCT algorithm and statistical analysis, we quantify the spatial configuration of promyelocytic leukemia nuclear bodies with respect to irregular-shaped SC35 domains. We show that the compartments are closer than expected under a null model for their spatial point distribution, and furthermore that their spatial association varies according to cell state. The methods reported are general and can readily be applied to quantify the spatial interactions of other nuclear compartments. PMID:19383481

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

Barriers and facilitators to health screening in men: A systematic review.

PubMed

Teo, Chin Hai; Ng, Chirk Jenn; Booth, Andrew; White, Alan

2016-09-01

Men have poorer health status and are less likely to attend health screening compared to women. This systematic review presents current evidence on the barriers and facilitators to engaging men in health screening. We included qualitative, quantitative and mixed-method studies identified through five electronic databases, contact with experts and reference mining. Two researchers selected and appraised the studies independently. Data extraction and synthesis were conducted using the 'best fit' framework synthesis method. 53 qualitative, 44 quantitative and 6 mixed-method studies were included. Factors influencing health screening uptake in men can be categorized into five domains: individual, social, health system, healthcare professional and screening procedure. The most commonly reported barriers are fear of getting the disease and low risk perception; for facilitators, they are perceived risk and benefits of screening. Male-dominant barriers include heterosexual -self-presentation, avoidance of femininity and lack of time. The partner's role is the most common male-dominant facilitator to screening. This systematic review provides a comprehensive overview of barriers and facilitators to health screening in men including the male-dominant factors. The findings are particularly useful for clinicians, researchers and policy makers who are developing interventions and policies to increase screening uptake in men. Copyright © 2016 Elsevier Ltd. All rights reserved.

A pyrosequencing assay for the quantitative methylation analysis of the PCDHB gene cluster, the major factor in neuroblastoma methylator phenotype.

PubMed

Banelli, Barbara; Brigati, Claudio; Di Vinci, Angela; Casciano, Ida; Forlani, Alessandra; Borzì, Luana; Allemanni, Giorgio; Romani, Massimo

2012-03-01

Epigenetic alterations are hallmarks of cancer and powerful biomarkers, whose clinical utilization is made difficult by the absence of standardization and of common methods of data interpretation. The coordinate methylation of many loci in cancer is defined as 'CpG island methylator phenotype' (CIMP) and identifies clinically distinct groups of patients. In neuroblastoma (NB), CIMP is defined by a methylation signature, which includes different loci, but its predictive power on outcome is entirely recapitulated by the PCDHB cluster only. We have developed a robust and cost-effective pyrosequencing-based assay that could facilitate the clinical application of CIMP in NB. This assay permits the unbiased simultaneous amplification and sequencing of 17 out of 19 genes of the PCDHB cluster for quantitative methylation analysis, taking into account all the sequence variations. As some of these variations were at CpG doublets, we bypassed the data interpretation conducted by the methylation analysis software to assign the corrected methylation value at these sites. The final result of the assay is the mean methylation level of 17 gene fragments in the protocadherin B cluster (PCDHB) cluster. We have utilized this assay to compare the methylation levels of the PCDHB cluster between high-risk and very low-risk NB patients, confirming the predictive value of CIMP. Our results demonstrate that the pyrosequencing-based assay herein described is a powerful instrument for the analysis of this gene cluster that may simplify the data comparison between different laboratories and, in perspective, could facilitate its clinical application. Furthermore, our results demonstrate that, in principle, pyrosequencing can be efficiently utilized for the methylation analysis of gene clusters with high internal homologies.

Wavelength Selection Method Based on Differential Evolution for Precise Quantitative Analysis Using Terahertz Time-Domain Spectroscopy.

PubMed

Li, Zhi; Chen, Weidong; Lian, Feiyu; Ge, Hongyi; Guan, Aihong

2017-12-01

Quantitative analysis of component mixtures is an important application of terahertz time-domain spectroscopy (THz-TDS) and has attracted broad interest in recent research. Although the accuracy of quantitative analysis using THz-TDS is affected by a host of factors, wavelength selection from the sample's THz absorption spectrum is the most crucial component. The raw spectrum consists of signals from the sample and scattering and other random disturbances that can critically influence the quantitative accuracy. For precise quantitative analysis using THz-TDS, the signal from the sample needs to be retained while the scattering and other noise sources are eliminated. In this paper, a novel wavelength selection method based on differential evolution (DE) is investigated. By performing quantitative experiments on a series of binary amino acid mixtures using THz-TDS, we demonstrate the efficacy of the DE-based wavelength selection method, which yields an error rate below 5%.

Quantitative and Qualitative Evaluations of the Enhanced Logo-autobiography Program for Korean-American Women.

PubMed

Sung, Kyung Mi; Bernstein, Kunsook

2017-12-01

This study extends Bernstein et al.'s (2016) investigation of the effects of the Enhanced Logo-autobiography Program on Korean-American women's depressive symptoms, coping strategies, purpose in life, and posttraumatic growth by analyzing quantitative and qualitative data. This study's participants significantly improved on quantitative measures of depression, coping strategies, purpose in life, and post-traumatic growth at eight weeks post-intervention and follow-up. The qualitative content analysis revealed 17 themes with five essential themes. The program's activity to promote purpose in life through posttraumatic growth facilitated participants' recovery from traumatic experiences. Standardized guidelines are needed to conduct this program in Korean community centers.

Calibration-free quantitative analysis of elemental ratios in intermetallic nanoalloys and nanocomposites using Laser Induced Breakdown Spectroscopy (LIBS).

PubMed

Davari, Seyyed Ali; Hu, Sheng; Mukherjee, Dibyendu

2017-03-01

Intermetallic nanoalloys (NAs) and nanocomposites (NCs) have increasingly gained prominence as efficient catalytic materials in electrochemical energy conversion and storage systems. But their morphology and chemical compositions play critical role in tuning their catalytic activities, and precious metal contents. While advanced microscopy techniques facilitate morphological characterizations, traditional chemical characterizations are either qualitative or extremely involved. In this study, we apply Laser Induced Breakdown Spectroscopy (LIBS) for quantitative compositional analysis of NAs and NCs synthesized with varied elemental ratios by our in-house built pulsed laser ablation technique. Specifically, elemental ratios of binary PtNi, PdCo (NAs) and PtCo (NCs) of different compositions are determined from LIBS measurements employing an internal calibration scheme using the bulk matrix species as internal standards. Morphology and qualitative elemental compositions of the aforesaid NAs and NCs are confirmed from Transmission Electron Microscopy (TEM) images and Energy Dispersive X-ray Spectroscopy (EDX) measurements. LIBS experiments are carried out in ambient conditions with the NA and NC samples drop cast on silicon wafers after centrifugation to increase their concentrations. The technique does not call for cumbersome sample preparations including acid digestions and external calibration standards commonly required in Inductively Coupled Plasma-Optical Emission Spectroscopy (ICP-OES) techniques. Yet the quantitative LIBS results are in good agreement with the results from ICP-OES measurements. Our results indicate the feasibility of using LIBS in future for rapid and in-situ quantitative chemical characterizations of wide classes of synthesized NAs and NCs. Copyright © 2016 Elsevier B.V. All rights reserved.

Joint analysis of binary and quantitative traits with data sharing and outcome-dependent sampling.

PubMed

Zheng, Gang; Wu, Colin O; Kwak, Minjung; Jiang, Wenhua; Joo, Jungnam; Lima, Joao A C

2012-04-01

We study the analysis of a joint association between a genetic marker with both binary (case-control) and quantitative (continuous) traits, where the quantitative trait values are only available for the cases due to data sharing and outcome-dependent sampling. Data sharing becomes common in genetic association studies, and the outcome-dependent sampling is the consequence of data sharing, under which a phenotype of interest is not measured for some subgroup. The trend test (or Pearson's test) and F-test are often, respectively, used to analyze the binary and quantitative traits. Because of the outcome-dependent sampling, the usual F-test can be applied using the subgroup with the observed quantitative traits. We propose a modified F-test by also incorporating the genotype frequencies of the subgroup whose traits are not observed. Further, a combination of this modified F-test and Pearson's test is proposed by Fisher's combination of their P-values as a joint analysis. Because of the correlation of the two analyses, we propose to use a Gamma (scaled chi-squared) distribution to fit the asymptotic null distribution for the joint analysis. The proposed modified F-test and the joint analysis can also be applied to test single trait association (either binary or quantitative trait). Through simulations, we identify the situations under which the proposed tests are more powerful than the existing ones. Application to a real dataset of rheumatoid arthritis is presented. © 2012 Wiley Periodicals, Inc.

Kinetic Analysis of Amylase Using Quantitative Benedict's and Iodine Starch Reagents

ERIC Educational Resources Information Center

Cochran, Beverly; Lunday, Deborah; Miskevich, Frank

2008-01-01

Quantitative analysis of carbohydrates is a fundamental analytical tool used in many aspects of biology and chemistry. We have adapted a technique developed by Mathews et al. using an inexpensive scanner and open-source image analysis software to quantify amylase activity using both the breakdown of starch and the appearance of glucose. Breakdown…

Investment appraisal using quantitative risk analysis.

PubMed

Johansson, Henrik

2002-07-01

Investment appraisal concerned with investments in fire safety systems is discussed. Particular attention is directed at evaluating, in terms of the Bayesian decision theory, the risk reduction that investment in a fire safety system involves. It is shown how the monetary value of the change from a building design without any specific fire protection system to one including such a system can be estimated by use of quantitative risk analysis, the results of which are expressed in terms of a Risk-adjusted net present value. This represents the intrinsic monetary value of investing in the fire safety system. The method suggested is exemplified by a case study performed in an Avesta Sheffield factory.

Survival Prediction in Pancreatic Ductal Adenocarcinoma by Quantitative Computed Tomography Image Analysis.

PubMed

Attiyeh, Marc A; Chakraborty, Jayasree; Doussot, Alexandre; Langdon-Embry, Liana; Mainarich, Shiana; Gönen, Mithat; Balachandran, Vinod P; D'Angelica, Michael I; DeMatteo, Ronald P; Jarnagin, William R; Kingham, T Peter; Allen, Peter J; Simpson, Amber L; Do, Richard K

2018-04-01

Pancreatic cancer is a highly lethal cancer with no established a priori markers of survival. Existing nomograms rely mainly on post-resection data and are of limited utility in directing surgical management. This study investigated the use of quantitative computed tomography (CT) features to preoperatively assess survival for pancreatic ductal adenocarcinoma (PDAC) patients. A prospectively maintained database identified consecutive chemotherapy-naive patients with CT angiography and resected PDAC between 2009 and 2012. Variation in CT enhancement patterns was extracted from the tumor region using texture analysis, a quantitative image analysis tool previously described in the literature. Two continuous survival models were constructed, with 70% of the data (training set) using Cox regression, first based only on preoperative serum cancer antigen (CA) 19-9 levels and image features (model A), and then on CA19-9, image features, and the Brennan score (composite pathology score; model B). The remaining 30% of the data (test set) were reserved for independent validation. A total of 161 patients were included in the analysis. Training and test sets contained 113 and 48 patients, respectively. Quantitative image features combined with CA19-9 achieved a c-index of 0.69 [integrated Brier score (IBS) 0.224] on the test data, while combining CA19-9, imaging, and the Brennan score achieved a c-index of 0.74 (IBS 0.200) on the test data. We present two continuous survival prediction models for resected PDAC patients. Quantitative analysis of CT texture features is associated with overall survival. Further work includes applying the model to an external dataset to increase the sample size for training and to determine its applicability.

Quantitative assessment of upper extremities motor function in multiple sclerosis.

PubMed

Daunoraviciene, Kristina; Ziziene, Jurgita; Griskevicius, Julius; Pauk, Jolanta; Ovcinikova, Agne; Kizlaitiene, Rasa; Kaubrys, Gintaras

2018-05-18

Upper extremity (UE) motor function deficits are commonly noted in multiple sclerosis (MS) patients and assessing it is challenging because of the lack of consensus regarding its definition. Instrumented biomechanical analysis of upper extremity movements can quantify coordination with different spatiotemporal measures and facilitate disability rating in MS patients. To identify objective quantitative parameters for more accurate evaluation of UE disability and relate it to existing clinical scores. Thirty-four MS patients and 24 healthy controls (CG) performed a finger-to-nose test as fast as possible and, in addition, clinical evaluation kinematic parameters of UE were measured by using inertial sensors. Generally, a higher disability score was associated with an increase of several temporal parameters, like slower task performance. The time taken to touch their nose was longer when the task was fulfilled with eyes closed. Time to peak angular velocity significantly changed in MS patients (EDSS > 5.0). The inter-joint coordination significantly decreases in MS patients (EDSS 3.0-5.5). Spatial parameters indicated that maximal ROM changes were in elbow flexion. Our findings have revealed that spatiotemporal parameters are related to the UE motor function and MS disability level. Moreover, they facilitate clinical rating by supporting clinical decisions with quantitative data.

Facilitation of self-transcendence in a breast cancer support group.

PubMed

Coward, D D

1998-01-01

To examine the feasibility and patterns of effectiveness of a breast cancer support group intervention specifically designed to facilitate self-transcendence views and perspectives that would enhance emotional and physical well-being. Pre-experimental design pilot intervention study with a quantitative approach to data analysis. Survivor-established breast cancer resource center in Austin, TX. Women with recently diagnosed breast cancer (N = 16) participating in 90-minute support group sessions that met weekly for eight weeks. Theory-driven support group intervention facilitated by an oncology clinical nurse specialist, a psychotherapist, and a breast cancer survivor. Activities planned for individual sessions were based on self-transcendence theory, cancer support group literature, and the facilitators' extensive previous support group experience. Self-transcendence, emotional well-being, physical well-being. Good networking, coordination, and follow-up were essential for participant recruitment and retention throughout the intervention period. Although specific theory-driven activities were planned for group sessions, facilitators maintained flexibility in meeting immediate concerns of the participants. Relationships among participants' scores on study variables indicated an association between self-transcendence and emotional well-being. Scores on self-transcendence and well-being variables at the end of the intervention increased from baseline, but only functional performance status, mood state, and satisfaction with life reached statistical significance. The pilot study was invaluable in providing direction for the conduct of future experimental studies. Provides preliminary support for the use of theory-driven activities for promotion of self-transcendence views and behaviors within a cancer support group setting.

Virtual OD: Facilitating Groups Online

ERIC Educational Resources Information Center

Milton, Judy; Watkins, Karen E.; Daley, Barbara J.

2005-01-01

This study examined the role of facilitators in nine virtual action learning groups. A qualitative analysis of the facilitators' interventions across all groups resulted in a typology that included group management, group process, and support interventions. A model showing the relationship among these categories proposes that effective…

Semantic Coherence Facilitates Distributional Learning.

PubMed

Ouyang, Long; Boroditsky, Lera; Frank, Michael C

2017-04-01

Computational models have shown that purely statistical knowledge about words' linguistic contexts is sufficient to learn many properties of words, including syntactic and semantic category. For example, models can infer that "postman" and "mailman" are semantically similar because they have quantitatively similar patterns of association with other words (e.g., they both tend to occur with words like "deliver," "truck," "package"). In contrast to these computational results, artificial language learning experiments suggest that distributional statistics alone do not facilitate learning of linguistic categories. However, experiments in this paradigm expose participants to entirely novel words, whereas real language learners encounter input that contains some known words that are semantically organized. In three experiments, we show that (a) the presence of familiar semantic reference points facilitates distributional learning and (b) this effect crucially depends both on the presence of known words and the adherence of these known words to some semantic organization. Copyright © 2016 Cognitive Science Society, Inc.

Quantitative analysis of biological tissues using Fourier transform-second-harmonic generation imaging

NASA Astrophysics Data System (ADS)

Ambekar Ramachandra Rao, Raghu; Mehta, Monal R.; Toussaint, Kimani C., Jr.

2010-02-01

We demonstrate the use of Fourier transform-second-harmonic generation (FT-SHG) imaging of collagen fibers as a means of performing quantitative analysis of obtained images of selected spatial regions in porcine trachea, ear, and cornea. Two quantitative markers, preferred orientation and maximum spatial frequency are proposed for differentiating structural information between various spatial regions of interest in the specimens. The ear shows consistent maximum spatial frequency and orientation as also observed in its real-space image. However, there are observable changes in the orientation and minimum feature size of fibers in the trachea indicating a more random organization. Finally, the analysis is applied to a 3D image stack of the cornea. It is shown that the standard deviation of the orientation is sensitive to the randomness in fiber orientation. Regions with variations in the maximum spatial frequency, but with relatively constant orientation, suggest that maximum spatial frequency is useful as an independent quantitative marker. We emphasize that FT-SHG is a simple, yet powerful, tool for extracting information from images that is not obvious in real space. This technique can be used as a quantitative biomarker to assess the structure of collagen fibers that may change due to damage from disease or physical injury.

Quantitative 3D analysis of bone in hip osteoarthritis using clinical computed tomography.

PubMed

Turmezei, Tom D; Treece, Graham M; Gee, Andrew H; Fotiadou, Anastasia F; Poole, Kenneth E S

2016-07-01

To assess the relationship between proximal femoral cortical bone thickness and radiological hip osteoarthritis using quantitative 3D analysis of clinical computed tomography (CT) data. Image analysis was performed on clinical CT imaging data from 203 female volunteers with a technique called cortical bone mapping (CBM). Colour thickness maps were created for each proximal femur. Statistical parametric mapping was performed to identify statistically significant differences in cortical bone thickness that corresponded with the severity of radiological hip osteoarthritis. Kellgren and Lawrence (K&L) grade, minimum joint space width (JSW) and a novel CT-based osteophyte score were also blindly assessed from the CT data. For each increase in K&L grade, cortical thickness increased by up to 25 % in distinct areas of the superolateral femoral head-neck junction and superior subchondral bone plate. For increasing severity of CT osteophytes, the increase in cortical thickness was more circumferential, involving a wider portion of the head-neck junction, with up to a 7 % increase in cortical thickness per increment in score. Results were not significant for minimum JSW. These findings indicate that quantitative 3D analysis of the proximal femur can identify changes in cortical bone thickness relevant to structural hip osteoarthritis. • CT is being increasingly used to assess bony involvement in osteoarthritis • CBM provides accurate and reliable quantitative analysis of cortical bone thickness • Cortical bone is thicker at the superior femoral head-neck with worse osteoarthritis • Regions of increased thickness co-locate with impingement and osteophyte formation • Quantitative 3D bone analysis could enable clinical disease prediction and therapy development.

[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.

Leadership Development Through Peer-Facilitated Simulation in Nursing Education.

PubMed

Brown, Karen M; Rode, Jennifer L

2018-01-01

Baccalaureate nursing graduates must possess leadership skills, yet few opportunities exist to cultivate leadership abilities in a clinical environment. Peer-facilitated learning may increase the leadership skills of competence, self-confidence, self-reflection, and role modeling. Facilitating human patient simulation provides opportunities to develop leadership skills. With faculty supervision, senior baccalaureate students led small-group simulation experiences with sophomore and junior peers and then conducted subsequent debriefings. Quantitative and qualitative descriptive data allowed evaluation of students' satisfaction with this teaching innovation and whether the experience affected students' desire to take on leadership roles. Students expressed satisfaction with the peer-facilitated simulation experience and confidence in mastering the content while developing necessary skills for practice. Peer-facilitated simulation provides an opportunity for leadership development and learning. Study results can inform the development of nursing curricula to best develop the leadership skills of nursing students. [J Nurs Educ. 2018;57(1):53-57.]. Copyright 2018, SLACK Incorporated.

Correlative SEM SERS for quantitative analysis of dimer nanoparticles.

PubMed

Timmermans, F J; Lenferink, A T M; van Wolferen, H A G M; Otto, C

2016-11-14

A Raman microscope integrated with a scanning electron microscope was used to investigate plasmonic structures by correlative SEM-SERS analysis. The integrated Raman-SEM microscope combines high-resolution electron microscopy information with SERS signal enhancement from selected nanostructures with adsorbed Raman reporter molecules. Correlative analysis is performed for dimers of two gold nanospheres. Dimers were selected on the basis of SEM images from multi aggregate samples. The effect of the orientation of the dimer with respect to the polarization state of the laser light and the effect of the particle gap size on the Raman signal intensity is observed. Additionally, calculations are performed to simulate the electric near field enhancement. These simulations are based on the morphologies observed by electron microscopy. In this way the experiments are compared with the enhancement factor calculated with near field simulations and are subsequently used to quantify the SERS enhancement factor. Large differences between experimentally observed and calculated enhancement factors are regularly detected, a phenomenon caused by nanoscale differences between the real and 'simplified' simulated structures. Quantitative SERS experiments reveal the structure induced enhancement factor, ranging from ∼200 to ∼20 000, averaged over the full nanostructure surface. The results demonstrate correlative Raman-SEM microscopy for the quantitative analysis of plasmonic particles and structures, thus enabling a new analytical method in the field of SERS and plasmonics.

Quantitative Analysis of the Interdisciplinarity of Applied Mathematics.

PubMed

Xie, Zheng; Duan, Xiaojun; Ouyang, Zhenzheng; Zhang, Pengyuan

2015-01-01

The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999-2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics.

Identification and quantitation of semi-crystalline microplastics using image analysis and differential scanning calorimetry.

PubMed

Rodríguez Chialanza, Mauricio; Sierra, Ignacio; Pérez Parada, Andrés; Fornaro, Laura

2018-06-01

There are several techniques used to analyze microplastics. These are often based on a combination of visual and spectroscopic techniques. Here we introduce an alternative workflow for identification and mass quantitation through a combination of optical microscopy with image analysis (IA) and differential scanning calorimetry (DSC). We studied four synthetic polymers with environmental concern: low and high density polyethylene (LDPE and HDPE, respectively), polypropylene (PP), and polyethylene terephthalate (PET). Selected experiments were conducted to investigate (i) particle characterization and counting procedures based on image analysis with open-source software, (ii) chemical identification of microplastics based on DSC signal processing, (iii) dependence of particle size on DSC signal, and (iv) quantitation of microplastics mass based on DSC signal. We describe the potential and limitations of these techniques to increase reliability for microplastic analysis. Particle size demonstrated to have particular incidence in the qualitative and quantitative performance of DSC signals. Both, identification (based on characteristic onset temperature) and mass quantitation (based on heat flow) showed to be affected by particle size. As a result, a proper sample treatment which includes sieving of suspended particles is particularly required for this analytical approach.

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

What do parents perceive are the barriers and facilitators to accessing psychological treatment for mental health problems in children and adolescents? A systematic review of qualitative and quantitative studies.

PubMed

Reardon, Tessa; Harvey, Kate; Baranowska, Magdalena; O'Brien, Doireann; Smith, Lydia; Creswell, Cathy

2017-06-01

A minority of children and adolescents with mental health problems access treatment. The reasons for poor rates of treatment access are not well understood. As parents are a key gatekeeper to treatment access, it is important to establish parents' views of barriers/facilitators to accessing treatment. The aims of this study are to synthesise findings from qualitative and quantitative studies that report parents' perceptions of barriers/facilitators to accessing treatment for mental health problems in children/adolescents. A systematic review and narrative synthesis were conducted. Forty-four studies were included in the review and were assessed in detail. Parental perceived barriers/facilitators relating to (1) systemic/structural issues; (2) views and attitudes towards services and treatment; (3) knowledge and understanding of mental health problems and the help-seeking process; and (4) family circumstances were identified. Findings highlight avenues for improving access to child mental health services, including increased provision that is free to service users and flexible to their needs, with opportunities to develop trusting, supportive relationships with professionals. Furthermore, interventions are required to improve parents' identification of mental health problems, reduce stigma for parents, and increase awareness of how to access services.

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.

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.

Quantitative Analysis of Food and Feed Samples with Droplet Digital PCR

PubMed Central

Morisset, Dany; Štebih, Dejan; Milavec, Mojca; Gruden, Kristina; Žel, Jana

2013-01-01

In this study, the applicability of droplet digital PCR (ddPCR) for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies) of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR) approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed. PMID:23658750

Quantitative Multispectral Analysis Of Discrete Subcellular Particles By Digital Imaging Fluorescence Microscopy (DIFM)

NASA Astrophysics Data System (ADS)

Dorey, C. K.; Ebenstein, David B.

1988-10-01

Subcellular localization of multiple biochemical markers is readily achieved through their characteristic autofluorescence or through use of appropriately labelled antibodies. Recent development of specific probes has permitted elegant studies in calcium and pH in living cells. However, each of these methods measured fluorescence at one wavelength; precise quantitation of multiple fluorophores at individual sites within a cell has not been possible. Using DIFM, we have achieved spectral analysis of discrete subcellular particles 1-2 gm in diameter. The fluorescence emission is broken into narrow bands by an interference monochromator and visualized through the combined use of a silicon intensified target (SIT) camera, a microcomputer based framegrabber with 8 bit resolution, and a color video monitor. Image acquisition, processing, analysis and display are under software control. The digitized image can be corrected for the spectral distortions induced by the wavelength dependent sensitivity of the camera, and the displayed image can be enhanced or presented in pseudocolor to facilitate discrimination of variation in pixel intensity of individual particles. For rapid comparison of the fluorophore composition of granules, a ratio image is produced by dividing the image captured at one wavelength by that captured at another. In the resultant ratio image, a granule which has a fluorophore composition different from the majority is selectively colored. This powerful system has been utilized to obtain spectra of endogenous autofluorescent compounds in discrete cellular organelles of human retinal pigment epithelium, and to measure immunohistochemically labelled components of the extracellular matrix associated with the human optic nerve.

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.

Race and Older Mothers’ Differentiation: A Sequential Quantitative and Qualitative Analysis

PubMed Central

Sechrist, Jori; Suitor, J. Jill; Riffin, Catherine; Taylor-Watson, Kadari; Pillemer, Karl

2011-01-01

The goal of this paper is to demonstrate a process by which qualitative and quantitative approaches are combined to reveal patterns in the data that are unlikely to be detected and confirmed by either method alone. Specifically, we take a sequential approach to combining qualitative and quantitative data to explore race differences in how mothers differentiate among their adult children. We began with a standard multivariate analysis examining race differences in mothers’ differentiation among their adult children regarding emotional closeness and confiding. Finding no race differences in this analysis, we conducted an in-depth comparison of the Black and White mothers’ narratives to determine whether there were underlying patterns that we had been unable to detect in our first analysis. Using this method, we found that Black mothers were substantially more likely than White mothers to emphasize interpersonal relationships within the family when describing differences among their children. In our final step, we developed a measure of familism based on the qualitative data and conducted a multivariate analysis to confirm the patterns revealed by the in-depth comparison of the mother’s narratives. We conclude that using such a sequential mixed methods approach to data analysis has the potential to shed new light on complex family relations. PMID:21967639

A thioacidolysis method tailored for higher‐throughput quantitative analysis of lignin monomers

PubMed Central

Foster, Cliff; Happs, Renee M.; Doeppke, Crissa; Meunier, Kristoffer; Gehan, Jackson; Yue, Fengxia; Lu, Fachuang; Davis, Mark F.

2016-01-01

Abstract Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β‐O‐4 linkages. Current thioacidolysis methods are low‐throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non‐chlorinated organic solvent and is tailored for higher‐throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1–2 mg of biomass per assay and has been quantified using fast‐GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, including standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day‐to‐day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. The method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses. PMID:27534715

A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

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

Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.

Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

A thioacidolysis method tailored for higher-throughput quantitative analysis of lignin monomers

DOE PAGES

Harman-Ware, Anne E.; Foster, Cliff; Happs, Renee M.; ...

2016-09-14

Thioacidolysis is a method used to measure the relative content of lignin monomers bound by β-O-4 linkages. Current thioacidolysis methods are low-throughput as they require tedious steps for reaction product concentration prior to analysis using standard GC methods. A quantitative thioacidolysis method that is accessible with general laboratory equipment and uses a non-chlorinated organic solvent and is tailored for higher-throughput analysis is reported. The method utilizes lignin arylglycerol monomer standards for calibration, requires 1-2 mg of biomass per assay and has been quantified using fast-GC techniques including a Low Thermal Mass Modular Accelerated Column Heater (LTM MACH). Cumbersome steps, includingmore » standard purification, sample concentrating and drying have been eliminated to help aid in consecutive day-to-day analyses needed to sustain a high sample throughput for large screening experiments without the loss of quantitation accuracy. As a result, the method reported in this manuscript has been quantitatively validated against a commonly used thioacidolysis method and across two different research sites with three common biomass varieties to represent hardwoods, softwoods, and grasses.« less

QuASAR: quantitative allele-specific analysis of reads.

PubMed

Harvey, Chris T; Moyerbrailean, Gregory A; Davis, Gordon O; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2015-04-15

Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. http://github.com/piquelab/QuASAR. fluca@wayne.edu or rpique@wayne.edu Supplementary Material is available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

QuASAR: quantitative allele-specific analysis of reads

PubMed Central

Harvey, Chris T.; Moyerbrailean, Gregory A.; Davis, Gordon O.; Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2015-01-01

Motivation: Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding of the functional role of non-coding sequences. However, eQTL studies are costly, requiring large sample sizes and genome-wide genotyping of each sample. In contrast, analysis of allele-specific expression (ASE) is becoming a popular approach to detect the effect of genetic variation on gene expression, even within a single individual. This is typically achieved by counting the number of RNA-seq reads matching each allele at heterozygous sites and testing the null hypothesis of a 1:1 allelic ratio. In principle, when genotype information is not readily available, it could be inferred from the RNA-seq reads directly. However, there are currently no existing methods that jointly infer genotypes and conduct ASE inference, while considering uncertainty in the genotype calls. Results: We present QuASAR, quantitative allele-specific analysis of reads, a novel statistical learning method for jointly detecting heterozygous genotypes and inferring ASE. The proposed ASE inference step takes into consideration the uncertainty in the genotype calls, while including parameters that model base-call errors in sequencing and allelic over-dispersion. We validated our method with experimental data for which high-quality genotypes are available. Results for an additional dataset with multiple replicates at different sequencing depths demonstrate that QuASAR is a powerful tool for ASE analysis when genotypes are not available. Availability and implementation: http://github.com/piquelab/QuASAR. Contact: fluca@wayne.edu or rpique@wayne.edu Supplementary information: Supplementary Material is available at Bioinformatics online. PMID:25480375

Machine learning-based quantitative texture analysis of CT images of small renal masses: Differentiation of angiomyolipoma without visible fat from renal cell carcinoma.

PubMed

Feng, Zhichao; Rong, Pengfei; Cao, Peng; Zhou, Qingyu; Zhu, Wenwei; Yan, Zhimin; Liu, Qianyun; Wang, Wei

2018-04-01

To evaluate the diagnostic performance of machine-learning based quantitative texture analysis of CT images to differentiate small (≤ 4 cm) angiomyolipoma without visible fat (AMLwvf) from renal cell carcinoma (RCC). This single-institutional retrospective study included 58 patients with pathologically proven small renal mass (17 in AMLwvf and 41 in RCC groups). Texture features were extracted from the largest possible tumorous regions of interest (ROIs) by manual segmentation in preoperative three-phase CT images. Interobserver reliability and the Mann-Whitney U test were applied to select features preliminarily. Then support vector machine with recursive feature elimination (SVM-RFE) and synthetic minority oversampling technique (SMOTE) were adopted to establish discriminative classifiers, and the performance of classifiers was assessed. Of the 42 extracted features, 16 candidate features showed significant intergroup differences (P < 0.05) and had good interobserver agreement. An optimal feature subset including 11 features was further selected by the SVM-RFE method. The SVM-RFE+SMOTE classifier achieved the best performance in discriminating between small AMLwvf and RCC, with the highest accuracy, sensitivity, specificity and AUC of 93.9 %, 87.8 %, 100 % and 0.955, respectively. Machine learning analysis of CT texture features can facilitate the accurate differentiation of small AMLwvf from RCC. • Although conventional CT is useful for diagnosis of SRMs, it has limitations. • Machine-learning based CT texture analysis facilitate differentiation of small AMLwvf from RCC. • The highest accuracy of SVM-RFE+SMOTE classifier reached 93.9 %. • Texture analysis combined with machine-learning methods might spare unnecessary surgery for AMLwvf.

Toward standardized quantitative image quality (IQ) assessment in computed tomography (CT): A comprehensive framework for automated and comparative IQ analysis based on ICRU Report 87.

PubMed

Pahn, Gregor; Skornitzke, Stephan; Schlemmer, Hans-Peter; Kauczor, Hans-Ulrich; Stiller, Wolfram

2016-01-01

Based on the guidelines from "Report 87: Radiation Dose and Image-quality Assessment in Computed Tomography" of the International Commission on Radiation Units and Measurements (ICRU), a software framework for automated quantitative image quality analysis was developed and its usability for a variety of scientific questions demonstrated. The extendable framework currently implements the calculation of the recommended Fourier image quality (IQ) metrics modulation transfer function (MTF) and noise-power spectrum (NPS), and additional IQ quantities such as noise magnitude, CT number accuracy, uniformity across the field-of-view, contrast-to-noise ratio (CNR) and signal-to-noise ratio (SNR) of simulated lesions for a commercially available cone-beam phantom. Sample image data were acquired with different scan and reconstruction settings on CT systems from different manufacturers. Spatial resolution is analyzed in terms of edge-spread function, line-spread-function, and MTF. 3D NPS is calculated according to ICRU Report 87, and condensed to 2D and radially averaged 1D representations. Noise magnitude, CT numbers, and uniformity of these quantities are assessed on large samples of ROIs. Low-contrast resolution (CNR, SNR) is quantitatively evaluated as a function of lesion contrast and diameter. Simultaneous automated processing of several image datasets allows for straightforward comparative assessment. The presented framework enables systematic, reproducible, automated and time-efficient quantitative IQ analysis. Consistent application of the ICRU guidelines facilitates standardization of quantitative assessment not only for routine quality assurance, but for a number of research questions, e.g. the comparison of different scanner models or acquisition protocols, and the evaluation of new technology or reconstruction methods. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Quantitative analysis of NMR spectra with chemometrics

NASA Astrophysics Data System (ADS)

Winning, H.; Larsen, F. H.; Bro, R.; Engelsen, S. B.

2008-01-01

The number of applications of chemometrics to series of NMR spectra is rapidly increasing due to an emerging interest for quantitative NMR spectroscopy e.g. in the pharmaceutical and food industries. This paper gives an analysis of advantages and limitations of applying the two most common chemometric procedures, Principal Component Analysis (PCA) and Multivariate Curve Resolution (MCR), to a designed set of 231 simple alcohol mixture (propanol, butanol and pentanol) 1H 400 MHz spectra. The study clearly demonstrates that the major advantage of chemometrics is the visualisation of larger data structures which adds a new exploratory dimension to NMR research. While robustness and powerful data visualisation and exploration are the main qualities of the PCA method, the study demonstrates that the bilinear MCR method is an even more powerful method for resolving pure component NMR spectra from mixtures when certain conditions are met.

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells.

PubMed

Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I

2018-05-09

We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell.

A meta-analysis of plant facilitation in coastal dune systems: responses, regions, and research gaps.

PubMed

Castanho, Camila de Toledo; Lortie, Christopher J; Zaitchik, Benjamin; Prado, Paulo Inácio

2015-01-01

Empirical studies in salt marshes, arid, and alpine systems support the hypothesis that facilitation between plants is an important ecological process in severe or 'stressful' environments. Coastal dunes are both abiotically stressful and frequently disturbed systems. Facilitation has been documented, but the evidence to date has not been synthesized. We did a systematic review with meta-analysis to highlight general research gaps in the study of plant interactions in coastal dunes and examine if regional and local factors influence the magnitude of facilitation in these systems. The 32 studies included in the systematic review were done in coastal dunes located in 13 countries around the world but the majority was in the temperate zone (63%). Most of the studies adopt only an observational approach to make inferences about facilitative interactions, whereas only 28% of the studies used both observational and experimental approaches. Among the factors we tested, only geographic region mediates the occurrence of facilitation more broadly in coastal dune systems. The presence of a neighbor positively influenced growth and survival in the tropics, whereas in temperate and subartic regions the effect was neutral for both response variables. We found no evidence that climatic and local factors, such as life-form and life stage of interacting plants, affect the magnitude of facilitation in coastal dunes. Overall, conclusions about plant facilitation in coastal dunes depend on the response variable measured and, more broadly, on the geographic region examined. However, the high variability and the limited number of studies, especially in tropical region, indicate we need to be cautious in the generalization of the conclusions. Anyway, coastal dunes provide an important means to explore topical issues in facilitation research including context dependency, local versus regional drivers of community structure, and the importance of gradients in shaping the outcome of net

Quantitation of zolpidem in biological fluids by electro-driven microextraction combined with HPLC-UV analysis.

PubMed

Yaripour, Saeid; Mohammadi, Ali; Esfanjani, Isa; Walker, Roderick B; Nojavan, Saeed

2018-01-01

In this study, for the first time, an electro-driven microextraction method named electromembrane extraction combined with a simple high performance liquid chromatography and ultraviolet detection was developed and validated for the quantitation of zolpidem in biological samples. Parameters influencing electromembrane extraction were evaluated and optimized. The membrane consisted of 2-ethylhexanol immobilized in the pores of a hollow fiber. As a driving force, a 150 V electric field was applied to facilitate the analyte migration from the sample matrix to an acceptor solution through a supported liquid membrane. The pHs of donor and acceptor solutions were optimized to 6.0 and 2.0, respectively. The enrichment factor was obtained >75 within 15 minutes. The effect of carbon nanotubes (as solid nano-sorbents) on the membrane performance and EME efficiency was evaluated. The method was linear over the range of 10-1000 ng/mL for zolpidem (R 2 >0.9991) with repeatability ( %RSD) between 0.3 % and 7.3 % ( n = 3). The limits of detection and quantitation were 3 and 10 ng/mL, respectively. The sensitivity of HPLC-UV for the determination of zolpidem was enhanced by electromembrane extraction. Finally, the method was employed for the quantitation of zolpidem in biological samples with relative recoveries in the range of 60-79 %.

Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis.

PubMed

Lindén, Rolf O; Eronen, Ville-Pekka; Aittokallio, Tero

2011-03-24

High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into the functional wiring diagrams of genetic interaction networks on a global scale. However, it is poorly known how well these quantitative interaction measurements agree across the screening approaches, which hinders their integrated use toward improving the coverage and quality of the genetic interaction maps in yeast and other organisms. Using large-scale data matrices from epistatic miniarray profiling (E-MAP), genetic interaction mapping (GIM), and synthetic genetic array (SGA) approaches, we carried out here a systematic comparative evaluation among these quantitative maps of genetic interactions in yeast. The relatively low association between the original interaction measurements or their customized scores could be improved using a matrix-based modelling framework, which enables the use of single- and double-mutant fitness estimates and measurements, respectively, when scoring genetic interactions. Toward an integrative analysis, we show how the detections from the different screening approaches can be combined to suggest novel positive and negative interactions which are complementary to those obtained using any single screening approach alone. The matrix approximation procedure has been made available to support the design and analysis of the future screening studies. We have shown here that even if the correlation between the currently available quantitative genetic interaction maps in yeast is relatively low, their comparability can be improved by means of our computational matrix approximation procedure, which will enable integrative analysis and detection of a wider spectrum of genetic interactions using data from the complementary screening approaches.

Quantitative phase-digital holographic microscopy: a new imaging modality to identify original cellular biomarkers of diseases

NASA Astrophysics Data System (ADS)

Marquet, P.; Rothenfusser, K.; Rappaz, B.; Depeursinge, C.; Jourdain, P.; Magistretti, P. J.

2016-03-01

Quantitative phase microscopy (QPM) has recently emerged as a powerful label-free technique in the field of living cell imaging allowing to non-invasively measure with a nanometric axial sensitivity cell structure and dynamics. Since the phase retardation of a light wave when transmitted through the observed cells, namely the quantitative phase signal (QPS), is sensitive to both cellular thickness and intracellular refractive index related to the cellular content, its accurate analysis allows to derive various cell parameters and monitor specific cell processes, which are very likely to identify new cell biomarkers. Specifically, quantitative phase-digital holographic microscopy (QP-DHM), thanks to its numerical flexibility facilitating parallelization and automation processes, represents an appealing imaging modality to both identify original cellular biomarkers of diseases as well to explore the underlying pathophysiological processes.

Low-dose CT for quantitative analysis in acute respiratory distress syndrome

PubMed Central

2013-01-01

Introduction The clinical use of serial quantitative computed tomography (CT) to characterize lung disease and guide the optimization of mechanical ventilation in patients with acute respiratory distress syndrome (ARDS) is limited by the risk of cumulative radiation exposure and by the difficulties and risks related to transferring patients to the CT room. We evaluated the effects of tube current-time product (mAs) variations on quantitative results in healthy lungs and in experimental ARDS in order to support the use of low-dose CT for quantitative analysis. Methods In 14 sheep chest CT was performed at baseline and after the induction of ARDS via intravenous oleic acid injection. For each CT session, two consecutive scans were obtained applying two different mAs: 60 mAs was paired with 140, 15 or 7.5 mAs. All other CT parameters were kept unaltered (tube voltage 120 kVp, collimation 32 × 0.5 mm, pitch 0.85, matrix 512 × 512, pixel size 0.625 × 0.625 mm). Quantitative results obtained at different mAs were compared via Bland-Altman analysis. Results Good agreement was observed between 60 mAs and 140 mAs and between 60 mAs and 15 mAs (all biases less than 1%). A further reduction of mAs to 7.5 mAs caused an increase in the bias of poorly aerated and nonaerated tissue (-2.9% and 2.4%, respectively) and determined a significant widening of the limits of agreement for the same compartments (-10.5% to 4.8% for poorly aerated tissue and -5.9% to 10.8% for nonaerated tissue). Estimated mean effective dose at 140, 60, 15 and 7.5 mAs corresponded to 17.8, 7.4, 2.0 and 0.9 mSv, respectively. Image noise of scans performed at 140, 60, 15 and 7.5 mAs corresponded to 10, 16, 38 and 74 Hounsfield units, respectively. Conclusions A reduction of effective dose up to 70% has been achieved with minimal effects on lung quantitative results. Low-dose computed tomography provides accurate quantitative results and could be used to characterize lung compartment distribution and

Oufti: An integrated software package for high-accuracy, high-throughput quantitative microscopy analysis

PubMed Central

Paintdakhi, Ahmad; Parry, Bradley; Campos, Manuel; Irnov, Irnov; Elf, Johan; Surovtsev, Ivan; Jacobs-Wagner, Christine

2016-01-01

Summary With the realization that bacteria display phenotypic variability among cells and exhibit complex subcellular organization critical for cellular function and behavior, microscopy has re-emerged as a primary tool in bacterial research during the last decade. However, the bottleneck in today’s single-cell studies is quantitative image analysis of cells and fluorescent signals. Here, we address current limitations through the development of Oufti, a stand-alone, open-source software package for automated measurements of microbial cells and fluorescence signals from microscopy images. Oufti provides computational solutions for tracking touching cells in confluent samples, handles various cell morphologies, offers algorithms for quantitative analysis of both diffraction and non-diffraction-limited fluorescence signals, and is scalable for high-throughput analysis of massive datasets, all with subpixel precision. All functionalities are integrated in a single package. The graphical user interface, which includes interactive modules for segmentation, image analysis, and post-processing analysis, makes the software broadly accessible to users irrespective of their computational skills. PMID:26538279

Improving image segmentation performance and quantitative analysis via a computer-aided grading methodology for optical coherence tomography retinal image analysis.

PubMed

Debuc, Delia Cabrera; Salinas, Harry M; Ranganathan, Sudarshan; Tátrai, Erika; Gao, Wei; Shen, Meixiao; Wang, Jianhua; Somfai, Gábor M; Puliafito, Carmen A

2010-01-01

We demonstrate quantitative analysis and error correction of optical coherence tomography (OCT) retinal images by using a custom-built, computer-aided grading methodology. A total of 60 Stratus OCT (Carl Zeiss Meditec, Dublin, California) B-scans collected from ten normal healthy eyes are analyzed by two independent graders. The average retinal thickness per macular region is compared with the automated Stratus OCT results. Intergrader and intragrader reproducibility is calculated by Bland-Altman plots of the mean difference between both gradings and by Pearson correlation coefficients. In addition, the correlation between Stratus OCT and our methodology-derived thickness is also presented. The mean thickness difference between Stratus OCT and our methodology is 6.53 microm and 26.71 microm when using the inner segment/outer segment (IS/OS) junction and outer segment/retinal pigment epithelium (OS/RPE) junction as the outer retinal border, respectively. Overall, the median of the thickness differences as a percentage of the mean thickness is less than 1% and 2% for the intragrader and intergrader reproducibility test, respectively. The measurement accuracy range of the OCT retinal image analysis (OCTRIMA) algorithm is between 0.27 and 1.47 microm and 0.6 and 1.76 microm for the intragrader and intergrader reproducibility tests, respectively. Pearson correlation coefficients demonstrate R(2)>0.98 for all Early Treatment Diabetic Retinopathy Study (ETDRS) regions. Our methodology facilitates a more robust and localized quantification of the retinal structure in normal healthy controls and patients with clinically significant intraretinal features.

Selective Weighted Least Squares Method for Fourier Transform Infrared Quantitative Analysis.

PubMed

Wang, Xin; Li, Yan; Wei, Haoyun; Chen, Xia

2017-06-01

Classical least squares (CLS) regression is a popular multivariate statistical method used frequently for quantitative analysis using Fourier transform infrared (FT-IR) spectrometry. Classical least squares provides the best unbiased estimator for uncorrelated residual errors with zero mean and equal variance. However, the noise in FT-IR spectra, which accounts for a large portion of the residual errors, is heteroscedastic. Thus, if this noise with zero mean dominates in the residual errors, the weighted least squares (WLS) regression method described in this paper is a better estimator than CLS. However, if bias errors, such as the residual baseline error, are significant, WLS may perform worse than CLS. In this paper, we compare the effect of noise and bias error in using CLS and WLS in quantitative analysis. Results indicated that for wavenumbers with low absorbance, the bias error significantly affected the error, such that the performance of CLS is better than that of WLS. However, for wavenumbers with high absorbance, the noise significantly affected the error, and WLS proves to be better than CLS. Thus, we propose a selective weighted least squares (SWLS) regression that processes data with different wavenumbers using either CLS or WLS based on a selection criterion, i.e., lower or higher than an absorbance threshold. The effects of various factors on the optimal threshold value (OTV) for SWLS have been studied through numerical simulations. These studies reported that: (1) the concentration and the analyte type had minimal effect on OTV; and (2) the major factor that influences OTV is the ratio between the bias error and the standard deviation of the noise. The last part of this paper is dedicated to quantitative analysis of methane gas spectra, and methane/toluene mixtures gas spectra as measured using FT-IR spectrometry and CLS, WLS, and SWLS. The standard error of prediction (SEP), bias of prediction (bias), and the residual sum of squares of the errors

Quantitative analysis of rib movement based on dynamic chest bone images: preliminary results

NASA Astrophysics Data System (ADS)

Tanaka, R.; Sanada, S.; Oda, M.; Mitsutaka, M.; Suzuki, K.; Sakuta, K.; Kawashima, H.

2014-03-01

Rib movement during respiration is one of the diagnostic criteria in pulmonary impairments. In general, the rib movement is assessed in fluoroscopy. However, the shadows of lung vessels and bronchi overlapping ribs prevent accurate quantitative analysis of rib movement. Recently, an image-processing technique for separating bones from soft tissue in static chest radiographs, called "bone suppression technique", has been developed. Our purpose in this study was to evaluate the usefulness of dynamic bone images created by the bone suppression technique in quantitative analysis of rib movement. Dynamic chest radiographs of 10 patients were obtained using a dynamic flat-panel detector (FPD). Bone suppression technique based on a massive-training artificial neural network (MTANN) was applied to the dynamic chest images to create bone images. Velocity vectors were measured in local areas on the dynamic bone images, which formed a map. The velocity maps obtained with bone and original images for scoliosis and normal cases were compared to assess the advantages of bone images. With dynamic bone images, we were able to quantify and distinguish movements of ribs from those of other lung structures accurately. Limited rib movements of scoliosis patients appeared as reduced rib velocity vectors. Vector maps in all normal cases exhibited left-right symmetric distributions, whereas those in abnormal cases showed nonuniform distributions. In conclusion, dynamic bone images were useful for accurate quantitative analysis of rib movements: Limited rib movements were indicated as a reduction of rib movement and left-right asymmetric distribution on vector maps. Thus, dynamic bone images can be a new diagnostic tool for quantitative analysis of rib movements without additional radiation dose.

Quantitative analysis of multiple sclerosis: a feasibility study

NASA Astrophysics Data System (ADS)

Li, Lihong; Li, Xiang; Wei, Xinzhou; Sturm, Deborah; Lu, Hongbing; Liang, Zhengrong

2006-03-01

Multiple Sclerosis (MS) is an inflammatory and demyelinating disorder of the central nervous system with a presumed immune-mediated etiology. For treatment of MS, the measurements of white matter (WM), gray matter (GM), and cerebral spinal fluid (CSF) are often used in conjunction with clinical evaluation to provide a more objective measure of MS burden. In this paper, we apply a new unifying automatic mixture-based algorithm for segmentation of brain tissues to quantitatively analyze MS. The method takes into account the following effects that commonly appear in MR imaging: 1) The MR data is modeled as a stochastic process with an inherent inhomogeneity effect of smoothly varying intensity; 2) A new partial volume (PV) model is built in establishing the maximum a posterior (MAP) segmentation scheme; 3) Noise artifacts are minimized by a priori Markov random field (MRF) penalty indicating neighborhood correlation from tissue mixture. The volumes of brain tissues (WM, GM) and CSF are extracted from the mixture-based segmentation. Experimental results of feasibility studies on quantitative analysis of MS are presented.

Quantitative structure-activity relationship analysis of the pharmacology of para-substituted methcathinone analogues.

PubMed

Bonano, J S; Banks, M L; Kolanos, R; Sakloth, F; Barnier, M L; Glennon, R A; Cozzi, N V; Partilla, J S; Baumann, M H; Negus, S S

2015-05-01

Methcathinone (MCAT) is a potent monoamine releaser and parent compound to emerging drugs of abuse including mephedrone (4-CH3 MCAT), the para-methyl analogue of MCAT. This study examined quantitative structure-activity relationships (QSAR) for MCAT and six para-substituted MCAT analogues on (a) in vitro potency to promote monoamine release via dopamine and serotonin transporters (DAT and SERT, respectively), and (b) in vivo modulation of intracranial self-stimulation (ICSS), a behavioural procedure used to evaluate abuse potential. Neurochemical and behavioural effects were correlated with steric (Es ), electronic (σp ) and lipophilic (πp ) parameters of the para substituents. For neurochemical studies, drug effects on monoamine release through DAT and SERT were evaluated in rat brain synaptosomes. For behavioural studies, drug effects were tested in male Sprague-Dawley rats implanted with electrodes targeting the medial forebrain bundle and trained to lever-press for electrical brain stimulation. MCAT and all six para-substituted analogues increased monoamine release via DAT and SERT and dose- and time-dependently modulated ICSS. In vitro selectivity for DAT versus SERT correlated with in vivo efficacy to produce abuse-related ICSS facilitation. In addition, the Es values of the para substituents correlated with both selectivity for DAT versus SERT and magnitude of ICSS facilitation. Selectivity for DAT versus SERT in vitro is a key determinant of abuse-related ICSS facilitation by these MCAT analogues, and steric aspects of the para substituent of the MCAT scaffold (indicated by Es ) are key determinants of this selectivity. © 2014 The British Pharmacological Society.

Quantitative structure–activity relationship analysis of the pharmacology of para-substituted methcathinone analogues

PubMed Central

Bonano, J S; Banks, M L; Kolanos, R; Sakloth, F; Barnier, M L; Glennon, R A; Cozzi, N V; Partilla, J S; Baumann, M H; Negus, S S

2015-01-01

Background and Purpose Methcathinone (MCAT) is a potent monoamine releaser and parent compound to emerging drugs of abuse including mephedrone (4-CH3 MCAT), the para-methyl analogue of MCAT. This study examined quantitative structure–activity relationships (QSAR) for MCAT and six para-substituted MCAT analogues on (a) in vitro potency to promote monoamine release via dopamine and serotonin transporters (DAT and SERT, respectively), and (b) in vivo modulation of intracranial self-stimulation (ICSS), a behavioural procedure used to evaluate abuse potential. Neurochemical and behavioural effects were correlated with steric (Es), electronic (σp) and lipophilic (πp) parameters of the para substituents. Experimental Approach For neurochemical studies, drug effects on monoamine release through DAT and SERT were evaluated in rat brain synaptosomes. For behavioural studies, drug effects were tested in male Sprague-Dawley rats implanted with electrodes targeting the medial forebrain bundle and trained to lever-press for electrical brain stimulation. Key Results MCAT and all six para-substituted analogues increased monoamine release via DAT and SERT and dose- and time-dependently modulated ICSS. In vitro selectivity for DAT versus SERT correlated with in vivo efficacy to produce abuse-related ICSS facilitation. In addition, the Es values of the para substituents correlated with both selectivity for DAT versus SERT and magnitude of ICSS facilitation. Conclusions and Implications Selectivity for DAT versus SERT in vitro is a key determinant of abuse-related ICSS facilitation by these MCAT analogues, and steric aspects of the para substituent of the MCAT scaffold (indicated by Es) are key determinants of this selectivity. PMID:25438806

Quality Assessments of Long-Term Quantitative Proteomic Analysis of Breast Cancer Xenograft Tissues

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

Zhou, Jian-Ying; Chen, Lijun; Zhang, Bai

The identification of protein biomarkers requires large-scale analysis of human specimens to achieve statistical significance. In this study, we evaluated the long-term reproducibility of an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics strategy using one channel for universal normalization across all samples. A total of 307 liquid chromatography tandem mass spectrometric (LC-MS/MS) analyses were completed, generating 107 one-dimensional (1D) LC-MS/MS datasets and 8 offline two-dimensional (2D) LC-MS/MS datasets (25 fractions for each set) for human-in-mouse breast cancer xenograft tissues representative of basal and luminal subtypes. Such large-scale studies require the implementation of robust metrics to assessmore » the contributions of technical and biological variability in the qualitative and quantitative data. Accordingly, we developed a quantification confidence score based on the quality of each peptide-spectrum match (PSM) to remove quantification outliers from each analysis. After combining confidence score filtering and statistical analysis, reproducible protein identification and quantitative results were achieved from LC-MS/MS datasets collected over a 16 month period.« less

Quantitative analysis of intermolecular interactions in orthorhombic rubrene

DOE PAGES

Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; ...

2015-08-14

Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically,more » the presence of C π...C πinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.« less

Quantitative analysis of titanium concentration using calibration-free laser-induced breakdown spectroscopy (LIBS)

NASA Astrophysics Data System (ADS)

Zaitun; Prasetyo, S.; Suliyanti, M. M.; Isnaeni; Herbani, Y.

2018-03-01

Laser-induced breakdown spectroscopy (LIBS) can be used for quantitative and qualitative analysis. Calibration-free LIBS (CF-LIBS) is a method to quantitatively analyze concentration of elements in a sample in local thermodynamic equilibrium conditions without using available matrix-matched calibration. In this study, we apply CF-LIBS for quantitative analysis of Ti in TiO2 sample. TiO2 powder sample was mixed with polyvinyl alcohol and formed into pellets. An Nd:YAG pulsed laser at a wavelength of 1064 nm was focused onto the sample to generate plasma. The spectrum of plasma was recorded using spectrophotometer then compared to NIST spectral line to determine energy levels and other parameters. The value of plasma temperature obtained using Boltzmann plot is 8127.29 K and electron density from calculation is 2.49×1016 cm-3. Finally, the concentration of Ti in TiO2 sample from this study is 97% that is in proximity with the sample certificate.

Quantitative refractive index distribution of single cell by combining phase-shifting interferometry and AFM imaging.

PubMed

Zhang, Qinnan; Zhong, Liyun; Tang, Ping; Yuan, Yingjie; Liu, Shengde; Tian, Jindong; Lu, Xiaoxu

2017-05-31

Cell refractive index, an intrinsic optical parameter, is closely correlated with the intracellular mass and concentration. By combining optical phase-shifting interferometry (PSI) and atomic force microscope (AFM) imaging, we constructed a label free, non-invasive and quantitative refractive index of single cell measurement system, in which the accurate phase map of single cell was retrieved with PSI technique and the cell morphology with nanoscale resolution was achieved with AFM imaging. Based on the proposed AFM/PSI system, we achieved quantitative refractive index distributions of single red blood cell and Jurkat cell, respectively. Further, the quantitative change of refractive index distribution during Daunorubicin (DNR)-induced Jurkat cell apoptosis was presented, and then the content changes of intracellular biochemical components were achieved. Importantly, these results were consistent with Raman spectral analysis, indicating that the proposed PSI/AFM based refractive index system is likely to become a useful tool for intracellular biochemical components analysis measurement, and this will facilitate its application for revealing cell structure and pathological state from a new perspective.

A Framework for Mixing Methods in Quantitative Measurement Development, Validation, and Revision: A Case Study

ERIC Educational Resources Information Center

Luyt, Russell

2012-01-01

A framework for quantitative measurement development, validation, and revision that incorporates both qualitative and quantitative methods is introduced. It extends and adapts Adcock and Collier's work, and thus, facilitates understanding of quantitative measurement development, validation, and revision as an integrated and cyclical set of…

Quantitative research.

PubMed

Watson, Roger

2015-04-01

This article describes the basic tenets of quantitative research. The concepts of dependent and independent variables are addressed and the concept of measurement and its associated issues, such as error, reliability and validity, are explored. Experiments and surveys – the principal research designs in quantitative research – are described and key features explained. The importance of the double-blind randomised controlled trial is emphasised, alongside the importance of longitudinal surveys, as opposed to cross-sectional surveys. Essential features of data storage are covered, with an emphasis on safe, anonymous storage. Finally, the article explores the analysis of quantitative data, considering what may be analysed and the main uses of statistics in analysis.

Quantitative analysis of background parenchymal enhancement in whole breast on MRI: Influence of menstrual cycle and comparison with a qualitative analysis.

PubMed

Jung, Yongsik; Jeong, Seong Kyun; Kang, Doo Kyoung; Moon, Yeorae; Kim, Tae Hee

2018-06-01

We quantitatively analyzed background parenchymal enhancement (BPE) in whole breast according to menstrual cycle and compared it with a qualitative analysis method. A data set of breast magnetic resonance imaging (MRI) from 273 breast cancer patients was used. For quantitative analysis, we used semiautomated in-house software with MATLAB. From each voxel of whole breast, the software calculated BPE using following equation: [(signal intensity [SI] at 1 min 30 s after contrast injection - baseline SI)/baseline SI] × 100%. In total, 53 patients had minimal, 108 mild, 87 moderate, and 25 marked BPE. On quantitative analysis, mean BPE values were 33.1% in the minimal, 42.1% in the mild, 59.1% in the moderate, and 81.9% in the marked BPE group showing significant difference (p = .009 for minimal vs. mild, p < 0.001 for other comparisons). Spearman's correlation test showed that there was strong significant correlation between qualitative and quantitative BPE (r = 0.63, p < 0.001). The mean BPE value was 48.7% for patients in the first week of the menstrual cycle, 43.5% in the second week, 49% in the third week, and 49.4% for those in the fourth week. The difference between the second and fourth weeks was significant (p = .005). Median, 90th percentile, and 10th percentile values were also significantly different between the second and fourth weeks but not different in other comparisons (first vs. second, first vs. third, first vs. fourth, second vs. third, or third vs. fourth). Quantitative analysis of BPE correlated well with the qualitative BPE grade. Quantitative BPE values were lowest in the second week and highest in the fourth week. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

The Quantitative Analysis of Chennai Automotive Industry Cluster

NASA Astrophysics Data System (ADS)

Bhaskaran, Ethirajan

2016-07-01

Chennai, also called as Detroit of India due to presence of Automotive Industry producing over 40 % of the India's vehicle and components. During 2001-2002, the Automotive Component Industries (ACI) in Ambattur, Thirumalizai and Thirumudivakkam Industrial Estate, Chennai has faced problems on infrastructure, technology, procurement, production and marketing. The objective is to study the Quantitative Performance of Chennai Automotive Industry Cluster before (2001-2002) and after the CDA (2008-2009). The methodology adopted is collection of primary data from 100 ACI using quantitative questionnaire and analyzing using Correlation Analysis (CA), Regression Analysis (RA), Friedman Test (FMT), and Kruskall Wallis Test (KWT).The CA computed for the different set of variables reveals that there is high degree of relationship between the variables studied. The RA models constructed establish the strong relationship between the dependent variable and a host of independent variables. The models proposed here reveal the approximate relationship in a closer form. KWT proves, there is no significant difference between three locations clusters with respect to: Net Profit, Production Cost, Marketing Costs, Procurement Costs and Gross Output. This supports that each location has contributed for development of automobile component cluster uniformly. The FMT proves, there is no significant difference between industrial units in respect of cost like Production, Infrastructure, Technology, Marketing and Net Profit. To conclude, the Automotive Industries have fully utilized the Physical Infrastructure and Centralised Facilities by adopting CDA and now exporting their products to North America, South America, Europe, Australia, Africa and Asia. The value chain analysis models have been implemented in all the cluster units. This Cluster Development Approach (CDA) model can be implemented in industries of under developed and developing countries for cost reduction and productivity

A Novel Quantitative Hemolytic Assay Coupled with Restriction Fragment Length Polymorphisms Analysis Enabled Early Diagnosis of Atypical Hemolytic Uremic Syndrome and Identified Unique Predisposing Mutations in Japan

PubMed Central

Yoshida, Yoko; Miyata, Toshiyuki; Matsumoto, Masanori; Shirotani-Ikejima, Hiroko; Uchida, Yumiko; Ohyama, Yoshifumi; Kokubo, Tetsuro; Fujimura, Yoshihiro

2015-01-01

For thrombotic microangiopathies (TMAs), the diagnosis of atypical hemolytic uremic syndrome (aHUS) is made by ruling out Shiga toxin-producing Escherichia coli (STEC)-associated HUS and ADAMTS13 activity-deficient thrombotic thrombocytopenic purpura (TTP), often using the exclusion criteria for secondary TMAs. Nowadays, assays for ADAMTS13 activity and evaluation for STEC infection can be performed within a few hours. However, a confident diagnosis of aHUS often requires comprehensive gene analysis of the alternative complement activation pathway, which usually takes at least several weeks. However, predisposing genetic abnormalities are only identified in approximately 70% of aHUS. To facilitate the diagnosis of complement-mediated aHUS, we describe a quantitative hemolytic assay using sheep red blood cells (RBCs) and human citrated plasma, spiked with or without a novel inhibitory anti-complement factor H (CFH) monoclonal antibody. Among 45 aHUS patients in Japan, 24% (11/45) had moderate-to-severe (≥50%) hemolysis, whereas the remaining 76% (34/45) patients had mild or no hemolysis (<50%). The former group is largely attributed to CFH-related abnormalities, and the latter group has C3-p.I1157T mutations (16/34), which were identified by restriction fragment length polymorphism (RFLP) analysis. Thus, a quantitative hemolytic assay coupled with RFLP analysis enabled the early diagnosis of complement-mediated aHUS in 60% (27/45) of patients in Japan within a week of presentation. We hypothesize that this novel quantitative hemolytic assay would be more useful in a Caucasian population, who may have a higher proportion of CFH mutations than Japanese patients. PMID:25951460

A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins.

PubMed

Hong, Qiuting; Ruhaak, L Renee; Stroble, Carol; Parker, Evan; Huang, Jincui; Maverakis, Emanual; Lebrilla, Carlito B

2015-12-04

A comprehensive glycan map was constructed for the top eight abundant glycoproteins in plasma using both specific and nonspecific enzyme digestions followed by nano liquid chromatography (LC)-chip/quadrupole time-of-flight mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) technique on a triple quadrupole MS was developed and applied to quantify immunoglobulins G, A, M, and their site-specific glycans simultaneously and directly from human serum/plasma without protein enrichments. A total of 64 glycopeptides and 15 peptides were monitored for IgG, IgA, and IgM in a 20 min ultra high performance (UP)LC gradient. The absolute protein contents were quantified using peptide calibration curves. The glycopeptide ion abundances were normalized to the respective protein abundances to separate protein glycosylation from protein expression. This technique yields higher method reproducibility and less sample loss when compared with the quantitation method that involves protein enrichments. The absolute protein quantitation has a wide linear range (3-4 orders of magnitude) and low limit of quantitation (femtomole level). This rapid and robust quantitation technique, which provides quantitative information for both proteins and glycosylation, will further facilitate disease biomarker discoveries.

Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

PubMed

Bergholt, Mads Sylvest; Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

2013-12-03

We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in

Development of quantitative exposure data for a pooled exposure-response analysis of 10 silica cohorts.

PubMed

Mannetje, Andrea 't; Steenland, Kyle; Checkoway, Harvey; Koskela, Riitta-Sisko; Koponen, Matti; Attfield, Michael; Chen, Jingqiong; Hnizdo, Eva; DeKlerk, Nicholas; Dosemeci, Mustafa

2002-08-01

Comprehensive quantitative silica exposure estimates over time, measured in the same units across a number of cohorts, would make possible a pooled exposure-response analysis for lung cancer. Such an analysis would help clarify the continuing controversy regarding whether silica causes lung cancer. Existing quantitative exposure data for 10 silica-exposed cohorts were retrieved from the original investigators. Occupation- and time-specific exposure estimates were either adopted/adapted or developed for each cohort, and converted to milligram per cubic meter (mg/m(3)) respirable crystalline silica. Quantitative exposure assignments were typically based on a large number (thousands) of raw measurements, or otherwise consisted of exposure estimates by experts (for two cohorts). Median exposure level of the cohorts ranged between 0.04 and 0.59 mg/m(3) respirable crystalline silica. Exposure estimates were partially validated via their successful prediction of silicosis in these cohorts. Existing data were successfully adopted or modified to create comparable quantitative exposure estimates over time for 10 silica-exposed cohorts, permitting a pooled exposure-response analysis. The difficulties encountered in deriving common exposure estimates across cohorts are discussed. Copyright 2002 Wiley-Liss, Inc.

NanoDrop Microvolume Quantitation of Nucleic Acids

PubMed Central

Desjardins, Philippe; Conklin, Deborah

2010-01-01

Biomolecular assays are continually being developed that use progressively smaller amounts of material, often precluding the use of conventional cuvette-based instruments for nucleic acid quantitation for those that can perform microvolume quantitation. The NanoDrop microvolume sample retention system (Thermo Scientific NanoDrop Products) functions by combining fiber optic technology and natural surface tension properties to capture and retain minute amounts of sample independent of traditional containment apparatus such as cuvettes or capillaries. Furthermore, the system employs shorter path lengths, which result in a broad range of nucleic acid concentration measurements, essentially eliminating the need to perform dilutions. Reducing the volume of sample required for spectroscopic analysis also facilitates the inclusion of additional quality control steps throughout many molecular workflows, increasing efficiency and ultimately leading to greater confidence in downstream results. The need for high-sensitivity fluorescent analysis of limited mass has also emerged with recent experimental advances. Using the same microvolume sample retention technology, fluorescent measurements may be performed with 2 μL of material, allowing fluorescent assays volume requirements to be significantly reduced. Such microreactions of 10 μL or less are now possible using a dedicated microvolume fluorospectrometer. Two microvolume nucleic acid quantitation protocols will be demonstrated that use integrated sample retention systems as practical alternatives to traditional cuvette-based protocols. First, a direct A260 absorbance method using a microvolume spectrophotometer is described. This is followed by a demonstration of a fluorescence-based method that enables reduced-volume fluorescence reactions with a microvolume fluorospectrometer. These novel techniques enable the assessment of nucleic acid concentrations ranging from 1 pg/ μL to 15,000 ng/ μL with minimal consumption of

Visualization and Quantitative Analysis of Crack-Tip Plastic Zone in Pure Nickel

NASA Astrophysics Data System (ADS)

Kelton, Randall; Sola, Jalal Fathi; Meletis, Efstathios I.; Huang, Haiying

2018-05-01

Changes in surface morphology have long been thought to be associated with crack propagation in metallic materials. We have studied areal surface texture changes around crack tips in an attempt to understand the correlations between surface texture changes and crack growth behavior. Detailed profiling of the fatigue sample surface was carried out at short fatigue intervals. An image processing algorithm was developed to calculate the surface texture changes. Quantitative analysis of the crack-tip plastic zone, crack-arrested sites near triple points, and large surface texture changes associated with crack release from arrested locations was carried out. The results indicate that surface texture imaging enables visualization of the development of plastic deformation around a crack tip. Quantitative analysis of the surface texture changes reveals the effects of local microstructures on the crack growth behavior.

Characterization of breast lesion using T1-perfusion magnetic resonance imaging: Qualitative vs. quantitative analysis.

PubMed

Thakran, S; Gupta, P K; Kabra, V; Saha, I; Jain, P; Gupta, R K; Singh, A

2018-06-14

The objective of this study was to quantify the hemodynamic parameters using first pass analysis of T 1 -perfusion magnetic resonance imaging (MRI) data of human breast and to compare these parameters with the existing tracer kinetic parameters, semi-quantitative and qualitative T 1 -perfusion analysis in terms of lesion characterization. MRI of the breast was performed in 50 women (mean age, 44±11 [SD] years; range: 26-75) years with a total of 15 benign and 35 malignant breast lesions. After pre-processing, T 1 -perfusion MRI data was analyzed using qualitative approach by two radiologists (visual inspection of the kinetic curve into types I, II or III), semi-quantitative (characterization of kinetic curve types using empirical parameters), generalized-tracer-kinetic-model (tracer kinetic parameters) and first pass analysis (hemodynamic-parameters). Chi-squared test, t-test, one-way analysis-of-variance (ANOVA) using Bonferroni post-hoc test and receiver-operating-characteristic (ROC) curve were used for statistical analysis. All quantitative parameters except leakage volume (Ve), qualitative (type-I and III) and semi-quantitative curves (type-I and III) provided significant differences (P<0.05) between benign and malignant lesions. Kinetic parameters, particularly volume transfer coefficient (K trans ) provided a significant difference (P<0.05) between all grades except grade-II vs III. The hemodynamic parameter (relative-leakage-corrected-breast-blood-volume [rBBVcorr) provided a statistically significant difference (P<0.05) between all grades. It also provided highest sensitivity and specificity among all parameters in differentiation between different grades of malignant breast lesions. Quantitative parameters, particularly rBBVcorr and K trans provided similar sensitivity and specificity in differentiating benign from malignant breast lesions for this cohort. Moreover, rBBVcorr provided better differentiation between different grades of malignant breast

Feasibility of high-resolution quantitative perfusion analysis in patients with heart failure.

PubMed

Sammut, Eva; Zarinabad, Niloufar; Wesolowski, Roman; Morton, Geraint; Chen, Zhong; Sohal, Manav; Carr-White, Gerry; Razavi, Reza; Chiribiri, Amedeo

2015-02-12

Cardiac magnetic resonance (CMR) is playing an expanding role in the assessment of patients with heart failure (HF). The assessment of myocardial perfusion status in HF can be challenging due to left ventricular (LV) remodelling and wall thinning, coexistent scar and respiratory artefacts. The aim of this study was to assess the feasibility of quantitative CMR myocardial perfusion analysis in patients with HF. A group of 58 patients with heart failure (HF; left ventricular ejection fraction, LVEF ≤ 50%) and 33 patients with normal LVEF (LVEF >50%), referred for suspected coronary artery disease, were studied. All subjects underwent quantitative first-pass stress perfusion imaging using adenosine according to standard acquisition protocols. The feasibility of quantitative perfusion analysis was then assessed using high-resolution, 3 T kt perfusion and voxel-wise Fermi deconvolution. 30/58 (52%) subjects in the HF group had underlying ischaemic aetiology. Perfusion abnormalities were seen amongst patients with ischaemic HF and patients with normal LV function. No regional perfusion defect was observed in the non-ischaemic HF group. Good agreement was found between visual and quantitative analysis across all groups. Absolute stress perfusion rate, myocardial perfusion reserve (MPR) and endocardial-epicardial MPR ratio identified areas with abnormal perfusion in the ischaemic HF group (p = 0.02; p = 0.04; p = 0.02, respectively). In the Normal LV group, MPR and endocardial-epicardial MPR ratio were able to distinguish between normal and abnormal segments (p = 0.04; p = 0.02 respectively). No significant differences of absolute stress perfusion rate or MPR were observed comparing visually normal segments amongst groups. Our results demonstrate the feasibility of high-resolution voxel-wise perfusion assessment in patients with HF.

A novel iris transillumination grading scale allowing flexible assessment with quantitative image analysis and visual matching.

PubMed

Wang, Chen; Brancusi, Flavia; Valivullah, Zaheer M; Anderson, Michael G; Cunningham, Denise; Hedberg-Buenz, Adam; Power, Bradley; Simeonov, Dimitre; Gahl, William A; Zein, Wadih M; Adams, David R; Brooks, Brian

2018-01-01

To develop a sensitive scale of iris transillumination suitable for clinical and research use, with the capability of either quantitative analysis or visual matching of images. Iris transillumination photographic images were used from 70 study subjects with ocular or oculocutaneous albinism. Subjects represented a broad range of ocular pigmentation. A subset of images was subjected to image analysis and ranking by both expert and nonexpert reviewers. Quantitative ordering of images was compared with ordering by visual inspection. Images were binned to establish an 8-point scale. Ranking consistency was evaluated using the Kendall rank correlation coefficient (Kendall's tau). Visual ranking results were assessed using Kendall's coefficient of concordance (Kendall's W) analysis. There was a high degree of correlation among the image analysis, expert-based and non-expert-based image rankings. Pairwise comparisons of the quantitative ranking with each reviewer generated an average Kendall's tau of 0.83 ± 0.04 (SD). Inter-rater correlation was also high with Kendall's W of 0.96, 0.95, and 0.95 for nonexpert, expert, and all reviewers, respectively. The current standard for assessing iris transillumination is expert assessment of clinical exam findings. We adapted an image-analysis technique to generate quantitative transillumination values. Quantitative ranking was shown to be highly similar to a ranking produced by both expert and nonexpert reviewers. This finding suggests that the image characteristics used to quantify iris transillumination do not require expert interpretation. Inter-rater rankings were also highly similar, suggesting that varied methods of transillumination ranking are robust in terms of producing reproducible results.

Automated model-based quantitative analysis of phantoms with spherical inserts in FDG PET scans.

PubMed

Ulrich, Ethan J; Sunderland, John J; Smith, Brian J; Mohiuddin, Imran; Parkhurst, Jessica; Plichta, Kristin A; Buatti, John M; Beichel, Reinhard R

2018-01-01

Quality control plays an increasingly important role in quantitative PET imaging and is typically performed using phantoms. The purpose of this work was to develop and validate a fully automated analysis method for two common PET/CT quality assurance phantoms: the NEMA NU-2 IQ and SNMMI/CTN oncology phantom. The algorithm was designed to only utilize the PET scan to enable the analysis of phantoms with thin-walled inserts. We introduce a model-based method for automated analysis of phantoms with spherical inserts. Models are first constructed for each type of phantom to be analyzed. A robust insert detection algorithm uses the model to locate all inserts inside the phantom. First, candidates for inserts are detected using a scale-space detection approach. Second, candidates are given an initial label using a score-based optimization algorithm. Third, a robust model fitting step aligns the phantom model to the initial labeling and fixes incorrect labels. Finally, the detected insert locations are refined and measurements are taken for each insert and several background regions. In addition, an approach for automated selection of NEMA and CTN phantom models is presented. The method was evaluated on a diverse set of 15 NEMA and 20 CTN phantom PET/CT scans. NEMA phantoms were filled with radioactive tracer solution at 9.7:1 activity ratio over background, and CTN phantoms were filled with 4:1 and 2:1 activity ratio over background. For quantitative evaluation, an independent reference standard was generated by two experts using PET/CT scans of the phantoms. In addition, the automated approach was compared against manual analysis, which represents the current clinical standard approach, of the PET phantom scans by four experts. The automated analysis method successfully detected and measured all inserts in all test phantom scans. It is a deterministic algorithm (zero variability), and the insert detection RMS error (i.e., bias) was 0.97, 1.12, and 1.48 mm for phantom

Quantitative analysis of dinuclear manganese(II) EPR spectra

NASA Astrophysics Data System (ADS)

Golombek, Adina P.; Hendrich, Michael P.

2003-11-01

A quantitative method for the analysis of EPR spectra from dinuclear Mn(II) complexes is presented. The complex [(Me 3TACN) 2Mn(II) 2(μ-OAc) 3]BPh 4 ( 1) (Me 3TACN= N, N', N''-trimethyl-1,4,7-triazacyclononane; OAc=acetate 1-; BPh 4=tetraphenylborate 1-) was studied with EPR spectroscopy at X- and Q-band frequencies, for both perpendicular and parallel polarizations of the microwave field, and with variable temperature (2-50 K). Complex 1 is an antiferromagnetically coupled dimer which shows signals from all excited spin manifolds, S=1 to 5. The spectra were simulated with diagonalization of the full spin Hamiltonian which includes the Zeeman and zero-field splittings of the individual manganese sites within the dimer, the exchange and dipolar coupling between the two manganese sites of the dimer, and the nuclear hyperfine coupling for each manganese ion. All possible transitions for all spin manifolds were simulated, with the intensities determined from the calculated probability of each transition. In addition, the non-uniform broadening of all resonances was quantitatively predicted using a lineshape model based on D- and r-strain. As the temperature is increased from 2 K, an 11-line hyperfine pattern characteristic of dinuclear Mn(II) is first observed from the S=3 manifold. D- and r-strain are the dominate broadening effects that determine where the hyperfine pattern will be resolved. A single unique parameter set was found to simulate all spectra arising for all temperatures, microwave frequencies, and microwave modes. The simulations are quantitative, allowing for the first time the determination of species concentrations directly from EPR spectra. Thus, this work describes the first method for the quantitative characterization of EPR spectra of dinuclear manganese centers in model complexes and proteins. The exchange coupling parameter J for complex 1 was determined ( J=-1.5±0.3 cm-1; H ex=-2J S1· S2) and found to be in agreement with a previous

Digital Holography, a metrological tool for quantitative analysis: Trends and future applications

NASA Astrophysics Data System (ADS)

Paturzo, Melania; Pagliarulo, Vito; Bianco, Vittorio; Memmolo, Pasquale; Miccio, Lisa; Merola, Francesco; Ferraro, Pietro

2018-05-01

A review on the last achievements of Digital Holography is reported in this paper, showing that this powerful method can be a key metrological tool for the quantitative analysis and non-invasive inspection of a variety of materials, devices and processes. Nowadays, its range of applications has been greatly extended, including the study of live biological matter and biomedical applications. This paper overviews the main progresses and future perspectives of digital holography, showing new optical configurations and investigating the numerical issues to be tackled for the processing and display of quantitative data.

A qualitative theory guided analysis of stroke survivors' perceived barriers and facilitators to physical activity.

PubMed

Nicholson, Sarah L; Donaghy, Marie; Johnston, Marie; Sniehotta, Falko F; van Wijck, Frederike; Johnston, Derek; Greig, Carolyn; McMurdo, Marion E T; Mead, Gillian

2014-01-01

After stroke, physical activity and physical fitness levels are low, impacting on health, activity and participation. It is unclear how best to support stroke survivors to increase physical activity. Little is known about the barriers and facilitators to physical activity after stroke. Thus, our aim was to explore stroke survivors' perceived barriers and facilitators to physical activity. Semi-structured interviews with 13 ambulatory stroke survivors exploring perceived barriers and facilitators to physical activity post stroke were conducted in participants' homes, audio-recorded and transcribed verbatim. The Theoretical Domains Framework (TDF) informed content analysis of the interview transcripts. Data saturation was reached after interviews with 13 participants (median age of 76 years (inter-quartile range (IQR) = 69-83 years). The median time since stroke was 345 d (IQR = 316-366 d). The most commonly reported TDF domains were "beliefs about capabilities", "environmental context and resources" and "social influence". The most commonly reported perceived motivators were: social interaction, beliefs of benefits of exercise, high self-efficacy and the necessity of routine behaviours. The most commonly reported perceived barriers were: lack of professional support on discharge from hospital and follow-up, transport issues to structured classes/interventions, lack of control and negative affect. Stroke survivors perceive several different barriers and facilitators to physical activity. Stroke services need to address barriers to physical activity and to build on facilitators to promote physical activity after stroke. Physical activity post stroke can improve physical fitness and function, yet physical activity remains low among stroke survivors. Understanding stroke survivors' perceived barriers and facilitators to physical activity is essential to develop targeted interventions to increase physical activity. Beliefs about capabilities, environmental

Evaluation of quantitative image analysis criteria for the high-resolution microendoscopic detection of neoplasia in Barrett's esophagus

NASA Astrophysics Data System (ADS)

Muldoon, Timothy J.; Thekkek, Nadhi; Roblyer, Darren; Maru, Dipen; Harpaz, Noam; Potack, Jonathan; Anandasabapathy, Sharmila; Richards-Kortum, Rebecca

2010-03-01

Early detection of neoplasia in patients with Barrett's esophagus is essential to improve outcomes. The aim of this ex vivo study was to evaluate the ability of high-resolution microendoscopic imaging and quantitative image analysis to identify neoplastic lesions in patients with Barrett's esophagus. Nine patients with pathologically confirmed Barrett's esophagus underwent endoscopic examination with biopsies or endoscopic mucosal resection. Resected fresh tissue was imaged with fiber bundle microendoscopy; images were analyzed by visual interpretation or by quantitative image analysis to predict whether the imaged sites were non-neoplastic or neoplastic. The best performing pair of quantitative features were chosen based on their ability to correctly classify the data into the two groups. Predictions were compared to the gold standard of histopathology. Subjective analysis of the images by expert clinicians achieved average sensitivity and specificity of 87% and 61%, respectively. The best performing quantitative classification algorithm relied on two image textural features and achieved a sensitivity and specificity of 87% and 85%, respectively. This ex vivo pilot trial demonstrates that quantitative analysis of images obtained with a simple microendoscope system can distinguish neoplasia in Barrett's esophagus with good sensitivity and specificity when compared to histopathology and to subjective image interpretation.

Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples

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

Clair, Geremy; Piehowski, Paul D.; Nicola, Teodora

Global proteomics approaches allow characterization of whole tissue lysates to an impressive depth. However, it is now increasingly recognized that to better understand the complexity of multicellular organisms, global protein profiling of specific spatially defined regions/substructures of tissues (i.e. spatially-resolved proteomics) is essential. Laser capture microdissection (LCM) enables microscopic isolation of defined regions of tissues preserving crucial spatial information. However, current proteomics workflows entail several manual sample preparation steps and are challenged by the microscopic mass-limited samples generated by LCM, and that impact measurement robustness, quantification, and throughput. Here, we coupled LCM with a fully automated sample preparation workflow thatmore » with a single manual step allows: protein extraction, tryptic digestion, peptide cleanup and LC-MS/MS analysis of proteomes from microdissected tissues. Benchmarking against the current state of the art in ultrasensitive global proteomic analysis, our approach demonstrated significant improvements in quantification and throughput. Using our LCM-SNaPP proteomics approach, we characterized to a depth of more than 3,400 proteins, the ontogeny of protein changes during normal lung development in laser capture microdissected alveolar tissue containing ~4,000 cells per sample. Importantly, the data revealed quantitative changes for 350 low abundance transcription factors and signaling molecules, confirming earlier transcript-level observations and defining seven modules of coordinated transcription factor/signaling molecule expression patterns, suggesting that a complex network of temporal regulatory control directs normal lung development with epigenetic regulation fine-tuning pre-natal developmental processes. Our LCM-proteomics approach facilitates efficient, spatially-resolved, ultrasensitive global proteomics analyses in high-throughput that will be enabling for several

Quantitative Analysis of Thermal Anomalies in the DFDP-2B Borehole, New Zealand

NASA Astrophysics Data System (ADS)

Janků-Čápová, Lucie; Sutherland, Rupert; Townend, John

2017-04-01

The DFDP-2B borehole, which was drilled in the Whataroa Valley, South Island, New Zealand in late 2014, provides a unique opportunity to study the conditions in the hanging wall of a plate boundary fault, the Alpine Fault, which is late in its seismic cycle. High geothermal gradient of > 125°C/km encountered in the borehole drew attention to the thermal structure of the valley, as well as of the Alpine Fault's hanging wall as a whole. A detailed analysis of temperature logs measured during drilling of the DFDP-2B borehole, reveals two distinct portions of the signal containing information on different processes. The long-wavelength portion of the temperature signal, i.e. the overall trend (hundreds of metres), reflects the response of the rock environment to the disturbance caused by drilling and permits an estimation of the thermal diffusivity of the rock based on the rate of temperature recovery. The short-wavelength (tens of metres to tens of centimetres) signal represents the local anomalies caused by lithological variations or, more importantly, by fluid flow into or out of the borehole along fractures. By analysing these distinct features, we can identify anomalous zones that manifest in other wireline data (resistivity, BHTV) and are likely attributable to permeable fractures. Here we present a novel method of quantitative analysis of the short-wavelength temperature anomalies. This method provides a precise and objective way to determine the position, width and amplitude of temperature anomalies and facilitates the interpretation of temperature logs, which is of a particular importance in estimation of flow in a fractured aquifer.

Quantitative magnetic resonance imaging phantoms: A review and the need for a system phantom.

PubMed

Keenan, Kathryn E; Ainslie, Maureen; Barker, Alex J; Boss, Michael A; Cecil, Kim M; Charles, Cecil; Chenevert, Thomas L; Clarke, Larry; Evelhoch, Jeffrey L; Finn, Paul; Gembris, Daniel; Gunter, Jeffrey L; Hill, Derek L G; Jack, Clifford R; Jackson, Edward F; Liu, Guoying; Russek, Stephen E; Sharma, Samir D; Steckner, Michael; Stupic, Karl F; Trzasko, Joshua D; Yuan, Chun; Zheng, Jie

2018-01-01

The MRI community is using quantitative mapping techniques to complement qualitative imaging. For quantitative imaging to reach its full potential, it is necessary to analyze measurements across systems and longitudinally. Clinical use of quantitative imaging can be facilitated through adoption and use of a standard system phantom, a calibration/standard reference object, to assess the performance of an MRI machine. The International Society of Magnetic Resonance in Medicine AdHoc Committee on Standards for Quantitative Magnetic Resonance was established in February 2007 to facilitate the expansion of MRI as a mainstream modality for multi-institutional measurements, including, among other things, multicenter trials. The goal of the Standards for Quantitative Magnetic Resonance committee was to provide a framework to ensure that quantitative measures derived from MR data are comparable over time, between subjects, between sites, and between vendors. This paper, written by members of the Standards for Quantitative Magnetic Resonance committee, reviews standardization attempts and then details the need, requirements, and implementation plan for a standard system phantom for quantitative MRI. In addition, application-specific phantoms and implementation of quantitative MRI are reviewed. Magn Reson Med 79:48-61, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Application of relativistic electrons for the quantitative analysis of trace elements

NASA Astrophysics Data System (ADS)

Hoffmann, D. H. H.; Brendel, C.; Genz, H.; Löw, W.; Richter, A.

1984-04-01

Particle induced X-ray emission methods (PIXE) have been extended to relativistic electrons to induce X-ray emission (REIXE) for quantitative trace-element analysis. The electron beam (20 ≤ E0≤ 70 MeV) was supplied by the Darmstadt electron linear accelerator DALINAC. Systematic measurements of absolute K-, L- and M-shell ionization cross sections revealed a scaling behaviour of inner-shell ionization cross sections from which X-ray production cross sections can be deduced for any element of interest for a quantitative sample investigation. Using a multielemental mineral monazite sample from Malaysia the sensitivity of REIXE is compared to well established methods of trace-element analysis like proton- and X-ray-induced X-ray fluorescence analysis. The achievable detection limit for very heavy elements amounts to about 100 ppm for the REIXE method. As an example of an application the investigation of a sample prepared from manganese nodules — picked up from the Pacific deep sea — is discussed, which showed the expected high mineral content of Fe, Ni, Cu and Ti, although the search for aliquots of Pt did not show any measurable content within an upper limit of 250 ppm.

An Analysis of Instructional Facilitators' Relationships with Teachers and Principals

ERIC Educational Resources Information Center

Range, Bret G.; Pijanowski, John C.; Duncan, Heather; Scherz, Susan; Hvidston, David

2014-01-01

This study examines the perspectives of Wyoming instructional facilitators, concerning three coaching constructs--namely, their instructional leadership roles, teachers' instructional practices, and the support that they receive from principals and teachers. Findings suggest that instructional facilitators were positive about their instructional…

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.

Comparative study of contrast-enhanced ultrasound qualitative and quantitative analysis for identifying benign and malignant breast tumor lumps.

PubMed

Liu, Jian; Gao, Yun-Hua; Li, Ding-Dong; Gao, Yan-Chun; Hou, Ling-Mi; Xie, Ting

2014-01-01

To compare the value of contrast-enhanced ultrasound (CEUS) qualitative and quantitative analysis in the identification of breast tumor lumps. Qualitative and quantitative indicators of CEUS for 73 cases of breast tumor lumps were retrospectively analyzed by univariate and multivariate approaches. Logistic regression was applied and ROC curves were drawn for evaluation and comparison. The CEUS qualitative indicator-generated regression equation contained three indicators, namely enhanced homogeneity, diameter line expansion and peak intensity grading, which demonstrated prediction accuracy for benign and malignant breast tumor lumps of 91.8%; the quantitative indicator-generated regression equation only contained one indicator, namely the relative peak intensity, and its prediction accuracy was 61.5%. The corresponding areas under the ROC curve for qualitative and quantitative analyses were 91.3% and 75.7%, respectively, which exhibited a statistically significant difference by the Z test (P<0.05). The ability of CEUS qualitative analysis to identify breast tumor lumps is better than with quantitative analysis.

Fast quantitative analysis of boric acid by gas chromatography-mass spectrometry coupled with a simple and selective derivatization reaction using triethanolamine.

PubMed

Zeng, Li-Min; Wang, Hao-Yang; Guo, Yin-Long

2010-03-01

A fast, selective, and sensitive GC-MS method has been developed and validated for the determination of boric acid in the drinking water by derivatization with triethanolamine. This analytic strategy successfully converts the inorganic, nonvolatile boric acid B(OH)(3) present in the drinking water to a volatile triethanolamine borate B(OCH(2)CH(2))(3)N in a quantitative manner, which facilitates the GC measurement. The SIM mode was applied in the analysis and showed high accuracy, specificity, and reproducibility, as well as reducing the matrix effect effectively. The calibration curve was obtained from 0.01 microg/mL to 10.0 microg/mL with a satisfactory correlation coefficient of 0.9988. The limit of detection for boric acid was 0.04 microg/L. Then the method was applied for detection of the amount of boric acid in bottled drinking water and the results are in accordance with the reported concentration value of boric acid. This study offers a perspective into the utility of GC-MS as an alternate quantitative tool for detection of B(OH)(3), even for detection of boron in various other samples by digesting the boron compounds to boric acid. Copyright 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

Novel quantitative analysis of autofluorescence images for oral cancer screening.

PubMed

Huang, Tze-Ta; Huang, Jehn-Shyun; Wang, Yen-Yun; Chen, Ken-Chung; Wong, Tung-Yiu; Chen, Yi-Chun; Wu, Che-Wei; Chan, Leong-Perng; Lin, Yi-Chu; Kao, Yu-Hsun; Nioka, Shoko; Yuan, Shyng-Shiou F; Chung, Pau-Choo

2017-05-01

VELscope® was developed to inspect oral mucosa autofluorescence. However, its accuracy is heavily dependent on the examining physician's experience. This study was aimed toward the development of a novel quantitative analysis of autofluorescence images for oral cancer screening. Patients with either oral cancer or precancerous lesions and a control group with normal oral mucosa were enrolled in this study. White light images and VELscope® autofluorescence images of the lesions were taken with a digital camera. The lesion in the image was chosen as the region of interest (ROI). The average intensity and heterogeneity of the ROI were calculated. A quadratic discriminant analysis (QDA) was utilized to compute boundaries based on sensitivity and specificity. 47 oral cancer lesions, 54 precancerous lesions, and 39 normal oral mucosae controls were analyzed. A boundary of specificity of 0.923 and a sensitivity of 0.979 between the oral cancer lesions and normal oral mucosae were validated. The oral cancer and precancerous lesions could also be differentiated from normal oral mucosae with a specificity of 0.923 and a sensitivity of 0.970. The novel quantitative analysis of the intensity and heterogeneity of VELscope® autofluorescence images used in this study in combination with a QDA classifier can be used to differentiate oral cancer and precancerous lesions from normal oral mucosae. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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

2011-11-01

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

Accuracy improvement of quantitative analysis by spatial confinement in laser-induced breakdown spectroscopy.

PubMed

Guo, L B; Hao, Z Q; Shen, M; Xiong, W; He, X N; Xie, Z Q; Gao, M; Li, X Y; Zeng, X Y; Lu, Y F

2013-07-29

To improve the accuracy of quantitative analysis in laser-induced breakdown spectroscopy, the plasma produced by a Nd:YAG laser from steel targets was confined by a cavity. A number of elements with low concentrations, such as vanadium (V), chromium (Cr), and manganese (Mn), in the steel samples were investigated. After the optimization of the cavity dimension and laser fluence, significant enhancement factors of 4.2, 3.1, and 2.87 in the emission intensity of V, Cr, and Mn lines, respectively, were achieved at a laser fluence of 42.9 J/cm(2) using a hemispherical cavity (diameter: 5 mm). More importantly, the correlation coefficient of the V I 440.85/Fe I 438.35 nm was increased from 0.946 (without the cavity) to 0.981 (with the cavity); and similar results for Cr I 425.43/Fe I 425.08 nm and Mn I 476.64/Fe I 492.05 nm were also obtained. Therefore, it was demonstrated that the accuracy of quantitative analysis with low concentration elements in steel samples was improved, because the plasma became uniform with spatial confinement. The results of this study provide a new pathway for improving the accuracy of quantitative analysis of LIBS.

The impact of mind-body medicine facilitation on affirming and enhancing professional identity in health care professions faculty.

PubMed

Talisman, Nicholas; Harazduk, Nancy; Rush, Christina; Graves, Kristi; Haramati, Aviad

2015-06-01

Georgetown University School of Medicine (GUSOM) offers medical students a course in mind-body medicine (MBM) that introduces them to tools that reduce stress and foster self-awareness. Previous studies reported decreases in students' perceived stress and increases in mindfulness-changes that were associated with increased empathic concern and other elements of professional identity formation. However, no reports have described the impact of an MBM course on the facilitators themselves. To explore whether MBM facilitation is associated with changes in professional identity, self-awareness, and/or perceived stress, 62 facilitators, trained by the GUSOM MBM program, were invited to complete two validated surveys: the Freiburg Mindfulness Inventory (FMI) and the Perceived Stress Scale (PSS). Forty-two participants also completed a six-item open-ended questionnaire addressing their experience in the context of their professional identity. Facilitators' scores were significantly lower on PSS and higher on FMI compared with normative controls (P < .05), and the two parameters were inversely correlated (-0.46, P < .01). Qualitative analysis revealed three main themes: (1) aspects of professional identity (with subthemes of communication; connections and community; empathy and active listening; and self-confidence); (2) self-care; and (3) mindful awareness. Preliminary findings will be extended with larger studies that examine longitudinal quantitative assessment of communication, connection, and self-confidence outcomes in MBM facilitators, and the impact of MBM facilitation on burnout and resilience.

Quantitative analysis of glycerophospholipids by LC-MS: acquisition, data handling, and interpretation

PubMed Central

Myers, David S.; Ivanova, Pavlina T.; Milne, Stephen B.; Brown, H. Alex

2012-01-01

As technology expands what it is possible to accurately measure, so too the challenges faced by modern mass spectrometry applications expand. A high level of accuracy in lipid quantitation across thousands of chemical species simultaneously is demanded. While relative changes in lipid amounts with varying conditions may provide initial insights or point to novel targets, there are many questions that require determination of lipid analyte absolute quantitation. Glycerophospholipids present a significant challenge in this regard, given the headgroup diversity, large number of possible acyl chain combinations, and vast range of ionization efficiency of species. Lipidomic output is being used more often not just for profiling of the masses of species, but also for highly-targeted flux-based measurements which put additional burdens on the quantitation pipeline. These first two challenges bring into sharp focus the need for a robust lipidomics workflow including deisotoping, differentiation from background noise, use of multiple internal standards per lipid class, and the use of a scriptable environment in order to create maximum user flexibility and maintain metadata on the parameters of the data analysis as it occurs. As lipidomics technology develops and delivers more output on a larger number of analytes, so must the sophistication of statistical post-processing also continue to advance. High-dimensional data analysis methods involving clustering, lipid pathway analysis, and false discovery rate limitation are becoming standard practices in a maturing field. PMID:21683157

Quantitation of zolpidem in biological fluids by electro-driven microextraction combined with HPLC-UV analysis

PubMed Central

Yaripour, Saeid; Mohammadi, Ali; Esfanjani, Isa; Walker, Roderick B.; Nojavan, Saeed

2018-01-01

In this study, for the first time, an electro-driven microextraction method named electromembrane extraction combined with a simple high performance liquid chromatography and ultraviolet detection was developed and validated for the quantitation of zolpidem in biological samples. Parameters influencing electromembrane extraction were evaluated and optimized. The membrane consisted of 2-ethylhexanol immobilized in the pores of a hollow fiber. As a driving force, a 150 V electric field was applied to facilitate the analyte migration from the sample matrix to an acceptor solution through a supported liquid membrane. The pHs of donor and acceptor solutions were optimized to 6.0 and 2.0, respectively. The enrichment factor was obtained >75 within 15 minutes. The effect of carbon nanotubes (as solid nano-sorbents) on the membrane performance and EME efficiency was evaluated. The method was linear over the range of 10-1000 ng/mL for zolpidem (R2 >0.9991) with repeatability ( %RSD) between 0.3 % and 7.3 % (n = 3). The limits of detection and quantitation were 3 and 10 ng/mL, respectively. The sensitivity of HPLC-UV for the determination of zolpidem was enhanced by electromembrane extraction. Finally, the method was employed for the quantitation of zolpidem in biological samples with relative recoveries in the range of 60-79 %. PMID:29805344

Quantitative analysis of major dibenzocyclooctane lignans in Schisandrae fructus by online TLC-DART-MS.

PubMed

Kim, Hye Jin; Oh, Myung Sook; Hong, Jongki; Jang, Young Pyo

2011-01-01

Direct analysis in real time (DART) ion source is a powerful ionising technique for the quick and easy detection of various organic molecules without any sample preparation steps, but the lack of quantitation capacity limits its extensive use in the field of phytochemical analysis. To improvise a new system which utilize DART-MS as a hyphenated detector for quantitation. A total extract of Schisandra chinensis fruit was analyzed on a TLC plate and three major lignan compounds were quantitated by three different methods of UV densitometry, TLC-DART-MS and HPLC-UV to compare the efficiency of each method. To introduce the TLC plate into the DART ion source at a constant velocity, a syringe pump was employed. The DART-MS total ion current chromatogram was recorded for the entire TLC plate. The concentration of each lignan compound was calculated from the calibration curve established with standard compound. Gomisin A, gomisin N and schisandrin were well separated on a silica-coated TLC plate and the specific ion current chromatograms were successfully acquired from the TLC-DART-MS system. The TLC-DART-MS system for the quantitation of natural products showed better linearity and specificity than TLC densitometry, and consumed less time and solvent than conventional HPLC method. A hyphenated system for the quantitation of phytochemicals from crude herbal drugs was successfully established. This system was shown to have a powerful analytical capacity for the prompt and efficient quantitation of natural products from crude drugs. Copyright © 2010 John Wiley & Sons, Ltd.

Quantitative Schlieren analysis applied to holograms of crystals grown on Spacelab 3

NASA Technical Reports Server (NTRS)

Brooks, Howard L.

1986-01-01

In order to extract additional information about crystals grown in the microgravity environment of Spacelab, a quantitative schlieren analysis technique was developed for use in a Holography Ground System of the Fluid Experiment System. Utilizing the Unidex position controller, it was possible to measure deviation angles produced by refractive index gradients of 0.5 milliradians. Additionally, refractive index gradient maps for any recorded time during the crystal growth were drawn and used to create solute concentration maps for the environment around the crystal. The technique was applied to flight holograms of Cell 204 of the Fluid Experiment System that were recorded during the Spacelab 3 mission on STS 51B. A triglycine sulfate crystal was grown under isothermal conditions in the cell and the data gathered with the quantitative schlieren analysis technique is consistent with a diffusion limited growth process.

The Facilitators and Barriers to Nurses’ Participation in Continuing Education Programs: A Mixed Method Explanatory Sequential Study

PubMed Central

Shahhosseini, Zohreh; Hamzehgardeshi, Zeinab

2015-01-01

Background: Since several factors affect nurses’ participation in Continuing Education, and that nurses’ Continuing Education affects patients’ and community health status, it is essential to know facilitators and barriers of participation in Continuing Education programs and plan accordingly. This mixed approach study aimed to investigate the facilitators and barriers of nurses’ participation, to explore nurses’ perception of the most common facilitators and barriers. Methods: An explanatory sequential mixed methods design with follow up explanations variant were used, and it involved collecting quantitative data (361 nurses) first and then explaining the quantitative results with in-depth interviews during a qualitative study. Results: The results showed that the mean score of facilitators to nurses’ participation in Continuing Education was significantly higher than the mean score of barriers (61.99±10.85 versus 51.17±12.83; p<0.001, t=12.23). The highest mean score of facilitators of nurses’ participation in Continuing Education was related to “Update my knowledge”. By reviewing the handwritings in qualitative phase, two main levels of updating information and professional skills were extracted as the most common facilitators and lack of support as the most common barrier to nurses’ participation in continuing education program. Conclusion: According to important role Continuing Education on professional skills, nurse managers should facilitate the nurse’ participation in the Continues Education. PMID:25948439

The facilitators and barriers to nurses' participation in continuing education programs: a mixed method explanatory sequential study.

PubMed

Shahhosseini, Zohreh; Hamzehgardeshi, Zeinab

2014-11-30

Since several factors affect nurses' participation in Continuing Education, and that nurses' Continuing Education affects patients' and community health status, it is essential to know facilitators and barriers of participation in Continuing Education programs and plan accordingly. This mixed approach study aimed to investigate the facilitators and barriers of nurses' participation, to explore nurses' perception of the most common facilitators and barriers. An explanatory sequential mixed methods design with follow up explanations variant were used, and it involved collecting quantitative data (361 nurses) first and then explaining the quantitative results with in-depth interviews during a qualitative study. The results showed that the mean score of facilitators to nurses' participation in Continuing Education was significantly higher than the mean score of barriers (61.99 ± 10.85 versus 51.17 ± 12.83; p<0.001, t=12.23). The highest mean score of facilitators of nurses' participation in Continuing Education was related to "Update my knowledge". By reviewing the handwritings in qualitative phase, two main levels of updating information and professional skills were extracted as the most common facilitators and lack of support as the most common barrier to nurses' participation in continuing education program. According to important role Continuing Education on professional skills, nurse managers should facilitate the nurse' participation in the Continues Education.

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.

Gene Level Meta-Analysis of Quantitative Traits by Functional Linear Models.

PubMed

Fan, Ruzong; Wang, Yifan; Boehnke, Michael; Chen, Wei; Li, Yun; Ren, Haobo; Lobach, Iryna; Xiong, Momiao

2015-08-01

Meta-analysis of genetic data must account for differences among studies including study designs, markers genotyped, and covariates. The effects of genetic variants may differ from population to population, i.e., heterogeneity. Thus, meta-analysis of combining data of multiple studies is difficult. Novel statistical methods for meta-analysis are needed. In this article, functional linear models are developed for meta-analyses that connect genetic data to quantitative traits, adjusting for covariates. The models can be used to analyze rare variants, common variants, or a combination of the two. Both likelihood-ratio test (LRT) and F-distributed statistics are introduced to test association between quantitative traits and multiple variants in one genetic region. Extensive simulations are performed to evaluate empirical type I error rates and power performance of the proposed tests. The proposed LRT and F-distributed statistics control the type I error very well and have higher power than the existing methods of the meta-analysis sequence kernel association test (MetaSKAT). We analyze four blood lipid levels in data from a meta-analysis of eight European studies. The proposed methods detect more significant associations than MetaSKAT and the P-values of the proposed LRT and F-distributed statistics are usually much smaller than those of MetaSKAT. The functional linear models and related test statistics can be useful in whole-genome and whole-exome association studies. Copyright © 2015 by the Genetics Society of America.

Large-scale quantitative analysis of painting arts.

PubMed

Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

2014-12-11

Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images - the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances.

Toward best practices in data processing and analysis for intact biotherapeutics by MS in quantitative bioanalysis.

PubMed

Kellie, John F; Kehler, Jonathan R; Karlinsey, Molly Z; Summerfield, Scott G

2017-12-01

Typically, quantitation of biotherapeutics from biological matrices by LC-MS is based on a surrogate peptide approach to determine molecule concentration. Recent efforts have focused on quantitation of the intact protein molecules or larger mass subunits of monoclonal antibodies. To date, there has been limited guidance for large or intact protein mass quantitation for quantitative bioanalysis. Intact- and subunit-level analyses of biotherapeutics from biological matrices are performed at 12-25 kDa mass range with quantitation data presented. Linearity, bias and other metrics are presented along with recommendations made on the viability of existing quantitation approaches. This communication is intended to start a discussion around intact protein data analysis and processing, recognizing that other published contributions will be required.

Quantitative local analysis of nonlinear systems

NASA Astrophysics Data System (ADS)

Topcu, Ufuk

This thesis investigates quantitative methods for local robustness and performance analysis of nonlinear dynamical systems with polynomial vector fields. We propose measures to quantify systems' robustness against uncertainties in initial conditions (regions-of-attraction) and external disturbances (local reachability/gain analysis). S-procedure and sum-of-squares relaxations are used to translate Lyapunov-type characterizations to sum-of-squares optimization problems. These problems are typically bilinear/nonconvex (due to local analysis rather than global) and their size grows rapidly with state/uncertainty space dimension. Our approach is based on exploiting system theoretic interpretations of these optimization problems to reduce their complexity. We propose a methodology incorporating simulation data in formal proof construction enabling more reliable and efficient search for robustness and performance certificates compared to the direct use of general purpose solvers. This technique is adapted both to region-of-attraction and reachability analysis. We extend the analysis to uncertain systems by taking an intentionally simplistic and potentially conservative route, namely employing parameter-independent rather than parameter-dependent certificates. The conservatism is simply reduced by a branch-and-hound type refinement procedure. The main thrust of these methods is their suitability for parallel computing achieved by decomposing otherwise challenging problems into relatively tractable smaller ones. We demonstrate proposed methods on several small/medium size examples in each chapter and apply each method to a benchmark example with an uncertain short period pitch axis model of an aircraft. Additional practical issues leading to a more rigorous basis for the proposed methodology as well as promising further research topics are also addressed. We show that stability of linearized dynamics is not only necessary but also sufficient for the feasibility of the

Quantitative descriptive analysis and principal component analysis for sensory characterization of Indian milk product cham-cham.

PubMed

Puri, Ritika; Khamrui, Kaushik; Khetra, Yogesh; Malhotra, Ravinder; Devraja, H C

2016-02-01

Promising development and expansion in the market of cham-cham, a traditional Indian dairy product is expected in the coming future with the organized production of this milk product by some large dairies. The objective of this study was to document the extent of variation in sensory properties of market samples of cham-cham collected from four different locations known for their excellence in cham-cham production and to find out the attributes that govern much of variation in sensory scores of this product using quantitative descriptive analysis (QDA) and principal component analysis (PCA). QDA revealed significant (p < 0.05) difference in sensory attributes of cham-cham among the market samples. PCA identified four significant principal components that accounted for 72.4 % of the variation in the sensory data. Factor scores of each of the four principal components which primarily correspond to sweetness/shape/dryness of interior, surface appearance/surface dryness, rancid and firmness attributes specify the location of each market sample along each of the axes in 3-D graphs. These findings demonstrate the utility of quantitative descriptive analysis for identifying and measuring attributes of cham-cham that contribute most to its sensory acceptability.

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

Improving image segmentation performance and quantitative analysis via a computer-aided grading methodology for optical coherence tomography retinal image analysis

NASA Astrophysics Data System (ADS)

Cabrera Debuc, Delia; Salinas, Harry M.; Ranganathan, Sudarshan; Tátrai, Erika; Gao, Wei; Shen, Meixiao; Wang, Jianhua; Somfai, Gábor M.; Puliafito, Carmen A.

2010-07-01

We demonstrate quantitative analysis and error correction of optical coherence tomography (OCT) retinal images by using a custom-built, computer-aided grading methodology. A total of 60 Stratus OCT (Carl Zeiss Meditec, Dublin, California) B-scans collected from ten normal healthy eyes are analyzed by two independent graders. The average retinal thickness per macular region is compared with the automated Stratus OCT results. Intergrader and intragrader reproducibility is calculated by Bland-Altman plots of the mean difference between both gradings and by Pearson correlation coefficients. In addition, the correlation between Stratus OCT and our methodology-derived thickness is also presented. The mean thickness difference between Stratus OCT and our methodology is 6.53 μm and 26.71 μm when using the inner segment/outer segment (IS/OS) junction and outer segment/retinal pigment epithelium (OS/RPE) junction as the outer retinal border, respectively. Overall, the median of the thickness differences as a percentage of the mean thickness is less than 1% and 2% for the intragrader and intergrader reproducibility test, respectively. The measurement accuracy range of the OCT retinal image analysis (OCTRIMA) algorithm is between 0.27 and 1.47 μm and 0.6 and 1.76 μm for the intragrader and intergrader reproducibility tests, respectively. Pearson correlation coefficients demonstrate R2>0.98 for all Early Treatment Diabetic Retinopathy Study (ETDRS) regions. Our methodology facilitates a more robust and localized quantification of the retinal structure in normal healthy controls and patients with clinically significant intraretinal features.

[Quality evaluation of rhubarb dispensing granules based on multi-component simultaneous quantitative analysis and bioassay].

PubMed

Tan, Peng; Zhang, Hai-Zhu; Zhang, Ding-Kun; Wu, Shan-Na; Niu, Ming; Wang, Jia-Bo; Xiao, Xiao-He

2017-07-01

This study attempts to evaluate the quality of Chinese formula granules by combined use of multi-component simultaneous quantitative analysis and bioassay. The rhubarb dispensing granules were used as the model drug for demonstrative study. The ultra-high performance liquid chromatography (UPLC) method was adopted for simultaneously quantitative determination of the 10 anthraquinone derivatives (such as aloe emodin-8-O-β-D-glucoside) in rhubarb dispensing granules; purgative biopotency of different batches of rhubarb dispensing granules was determined based on compound diphenoxylate tablets-induced mouse constipation model; blood activating biopotency of different batches of rhubarb dispensing granules was determined based on in vitro rat antiplatelet aggregation model; SPSS 22.0 statistical software was used for correlation analysis between 10 anthraquinone derivatives and purgative biopotency, blood activating biopotency. The results of multi-components simultaneous quantitative analysisshowed that there was a great difference in chemical characterizationand certain differences inpurgative biopotency and blood activating biopotency among 10 batches of rhubarb dispensing granules. The correlation analysis showed that the intensity of purgative biopotency was significantly correlated with the content of conjugated anthraquinone glycosides (P<0.01), and the intensity of blood activating biopotency was significantly correlated with the content of free anthraquinone (P<0.01). In summary, the combined use of multi-component simultaneous quantitative analysis and bioassay can achieve objective quantification and more comprehensive reflection on overall quality difference among different batches of rhubarb dispensing granules. Copyright© by the Chinese Pharmaceutical Association.

A Quantitative Content Analysis of Mercer University MEd, EdS, and Doctoral Theses

ERIC Educational Resources Information Center

Randolph, Justus J.; Gaiek, Lura S.; White, Torian A.; Slappey, Lisa A.; Chastain, Andrea; Harris, Rose Prejean

2010-01-01

Quantitative content analysis of a body of research not only helps budding researchers understand the culture, language, and expectations of scholarship, it helps identify deficiencies and inform policy and practice. Because of these benefits, an analysis of a census of 980 Mercer University MEd, EdS, and doctoral theses was conducted. Each thesis…

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.

Facilitators and barriers to external cephalic version for breech presentation at term among health care providers in the Netherlands: a quantitative analysis.

PubMed

Rosman, Ageeth N; Vlemmix, Floortje; Beuckens, Antje; Rijnders, Marlies E; Opmeer, Brent C; Mol, Ben Willem J; Kok, Marjolein; Fleuren, Margot A H

2014-03-01

guidelines recommend that external cephalic version (ECV) should be offered to all women with a fetus in breech presentation at term. However, only 50-60% of the women receive an ECV attempt. We explored the determinants (barriers and facilitators) affecting the uptake of the guidelines among gynaecologists and midwives in the Netherlands. national online survey. the Netherlands. gynaecologists and midwives. in the online survey, we identified the determinants that positively or negatively influenced the professionals׳ adherence to three key recommendations in the guidelines: (a) counselling, (b) advising for ECV, (c) arranging an ECV. Determinants were identified in a previously performed qualitative study and were categorised into five underlying constructs; attitude towards ECV, professional obligation, outcome expectations, self-efficacy and preconditions for successful ECV. We performed a multivariate analysis to assess the importance of the different constructs for adherence to the guideline. 364 professionals responded to the survey. Adherence varied: 84% counselled, 73% advised, and 82% arranged an ECV for (almost) all their clients. Although 90% of respondents considered ECV to be an effective treatment for preventing caesarean childbirths, only 30% agreed that 'every client should undergo ECV'. Self-efficacy (perceived skills) was the most important determinant influencing adherence. self-efficacy appears to be the most significant determinant for counselling, advising and arranging an ECV. to improve adherence to the guidelines on ECV we must improve self-efficacy. Copyright © 2014. Published by Elsevier Ltd.

Quantitative analysis of fragrance in selectable one dimensional or two dimensional gas chromatography-mass spectrometry with simultaneous detection of multiple detectors in single injection.

PubMed

Tan, Hui Peng; Wan, Tow Shi; Min, Christina Liew Shu; Osborne, Murray; Ng, Khim Hui

2014-03-14

A selectable one-dimensional ((1)D) or two-dimensional ((2)D) gas chromatography-mass spectrometry (GC-MS) system coupled with flame ionization detector (FID) and olfactory detection port (ODP) was employed in this study to analyze perfume oil and fragrance in shower gel. A split/splitless (SSL) injector and a programmable temperature vaporization (PTV) injector are connected via a 2-way splitter of capillary flow technology (CFT) in this selectable (1)D/(2)D GC-MS/FID/ODP system to facilitate liquid sample injections and thermal desorption (TD) for stir bar sorptive extraction (SBSE) technique, respectively. The dual-linked injectors set-up enable the use of two different injector ports (one at a time) in single sequence run without having to relocate the (1)D capillary column from one inlet to another. Target analytes were separated in (1)D GC-MS/FID/ODP and followed by further separation of co-elution mixture from (1)D in (2)D GC-MS/FID/ODP in single injection without any instrumental reconfiguration. A (1)D/(2)D quantitative analysis method was developed and validated for its repeatability - tR; calculated linear retention indices (LRI); response ratio in both MS and FID signal, limit of detection (LOD), limit of quantitation (LOQ), as well as linearity over a concentration range. The method was successfully applied in quantitative analysis of perfume solution at different concentration level (RSD≤0.01%, n=5) and shower gel spiked with perfume at different dosages (RSD≤0.04%, n=5) with good recovery (96-103% for SSL injection; 94-107% for stir bar sorptive extraction-thermal desorption (SBSE-TD). Copyright © 2014 Elsevier B.V. All rights reserved.

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

PubMed

Prescott, Jeffrey William

2013-02-01

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

Quantitative analysis of microtubule orientation in interdigitated leaf pavement cells

PubMed Central

Akita, Kae; Higaki, Takumi; Kutsuna, Natsumaro; Hasezawa, Seiichiro

2015-01-01

Leaf pavement cells are shaped like a jigsaw puzzle in most dicotyledon species. Molecular genetic studies have identified several genes required for pavement cells morphogenesis and proposed that microtubules play crucial roles in the interdigitation of pavement cells. In this study, we performed quantitative analysis of cortical microtubule orientation in leaf pavement cells in Arabidopsis thaliana. We captured confocal images of cortical microtubules in cotyledon leaf epidermis expressing GFP-tubulinβ and quantitatively evaluated the microtubule orientations relative to the pavement cell growth axis using original image processing techniques. Our results showed that microtubules kept parallel orientations to the growth axis during pavement cell growth. In addition, we showed that immersion treatment of seed cotyledons in solutions containing tubulin polymerization and depolymerization inhibitors decreased pavement cell complexity. Treatment with oryzalin and colchicine inhibited the symmetric division of guard mother cells. PMID:26039484

Quantitative analysis of microtubule orientation in interdigitated leaf pavement cells.

PubMed

Akita, Kae; Higaki, Takumi; Kutsuna, Natsumaro; Hasezawa, Seiichiro

2015-01-01

Leaf pavement cells are shaped like a jigsaw puzzle in most dicotyledon species. Molecular genetic studies have identified several genes required for pavement cells morphogenesis and proposed that microtubules play crucial roles in the interdigitation of pavement cells. In this study, we performed quantitative analysis of cortical microtubule orientation in leaf pavement cells in Arabidopsis thaliana. We captured confocal images of cortical microtubules in cotyledon leaf epidermis expressing GFP-tubulinβ and quantitatively evaluated the microtubule orientations relative to the pavement cell growth axis using original image processing techniques. Our results showed that microtubules kept parallel orientations to the growth axis during pavement cell growth. In addition, we showed that immersion treatment of seed cotyledons in solutions containing tubulin polymerization and depolymerization inhibitors decreased pavement cell complexity. Treatment with oryzalin and colchicine inhibited the symmetric division of guard mother cells.

FLIPPER, a combinatorial probe for correlated live imaging and electron microscopy, allows identification and quantitative analysis of various cells and organelles.

PubMed

Kuipers, Jeroen; van Ham, Tjakko J; Kalicharan, Ruby D; Veenstra-Algra, Anneke; Sjollema, Klaas A; Dijk, Freark; Schnell, Ulrike; Giepmans, Ben N G

2015-04-01

Ultrastructural examination of cells and tissues by electron microscopy (EM) yields detailed information on subcellular structures. However, EM is typically restricted to small fields of view at high magnification; this makes quantifying events in multiple large-area sample sections extremely difficult. Even when combining light microscopy (LM) with EM (correlated LM and EM: CLEM) to find areas of interest, the labeling of molecules is still a challenge. We present a new genetically encoded probe for CLEM, named "FLIPPER", which facilitates quantitative analysis of ultrastructural features in cells. FLIPPER consists of a fluorescent protein (cyan, green, orange, or red) for LM visualization, fused to a peroxidase allowing visualization of targets at the EM level. The use of FLIPPER is straightforward and because the module is completely genetically encoded, cells can be optimally prepared for EM examination. We use FLIPPER to quantify cellular morphology at the EM level in cells expressing a normal and disease-causing point-mutant cell-surface protein called EpCAM (epithelial cell adhesion molecule). The mutant protein is retained in the endoplasmic reticulum (ER) and could therefore alter ER function and morphology. To reveal possible ER alterations, cells were co-transfected with color-coded full-length or mutant EpCAM and a FLIPPER targeted to the ER. CLEM examination of the mixed cell population allowed color-based cell identification, followed by an unbiased quantitative analysis of the ER ultrastructure by EM. Thus, FLIPPER combines bright fluorescent proteins optimized for live imaging with high sensitivity for EM labeling, thereby representing a promising tool for CLEM.

Accuracy of a remote quantitative image analysis in the whole slide images.

PubMed

Słodkowska, Janina; Markiewicz, Tomasz; Grala, Bartłomiej; Kozłowski, Wojciech; Papierz, Wielisław; Pleskacz, Katarzyna; Murawski, Piotr

2011-03-30

The rationale for choosing a remote quantitative method supporting a diagnostic decision requires some empirical studies and knowledge on scenarios including valid telepathology standards. The tumours of the central nervous system [CNS] are graded on the base of the morphological features and the Ki-67 labelling Index [Ki-67 LI]. Various methods have been applied for Ki-67 LI estimation. Recently we have introduced the Computerized Analysis of Medical Images [CAMI] software for an automated Ki-67 LI counting in the digital images. Aims of our study was to explore the accuracy and reliability of a remote assessment of Ki-67 LI with CAMI software applied to the whole slide images [WSI]. The WSI representing CNS tumours: 18 meningiomas and 10 oligodendrogliomas were stored on the server of the Warsaw University of Technology. The digital copies of entire glass slides were created automatically by the Aperio ScanScope CS with objective 20x or 40x. Aperio's Image Scope software provided functionality for a remote viewing of WSI. The Ki-67 LI assessment was carried on within 2 out of 20 selected fields of view (objective 40x) representing the highest labelling areas in each WSI. The Ki-67 LI counting was performed by 3 various methods: 1) the manual reading in the light microscope - LM, 2) the automated counting with CAMI software on the digital images - DI , and 3) the remote quantitation on the WSIs - as WSI method. The quality of WSIs and technical efficiency of the on-line system were analysed. The comparative statistical analysis was performed for the results obtained by 3 methods of Ki-67 LI counting. The preliminary analysis showed that in 18% of WSI the results of Ki-67 LI differed from those obtained in other 2 methods of counting when the quality of the glass slides was below the standard range. The results of our investigations indicate that the remote automated Ki-67 LI analysis performed with the CAMI algorithm on the whole slide images of meningiomas and

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.

Mixing Qualitative and Quantitative Methods: Insights into Design and Analysis Issues

ERIC Educational Resources Information Center

Lieber, Eli

2009-01-01

This article describes and discusses issues related to research design and data analysis in the mixing of qualitative and quantitative methods. It is increasingly desirable to use multiple methods in research, but questions arise as to how best to design and analyze the data generated by mixed methods projects. I offer a conceptualization for such…

A Systematic Approach for Quantitative Analysis of Multidisciplinary Design Optimization Framework

NASA Astrophysics Data System (ADS)

Kim, Sangho; Park, Jungkeun; Lee, Jeong-Oog; Lee, Jae-Woo

An efficient Multidisciplinary Design and Optimization (MDO) framework for an aerospace engineering system should use and integrate distributed resources such as various analysis codes, optimization codes, Computer Aided Design (CAD) tools, Data Base Management Systems (DBMS), etc. in a heterogeneous environment, and need to provide user-friendly graphical user interfaces. In this paper, we propose a systematic approach for determining a reference MDO framework and for evaluating MDO frameworks. The proposed approach incorporates two well-known methods, Analytic Hierarchy Process (AHP) and Quality Function Deployment (QFD), in order to provide a quantitative analysis of the qualitative criteria of MDO frameworks. Identification and hierarchy of the framework requirements and the corresponding solutions for the reference MDO frameworks, the general one and the aircraft oriented one were carefully investigated. The reference frameworks were also quantitatively identified using AHP and QFD. An assessment of three in-house frameworks was then performed. The results produced clear and useful guidelines for improvement of the in-house MDO frameworks and showed the feasibility of the proposed approach for evaluating an MDO framework without a human interference.

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.

Application of magnetic carriers to two examples of quantitative cell analysis

NASA Astrophysics Data System (ADS)

Zhou, Chen; Qian, Zhixi; Choi, Young Suk; David, Allan E.; Todd, Paul; Hanley, Thomas R.

2017-04-01

The use of magnetophoretic mobility as a surrogate for fluorescence intensity in quantitative cell analysis was investigated. The objectives of quantitative fluorescence flow cytometry include establishing a level of labeling for the setting of parameters in fluorescence activated cell sorters (FACS) and the determination of levels of uptake of fluorescently labeled substrates by living cells. Likewise, the objectives of quantitative magnetic cytometry include establishing a level of labeling for the setting of parameters in flowing magnetic cell sorters and the determination of levels of uptake of magnetically labeled substrates by living cells. The magnetic counterpart to fluorescence intensity is magnetophoretic mobility, defined as the velocity imparted to a suspended cell per unit of magnetic ponderomotive force. A commercial velocimeter available for making this measurement was used to demonstrate both applications. Cultured Gallus lymphoma cells were immunolabeled with commercial magnetic beads and shown to have adequate magnetophoretic mobility to be separated by a novel flowing magnetic separator. Phagocytosis of starch nanoparticles having magnetic cores by cultured Chinese hamster ovary cells, a CHO line, was quantified on the basis of magnetophoretic mobility.

On sweat analysis for quantitative estimation of dehydration during physical exercise.

PubMed

Ring, Matthias; Lohmueller, Clemens; Rauh, Manfred; Eskofier, Bjoern M

2015-08-01

Quantitative estimation of water loss during physical exercise is of importance because dehydration can impair both muscular strength and aerobic endurance. A physiological indicator for deficit of total body water (TBW) might be the concentration of electrolytes in sweat. It has been shown that concentrations differ after physical exercise depending on whether water loss was replaced by fluid intake or not. However, to the best of our knowledge, this fact has not been examined for its potential to quantitatively estimate TBW loss. Therefore, we conducted a study in which sweat samples were collected continuously during two hours of physical exercise without fluid intake. A statistical analysis of these sweat samples revealed significant correlations between chloride concentration in sweat and TBW loss (r = 0.41, p <; 0.01), and between sweat osmolality and TBW loss (r = 0.43, p <; 0.01). A quantitative estimation of TBW loss resulted in a mean absolute error of 0.49 l per estimation. Although the precision has to be improved for practical applications, the present results suggest that TBW loss estimation could be realizable using sweat samples.

Implementing a Quantitative Analysis Design Tool for Future Generation Interfaces

DTIC Science & Technology

2012-03-01

with Remotely Piloted Aircraft (RPA) has resulted in the need of a platform to evaluate interface design. The Vigilant Spirit Control Station ( VSCS ...Spirit interface. A modified version of the HCI Index was successfully applied to perform a quantitative analysis of the baseline VSCS interface and...time of the original VSCS interface. These results revealed the effectiveness of the tool and demonstrated in the design of future generation

A quantitative analysis of coupled oscillations using mobile accelerometer sensors

NASA Astrophysics Data System (ADS)

Castro-Palacio, Juan Carlos; Velázquez-Abad, Luisberis; Giménez, Fernando; Monsoriu, Juan A.

2013-05-01

In this paper, smartphone acceleration sensors were used to perform a quantitative analysis of mechanical coupled oscillations. Symmetric and asymmetric normal modes were studied separately in the first two experiments. In the third, a coupled oscillation was studied as a combination of the normal modes. Results indicate that acceleration sensors of smartphones, which are very familiar to students, represent valuable measurement instruments for introductory and first-year physics courses.

Applying Knowledge of Quantitative Design and Analysis

ERIC Educational Resources Information Center

Baskas, Richard S.

2011-01-01

This study compared and contrasted two quantitative scholarly articles in relation to their research designs. Their designs were analyzed by the comparison of research references and research specific vocabulary to describe how various research methods were used. When researching and analyzing quantitative scholarly articles, it is imperative to…

Quantitative analysis of wet-heat inactivation in bovine spongiform encephalopathy

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

Matsuura, Yuichi; Ishikawa, Yukiko; Bo, Xiao

2013-03-01

Highlights: ► We quantitatively analyzed wet-heat inactivation of the BSE agent. ► Infectivity of the BSE macerate did not survive 155 °C wet-heat treatment. ► Once the sample was dehydrated, infectivity was observed even at 170 °C. ► A quantitative PMCA assay was used to evaluate the degree of BSE inactivation. - Abstract: The bovine spongiform encephalopathy (BSE) agent is resistant to conventional microbial inactivation procedures and thus threatens the safety of cattle products and by-products. To obtain information necessary to assess BSE inactivation, we performed quantitative analysis of wet-heat inactivation of infectivity in BSE-infected cattle spinal cords. Using amore » highly sensitive bioassay, we found that infectivity in BSE cattle macerates fell with increase in temperatures from 133 °C to 150 °C and was not detected in the samples subjected to temperatures above 155 °C. In dry cattle tissues, infectivity was detected even at 170 °C. Thus, BSE infectivity reduces with increase in wet-heat temperatures but is less affected when tissues are dehydrated prior to the wet-heat treatment. The results of the quantitative protein misfolding cyclic amplification assay also demonstrated that the level of the protease-resistant prion protein fell below the bioassay detection limit by wet-heat at 155 °C and higher and could help assess BSE inactivation. Our results show that BSE infectivity is strongly resistant to wet-heat inactivation and that it is necessary to pay attention to BSE decontamination in recycled cattle by-products.« less

A quantitative analysis of IRAS maps of molecular clouds

NASA Technical Reports Server (NTRS)

Wiseman, Jennifer J.; Adams, Fred C.

1994-01-01

We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

Feared consequences of panic attacks in panic disorder: a qualitative and quantitative analysis.

PubMed

Raffa, Susan D; White, Kamila S; Barlow, David H

2004-01-01

Cognitions are hypothesized to play a central role in panic disorder (PD). Previous studies have used questionnaires to assess cognitive content, focusing on prototypical cognitions associated with PD; however, few studies have qualitatively examined cognitions associated with the feared consequences of panic attacks. The purpose of this study was to conduct a qualitative and quantitative analysis of feared consequences of panic attacks. The initial, qualitative analysis resulted in the development of 32 categories of feared consequences. The categories were derived from participant responses to a standardized, semi-structured question (n = 207). Five expert-derived categories were then utilized to quantitatively examine the relationship between cognitions and indicators of PD severity. Cognitions did not predict PD severity; however, correlational analyses indicated some predictive validity to the expert-derived categories. The qualitative analysis identified additional areas of patient-reported concern not included in previous research that may be important in the assessment and treatment of PD.

Do Gender-Specific and High-Resolution Three Dimensional Body Charts Facilitate the Communication of Pain for Women? A Quantitative and Qualitative Study

PubMed Central

Egsgaard, Line Lindhardt

2016-01-01

Background Chronic pain is more prevalent among women; however, the majority of standardized pain drawings are often collected using male-like androgynous body representations. Objective The purpose of this study was to assess whether gender-specific and high-resolution three-dimensional (3D) body charts facilitate the communication of pain for women. Methods Using mixed-methods and a cross-over design, female patients with chronic pain were asked to provide detailed drawings of their current pain on masculine and feminine two-dimensional (2D) body schemas (N=41, Part I) or on female 2D and 3D high-resolution body schemas (N=41, Part II) on a computer tablet. The consistency of the drawings between body charts were assessed by intraclass correlation coefficient (ICC) and Bland-Altman plots. Semistructured interviews and a preference questionnaire were then used to obtain qualitative and quantitative responses of the drawing experience. Results The consistency between body charts were high (Part I: ICC=0.980, Part II: ICC=0.994). The preference ratio for the masculine to feminine body schemas were 6:35 and 18:23 for the 2D to 3D female body charts. Patients reported that the 3D body chart enabled a more accurate expression of their pain due to the detailed contours of the musculature and bone structure, however, patients also reported the 3D body chart was too human and believed that skin-like appearance limited ‘deep pain’ expressions. Conclusions Providing gender-specific body charts may facilitate the communication of pain and the level of detail (2D vs 3D body charts) should be used according to patients’ needs. PMID:27440737

Simulating realistic predator signatures in quantitative fatty acid signature analysis

USGS Publications Warehouse

Bromaghin, Jeffrey F.

2015-01-01

Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

Kinetics analysis and quantitative calculations for the successive radioactive decay process

NASA Astrophysics Data System (ADS)

Zhou, Zhiping; Yan, Deyue; Zhao, Yuliang; Chai, Zhifang

2015-01-01

The general radioactive decay kinetics equations with branching were developed and the analytical solutions were derived by Laplace transform method. The time dependence of all the nuclide concentrations can be easily obtained by applying the equations to any known radioactive decay series. Taking the example of thorium radioactive decay series, the concentration evolution over time of various nuclide members in the family has been given by the quantitative numerical calculations with a computer. The method can be applied to the quantitative prediction and analysis for the daughter nuclides in the successive decay with branching of the complicated radioactive processes, such as the natural radioactive decay series, nuclear reactor, nuclear waste disposal, nuclear spallation, synthesis and identification of superheavy nuclides, radioactive ion beam physics and chemistry, etc.

Dispersal of Invasive Forest Insects via Recreational Firewood: A Quantitative Analysis

Treesearch

Frank H. Koch; Denys Yemshanov; Roger D. Magarey; William D. Smith

2012-01-01

Recreational travel is a recognized vector for the spread of invasive species in North America. However, there has been little quantitative analysis of the risks posed by such travel and the associated transport of firewood. In this study, we analyzed the risk of forest insect spread with firewood and estimated related dispersal parameters for application in...

Inter-rater reliability of motor unit number estimates and quantitative motor unit analysis in the tibialis anterior muscle.

PubMed

Boe, S G; Dalton, B H; Harwood, B; Doherty, T J; Rice, C L

2009-05-01

To establish the inter-rater reliability of decomposition-based quantitative electromyography (DQEMG) derived motor unit number estimates (MUNEs) and quantitative motor unit (MU) analysis. Using DQEMG, two examiners independently obtained a sample of needle and surface-detected motor unit potentials (MUPs) from the tibialis anterior muscle from 10 subjects. Coupled with a maximal M wave, surface-detected MUPs were used to derive a MUNE for each subject and each examiner. Additionally, size-related parameters of the individual MUs were obtained following quantitative MUP analysis. Test-retest MUNE values were similar with high reliability observed between examiners (ICC=0.87). Additionally, MUNE variability from test-retest as quantified by a 95% confidence interval was relatively low (+/-28 MUs). Lastly, quantitative data pertaining to MU size, complexity and firing rate were similar between examiners. MUNEs and quantitative MU data can be obtained with high reliability by two independent examiners using DQEMG. Establishing the inter-rater reliability of MUNEs and quantitative MU analysis using DQEMG is central to the clinical applicability of the technique. In addition to assessing response to treatments over time, multiple clinicians may be involved in the longitudinal assessment of the MU pool of individuals with disorders of the central or peripheral nervous system.

Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.

ERIC Educational Resources Information Center

Hill, Devon W.; And Others

1988-01-01

Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)

Barriers, facilitators and preferences for the physical activity of school children. Rationale and methods of a mixed study

PubMed Central

2012-01-01

Background Physical activity interventions in schools environment seem to have shown some effectiveness in the control of the current obesity epidemic in children. However the complexity of behaviors and the diversity of influences related to this problem suggest that we urgently need new lines of insight about how to support comprehensive population strategies of intervention. The aim of this study was to know the perceptions of the children from Cuenca, about their environmental barriers, facilitators and preferences for physical activity. Methods/Design We used a mixed-method design by combining two qualitative methods (analysis of individual drawings and focus groups) together with the quantitative measurement of physical activity through accelerometers, in a theoretical sample of 121 children aged 9 and 11 years of schools in the province of Cuenca, Spain. Conclusions Mixed-method study is an appropriate strategy to know the perceptions of children about barriers and facilitators for physical activity, using both qualitative methods for a deeply understanding of their points of view, and quantitative methods for triangulate the discourse of participants with empirical data. We consider that this is an innovative approach that could provide knowledges for the development of more effective interventions to prevent childhood overweight. PMID:22978490

Large-Scale Quantitative Analysis of Painting Arts

PubMed Central

Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

2014-01-01

Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images – the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances. PMID:25501877

Quantitative analysis of three chiral pesticide enantiomers by high-performance column liquid chromatography.

PubMed

Wang, Peng; Liu, Donghui; Gu, Xu; Jiang, Shuren; Zhou, Zhiqiang

2008-01-01

Methods for the enantiomeric quantitative determination of 3 chiral pesticides, paclobutrazol, myclobutanil, and uniconazole, and their residues in soil and water are reported. An effective chiral high-performance liquid chromatographic (HPLC)-UV method using an amylose-tris(3,5-dimethylphenylcarbamate; AD) column was developed for resolving the enantiomers and quantitative determination. The enantiomers were identified by a circular dichroism detector. Validation involved complete resolution of each of the 2 enantiomers, plus determination of linearity, precision, and limit of detection (LOD). The pesticide enantiomers were isolated by solvent extraction from soil and C18 solid-phase extraction from water. The 2 enantiomers of the 3 pesticides could be completely separated on the AD column using n-hexane isopropanol mobile phase. The linearity and precision results indicated that the method was reliable for the quantitative analysis of the enantiomers. LODs were 0.025, 0.05, and 0.05 mg/kg for each enantiomer of paclobutrazol, myclobutanil, and uniconazole, respectively. Recovery and precision data showed that the pretreatment procedures were satisfactory for enantiomer extraction and cleanup. This method can be used for optical purity determination of technical material and analysis of environmental residues.

Cardiac imaging: working towards fully-automated machine analysis & interpretation.

PubMed

Slomka, Piotr J; Dey, Damini; Sitek, Arkadiusz; Motwani, Manish; Berman, Daniel S; Germano, Guido

2017-03-01

Non-invasive imaging plays a critical role in managing patients with cardiovascular disease. Although subjective visual interpretation remains the clinical mainstay, quantitative analysis facilitates objective, evidence-based management, and advances in clinical research. This has driven developments in computing and software tools aimed at achieving fully automated image processing and quantitative analysis. In parallel, machine learning techniques have been used to rapidly integrate large amounts of clinical and quantitative imaging data to provide highly personalized individual patient-based conclusions. Areas covered: This review summarizes recent advances in automated quantitative imaging in cardiology and describes the latest techniques which incorporate machine learning principles. The review focuses on the cardiac imaging techniques which are in wide clinical use. It also discusses key issues and obstacles for these tools to become utilized in mainstream clinical practice. Expert commentary: Fully-automated processing and high-level computer interpretation of cardiac imaging are becoming a reality. Application of machine learning to the vast amounts of quantitative data generated per scan and integration with clinical data also facilitates a move to more patient-specific interpretation. These developments are unlikely to replace interpreting physicians but will provide them with highly accurate tools to detect disease, risk-stratify, and optimize patient-specific treatment. However, with each technological advance, we move further from human dependence and closer to fully-automated machine interpretation.

Cardiac imaging: working towards fully-automated machine analysis & interpretation

PubMed Central

Slomka, Piotr J; Dey, Damini; Sitek, Arkadiusz; Motwani, Manish; Berman, Daniel S; Germano, Guido

2017-01-01

Introduction Non-invasive imaging plays a critical role in managing patients with cardiovascular disease. Although subjective visual interpretation remains the clinical mainstay, quantitative analysis facilitates objective, evidence-based management, and advances in clinical research. This has driven developments in computing and software tools aimed at achieving fully automated image processing and quantitative analysis. In parallel, machine learning techniques have been used to rapidly integrate large amounts of clinical and quantitative imaging data to provide highly personalized individual patient-based conclusions. Areas covered This review summarizes recent advances in automated quantitative imaging in cardiology and describes the latest techniques which incorporate machine learning principles. The review focuses on the cardiac imaging techniques which are in wide clinical use. It also discusses key issues and obstacles for these tools to become utilized in mainstream clinical practice. Expert commentary Fully-automated processing and high-level computer interpretation of cardiac imaging are becoming a reality. Application of machine learning to the vast amounts of quantitative data generated per scan and integration with clinical data also facilitates a move to more patient-specific interpretation. These developments are unlikely to replace interpreting physicians but will provide them with highly accurate tools to detect disease, risk-stratify, and optimize patient-specific treatment. However, with each technological advance, we move further from human dependence and closer to fully-automated machine interpretation. PMID:28277804

A Content Analysis of Quantitative Research in Journal of Marital and Family Therapy: A 10-Year Review.

PubMed

Parker, Elizabeth O; Chang, Jennifer; Thomas, Volker

2016-01-01

We examined the trends of quantitative research over the past 10 years in the Journal of Marital and Family Therapy (JMFT). Specifically, within the JMFT, we investigated the types and trends of research design and statistical analysis within the quantitative research that was published in JMFT from 2005 to 2014. We found that while the amount of peer-reviewed articles have increased over time, the percentage of quantitative research has remained constant. We discussed the types and trends of statistical analysis and the implications for clinical work and training programs in the field of marriage and family therapy. © 2016 American Association for Marriage and Family Therapy.

Online interprofessional education facilitation: A scoping review.

PubMed

Evans, Sherryn Maree; Ward, Catherine; Reeves, Scott

2018-04-22

The use of online media to deliver interprofessional education (IPE) is becoming more prevalent across health professions education settings. Facilitation of IPE activities is known to be critical to the effective delivery of IPE, however, specifics about the nature of online IPE facilitation remains unclear. To explore the health professions education literature to understand the extent, range and nature of research on online IPE facilitation. Scoping review methodology was used to guide a search of four electronic databases for relevant papers. Of the 2095 abstracts initially identified, after screening of both abstracts and full-text papers, 10 studies were selected for inclusion in this review. Following abstraction of key information from each study, a thematic analysis was undertaken. Three key themes emerged to describe the nature of the IPE facilitation literature: (1) types of online IPE facilitation contributions, (2) the experience of online IPE facilitation and (3) personal outcomes of online IPE facilitation. These IPE facilitation themes were particularly focused on facilitation of interprofessional student teams on an asynchronous basis. While the included studies provide some insight into the nature of online IPE facilitation, future research is needed to better understand facilitator contributions, and the facilitation experience and associated outcomes, both relating to synchronous and asynchronous online environments.

The other half of the story: effect size analysis in quantitative research.

PubMed

Maher, Jessica Middlemis; Markey, Jonathan C; Ebert-May, Diane

2013-01-01

Statistical significance testing is the cornerstone of quantitative research, but studies that fail to report measures of effect size are potentially missing a robust part of the analysis. We provide a rationale for why effect size measures should be included in quantitative discipline-based education research. Examples from both biological and educational research demonstrate the utility of effect size for evaluating practical significance. We also provide details about some effect size indices that are paired with common statistical significance tests used in educational research and offer general suggestions for interpreting effect size measures. Finally, we discuss some inherent limitations of effect size measures and provide further recommendations about reporting confidence intervals.

Quantitative analysis of terahertz spectra for illicit drugs using adaptive-range micro-genetic algorithm

NASA Astrophysics Data System (ADS)

Chen, Yi; Ma, Yong; Lu, Zheng; Peng, Bei; Chen, Qin

2011-08-01

In the field of anti-illicit drug applications, many suspicious mixture samples might consist of various drug components—for example, a mixture of methamphetamine, heroin, and amoxicillin—which makes spectral identification very difficult. A terahertz spectroscopic quantitative analysis method using an adaptive range micro-genetic algorithm with a variable internal population (ARVIPɛμGA) has been proposed. Five mixture cases are discussed using ARVIPɛμGA driven quantitative terahertz spectroscopic analysis in this paper. The devised simulation results show agreement with the previous experimental results, which suggested that the proposed technique has potential applications for terahertz spectral identifications of drug mixture components. The results show agreement with the results obtained using other experimental and numerical techniques.

A Systematic Review of Barriers and Facilitators to Minority Research Participation Among African Americans, Latinos, Asian Americans, and Pacific Islanders

PubMed Central

Duran, Nelida; Norris, Keith

2014-01-01

To assess the experienced or perceived barriers and facilitators to health research participation for major US racial/ethnic minority populations, we conducted a systematic review of qualitative and quantitative studies from a search on PubMed and Web of Science from January 2000 to December 2011. With 44 articles included in the review, we found distinct and shared barriers and facilitators. Despite different expressions of mistrust, all groups represented in these studies were willing to participate for altruistic reasons embedded in cultural and community priorities. Greater comparative understanding of barriers and facilitators to racial/ethnic minorities’ research participation can improve population-specific recruitment and retention strategies and could better inform future large-scale prospective quantitative and in-depth ethnographic studies. PMID:24328648

Facilitators and barriers to quality of care in maternal, newborn and child health: a global situational analysis through metareview

PubMed Central

Nair, Manisha; Yoshida, Sachiyo; Lambrechts, Thierry; Boschi-Pinto, Cynthia; Bose, Krishna; Mason, Elizabeth Mary; Mathai, Matthews

2014-01-01

Objective Conduct a global situational analysis to identify the current facilitators and barriers to improving quality of care (QoC) for pregnant women, newborns and children. Study design Metareview of published and unpublished systematic reviews and meta-analyses conducted between January 2000 and March 2013 in any language. Assessment of Multiple Systematic Reviews (AMSTAR) is used to assess the methodological quality of systematic reviews. Settings Health systems of all countries. Study outcome: QoC measured using surrogate indicators––effective, efficient, accessible, acceptable/patient centred, equitable and safe. Analysis Conducted in two phases (1) qualitative synthesis of extracted data to identify and group the facilitators and barriers to improving QoC, for each of the three population groups, into the six domains of WHO's framework and explore new domains and (2) an analysis grid to map the common facilitators and barriers. Results We included 98 systematic reviews with 110 interventions to improve QoC from countries globally. The facilitators and barriers identified fitted the six domains of WHO's framework––information, patient–population engagement, leadership, regulations and standards, organisational capacity and models of care. Two new domains, ‘communication’ and ‘satisfaction’, were generated. Facilitators included active and regular interpersonal communication between users and providers; respect, confidentiality, comfort and support during care provision; engaging users in decision-making; continuity of care and effective audit and feedback mechanisms. Key barriers identified were language barriers in information and communication; power difference between users and providers; health systems not accounting for user satisfaction; variable standards of implementation of standard guidelines; shortage of resources in health facilities and lack of studies assessing the role of leadership in improving QoC. These were common across

iTRAQ-Based Quantitative Proteomic Analysis of the Antimicrobial Mechanism of Peptide F1 against Escherichia coli.

PubMed

Miao, Jianyin; Chen, Feilong; Duan, Shan; Gao, Xiangyang; Liu, Guo; Chen, Yunjiao; Dixon, William; Xiao, Hang; Cao, Yong

2015-08-19

Antimicrobial peptides have received increasing attention in the agricultural and food industries due to their potential to control pathogens. However, to facilitate the development of novel peptide-based antimicrobial agents, details regarding the molecular mechanisms of these peptides need to be elucidated. The aim of this study was to investigate the antimicrobial mechanism of peptide F1, a bacteriocin found in Tibetan kefir, against Escherichia coli at protein levels using iTRAQ-based quantitative proteomic analysis. In response to treatment with peptide F1, 31 of the 280 identified proteins in E. coli showed alterations in their expression, including 10 down-regulated proteins and 21 up-regulated proteins. These 31 proteins all possess different molecular functions and are involved in different molecular pathways, as is evident in referencing the Kyoto Encyclopedia of Genes and Genomes pathways. Specifically, pathways that were significantly altered in E. coli in response to peptide F1 treatment include the tricarboxylic acid cycle, oxidative phosphorylation, glycerophospholipid metabolism, and the cell cycle-caulobacter pathways, which was also associated with inhibition of the cell growth, induction of morphological changes, and cell death. The results provide novel insights into the molecular mechanisms of antimicrobial peptides.

Quantitative analysis of protein-ligand interactions by NMR.

PubMed

Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

2016-08-01

Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

Barriers and facilitators among health professionals in primary care to prevention of cardiometabolic diseases: A systematic review.

PubMed

Wändell, Per E; de Waard, Anne-Karien M; Holzmann, Martin J; Gornitzki, Carl; Lionis, Christos; de Wit, Niek; Søndergaard, Jens; Sønderlund, Anders L; Kral, Norbert; Seifert, Bohumil; Korevaar, Joke C; Schellevis, François G; Carlsson, Axel C

2018-01-29

The aim of this study is to identify potential facilitators and barriers for health care professionals to undertake selective prevention of cardiometabolic diseases (CMD) in primary health care. We developed a search string for Medline, Embase, Cinahl and PubMed. We also screened reference lists of relevant articles to retain barriers and facilitators for prevention of CMD. We found 19 qualitative studies, 7 quantitative studies and 2 mixed qualitative and quantitative studies. In terms of five overarching categories, the most frequently reported barriers and facilitators were as follows: Structural (barriers: time restraints, ineffective counselling and interventions, insufficient reimbursement and problems with guidelines; facilitators: feasible and effective counselling and interventions, sufficient assistance and support, adequate referral, and identification of obstacles), Organizational (barriers: general organizational problems, role of practice, insufficient IT support, communication problems within health teams and lack of support services, role of staff, lack of suitable appointment times; facilitators: structured practice, IT support, flexibility of counselling, sufficient logistic/practical support and cooperation with allied health staff/community resources, responsibility to offer and importance of prevention), Professional (barriers: insufficient counselling skills, lack of knowledge and of experience; facilitators: sufficient training, effective in motivating patients), Patient-related factors (barriers: low adherence, causes problems for patients; facilitators: strong GP-patient relationship, appreciation from patients), and Attitudinal (barriers: negative attitudes to prevention; facilitators: positive attitudes of importance of prevention). We identified several frequently reported barriers and facilitators for prevention of CMD, which may be used in designing future implementation and intervention studies. © The Author(s) 2018. Published by

Randomised controlled non-inferiority trial of primary care-based facilitated access to an alcohol reduction website: cost-effectiveness analysis.

PubMed

Hunter, Rachael; Wallace, Paul; Struzzo, Pierluigi; Vedova, Roberto Della; Scafuri, Francesca; Tersar, Costanza; Lygidakis, Charilaos; McGregor, Richard; Scafato, Emanuele; Freemantle, Nick

2017-11-03

To evaluate the 12-month costs and quality-adjusted life years (QALYs) gained to the Italian National Health Service of facilitated access to a website for hazardous drinkers compared with a standard face-to-face brief intervention (BI). Randomised 1:1 non-inferiority trial. Practices of 58 general practitioners (GPs) in Italy. Of 9080 patients (>18 years old) approached to take part in the trial, 4529 (49·9%) logged on to the website and 3841 (84.8%) undertook online screening for hazardous drinking. 822 (21.4%) screened positive and 763 (19.9%) were recruited to the trial. Patients were randomised to receive either a face-to-face BI or access via a brochure from their GP to an alcohol reduction website (facilitated access). The primary outcome is the cost per QALY gained of facilitated access compared with face-to-face. A secondary analysis includes total costs and benefits per 100 patients, including number of hazardous drinkers prevented at 12 months. The average time required for the face-to-face BI was 8 min (95% CI 7.5 min to 8.6 min). Given the maximum time taken for facilitated access of 5 min, face-to-face is an additional 3 min: equivalent to having time for another GP appointment for every three patients referred to the website. Complete case analysis adjusting for baseline the difference in QALYs for facilitated access is 0.002 QALYs per patient (95% CI -0.007 to 0.011). Facilitated access to a website to reduce hazardous drinking costs less than a face-to-face BI given by a GP with no worse outcomes. The lower cost of facilitated access, particularly in regards to investment of time, may facilitate the increase in provision of BIs for hazardous drinking. NCT01638338;Post-results. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Randomised controlled non-inferiority trial of primary care-based facilitated access to an alcohol reduction website: cost-effectiveness analysis

PubMed Central

Wallace, Paul; Struzzo, Pierluigi; Vedova, Roberto Della; Scafuri, Francesca; Tersar, Costanza; Lygidakis, Charilaos; McGregor, Richard; Scafato, Emanuele; Freemantle, Nick

2017-01-01

Objectives To evaluate the 12-month costs and quality-adjusted life years (QALYs) gained to the Italian National Health Service of facilitated access to a website for hazardous drinkers compared with a standard face-to-face brief intervention (BI). Design Randomised 1:1 non-inferiority trial. Setting Practices of 58 general practitioners (GPs) in Italy. Participants Of 9080 patients (>18 years old) approached to take part in the trial, 4529 (49·9%) logged on to the website and 3841 (84.8%) undertook online screening for hazardous drinking. 822 (21.4%) screened positive and 763 (19.9%) were recruited to the trial. Interventions Patients were randomised to receive either a face-to-face BI or access via a brochure from their GP to an alcohol reduction website (facilitated access). Primary and secondary outcome measures The primary outcome is the cost per QALY gained of facilitated access compared with face-to-face. A secondary analysis includes total costs and benefits per 100 patients, including number of hazardous drinkers prevented at 12 months. Results The average time required for the face-to-face BI was 8 min (95% CI 7.5 min to 8.6 min). Given the maximum time taken for facilitated access of 5 min, face-to-face is an additional 3 min: equivalent to having time for another GP appointment for every three patients referred to the website. Complete case analysis adjusting for baseline the difference in QALYs for facilitated access is 0.002 QALYs per patient (95% CI −0.007 to 0.011). Conclusions Facilitated access to a website to reduce hazardous drinking costs less than a face-to-face BI given by a GP with no worse outcomes. The lower cost of facilitated access, particularly in regards to investment of time, may facilitate the increase in provision of BIs for hazardous drinking. Trial registration number NCT01638338;Post-results. PMID:29102983

Principles, performance, and applications of spectral reconstitution (SR) in quantitative analysis of oils by Fourier transform infrared spectroscopy (FT-IR).

PubMed

García-González, Diego L; Sedman, Jacqueline; van de Voort, Frederik R

2013-04-01

Spectral reconstitution (SR) is a dilution technique developed to facilitate the rapid, automated, and quantitative analysis of viscous oil samples by Fourier transform infrared spectroscopy (FT-IR). This technique involves determining the dilution factor through measurement of an absorption band of a suitable spectral marker added to the diluent, and then spectrally removing the diluent from the sample and multiplying the resulting spectrum to compensate for the effect of dilution on the band intensities. The facsimile spectrum of the neat oil thus obtained can then be qualitatively or quantitatively analyzed for the parameter(s) of interest. The quantitative performance of the SR technique was examined with two transition-metal carbonyl complexes as spectral markers, chromium hexacarbonyl and methylcyclopentadienyl manganese tricarbonyl. The estimation of the volume fraction (VF) of the diluent in a model system, consisting of canola oil diluted to various extents with odorless mineral spirits, served as the basis for assessment of these markers. The relationship between the VF estimates and the true volume fraction (VF(t)) was found to be strongly dependent on the dilution ratio and also depended, to a lesser extent, on the spectral resolution. These dependences are attributable to the effect of changes in matrix polarity on the bandwidth of the ν(CO) marker bands. Excellent VF(t) estimates were obtained by making a polarity correction devised with a variance-spectrum-delineated correction equation. In the absence of such a correction, SR was shown to introduce only a minor and constant bias, provided that polarity differences among all the diluted samples analyzed were minimal. This bias can be built into the calibration of a quantitative FT-IR analytical method by subjecting appropriate calibration standards to the same SR procedure as the samples to be analyzed. The primary purpose of the SR technique is to simplify preparation of diluted samples such that

Visualisation and quantitative analysis of the rodent malaria liver stage by real time imaging.

PubMed

Ploemen, Ivo H J; Prudêncio, Miguel; Douradinha, Bruno G; Ramesar, Jai; Fonager, Jannik; van Gemert, Geert-Jan; Luty, Adrian J F; Hermsen, Cornelus C; Sauerwein, Robert W; Baptista, Fernanda G; Mota, Maria M; Waters, Andrew P; Que, Ivo; Lowik, Clemens W G M; Khan, Shahid M; Janse, Chris J; Franke-Fayard, Blandine M D

2009-11-18

The quantitative analysis of Plasmodium development in the liver in laboratory animals in cultured cells is hampered by low parasite infection rates and the complicated methods required to monitor intracellular development. As a consequence, this important phase of the parasite's life cycle has been poorly studied compared to blood stages, for example in screening anti-malarial drugs. Here we report the use of a transgenic P. berghei parasite, PbGFP-Luc(con), expressing the bioluminescent reporter protein luciferase to visualize and quantify parasite development in liver cells both in culture and in live mice using real-time luminescence imaging. The reporter-parasite based quantification in cultured hepatocytes by real-time imaging or using a microplate reader correlates very well with established quantitative RT-PCR methods. For the first time the liver stage of Plasmodium is visualized in whole bodies of live mice and we were able to discriminate as few as 1-5 infected hepatocytes per liver in mice using 2D-imaging and to identify individual infected hepatocytes by 3D-imaging. The analysis of liver infections by whole body imaging shows a good correlation with quantitative RT-PCR analysis of extracted livers. The luminescence-based analysis of the effects of various drugs on in vitro hepatocyte infection shows that this method can effectively be used for in vitro screening of compounds targeting Plasmodium liver stages. Furthermore, by analysing the effect of primaquine and tafenoquine in vivo we demonstrate the applicability of real time imaging to assess parasite drug sensitivity in the liver. The simplicity and speed of quantitative analysis of liver-stage development by real-time imaging compared to the PCR methodologies, as well as the possibility to analyse liver development in live mice without surgery, opens up new possibilities for research on Plasmodium liver infections and for validating the effect of drugs and vaccines on the liver stage of

Visualisation and Quantitative Analysis of the Rodent Malaria Liver Stage by Real Time Imaging

PubMed Central

Douradinha, Bruno G.; Ramesar, Jai; Fonager, Jannik; van Gemert, Geert-Jan; Luty, Adrian J. F.; Hermsen, Cornelus C.; Sauerwein, Robert W.; Baptista, Fernanda G.; Mota, Maria M.; Waters, Andrew P.; Que, Ivo; Lowik, Clemens W. G. M.; Khan, Shahid M.; Janse, Chris J.; Franke-Fayard, Blandine M. D.

2009-01-01

The quantitative analysis of Plasmodium development in the liver in laboratory animals in cultured cells is hampered by low parasite infection rates and the complicated methods required to monitor intracellular development. As a consequence, this important phase of the parasite's life cycle has been poorly studied compared to blood stages, for example in screening anti-malarial drugs. Here we report the use of a transgenic P. berghei parasite, PbGFP-Luccon, expressing the bioluminescent reporter protein luciferase to visualize and quantify parasite development in liver cells both in culture and in live mice using real-time luminescence imaging. The reporter-parasite based quantification in cultured hepatocytes by real-time imaging or using a microplate reader correlates very well with established quantitative RT-PCR methods. For the first time the liver stage of Plasmodium is visualized in whole bodies of live mice and we were able to discriminate as few as 1–5 infected hepatocytes per liver in mice using 2D-imaging and to identify individual infected hepatocytes by 3D-imaging. The analysis of liver infections by whole body imaging shows a good correlation with quantitative RT-PCR analysis of extracted livers. The luminescence-based analysis of the effects of various drugs on in vitro hepatocyte infection shows that this method can effectively be used for in vitro screening of compounds targeting Plasmodium liver stages. Furthermore, by analysing the effect of primaquine and tafenoquine in vivo we demonstrate the applicability of real time imaging to assess parasite drug sensitivity in the liver. The simplicity and speed of quantitative analysis of liver-stage development by real-time imaging compared to the PCR methodologies, as well as the possibility to analyse liver development in live mice without surgery, opens up new possibilities for research on Plasmodium liver infections and for validating the effect of drugs and vaccines on the liver stage of

Systematic review of quantitative clinical gait analysis in patients with dementia.

PubMed

van Iersel, M B; Hoefsloot, W; Munneke, M; Bloem, B R; Olde Rikkert, M G M

2004-02-01

Diminished mobility often accompanies dementia and has a great impact on independence and quality of life. New treatment strategies for dementia are emerging, but the effects on gait remains to be studied objectively. In this review we address the general effects of dementia on gait as revealed by quantitative gait analysis. A systematic literature search with the (MESH) terms: 'dementia' and 'gait disorders' in Medline, CC, Psychlit and CinaHL between 1980-2002. Main inclusion criteria: controlled studies; patients with dementia; quantitative gait data. Seven publications met the inclusion criteria. All compared gait in Alzheimer's Disease (AD) with healthy elderly controls; one also assessed gait in Vascular Dementia (VaD). The methodology used was inconsistent and often had many shortcomings. However, there were several consistent findings: walking velocity decreased in dementia compared to healthy controls and decreased further with progressing severity of dementia. VaD was associated with a significant decrease in walking velocity compared to AD subjects. Dementia was associated with a shortened step length, an increased double support time and step to step variability. Gait in dementia is hardly analyzed in a well-designed manner. Despite this, the literature suggests that quantitative gait analysis can be sufficiently reliable and responsive to measure decline in walking velocity between subjects with and without dementia. More research is required to assess, both on an individual and a group level, how the minimal clinically relevant changes in gait in elderly demented patients should be defined and what would be the most responsive method to measure these changes.

Barriers and facilitators to the implementation of physical activity policies in schools: A systematic review.

PubMed

Nathan, Nicole; Elton, Ben; Babic, Mark; McCarthy, Nicole; Sutherland, Rachel; Presseau, Justin; Seward, Kirsty; Hodder, Rebecca; Booth, Debbie; Yoong, Sze Lin; Wolfenden, Luke

2018-02-01

Research consistently indicates that schools fail to implement mandatory physical activity policies. This review aimed to describe factors (barriers and facilitators) that may influence the implementation of school physical activity policies which specify the time or intensity that physical activity should be implemented and to map these factors to a theoretical framework. A systematic search was undertaken in six databases for quantitative or qualitative studies published between 1995-March 2016 that examined teachers', principals' or school administrators' reported barriers and/or facilitators to implementing mandated school physical activity policies. Two independent reviewers screened texts, extracted and coded data from identified articles using the Theoretical Domains Framework (TDF). Of the 10,346 articles identified, 17 studies met the inclusion criteria (8 quantitative, 9 qualitative). Barriers and facilitators identified in qualitative studies covered 9 and 10 TDF domains respectively. Barriers and facilitators reported in quantitative studies covered 8 TDF domains each. The most common domains identified were: 'environmental context and resources' (e.g., availability of equipment, time or staff), 'goals' (e.g., the perceived priority of the policy in the school), 'social influences' (e.g., support from school boards), and 'skills' (e.g., teachers' ability to implement the policy). Implementation support strategies that target these factors may represent promising means to improve implementation of physical activity policies and increase physical activity among school-aged children. Future studies assessing factors that influence school implementation of physical activity policies would benefit from using a comprehensive framework to help identify if any domains have been overlooked in the current literature. This review was prospectively registered with PROSPERO (CRD42016051649) on the 8th December 2016. Copyright © 2017 Elsevier Inc. All rights

Quantitative Analysis of a Hybrid Electric HMMWV for Fuel Economy Improvement

DTIC Science & Technology

2012-05-01

HMMWV of equivalent size. Hybrid vehicle powertrains show improved fuel economy gains due to optimized engine operation and regenerative braking . In... regenerative braking . Validated vehicle models as well as data collected on test tracks are used in the quantitative analysis. The regenerative braking ...hybrid electric vehicle, drive cycle, fuel economy, engine efficiency, regenerative braking . 1 Introduction The US Army (Tank Automotive

SU-G-206-01: A Fully Automated CT Tool to Facilitate Phantom Image QA for Quantitative Imaging in Clinical Trials

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

Wahi-Anwar, M; Lo, P; Kim, H

Purpose: The use of Quantitative Imaging (QI) methods in Clinical Trials requires both verification of adherence to a specified protocol and an assessment of scanner performance under that protocol, which are currently accomplished manually. This work introduces automated phantom identification and image QA measure extraction towards a fully-automated CT phantom QA system to perform these functions and facilitate the use of Quantitative Imaging methods in clinical trials. Methods: This study used a retrospective cohort of CT phantom scans from existing clinical trial protocols - totaling 84 phantoms, across 3 phantom types using various scanners and protocols. The QA system identifiesmore » the input phantom scan through an ensemble of threshold-based classifiers. Each classifier - corresponding to a phantom type - contains a template slice, which is compared to the input scan on a slice-by-slice basis, resulting in slice-wise similarity metric values for each slice compared. Pre-trained thresholds (established from a training set of phantom images matching the template type) are used to filter the similarity distribution, and the slice with the most optimal local mean similarity, with local neighboring slices meeting the threshold requirement, is chosen as the classifier’s matched slice (if it existed). The classifier with the matched slice possessing the most optimal local mean similarity is then chosen as the ensemble’s best matching slice. If the best matching slice exists, image QA algorithm and ROIs corresponding to the matching classifier extracted the image QA measures. Results: Automated phantom identification performed with 84.5% accuracy and 88.8% sensitivity on 84 phantoms. Automated image quality measurements (following standard protocol) on identified water phantoms (n=35) matched user QA decisions with 100% accuracy. Conclusion: We provide a fullyautomated CT phantom QA system consistent with manual QA performance. Further work will include

Techniques for quantitative LC-MS/MS analysis of protein therapeutics: advances in enzyme digestion and immunocapture.

PubMed

Fung, Eliza N; Bryan, Peter; Kozhich, Alexander

2016-04-01

LC-MS/MS has been investigated to quantify protein therapeutics in biological matrices. The protein therapeutics is digested by an enzyme to generate surrogate peptide(s) before LC-MS/MS analysis. One challenge is isolating protein therapeutics in the presence of large number of endogenous proteins in biological matrices. Immunocapture, in which a capture agent is used to preferentially bind the protein therapeutics over other proteins, is gaining traction. The protein therapeutics is eluted for digestion and LC-MS/MS analysis. One area of tremendous potential for immunocapture-LC-MS/MS is to obtain quantitative data where ligand-binding assay alone is not sufficient, for example, quantitation of antidrug antibody complexes. Herein, we present an overview of recent advance in enzyme digestion and immunocapture applicable to protein quantitation.

Facilitating Facilitators: Enhancing PBL through a Structured Facilitator Development Program

ERIC Educational Resources Information Center

Salinitri, Francine D.; Wilhelm, Sheila M.; Crabtree, Brian L.

2015-01-01

With increasing adoption of the problem-based learning (PBL) model, creative approaches to enhancing facilitator training and optimizing resources to maintain effective learning in small groups is essential. We describe a theoretical framework for the development of a PBL facilitator training program that uses the constructivist approach as the…

Quantitative option analysis for implementation and management of landfills.

PubMed

Kerestecioğlu, Merih

2016-09-01

The selection of the most feasible strategy for implementation of landfills is a challenging step. Potential implementation options of landfills cover a wide range, from conventional construction contracts to the concessions. Montenegro, seeking to improve the efficiency of the public services while maintaining affordability, was considering privatisation as a way to reduce public spending on service provision. In this study, to determine the most feasible model for construction and operation of a regional landfill, a quantitative risk analysis was implemented with four steps: (i) development of a global risk matrix; (ii) assignment of qualitative probabilities of occurrences and magnitude of impacts; (iii) determination of the risks to be mitigated, monitored, controlled or ignored; (iv) reduction of the main risk elements; and (v) incorporation of quantitative estimates of probability of occurrence and expected impact for each risk element in the reduced risk matrix. The evaluated scenarios were: (i) construction and operation of the regional landfill by the public sector; (ii) construction and operation of the landfill by private sector and transfer of the ownership to the public sector after a pre-defined period; and (iii) operation of the landfill by the private sector, without ownership. The quantitative risk assessment concluded that introduction of a public private partnership is not the most feasible option, unlike the common belief in several public institutions in developing countries. A management contract for the first years of operation was advised to be implemented, after which, a long term operating contract may follow. © The Author(s) 2016.

An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.

PubMed

Vu, Trung N; Valkenborg, Dirk; Smets, Koen; Verwaest, Kim A; Dommisse, Roger; Lemière, Filip; Verschoren, Alain; Goethals, Bart; Laukens, Kris

2011-10-20

Nuclear magnetic resonance spectroscopy (NMR) is a powerful technique to reveal and compare quantitative metabolic profiles of biological tissues. However, chemical and physical sample variations make the analysis of the data challenging, and typically require the application of a number of preprocessing steps prior to data interpretation. For example, noise reduction, normalization, baseline correction, peak picking, spectrum alignment and statistical analysis are indispensable components in any NMR analysis pipeline. We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. The workflow performance was evaluated using a previously published dataset. Correlation maps, spectral and grey scale plots show clear improvements in comparison to other methods, and the down

Forensic toxicology in drug-facilitated sexual assault.

PubMed

Dinis-Oliveira, Ricardo Jorge; Magalhães, Teresa

2013-09-01

The low rates of reporting, prosecution and conviction that characterize sexual assault, is likely even more evident in drug-facilitated cases. Typically, in these crimes, victims are incapacitated and left unable to resist sexual advances, unconscious, unable to fight off the abuser or to say "no" and unable to clearly remember the circumstances surrounding the events due to anterograde amnesia. The consequence is the delay in performing toxicological analysis aggravated by the reluctance of the victim to disclose the crime. Moreover since "date rape drugs" are often consumed with ethanol and exhibit similar toxicodynamic effects, the diagnosis is erroneously performed as being classical ethanol intoxication. Therefore, it is imperative to rapidly consider toxicological analysis in drug-facilitated sexual assaults. The major focus of this review is to harmonize practical approaches and guidelines to rapidly uncover drug-facilitated sexual assault, namely issues related to when to perform toxicological analysis, toxicological requests, samples to be collected, storage, preservation and transport precautions and xenobiotics or endobiotics to be analyzed.

Quantitative morphometric analysis for the tectonic characterisation of northern Tunisia.

NASA Astrophysics Data System (ADS)

Camafort, Miquel; Pérez-Peña, José Vicente; Booth-Rea, Guillermo; Ranero, César R.; Gràcia, Eulàlia; Azañón, José Miguel; Melki, Fetheddine; Ouadday, Mohamed

2016-04-01

Northern Tunisia is characterized by low deformation rates and low to moderate seismicity. Although instrumental seismicity reaches maximum magnitudes of Mw 5.5, some historical earthquakes have occurred with catastrophic consequences in this region. Aiming to improve our knowledge of active tectonics in Tunisia, we carried out both a quantitative morphometric analysis and field study in the north-western region. We applied different morphometric tools, like river profiles, knickpoint analysis, hypsometric curves and integrals and drainage pattern anomalies in order to differentiate between zones with high or low recent tectonic activity. This analysis helps identifying uplift and subsidence zones, which we relate to fault activity. Several active faults in a sparse distribution were identified. A selected sector was studied with a field campaign to test the results obtained with the quantitative analysis. During the fieldwork we identified geological evidence of recent activity and a considerable seismogenic potential along El Alia-Teboursouk (ETF) and Dkhila (DF) faults. The ETF fault could be responsible of one of the most devastating historical earthquakes in northern Tunisia that destroyed Utique in 412 A.D. Geological evidence include fluvial terraces folded by faults, striated and cracked pebbles, clastic dikes, sand volcanoes, coseismic cracks, etc. Although not reflected in the instrumental seismicity, our results support an important seismic hazard, evidenced by the several active tectonic structures identified and the two seismogenic faults described. After obtaining the current active tectonic framework of Tunisia we discuss our results within the western Mediterranean trying to contribute to the understanding of the western Mediterranean tectonic context. With our results, we suggest that the main reason explaining the sparse and scarce seismicity of the area in contrast with the adjacent parts of the Nubia-Eurasia boundary is due to its extended

Economic analysis of light brown apple moth using GIS and quantitative modeling

Treesearch

Glenn Fowler; Lynn Garrett; Alison Neeley; Roger Magarey; Dan Borchert; Brian Spears

2011-01-01

We conducted an economic analysis of the light brown apple moth (LBAM), (piphyas postvittana (Walker)), whose presence in California has resulted in a regulatory program. Our objective was to quantitatively characterize the economic costs to apple, grape, orange, and pear crops that would result from LBAM's introduction into the continental...

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

Quantitative analysis of the anti-noise performance of an m-sequence in an electromagnetic method

NASA Astrophysics Data System (ADS)

Yuan, Zhe; Zhang, Yiming; Zheng, Qijia

2018-02-01

An electromagnetic method with a transmitted waveform coded by an m-sequence achieved better anti-noise performance compared to the conventional manner with a square-wave. The anti-noise performance of the m-sequence varied with multiple coding parameters; hence, a quantitative analysis of the anti-noise performance for m-sequences with different coding parameters was required to optimize them. This paper proposes the concept of an identification system, with the identified Earth impulse response obtained by measuring the system output with the input of the voltage response. A quantitative analysis of the anti-noise performance of the m-sequence was achieved by analyzing the amplitude-frequency response of the corresponding identification system. The effects of the coding parameters on the anti-noise performance are summarized by numerical simulation, and their optimization is further discussed in our conclusions; the validity of the conclusions is further verified by field experiment. The quantitative analysis method proposed in this paper provides a new insight into the anti-noise mechanism of the m-sequence, and could be used to evaluate the anti-noise performance of artificial sources in other time-domain exploration methods, such as the seismic method.

Quantitative and Qualitative Analysis of Bacteria in Er(III) Solution by Thin-Film Magnetopheresis

PubMed Central

Zborowski, Maciej; Tada, Yoko; Malchesky, Paul S.; Hall, Geraldine S.

1993-01-01

Magnetic deposition, quantitation, and identification of bacteria reacting with the paramagnetic trivalent lanthanide ion, Er3+, was evaluated. The magnetic deposition method was dubbed thin-film magnetopheresis. The optimization of the magnetic deposition protocol was accomplished with Escherichia coli as a model organism in 150 mM NaCl and 5 mM ErCl3 solution. Three gram-positive bacteria, Staphylococcus epidermidis, Staphylococcus saprophyticus, and Enterococcus faecalis, and four gram-negative bacteria, E. coli, Pseudomonas aeruginosa, Proteus mirabilis, and Klebsiella pneumoniae, were subsequently investigated. Quantitative analysis consisted of the microscopic cell count and a scattered-light scanning of the magnetically deposited material aided by the computer data acquisition system. Qualitative analysis consisted of Gram stain differentiation and fluorescein isothiocyanate staining in combination with selected antisera against specific types of bacteria on the solid substrate. The magnetic deposition protocol allowed quantitative detection of E. coli down to the concentration of 105 CFU ml-1, significant in clinical diagnosis applications such as urinary tract infections. Er3+ did not interfere with the typical appearance of the Gram-stained bacteria nor with the antigen recognition by the antibody in the immunohistological evaluations. Indirect antiserum-fluorescein isothiocyanate labelling correctly revealed the presence of E. faecalis and P. aeruginosa in the magnetically deposited material obtained from the mixture of these two bacterial species. On average, the reaction of gram-positive organisms was significantly stronger to the magnetic field in the presence of Er3+ than the reaction of gram-negative organisms. The thin-film magnetophoresis offers promise as a rapid method for quantitative and qualitative analysis of bacteria in solutions such as urine or environmental water. Images PMID:16348916

Quantitative analysis of domain texture in polycrystalline barium titanate by polarized Raman microprobe spectroscopy

NASA Astrophysics Data System (ADS)

Sakashita, Tatsuo; Chazono, Hirokazu; Pezzotti, Giuseppe

2007-12-01

A quantitative determination of domain distribution in polycrystalline barium titanate (BaTiO3, henceforth BT) ceramics has been pursued with the aid of a microprobe polarized Raman spectrometer. The crystallographic texture and domain orientation distribution of BT ceramics, which switched upon applying stress according to ferroelasticity principles, were determined from the relative intensity of selected phonon modes, taking into consideration a theoretical analysis of the angular dependence of phonon mode intensity for the tetragonal BT phase. Furthermore, the angular dependence of Raman intensity measured in polycrystalline BT depended on the statistical distribution of domain angles in the laser microprobe, which was explicitly taken into account in this work for obtaining a quantitative analysis of domain orientation for in-plane textured BT polycrystalline materials.

Quantitative analysis of surface characteristics and morphology in Death Valley, California using AIRSAR data

NASA Technical Reports Server (NTRS)

Kierein-Young, K. S.; Kruse, F. A.; Lefkoff, A. B.

1992-01-01

The Jet Propulsion Laboratory Airborne Synthetic Aperture Radar (JPL-AIRSAR) is used to collect full polarimetric measurements at P-, L-, and C-bands. These data are analyzed using the radar analysis and visualization environment (RAVEN). The AIRSAR data are calibrated using in-scene corner reflectors to allow for quantitative analysis of the radar backscatter. RAVEN is used to extract surface characteristics. Inversion models are used to calculate quantitative surface roughness values and fractal dimensions. These values are used to generate synthetic surface plots that represent the small-scale surface structure of areas in Death Valley. These procedures are applied to a playa, smooth salt-pan, and alluvial fan surfaces in Death Valley. Field measurements of surface roughness are used to verify the accuracy.

Qualitative and quantitative analysis of mixtures of compounds containing both hydrogen and deuterium

NASA Technical Reports Server (NTRS)

Crespi, H. L.; Harkness, L.; Katz, J. J.; Norman, G.; Saur, W.

1969-01-01

Method allows qualitative and quantitative analysis of mixtures of partially deuterated compounds. Nuclear magnetic resonance spectroscopy determines location and amount of deuterium in organic compounds but not fully deuterated compounds. Mass spectroscopy can detect fully deuterated species but not the location.

Quantitative evaluation of translational medicine based on scientometric analysis and information extraction.

PubMed

Zhang, Yin; Diao, Tianxi; Wang, Lei

2014-12-01

Designed to advance the two-way translational process between basic research and clinical practice, translational medicine has become one of the most important areas in biomedicine. The quantitative evaluation of translational medicine is valuable for the decision making of global translational medical research and funding. Using the scientometric analysis and information extraction techniques, this study quantitatively analyzed the scientific articles on translational medicine. The results showed that translational medicine had significant scientific output and impact, specific core field and institute, and outstanding academic status and benefit. While it is not considered in this study, the patent data are another important indicators that should be integrated in the relevant research in the future. © 2014 Wiley Periodicals, Inc.

Quantitative Analysis Tools and Digital Phantoms for Deformable Image Registration Quality Assurance.

PubMed

Kim, Haksoo; Park, Samuel B; Monroe, James I; Traughber, Bryan J; Zheng, Yiran; Lo, Simon S; Yao, Min; Mansur, David; Ellis, Rodney; Machtay, Mitchell; Sohn, Jason W

2015-08-01

This article proposes quantitative analysis tools and digital phantoms to quantify intrinsic errors of deformable image registration (DIR) systems and establish quality assurance (QA) procedures for clinical use of DIR systems utilizing local and global error analysis methods with clinically realistic digital image phantoms. Landmark-based image registration verifications are suitable only for images with significant feature points. To address this shortfall, we adapted a deformation vector field (DVF) comparison approach with new analysis techniques to quantify the results. Digital image phantoms are derived from data sets of actual patient images (a reference image set, R, a test image set, T). Image sets from the same patient taken at different times are registered with deformable methods producing a reference DVFref. Applying DVFref to the original reference image deforms T into a new image R'. The data set, R', T, and DVFref, is from a realistic truth set and therefore can be used to analyze any DIR system and expose intrinsic errors by comparing DVFref and DVFtest. For quantitative error analysis, calculating and delineating differences between DVFs, 2 methods were used, (1) a local error analysis tool that displays deformation error magnitudes with color mapping on each image slice and (2) a global error analysis tool that calculates a deformation error histogram, which describes a cumulative probability function of errors for each anatomical structure. Three digital image phantoms were generated from three patients with a head and neck, a lung and a liver cancer. The DIR QA was evaluated using the case with head and neck. © The Author(s) 2014.

Improved Protein Arrays for Quantitative Systems Analysis of the Dynamics of Signaling Pathway Interactions

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

Yang, Chin-Rang

Astronauts and workers in nuclear plants who repeatedly exposed to low doses of ionizing radiation (IR, <10 cGy) are likely to incur specific changes in signal transduction and gene expression in various tissues of their body. Remarkable advances in high throughput genomics and proteomics technologies enable researchers to broaden their focus from examining single gene/protein kinetics to better understanding global gene/protein expression profiling and biological pathway analyses, namely Systems Biology. An ultimate goal of systems biology is to develop dynamic mathematical models of interacting biological systems capable of simulating living systems in a computer. This Glue Grant is to complementmore » Dr. Boothman’s existing DOE grant (No. DE-FG02-06ER64186) entitled “The IGF1/IGF-1R-MAPK-Secretory Clusterin (sCLU) Pathway: Mediator of a Low Dose IR-Inducible Bystander Effect” to develop sensitive and quantitative proteomic technology that suitable for low dose radiobiology researches. An improved version of quantitative protein array platform utilizing linear Quantum dot signaling for systematically measuring protein levels and phosphorylation states for systems biology modeling is presented. The signals are amplified by a confocal laser Quantum dot scanner resulting in ~1000-fold more sensitivity than traditional Western blots and show the good linearity that is impossible for the signals of HRP-amplification. Therefore this improved protein array technology is suitable to detect weak responses of low dose radiation. Software is developed to facilitate the quantitative readout of signaling network activities. Kinetics of EGFRvIII mutant signaling was analyzed to quantify cross-talks between EGFR and other signaling pathways.« less

Quantitative analysis of the polarization characteristics of atherosclerotic plaques

NASA Astrophysics Data System (ADS)

Gubarkova, Ekaterina V.; Kirillin, Michail Y.; Dudenkova, Varvara V.; Kiseleva, Elena B.; Moiseev, Alexander A.; Gelikonov, Grigory V.; Timofeeva, Lidia B.; Fiks, Ilya I.; Feldchtein, Felix I.; Gladkova, Natalia D.

2016-04-01

In this study we demonstrate the capability of cross-polarization optical coherence tomography (CP OCT) to assess collagen and elastin fibers condition in atherosclerotic plaques basing on ratio of the OCT signal levels in cross- and co- polarizations. We consider the depolarization factor (DF) and the effective birefringence (Δn) as quantitative characteristics of CP OCT images. We revealed that calculation of both DF and Δn in the region of interest (fibrous cap) yields a statistically significant difference between stable and unstable plaques (0.46+/-0.21 vs 0.09+/-0.04 for IDF; (4.7+/-1.0)•10-4 vs (2.5+/-0.7)•10-4 for Δn p<0.05). In parallel with CP OCT we used the nonlinear microscopy for analysis of thin cross-section of atherosclerotic plaque, revealing the different average isotropy index of collagen and elastin fibers for stable and unstable plaques (0.30 +/- 0.10 vs 0.70 +/- 0.08; p<0.001). The proposed approach for quantitative assessment of CP OCT images allows cross-scattering and birefringence characterization of stable and unstable atherosclerotic plaques.

Simultaneous quantitative analysis of main components in linderae reflexae radix with one single marker.

PubMed

Wang, Li-Li; Zhang, Yun-Bin; Sun, Xiao-Ya; Chen, Sui-Qing

2016-05-08

Establish a quantitative analysis of multi-components by the single marker (QAMS) method for quality evaluation and validate its feasibilities by the simultaneous quantitative assay of four main components in Linderae Reflexae Radix. Four main components of pinostrobin, pinosylvin, pinocembrin, and 3,5-dihydroxy-2-(1- p -mentheneyl)- trans -stilbene were selected as analytes to evaluate the quality by RP-HPLC coupled with a UV-detector. The method was evaluated by a comparison of the quantitative results between the external standard method and QAMS with a different HPLC system. The results showed that no significant differences were found in the quantitative results of the four contents of Linderae Reflexae Radix determined by the external standard method and QAMS (RSD <3%). The contents of four analytes (pinosylvin, pinocembrin, pinostrobin, and Reflexanbene I) in Linderae Reflexae Radix were determined by the single marker of pinosylvin. This fingerprint was the spectra determined by Shimadzu LC-20AT and Waters e2695 HPLC that were equipped with three different columns.

Quantitative analysis of peel-off degree for printed electronics

NASA Astrophysics Data System (ADS)

Park, Janghoon; Lee, Jongsu; Sung, Ki-Hak; Shin, Kee-Hyun; Kang, Hyunkyoo

2018-02-01

We suggest a facile methodology of peel-off degree evaluation by image processing on printed electronics. The quantification of peeled and printed areas was performed using open source programs. To verify the accuracy of methods, we manually removed areas from the printed circuit that was measured, resulting in 96.3% accuracy. The sintered patterns showed a decreasing tendency in accordance with the increase in the energy density of an infrared lamp, and the peel-off degree increased. Thus, the comparison between both results was presented. Finally, the correlation between performance characteristics was determined by quantitative analysis.

Quantitative analysis of multi-component gas mixture based on AOTF-NIR spectroscopy

NASA Astrophysics Data System (ADS)

Hao, Huimin; Zhang, Yong; Liu, Junhua

2007-12-01

Near Infrared (NIR) spectroscopy analysis technology has attracted many eyes and has wide application in many domains in recent years because of its remarkable advantages. But the NIR spectrometer can only be used for liquid and solid analysis by now. In this paper, a new quantitative analysis method of gas mixture by using new generation NIR spectrometer is explored. To collect the NIR spectra of gas mixtures, a vacuumable gas cell was designed and assembled to Luminar 5030-731 Acousto-Optic Tunable Filter (AOTF)-NIR spectrometer. Standard gas samples of methane (CH 4), ethane (C IIH 6) and propane (C 3H 8) are diluted with super pure nitrogen via precision volumetric gas flow controllers to obtain gas mixture samples of different concentrations dynamically. The gas mixtures were injected into the gas cell and the spectra of wavelength between 1100nm-2300nm were collected. The feature components extracted from gas mixture spectra by using Partial Least Squares (PLS) were used as the inputs of the Support Vector Regress Machine (SVR) to establish the quantitative analysis model. The effectiveness of the model is tested by the samples of predicting set. The prediction Root Mean Square Error (RMSE) of CH 4, C IIH 6 and C 3H 8 is respectively 1.27%, 0.89%, and 1.20% when the concentrations of component gas are over 0.5%. It shows that the AOTF-NIR spectrometer with gas cell can be used for gas mixture analysis. PLS combining with SVR has a good performance in NIR spectroscopy analysis. This paper provides the bases for extending the application of NIR spectroscopy analysis to gas detection.

Quantitative blood group typing using surface plasmon resonance.

PubMed

Then, Whui Lyn; Aguilar, Marie-Isabel; Garnier, Gil

2015-11-15

The accurate and reliable typing of blood groups is essential prior to blood transfusion. While current blood typing methods are well established, results are subjective and heavily reliant on analysis by trained personnel. Techniques for quantifying blood group antibody-antigen interactions are also very limited. Many biosensing systems rely on surface plasmon resonance (SPR) detection to quantify biomolecular interactions. While SPR has been widely used for characterizing antibody-antigen interactions, measuring antibody interactions with whole cells is significantly less common. Previous studies utilized SPR for blood group antigen detection, however, showed poor regeneration causing loss of functionality after a single use. In this study, a fully regenerable, multi-functional platform for quantitative blood group typing via SPR detection is achieved by immobilizing anti-human IgG antibody to the sensor surface, which binds to the Fc region of human IgG antibodies. The surface becomes an interchangeable platform capable of quantifying the blood group interactions between red blood cells (RBCs) and IgG antibodies. As with indirect antiglobulin tests (IAT), which use IgG antibodies for detection, IgG antibodies are initially incubated with RBCs. This facilitates binding to the immobilized monolayer and allows for quantitative blood group detection. Using the D-antigen as an example, a clear distinction between positive (>500 RU) and negative (<100 RU) RBCs is achieved using anti-D IgG. Complete regeneration of the anti-human IgG surface is also successful, showing negligible degradation of the surface after more than 100 regenerations. This novel approach is validated with human-sourced whole blood samples to demonstrate an interesting alternative for quantitative blood grouping using SPR analysis. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

Identifying Perceived Barriers and Facilitators to Culturally Competent Practice for School Social Workers

ERIC Educational Resources Information Center

Teasley, Martell; Gourdine, Ruby; Canfield, James

2010-01-01

This study presents descriptive findings from self-reported qualitative and quantitative data on barriers and facilitators to culturally competent school social work practice. The study highlights the need for the development of evaluative methods for the purpose of examining how elements within the practice environment affect school social work…

A Data Analysis Pipeline Accounting for Artifacts in Tox21 Quantitative High-Throughput Screening Assays

PubMed Central

Hsieh, Jui-Hua; Sedykh, Alexander; Huang, Ruili; Xia, Menghang; Tice, Raymond R.

2015-01-01

A main goal of the U.S. Tox21 program is to profile a 10K-compound library for activity against a panel of stress-related and nuclear receptor signaling pathway assays using a quantitative high-throughput screening (qHTS) approach. However, assay artifacts, including nonreproducible signals and assay interference (e.g., autofluorescence), complicate compound activity interpretation. To address these issues, we have developed a data analysis pipeline that includes an updated signal noise–filtering/curation protocol and an assay interference flagging system. To better characterize various types of signals, we adopted a weighted version of the area under the curve (wAUC) to quantify the amount of activity across the tested concentration range in combination with the assay-dependent point-of-departure (POD) concentration. Based on the 32 Tox21 qHTS assays analyzed, we demonstrate that signal profiling using wAUC affords the best reproducibility (Pearson's r = 0.91) in comparison with the POD (0.82) only or the AC50 (i.e., half-maximal activity concentration, 0.81). Among the activity artifacts characterized, cytotoxicity is the major confounding factor; on average, about 8% of Tox21 compounds are affected, whereas autofluorescence affects less than 0.5%. To facilitate data evaluation, we implemented two graphical user interface applications, allowing users to rapidly evaluate the in vitro activity of Tox21 compounds. PMID:25904095

A Data Analysis Pipeline Accounting for Artifacts in Tox21 Quantitative High-Throughput Screening Assays.

PubMed

Hsieh, Jui-Hua; Sedykh, Alexander; Huang, Ruili; Xia, Menghang; Tice, Raymond R

2015-08-01

A main goal of the U.S. Tox21 program is to profile a 10K-compound library for activity against a panel of stress-related and nuclear receptor signaling pathway assays using a quantitative high-throughput screening (qHTS) approach. However, assay artifacts, including nonreproducible signals and assay interference (e.g., autofluorescence), complicate compound activity interpretation. To address these issues, we have developed a data analysis pipeline that includes an updated signal noise-filtering/curation protocol and an assay interference flagging system. To better characterize various types of signals, we adopted a weighted version of the area under the curve (wAUC) to quantify the amount of activity across the tested concentration range in combination with the assay-dependent point-of-departure (POD) concentration. Based on the 32 Tox21 qHTS assays analyzed, we demonstrate that signal profiling using wAUC affords the best reproducibility (Pearson's r = 0.91) in comparison with the POD (0.82) only or the AC(50) (i.e., half-maximal activity concentration, 0.81). Among the activity artifacts characterized, cytotoxicity is the major confounding factor; on average, about 8% of Tox21 compounds are affected, whereas autofluorescence affects less than 0.5%. To facilitate data evaluation, we implemented two graphical user interface applications, allowing users to rapidly evaluate the in vitro activity of Tox21 compounds. © 2015 Society for Laboratory Automation and Screening.

Analysis of specific RNA in cultured cells through quantitative integration of q-PCR and N-SIM single cell FISH images: Application to hormonal stimulation of StAR transcription.

PubMed

Lee, Jinwoo; Foong, Yee Hoon; Musaitif, Ibrahim; Tong, Tiegang; Jefcoate, Colin

2016-07-05

The steroidogenic acute regulatory protein (StAR) has been proposed to serve as the switch that can turn on/off steroidogenesis. We investigated the events that facilitate dynamic StAR transcription in response to cAMP stimulation in MA-10 Leydig cells, focusing on splicing anomalies at StAR gene loci. We used 3' reverse primers in a single reaction to respectively quantify StAR primary (p-RNA), spliced (sp-RNA/mRNA), and extended 3' untranslated region (UTR) transcripts, which were quantitatively imaged by high-resolution fluorescence in situ hybridization (FISH). This approach delivers spatio-temporal resolution of initiation and splicing at single StAR loci, and transfers individual mRNA molecules to cytoplasmic sites. Gene expression was biphasic, initially showing slow splicing, transitioning to concerted splicing. The alternative 3.5-kb mRNAs were distinguished through the use of extended 3'UTR probes, which exhibited distinctive mitochondrial distribution. Combining quantitative PCR and FISH enables imaging of localization of RNA expression and analysis of RNA processing rates. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Quantitative analysis of benzodiazepines in vitreous humor by high-performance liquid chromatography

PubMed Central

Bazmi, Elham; Behnoush, Behnam; Akhgari, Maryam; Bahmanabadi, Leila

2016-01-01

Objective: Benzodiazepines are frequently screened drugs in emergency toxicology, drugs of abuse testing, and in forensic cases. As the variations of benzodiazepines concentrations in biological samples during bleeding, postmortem changes, and redistribution could be biasing forensic medicine examinations, hence selecting a suitable sample and a validated accurate method is essential for the quantitative analysis of these main drug categories. The aim of this study was to develop a valid method for the determination of four benzodiazepines (flurazepam, lorazepam, alprazolam, and diazepam) in vitreous humor using liquid–liquid extraction and high-performance liquid chromatography. Methods: Sample preparation was carried out using liquid–liquid extraction with n-hexane: ethyl acetate and subsequent detection by high-performance liquid chromatography method coupled to diode array detector. This method was applied to quantify benzodiazepines in 21 authentic vitreous humor samples. Linear curve for each drug was obtained within the range of 30–3000 ng/mL with coefficient of correlation higher than 0.99. Results: The limit of detection and quantitation were 30 and 100 ng/mL respectively for four drugs. The method showed an appropriate intra- and inter-day precision (coefficient of variation < 10%). Benzodiazepines recoveries were estimated to be over 80%. The method showed high selectivity; no additional peak due to interfering substances in samples was observed. Conclusion: The present method was selective, sensitive, accurate, and precise for the quantitative analysis of benzodiazepines in vitreous humor samples in forensic toxicology laboratory. PMID:27635251

Analysis of high accuracy, quantitative proteomics data in the MaxQB database.

PubMed

Schaab, Christoph; Geiger, Tamar; Stoehr, Gabriele; Cox, Juergen; Mann, Matthias

2012-03-01

MS-based proteomics generates rapidly increasing amounts of precise and quantitative information. Analysis of individual proteomic experiments has made great strides, but the crucial ability to compare and store information across different proteome measurements still presents many challenges. For example, it has been difficult to avoid contamination of databases with low quality peptide identifications, to control for the inflation in false positive identifications when combining data sets, and to integrate quantitative data. Although, for example, the contamination with low quality identifications has been addressed by joint analysis of deposited raw data in some public repositories, we reasoned that there should be a role for a database specifically designed for high resolution and quantitative data. Here we describe a novel database termed MaxQB that stores and displays collections of large proteomics projects and allows joint analysis and comparison. We demonstrate the analysis tools of MaxQB using proteome data of 11 different human cell lines and 28 mouse tissues. The database-wide false discovery rate is controlled by adjusting the project specific cutoff scores for the combined data sets. The 11 cell line proteomes together identify proteins expressed from more than half of all human genes. For each protein of interest, expression levels estimated by label-free quantification can be visualized across the cell lines. Similarly, the expression rank order and estimated amount of each protein within each proteome are plotted. We used MaxQB to calculate the signal reproducibility of the detected peptides for the same proteins across different proteomes. Spearman rank correlation between peptide intensity and detection probability of identified proteins was greater than 0.8 for 64% of the proteome, whereas a minority of proteins have negative correlation. This information can be used to pinpoint false protein identifications, independently of peptide database

Barriers and facilitators to healthy eating for nurses in the workplace: an integrative review.

PubMed

Nicholls, Rachel; Perry, Lin; Duffield, Christine; Gallagher, Robyn; Pierce, Heather

2017-05-01

The aim was to conduct an integrative systematic review to identify barriers and facilitators to healthy eating for working nurses. There is growing recognition of the influence of the workplace environment on the eating habits of the workforce, which in turn may contribute to increased overweight and obesity. Overweight and obesity exact enormous costs in terms of reduced well-being, worker productivity and increased risk of non-communicable diseases. The workplace is an ideal place to intervene and support healthy behaviours. This review aimed to identify barriers and facilitators to nurses' healthy eating in the workplace. Integrative mixed method review. Five electronic databases were searched: CINAHL, MEDLINE, PROQUEST Health and Medicine, ScienceDirect and PsycINFO. Reference lists were searched. Included papers were published in English between 2000-2016. Of 26 included papers, 21 were qualitative and five quantitative. An integrative literature review was undertaken. Quality appraisal of included studies used standardized checklists. A social-ecological framework was used to examine workplace facilitators and constraints to healthy eating, derived from the literature. Emergent themes were identified by thematic analysis. Review participants were Registered, Enrolled and/or Nurse Assistants primarily working in hospitals in middle or high income countries. The majority of studies reported barriers to healthy eating related to adverse work schedules, individual barriers, aspects of the physical workplace environment and social eating practices at work. Few facilitators were reported. Overall, studies found the workplace exerts a considerable negative influence on nurses' dietary intake. Reorientation of the workplace to promote healthy eating among nurses is required. © 2016 John Wiley & Sons Ltd.

Quantitative Risk Analysis

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

Helms, J.

2017-02-10

The US energy sector is vulnerable to multiple hazards including both natural disasters and malicious attacks from an intelligent adversary. The question that utility owners, operators and regulators face is how to prioritize their investments to mitigate the risks from a hazard that can have the most impact on the asset of interest. In order to be able to understand their risk landscape and develop a prioritized mitigation strategy, they must quantify risk in a consistent way across all hazards their asset is facing. Without being able to quantitatively measure risk, it is not possible to defensibly prioritize security investmentsmore » or evaluate trade-offs between security and functionality. Development of a methodology that will consistently measure and quantify risk across different hazards is needed.« less

Comparison among Reconstruction Algorithms for Quantitative Analysis of 11C-Acetate Cardiac PET Imaging.

PubMed

Shi, Ximin; Li, Nan; Ding, Haiyan; Dang, Yonghong; Hu, Guilan; Liu, Shuai; Cui, Jie; Zhang, Yue; Li, Fang; Zhang, Hui; Huo, Li

2018-01-01

Kinetic modeling of dynamic 11 C-acetate PET imaging provides quantitative information for myocardium assessment. The quality and quantitation of PET images are known to be dependent on PET reconstruction methods. This study aims to investigate the impacts of reconstruction algorithms on the quantitative analysis of dynamic 11 C-acetate cardiac PET imaging. Suspected alcoholic cardiomyopathy patients ( N = 24) underwent 11 C-acetate dynamic PET imaging after low dose CT scan. PET images were reconstructed using four algorithms: filtered backprojection (FBP), ordered subsets expectation maximization (OSEM), OSEM with time-of-flight (TOF), and OSEM with both time-of-flight and point-spread-function (TPSF). Standardized uptake values (SUVs) at different time points were compared among images reconstructed using the four algorithms. Time-activity curves (TACs) in myocardium and blood pools of ventricles were generated from the dynamic image series. Kinetic parameters K 1 and k 2 were derived using a 1-tissue-compartment model for kinetic modeling of cardiac flow from 11 C-acetate PET images. Significant image quality improvement was found in the images reconstructed using iterative OSEM-type algorithms (OSME, TOF, and TPSF) compared with FBP. However, no statistical differences in SUVs were observed among the four reconstruction methods at the selected time points. Kinetic parameters K 1 and k 2 also exhibited no statistical difference among the four reconstruction algorithms in terms of mean value and standard deviation. However, for the correlation analysis, OSEM reconstruction presented relatively higher residual in correlation with FBP reconstruction compared with TOF and TPSF reconstruction, and TOF and TPSF reconstruction were highly correlated with each other. All the tested reconstruction algorithms performed similarly for quantitative analysis of 11 C-acetate cardiac PET imaging. TOF and TPSF yielded highly consistent kinetic parameter results with superior

Meta-analysis is not an exact science: Call for guidance on quantitative synthesis decisions.

PubMed

Haddaway, Neal R; Rytwinski, Trina

2018-05-01

Meta-analysis is becoming increasingly popular in the field of ecology and environmental management. It increases the effective power of analyses relative to single studies, and allows researchers to investigate effect modifiers and sources of heterogeneity that could not be easily examined within single studies. Many systematic reviewers will set out to conduct a meta-analysis as part of their synthesis, but meta-analysis requires a niche set of skills that are not widely held by the environmental research community. Each step in the process of carrying out a meta-analysis requires decisions that have both scientific and statistical implications. Reviewers are likely to be faced with a plethora of decisions over which effect size to choose, how to calculate variances, and how to build statistical models. Some of these decisions may be simple based on appropriateness of the options. At other times, reviewers must choose between equally valid approaches given the information available to them. This presents a significant problem when reviewers are attempting to conduct a reliable synthesis, such as a systematic review, where subjectivity is minimised and all decisions are documented and justified transparently. We propose three urgent, necessary developments within the evidence synthesis community. Firstly, we call on quantitative synthesis experts to improve guidance on how to prepare data for quantitative synthesis, providing explicit detail to support systematic reviewers. Secondly, we call on journal editors and evidence synthesis coordinating bodies (e.g. CEE) to ensure that quantitative synthesis methods are adequately reported in a transparent and repeatable manner in published systematic reviews. Finally, where faced with two or more broadly equally valid alternative methods or actions, reviewers should conduct multiple analyses, presenting all options, and discussing the implications of the different analytical approaches. We believe it is vital to tackle

Evaluation of coronary stenosis with the aid of quantitative image analysis in histological cross sections.

PubMed

Dulohery, Kate; Papavdi, Asteria; Michalodimitrakis, Manolis; Kranioti, Elena F

2012-11-01

Coronary artery atherosclerosis is a hugely prevalent condition in the Western World and is often encountered during autopsy. Atherosclerotic plaques can cause luminal stenosis: which, if over a significant level (75%), is said to contribute to cause of death. Estimation of stenosis can be macroscopically performed by the forensic pathologists at the time of autopsy or by microscopic examination. This study compares macroscopic estimation with quantitative microscopic image analysis with a particular focus on the assessment of significant stenosis (>75%). A total of 131 individuals were analysed. The sample consists of an atherosclerotic group (n=122) and a control group (n=9). The results of the two methods were significantly different from each other (p=0.001) and the macroscopic method gave a greater percentage stenosis by an average of 3.5%. Also, histological examination of coronary artery stenosis yielded a difference in significant stenosis in 11.5% of cases. The differences were attributed to either histological quantitative image analysis underestimation; gross examination overestimation; or, a combination of both. The underestimation may have come from tissue shrinkage during tissue processing for histological specimen. The overestimation from the macroscopic assessment can be attributed to the lumen shape, to the examiner observer error or to a possible bias to diagnose coronary disease when no other cause of death is apparent. The results indicate that the macroscopic estimation is open to more biases and that histological quantitative image analysis only gives a precise assessment of stenosis ex vivo. Once tissue shrinkage, if any, is accounted for then histological quantitative image analysis will yield a more accurate assessment of in vivo stenosis. It may then be considered a complementary tool for the examination of coronary stenosis. Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Quantitative image analysis for investigating cell-matrix interactions

NASA Astrophysics Data System (ADS)

Burkel, Brian; Notbohm, Jacob

2017-07-01

The extracellular matrix provides both chemical and physical cues that control cellular processes such as migration, division, differentiation, and cancer progression. Cells can mechanically alter the matrix by applying forces that result in matrix displacements, which in turn may localize to form dense bands along which cells may migrate. To quantify the displacements, we use confocal microscopy and fluorescent labeling to acquire high-contrast images of the fibrous material. Using a technique for quantitative image analysis called digital volume correlation, we then compute the matrix displacements. Our experimental technology offers a means to quantify matrix mechanics and cell-matrix interactions. We are now using these experimental tools to modulate mechanical properties of the matrix to study cell contraction and migration.

Quantitative spectral and orientational analysis in surface sum frequency generation vibrational spectroscopy (SFG-VS)

NASA Astrophysics Data System (ADS)

Wang, Hong-Fei; Gan, Wei; Lu, Rong; Rao, Yi; Wu, Bao-Hua

Sum frequency generation vibrational spectroscopy (SFG-VS) has been proven to be a uniquely effective spectroscopic technique in the investigation of molecular structure and conformations, as well as the dynamics of molecular interfaces. However, the ability to apply SFG-VS to complex molecular interfaces has been limited by the ability to abstract quantitative information from SFG-VS experiments. In this review, we try to make assessments of the limitations, issues and techniques as well as methodologies in quantitative orientational and spectral analysis with SFG-VS. Based on these assessments, we also try to summarize recent developments in methodologies on quantitative orientational and spectral analysis in SFG-VS, and their applications to detailed analysis of SFG-VS data of various vapour/neat liquid interfaces. A rigorous formulation of the polarization null angle (PNA) method is given for accurate determination of the orientational parameter D = /, and comparison between the PNA method with the commonly used polarization intensity ratio (PIR) method is discussed. The polarization and incident angle dependencies of the SFG-VS intensity are also reviewed, in the light of how experimental arrangements can be optimized to effectively abstract crucial information from the SFG-VS experiments. The values and models of the local field factors in the molecular layers are discussed. In order to examine the validity and limitations of the bond polarizability derivative model, the general expressions for molecular hyperpolarizability tensors and their expression with the bond polarizability derivative model for C3v, C2v and C∞v molecular groups are given in the two appendixes. We show that the bond polarizability derivative model can quantitatively describe many aspects of the intensities observed in the SFG-VS spectrum of the vapour/neat liquid interfaces in different polarizations. Using the polarization analysis in SFG-VS, polarization selection

Quantitative Analysis of Color Differences within High Contrast, Low Power Reversible Electrophoretic Displays

DOE PAGES

Giera, Brian; Bukosky, Scott; Lee, Elaine; ...

2018-01-23

Here, quantitative color analysis is performed on videos of high contrast, low power reversible electrophoretic deposition (EPD)-based displays operated under different applied voltages. This analysis is coded in an open-source software, relies on a color differentiation metric, ΔE * 00, derived from digital video, and provides an intuitive relationship between the operating conditions of the devices and their performance. Time-dependent ΔE * 00 color analysis reveals color relaxation behavior, recoverability for different voltage sequences, and operating conditions that can lead to optimal performance.

Quantitative Analysis of Color Differences within High Contrast, Low Power Reversible Electrophoretic Displays

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

Giera, Brian; Bukosky, Scott; Lee, Elaine

Here, quantitative color analysis is performed on videos of high contrast, low power reversible electrophoretic deposition (EPD)-based displays operated under different applied voltages. This analysis is coded in an open-source software, relies on a color differentiation metric, ΔE * 00, derived from digital video, and provides an intuitive relationship between the operating conditions of the devices and their performance. Time-dependent ΔE * 00 color analysis reveals color relaxation behavior, recoverability for different voltage sequences, and operating conditions that can lead to optimal performance.

A Quantitative Analysis of the Extrinsic and Intrinsic Turnover Factors of Relational Database Support Professionals

ERIC Educational Resources Information Center

Takusi, Gabriel Samuto

2010-01-01

This quantitative analysis explored the intrinsic and extrinsic turnover factors of relational database support specialists. Two hundred and nine relational database support specialists were surveyed for this research. The research was conducted based on Hackman and Oldham's (1980) Job Diagnostic Survey. Regression analysis and a univariate ANOVA…

A Quantitative Analysis of Pulsed Signals Emitted by Wild Bottlenose Dolphins.

PubMed

Luís, Ana Rita; Couchinho, Miguel N; Dos Santos, Manuel E

2016-01-01

Common bottlenose dolphins (Tursiops truncatus), produce a wide variety of vocal emissions for communication and echolocation, of which the pulsed repertoire has been the most difficult to categorize. Packets of high repetition, broadband pulses are still largely reported under a general designation of burst-pulses, and traditional attempts to classify these emissions rely mainly in their aural characteristics and in graphical aspects of spectrograms. Here, we present a quantitative analysis of pulsed signals emitted by wild bottlenose dolphins, in the Sado estuary, Portugal (2011-2014), and test the reliability of a traditional classification approach. Acoustic parameters (minimum frequency, maximum frequency, peak frequency, duration, repetition rate and inter-click-interval) were extracted from 930 pulsed signals, previously categorized using a traditional approach. Discriminant function analysis revealed a high reliability of the traditional classification approach (93.5% of pulsed signals were consistently assigned to their aurally based categories). According to the discriminant function analysis (Wilk's Λ = 0.11, F3, 2.41 = 282.75, P < 0.001), repetition rate is the feature that best enables the discrimination of different pulsed signals (structure coefficient = 0.98). Classification using hierarchical cluster analysis led to a similar categorization pattern: two main signal types with distinct magnitudes of repetition rate were clustered into five groups. The pulsed signals, here described, present significant differences in their time-frequency features, especially repetition rate (P < 0.001), inter-click-interval (P < 0.001) and duration (P < 0.001). We document the occurrence of a distinct signal type-short burst-pulses, and highlight the existence of a diverse repertoire of pulsed vocalizations emitted in graded sequences. The use of quantitative analysis of pulsed signals is essential to improve classifications and to better assess the contexts of

Acousto-Optic Tunable Filter Spectroscopic Instrumentation for Quantitative Near-Ir Analysis of Organic Materials.

NASA Astrophysics Data System (ADS)

Eilert, Arnold James

1995-01-01

The utility of near-IR spectroscopy for routine quantitative analyses of a wide variety of compositional, chemical, or physical parameters of organic materials is well understood. It can be used for relatively fast and inexpensive non-destructive bulk material analysis before, during, and after processing. It has been demonstrated as being a particularly useful technique for numerous analytical applications in cereal (food and feed) science and industry. Further fulfillment of the potential of near-IR spectroscopic analysis, both in the process and laboratory environment, is reliant upon the development of instrumentation that is capable of meeting the challenges of increasingly difficult applications. One approach to the development of near-IR spectroscopic instrumentation that holds a great deal of promise is acousto-optic tunable filter (AOTF) technology. A combination of attributes offered by AOTF spectrometry, including speed, optical throughput, wavelength reproducibility, ruggedness (no -moving-parts operation) and flexibility, make it particularly desirable for numerous applications. A series of prototype (research model) acousto -optic tunable filter instruments were developed and tested in order to investigate the feasibility of the technology for quantitative near-IR spectrometry. Development included design, component procurement, assembly and/or configuration of the optical and electronic subsystems of which each functional spectrometer arrangement was comprised, as well as computer interfacing and acquisition/control software development. Investigation of this technology involved an evolution of several operational spectrometer systems, each of which offered improvements over its predecessor. Appropriate testing was conducted at various stages of development. Demonstrations of the potential applicability of our AOTF spectrometer to quantitative process monitoring or laboratory analysis of numerous organic substances, including food materials, were

Quantitative analysis of Si1-xGex alloy films by SIMS and XPS depth profiling using a reference material

NASA Astrophysics Data System (ADS)

Oh, Won Jin; Jang, Jong Shik; Lee, Youn Seoung; Kim, Ansoon; Kim, Kyung Joong

2018-02-01

Quantitative analysis methods of multi-element alloy films were compared. The atomic fractions of Si1-xGex alloy films were measured by depth profiling analysis with secondary ion mass spectrometry (SIMS) and X-ray Photoelectron Spectroscopy (XPS). Intensity-to-composition conversion factor (ICF) was used as a mean to convert the intensities to compositions instead of the relative sensitivity factors. The ICFs were determined from a reference Si1-xGex alloy film by the conventional method, average intensity (AI) method and total number counting (TNC) method. In the case of SIMS, although the atomic fractions measured by oxygen ion beams were not quantitative due to severe matrix effect, the results by cesium ion beam were very quantitative. The quantitative analysis results by SIMS using MCs2+ ions are comparable to the results by XPS. In the case of XPS, the measurement uncertainty was highly improved by the AI method and TNC method.

Qualitative and Quantitative Analysis for Facial Complexion in Traditional Chinese Medicine

PubMed Central

Zhao, Changbo; Li, Guo-zheng; Li, Fufeng; Wang, Zhi; Liu, Chang

2014-01-01

Facial diagnosis is an important and very intuitive diagnostic method in Traditional Chinese Medicine (TCM). However, due to its qualitative and experience-based subjective property, traditional facial diagnosis has a certain limitation in clinical medicine. The computerized inspection method provides classification models to recognize facial complexion (including color and gloss). However, the previous works only study the classification problems of facial complexion, which is considered as qualitative analysis in our perspective. For quantitative analysis expectation, the severity or degree of facial complexion has not been reported yet. This paper aims to make both qualitative and quantitative analysis for facial complexion. We propose a novel feature representation of facial complexion from the whole face of patients. The features are established with four chromaticity bases splitting up by luminance distribution on CIELAB color space. Chromaticity bases are constructed from facial dominant color using two-level clustering; the optimal luminance distribution is simply implemented with experimental comparisons. The features are proved to be more distinctive than the previous facial complexion feature representation. Complexion recognition proceeds by training an SVM classifier with the optimal model parameters. In addition, further improved features are more developed by the weighted fusion of five local regions. Extensive experimental results show that the proposed features achieve highest facial color recognition performance with a total accuracy of 86.89%. And, furthermore, the proposed recognition framework could analyze both color and gloss degrees of facial complexion by learning a ranking function. PMID:24967342

Seniors' online communities: a quantitative content analysis.

PubMed

Nimrod, Galit

2010-06-01

To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. There was a constant increase in the daily activity level during the research period. Content analysis identified 13 main subjects discussed in the communities, including (in descending order) "Fun on line," "Retirement," "Family," "Health," "Work and Study," "Recreation" "Finance," "Religion and Spirituality," "Technology," "Aging," "Civic and Social," "Shopping," and "Travels." The overall tone was somewhat more positive than negative. The findings suggest that the utilities of Information and Communications Technologies for older adults that were identified in previous research are valid for seniors' online communities as well. However, the findings suggest several other possible benefits, which may be available only to online communities. The communities may provide social support, contribute to self-preservation, and serve as an opportunity for self-discovery and growth. Because they offer both leisure activity and an expanded social network, it is suggested that active participation in the communities may contribute to the well-being of older adults. Directions for future research and applied implications are further discussed.

New approaches for the analysis of confluent cell layers with quantitative phase digital holographic microscopy

NASA Astrophysics Data System (ADS)

Pohl, L.; Kaiser, M.; Ketelhut, S.; Pereira, S.; Goycoolea, F.; Kemper, Björn

2016-03-01

Digital holographic microscopy (DHM) enables high resolution non-destructive inspection of technical surfaces and minimally-invasive label-free live cell imaging. However, the analysis of confluent cell layers represents a challenge as quantitative DHM phase images in this case do not provide sufficient information for image segmentation, determination of the cellular dry mass or calculation of the cell thickness. We present novel strategies for the analysis of confluent cell layers with quantitative DHM phase contrast utilizing a histogram based-evaluation procedure. The applicability of our approach is illustrated by quantification of drug induced cell morphology changes and it is shown that the method is capable to quantify reliable global morphology changes of confluent cell layers.

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.

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.

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.

A review on recent developments in mass spectrometry instrumentation and quantitative tools advancing bacterial proteomics.

PubMed

Van Oudenhove, Laurence; Devreese, Bart

2013-06-01

Proteomics has evolved substantially since its early days, some 20 years ago. In this mini-review, we aim to provide an overview of general methodologies and more recent developments in mass spectrometric approaches used for relative and absolute quantitation of proteins. Enhancement of sensitivity of the mass spectrometers as well as improved sample preparation and protein fractionation methods are resulting in a more comprehensive analysis of proteomes. We also document some upcoming trends for quantitative proteomics such as the use of label-free quantification methods. Hopefully, microbiologists will continue to explore proteomics as a tool in their research to understand the adaptation of microorganisms to their ever changing environment. We encourage them to incorporate some of the described new developments in mass spectrometry to facilitate their analyses and improve the general knowledge of the fascinating world of microorganisms.

Direct comparison of low- and mid-frequency Raman spectroscopy for quantitative solid-state pharmaceutical analysis.

PubMed

Lipiäinen, Tiina; Fraser-Miller, Sara J; Gordon, Keith C; Strachan, Clare J

2018-02-05

This study considers the potential of low-frequency (terahertz) Raman spectroscopy in the quantitative analysis of ternary mixtures of solid-state forms. Direct comparison between low-frequency and mid-frequency spectral regions for quantitative analysis of crystal form mixtures, without confounding sampling and instrumental variations, is reported for the first time. Piroxicam was used as a model drug, and the low-frequency spectra of piroxicam forms β, α2 and monohydrate are presented for the first time. These forms show clear spectral differences in both the low- and mid-frequency regions. Both spectral regions provided quantitative models suitable for predicting the mixture compositions using partial least squares regression (PLSR), but the low-frequency data gave better models, based on lower errors of prediction (2.7, 3.1 and 3.2% root-mean-square errors of prediction [RMSEP] values for the β, α2 and monohydrate forms, respectively) than the mid-frequency data (6.3, 5.4 and 4.8%, for the β, α2 and monohydrate forms, respectively). The better performance of low-frequency Raman analysis was attributed to larger spectral differences between the solid-state forms, combined with a higher signal-to-noise ratio. Copyright © 2017 Elsevier B.V. All rights reserved.

Watershed Planning within a Quantitative Scenario Analysis Framework.

PubMed

Merriam, Eric R; Petty, J Todd; Strager, Michael P

2016-07-24

There is a critical need for tools and methodologies capable of managing aquatic systems within heavily impacted watersheds. Current efforts often fall short as a result of an inability to quantify and predict complex cumulative effects of current and future land use scenarios at relevant spatial scales. The goal of this manuscript is to provide methods for conducting a targeted watershed assessment that enables resource managers to produce landscape-based cumulative effects models for use within a scenario analysis management framework. Sites are first selected for inclusion within the watershed assessment by identifying sites that fall along independent gradients and combinations of known stressors. Field and laboratory techniques are then used to obtain data on the physical, chemical, and biological effects of multiple land use activities. Multiple linear regression analysis is then used to produce landscape-based cumulative effects models for predicting aquatic conditions. Lastly, methods for incorporating cumulative effects models within a scenario analysis framework for guiding management and regulatory decisions (e.g., permitting and mitigation) within actively developing watersheds are discussed and demonstrated for 2 sub-watersheds within the mountaintop mining region of central Appalachia. The watershed assessment and management approach provided herein enables resource managers to facilitate economic and development activity while protecting aquatic resources and producing opportunity for net ecological benefits through targeted remediation.

A combined qualitative and quantitative procedure for the chemical analysis of urinary calculi

PubMed Central

Hodgkinson, A.

1971-01-01

A better understanding of the physico-chemical principles underlying the formation of calculus has led to a need for more precise information on the chemical composition of stones. A combined qualitative and quantitative procedure for the chemical analysis of urinary calculi which is suitable for routine use is presented. The procedure involves five simple qualitative tests followed by the quantitative determination of calcium, magnesium, inorganic phosphate, and oxalate. These data are used to calculate the composition of the stone in terms of calcium oxalate, apatite, and magnesium ammonium phosphate. Analytical results and derived values for five representative types of calculi are presented. PMID:5551382

Quantitative analysis of the mixtures of illicit drugs using terahertz time-domain spectroscopy

NASA Astrophysics Data System (ADS)

Jiang, Dejun; Zhao, Shusen; Shen, Jingling

2008-03-01

A method was proposed to quantitatively inspect the mixtures of illicit drugs with terahertz time-domain spectroscopy technique. The mass percentages of all components in a mixture can be obtained by linear regression analysis, on the assumption that all components in the mixture and their absorption features be known. For illicit drugs were scarce and expensive, firstly we used common chemicals, Benzophenone, Anthraquinone, Pyridoxine hydrochloride and L-Ascorbic acid in the experiment. Then illicit drugs and a common adulterant, methamphetamine and flour, were selected for our experiment. Experimental results were in significant agreement with actual content, which suggested that it could be an effective method for quantitative identification of illicit drugs.

Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

NASA Technical Reports Server (NTRS)

Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

2006-01-01

A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

Quantitative proteomic analysis of human lung tumor xenografts treated with the ectopic ATP synthase inhibitor citreoviridin.

PubMed

Wu, Yi-Hsuan; Hu, Chia-Wei; Chien, Chih-Wei; Chen, Yu-Ju; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

2013-01-01

ATP synthase is present on the plasma membrane of several types of cancer cells. Citreoviridin, an ATP synthase inhibitor, selectively suppresses the proliferation and growth of lung cancer without affecting normal cells. However, the global effects of targeting ectopic ATP synthase in vivo have not been well defined. In this study, we performed quantitative proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ) and provided a comprehensive insight into the complicated regulation by citreoviridin in a lung cancer xenograft model. With high reproducibility of the quantitation, we obtained quantitative proteomic profiling with 2,659 proteins identified. Bioinformatics analysis of the 141 differentially expressed proteins selected by their relative abundance revealed that citreoviridin induces alterations in the expression of glucose metabolism-related enzymes in lung cancer. The up-regulation of enzymes involved in gluconeogenesis and storage of glucose indicated that citreoviridin may reduce the glycolytic intermediates for macromolecule synthesis and inhibit cell proliferation. Using comprehensive proteomics, the results identify metabolic aspects that help explain the antitumorigenic effect of citreoviridin in lung cancer, which may lead to a better understanding of the links between metabolism and tumorigenesis in cancer therapy.

Quantitative Proteomic Analysis of Human Lung Tumor Xenografts Treated with the Ectopic ATP Synthase Inhibitor Citreoviridin

PubMed Central

Wu, Yi-Hsuan; Hu, Chia-Wei; Chien, Chih-Wei; Chen, Yu-Ju; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

2013-01-01

ATP synthase is present on the plasma membrane of several types of cancer cells. Citreoviridin, an ATP synthase inhibitor, selectively suppresses the proliferation and growth of lung cancer without affecting normal cells. However, the global effects of targeting ectopic ATP synthase in vivo have not been well defined. In this study, we performed quantitative proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ) and provided a comprehensive insight into the complicated regulation by citreoviridin in a lung cancer xenograft model. With high reproducibility of the quantitation, we obtained quantitative proteomic profiling with 2,659 proteins identified. Bioinformatics analysis of the 141 differentially expressed proteins selected by their relative abundance revealed that citreoviridin induces alterations in the expression of glucose metabolism-related enzymes in lung cancer. The up-regulation of enzymes involved in gluconeogenesis and storage of glucose indicated that citreoviridin may reduce the glycolytic intermediates for macromolecule synthesis and inhibit cell proliferation. Using comprehensive proteomics, the results identify metabolic aspects that help explain the antitumorigenic effect of citreoviridin in lung cancer, which may lead to a better understanding of the links between metabolism and tumorigenesis in cancer therapy. PMID:23990911

PANDA-view: An easy-to-use tool for statistical analysis and visualization of quantitative proteomics data.

PubMed

Chang, Cheng; Xu, Kaikun; Guo, Chaoping; Wang, Jinxia; Yan, Qi; Zhang, Jian; He, Fuchu; Zhu, Yunping

2018-05-22

Compared with the numerous software tools developed for identification and quantification of -omics data, there remains a lack of suitable tools for both downstream analysis and data visualization. To help researchers better understand the biological meanings in their -omics data, we present an easy-to-use tool, named PANDA-view, for both statistical analysis and visualization of quantitative proteomics data and other -omics data. PANDA-view contains various kinds of analysis methods such as normalization, missing value imputation, statistical tests, clustering and principal component analysis, as well as the most commonly-used data visualization methods including an interactive volcano plot. Additionally, it provides user-friendly interfaces for protein-peptide-spectrum representation of the quantitative proteomics data. PANDA-view is freely available at https://sourceforge.net/projects/panda-view/. 1987ccpacer@163.com and zhuyunping@gmail.com. Supplementary data are available at Bioinformatics online.

Comparative study of two protocols for quantitative image-analysis of serotonin transporter clustering in lymphocytes, a putative biomarker of therapeutic efficacy in major depression.

PubMed

Romay-Tallon, Raquel; Rivera-Baltanas, Tania; Allen, Josh; Olivares, Jose M; Kalynchuk, Lisa E; Caruncho, Hector J

2017-01-01

The pattern of serotonin transporter clustering on the plasma membrane of lymphocytes extracted from human whole blood samples has been identified as a putative biomarker of therapeutic efficacy in major depression. Here we evaluated the possibility of performing a similar analysis using blood smears obtained from rats, and from control human subjects and depression patients. We hypothesized that we could optimize a protocol to make the analysis of serotonin protein clustering in blood smears comparable to the analysis of serotonin protein clustering using isolated lymphocytes. Our data indicate that blood smears require a longer fixation time and longer times of incubation with primary and secondary antibodies. In addition, one needs to optimize the image analysis settings for the analysis of smears. When these steps are followed, the quantitative analysis of both the number and size of serotonin transporter clusters on the plasma membrane of lymphocytes is similar using both blood smears and isolated lymphocytes. The development of this novel protocol will greatly facilitate the collection of appropriate samples by eliminating the necessity and cost of specialized personnel for drawing blood samples, and by being a less invasive procedure. Therefore, this protocol will help us advance the validation of membrane protein clustering in lymphocytes as a biomarker of therapeutic efficacy in major depression, and bring it closer to its clinical application.

Functional linear models for association analysis of quantitative traits.

PubMed

Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

2013-11-01

Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. © 2013 WILEY

Customized Body Mapping to Facilitate the Ergonomic Design of Sportswear.

PubMed

Cao, Mingliang; Li, Yi; Guo, Yueping; Yao, Lei; Pan, Zhigeng

2016-01-01

A successful high-performance sportswear design that considers human factors should result in a significant increase in thermal comfort and reduce energy loss. The authors describe a body-mapping approach that facilitates the effective ergonomic design of sportswear. Their general framework can be customized based on the functional requirements of various sports and sportswear, the desired combination and selection of mapping areas for the human body, and customized quantitative data distribution of target physiological indicators.

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.

Recommendations for Quantitative Analysis of Small Molecules by Matrix-assisted laser desorption ionization mass spectrometry

PubMed Central

Wang, Poguang; Giese, Roger W.

2017-01-01

Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been used for quantitative analysis of small molecules for many years. It is usually preceded by an LC separation step when complex samples are tested. With the development several years ago of “modern MALDI” (automation, high repetition laser, high resolution peaks), the ease of use and performance of MALDI as a quantitative technique greatly increased. This review focuses on practical aspects of modern MALDI for quantitation of small molecules conducted in an ordinary way (no special reagents, devices or techniques for the spotting step of MALDI), and includes our ordinary, preferred Methods The review is organized as 18 recommendations with accompanying explanations, criticisms and exceptions. PMID:28118972

Esophagram findings in cervical esophageal stenosis: A case-controlled quantitative analysis.

PubMed

West, Jacob; Kim, Cherine H; Reichert, Zachary; Krishna, Priya; Crawley, Brianna K; Inman, Jared C

2018-01-04

Cervical esophageal stenosis is often diagnosed with a qualitative evaluation of a barium esophagram. Although the esophagram is frequently the initial screening exam for dysphagia, a clear objective standard for stenosis has not been defined. In this study, we measured esophagram diameters in order to establish a quantitative standard for defining cervical esophageal stenosis that requires surgical intervention. Single institution case-control study. Patients with clinically significant cervical esophageal stenosis defined by moderate symptoms of dysphagia (Functional Outcome Swallowing Scale > 2 and Functional Oral Intake Scale < 6) persisting for 6 months and responding to dilation treatment were matched with age, sex, and height controls. Both qualitative and quantitative barium esophagram measurements for the upper, mid-, and lower vertebral bodies of C5 through T1 were analyzed in lateral, oblique, and anterior-posterior views. Stenotic patients versus nonstenotic controls showed no significant differences in age, sex, height, body mass index, or ethnicity. Stenosis was most commonly at the sixth cervical vertebra (C 6) lower border and C7 upper border. The mean intraesophageal minimum/maximum ratios of controls and stenotic groups in the lateral view were 0.63 ± 0.08 and 0.36 ± 0.12, respectively (P < 0.0001). Receiver operating characteristic analysis of the minimum/maximum ratios, with a <0.50 ratio delineating stenosis, demonstrated that lateral view measurements had the best diagnostic ability. The sensitivity of the radiologists' qualitative interpretation was 56%. With application of lateral intraesophageal minimum/maximum ratios, we observed improved sensitivity to 94% of the esophagram, detecting clinically significant stenosis. Applying quantitative determinants in esophagram analysis may improve the sensitivity of detecting cervical esophageal stenosis in dysphagic patients who may benefit from surgical therapy. IIIb

NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

PubMed

Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

2018-01-01

We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

Facilitating Grant Proposal Writing in Health Behaviors for University Faculty: A Descriptive Study

PubMed Central

Stein, L. A. R.; Clair, M.; Lebeau, R.; Prochaska, J. O.; Rossi, J. S.; Swift, J.

2015-01-01

Grant proposal writing in the behavioral sciences is important for fiscal reasons and scientific reasons at many universities. This report describes a grant proposal–writing seminar series provided to University faculty (N = 20) and explores factors facilitating and impeding writing. Summary statistics are provided for quantitative data. Free responses were sorted by independent raters into meaningful categories. As a consequence of the training, 45% planned to submit within 18 months; 80% of grant proposals targeted NIH. At 1-year follow-up, 40% actually submitted grants. Factors impeding grant proposal writing included competing professional demands; factors facilitating writing included regularly scheduled feedback on written proposal sections and access to expert collaborators. Obtaining grants generates financial resources, facilitates training experiences, and vastly contributes to the growth and dissemination of the knowledge base in an area. PMID:21444921

Excitation wavelength selection for quantitative analysis of carotenoids in tomatoes using Raman spectroscopy.

PubMed

Hara, Risa; Ishigaki, Mika; Kitahama, Yasutaka; Ozaki, Yukihiro; Genkawa, Takuma

2018-08-30

The difference in Raman spectra for different excitation wavelengths (532 nm, 785 nm, and 1064 nm) was investigated to identify an appropriate wavelength for the quantitative analysis of carotenoids in tomatoes. For the 532 nm-excited Raman spectra, the intensity of the peak assigned to the carotenoid has no correlation with carotenoid concentration, and the peak shift reflects carotenoid composition changing from lycopene to β-carotene and lutein. Thus, 532 nm-excited Raman spectra are useful for the qualitative analysis of carotenoids. For the 785 nm- and 1064 nm-excited Raman spectra, the peak intensity of the carotenoid showed good correlation with carotenoid concentration; thus, regression models for carotenoid concentration were developed using these Raman spectra and partial least squares regression. A regression model designed using the 785 nm-excited Raman spectra showed a better result than the 532 nm- and 1064 nm-excited Raman spectra. Therefore, it can be concluded that 785 nm is the most suitable excitation wavelength for the quantitative analysis of carotenoid concentration in tomatoes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantitative analysis of comparative genomic hybridization

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

Manoir, S. du; Bentz, M.; Joos, S.

1995-01-01

Comparative genomic hybridization (CGH) is a new molecular cytogenetic method for the detection of chromosomal imbalances. Following cohybridization of DNA prepared from a sample to be studied and control DNA to normal metaphase spreads, probes are detected via different fluorochromes. The ratio of the test and control fluorescence intensities along a chromosome reflects the relative copy number of segments of a chromosome in the test genome. Quantitative evaluation of CGH experiments is required for the determination of low copy changes, e.g., monosomy or trisomy, and for the definition of the breakpoints involved in unbalanced rearrangements. In this study, a programmore » for quantitation of CGH preparations is presented. This program is based on the extraction of the fluorescence ratio profile along each chromosome, followed by averaging of individual profiles from several metaphase spreads. Objective parameters critical for quantitative evaluations were tested, and the criteria for selection of suitable CGH preparations are described. The granularity of the chromosome painting and the regional inhomogeneity of fluorescence intensities in metaphase spreads proved to be crucial parameters. The coefficient of variation of the ratio value for chromosomes in balanced state (CVBS) provides a general quality criterion for CGH experiments. Different cutoff levels (thresholds) of average fluorescence ratio values were compared for their specificity and sensitivity with regard to the detection of chromosomal imbalances. 27 refs., 15 figs., 1 tab.« less

Verbal Rehearsal and Memory in Children with Closed Head Injury: A Quantitative and Qualitative Analysis.

ERIC Educational Resources Information Center

Harris, Jessica R.

1996-01-01

Nine closed head injured (CHI) children (mean age 11 years) with post-onset intervals of 7 months to 8 years were given an overt free recall task. Quantitative analysis suggested inefficient passive rehearsal strategy by severely injured subjects. Qualitative analysis revealed differences between CHI children and controls in rehearsal strategies,…

The emergence of global health partnerships as facilitators of access to medication in Africa: a narrative policy analysis.

PubMed

Ngoasong, Michael Zisuh

2009-03-01

Over the last decade global health partnerships (GHPs) have been formed to provide a better policy response to Africa's health problems. This paper uses narrative policy analysis to explain the historical processes and challenges facing national and global health policy in facilitating access to medication in African countries. An overview of the historical context of events leading to the creation of GHPs is followed by a content and context analysis of two GHPs - Roll Back Malaria partnership and the Accelerating Access Initiative. The historical narratives implicitly reflect the context in which policy decisions are produced and implemented. The deployment of GHPs in Africa reflects a convergence of the competing and conflicting narratives, in relating to strategies previously promoted by various multilateral and bilateral development agencies, international civil society organizations, and the private commercial industry to facilitate access to medication.

Medical students' and facilitators' experiences of an Early Professional Contact course: active and motivated students, strained facilitators.

PubMed

von Below, Bernhard; Hellquist, Gunilla; Rödjer, Stig; Gunnarsson, Ronny; Björkelund, Cecilia; Wahlqvist, Mats

2008-12-02

Today, medical students are introduced to patient contact, communication skills, and clinical examination in the preclinical years of the curriculum with the purpose of gaining clinical experience. These courses are often evaluated from the student perspective. Reports with an additional emphasis on the facilitator perspective are scarce. According to constructive alignment, an influential concept from research in higher education, the learning climate between students and teachers is also of great importance. In this paper, we approach the learning climate by studying both students' and facilitators' course experiences.In 2001, a new "Early Professional Contact" longitudinal strand through term 1-4, was introduced at the Sahlgrenska Academy, University of Gothenburg, Sweden. General practitioners and hospital specialists were facilitators.The aim of this study was to assess and analyse students' and clinical facilitators' experiences of the Early Professional Contact course and to illuminate facilitators' working conditions. Inspired by a Swedish adaptation of the Course Experience Questionnaire, an Early Professional Contact Questionnaire was constructed. In 2003, on the completion of the first longitudinal strand, a student and facilitator version was distributed to 86 students and 21 facilitators. In the analysis, both Chi-square and the Mann-Whitney tests were used. Sixty students (70%) and 15 facilitators (71%) completed the questionnaire. Both students and facilitators were satisfied with the course. Students reported gaining iiration for their future work as doctors along with increased confidence in meeting patients. They also reported increased motivation for biomedical studies. Differences in attitudes between facilitators and students were found. Facilitators experienced a greater workload, less reasonable demands and less support, than students. In this project, a new Early Professional Contact course was analysed from both student and facilitator

Dual-color dual-focus line-scanning FCS for quantitative analysis of receptor-ligand interactions in living specimens.

PubMed

Dörlich, René M; Chen, Qing; Niklas Hedde, Per; Schuster, Vittoria; Hippler, Marc; Wesslowski, Janine; Davidson, Gary; Nienhaus, G Ulrich

2015-05-07

Cellular communication in multi-cellular organisms is mediated to a large extent by a multitude of cell-surface receptors that bind specific ligands. An in-depth understanding of cell signaling networks requires quantitative information on ligand-receptor interactions within living systems. In principle, fluorescence correlation spectroscopy (FCS) based methods can provide such data, but live-cell applications have proven extremely challenging. Here, we have developed an integrated dual-color dual-focus line-scanning fluorescence correlation spectroscopy (2c2f lsFCS) technique that greatly facilitates live-cell and tissue experiments. Absolute ligand and receptor concentrations and their diffusion coefficients within the cell membrane can be quantified without the need to perform additional calibration experiments. We also determine the concentration of ligands diffusing in the medium outside the cell within the same experiment by using a raster image correlation spectroscopy (RICS) based analysis. We have applied this robust technique to study the interactions of two Wnt antagonists, Dickkopf1 and Dickkopf2 (Dkk1/2), to their cognate receptor, low-density-lipoprotein-receptor related protein 6 (LRP6), in the plasma membrane of living HEK293T cells. We obtained significantly lower affinities than previously reported using in vitro studies, underscoring the need to measure such data on living cells or tissues.

Quantitative Analysis of NAD Synthesis-Breakdown Fluxes.

PubMed

Liu, Ling; Su, Xiaoyang; Quinn, William J; Hui, Sheng; Krukenberg, Kristin; Frederick, David W; Redpath, Philip; Zhan, Le; Chellappa, Karthikeyani; White, Eileen; Migaud, Marie; Mitchison, Timothy J; Baur, Joseph A; Rabinowitz, Joshua D

2018-05-01

The redox cofactor nicotinamide adenine dinucleotide (NAD) plays a central role in metabolism and is a substrate for signaling enzymes including poly-ADP-ribose-polymerases (PARPs) and sirtuins. NAD concentration falls during aging, which has triggered intense interest in strategies to boost NAD levels. A limitation in understanding NAD metabolism has been reliance on concentration measurements. Here, we present isotope-tracer methods for NAD flux quantitation. In cell lines, NAD was made from nicotinamide and consumed largely by PARPs and sirtuins. In vivo, NAD was made from tryptophan selectively in the liver, which then excreted nicotinamide. NAD fluxes varied widely across tissues, with high flux in the small intestine and spleen and low flux in the skeletal muscle. Intravenous administration of nicotinamide riboside or mononucleotide delivered intact molecules to multiple tissues, but the same agents given orally were metabolized to nicotinamide in the liver. Thus, flux analysis can reveal tissue-specific NAD metabolism. Copyright © 2018 Elsevier Inc. All rights reserved.

Understanding Quantitative and Qualitative Research in Early Childhood Education.

ERIC Educational Resources Information Center

Goodwin, William L.; Goodwin, Laura D.

This book describes the research process in order to facilitate understanding of the process and its products, especially as they pertain to early childhood education. It examines both quantitative and qualitative research methods, emphasizing ways in which they can be used together to fully study a given phenomenon or topic. Chapter 1 examines…

Quantitative coronary plaque analysis predicts high-risk plaque morphology on coronary computed tomography angiography: results from the ROMICAT II trial.

PubMed

Liu, Ting; Maurovich-Horvat, Pál; Mayrhofer, Thomas; Puchner, Stefan B; Lu, Michael T; Ghemigian, Khristine; Kitslaar, Pieter H; Broersen, Alexander; Pursnani, Amit; Hoffmann, Udo; Ferencik, Maros

2018-02-01

Semi-automated software can provide quantitative assessment of atherosclerotic plaques on coronary CT angiography (CTA). The relationship between established qualitative high-risk plaque features and quantitative plaque measurements has not been studied. We analyzed the association between quantitative plaque measurements and qualitative high-risk plaque features on coronary CTA. We included 260 patients with plaque who underwent coronary CTA in the Rule Out Myocardial Infarction/Ischemia Using Computer Assisted Tomography (ROMICAT) II trial. Quantitative plaque assessment and qualitative plaque characterization were performed on a per coronary segment basis. Quantitative coronary plaque measurements included plaque volume, plaque burden, remodeling index, and diameter stenosis. In qualitative analysis, high-risk plaque was present if positive remodeling, low CT attenuation plaque, napkin-ring sign or spotty calcium were detected. Univariable and multivariable logistic regression analyses were performed to assess the association between quantitative and qualitative high-risk plaque assessment. Among 888 segments with coronary plaque, high-risk plaque was present in 391 (44.0%) segments by qualitative analysis. In quantitative analysis, segments with high-risk plaque had higher total plaque volume, low CT attenuation plaque volume, plaque burden and remodeling index. Quantitatively assessed low CT attenuation plaque volume (odds ratio 1.12 per 1 mm 3 , 95% CI 1.04-1.21), positive remodeling (odds ratio 1.25 per 0.1, 95% CI 1.10-1.41) and plaque burden (odds ratio 1.53 per 0.1, 95% CI 1.08-2.16) were associated with high-risk plaque. Quantitative coronary plaque characteristics (low CT attenuation plaque volume, positive remodeling and plaque burden) measured by semi-automated software correlated with qualitative assessment of high-risk plaque features.

Preparing palliative home care nurses to act as facilitators for physicians' learning: Evaluation of a training programme.

PubMed

Pype, Peter; Mertens, Fien; Wens, Johan; Stes, Ann; Van den Eynden, Bart; Deveugele, Myriam

2015-05-01

Palliative care requires a multidisciplinary care team. General practitioners often ask specialised palliative home care teams for support. Working with specialised nurses offers learning opportunities, also called workplace learning. This can be enhanced by the presence of a learning facilitator. To describe the development and evaluation of a training programme for nurses in primary care. The programme aimed to prepare palliative home care team nurses to act as facilitators for general practitioners' workplace learning. A one-group post-test only design (quantitative) and semi-structured interviews (qualitative) were used. A multifaceted train-the-trainer programme was designed. Evaluation was done through assignments with individual feedback, summative assessment through videotaped encounters with simulation-physicians and individual interviews after a period of practice implementation. A total of 35 nurses followed the programme. The overall satisfaction was high. Homework assignments interfered with the practice workload but showed to be fundamental in translating theory into practice. Median score on the summative assessment was 7 out of 14 with range 1-13. Interviews revealed some aspects of the training (e.g. incident analysis) to be too difficult for implementation or to be in conflict with personal preferences (focus on patient care instead of facilitating general practitioners' learning). Training palliative home care team nurses as facilitator of general practitioners' workplace learning is a feasible but complex intervention. Personal characteristics, interpersonal relationships and contextual variables have to be taken into account. Training expert palliative care nurses to facilitate general practitioners' workplace learning requires careful and individualised mentoring. © The Author(s) 2014.

[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.

Quantitative Analysis of Venus Radar Backscatter Data in ArcGIS

NASA Technical Reports Server (NTRS)

Long, S. M.; Grosfils, E. B.

2005-01-01

Ongoing mapping of the Ganiki Planitia (V14) quadrangle of Venus and definition of material units has involved an integrated but qualitative analysis of Magellan radar backscatter images and topography using standard geomorphological mapping techniques. However, such analyses do not take full advantage of the quantitative information contained within the images. Analysis of the backscatter coefficient allows a much more rigorous statistical comparison between mapped units, permitting first order selfsimilarity tests of geographically separated materials assigned identical geomorphological labels. Such analyses cannot be performed directly on pixel (DN) values from Magellan backscatter images, because the pixels are scaled to the Muhleman law for radar echoes on Venus and are not corrected for latitudinal variations in incidence angle. Therefore, DN values must be converted based on pixel latitude back to their backscatter coefficient values before accurate statistical analysis can occur. Here we present a method for performing the conversions and analysis of Magellan backscatter data using commonly available ArcGIS software and illustrate the advantages of the process for geological mapping.

Quantitative assessment of skin, hair, and iris variation in a diverse sample of individuals and associated genetic variation.

PubMed

Norton, Heather L; Edwards, Melissa; Krithika, S; Johnson, Monique; Werren, Elizabeth A; Parra, Esteban J

2016-08-01

The main goals of this study are to 1) quantitatively measure skin, hair, and iris pigmentation in a diverse sample of individuals, 2) describe variation within and between these samples, and 3) demonstrate how quantitative measures can facilitate genotype-phenotype association tests. We quantitatively characterize skin, hair, and iris pigmentation using the Melanin (M) Index (skin) and CIELab values (hair) in 1,450 individuals who self-identify as African American, East Asian, European, Hispanic, or South Asian. We also quantify iris pigmentation in a subset of these individuals using CIELab values from high-resolution iris photographs. We compare mean skin M index and hair and iris CIELab values among populations using ANOVA and MANOVA respectively and test for genotype-phenotype associations in the European sample. All five populations are significantly different for skin (P <2 × 10(-16) ) and hair color (P <2 × 10(-16) ). Our quantitative analysis of iris and hair pigmentation reinforces the continuous, rather than discrete, nature of these traits. We confirm the association of three loci (rs16891982, rs12203592, and rs12913832) with skin pigmentation and four loci (rs12913832, rs12203592, rs12896399, and rs16891982) with hair pigmentation. Interestingly, the derived rs12203592 T allele located within the IRF4 gene is associated with lighter skin but darker hair color. The quantitative methods used here provide a fine-scale assessment of pigmentation phenotype and facilitate genotype-phenotype associations, even with relatively small sample sizes. This represents an important expansion of current investigations into pigmentation phenotype and associated genetic variation by including non-European and admixed populations. Am J Phys Anthropol 160:570-581, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

[Evaluation on methodological problems in reports concerning quantitative analysis of syndrome differentiation of diabetes mellitus].

PubMed

Chen, Bi-Cang; Wu, Qiu-Ying; Xiang, Cheng-Bin; Zhou, Yi; Guo, Ling-Xiang; Zhao, Neng-Jiang; Yang, Shu-Yu

2006-01-01

To evaluate the quality of reports published in recent 10 years in China about quantitative analysis of syndrome differentiation for diabetes mellitus (DM) in order to explore the methodological problems in these reports and find possible solutions. The main medical literature databases in China were searched. Thirty-one articles were included and evaluated by the principles of clinical epidemiology. There were many mistakes and deficiencies in these articles, such as clinical trial designs, diagnosis criteria for DM, standards of syndrome differentiation of DM, case inclusive and exclusive criteria, sample size and estimation, data comparability and statistical methods. It is necessary and important to improve the quality of reports concerning quantitative analysis of syndrome differentiation of DM in light of the principles of clinical epidemiology.

[Influence of sample surface roughness on mathematical model of NIR quantitative analysis of wood density].

PubMed

Huang, An-Min; Fei, Ben-Hua; Jiang, Ze-Hui; Hse, Chung-Yun

2007-09-01

Near infrared spectroscopy is widely used as a quantitative method, and the main multivariate techniques consist of regression methods used to build prediction models, however, the accuracy of analysis results will be affected by many factors. In the present paper, the influence of different sample roughness on the mathematical model of NIR quantitative analysis of wood density was studied. The result of experiments showed that if the roughness of predicted samples was consistent with that of calibrated samples, the result was good, otherwise the error would be much higher. The roughness-mixed model was more flexible and adaptable to different sample roughness. The prediction ability of the roughness-mixed model was much better than that of the single-roughness model.

Applying Quantitative Approaches to the Formative Evaluation of Antismoking Campaign Messages

PubMed Central

Parvanta, Sarah; Gibson, Laura; Forquer, Heather; Shapiro-Luft, Dina; Dean, Lorraine; Freres, Derek; Lerman, Caryn; Mallya, Giridhar; Moldovan-Johnson, Mihaela; Tan, Andy; Cappella, Joseph; Hornik, Robert

2014-01-01

This article shares an in-depth summary of a formative evaluation that used quantitative data to inform the development and selection of promotional ads for the antismoking communication component of a social marketing campaign. A foundational survey provided cross-sectional data to identify beliefs about quitting smoking that campaign messages should target, as well as beliefs to avoid. Pretesting draft ads against quantitative indicators of message effectiveness further facilitated the selection and rejection of final campaign ads. Finally, we consider lessons learned from the process of balancing quantitative methods and judgment to make formative decisions about more and less promising persuasive messages for campaigns. PMID:24817829

Facilitation of an end-of-life care programme into practice within UK nursing care homes: A mixed-methods study.

PubMed

Kinley, Julie; Preston, Nancy; Froggatt, Katherine

2018-06-01

The predicted demographic changes internationally have implications for the nature of care that older people receive and place of care as they age. Healthcare policy now promotes the implementation of end-of-life care interventions to improve care delivery within different settings. The Gold Standards Framework in Care Homes (GSFCH) programme is one end-of-life care initiative recommended by the English Department of Health. Only a small number of care homes that start the programme complete it, which raises questions about the implementation process. To identify the type, role, impact and cost of facilitation when implementing the GSFCH programme into nursing care home practice. A mixed-methods study. Nursing care homes in south-east England. Staff from 38 nursing care homes undertaking the GSFCH programme. Staff in 24 nursing care homes received high facilitation. Of those, 12 also received action learning. The remaining 14 nursing care homes received usual local facilitation of the GSFCH programme. Study data were collected from staff employed within nursing care homes (home managers and GSFCH coordinators) and external facilitators associated with the homes. Data collection included interviews, surveys and facilitator activity logs. Following separate quantitative (descriptive statistics) and qualitative (template) data analysis the data sets were integrated by 'following a thread'. This paper reports study data in relation to facilitation. Three facilitation approaches were provided to nursing home staff when implementing the GSFCH programme: 'fitting it in' facilitation; 'as requested' facilitation; and 'being present' facilitation. 'Being present' facilitation most effectively enabled the completion of the programme, through to accreditation. However, it was not sufficient to just be present. Without mastery and commitment, from all participants, including the external facilitator, learning and initiation of change failed to occur. Implementation of the

Teaching Fundamental Skills in Microsoft Excel to First-Year Students in Quantitative Analysis

ERIC Educational Resources Information Center

Rubin, Samuel J.; Abrams, Binyomin

2015-01-01

Despite their technological savvy, most students entering university lack the necessary computer skills to succeed in a quantitative analysis course, in which they are often expected to input, analyze, and plot results of experiments without any previous formal education in Microsoft Excel or similar programs. This lack of formal education results…

Using multiple PCR and CE with chemiluminescence detection for simultaneous qualitative and quantitative analysis of genetically modified organism.

PubMed

Guo, Longhua; Qiu, Bin; Chi, Yuwu; Chen, Guonan

2008-09-01

In this paper, an ultrasensitive CE-CL detection system coupled with a novel double-on-column coaxial flow detection interface was developed for the detection of PCR products. A reliable procedure based on this system had been demonstrated for qualitative and quantitative analysis of genetically modified organism-the detection of Roundup Ready Soy (RRS) samples was presented as an example. The promoter, terminator, function and two reference genes of RRS were amplified with multiplex PCR simultaneously. After that, the multiplex PCR products were labeled with acridinium ester at the 5'-terminal through an amino modification and then analyzed by the proposed CE-CL system. Reproducibility of analysis times and peak heights for the CE-CL analysis were determined to be better than 0.91 and 3.07% (RSD, n=15), respectively, for three consecutive days. It was shown that this method could accurately and qualitatively detect RRS standards and the simulative samples. The evaluation in terms of quantitative analysis of RRS provided by this new method was confirmed by comparing our assay results with those of the standard real-time quantitative PCR (RT-QPCR) using SYBR Green I dyes. The results showed a good coherence between the two methods. This approach demonstrated the possibility for accurate qualitative and quantitative detection of GM plants in a single run.

Testicular Dysgenesis Syndrome and the Estrogen Hypothesis: A Quantitative Meta-Analysis

PubMed Central

Martin, Olwenn V.; Shialis, Tassos; Lester, John N.; Scrimshaw, Mark D.; Boobis, Alan R.; Voulvoulis, Nikolaos

2008-01-01

Background Male reproductive tract abnormalities such as hypospadias and cryptorchidism, and testicular cancer have been proposed to comprise a common syndrome together with impaired spermatogenesis with a common etiology resulting from the disruption of gonadal development during fetal life, the testicular dysgenesis syndrome (TDS). The hypothesis that in utero exposure to estrogenic agents could induce these disorders was first proposed in 1993. The only quantitative summary estimate of the association between prenatal exposure to estrogenic agents and testicular cancer was published over 10 years ago, and other systematic reviews of the association between estrogenic compounds, other than the potent pharmaceutical estrogen diethylstilbestrol (DES), and TDS end points have remained inconclusive. Objectives We conducted a quantitative meta-analysis of the association between the end points related to TDS and prenatal exposure to estrogenic agents. Inclusion in this analysis was based on mechanistic criteria, and the plausibility of an estrogen receptor (ER)-α–mediated mode of action was specifically explored. Results We included in this meta-analysis eight studies investigating the etiology of hypospadias and/or cryptorchidism that had not been identified in previous systematic reviews. Four additional studies of pharmaceutical estrogens yielded a statistically significant updated summary estimate for testicular cancer. Conclusions The doubling of the risk ratios for all three end points investigated after DES exposure is consistent with a shared etiology and the TDS hypothesis but does not constitute evidence of an estrogenic mode of action. Results of the subset analyses point to the existence of unidentified sources of heterogeneity between studies or within the study population. PMID:18288311

Testicular dysgenesis syndrome and the estrogen hypothesis: a quantitative meta-analysis.

PubMed

Martin, Olwenn V; Shialis, Tassos; Lester, John N; Scrimshaw, Mark D; Boobis, Alan R; Voulvoulis, Nikolaos

2008-02-01

Male reproductive tract abnormalities such as hypospadias and cryptorchidism, and testicular cancer have been proposed to comprise a common syndrome together with impaired spermatogenesis with a common etiology resulting from the disruption of gonadal development during fetal life, the testicular dysgenesis syndrome (TDS). The hypothesis that in utero exposure to estrogenic agents could induce these disorders was first proposed in 1993. The only quantitative summary estimate of the association between prenatal exposure to estrogenic agents and testicular cancer was published over 10 years ago, and other systematic reviews of the association between estrogenic compounds, other than the potent pharmaceutical estrogen diethylstilbestrol (DES), and TDS end points have remained inconclusive. We conducted a quantitative meta-analysis of the association between the end points related to TDS and prenatal exposure to estrogenic agents. Inclusion in this analysis was based on mechanistic criteria, and the plausibility of an estrogen receptor (ER)-alpha-mediated mode of action was specifically explored. We included in this meta-analysis eight studies investigating the etiology of hypospadias and/or cryptorchidism that had not been identified in previous systematic reviews. Four additional studies of pharmaceutical estrogens yielded a statistically significant updated summary estimate for testicular cancer. The doubling of the risk ratios for all three end points investigated after DES exposure is consistent with a shared etiology and the TDS hypothesis but does not constitute evidence of an estrogenic mode of action. Results of the subset analyses point to the existence of unidentified sources of heterogeneity between studies or within the study population.

Detection, monitoring, and quantitative analysis of wildfires with the BIRD satellite

NASA Astrophysics Data System (ADS)

Oertel, Dieter A.; Briess, Klaus; Lorenz, Eckehard; Skrbek, Wolfgang; Zhukov, Boris

2004-02-01

Increasing concern about environment and interest to avoid losses led to growing demands on space borne fire detection, monitoring and quantitative parameter estimation of wildfires. The global change research community intends to quantify the amount of gaseous and particulate matter emitted from vegetation fires, peat fires and coal seam fires. The DLR Institute of Space Sensor Technology and Planetary Exploration (Berlin-Adlershof) developed a small satellite called BIRD (Bi-spectral Infrared Detection) which carries a sensor package specially designed for fire detection. BIRD was launched as a piggy-back satellite on October 22, 2001 with ISRO"s Polar Satellite Launch Vehicle (PSLV). It is circling the Earth on a polar and sun-synchronous orbit at an altitude of 572 km and it is providing unique data for detailed analysis of high temperature events on Earth surface. The BIRD sensor package is dedicated for high resolution and reliable fire recognition. Active fire analysis is possible in the sub-pixel domain. The leading channel for fire detection and monitoring is the MIR channel at 3.8 μm. The rejection of false alarms is based on procedures using MIR/NIR (Middle Infra Red/Near Infra Red) and MIR/TIR (Middle Infra Red/Thermal Infra Red) radiance ratio thresholds. Unique results of BIRD wildfire detection and analysis over fire prone regions in Australia and Asia will be presented. BIRD successfully demonstrates innovative fire recognition technology for small satellites which permit to retrieve quantitative characteristics of active burning wildfires, such as the equivalent fire temperature, fire area, radiative energy release, fire front length and fire front strength.

Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome

PubMed Central

Chaudhuri, Roy R.; Yu, Lu; Kanji, Alpa; Perkins, Timothy T.; Gardner, Paul P.; Choudhary, Jyoti; Maskell, Duncan J.

2011-01-01

Campylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community. PMID:21816880

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. PMID:24861615

‘In the Moment’: An Analysis of Facilitator Impact During a Quality Improvement Process

PubMed Central

Shaw, Erik; Looney, Anna; Chase, Sabrina; Navalekar, Rohini; Stello, Brian; Lontok, Oliver; Crabtree, Benjamin

2010-01-01

Facilitators frequently act ‘in the moment’ – deciding if, when and how to intervene into group process discussions. This paper offers a unique look at how facilitators impacted eleven primary care teams engaged in a 12-week quality improvement (QI) process. Participating in a federally funded QI trial, primary care practices in New Jersey and Pennsylvania formed practice-based teams comprised of physicians, nurses, administrative staff, and patients. External facilitators met with each team to help them identify and implement changes aimed at improving the organization, work relationships, office functions, and patient care. Audio-recordings of the meetings and descriptive field notes were collected. These qualitative data provided information on how facilitators acted ‘in the moment’ and how their interventions impacted group processes over time. Our findings reveal that facilitators impacted groups in multiple ways throughout the QI process, rather than through a linear progression of stages or events. We present five case examples that show what acting ‘in the moment’ looked like during the QI meetings and how these facilitator actions/interventions impacted the primary care teams. These accounts provide practical lessons learned and insights into effective facilitation that may encourage others in their own facilitation work and offer beneficial strategies to facilitators in other contexts. PMID:22557936

Tau-U: A Quantitative Approach for Analysis of Single-Case Experimental Data in Aphasia.

PubMed

Lee, Jaime B; Cherney, Leora R

2018-03-01

Tau-U is a quantitative approach for analyzing single-case experimental design (SCED) data. It combines nonoverlap between phases with intervention phase trend and can correct for a baseline trend (Parker, Vannest, & Davis, 2011). We demonstrate the utility of Tau-U by comparing it with the standardized mean difference approach (Busk & Serlin, 1992) that is widely reported within the aphasia SCED literature. Repeated writing measures from 3 participants with chronic aphasia who received computer-based writing treatment are analyzed visually and quantitatively using both Tau-U and the standardized mean difference approach. Visual analysis alone was insufficient for determining an effect between the intervention and writing improvement. The standardized mean difference yielded effect sizes ranging from 4.18 to 26.72 for trained items and 1.25 to 3.20 for untrained items. Tau-U yielded significant (p < .05) effect sizes for 2 of 3 participants for trained probes and 1 of 3 participants for untrained probes. A baseline trend correction was applied to data from 2 of 3 participants. Tau-U has the unique advantage of allowing for the correction of an undesirable baseline trend. Although further study is needed, Tau-U shows promise as a quantitative approach to augment visual analysis of SCED data in aphasia.

Power Analysis of Artificial Selection Experiments Using Efficient Whole Genome Simulation of Quantitative Traits

PubMed Central

Kessner, Darren; Novembre, John

2015-01-01

Evolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTL) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTL under selection affects the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50–100%) can be explained by detected QTL in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates. PMID:25672748

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

PubMed

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

2008-02-01

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

Facilitating LOS Debriefings: A Training Manual

NASA Technical Reports Server (NTRS)

McDonnell, Lori K.; Jobe, Kimberly K.; Dismukes, R. Key

1997-01-01

This manual is a practical guide to help airline instructors effectively facilitate debriefings of Line Oriented Simulations (LOS). It is based on a recently completed study of Line Oriented Flight Training (LOFT) debriefings at several U.S. airlines. This manual presents specific facilitation tools instructors can use to achieve debriefing objectives. The approach of the manual is to be flexible so it can be tailored to the individual needs of each airline. Part One clarifies the purpose and objectives of facilitation in the LOS setting. Part Two provides recommendations for clarifying roles and expectations and presents a model for organizing discussion. Part Tree suggests techniques for eliciting active crew participation and in-depth analysis and evaluation. Finally, in Part Four, these techniques are organized according to the facilitation model. Examples of how to effectively use the techniques are provided throughout, including strategies to try when the debriefing objectives are not being fully achieved.

Optimization of homonuclear 2D NMR for fast quantitative analysis: application to tropine-nortropine mixtures.

PubMed

Giraudeau, Patrick; Guignard, Nadia; Hillion, Emilie; Baguet, Evelyne; Akoka, Serge

2007-03-12

Quantitative analysis by (1)H NMR is often hampered by heavily overlapping signals that may occur for complex mixtures, especially those containing similar compounds. Bidimensional homonuclear NMR spectroscopy can overcome this difficulty. A thorough review of acquisition and post-processing parameters was carried out to obtain accurate and precise, quantitative 2D J-resolved and DQF-COSY spectra in a much reduced time, thus limiting the spectrometer instabilities in the course of time. The number of t(1) increments was reduced as much as possible, and standard deviation was improved by optimization of spectral width, number of transients, phase cycling and apodization function. Localized polynomial baseline corrections were applied to the relevant chemical shift areas. Our method was applied to tropine-nortropine mixtures. Quantitative J-resolved spectra were obtained in less than 3 min and quantitative DQF-COSY spectra in 12 min, with an accuracy of 3% for J-spectroscopy and 2% for DQF-COSY, and a standard deviation smaller than 1%.

Combining qualitative and quantitative research within mixed method research designs: a methodological review.

PubMed

Östlund, Ulrika; Kidd, Lisa; Wengström, Yvonne; Rowa-Dewar, Neneh

2011-03-01

It has been argued that mixed methods research can be useful in nursing and health science because of the complexity of the phenomena studied. However, the integration of qualitative and quantitative approaches continues to be one of much debate and there is a need for a rigorous framework for designing and interpreting mixed methods research. This paper explores the analytical approaches (i.e. parallel, concurrent or sequential) used in mixed methods studies within healthcare and exemplifies the use of triangulation as a methodological metaphor for drawing inferences from qualitative and quantitative findings originating from such analyses. This review of the literature used systematic principles in searching CINAHL, Medline and PsycINFO for healthcare research studies which employed a mixed methods approach and were published in the English language between January 1999 and September 2009. In total, 168 studies were included in the results. Most studies originated in the United States of America (USA), the United Kingdom (UK) and Canada. The analytic approach most widely used was parallel data analysis. A number of studies used sequential data analysis; far fewer studies employed concurrent data analysis. Very few of these studies clearly articulated the purpose for using a mixed methods design. The use of the methodological metaphor of triangulation on convergent, complementary, and divergent results from mixed methods studies is exemplified and an example of developing theory from such data is provided. A trend for conducting parallel data analysis on quantitative and qualitative data in mixed methods healthcare research has been identified in the studies included in this review. Using triangulation as a methodological metaphor can facilitate the integration of qualitative and quantitative findings, help researchers to clarify their theoretical propositions and the basis of their results. This can offer a better understanding of the links between theory and

High-throughput analysis of the protein sequence-stability landscape using a quantitative "yeast surface two-hybrid" system and fragment reconstitution

PubMed Central

Dutta, Sanjib; Koide, Akiko; Koide, Shohei

2008-01-01

Stability evaluation of many mutants can lead to a better understanding of the sequence determinants of a structural motif and of factors governing protein stability and protein evolution. The traditional biophysical analysis of protein stability is low throughput, limiting our ability to widely explore the sequence space in a quantitative manner. In this study, we have developed a high-throughput library screening method for quantifying stability changes, which is based on protein fragment reconstitution and yeast surface display. Our method exploits the thermodynamic linkage between protein stability and fragment reconstitution and the ability of the yeast surface display technique to quantitatively evaluate protein-protein interactions. The method was applied to a fibronectin type III (FN3) domain. Characterization of fragment reconstitution was facilitated by the co-expression of two FN3 fragments, thus establishing a "yeast surface two-hybrid" method. Importantly, our method does not rely on competition between clones and thus eliminates a common limitation of high-throughput selection methods in which the most stable variants are predominantly recovered. Thus, it allows for the isolation of sequences that exhibits a desired level of stability. We identified over one hundred unique sequences for a β-bulge motif, which was significantly more informative than natural sequences of the FN3 family in revealing the sequence determinants for the β-bulge. Our method provides a powerful means to rapidly assess stability of many variants, to systematically assess contribution of different factors to protein stability and to enhance protein stability. PMID:18674545

Quantitative analysis of global veterinary human resources.

PubMed

Kouba, V

2003-12-01

This analysis of global veterinary personnel was based on the available quantitative data reported by individual countries to international organisations. The analysis begins with a time series of globally reported numbers of veterinarians, starting in the year 1959 (140,391). In 2000 this number reached 691,379. Of this total, 27.77% of veterinarians were working as government officials, 15.38% were working in laboratories, universities and training institutions and 46.33% were working as private practitioners. The ratio of veterinarians to technicians was 1:0.63. The global average of resources serviced by each veterinarian was as follows: 8,760 inhabitants; 189 km2 of land area and 20 km2 of arable land; 1,925 cattle, 242 buffaloes, 87 horses, 1,309 pigs, 1,533 sheep and 20,714 chickens; in abattoirs: 401 slaughtered cattle, 699 slaughtered sheep and 1,674 slaughtered pigs; the production of 336 tonnes (t) of meat, 708 t cow milk and 74 t hen eggs; in international trade: 12 cattle, 23 sheep, 22 pigs, 1 horse, 1,086 chickens, 33 t meat and meat products; 2,289 units of livestock (50 minutes of annual veterinary working time for each unit). These averages were also analysed according to employment categories. The author also discusses factors influencing veterinary personnel analyses and planning.

Quantitative Analysis of the Usage of the COSMOS Science Education Portal

NASA Astrophysics Data System (ADS)

Sotiriou, Sofoklis; Bogner, Franz X.; Neofotistos, George

2011-08-01

A quantitative method of mapping the web usage of an innovative educational portal is applied to analyze the behaviour of users of the COSMOS Science Education Portal. The COSMOS Portal contains user-generated resources (that are uploaded by its users). It has been designed to support a science teacher's search, retrieval and access to both, scientific and educational resources. It also aims to introduce in and familiarize teachers with an innovative methodology for designing, expressing and representing educational practices in a commonly understandable way through the use of user-friendly authoring tools that are available through the portal. As a new science education portal that includes user-generated content, the COSMOS Portal encounters the well-known "new product/service challenge": to convince the users to use its tools, which facilitate quite fast lesson planning and lesson preparation activities. To respond to this challenge, the COSMOS Portal operators implemented a validation process by analyzing the usage data of the portal in a 10 month time-period. The data analyzed comprised: (a) the temporal evolution of the number of contributors and the amount of content uploaded to the COSMOS Portal; (b) the number of portal visitors (categorized as all-visitors, new-visitors, and returning-visitors) and (c) visitor loyalty parameters (such as page-views; pages/visit; average time on site; depth of visit; length of visit). The data is augmented with data associated with the usage context (e.g. the time of day when most of the activities in the portal take place). The quantitative results indicate that the exponential growth of the contributors to the COSMOS Portal is followed by an exponential growth of the uploaded content. Furthermore, the web usage statistics demonstrate significant changes in users' behaviour during the period under study, with returning visitors using the COSMOS Portal more frequently, mainly for lesson planning and preparation (in the

A Reproducible Computerized Method for Quantitation of Capillary Density using Nailfold Capillaroscopy.

PubMed

Cheng, Cynthia; Lee, Chadd W; Daskalakis, Constantine

2015-10-27

Capillaroscopy is a non-invasive, efficient, relatively inexpensive and easy to learn methodology for directly visualizing the microcirculation. The capillaroscopy technique can provide insight into a patient's microvascular health, leading to a variety of potentially valuable dermatologic, ophthalmologic, rheumatologic and cardiovascular clinical applications. In addition, tumor growth may be dependent on angiogenesis, which can be quantitated by measuring microvessel density within the tumor. However, there is currently little to no standardization of techniques, and only one publication to date reports the reliability of a currently available, complex computer based algorithms for quantitating capillaroscopy data.(1) This paper describes a new, simpler, reliable, standardized capillary counting algorithm for quantitating nailfold capillaroscopy data. A simple, reproducible computerized capillaroscopy algorithm such as this would facilitate more widespread use of the technique among researchers and clinicians. Many researchers currently analyze capillaroscopy images by hand, promoting user fatigue and subjectivity of the results. This paper describes a novel, easy-to-use automated image processing algorithm in addition to a reproducible, semi-automated counting algorithm. This algorithm enables analysis of images in minutes while reducing subjectivity; only a minimal amount of training time (in our experience, less than 1 hr) is needed to learn the technique.

A Reproducible Computerized Method for Quantitation of Capillary Density using Nailfold Capillaroscopy

PubMed Central

Daskalakis, Constantine

2015-01-01

Capillaroscopy is a non-invasive, efficient, relatively inexpensive and easy to learn methodology for directly visualizing the microcirculation. The capillaroscopy technique can provide insight into a patient’s microvascular health, leading to a variety of potentially valuable dermatologic, ophthalmologic, rheumatologic and cardiovascular clinical applications. In addition, tumor growth may be dependent on angiogenesis, which can be quantitated by measuring microvessel density within the tumor. However, there is currently little to no standardization of techniques, and only one publication to date reports the reliability of a currently available, complex computer based algorithms for quantitating capillaroscopy data.1 This paper describes a new, simpler, reliable, standardized capillary counting algorithm for quantitating nailfold capillaroscopy data. A simple, reproducible computerized capillaroscopy algorithm such as this would facilitate more widespread use of the technique among researchers and clinicians. Many researchers currently analyze capillaroscopy images by hand, promoting user fatigue and subjectivity of the results. This paper describes a novel, easy-to-use automated image processing algorithm in addition to a reproducible, semi-automated counting algorithm. This algorithm enables analysis of images in minutes while reducing subjectivity; only a minimal amount of training time (in our experience, less than 1 hr) is needed to learn the technique. PMID:26554744

A Quantitative Features Analysis of Recommended No- and Low-Cost Preschool E-Books

ERIC Educational Resources Information Center

Parette, Howard P.; Blum, Craig; Luthin, Katie

2015-01-01

In recent years, recommended e-books have drawn increasing attention from early childhood education professionals. This study applied a quantitative descriptive features analysis of cost (n = 70) and no-cost (n = 60) e-books recommended by the Texas Computer Education Association. While t tests revealed no statistically significant differences…

Screening hypochromism (sieve effect) in red blood cells: a quantitative analysis

PubMed Central

Razi Naqvi, K.

2014-01-01

Multiwavelength UV-visible spectroscopy, Kramers-Kronig analysis, and several other experimental and theoretical tools have been applied over the last several decades to fathom absorption and scattering of light by suspensions of micron-sized pigmented particles, including red blood cells, but a satisfactory quantitative analysis of the difference between the absorption spectra of suspension of intact and lysed red blood cells is still lacking. It is stressed that such a comparison is meaningful only if the pertinent spectra are free from, or have been corrected for, scattering losses, and it is shown that Duysens’ theory can, whereas that of Vekshin cannot, account satisfactorily for the observed hypochromism of suspensions of red blood cells. PMID:24761307

Screening hypochromism (sieve effect) in red blood cells: a quantitative analysis.

PubMed

Razi Naqvi, K

2014-04-01

Multiwavelength UV-visible spectroscopy, Kramers-Kronig analysis, and several other experimental and theoretical tools have been applied over the last several decades to fathom absorption and scattering of light by suspensions of micron-sized pigmented particles, including red blood cells, but a satisfactory quantitative analysis of the difference between the absorption spectra of suspension of intact and lysed red blood cells is still lacking. It is stressed that such a comparison is meaningful only if the pertinent spectra are free from, or have been corrected for, scattering losses, and it is shown that Duysens' theory can, whereas that of Vekshin cannot, account satisfactorily for the observed hypochromism of suspensions of red blood cells.

Argumentation: A Methodology to Facilitate Critical Thinking.

PubMed

Makhene, Agnes

2017-06-20

Caring is a difficult nursing activity that involves a complex nature of a human being in need of complex decision-making and problem solving through the critical thinking process. It is mandatory that critical thinking is facilitated in general and in nursing education particularly in order to render care in diverse multicultural patient care settings. This paper aims to describe how argumentation can be used to facilitate critical thinking in learners. A qualitative, exploratory and descriptive design that is contextual was used. Purposive sampling method was used to draw a sample and Miles and Huberman methodology of qualitative analysis was used to analyse data. Lincoln and Guba's strategies were employed to ensure trustworthiness, while Dhai and McQuoid-Mason's principles of ethical consideration were used. Following data analysis the findings were integrated within literature which culminated into the formulation of guidelines that can be followed when using argumentation as a methodology to facilitate critical thinking.

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

PubMed

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

2013-10-02

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

Quantitative analysis of Al-Si alloy using calibration free laser induced breakdown spectroscopy (CF-LIBS)

NASA Astrophysics Data System (ADS)

Shakeel, Hira; Haq, S. U.; Aisha, Ghulam; Nadeem, Ali

2017-06-01

The quantitative analysis of the standard aluminum-silicon alloy has been performed using calibration free laser induced breakdown spectroscopy (CF-LIBS). The plasma was produced using the fundamental harmonic (1064 nm) of the Nd: YAG laser and the emission spectra were recorded at 3.5 μs detector gate delay. The qualitative analysis of the emission spectra confirms the presence of Mg, Al, Si, Ti, Mn, Fe, Ni, Cu, Zn, Sn, and Pb in the alloy. The background subtracted and self-absorption corrected emission spectra were used for the estimation of plasma temperature as 10 100 ± 300 K. The plasma temperature and self-absorption corrected emission lines of each element have been used for the determination of concentration of each species present in the alloy. The use of corrected emission intensities and accurate evaluation of plasma temperature yield reliable quantitative analysis up to a maximum 2.2% deviation from reference sample concentration.

Quantitative trace analysis of complex mixtures using SABRE hyperpolarization.

PubMed

Eshuis, Nan; van Weerdenburg, Bram J A; Feiters, Martin C; Rutjes, Floris P J T; Wijmenga, Sybren S; Tessari, Marco

2015-01-26

Signal amplification by reversible exchange (SABRE) is an emerging nuclear spin hyperpolarization technique that strongly enhances NMR signals of small molecules in solution. However, such signal enhancements have never been exploited for concentration determination, as the efficiency of SABRE can strongly vary between different substrates or even between nuclear spins in the same molecule. The first application of SABRE for the quantitative analysis of a complex mixture is now reported. Despite the inherent complexity of the system under investigation, which involves thousands of competing binding equilibria, analytes at concentrations in the low micromolar range could be quantified from single-scan SABRE spectra using a standard-addition approach. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diagnostic value of (99m)Tc-3PRGD2 scintimammography for differentiation of malignant from benign breast lesions: Comparison of visual and semi-quantitative analysis.

PubMed

Chen, Qianqian; Xie, Qian; Zhao, Min; Chen, Bin; Gao, Shi; Zhang, Haishan; Xing, Hua; Ma, Qingjie

2015-01-01