Quantification of miRNAs by a simple and specific qPCR method

DEFF Research Database (Denmark)

Cirera Salicio, Susanna; Busk, Peter K.

2014-01-01

MicroRNAs (miRNAs) are powerful regulators of gene expression at posttranscriptional level and play important roles in many biological processes and in disease. The rapid pace of the emerging field of miRNAs has opened new avenues for development of techniques to quantitatively determine mi...... in miRNA quantification. Furthermore, the method is easy to perform with common laboratory reagents, which allows miRNA quantification at low cost....

A fast and robust hepatocyte quantification algorithm including vein processing

Directory of Open Access Journals (Sweden)

Homeyer André

2010-03-01

Full Text Available Abstract Background Quantification of different types of cells is often needed for analysis of histological images. In our project, we compute the relative number of proliferating hepatocytes for the evaluation of the regeneration process after partial hepatectomy in normal rat livers. Results Our presented automatic approach for hepatocyte (HC quantification is suitable for the analysis of an entire digitized histological section given in form of a series of images. It is the main part of an automatic hepatocyte quantification tool that allows for the computation of the ratio between the number of proliferating HC-nuclei and the total number of all HC-nuclei for a series of images in one processing run. The processing pipeline allows us to obtain desired and valuable results for a wide range of images with different properties without additional parameter adjustment. Comparing the obtained segmentation results with a manually retrieved segmentation mask which is considered to be the ground truth, we achieve results with sensitivity above 90% and false positive fraction below 15%. Conclusions The proposed automatic procedure gives results with high sensitivity and low false positive fraction and can be applied to process entire stained sections.

Direct qPCR quantification using the Quantifiler(®) Trio DNA quantification kit.

Science.gov (United States)

Liu, Jason Yingjie

2014-11-01

The effectiveness of a direct quantification assay is essential to the adoption of the combined direct quantification/direct STR workflow. In this paper, the feasibility of using the Quantifiler(®) Trio DNA quantification kit for the direct quantification of forensic casework samples was investigated. Both low-level touch DNA samples and blood samples were collected on PE swabs and quantified directly. The increased sensitivity of the Quantifiler(®) Trio kit enabled the detection of less than 10pg of DNA in unprocessed touch samples and also minimizes the stochastic effect experienced by different targets in the same sample. The DNA quantity information obtained from a direct quantification assay using the Quantifiler(®) Trio kit can also be used to accurately estimate the optimal input DNA quantity for a direct STR amplification reaction. The correlation between the direct quantification results (Quantifiler(®) Trio kit) and the direct STR results (GlobalFiler™ PCR amplification kit(*)) for low-level touch DNA samples indicates that direct quantification using the Quantifiler(®) Trio DNA quantification kit is more reliable than the Quantifiler(®) Duo DNA quantification kit for predicting the STR results of unprocessed touch DNA samples containing less than 10pg of DNA. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Predicting medical professionals' intention to allow family presence during resuscitation: A cross sectional survey.

Science.gov (United States)

Lai, Meng-Kuan; Aritejo, Bayu Aji; Tang, Jing-Shia; Chen, Chien-Liang; Chuang, Chia-Chang

2017-05-01

Family presence during resuscitation is an emerging trend, yet it remains controversial, even in countries with relatively high acceptance of family presence during resuscitation among medical professionals. Family presence during resuscitation is not common in many countries, and medical professionals in these regions are unfamiliar with family presence during resuscitation. Therefore, this study predicted the medical professionals' intention to allow family presence during resuscitation by applying the theory of planned behaviour. A cross-sectional survey. A single medical centre in southern Taiwan. Medical staffs including physicians and nurses in a single medical centre (n=714). A questionnaire was constructed to measure the theory of planned behaviour constructs of attitudes, subjective norms, perceived behavioural control, and behavioural intentions as well as the awareness of family presence during resuscitation and demographics. In total, 950 questionnaires were distributed to doctors and nurses in a medical centre. Among the 714 valid questionnaires, only 11 participants were aware of any association in Taiwan that promotes family presence during resuscitation; 94.7% replied that they were unsure (30.4%) or that their unit did not have a family presence during resuscitation policy (74.8%). Regression analysis was performed to predict medical professionals' intention to allow family presence during resuscitation. The results indicated that only positive attitudes and subjective norms regarding family presence during resuscitation and clinical tenure could predict the intention to allow family presence during resuscitation. Because Family presence during resuscitation practice is not common in Taiwan and only 26.19% of the participants agreed to both items measuring the intention to allow family presence during resuscitation, we recommend the implementation of a family presence during resuscitation education program that will enhance the positive beliefs

Comparison of DNA Quantification Methods for Next Generation Sequencing.

Science.gov (United States)

Robin, Jérôme D; Ludlow, Andrew T; LaRanger, Ryan; Wright, Woodring E; Shay, Jerry W

2016-04-06

Next Generation Sequencing (NGS) is a powerful tool that depends on loading a precise amount of DNA onto a flowcell. NGS strategies have expanded our ability to investigate genomic phenomena by referencing mutations in cancer and diseases through large-scale genotyping, developing methods to map rare chromatin interactions (4C; 5C and Hi-C) and identifying chromatin features associated with regulatory elements (ChIP-seq, Bis-Seq, ChiA-PET). While many methods are available for DNA library quantification, there is no unambiguous gold standard. Most techniques use PCR to amplify DNA libraries to obtain sufficient quantities for optical density measurement. However, increased PCR cycles can distort the library's heterogeneity and prevent the detection of rare variants. In this analysis, we compared new digital PCR technologies (droplet digital PCR; ddPCR, ddPCR-Tail) with standard methods for the titration of NGS libraries. DdPCR-Tail is comparable to qPCR and fluorometry (QuBit) and allows sensitive quantification by analysis of barcode repartition after sequencing of multiplexed samples. This study provides a direct comparison between quantification methods throughout a complete sequencing experiment and provides the impetus to use ddPCR-based quantification for improvement of NGS quality.

Comparison of Suitability of the Most Common Ancient DNA Quantification Methods.

Science.gov (United States)

Brzobohatá, Kristýna; Drozdová, Eva; Smutný, Jiří; Zeman, Tomáš; Beňuš, Radoslav

2017-04-01

Ancient DNA (aDNA) extracted from historical bones is damaged and fragmented into short segments, present in low quantity, and usually copurified with microbial DNA. A wide range of DNA quantification methods are available. The aim of this study was to compare the five most common DNA quantification methods for aDNA. Quantification methods were tested on DNA extracted from skeletal material originating from an early medieval burial site. The tested methods included ultraviolet (UV) absorbance, real-time quantitative polymerase chain reaction (qPCR) based on SYBR ® green detection, real-time qPCR based on a forensic kit, quantification via fluorescent dyes bonded to DNA, and fragmentary analysis. Differences between groups were tested using a paired t-test. Methods that measure total DNA present in the sample (NanoDrop ™ UV spectrophotometer and Qubit ® fluorometer) showed the highest concentrations. Methods based on real-time qPCR underestimated the quantity of aDNA. The most accurate method of aDNA quantification was fragmentary analysis, which also allows DNA quantification of the desired length and is not affected by PCR inhibitors. Methods based on the quantification of the total amount of DNA in samples are unsuitable for ancient samples as they overestimate the amount of DNA presumably due to the presence of microbial DNA. Real-time qPCR methods give undervalued results due to DNA damage and the presence of PCR inhibitors. DNA quantification methods based on fragment analysis show not only the quantity of DNA but also fragment length.

The role of PET quantification in cardiovascular imaging.

Science.gov (United States)

Slomka, Piotr; Berman, Daniel S; Alexanderson, Erick; Germano, Guido

2014-08-01

Positron Emission Tomography (PET) has several clinical and research applications in cardiovascular imaging. Myocardial perfusion imaging with PET allows accurate global and regional measurements of myocardial perfusion, myocardial blood flow and function at stress and rest in one exam. Simultaneous assessment of function and perfusion by PET with quantitative software is currently the routine practice. Combination of ejection fraction reserve with perfusion information may improve the identification of severe disease. The myocardial viability can be estimated by quantitative comparison of fluorodeoxyglucose ( 18 FDG) and rest perfusion imaging. The myocardial blood flow and coronary flow reserve measurements are becoming routinely included in the clinical assessment due to enhanced dynamic imaging capabilities of the latest PET/CT scanners. Absolute flow measurements allow evaluation of the coronary microvascular dysfunction and provide additional prognostic and diagnostic information for coronary disease. Standard quantitative approaches to compute myocardial blood flow from kinetic PET data in automated and rapid fashion have been developed for 13 N-ammonia, 15 O-water and 82 Rb radiotracers. The agreement between software methods available for such analysis is excellent. Relative quantification of 82 Rb PET myocardial perfusion, based on comparisons to normal databases, demonstrates high performance for the detection of obstructive coronary disease. New tracers, such as 18 F-flurpiridaz may allow further improvements in the disease detection. Computerized analysis of perfusion at stress and rest reduces the variability of the assessment as compared to visual analysis. PET quantification can be enhanced by precise coregistration with CT angiography. In emerging clinical applications, the potential to identify vulnerable plaques by quantification of atherosclerotic plaque uptake of 18 FDG and 18 F-sodium fluoride tracers in carotids, aorta and coronary arteries

Emphysema quantification from CT scans using novel application of diaphragm curvature estimation: comparison with standard quantification methods and pulmonary function data

Science.gov (United States)

Keller, Brad M.; Reeves, Anthony P.; Yankelevitz, David F.; Henschke, Claudia I.; Barr, R. Graham

2009-02-01

Emphysema is a disease of the lungs that destroys the alveolar air sacs and induces long-term respiratory dysfunction. CT scans allow for the imaging of the anatomical basis of emphysema and quantification of the underlying disease state. Several measures have been introduced for the quantification emphysema directly from CT data; most,however, are based on the analysis of density information provided by the CT scans, which vary by scanner and can be hard to standardize across sites and time. Given that one of the anatomical variations associated with the progression of emphysema is the flatting of the diaphragm due to the loss of elasticity in the lung parenchyma, curvature analysis of the diaphragm would provide information about emphysema from CT. Therefore, we propose a new, non-density based measure of the curvature of the diaphragm that would allow for further quantification methods in a robust manner. To evaluate the new method, 24 whole-lung scans were analyzed using the ratios of the lung height and diaphragm width to diaphragm height as curvature estimates as well as using the emphysema index as comparison. Pearson correlation coefficients showed a strong trend of several of the proposed diaphragm curvature measures to have higher correlations, of up to r=0.57, with DLCO% and VA than did the emphysema index. Furthermore, we found emphysema index to have only a 0.27 correlation to the proposed measures, indicating that the proposed measures evaluate different aspects of the disease.

Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA.

Science.gov (United States)

Shahal, Tamar; Gilat, Noa; Michaeli, Yael; Redy-Keisar, Orit; Shabat, Doron; Ebenstein, Yuval

2014-08-19

5-Hydroxymethylcytosine (5hmC), a modified form of the DNA base cytosine, is an important epigenetic mark linked to regulation of gene expression in development, and tumorigenesis. We have developed a spectroscopic method for a global quantification of 5hmC in genomic DNA. The assay is performed within a multiwell plate, which allows simultaneous recording of up to 350 samples. Our quantification procedure of 5hmC is direct, simple, and rapid. It relies on a two-step protocol that consists of enzymatic glucosylation of 5hmC with an azide-modified glucose, followed by a "click reaction" with an alkyne-fluorescent tag. The fluorescence intensity recorded from the DNA sample is proportional to its 5hmC content and can be quantified by a simple plate reader measurement. This labeling technique is specific and highly sensitive, allowing detection of 5hmC down to 0.002% of the total nucleotides. Our results reveal significant variations in the 5hmC content obtained from different mouse tissues, in agreement with previously reported data.

Good quantification practices of flavours and fragrances by mass spectrometry.

Science.gov (United States)

Begnaud, Frédéric; Chaintreau, Alain

2016-10-28

Over the past 15 years, chromatographic techniques with mass spectrometric detection have been increasingly used to monitor the rapidly expanded list of regulated flavour and fragrance ingredients. This trend entails a need for good quantification practices suitable for complex media, especially for multi-analytes. In this article, we present experimental precautions needed to perform the analyses and ways to process the data according to the most recent approaches. This notably includes the identification of analytes during their quantification and method validation, when applied to real matrices, based on accuracy profiles. A brief survey of application studies based on such practices is given.This article is part of the themed issue 'Quantitative mass spectrometry'. © 2016 The Authors.

Strategy study of quantification harmonization of SUV in PET/CT images

International Nuclear Information System (INIS)

Fischer, Andreia Caroline Fischer da Silveira

2014-01-01

In clinical practice, PET/CT images are often analyzed qualitatively by visual comparison of tumor lesions and normal tissues uptake; and semi-quantitatively by means of a parameter called SUV (Standardized Uptake Value). To ensure that longitudinal studies acquired on different scanners are interchangeable, and information of quantification is comparable, it is necessary to establish a strategy to harmonize the quantification of SUV. The aim of this study is to evaluate the strategy to harmonize the quantification of PET/CT images, performed with different scanner models and manufacturers. For this purpose, a survey of the technical characteristics of equipment and acquisition protocols of clinical images of different services of PET/CT in the state of Rio Grande do Sul was conducted. For each scanner, the accuracy of SUV quantification, and the Recovery Coefficient (RC) curves were determined, using the reconstruction parameters clinically relevant and available. From these data, harmonized performance specifications among the evaluated scanners were identified, as well as the algorithm that produces, for each one, the most accurate quantification. Finally, the most appropriate reconstruction parameters to harmonize the SUV quantification in each scanner, either regionally or internationally were identified. It was found that the RC values of the analyzed scanners proved to be overestimated by up to 38%, particularly for objects larger than 17mm. These results demonstrate the need for further optimization, through the reconstruction parameters modification, and even the change of the reconstruction algorithm used in each scanner. It was observed that there is a decoupling between the best image for PET/CT qualitative analysis and the best image for quantification studies. Thus, the choice of reconstruction method should be tied to the purpose of the PET/CT study in question, since the same reconstruction algorithm is not adequate, in one scanner, for qualitative

Uncertainty Quantification of CFD Data Generated for a Model Scramjet Isolator Flowfield

Science.gov (United States)

Baurle, R. A.; Axdahl, E. L.

2017-01-01

Computational fluid dynamics is now considered to be an indispensable tool for the design and development of scramjet engine components. Unfortunately, the quantification of uncertainties is rarely addressed with anything other than sensitivity studies, so the degree of confidence associated with the numerical results remains exclusively with the subject matter expert that generated them. This practice must be replaced with a formal uncertainty quantification process for computational fluid dynamics to play an expanded role in the system design, development, and flight certification process. Given the limitations of current hypersonic ground test facilities, this expanded role is believed to be a requirement by some in the hypersonics community if scramjet engines are to be given serious consideration as a viable propulsion system. The present effort describes a simple, relatively low cost, nonintrusive approach to uncertainty quantification that includes the basic ingredients required to handle both aleatoric (random) and epistemic (lack of knowledge) sources of uncertainty. The nonintrusive nature of the approach allows the computational fluid dynamicist to perform the uncertainty quantification with the flow solver treated as a "black box". Moreover, a large fraction of the process can be automated, allowing the uncertainty assessment to be readily adapted into the engineering design and development workflow. In the present work, the approach is applied to a model scramjet isolator problem where the desire is to validate turbulence closure models in the presence of uncertainty. In this context, the relevant uncertainty sources are determined and accounted for to allow the analyst to delineate turbulence model-form errors from other sources of uncertainty associated with the simulation of the facility flow.

The quantification of free Amadori compounds and amino acids allows to model the bound Maillard reaction products formation in soybean products

NARCIS (Netherlands)

Troise, Antonio Dario; Wiltafsky, Markus; Fogliano, Vincenzo; Vitaglione, Paola

2018-01-01

The quantification of protein bound Maillard reaction products (MRPs) is still a challenge in food chemistry. Protein hydrolysis is the bottleneck step: it is time consuming and the protein degradation is not always complete. In this study, the quantitation of free amino acids and Amadori products

Aspect-Oriented Programming is Quantification and Obliviousness

Science.gov (United States)

Filman, Robert E.; Friedman, Daniel P.; Norvig, Peter (Technical Monitor)

2000-01-01

This paper proposes that the distinguishing characteristic of Aspect-Oriented Programming (AOP) systems is that they allow programming by making quantified programmatic assertions over programs written by programmers oblivious to such assertions. Thus, AOP systems can be analyzed with respect to three critical dimensions: the kinds of quantifications allowed, the nature of the actions that can be asserted, and the mechanism for combining base-level actions with asserted actions. Consequences of this perspective are the recognition that certain systems are not AOP and that some mechanisms are expressive enough to allow programming an AOP system within them. A corollary is that while AOP can be applied to Object-Oriented Programming, it is an independent concept applicable to other programming styles.

1H NMR quantification in very dilute toxin solutions: application to anatoxin-a analysis.

Science.gov (United States)

Dagnino, Denise; Schripsema, Jan

2005-08-01

A complete procedure is described for the extraction, detection and quantification of anatoxin-a in biological samples. Anatoxin-a is extracted from biomass by a routine acid base extraction. The extract is analysed by GC-MS, without the need of derivatization, with a detection limit of 0.5 ng. A method was developed for the accurate quantification of anatoxin-a in the standard solution to be used for the calibration of the GC analysis. 1H NMR allowed the accurate quantification of microgram quantities of anatoxin-a. The accurate quantification of compounds in standard solutions is rarely discussed, but for compounds like anatoxin-a (toxins with prices in the range of a million dollar a gram), of which generally only milligram quantities or less are available, this factor in the quantitative analysis is certainly not trivial. The method that was developed can easily be adapted for the accurate quantification of other toxins in very dilute solutions.

Developmental validation of the Quantifiler(®) HP and Trio Kits for human DNA quantification in forensic samples.

Science.gov (United States)

Holt, Allison; Wootton, Sharon Chao; Mulero, Julio J; Brzoska, Pius M; Langit, Emanuel; Green, Robert L

2016-03-01

The quantification of human genomic DNA is a necessary first step in the DNA casework sample analysis workflow. DNA quantification determines optimal sample input amounts for subsequent STR (short tandem repeat) genotyping procedures, as well as being a useful screening tool to identify samples most likely to provide probative genotypic evidence. To better mesh with the capabilities of newest-generation STR analysis assays, the Quantifiler(®) HP and Quantifiler(®) Trio DNA Quantification Kits were designed for greater detection sensitivity and more robust performance with samples that contain PCR inhibitors or degraded DNA. The new DNA quantification kits use multiplex TaqMan(®) assay-based fluorescent probe technology to simultaneously quantify up to three human genomic targets, allowing samples to be assessed for total human DNA, male contributor (i.e., Y-chromosome) DNA, as well as a determination of DNA degradation state. The Quantifiler HP and Trio Kits use multiple-copy loci to allow for significantly improved sensitivity compared to earlier-generation kits that employ single-copy target loci. The kits' improved performance provides better predictive ability for results with downstream, newest-generation STR assays, and their shortened time-to-result allows more efficient integration into the forensic casework analysis workflow. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Rapid Quantification and Validation of Lipid Concentrations within Liposomes

Directory of Open Access Journals (Sweden)

Carla B. Roces

2016-09-01

Full Text Available Quantification of the lipid content in liposomal adjuvants for subunit vaccine formulation is of extreme importance, since this concentration impacts both efficacy and stability. In this paper, we outline a high performance liquid chromatography-evaporative light scattering detector (HPLC-ELSD method that allows for the rapid and simultaneous quantification of lipid concentrations within liposomal systems prepared by three liposomal manufacturing techniques (lipid film hydration, high shear mixing, and microfluidics. The ELSD system was used to quantify four lipids: 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC, cholesterol, dimethyldioctadecylammonium (DDA bromide, and ᴅ-(+-trehalose 6,6′-dibehenate (TDB. The developed method offers rapidity, high sensitivity, direct linearity, and a good consistency on the responses (R2 > 0.993 for the four lipids tested. The corresponding limit of detection (LOD and limit of quantification (LOQ were 0.11 and 0.36 mg/mL (DMPC, 0.02 and 0.80 mg/mL (cholesterol, 0.06 and 0.20 mg/mL (DDA, and 0.05 and 0.16 mg/mL (TDB, respectively. HPLC-ELSD was shown to be a rapid and effective method for the quantification of lipids within liposome formulations without the need for lipid extraction processes.

Photochemical Microscale Electrophoresis Allows Fast Quantification of Biomolecule Binding.

Science.gov (United States)

Möller, Friederike M; Kieß, Michael; Braun, Dieter

2016-04-27

Intricate spatiotemporal patterns emerge when chemical reactions couple to physical transport. We induce electrophoretic transport by a confined photochemical reaction and use it to infer the binding strength of a second, biomolecular binding reaction under physiological conditions. To this end, we use the photoactive compound 2-nitrobenzaldehyde, which releases a proton upon 375 nm irradiation. The charged photoproducts locally perturb electroneutrality due to differential diffusion, giving rise to an electric potential Φ in the 100 μV range on the micrometer scale. Electrophoresis of biomolecules in this field is counterbalanced by back-diffusion within seconds. The biomolecule concentration is measured by fluorescence and settles proportionally to exp(-μ/D Φ). Typically, binding alters either the diffusion coefficient D or the electrophoretic mobility μ. Hence, the local biomolecule fluorescence directly reflects the binding state. A fit to the law of mass action reveals the dissociation constant of the binding reaction. We apply this approach to quantify the binding of the aptamer TBA15 to its protein target human-α-thrombin and to probe the hybridization of DNA. Dissociation constants in the nanomolar regime were determined and match both results in literature and in control experiments using microscale thermophoresis. As our approach is all-optical, isothermal and requires only nanoliter volumes at nanomolar concentrations, it will allow for the fast screening of biomolecule binding in low volume multiwell formats.

Convex geometry of quantum resource quantification

Science.gov (United States)

Regula, Bartosz

2018-01-01

We introduce a framework unifying the mathematical characterisation of different measures of general quantum resources and allowing for a systematic way to define a variety of faithful quantifiers for any given convex quantum resource theory. The approach allows us to describe many commonly used measures such as matrix norm-based quantifiers, robustness measures, convex roof-based measures, and witness-based quantifiers together in a common formalism based on the convex geometry of the underlying sets of resource-free states. We establish easily verifiable criteria for a measure to possess desirable properties such as faithfulness and strong monotonicity under relevant free operations, and show that many quantifiers obtained in this framework indeed satisfy them for any considered quantum resource. We derive various bounds and relations between the measures, generalising and providing significantly simplified proofs of results found in the resource theories of quantum entanglement and coherence. We also prove that the quantification of resources in this framework simplifies for pure states, allowing us to obtain more easily computable forms of the considered measures, and show that many of them are in fact equal on pure states. Further, we investigate the dual formulation of resource quantifiers, which provide a characterisation of the sets of resource witnesses. We present an explicit application of the results to the resource theories of multi-level coherence, entanglement of Schmidt number k, multipartite entanglement, as well as magic states, providing insight into the quantification of the four resources by establishing novel quantitative relations and introducing new quantifiers, such as a measure of entanglement of Schmidt number k which generalises the convex roof-extended negativity, a measure of k-coherence which generalises the \

Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix

Science.gov (United States)

Klymus, Katy E.; Richter, Catherine A.; Chapman, Duane C.; Paukert, Craig P.

2015-01-01

Wildlife managers can more easily mitigate the effects of invasive species if action takes place before a population becomes established. Such early detection requires sensitive survey tools that can detect low numbers of individuals. Due to their high sensitivity, environmental DNA (eDNA) surveys hold promise as an early detection method for aquatic invasive species. Quantification of eDNA amounts may also provide data on species abundance and timing of an organism’s presence, allowing managers to successfully combat the spread of ecologically damaging species. To better understand the link between eDNA and an organism’s presence, it is crucial to know how eDNA is shed into the environment. Our study used quantitative PCR (qPCR) and controlled laboratory experiments to measure the amount of eDNA that two species of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) shed into the water. We first measured how much eDNA a single fish sheds and the variability of these measurements. Then, in a series of manipulative lab experiments, we studied how temperature, biomass (grams of fish), and diet affect the shedding rate of eDNA by these fish. We found that eDNA amounts exhibit a positive relationship with fish biomass, and that feeding could increase the amount of eDNA shed by ten-fold, whereas water temperature did not have an effect. Our results demonstrate that quantification of eDNA may be useful for predicting carp density, as well as densities of other rare or invasive species.

3D automatic quantification applied to optically sectioned images to improve microscopy analysis

Directory of Open Access Journals (Sweden)

JE Diaz-Zamboni

2009-08-01

Full Text Available New fluorescence microscopy techniques, such as confocal or digital deconvolution microscopy, allow to easily obtain three-dimensional (3D information from specimens. However, there are few 3D quantification tools that allow extracting information of these volumes. Therefore, the amount of information acquired by these techniques is difficult to manipulate and analyze manually. The present study describes a model-based method, which for the first time shows 3D visualization and quantification of fluorescent apoptotic body signals, from optical serial sections of porcine hepatocyte spheroids correlating them to their morphological structures. The method consists on an algorithm that counts apoptotic bodies in a spheroid structure and extracts information from them, such as their centroids in cartesian and radial coordinates, relative to the spheroid centre, and their integrated intensity. 3D visualization of the extracted information, allowed us to quantify the distribution of apoptotic bodies in three different zones of the spheroid.

Quantification and presence of human ancient DNA in burial place ...

African Journals Online (AJOL)

Quantification and presence of human ancient DNA in burial place remains of Turkey using real time polymerase chain reaction. ... A published real-time PCR assay, which allows for the combined analysis of nuclear or ancient DNA and mitochondrial DNA, was modified. This approach can be used for recovering DNA from ...

A survey of tools for the analysis of quantitative PCR (qPCR) data.

Science.gov (United States)

Pabinger, Stephan; Rödiger, Stefan; Kriegner, Albert; Vierlinger, Klemens; Weinhäusel, Andreas

2014-09-01

Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

Quantification of trace metals in water using complexation and filter concentration.

Science.gov (United States)

Dolgin, Bella; Bulatov, Valery; Japarov, Julia; Elish, Eyal; Edri, Elad; Schechter, Israel

2010-06-15

Various metals undergo complexation with organic reagents, resulting in colored products. In practice, their molar absorptivities allow for quantification in the ppm range. However, a proper pre-concentration of the colored complex on paper filter lowers the quantification limit to the low ppb range. In this study, several pre-concentration techniques have been examined and compared: filtering the already complexed mixture, complexation on filter, and dipping of dye-covered filter in solution. The best quantification has been based on the ratio of filter reflectance at a certain wavelength to that at zero metal concentration. The studied complex formations (Ni ions with TAN and Cd ions with PAN) involve production of nanoparticle suspensions, which are associated with complicated kinetics. The kinetics of the complexation of Ni ions with TAN has been investigated and optimum timing could be found. Kinetic optimization in regard to some interferences has also been suggested.

Absolute and direct microRNA quantification using DNA-gold nanoparticle probes.

Science.gov (United States)

Degliangeli, Federica; Kshirsagar, Prakash; Brunetti, Virgilio; Pompa, Pier Paolo; Fiammengo, Roberto

2014-02-12

DNA-gold nanoparticle probes are implemented in a simple strategy for direct microRNA (miRNA) quantification. Fluorescently labeled DNA-probe strands are immobilized on PEGylated gold nanoparticles (AuNPs). In the presence of target miRNA, DNA-RNA heteroduplexes are formed and become substrate for the endonuclease DSN (duplex-specific nuclease). Enzymatic hydrolysis of the DNA strands yields a fluorescence signal due to diffusion of the fluorophores away from the gold surface. We show that the molecular design of our DNA-AuNP probes, with the DNA strands immobilized on top of the PEG-based passivation layer, results in nearly unaltered enzymatic activity toward immobilized heteroduplexes compared to substrates free in solution. The assay, developed in a real-time format, allows absolute quantification of as little as 0.2 fmol of miR-203. We also show the application of the assay for direct quantification of cancer-related miR-203 and miR-21 in samples of extracted total RNA from cell cultures. The possibility of direct and absolute quantification may significantly advance the use of microRNAs as biomarkers in the clinical praxis.

Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography.

Science.gov (United States)

Loss, Leandro A; Bebis, George; Chang, Hang; Auer, Manfred; Sarkar, Purbasha; Parvin, Bahram

2012-10-01

Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides.

Improved perfusion quantification in FAIR imaging by offset correction

DEFF Research Database (Denmark)

Sidaros, Karam; Andersen, Irene Klærke; Gesmar, Henrik

2001-01-01

Perfusion quantification using pulsed arterial spin labeling has been shown to be sensitive to the RF pulse slice profiles. Therefore, in Flow-sensitive Alternating-Inversion Recovery (FAIR) imaging the slice selective (ss) inversion slab is usually three to four times thicker than the imaging...... slice. However, this reduces perfusion sensitivity due to the increased transit delay of the incoming blood with unperturbed spins. In the present article, the dependence of the magnetization on the RF pulse slice profiles is inspected both theoretically and experimentally. A perfusion quantification...... model is presented that allows the use of thinner ss inversion slabs by taking into account the offset of RF slice profiles between ss and nonselective inversion slabs. This model was tested in both phantom and human studies. Magn Reson Med 46:193-197, 2001...

Mixture quantification using PLS in plastic scintillation measurements

Energy Technology Data Exchange (ETDEWEB)

Bagan, H.; Tarancon, A.; Rauret, G. [Departament de Quimica Analitica, Universitat de Barcelona, Diagonal 647, E-08028 Barcelona (Spain); Garcia, J.F., E-mail: jfgarcia@ub.ed [Departament de Quimica Analitica, Universitat de Barcelona, Diagonal 647, E-08028 Barcelona (Spain)

2011-06-15

This article reports the capability of plastic scintillation (PS) combined with multivariate calibration (Partial least squares; PLS) to detect and quantify alpha and beta emitters in mixtures. While several attempts have been made with this purpose in mind using liquid scintillation (LS), no attempt was done using PS that has the great advantage of not producing mixed waste after the measurements are performed. Following this objective, ternary mixtures of alpha and beta emitters ({sup 241}Am, {sup 137}Cs and {sup 90}Sr/{sup 90}Y) have been quantified. Procedure optimisation has evaluated the use of the net spectra or the sample spectra, the inclusion of different spectra obtained at different values of the Pulse Shape Analysis parameter and the application of the PLS1 or PLS2 algorithms. The conclusions show that the use of PS+PLS2 applied to the sample spectra, without the use of any pulse shape discrimination, allows quantification of the activities with relative errors less than 10% in most of the cases. This procedure not only allows quantification of mixtures but also reduces measurement time (no blanks are required) and the application of this procedure does not require detectors that include the pulse shape analysis parameter.

Molecular quantification of environmental DNA using microfluidics and digital PCR.

Science.gov (United States)

Hoshino, Tatsuhiko; Inagaki, Fumio

2012-09-01

Real-time PCR has been widely used to evaluate gene abundance in natural microbial habitats. However, PCR-inhibitory substances often reduce the efficiency of PCR, leading to the underestimation of target gene copy numbers. Digital PCR using microfluidics is a new approach that allows absolute quantification of DNA molecules. In this study, digital PCR was applied to environmental samples, and the effect of PCR inhibitors on DNA quantification was tested. In the control experiment using λ DNA and humic acids, underestimation of λ DNA at 1/4400 of the theoretical value was observed with 6.58 ng μL(-1) humic acids. In contrast, digital PCR provided accurate quantification data with a concentration of humic acids up to 9.34 ng μL(-1). The inhibitory effect of paddy field soil extract on quantification of the archaeal 16S rRNA gene was also tested. By diluting the DNA extract, quantified copy numbers from real-time PCR and digital PCR became similar, indicating that dilution was a useful way to remedy PCR inhibition. The dilution strategy was, however, not applicable to all natural environmental samples. For example, when marine subsurface sediment samples were tested the copy number of archaeal 16S rRNA genes was 1.04×10(3) copies/g-sediment by digital PCR, whereas real-time PCR only resulted in 4.64×10(2) copies/g-sediment, which was most likely due to an inhibitory effect. The data from this study demonstrated that inhibitory substances had little effect on DNA quantification using microfluidics and digital PCR, and showed the great advantages of digital PCR in accurate quantifications of DNA extracted from various microbial habitats. Copyright © 2012 Elsevier GmbH. All rights reserved.

A Novel Assay for Easy and Rapid Quantification of Helicobacter pylori Adhesion

DEFF Research Database (Denmark)

Skindersoe, Mette E; Rasmussen, Lone; Andersen, Leif P

2015-01-01

BACKGROUND: Reducing adhesion of Helicobacter pylori to gastric epithelial cells could be a new way to counteract infections with this organism. We here present a novel method for quantification of Helicobacter pylori adhesion to cells. METHODS: Helicobacter pylori is allowed to adhere to AGS...

Characterization and quantification of preferential flow in fractured rock systems, using resistivity tomography

CSIR Research Space (South Africa)

May, F

2010-11-01

Full Text Available , N Jovanovic2 and A Rozanov1 University of Stellenbosch1 and Council for Scientific and Industrial Research (CSIR)2 Characterization and quantification of preferential flow in fractured rock systems, using resistivity tomography Introduction... of slow and fast flowing pathways. Materials and Methods TABLE 1 DATE, TIME AND WEATHER CONDITIONS DURING RESISTIVITY TOMOGRAPHY SURVEY Survey No. Date Start time End time Precipitation (mm) Description KB001 8/27/2010 12H00 13H40 0.0 Sunny KB002 8...

Collaborative framework for PIV uncertainty quantification: comparative assessment of methods

International Nuclear Information System (INIS)

Sciacchitano, Andrea; Scarano, Fulvio; Neal, Douglas R; Smith, Barton L; Warner, Scott O; Vlachos, Pavlos P; Wieneke, Bernhard

2015-01-01

A posteriori uncertainty quantification of particle image velocimetry (PIV) data is essential to obtain accurate estimates of the uncertainty associated with a given experiment. This is particularly relevant when measurements are used to validate computational models or in design and decision processes. In spite of the importance of the subject, the first PIV uncertainty quantification (PIV-UQ) methods have been developed only in the last three years. The present work is a comparative assessment of four approaches recently proposed in the literature: the uncertainty surface method (Timmins et al 2012), the particle disparity approach (Sciacchitano et al 2013), the peak ratio criterion (Charonko and Vlachos 2013) and the correlation statistics method (Wieneke 2015). The analysis is based upon experiments conducted for this specific purpose, where several measurement techniques are employed simultaneously. The performances of the above approaches are surveyed across different measurement conditions and flow regimes. (paper)

Quantification practices in the nuclear industry

International Nuclear Information System (INIS)

1986-01-01

In this chapter the quantification of risk practices adopted by the nuclear industries in Germany, Britain and France are examined as representative of the practices adopted throughout Europe. From this examination a number of conclusions are drawn about the common features of the practices adopted. In making this survey, the views expressed in the report of the Task Force on Safety Goals/Objectives appointed by the Commission of the European Communities, are taken into account. For each country considered, the legal requirements for presentation of quantified risk assessment as part of the licensing procedure are examined, and the way in which the requirements have been developed for practical application are then examined. (author)

Quantification of prebiotics in commercial infant formulas.

Science.gov (United States)

Sabater, Carlos; Prodanov, Marin; Olano, Agustín; Corzo, Nieves; Montilla, Antonia

2016-03-01

Since breastfeeding is not always possible, infant formulas (IFs) are supplemented with prebiotic oligosaccharides, such as galactooligosaccharides (GOS) and/or fructooligosaccharides (FOS) to exert similar effects to those of the breast milk. Nowadays, a great number of infant formulas enriched with prebiotics are disposal in the market, however there are scarce data about their composition. In this study, the combined use of two chromatographic methods (GC-FID and HPLC-RID) for the quantification of carbohydrates present in commercial infant formulas have been used. According to the results obtained by GC-FID for products containing prebiotics, the content of FOS, GOS and GOS/FOS was in the ranges of 1.6-5.0, 1.7-3.2, and 0.08-0.25/2.3-3.8g/100g of product, respectively. HPLC-RID analysis allowed quantification of maltodextrins with degree of polymerization (DP) up to 19. The methodology proposed here may be used for routine quality control of infant formula and other food ingredients containing prebiotics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantification of lung fibrosis and emphysema in mice using automated micro-computed tomography.

Directory of Open Access Journals (Sweden)

Ellen De Langhe

Full Text Available BACKGROUND: In vivo high-resolution micro-computed tomography allows for longitudinal image-based measurements in animal models of lung disease. The combination of repetitive high resolution imaging with fully automated quantitative image analysis in mouse models of lung fibrosis lung benefits preclinical research. This study aimed to develop and validate such an automated micro-computed tomography analysis algorithm for quantification of aerated lung volume in mice; an indicator of pulmonary fibrosis and emphysema severity. METHODOLOGY: Mice received an intratracheal instillation of bleomycin (n = 8, elastase (0.25 U elastase n = 9, 0.5 U elastase n = 8 or saline control (n = 6 for fibrosis, n = 5 for emphysema. A subset of mice was scanned without intervention, to evaluate potential radiation-induced toxicity (n = 4. Some bleomycin-instilled mice were treated with imatinib for proof of concept (n = 8. Mice were scanned weekly, until four weeks after induction, when they underwent pulmonary function testing, lung histology and collagen quantification. Aerated lung volumes were calculated with our automated algorithm. PRINCIPAL FINDINGS: Our automated image-based aerated lung volume quantification method is reproducible with low intra-subject variability. Bleomycin-treated mice had significantly lower scan-derived aerated lung volumes, compared to controls. Aerated lung volume correlated with the histopathological fibrosis score and total lung collagen content. Inversely, a dose-dependent increase in lung volume was observed in elastase-treated mice. Serial scanning of individual mice is feasible and visualized dynamic disease progression. No radiation-induced toxicity was observed. Three-dimensional images provided critical topographical information. CONCLUSIONS: We report on a high resolution in vivo micro-computed tomography image analysis algorithm that runs fully automated and allows quantification of aerated lung volume in mice. This

Deep learning approach for the detection and quantification of intraretinal cystoid fluid in multivendor optical coherence tomography

Science.gov (United States)

Venhuizen, Freerk G.; van Ginneken, Bram; Liefers, Bart; van Asten, Freekje; Schreur, Vivian; Fauser, Sascha; Hoyng, Carel; Theelen, Thomas; Sánchez, Clara I.

2018-01-01

We developed a deep learning algorithm for the automatic segmentation and quantification of intraretinal cystoid fluid (IRC) in spectral domain optical coherence tomography (SD-OCT) volumes independent of the device used for acquisition. A cascade of neural networks was introduced to include prior information on the retinal anatomy, boosting performance significantly. The proposed algorithm approached human performance reaching an overall Dice coefficient of 0.754 ± 0.136 and an intraclass correlation coefficient of 0.936, for the task of IRC segmentation and quantification, respectively. The proposed method allows for fast quantitative IRC volume measurements that can be used to improve patient care, reduce costs, and allow fast and reliable analysis in large population studies. PMID:29675301

Accurate Quantification of Cardiovascular Biomarkers in Serum Using Protein Standard Absolute Quantification (PSAQ™) and Selected Reaction Monitoring*

Science.gov (United States)

Huillet, Céline; Adrait, Annie; Lebert, Dorothée; Picard, Guillaume; Trauchessec, Mathieu; Louwagie, Mathilde; Dupuis, Alain; Hittinger, Luc; Ghaleh, Bijan; Le Corvoisier, Philippe; Jaquinod, Michel; Garin, Jérôme; Bruley, Christophe; Brun, Virginie

2012-01-01

Development of new biomarkers needs to be significantly accelerated to improve diagnostic, prognostic, and toxicity monitoring as well as therapeutic follow-up. Biomarker evaluation is the main bottleneck in this development process. Selected Reaction Monitoring (SRM) combined with stable isotope dilution has emerged as a promising option to speed this step, particularly because of its multiplexing capacities. However, analytical variabilities because of upstream sample handling or incomplete trypsin digestion still need to be resolved. In 2007, we developed the PSAQ™ method (Protein Standard Absolute Quantification), which uses full-length isotope-labeled protein standards to quantify target proteins. In the present study we used clinically validated cardiovascular biomarkers (LDH-B, CKMB, myoglobin, and troponin I) to demonstrate that the combination of PSAQ and SRM (PSAQ-SRM) allows highly accurate biomarker quantification in serum samples. A multiplex PSAQ-SRM assay was used to quantify these biomarkers in clinical samples from myocardial infarction patients. Good correlation between PSAQ-SRM and ELISA assay results was found and demonstrated the consistency between these analytical approaches. Thus, PSAQ-SRM has the capacity to improve both accuracy and reproducibility in protein analysis. This will be a major contribution to efficient biomarker development strategies. PMID:22080464

Identification of spectral regions for the quantification of red wine tannins with fourier transform mid-infrared spectroscopy.

Science.gov (United States)

Jensen, Jacob S; Egebo, Max; Meyer, Anne S

2008-05-28

Accomplishment of fast tannin measurements is receiving increased interest as tannins are important for the mouthfeel and color properties of red wines. Fourier transform mid-infrared spectroscopy allows fast measurement of different wine components, but quantification of tannins is difficult due to interferences from spectral responses of other wine components. Four different variable selection tools were investigated for the identification of the most important spectral regions which would allow quantification of tannins from the spectra using partial least-squares regression. The study included the development of a new variable selection tool, iterative backward elimination of changeable size intervals PLS. The spectral regions identified by the different variable selection methods were not identical, but all included two regions (1485-1425 and 1060-995 cm(-1)), which therefore were concluded to be particularly important for tannin quantification. The spectral regions identified from the variable selection methods were used to develop calibration models. All four variable selection methods identified regions that allowed an improved quantitative prediction of tannins (RMSEP = 69-79 mg of CE/L; r = 0.93-0.94) as compared to a calibration model developed using all variables (RMSEP = 115 mg of CE/L; r = 0.87). Only minor differences in the performance of the variable selection methods were observed.

Rapid quantification of biomarkers during kerogen microscale pyrolysis

Energy Technology Data Exchange (ETDEWEB)

Stott, A.W.; Abbott, G.D. [Fossil Fuels and Environmental Geochemistry NRG, The University, Newcastle-upon-Tyne (United Kingdom)

1995-02-01

A rapid, reproducible method incorporating closed system microscale pyrolysis and thermal desorption-gas chromatography/mass spectrometry has been developed and applied to the quantification of sterane biomarkers released during pyrolysis of the Messel oil shale kerogen under confined conditions. This method allows a substantial experimental concentration-time data set to be collected at accurately controlled temperatures, due to the low thermal inertia of the microscale borosilicate glass reaction vessels, which facilitates kinetic studies of biomarker reactions during kerogen microscale pyrolysis

Strawberry: Fast and accurate genome-guided transcript reconstruction and quantification from RNA-Seq.

Science.gov (United States)

Liu, Ruolin; Dickerson, Julie

2017-11-01

We propose a novel method and software tool, Strawberry, for transcript reconstruction and quantification from RNA-Seq data under the guidance of genome alignment and independent of gene annotation. Strawberry consists of two modules: assembly and quantification. The novelty of Strawberry is that the two modules use different optimization frameworks but utilize the same data graph structure, which allows a highly efficient, expandable and accurate algorithm for dealing large data. The assembly module parses aligned reads into splicing graphs, and uses network flow algorithms to select the most likely transcripts. The quantification module uses a latent class model to assign read counts from the nodes of splicing graphs to transcripts. Strawberry simultaneously estimates the transcript abundances and corrects for sequencing bias through an EM algorithm. Based on simulations, Strawberry outperforms Cufflinks and StringTie in terms of both assembly and quantification accuracies. Under the evaluation of a real data set, the estimated transcript expression by Strawberry has the highest correlation with Nanostring probe counts, an independent experiment measure for transcript expression. Strawberry is written in C++14, and is available as open source software at https://github.com/ruolin/strawberry under the MIT license.

Tool for objective quantification of pulmonary sequelae in monitoring of patients with tuberculosis

International Nuclear Information System (INIS)

Giacomini, Guilherme; Alvarez, Matheus; Pina, Diana R. de; Bacchim Neto, Fernando A.; Pereira, Paulo C.M.; Ribeiro, Sergio M.; Miranda, Jose Ricardo de A.

2014-01-01

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is an ancient infectious disease that remains a global health problem. Chest radiography is the method commonly employed in assessing the evolution of TB. However, lung damage quantification methods are usually performed on a computerized tomography (CT). This objective quantification is important in the radiological monitoring of the patient by assessing the progression and treatment of TB. However, precise quantification is not feasible by the number of CT examinations necessary due to the high dose subjected to the patient and high cost to the institution. The purpose of this work is to develop a tool to quantify pulmonary sequelae caused by TB through chest X-rays. Aiming the proposed objective, a computational algorithm was developed, creating a three-dimensional representation of the lungs, with regions of dilated sequelae inside. It also made the quantification of pulmonary sequelae of these patients through CT scans performed in upcoming dates, minimizing the differences in disease progression. The measurements from the two methods were compared with results suggest that the effectiveness and applicability of the developed tool, allowing lower doses radiological monitoring of the patient during treatment

Quantification in emission tomography

International Nuclear Information System (INIS)

Buvat, Irene

2011-11-01

The objective of this lecture is to understand the possibilities and limitations of the quantitative analysis of single photon emission computed tomography (SPECT) and positron emission tomography (PET) images. It is also to identify the conditions to be fulfilled to obtain reliable quantitative measurements from images. Content: 1 - Introduction: Quantification in emission tomography - definition and challenges; quantification biasing phenomena 2 - Main problems impacting quantification in PET and SPECT: problems, consequences, correction methods, results (Attenuation, scattering, partial volume effect, movement, un-stationary spatial resolution in SPECT, fortuitous coincidences in PET, standardisation in PET); 3 - Synthesis: accessible efficiency, know-how, Precautions, beyond the activity measurement

Accident sequence quantification with KIRAP

Energy Technology Data Exchange (ETDEWEB)

Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong

1997-01-01

The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP`s cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs.

Accident sequence quantification with KIRAP

International Nuclear Information System (INIS)

Kim, Tae Un; Han, Sang Hoon; Kim, Kil You; Yang, Jun Eon; Jeong, Won Dae; Chang, Seung Cheol; Sung, Tae Yong; Kang, Dae Il; Park, Jin Hee; Lee, Yoon Hwan; Hwang, Mi Jeong.

1997-01-01

The tasks of probabilistic safety assessment(PSA) consists of the identification of initiating events, the construction of event tree for each initiating event, construction of fault trees for event tree logics, the analysis of reliability data and finally the accident sequence quantification. In the PSA, the accident sequence quantification is to calculate the core damage frequency, importance analysis and uncertainty analysis. Accident sequence quantification requires to understand the whole model of the PSA because it has to combine all event tree and fault tree models, and requires the excellent computer code because it takes long computation time. Advanced Research Group of Korea Atomic Energy Research Institute(KAERI) has developed PSA workstation KIRAP(Korea Integrated Reliability Analysis Code Package) for the PSA work. This report describes the procedures to perform accident sequence quantification, the method to use KIRAP's cut set generator, and method to perform the accident sequence quantification with KIRAP. (author). 6 refs

Quantification of low-expressed mRNA using 5' LNA-containing real-time PCR primers

International Nuclear Information System (INIS)

Malgoyre, A.; Banzet, S.; Mouret, C.; Bigard, A.X.; Peinnequin, A.

2007-01-01

Real-time RT-PCR is the most sensitive and accurate method for mRNA quantification. Using specific recombinant DNA as a template, real-time PCR allows accurate quantification within a 7-log range and increased sensitivity below 10 copies. However, when using RT-PCR to quantify mRNA in biological samples, a stochastic off-targeted amplification can occur. Classical adjustments of assay parameters have minimal effects on such amplification. This undesirable amplification appears mostly to be dependent on specific to non-specific target ratio rather than on the absolute quantity of the specific target. This drawback, which decreases assay reliability, mostly appears when quantifying low-expressed transcript in a whole organ. An original primer design using properties of LNA allows to block off-target amplification. 5'-LNA substitution strengthens 5'-hybridization. Consequently on-target hybridization is stabilized and the probability for the off-target to lead to amplification is decreased

Quantification of complex modular architecture in plants.

Science.gov (United States)

Reeb, Catherine; Kaandorp, Jaap; Jansson, Fredrik; Puillandre, Nicolas; Dubuisson, Jean-Yves; Cornette, Raphaël; Jabbour, Florian; Coudert, Yoan; Patiño, Jairo; Flot, Jean-François; Vanderpoorten, Alain

2018-04-01

Morphometrics, the assignment of quantities to biological shapes, is a powerful tool to address taxonomic, evolutionary, functional and developmental questions. We propose a novel method for shape quantification of complex modular architecture in thalloid plants, whose extremely reduced morphologies, combined with the lack of a formal framework for thallus description, have long rendered taxonomic and evolutionary studies extremely challenging. Using graph theory, thalli are described as hierarchical series of nodes and edges, allowing for accurate, homologous and repeatable measurements of widths, lengths and angles. The computer program MorphoSnake was developed to extract the skeleton and contours of a thallus and automatically acquire, at each level of organization, width, length, angle and sinuosity measurements. Through the quantification of leaf architecture in Hymenophyllum ferns (Polypodiopsida) and a fully worked example of integrative taxonomy in the taxonomically challenging thalloid liverwort genus Riccardia, we show that MorphoSnake is applicable to all ramified plants. This new possibility of acquiring large numbers of quantitative traits in plants with complex modular architectures opens new perspectives of applications, from the development of rapid species identification tools to evolutionary analyses of adaptive plasticity. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Comparison of five DNA quantification methods

DEFF Research Database (Denmark)

Nielsen, Karsten; Mogensen, Helle Smidt; Hedman, Johannes

2008-01-01

Six commercial preparations of human genomic DNA were quantified using five quantification methods: UV spectrometry, SYBR-Green dye staining, slot blot hybridization with the probe D17Z1, Quantifiler Human DNA Quantification kit and RB1 rt-PCR. All methods measured higher DNA concentrations than...... Quantification kit in two experiments. The measured DNA concentrations with Quantifiler were 125 and 160% higher than expected based on the manufacturers' information. When the Quantifiler human DNA standard (Raji cell line) was replaced by the commercial human DNA preparation G147A (Promega) to generate the DNA...... standard curve in the Quantifiler Human DNA Quantification kit, the DNA quantification results of the human DNA preparations were 31% higher than expected based on the manufacturers' information. The results indicate a calibration problem with the Quantifiler human DNA standard for its use...

Quantification of cellular uptake of DNA nanostructures by qPCR.

Science.gov (United States)

Okholm, Anders Hauge; Nielsen, Jesper Sejrup; Vinther, Mathias; Sørensen, Rasmus Schøler; Schaffert, David; Kjems, Jørgen

2014-05-15

DNA nanostructures facilitating drug delivery are likely soon to be realized. In the past few decades programmed self-assembly of DNA building blocks have successfully been employed to construct sophisticated nanoscale objects. By conjugating functionalities to DNA, other molecules such as peptides, proteins and polymers can be precisely positioned on DNA nanostructures. This exceptional ability to produce modular nanoscale devices with tunable and controlled behavior has initiated an interest in employing DNA nanostructures for drug delivery. However, to obtain this the relationship between cellular interactions and structural and functional features of the DNA delivery device must be thoroughly investigated. Here, we present a rapid and robust method for the precise quantification of the component materials of DNA origami structures capable of entering cells in vitro. The quantification is performed by quantitative polymerase chain reaction, allowing a linear dynamic range of detection of five orders of magnitude. We demonstrate the use of this method for high-throughput screening, which could prove efficient to identify key features of DNA nanostructures enabling cell penetration. The method described here is suitable for quantification of in vitro uptake studies but should easily be extended to quantify DNA nanostructures in blood or tissue samples. Copyright © 2014 Elsevier Inc. All rights reserved.

Theoretical Study of Penalized-Likelihood Image Reconstruction for Region of Interest Quantification

International Nuclear Information System (INIS)

Qi, Jinyi; Huesman, Ronald H.

2006-01-01

Region of interest (ROI) quantification is an important task in emission tomography (e.g., positron emission tomography and single photon emission computed tomography). It is essential for exploring clinical factors such as tumor activity, growth rate, and the efficacy of therapeutic interventions. Statistical image reconstruction methods based on the penalized maximum-likelihood (PML) or maximum a posteriori principle have been developed for emission tomography to deal with the low signal-to-noise ratio of the emission data. Similar to the filter cut-off frequency in the filtered backprojection method, the regularization parameter in PML reconstruction controls the resolution and noise tradeoff and, hence, affects ROI quantification. In this paper, we theoretically analyze the performance of ROI quantification in PML reconstructions. Building on previous work, we derive simplified theoretical expressions for the bias, variance, and ensemble mean-squared-error (EMSE) of the estimated total activity in an ROI that is surrounded by a uniform background. When the mean and covariance matrix of the activity inside the ROI are known, the theoretical expressions are readily computable and allow for fast evaluation of image quality for ROI quantification with different regularization parameters. The optimum regularization parameter can then be selected to minimize the EMSE. Computer simulations are conducted for small ROIs with variable uniform uptake. The results show that the theoretical predictions match the Monte Carlo results reasonably well

New technique using [125I]labeled rose bengal for the quantification in blood samples of pipecuronium bromide, a muscle relaxant drug

International Nuclear Information System (INIS)

Schopfer, C.; Benakis, A.; Pittet, J.-F.; Tassonyi, E.

1991-01-01

A new technique involving the use of [ 125 I]labeled rose bengal for the quantification of pipecuronium bromide (a muscle relaxant drug) is presented. This technique, which is based on the ability of rose bengal to react with pipecuronium and then form a complex which can be extracted into an organic solvent, involves two steps: the purification and labeling of rose bengal with 125 I, and the quantification of pipecuronium. The specific activity of the compound (106 μCi/mg) allows for the quantification of pipecuronium in biological samples at concentrations as low as 5 ng/ml. (author)

Quantification of viral DNA during HIV-1 infection: A review of relevant clinical uses and laboratory methods.

Science.gov (United States)

Alidjinou, E K; Bocket, L; Hober, D

2015-02-01

Effective antiretroviral therapy usually leads to undetectable HIV-1 RNA in the plasma. However, the virus persists in some cells of infected patients as various DNA forms, both integrated and unintegrated. This reservoir represents the greatest challenge to the complete cure of HIV-1 infection and its characteristics highly impact the course of the disease. The quantification of HIV-1 DNA in blood samples constitutes currently the most practical approach to measure this residual infection. Real-time quantitative PCR (qPCR) is the most common method used for HIV-DNA quantification and many strategies have been developed to measure the different forms of HIV-1 DNA. In the literature, several "in-house" PCR methods have been used and there is a need for standardization to have comparable results. In addition, qPCR is limited for the precise quantification of low levels by background noise. Among new assays in development, digital PCR was shown to allow an accurate quantification of HIV-1 DNA. Total HIV-1 DNA is most commonly measured in clinical routine. The absolute quantification of proviruses and unintegrated forms is more often used for research purposes. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Quantification of residual host cell DNA in adenoviral vectors produced on PER.C6 cells

NARCIS (Netherlands)

Gijsbers, Linda; Koel, Björn; Weggeman, Miranda; Goudsmit, Jaap; Havenga, Menzo; Marzio, Giuseppe

2005-01-01

Recombinant adenoviral vectors for gene therapy and vaccination are routinely prepared on cultures of immortalized cells, allowing the production of vector batches of high titer and consistent quality. Quantification of residual DNA from the producing cell line is part of the purity tests for

Automatic Drusen Quantification and Risk Assessment of Age-related Macular Degeneration on Color Fundus Images

NARCIS (Netherlands)

Grinsven, M.J.J.P. van; Lechanteur, Y.T.E.; Ven, J.P.H. van de; Ginneken, B. van; Hoyng, C.B.; Theelen, T.; Sanchez, C.I.

2013-01-01

PURPOSE: To evaluate a machine learning algorithm that allows for computer aided diagnosis (CAD) of non-advanced age-related macular degeneration (AMD) by providing an accurate detection and quantification of drusen location, area and size. METHODS: Color fundus photographs of 407 eyes without AMD

Structure determination of electrodeposited zinc-nickel alloys: thermal stability and quantification using XRD and potentiodynamic dissolution

International Nuclear Information System (INIS)

Fedi, B.; Gigandet, M.P.; Hihn, J-Y; Mierzejewski, S.

2016-01-01

Highlights: • Quantification of zinc-nickel phases between 1,2% and 20%. • Coupling XRD to partial potentiodynamic dissolution. • Deconvolution of anodic stripping curves. • Phase quantification after annealing. - Abstract: Electrodeposited zinc-nickel coatings obtained by electrodeposition reveal the presence of metastable phases in various quantities, thus requiring their identification, a study of their thermal stability, and, finally, determination of their respective proportions. By combining XRD measurement with partial potentiodynamic dissolution, anodic peaks were indexed to allow their quantification. Quantification of electrodeposited zinc-nickel alloys approximately 10 μm thick was thus carried out on nickel content between 1.2% and 20%, and exhibited good accuracy. This method was then extended to the same set of alloys after annealing (250 °C, 2 h), thus bringing the structural organization closer to its thermodynamic equilibrium. The result obtained ensures better understanding of crystallization of metastable phases and of phase proportion evolution in a bi-phasic zinc-nickel coating. Finally, the presence of a monophase γ and its thermal stability in the 12% to 15% range provides important information for coating anti-corrosion behavior.

Whole farm quantification of GHG emissions within smallholder farms in developing countries

International Nuclear Information System (INIS)

Seebauer, Matthias

2014-01-01

The IPCC has compiled the best available scientific methods into published guidelines for estimating greenhouse gas emissions and emission removals from the land-use sector. In order to evaluate existing GHG quantification tools to comprehensively quantify GHG emissions and removals in smallholder conditions, farm scale quantification was tested with farm data from Western Kenya. After conducting a cluster analysis to identify different farm typologies GHG quantification was exercised using the VCS SALM methodology complemented with IPCC livestock emission factors and the cool farm tool. The emission profiles of four farm clusters representing the baseline conditions in the year 2009 are compared with 2011 where farmers adopted sustainable land management practices (SALM). The results demonstrate the variation in both the magnitude of the estimated GHG emissions per ha between different smallholder farm typologies and the emissions estimated by applying two different accounting tools. The farm scale quantification further shows that the adoption of SALM has a significant impact on emission reduction and removals and the mitigation benefits range between 4 and 6.5 tCO 2  ha −1  yr −1 with significantly different mitigation benefits depending on typologies of the crop–livestock systems, their different agricultural practices, as well as adoption rates of improved practices. However, the inherent uncertainty related to the emission factors applied by accounting tools has substantial implications for reported agricultural emissions. With regard to uncertainty related to activity data, the assessment confirms the high variability within different farm types as well as between different parameters surveyed to comprehensively quantify GHG emissions within smallholder farms. (paper)

Photoacoustic bio-quantification of graphene based nanomaterials at a single cell level (Conference Presentation)

Science.gov (United States)

Nedosekin, Dmitry A.; Nolan, Jacqueline; Biris, Alexandru S.; Zharov, Vladimir P.

2017-03-01

Arkansas Nanomedicine Center at the University of Arkansas for Medical Sciences in collaboration with other Arkansas Universities and the FDA-based National Center of Toxicological Research in Jefferson, AR is developing novel techniques for rapid quantification of graphene-based nanomaterials (GBNs) in various biological samples. All-carbon GBNs have wide range of potential applications in industry, agriculture, food processing and medicine; however, quantification of GBNs is difficult in carbon reach biological tissues. The accurate quantification of GBNs is essential for research on material toxicity and the development of GBNs-based drug delivery platforms. We have developed microscopy and cytometry platforms for detection and quantification of GBNs in single cells, tissue and blood samples using photoacoustic contrast of GBNs. We demonstrated PA quantification of individual graphene uptake by single cells. High-resolution PA microscopy provided mapping of GBN distribution within live cells to establish correlation with intracellular toxic phenomena using apoptotic and necrotic assays. This new methodology and corresponding technical platform provide the insight on possible toxicological risks of GBNs at singe cells levels. In addition, in vivo PA image flow cytometry demonstrated the capability to monitor of GBNs pharmacokinetics in mouse model and to map the resulting biodistribution of GBNs in mouse tissues. The integrated PA platform provided an unprecedented sensitivity toward GBNs and allowed to enhance conventional toxicology research by providing a direct correlation between uptake of GBNs at a single cell level and cell viability status.

Feasibility and accuracy of dual-layer spectral detector computed tomography for quantification of gadolinium: a phantom study.

Science.gov (United States)

van Hamersvelt, Robbert W; Willemink, Martin J; de Jong, Pim A; Milles, Julien; Vlassenbroek, Alain; Schilham, Arnold M R; Leiner, Tim

2017-09-01

The aim of this study was to evaluate the feasibility and accuracy of dual-layer spectral detector CT (SDCT) for the quantification of clinically encountered gadolinium concentrations. The cardiac chamber of an anthropomorphic thoracic phantom was equipped with 14 tubular inserts containing different gadolinium concentrations, ranging from 0 to 26.3 mg/mL (0.0, 0.1, 0.2, 0.4, 0.5, 1.0, 2.0, 3.0, 4.0, 5.1, 10.6, 15.7, 20.7 and 26.3 mg/mL). Images were acquired using a novel 64-detector row SDCT system at 120 and 140 kVp. Acquisitions were repeated five times to assess reproducibility. Regions of interest (ROIs) were drawn on three slices per insert. A spectral plot was extracted for every ROI and mean attenuation profiles were fitted to known attenuation profiles of water and pure gadolinium using in-house-developed software to calculate gadolinium concentrations. At both 120 and 140 kVp, excellent correlations between scan repetitions and true and measured gadolinium concentrations were found (R > 0.99, P  0.99, CI 0.99-1.00). Relative mean measurement errors stayed below 10% down to 2.0 mg/mL true gadolinium concentration at 120 kVp and below 5% down to 1.0 mg/mL true gadolinium concentration at 140 kVp. SDCT allows for accurate quantification of gadolinium at both 120 and 140 kVp. Lowest measurement errors were found for 140 kVp acquisitions. • Gadolinium quantification may be useful in patients with contraindication to iodine. • Dual-layer spectral detector CT allows for overall accurate quantification of gadolinium. • Interscan variability of gadolinium quantification using SDCT material decomposition is excellent.

Lung involvement quantification in chest radiographs

International Nuclear Information System (INIS)

Giacomini, Guilherme; Alvarez, Matheus; Oliveira, Marcela de; Miranda, Jose Ricardo A.; Pina, Diana R.; Pereira, Paulo C.M.; Ribeiro, Sergio M.

2014-01-01

Tuberculosis (TB) caused by Mycobacterium tuberculosis, is an infectious disease which remains a global health problem. The chest radiography is the commonly method employed to assess the TB's evolution. The methods for quantification of abnormalities of chest are usually performed on CT scans (CT). This quantification is important to assess the TB evolution and treatment and comparing different treatments. However, precise quantification is not feasible for the amount of CT scans required. The purpose of this work is to develop a methodology for quantification of lung damage caused by TB through chest radiographs. It was developed an algorithm for computational processing of exams in Matlab, which creates a lungs' 3D representation, with compromised dilated regions inside. The quantification of lung lesions was also made for the same patients through CT scans. The measurements from the two methods were compared and resulting in strong correlation. Applying statistical Bland and Altman, all samples were within the limits of agreement, with a confidence interval of 95%. The results showed an average variation of around 13% between the two quantification methods. The results suggest the effectiveness and applicability of the method developed, providing better risk-benefit to the patient and cost-benefit ratio for the institution. (author)

Fluorescent quantification of melanin.

Science.gov (United States)

Fernandes, Bruno; Matamá, Teresa; Guimarães, Diana; Gomes, Andreia; Cavaco-Paulo, Artur

2016-11-01

Melanin quantification is reportedly performed by absorption spectroscopy, commonly at 405 nm. Here, we propose the implementation of fluorescence spectroscopy for melanin assessment. In a typical in vitro assay to assess melanin production in response to an external stimulus, absorption spectroscopy clearly overvalues melanin content. This method is also incapable of distinguishing non-melanotic/amelanotic control cells from those that are actually capable of performing melanogenesis. Therefore, fluorescence spectroscopy is the best method for melanin quantification as it proved to be highly specific and accurate, detecting even small variations in the synthesis of melanin. This method can also be applied to the quantification of melanin in more complex biological matrices like zebrafish embryos and human hair. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Identification and Quantification of Carbonate Species Using Rock-Eval Pyrolysis

Directory of Open Access Journals (Sweden)

Pillot D.

2013-03-01

Full Text Available This paper presents a new reliable and rapid method to characterise and quantify carbonates in solid samples based on monitoring the CO2 flux emitted by progressive thermal decomposition of carbonates during a programmed heating. The different peaks of destabilisation allow determining the different types of carbonates present in the analysed sample. The quantification of each peak gives the respective proportions of these different types of carbonates in the sample. In addition to the chosen procedure presented in this paper, using a standard Rock-Eval 6 pyrolyser, calibration characteristic profiles are also presented for the most common carbonates in nature. This method should allow different types of application for different disciplines, either academic or industrial.

FRANX. Application for analysis and quantification of the APS fire; FRANK. Aplicacion para el analisis y cuantificacion de los APS de incendios

Energy Technology Data Exchange (ETDEWEB)

Snchez, A.; Osorio, F.; Ontoso, N.

2014-07-01

The FRANX application has been developed by EPRI within the Risk and Reliability User Group in order to facilitate the process of quantification and updating APS Fire (also covers floods and earthquakes). By applying fire scenarios are quantified in the central integrating the tasks performed during the APS fire. This paper describes the main features of the program to allow quantification of an APS Fire. (Author)

An uncertainty inventory demonstration - a primary step in uncertainty quantification

Energy Technology Data Exchange (ETDEWEB)

Langenbrunner, James R. [Los Alamos National Laboratory; Booker, Jane M [Los Alamos National Laboratory; Hemez, Francois M [Los Alamos National Laboratory; Salazar, Issac F [Los Alamos National Laboratory; Ross, Timothy J [UNM

2009-01-01

Tools, methods, and theories for assessing and quantifying uncertainties vary by application. Uncertainty quantification tasks have unique desiderata and circumstances. To realistically assess uncertainty requires the engineer/scientist to specify mathematical models, the physical phenomena of interest, and the theory or framework for assessments. For example, Probabilistic Risk Assessment (PRA) specifically identifies uncertainties using probability theory, and therefore, PRA's lack formal procedures for quantifying uncertainties that are not probabilistic. The Phenomena Identification and Ranking Technique (PIRT) proceeds by ranking phenomena using scoring criteria that results in linguistic descriptors, such as importance ranked with words, 'High/Medium/Low.' The use of words allows PIRT to be flexible, but the analysis may then be difficult to combine with other uncertainty theories. We propose that a necessary step for the development of a procedure or protocol for uncertainty quantification (UQ) is the application of an Uncertainty Inventory. An Uncertainty Inventory should be considered and performed in the earliest stages of UQ.

Absolute quantification of Bovine Viral Diarrhea Virus (BVDV) RNA by the digital PCR technique

Science.gov (United States)

Flatschart, R. B.; Almeida, D. O.; Heinemann, M. B.; Medeiros, M. N.; Granjeiro, J. M.; Folgueras-Flatschart, A. V.

2015-01-01

The quality control of cell lines used in research and industry is critical to ensure confidence in experimental results and to guarantee the safety of biopharmaceuticals to consumers. The BVDV is a common adventitious agent in many cell lines. We preliminarly evaluate the use of Digital Droplet PCR (ddPCR) for the detection and enumeration of genome copies of BVDV in cell culture and on FBS. The application of a commercial Real-Time PCR kit with the ddPCR technique was successful on different matrices. The technique allowed the absolute quantification of the genome without the use of calibration standards, suggesting its promising application on the development of reference materials for quantification of nucleic acids.

Verb aspect, alternations and quantification

Directory of Open Access Journals (Sweden)

Svetla Koeva

2015-11-01

Full Text Available Verb aspect, alternations and quantification In this paper we are briefly discuss the nature of Bulgarian verb aspect and argue that the verb aspect pairs are different lexical units with different (although related meaning, different argument structure (reflecting categories, explicitness and referential status of arguments and different sets of semantic and syntactic alternations. The verb prefixes resulting in perfective verbs derivation in some cases can be interpreted as lexical quantifiers as well. Thus the Bulgarian verb aspect is related (in different way both with the potential for the generation of alternations and with the prefixal lexical quantification. It is shown that the scope of the lexical quantification by means of verbal prefixes is the quantified verb phrase and the scope remains constant in all derived alternations. The paper concerns the basic issues of these complex problems, while the detailed description of the conditions satisfying particular alternation or particular lexical quantification are subject of a more detailed study.

The Qiagen Investigator® Quantiplex HYres as an alternative kit for DNA quantification.

Science.gov (United States)

Frégeau, Chantal J; Laurin, Nancy

2015-05-01

The Investigator® Quantiplex HYres kit was evaluated as a potential replacement for dual DNA quantification of casework samples. This kit was determined to be highly sensitive with a limit of quantification and limit of detection of 0.0049ng/μL and 0.0003ng/μL, respectively, for both human and male DNA, using full or half reaction volumes. It was also accurate in assessing the amount of male DNA present in 96 mock and actual casework male:female mixtures (various ratios) processed in this exercise. The close correlation between the male/human DNA ratios expressed in percentages derived from the Investigator® Quantiplex HYres quantification results and the male DNA proportion calculated in mixed AmpFlSTR® Profiler® Plus or AmpFlSTR® Identifiler® Plus profiles, using the Amelogenin Y peak and STR loci, allowed guidelines to be developed to facilitate decisions regarding when to submit samples to Y-STR rather than autosomal STR profiling. The internal control (IC) target was shown to be more sensitive to inhibitors compared to the human and male DNA targets included in the Investigator® Quantiplex HYres kit serving as a good quality assessor of DNA extracts. The new kit met our criteria of enhanced sensitivity, accuracy, consistency, reliability and robustness for casework DNA quantification. Crown Copyright © 2015. Published by Elsevier Ireland Ltd. All rights reserved.

Optical coherence tomography assessment and quantification of intracoronary thrombus: Status and perspectives

International Nuclear Information System (INIS)

Porto, Italo; Mattesini, Alessio; Valente, Serafina; Prati, Francesco; Crea, Filippo; Bolognese, Leonardo

2015-01-01

Coronary angiography is the “golden standard” imaging technique in interventional cardiology and it is still widely used to guide interventions. A major drawback of this technique, however, is that it is inaccurate in the evaluation and quantification of intracoronary thrombus burden, a critical prognosticator and predictor of intraprocedural complications in acute coronary syndromes. The introduction of optical coherence tomography (OCT) holds the promise of overcoming this important limitation, as near-infrared light is uniquely sensitive to hemoglobin, the pigment of red blood cells trapped in the thrombus. This narrative review will focus on the use of OCT for the assessment, evaluation and quantification of intracoronary thrombosis. - Highlights: • Thrombotic burden in acute coronary syndromes Is not adequately evaluated by standard coronary angiography, whereas Optical Coherence Tomography is exquisitely sensitive to the hemoglobin contained in red blood cells and can be used to precisely quantify thrombus. • Both research and clinical applications have been developed using the OCT-based evaluation of thrombus. In particular, whereas precise quantification scores are useful for comparing antithrombotic therapies in randomized trials, both pharmacological and mechanical, the most important practical applications for OCT-based assessment of thrombus are the individuation of culprit lesions in the context of diffuse atheromata in acute coronary syndromes, and the so-called “delayed stenting” strategies. • Improvements in 3D rendering techniques are on the verge of revolutionizing OCT-based thrombus assessment, allowing extremely precise quantification of the thrombotic burden

Optical coherence tomography assessment and quantification of intracoronary thrombus: Status and perspectives

Energy Technology Data Exchange (ETDEWEB)

Porto, Italo, E-mail: italo.porto@gmail.com [Interventional Cardiology Unit, San Donato Hospital, Arezzo (Italy); Mattesini, Alessio; Valente, Serafina [Interventional Cardiology Unit, Careggi Hospital, Florence (Italy); Prati, Francesco [Interventional Cardiology San Giovanni Hospital, Rome (Italy); CLI foundation (Italy); Crea, Filippo [Department of Cardiovascular Sciences, Catholic University of the Sacred Heart, Rome (Italy); Bolognese, Leonardo [Interventional Cardiology Unit, San Donato Hospital, Arezzo (Italy)

2015-04-15

Coronary angiography is the “golden standard” imaging technique in interventional cardiology and it is still widely used to guide interventions. A major drawback of this technique, however, is that it is inaccurate in the evaluation and quantification of intracoronary thrombus burden, a critical prognosticator and predictor of intraprocedural complications in acute coronary syndromes. The introduction of optical coherence tomography (OCT) holds the promise of overcoming this important limitation, as near-infrared light is uniquely sensitive to hemoglobin, the pigment of red blood cells trapped in the thrombus. This narrative review will focus on the use of OCT for the assessment, evaluation and quantification of intracoronary thrombosis. - Highlights: • Thrombotic burden in acute coronary syndromes Is not adequately evaluated by standard coronary angiography, whereas Optical Coherence Tomography is exquisitely sensitive to the hemoglobin contained in red blood cells and can be used to precisely quantify thrombus. • Both research and clinical applications have been developed using the OCT-based evaluation of thrombus. In particular, whereas precise quantification scores are useful for comparing antithrombotic therapies in randomized trials, both pharmacological and mechanical, the most important practical applications for OCT-based assessment of thrombus are the individuation of culprit lesions in the context of diffuse atheromata in acute coronary syndromes, and the so-called “delayed stenting” strategies. • Improvements in 3D rendering techniques are on the verge of revolutionizing OCT-based thrombus assessment, allowing extremely precise quantification of the thrombotic burden.

A Java program for LRE-based real-time qPCR that enables large-scale absolute quantification.

Science.gov (United States)

Rutledge, Robert G

2011-03-02

Linear regression of efficiency (LRE) introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples.

Virus detection and quantification using electrical parameters

Science.gov (United States)

Ahmad, Mahmoud Al; Mustafa, Farah; Ali, Lizna M.; Rizvi, Tahir A.

2014-10-01

Here we identify and quantitate two similar viruses, human and feline immunodeficiency viruses (HIV and FIV), suspended in a liquid medium without labeling, using a semiconductor technique. The virus count was estimated by calculating the impurities inside a defined volume by observing the change in electrical parameters. Empirically, the virus count was similar to the absolute value of the ratio of the change of the virus suspension dopant concentration relative to the mock dopant over the change in virus suspension Debye volume relative to mock Debye volume. The virus type was identified by constructing a concentration-mobility relationship which is unique for each kind of virus, allowing for a fast (within minutes) and label-free virus quantification and identification. For validation, the HIV and FIV virus preparations were further quantified by a biochemical technique and the results obtained by both approaches corroborated well. We further demonstrate that the electrical technique could be applied to accurately measure and characterize silica nanoparticles that resemble the virus particles in size. Based on these results, we anticipate our present approach to be a starting point towards establishing the foundation for label-free electrical-based identification and quantification of an unlimited number of viruses and other nano-sized particles.

Direct liquid chromatography method for the simultaneous quantification of hydroxytyrosol and tyrosol in red wines.

Science.gov (United States)

Piñeiro, Zulema; Cantos-Villar, Emma; Palma, Miguel; Puertas, Belen

2011-11-09

A validated HPLC method with fluorescence detection for the simultaneous quantification of hydroxytyrosol and tyrosol in red wines is described. Detection conditions for both compounds were optimized (excitation at 279 and 278 and emission at 631 and 598 nm for hydroxytyrosol and tyrosol, respectively). The validation of the analytical method was based on selectivity, linearity, robustness, detection and quantification limits, repeatability, and recovery. The detection and quantification limits in red wines were set at 0.023 and 0.076 mg L(-1) for hydroxytyrosol and at 0.007 and 0.024 mg L(-1) for tyrosol determination, respectively. Precision values, both within-day and between-day (n = 5), remained below 3% for both compounds. In addition, a fractional factorial experimental design was developed to analyze the influence of six different conditions on analysis. The final optimized HPLC-fluorescence method allowed the analysis of 30 nonpretreated Spanish red wines to evaluate their hydroxytyrosol and tyrosol contents.

Uncertainty quantification theory, implementation, and applications

CERN Document Server

Smith, Ralph C

2014-01-01

The field of uncertainty quantification is evolving rapidly because of increasing emphasis on models that require quantified uncertainties for large-scale applications, novel algorithm development, and new computational architectures that facilitate implementation of these algorithms. Uncertainty Quantification: Theory, Implementation, and Applications provides readers with the basic concepts, theory, and algorithms necessary to quantify input and response uncertainties for simulation models arising in a broad range of disciplines. The book begins with a detailed discussion of applications where uncertainty quantification is critical for both scientific understanding and policy. It then covers concepts from probability and statistics, parameter selection techniques, frequentist and Bayesian model calibration, propagation of uncertainties, quantification of model discrepancy, surrogate model construction, and local and global sensitivity analysis. The author maintains a complementary web page where readers ca...

Simultaneous Assessment of Cardiomyocyte DNA Synthesis and Ploidy: A Method to Assist Quantification of Cardiomyocyte Regeneration and Turnover.

Science.gov (United States)

Richardson, Gavin D

2016-05-23

Although it is accepted that the heart has a limited potential to regenerate cardiomyocytes following injury and that low levels of cardiomyocyte turnover occur during normal ageing, quantification of these events remains challenging. This is in part due to the rarity of the process and the fact that multiple cellular sources contribute to myocardial maintenance. Furthermore, DNA duplication within cardiomyocytes often leads to a polyploid cardiomyocyte and only rarely leads to new cardiomyocytes by cellular division. In order to accurately quantify cardiomyocyte turnover discrimination between these processes is essential. The protocol described here employs long term nucleoside labeling in order to label all nuclei which have arisen as a result of DNA replication and cardiomyocyte nuclei identified by utilizing nuclei isolation and subsequent PCM1 immunolabeling. Together this allows the accurate and sensitive identification of the nucleoside labeling of the cardiomyocyte nuclei population. Furthermore, 4',6-diamidino-2-phenylindole labeling and analysis of nuclei ploidy, enables the discrimination of neo-cardiomyocyte nuclei from nuclei which have incorporated nucleoside during polyploidization. Although this method cannot control for cardiomyocyte binucleation, it allows a rapid and robust quantification of neo-cardiomyocyte nuclei while accounting for polyploidization. This method has a number of downstream applications including assessing the potential therapeutics to enhance cardiomyocyte regeneration or investigating the effects of cardiac disease on cardiomyocyte turnover and ploidy. This technique is also compatible with additional downstream immunohistological techniques, allowing quantification of nucleoside incorporation in all cardiac cell types.

Multivariate Analysis for Quantification of Plutonium(IV) in Nitric Acid Based on Absorption Spectra

Energy Technology Data Exchange (ETDEWEB)

Lines, Amanda M. [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Adami, Susan R. [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Sinkov, Sergey I. [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Lumetta, Gregg J. [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; Bryan, Samuel A. [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States

2017-08-09

Development of more effective, reliable, and fast methods for monitoring process streams is a growing opportunity for analytical applications. Many fields can benefit from on-line monitoring, including the nuclear fuel cycle where improved methods for monitoring radioactive materials will facilitate maintenance of proper safeguards and ensure safe and efficient processing of materials. On-line process monitoring with a focus on optical spectroscopy can provide a fast, non-destructive method for monitoring chemical species. However, identification and quantification of species can be hindered by the complexity of the solutions if bands overlap or show condition-dependent spectral features. Plutonium (IV) is one example of a species which displays significant spectral variation with changing nitric acid concentration. Single variate analysis (i.e. Beer’s Law) is difficult to apply to the quantification of Pu(IV) unless the nitric acid concentration is known and separate calibration curves have been made for all possible acid strengths. Multivariate, or chemometric, analysis is an approach that allows for the accurate quantification of Pu(IV) without a priori knowledge of nitric acid concentration.

Inter-laboratory assessment of different digital PCR platforms for quantification of human cytomegalovirus DNA.

Science.gov (United States)

Pavšič, Jernej; Devonshire, Alison; Blejec, Andrej; Foy, Carole A; Van Heuverswyn, Fran; Jones, Gerwyn M; Schimmel, Heinz; Žel, Jana; Huggett, Jim F; Redshaw, Nicholas; Karczmarczyk, Maria; Mozioğlu, Erkan; Akyürek, Sema; Akgöz, Müslüm; Milavec, Mojca

2017-04-01

Quantitative PCR (qPCR) is an important tool in pathogen detection. However, the use of different qPCR components, calibration materials and DNA extraction methods reduces comparability between laboratories, which can result in false diagnosis and discrepancies in patient care. The wider establishment of a metrological framework for nucleic acid tests could improve the degree of standardisation of pathogen detection and the quantification methods applied in the clinical context. To achieve this, accurate methods need to be developed and implemented as reference measurement procedures, and to facilitate characterisation of suitable certified reference materials. Digital PCR (dPCR) has already been used for pathogen quantification by analysing nucleic acids. Although dPCR has the potential to provide robust and accurate quantification of nucleic acids, further assessment of its actual performance characteristics is needed before it can be implemented in a metrological framework, and to allow adequate estimation of measurement uncertainties. Here, four laboratories demonstrated reproducibility (expanded measurement uncertainties below 15%) of dPCR for quantification of DNA from human cytomegalovirus, with no calibration to a common reference material. Using whole-virus material and extracted DNA, an intermediate precision (coefficients of variation below 25%) between three consecutive experiments was noted. Furthermore, discrepancies in estimated mean DNA copy number concentrations between laboratories were less than twofold, with DNA extraction as the main source of variability. These data demonstrate that dPCR offers a repeatable and reproducible method for quantification of viral DNA, and due to its satisfactory performance should be considered as candidate for reference methods for implementation in a metrological framework.

Effects of humic acid on DNA quantification with Quantifiler® Human DNA Quantification kit and short tandem repeat amplification efficiency.

Science.gov (United States)

Seo, Seung Bum; Lee, Hye Young; Zhang, Ai Hua; Kim, Hye Yeon; Shin, Dong Hoon; Lee, Soong Deok

2012-11-01

Correct DNA quantification is an essential part to obtain reliable STR typing results. Forensic DNA analysts often use commercial kits for DNA quantification; among them, real-time-based DNA quantification kits are most frequently used. Incorrect DNA quantification due to the presence of PCR inhibitors may affect experiment results. In this study, we examined the alteration degree of DNA quantification results estimated in DNA samples containing a PCR inhibitor by using a Quantifiler® Human DNA Quantification kit. For experiments, we prepared approximately 0.25 ng/μl DNA samples containing various concentrations of humic acid (HA). The quantification results were 0.194-0.303 ng/μl at 0-1.6 ng/μl HA (final concentration in the Quantifiler reaction) and 0.003-0.168 ng/μl at 2.4-4.0 ng/μl HA. Most DNA quantity was undetermined when HA concentration was higher than 4.8 ng/μl HA. The C (T) values of an internal PCR control (IPC) were 28.0-31.0, 36.5-37.1, and undetermined at 0-1.6, 2.4, and 3.2 ng/μl HA. These results indicate that underestimated DNA quantification results may be obtained in the DNA sample with high C (T) values of IPC. Thus, researchers should carefully interpret the DNA quantification results. We additionally examined the effects of HA on the STR amplification by using an Identifiler® kit and a MiniFiler™ kit. Based on the results of this study, it is thought that a better understanding of various effects of HA would help researchers recognize and manipulate samples containing HA.

A Java program for LRE-based real-time qPCR that enables large-scale absolute quantification.

Directory of Open Access Journals (Sweden)

Robert G Rutledge

Full Text Available BACKGROUND: Linear regression of efficiency (LRE introduced a new paradigm for real-time qPCR that enables large-scale absolute quantification by eliminating the need for standard curves. Developed through the application of sigmoidal mathematics to SYBR Green I-based assays, target quantity is derived directly from fluorescence readings within the central region of an amplification profile. However, a major challenge of implementing LRE quantification is the labor intensive nature of the analysis. FINDINGS: Utilizing the extensive resources that are available for developing Java-based software, the LRE Analyzer was written using the NetBeans IDE, and is built on top of the modular architecture and windowing system provided by the NetBeans Platform. This fully featured desktop application determines the number of target molecules within a sample with little or no intervention by the user, in addition to providing extensive database capabilities. MS Excel is used to import data, allowing LRE quantification to be conducted with any real-time PCR instrument that provides access to the raw fluorescence readings. An extensive help set also provides an in-depth introduction to LRE, in addition to guidelines on how to implement LRE quantification. CONCLUSIONS: The LRE Analyzer provides the automated analysis and data storage capabilities required by large-scale qPCR projects wanting to exploit the many advantages of absolute quantification. Foremost is the universal perspective afforded by absolute quantification, which among other attributes, provides the ability to directly compare quantitative data produced by different assays and/or instruments. Furthermore, absolute quantification has important implications for gene expression profiling in that it provides the foundation for comparing transcript quantities produced by any gene with any other gene, within and between samples.

Quantification of local mobilities

DEFF Research Database (Denmark)

Zhang, Y. B.

2018-01-01

A new method for quantification of mobilities of local recrystallization boundary segments is presented. The quantification is based on microstructures characterized using electron microscopy and on determination of migration velocities and driving forces for local boundary segments. Pure aluminium...... is investigated and the results show that even for a single recrystallization boundary, different boundary segments migrate differently, and the differences can be understood based on variations in mobilities and local deformed microstructures. The present work has important implications for understanding...

Development of Quantification Method for Bioluminescence Imaging

International Nuclear Information System (INIS)

Kim, Hyeon Sik; Min, Jung Joon; Lee, Byeong Il; Choi, Eun Seo; Tak, Yoon O; Choi, Heung Kook; Lee, Ju Young

2009-01-01

Optical molecular luminescence imaging is widely used for detection and imaging of bio-photons emitted by luminescent luciferase activation. The measured photons in this method provide the degree of molecular alteration or cell numbers with the advantage of high signal-to-noise ratio. To extract useful information from the measured results, the analysis based on a proper quantification method is necessary. In this research, we propose a quantification method presenting linear response of measured light signal to measurement time. We detected the luminescence signal by using lab-made optical imaging equipment of animal light imaging system (ALIS) and different two kinds of light sources. One is three bacterial light-emitting sources containing different number of bacteria. The other is three different non-bacterial light sources emitting very weak light. By using the concept of the candela and the flux, we could derive simplified linear quantification formula. After experimentally measuring light intensity, the data was processed with the proposed quantification function. We could obtain linear response of photon counts to measurement time by applying the pre-determined quantification function. The ratio of the re-calculated photon counts and measurement time present a constant value although different light source was applied. The quantification function for linear response could be applicable to the standard quantification process. The proposed method could be used for the exact quantitative analysis in various light imaging equipment with presenting linear response behavior of constant light emitting sources to measurement time

Development and validation of an open source quantification tool for DSC-MRI studies.

Science.gov (United States)

Gordaliza, P M; Mateos-Pérez, J M; Montesinos, P; Guzmán-de-Villoria, J A; Desco, M; Vaquero, J J

2015-03-01

This work presents the development of an open source tool for the quantification of dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion studies. The development of this tool is motivated by the lack of open source tools implemented on open platforms to allow external developers to implement their own quantification methods easily and without the need of paying for a development license. This quantification tool was developed as a plugin for the ImageJ image analysis platform using the Java programming language. A modular approach was used in the implementation of the components, in such a way that the addition of new methods can be done without breaking any of the existing functionalities. For the validation process, images from seven patients with brain tumors were acquired and quantified with the presented tool and with a widely used clinical software package. The resulting perfusion parameters were then compared. Perfusion parameters and the corresponding parametric images were obtained. When no gamma-fitting is used, an excellent agreement with the tool used as a gold-standard was obtained (R(2)>0.8 and values are within 95% CI limits in Bland-Altman plots). An open source tool that performs quantification of perfusion studies using magnetic resonance imaging has been developed and validated using a clinical software package. It works as an ImageJ plugin and the source code has been published with an open source license. Copyright © 2015 Elsevier Ltd. All rights reserved.

A novel synthetic quantification standard including virus and internal report targets: application for the detection and quantification of emerging begomoviruses on tomato.

Science.gov (United States)

Péréfarres, Frédéric; Hoareau, Murielle; Chiroleu, Frédéric; Reynaud, Bernard; Dintinger, Jacques; Lett, Jean-Michel

2011-08-05

real-time PCRs were developed in association with a novel strategy for the quantification standard. These assays should be of a great interest for breeding programs and epidemiological surveys to monitor viral populations.

A novel synthetic quantification standard including virus and internal report targets: application for the detection and quantification of emerging begomoviruses on tomato

Directory of Open Access Journals (Sweden)

Lett Jean-Michel

2011-08-01

quantify a wide range of begomoviruses, five duplex real-time PCRs were developed in association with a novel strategy for the quantification standard. These assays should be of a great interest for breeding programs and epidemiological surveys to monitor viral populations.

Quantification of fossil organic matter in contaminated sediments from an industrial watershed: Validation of the quantitative multimolecular approach by radiocarbon analysis

International Nuclear Information System (INIS)

Jeanneau, Laurent; Faure, Pierre

2010-01-01

The quantitative multimolecular approach (QMA) based on an exhaustive identification and quantification of molecules from the extractable organic matter (EOM) has been recently developed in order to investigate organic contamination in sediments by a more complete method than the restrictive quantification of target contaminants. Such an approach allows (i) the comparison between natural and anthropogenic inputs, (ii) between modern and fossil organic matter and (iii) the differentiation between several anthropogenic sources. However QMA is based on the quantification of molecules recovered by organic solvent and then analyzed by gas chromatography-mass spectrometry, which represent a small fraction of sedimentary organic matter (SOM). In order to extend the conclusions of QMA to SOM, radiocarbon analyses have been performed on organic extracts and decarbonated sediments. This analysis allows (i) the differentiation between modern biomass (contemporary 14 C) and fossil organic matter ( 14 C-free) and (ii) the calculation of the modern carbon percentage (PMC). At the confluence between Fensch and Moselle Rivers, a catchment highly contaminated by both industrial activities and urbanization, PMC values in decarbonated sediments are well correlated with the percentage of natural molecular markers determined by QMA. It highlights that, for this type of contamination by fossil organic matter inputs, the conclusions of QMA can be scaled up to SOM. QMA is an efficient environmental diagnostic tool that leads to a more realistic quantification of fossil organic matter in sediments.

Quantification of dsDNA using the Hitachi F-7000 Fluorescence Spectrophotometer and PicoGreen dye.

Science.gov (United States)

Moreno, Luis A; Cox, Kendra L

2010-11-05

Quantification of DNA, especially in small concentrations, is an important task with a wide range of biological applications including standard molecular biology assays such as synthesis and purification of DNA, diagnostic applications such as quantification of DNA amplification products, and detection of DNA molecules in drug preparations. During this video we will demonstrate the capability of the Hitachi F-7000 Fluorescence Spectrophotometer equipped with a Micro Plate Reader accessory to perform dsDNA quantification using Molecular Probes Quant-it PicoGreen dye reagent kit. The F-7000 Fluorescence Spectrophotometer offers high sensitivity and high speed measurements. It is a highly flexible system capable of measuring fluorescence, luminescence, and phosphorescence. Several measuring modes are available, including wavelength scan, time scan, photometry and 3-D scan measurement. The spectrophotometer has sensitivity in the range of 50 picomoles of fluorescein when using a 300 μL sample volume in the microplate, and is capable of measuring scan speeds of 60,000 nm/minute. It also has a wide dynamic range of up to 5 orders of magnitude which allows for the use of calibration curves over a wide range of concentrations. The optical system uses all reflective optics for maximum energy and sensitivity. The standard wavelength range is 200 to 750 nm, and can be extended to 900 nm when using one of the optional near infrared photomultipliers. The system allows optional temperature control for the plate reader from 5 to 60 degrees Celsius using an optional external temperature controlled liquid circulator. The microplate reader allows for the use of 96 well microplates, and the measuring speed for 96 wells is less than 60 seconds when using the kinetics mode. Software controls for the F-7000 and Microplate Reader are also highly flexible. Samples may be set in either column or row formats, and any combination of wells may be chosen for sample measurements. This allows

Quantification in single photon emission computed tomography (SPECT)

International Nuclear Information System (INIS)

Buvat, Irene

2005-01-01

The objective of this lecture is to understand the possibilities and limitations of the quantitative analysis of single photon emission computed tomography (SPECT) images. It is also to identify the conditions to be fulfilled to obtain reliable quantitative measurements from images. Content: 1 - Introduction: Quantification in emission tomography - definition and challenges; quantification biasing phenomena; 2 - quantification in SPECT, problems and correction methods: Attenuation, scattering, un-stationary spatial resolution, partial volume effect, movement, tomographic reconstruction, calibration; 3 - Synthesis: actual quantification accuracy; 4 - Beyond the activity concentration measurement

Development of a VHH-Based Erythropoietin Quantification Assay

DEFF Research Database (Denmark)

Kol, Stefan; Beuchert Kallehauge, Thomas; Adema, Simon

2015-01-01

Erythropoietin (EPO) quantification during cell line selection and bioreactor cultivation has traditionally been performed with ELISA or HPLC. As these techniques suffer from several drawbacks, we developed a novel EPO quantification assay. A camelid single-domain antibody fragment directed against...... human EPO was evaluated as a capturing antibody in a label-free biolayer interferometry-based quantification assay. Human recombinant EPO can be specifically detected in Chinese hamster ovary cell supernatants in a sensitive and pH-dependent manner. This method enables rapid and robust quantification...

Real-time PCR protocols for the quantification of the begomovirus tomato yellow leaf curl Sardinia virus in tomato plants and in its insect vector.

Science.gov (United States)

Noris, Emanuela; Miozzi, Laura

2015-01-01

Tomato yellow leaf curl Sardinia virus (TYLCSV) (Geminiviridae) is an important pathogen, transmitted by the whitefly Bemisia tabaci, that severely affects the tomato production in the Mediterranean basin. Here, we describe real-time PCR protocols suitable for relative and absolute quantification of TYLCSV in tomato plants and in whitefly extracts. Using primers and probe specifically designed for TYLCSV, the protocols for relative quantification allow to compare the amount of TYLCSV present in different plant or whitefly samples, normalized to the amount of DNA present in each sample using endogenous tomato or Bemisia genes as internal references. The absolute quantification protocol allows to calculate the number of genomic units of TYLCSV over the genomic units of the plant host (tomato), with a sensitivity of as few as ten viral genome copies per sample. The described protocols are potentially suitable for several applications, such as plant breeding for resistance, analysis of virus replication, and virus-vector interaction studies.

Quantification of silver nanoparticle uptake and distribution within individual human macrophages by FIB/SEM slice and view.

Science.gov (United States)

Guehrs, Erik; Schneider, Michael; Günther, Christian M; Hessing, Piet; Heitz, Karen; Wittke, Doreen; López-Serrano Oliver, Ana; Jakubowski, Norbert; Plendl, Johanna; Eisebitt, Stefan; Haase, Andrea

2017-03-21

Quantification of nanoparticle (NP) uptake in cells or tissues is very important for safety assessment. Often, electron microscopy based approaches are used for this purpose, which allow imaging at very high resolution. However, precise quantification of NP numbers in cells and tissues remains challenging. The aim of this study was to present a novel approach, that combines precise quantification of NPs in individual cells together with high resolution imaging of their intracellular distribution based on focused ion beam/ scanning electron microscopy (FIB/SEM) slice and view approaches. We quantified cellular uptake of 75 nm diameter citrate stabilized silver NPs (Ag 75 Cit) into an individual human macrophage derived from monocytic THP-1 cells using a FIB/SEM slice and view approach. Cells were treated with 10 μg/ml for 24 h. We investigated a single cell and found in total 3138 ± 722 silver NPs inside this cell. Most of the silver NPs were located in large agglomerates, only a few were found in clusters of fewer than five NPs. Furthermore, we cross-checked our results by using inductively coupled plasma mass spectrometry and could confirm the FIB/SEM results. Our approach based on FIB/SEM slice and view is currently the only one that allows the quantification of the absolute dose of silver NPs in individual cells and at the same time to assess their intracellular distribution at high resolution. We therefore propose to use FIB/SEM slice and view to systematically analyse the cellular uptake of various NPs as a function of size, concentration and incubation time.

An EPGPT-based approach for uncertainty quantification

International Nuclear Information System (INIS)

Wang, C.; Abdel-Khalik, H. S.

2012-01-01

Generalized Perturbation Theory (GPT) has been widely used by many scientific disciplines to perform sensitivity analysis and uncertainty quantification. This manuscript employs recent developments in GPT theory, collectively referred to as Exact-to-Precision Generalized Perturbation Theory (EPGPT), to enable uncertainty quantification for computationally challenging models, e.g. nonlinear models associated with many input parameters and many output responses and with general non-Gaussian parameters distributions. The core difference between EPGPT and existing GPT is in the way the problem is formulated. GPT formulates an adjoint problem that is dependent on the response of interest. It tries to capture via the adjoint solution the relationship between the response of interest and the constraints on the state variations. EPGPT recasts the problem in terms of a smaller set of what is referred to as the 'active' responses which are solely dependent on the physics model and the boundary and initial conditions rather than on the responses of interest. The objective of this work is to apply an EPGPT methodology to propagate cross-sections variations in typical reactor design calculations. The goal is to illustrate its use and the associated impact for situations where the typical Gaussian assumption for parameters uncertainties is not valid and when nonlinear behavior must be considered. To allow this demonstration, exaggerated variations will be employed to stimulate nonlinear behavior in simple prototypical neutronics models. (authors)

In vivo MRS metabolite quantification using genetic optimization

Science.gov (United States)

Papakostas, G. A.; Karras, D. A.; Mertzios, B. G.; van Ormondt, D.; Graveron-Demilly, D.

2011-11-01

The in vivo quantification of metabolites' concentrations, revealed in magnetic resonance spectroscopy (MRS) spectra, constitutes the main subject under investigation in this work. Significant contributions based on artificial intelligence tools, such as neural networks (NNs), with good results have been presented lately but have shown several drawbacks, regarding their quantification accuracy under difficult conditions. A general framework that encounters the quantification procedure as an optimization problem, which is solved using a genetic algorithm (GA), is proposed in this paper. Two different lineshape models are examined, while two GA configurations are applied on artificial data. Moreover, the introduced quantification technique deals with metabolite peaks' overlapping, a considerably difficult situation occurring under real conditions. Appropriate experiments have proved the efficiency of the introduced methodology, in artificial MRS data, by establishing it as a generic metabolite quantification procedure.

In vivo MRS metabolite quantification using genetic optimization

International Nuclear Information System (INIS)

Papakostas, G A; Mertzios, B G; Karras, D A; Van Ormondt, D; Graveron-Demilly, D

2011-01-01

The in vivo quantification of metabolites' concentrations, revealed in magnetic resonance spectroscopy (MRS) spectra, constitutes the main subject under investigation in this work. Significant contributions based on artificial intelligence tools, such as neural networks (NNs), with good results have been presented lately but have shown several drawbacks, regarding their quantification accuracy under difficult conditions. A general framework that encounters the quantification procedure as an optimization problem, which is solved using a genetic algorithm (GA), is proposed in this paper. Two different lineshape models are examined, while two GA configurations are applied on artificial data. Moreover, the introduced quantification technique deals with metabolite peaks' overlapping, a considerably difficult situation occurring under real conditions. Appropriate experiments have proved the efficiency of the introduced methodology, in artificial MRS data, by establishing it as a generic metabolite quantification procedure

Myoblots: dystrophin quantification by in-cell western assay for a streamlined development of Duchenne muscular dystrophy (DMD) treatments.

Science.gov (United States)

Ruiz-Del-Yerro, E; Garcia-Jimenez, I; Mamchaoui, K; Arechavala-Gomeza, V

2017-10-31

New therapies for neuromuscular disorders are often mutation specific and require to be studied in patient's cell cultures. In Duchenne muscular dystrophy (DMD) dystrophin restoration drugs are being developed but as muscle cell cultures from DMD patients are scarce and do not grow or differentiate well, only a limited number of candidate drugs are tested. Moreover, dystrophin quantification by western blotting requires a large number of cultured cells; so fewer compounds are as thoroughly screened as is desirable. We aimed to develop a quantitative assessment tool using fewer cells to contribute in the study of dystrophin and to identify better drug candidates. An 'in-cell western' assay is a quantitative immunofluorescence assay performed in cell culture microplates that allows protein quantification directly in culture, allowing a higher number of experimental repeats and throughput. We have optimized the assay ('myoblot') to be applied to the study of differentiated myoblast cultures. After an exhaustive optimization of the technique to adapt it to the growth and differentiation rates of our cultures and the low intrinsic expression of our proteins of interests, our myoblot protocol allows the quantification of dystrophin and other muscle-associated proteins in muscle cell cultures. We are able to distinguish accurately between the different sets of patients based on their dystrophin expression and detect dystrophin restoration after treatment. We expect that this new tool to quantify muscle proteins in DMD and other muscle disorders will aid in their diagnosis and in the development of new therapies. © 2017 British Neuropathological Society.

Self-optimized construction of transition rate matrices from accelerated atomistic simulations with Bayesian uncertainty quantification

Science.gov (United States)

Swinburne, Thomas D.; Perez, Danny

2018-05-01

A massively parallel method to build large transition rate matrices from temperature-accelerated molecular dynamics trajectories is presented. Bayesian Markov model analysis is used to estimate the expected residence time in the known state space, providing crucial uncertainty quantification for higher-scale simulation schemes such as kinetic Monte Carlo or cluster dynamics. The estimators are additionally used to optimize where exploration is performed and the degree of temperature acceleration on the fly, giving an autonomous, optimal procedure to explore the state space of complex systems. The method is tested against exactly solvable models and used to explore the dynamics of C15 interstitial defects in iron. Our uncertainty quantification scheme allows for accurate modeling of the evolution of these defects over timescales of several seconds.

TENORM radiological survey of Utica and Marcellus Shale

International Nuclear Information System (INIS)

Ying, Leong; O’Connor, Frank

2013-01-01

Comprehensive on-site radiological survey of processed sludge drilled materials extracted from the oil and gas production activities in the Utica and Marcellus Shale in Ohio has been conducted with a shielded isotopic identifier incorporating an advanced patented algorithmic processor to measure low-activity levels in compliance with environmental standards. - highlights: • First on-site radiological survey of processed shale sludge from oil and gas fields. • Mobile spectroscopic radiation inspection system with shielding for low-activity measurements. • Quantification of Ra-226 and Ra-228 radionuclides contamination in soil samples

Detection and Quantification of the Entomopathogenic Fungal Endophyte Beauveria bassiana in Plants by Nested and Quantitative PCR.

Science.gov (United States)

Garrido-Jurado, Inmaculada; Landa, Blanca B; Quesada-Moraga, Enrique

2016-01-01

The described protocol allows detecting as low as 10 fg the entomopathogenic fungal endophyte Beauveria bassiana in host plants by using a two-step nested PCR with the ITS1F/ITS4 and BB.fw and BB.rv primer pairs. On the other hand, a qPCR protocol using BB.fw and BB.rv primers is also available allowing the quantification of up to 26 fg of B. bassiana DNA per 20 ng of leaf DNA.

Quantification of video-taped images in microcirculation research using inexpensive imaging software (Adobe Photoshop).

Science.gov (United States)

Brunner, J; Krummenauer, F; Lehr, H A

2000-04-01

Study end-points in microcirculation research are usually video-taped images rather than numeric computer print-outs. Analysis of these video-taped images for the quantification of microcirculatory parameters usually requires computer-based image analysis systems. Most software programs for image analysis are custom-made, expensive, and limited in their applicability to selected parameters and study end-points. We demonstrate herein that an inexpensive, commercially available computer software (Adobe Photoshop), run on a Macintosh G3 computer with inbuilt graphic capture board provides versatile, easy to use tools for the quantification of digitized video images. Using images obtained by intravital fluorescence microscopy from the pre- and postischemic muscle microcirculation in the skinfold chamber model in hamsters, Photoshop allows simple and rapid quantification (i) of microvessel diameters, (ii) of the functional capillary density and (iii) of postischemic leakage of FITC-labeled high molecular weight dextran from postcapillary venules. We present evidence of the technical accuracy of the software tools and of a high degree of interobserver reliability. Inexpensive commercially available imaging programs (i.e., Adobe Photoshop) provide versatile tools for image analysis with a wide range of potential applications in microcirculation research.

Wiki Surveys: Open and Quantifiable Social Data Collection

Science.gov (United States)

Salganik, Matthew J.; Levy, Karen E. C.

2015-01-01

In the social sciences, there is a longstanding tension between data collection methods that facilitate quantification and those that are open to unanticipated information. Advances in technology now enable new, hybrid methods that combine some of the benefits of both approaches. Drawing inspiration from online information aggregation systems like Wikipedia and from traditional survey research, we propose a new class of research instruments called wiki surveys. Just as Wikipedia evolves over time based on contributions from participants, we envision an evolving survey driven by contributions from respondents. We develop three general principles that underlie wiki surveys: they should be greedy, collaborative, and adaptive. Building on these principles, we develop methods for data collection and data analysis for one type of wiki survey, a pairwise wiki survey. Using two proof-of-concept case studies involving our free and open-source website www.allourideas.org, we show that pairwise wiki surveys can yield insights that would be difficult to obtain with other methods. PMID:25992565

Wiki surveys: open and quantifiable social data collection.

Science.gov (United States)

Salganik, Matthew J; Levy, Karen E C

2015-01-01

In the social sciences, there is a longstanding tension between data collection methods that facilitate quantification and those that are open to unanticipated information. Advances in technology now enable new, hybrid methods that combine some of the benefits of both approaches. Drawing inspiration from online information aggregation systems like Wikipedia and from traditional survey research, we propose a new class of research instruments called wiki surveys. Just as Wikipedia evolves over time based on contributions from participants, we envision an evolving survey driven by contributions from respondents. We develop three general principles that underlie wiki surveys: they should be greedy, collaborative, and adaptive. Building on these principles, we develop methods for data collection and data analysis for one type of wiki survey, a pairwise wiki survey. Using two proof-of-concept case studies involving our free and open-source website www.allourideas.org, we show that pairwise wiki surveys can yield insights that would be difficult to obtain with other methods.

Rapid Quantification of Low-Viscosity Acetyl-Triacylglycerols Using Electrospray Ionization Mass Spectrometry.

Science.gov (United States)

Bansal, Sunil; Durrett, Timothy P

2016-09-01

Acetyl-triacylglycerols (acetyl-TAG) possess an sn-3 acetate group, which confers useful chemical and physical properties to these unusual triacylglycerols (TAG). Current methods for quantification of acetyl-TAG are time consuming and do not provide any information on the molecular species profile. Electrospray ionization mass spectrometry (ESI-MS)-based methods can overcome these drawbacks. However, the ESI-MS signal intensity for TAG depends on the aliphatic chain length and unsaturation index of the molecule. Therefore response factors for different molecular species need to be determined before any quantification. The effects of the chain length and the number of double-bonds of the sn-1/2 acyl groups on the signal intensity for the neutral loss of short chain length sn-3 groups were quantified using a series of synthesized sn-3 specific structured TAG. The signal intensity for the neutral loss of the sn-3 acyl group was found to negatively correlated with the aliphatic chain length and unsaturation index of the sn-1/2 acyl groups. The signal intensity of the neutral loss of the sn-3 acyl group was also negatively correlated with the size of that chain. Further, the position of the group undergoing neutral loss was also important, with the signal from an sn-2 acyl group much lower than that from one located at sn-3. Response factors obtained from these analyses were used to develop a method for the absolute quantification of acetyl-TAG. The increased sensitivity of this ESI-MS-based approach allowed successful quantification of acetyl-TAG in various biological settings, including the products of in vitro enzyme activity assays.

Elemental labelling combined with liquid chromatography inductively coupled plasma mass spectrometry for quantification of biomolecules: A review

International Nuclear Information System (INIS)

Kretschy, Daniela; Koellensperger, Gunda; Hann, Stephan

2012-01-01

Highlights: ► Survey of bio-analytical approaches utilizing biomolecule labelling. ► Detailed discussion of methodology and chemistry of elemental labelling. ► Biomedical and bio-analytical applications of elemental labelling. ► FI-ICP-MS and LC–ICP-MS for quantification of elemental labelled biomolecules. ► Review of selected applications. - Abstract: This article reviews novel quantification concepts where elemental labelling is combined with flow injection inductively coupled plasma mass spectrometry (FI-ICP-MS) or liquid chromatography inductively coupled plasma mass spectrometry (LC–ICP-MS), and employed for quantification of biomolecules such as proteins, peptides and related molecules in challenging sample matrices. In the first sections an overview on general aspects of biomolecule quantification, as well as of labelling will be presented emphasizing the potential, which lies in such methodological approaches. In this context, ICP-MS as detector provides high sensitivity, selectivity and robustness in biological samples and offers the capability for multiplexing and isotope dilution mass spectrometry (IDMS). Fundamental methodology of elemental labelling will be highlighted and analytical, as well as biomedical applications will be presented. A special focus will lie on established applications underlining benefits and bottlenecks of such approaches for the implementation in real life analysis. Key research made in this field will be summarized and a perspective for future developments including sophisticated and innovative applications will given.

Identification and Quantification of Celery Allergens Using Fiber Optic Surface Plasmon Resonance PCR.

Science.gov (United States)

Daems, Devin; Peeters, Bernd; Delport, Filip; Remans, Tony; Lammertyn, Jeroen; Spasic, Dragana

2017-07-31

Abstract : Accurate identification and quantification of allergens is key in healthcare, biotechnology and food quality and safety. Celery ( Apium graveolens ) is one of the most important elicitors of food allergic reactions in Europe. Currently, the golden standards to identify, quantify and discriminate celery in a biological sample are immunoassays and two-step molecular detection assays in which quantitative PCR (qPCR) is followed by a high-resolution melting analysis (HRM). In order to provide a DNA-based, rapid and simple detection method suitable for one-step quantification, a fiber optic PCR melting assay (FO-PCR-MA) was developed to determine different concentrations of celery DNA (1 pM-0.1 fM). The presented method is based on the hybridization and melting of DNA-coated gold nanoparticles to the FO sensor surface in the presence of the target gene (mannitol dehydrogenase, Mtd ). The concept was not only able to reveal the presence of celery DNA, but also allowed for the cycle-to-cycle quantification of the target sequence through melting analysis. Furthermore, the developed bioassay was benchmarked against qPCR followed by HRM, showing excellent agreement ( R ² = 0.96). In conclusion, this innovative and sensitive diagnostic test could further improve food quality control and thus have a large impact on allergen induced healthcare problems.

Offshore wind turbine risk quantification/evaluation under extreme environmental conditions

International Nuclear Information System (INIS)

Taflanidis, Alexandros A.; Loukogeorgaki, Eva; Angelides, Demos C.

2013-01-01

A simulation-based framework is discussed in this paper for quantification/evaluation of risk and development of automated risk assessment tools, focusing on applications to offshore wind turbines under extreme environmental conditions. The framework is founded on a probabilistic characterization of the uncertainty in the models for the excitation, the turbine and its performance. Risk is then quantified as the expected value of some risk consequence measure over the probability distributions considered for the uncertain model parameters. Stochastic simulation is proposed for the risk assessment, corresponding to the evaluation of some associated probabilistic integral quantifying risk, as it allows for the adoption of comprehensive computational models for describing the dynamic turbine behavior. For improvement of the computational efficiency, a surrogate modeling approach is introduced based on moving least squares response surface approximations. The assessment is also extended to a probabilistic sensitivity analysis that identifies the importance of each of the uncertain model parameters, i.e. risk factors, towards the total risk as well as towards each of the failure modes contributing to this risk. The versatility and computational efficiency of the advocated approaches is finally exploited to support the development of standalone risk assessment applets for automated implementation of the probabilistic risk quantification/assessment. -- Highlights: ► A simulation-based risk quantification/assessment framework is discussed. ► Focus is on offshore wind turbines under extreme environmental conditions. ► Approach is founded on probabilistic description of excitation/system model parameters. ► Surrogate modeling is adopted for improved computational efficiency. ► Standalone risk assessment applets for automated implementation are supported

Evidence-based quantification of uncertainties induced via simulation-based modeling

International Nuclear Information System (INIS)

Riley, Matthew E.

2015-01-01

The quantification of uncertainties in simulation-based modeling traditionally focuses upon quantifying uncertainties in the parameters input into the model, referred to as parametric uncertainties. Often neglected in such an approach are the uncertainties induced by the modeling process itself. This deficiency is often due to a lack of information regarding the problem or the models considered, which could theoretically be reduced through the introduction of additional data. Because of the nature of this epistemic uncertainty, traditional probabilistic frameworks utilized for the quantification of uncertainties are not necessarily applicable to quantify the uncertainties induced in the modeling process itself. This work develops and utilizes a methodology – incorporating aspects of Dempster–Shafer Theory and Bayesian model averaging – to quantify uncertainties of all forms for simulation-based modeling problems. The approach expands upon classical parametric uncertainty approaches, allowing for the quantification of modeling-induced uncertainties as well, ultimately providing bounds on classical probability without the loss of epistemic generality. The approach is demonstrated on two different simulation-based modeling problems: the computation of the natural frequency of a simple two degree of freedom non-linear spring mass system and the calculation of the flutter velocity coefficient for the AGARD 445.6 wing given a subset of commercially available modeling choices. - Highlights: • Modeling-induced uncertainties are often mishandled or ignored in the literature. • Modeling-induced uncertainties are epistemic in nature. • Probabilistic representations of modeling-induced uncertainties are restrictive. • Evidence theory and Bayesian model averaging are integrated. • Developed approach is applicable for simulation-based modeling problems

In situ Biofilm Quantification in Bioelectrochemical Systems by using Optical Coherence Tomography.

Science.gov (United States)

Molenaar, Sam D; Sleutels, Tom; Pereira, Joao; Iorio, Matteo; Borsje, Casper; Zamudio, Julian A; Fabregat-Santiago, Francisco; Buisman, Cees J N; Ter Heijne, Annemiek

2018-04-25

Detailed studies of microbial growth in bioelectrochemical systems (BESs) are required for their suitable design and operation. Here, we report the use of optical coherence tomography (OCT) as a tool for in situ and noninvasive quantification of biofilm growth on electrodes (bioanodes). An experimental platform is designed and described in which transparent electrodes are used to allow real-time, 3D biofilm imaging. The accuracy and precision of the developed method is assessed by relating the OCT results to well-established standards for biofilm quantification (chemical oxygen demand (COD) and total N content) and show high correspondence to these standards. Biofilm thickness observed by OCT ranged between 3 and 90 μm for experimental durations ranging from 1 to 24 days. This translated to growth yields between 38 and 42 mgCODbiomass  gCODacetate -1 at an anode potential of -0.35 V versus Ag/AgCl. Time-lapse observations of an experimental run performed in duplicate show high reproducibility in obtained microbial growth yield by the developed method. As such, we identify OCT as a powerful tool for conducting in-depth characterizations of microbial growth dynamics in BESs. Additionally, the presented platform allows concomitant application of this method with various optical and electrochemical techniques. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

A method for the 3-D quantification of bridging ligaments during crack propagation

International Nuclear Information System (INIS)

Babout, L.; Janaszewski, M.; Marrow, T.J.; Withers, P.J.

2011-01-01

This letter shows how a hole-closing algorithm can be used to identify and quantify crack-bridging ligaments from a sequence of X-ray tomography images of intergranular stress corrosion cracking. This allows automatic quantification of the evolution of bridging ligaments through the crack propagation sequence providing fracture mechanics insight previously unobtainable from fractography. The method may also be applied to other three-dimensional materials science problems, such as closing walls in foams.

Method for inverting reflection trace data from 3-D and 4-D seismic surveys and identifying subsurface fluid and pathways in and among hydrocarbon reservoirs based on impedance models

Science.gov (United States)

He, W.; Anderson, R.N.

1998-08-25

A method is disclosed for inverting 3-D seismic reflection data obtained from seismic surveys to derive impedance models for a subsurface region, and for inversion of multiple 3-D seismic surveys (i.e., 4-D seismic surveys) of the same subsurface volume, separated in time to allow for dynamic fluid migration, such that small scale structure and regions of fluid and dynamic fluid flow within the subsurface volume being studied can be identified. The method allows for the mapping and quantification of available hydrocarbons within a reservoir and is thus useful for hydrocarbon prospecting and reservoir management. An iterative seismic inversion scheme constrained by actual well log data which uses a time/depth dependent seismic source function is employed to derive impedance models from 3-D and 4-D seismic datasets. The impedance values can be region grown to better isolate the low impedance hydrocarbon bearing regions. Impedance data derived from multiple 3-D seismic surveys of the same volume can be compared to identify regions of dynamic evolution and bypassed pay. Effective Oil Saturation or net oil thickness can also be derived from the impedance data and used for quantitative assessment of prospective drilling targets and reservoir management. 20 figs.

A performance study on three qPCR quantification kits and their compatibilities with the 6-dye DNA profiling systems.

Science.gov (United States)

Lin, Sze-Wah; Li, Christina; Ip, Stephen C Y

2018-03-01

DNA quantification plays an integral role in forensic DNA profiling. Not only does it estimate the total amount of amplifiable human autosomal and male DNA to ensure optimal amplification of target DNA for subsequent analysis, but also assesses the extraction efficiency and purity of the DNA extract. Latest DNA quantification systems even offer an estimate for the degree of DNA degradation in a sample. Here, we report the performance of three new generation qPCR kits, namely Investigator ® Quantiplex HYres Kit from QIAGEN, Quantifiler ® Trio DNA Quantification Kit from Applied Biosystems™, and PowerQuant ® System from Promega, and their compatibilities with three 6-dye DNA profiling systems. Our results have demonstrated that all three kits generate standard curves with satisfactory consistency and reproducibility, and are capable of screening out traces of male DNA in the presence of 30-fold excess of female DNA. They also exhibit a higher tolerance to PCR inhibition than Quantifiler ® Human DNA Quantification Kit from Applied Biosystems™ in autosomal DNA quantification. PowerQuant ® , as compared to Quantiplex HYres and Quantifiler ® Trio, shows a better precision for both autosomal and male DNA quantifications. Quantifiler ® Trio and PowerQuant ® in contrast to Quantiplex HYres offer better correlations with lower discrepancies between autosomal and male DNA quantification, and their additional degradation index features provide a detection platform for inhibited and/or degraded DNA template. Regarding the compatibility between these quantification and profiling systems: (1) both Quantifiler ® Trio and PowerQuant ® work well with GlobalFiler and Fusion 6C, allowing a fairly accurate prediction of their DNA typing results based on the quantification values; (2) Quantiplex HYres offers a fairly reliable IPC system for detecting any potential inhibitions on Investigator 24plex, whereas Quantifiler ® Trio and PowerQuant ® suit better for Global

A simple method to improve the quantification accuracy of energy-dispersive X-ray microanalysis

International Nuclear Information System (INIS)

Walther, T

2008-01-01

Energy-dispersive X-ray spectroscopy in a transmission electron microscope is a standard tool for chemical microanalysis and routinely provides qualitative information on the presence of all major elements above Z=5 (boron) in a sample. Spectrum quantification relies on suitable corrections for absorption and fluorescence, in particular for thick samples and soft X-rays. A brief presentation is given of an easy way to improve quantification accuracy by evaluating the intensity ratio of two measurements acquired at different detector take-off angles. As the take-off angle determines the effective sample thickness seen by the detector this method corresponds to taking two measurements from the same position at two different thicknesses, which allows to correct absorption and fluorescence more reliably. An analytical solution for determining the depth of a feature embedded in the specimen foil is also provided.

Evolution of allowable stresses in shear for lumber

Science.gov (United States)

Robert L. Ethington; William L. Galligan; Henry M. Montrey; Alan D. Freas

1979-01-01

This paper surveys research leading to allowable shear stress parallel to grain for lumber. In early flexure tests of lumber, some pieces failed in shear. The estimated shear stress at time of failure was generally lower than shear strength measured on small, clear, straight-grained specimens. This and other engineering observations gave rise to adjustments that...

Detection, mapping, and quantification of single walled carbon nanotubes in histological specimens with photoacoustic microscopy.

Science.gov (United States)

Avti, Pramod K; Hu, Song; Favazza, Christopher; Mikos, Antonios G; Jansen, John A; Shroyer, Kenneth R; Wang, Lihong V; Sitharaman, Balaji

2012-01-01

In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM) was investigated to detect, map, and quantify trace amounts [nanograms (ng) to micrograms (µg)] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds). Optical-resolution (OR) and acoustic-resolution (AR)--Photoacoustic microscopy (PAM) was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR) fluorescence microscopy). Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections. The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs.

Detection, mapping, and quantification of single walled carbon nanotubes in histological specimens with photoacoustic microscopy.

Directory of Open Access Journals (Sweden)

Pramod K Avti

Full Text Available In the present study, the efficacy of multi-scale photoacoustic microscopy (PAM was investigated to detect, map, and quantify trace amounts [nanograms (ng to micrograms (µg] of SWCNTs in a variety of histological tissue specimens consisting of cancer and benign tissue biopsies (histological specimens from implanted tissue engineering scaffolds.Optical-resolution (OR and acoustic-resolution (AR--Photoacoustic microscopy (PAM was employed to detect, map and quantify the SWCNTs in a variety of tissue histological specimens and compared with other optical techniques (bright-field optical microscopy, Raman microscopy, near infrared (NIR fluorescence microscopy.Both optical-resolution and acoustic-resolution PAM, allow the detection and quantification of SWCNTs in histological specimens with scalable spatial resolution and depth penetration. The noise-equivalent detection sensitivity to SWCNTs in the specimens was calculated to be as low as ∼7 pg. Image processing analysis further allowed the mapping, distribution, and quantification of the SWCNTs in the histological sections.The results demonstrate the potential of PAM as a promising imaging technique to detect, map, and quantify SWCNTs in histological specimens, and could complement the capabilities of current optical and electron microscopy techniques in the analysis of histological specimens containing SWCNTs.

Digital PCR for direct quantification of viruses without DNA extraction.

Science.gov (United States)

Pavšič, Jernej; Žel, Jana; Milavec, Mojca

2016-01-01

DNA extraction before amplification is considered an essential step for quantification of viral DNA using real-time PCR (qPCR). However, this can directly affect the final measurements due to variable DNA yields and removal of inhibitors, which leads to increased inter-laboratory variability of qPCR measurements and reduced agreement on viral loads. Digital PCR (dPCR) might be an advantageous methodology for the measurement of virus concentrations, as it does not depend on any calibration material and it has higher tolerance to inhibitors. DNA quantification without an extraction step (i.e. direct quantification) was performed here using dPCR and two different human cytomegalovirus whole-virus materials. Two dPCR platforms were used for this direct quantification of the viral DNA, and these were compared with quantification of the extracted viral DNA in terms of yield and variability. Direct quantification of both whole-virus materials present in simple matrices like cell lysate or Tris-HCl buffer provided repeatable measurements of virus concentrations that were probably in closer agreement with the actual viral load than when estimated through quantification of the extracted DNA. Direct dPCR quantification of other viruses, reference materials and clinically relevant matrices is now needed to show the full versatility of this very promising and cost-efficient development in virus quantification.

A universal real-time PCR assay for the quantification of group-M HIV-1 proviral load.

Science.gov (United States)

Malnati, Mauro S; Scarlatti, Gabriella; Gatto, Francesca; Salvatori, Francesca; Cassina, Giulia; Rutigliano, Teresa; Volpi, Rosy; Lusso, Paolo

2008-01-01

Quantification of human immunodeficiency virus type-1 (HIV-1) proviral DNA is increasingly used to measure the HIV-1 cellular reservoirs, a helpful marker to evaluate the efficacy of antiretroviral therapeutic regimens in HIV-1-infected individuals. Furthermore, the proviral DNA load represents a specific marker for the early diagnosis of perinatal HIV-1 infection and might be predictive of HIV-1 disease progression independently of plasma HIV-1 RNA levels and CD4(+) T-cell counts. The high degree of genetic variability of HIV-1 poses a serious challenge for the design of a universal quantitative assay capable of detecting all the genetic subtypes within the main (M) HIV-1 group with similar efficiency. Here, we describe a highly sensitive real-time PCR protocol that allows for the correct quantification of virtually all group-M HIV-1 strains with a higher degree of accuracy compared with other methods. The protocol involves three stages, namely DNA extraction/lysis, cellular DNA quantification and HIV-1 proviral load assessment. Owing to the robustness of the PCR design, this assay can be performed on crude cellular extracts, and therefore it may be suitable for the routine analysis of clinical samples even in developing countries. An accurate quantification of the HIV-1 proviral load can be achieved within 1 d from blood withdrawal.

Bathymetric survey and estimation of the water balance of Lake ...

African Journals Online (AJOL)

Quantification of the water balance components and bathymetric survey is very crucial for sustainable management of lake waters. This paper focuses on the bathymetry and the water balance of the crater Lake Ardibo, recently utilized for irrigation. The bathymetric map of the lake is established at a contour interval of 10 ...

Ex vivo activity quantification in micrometastases at the cellular scale using the α-camera technique

DEFF Research Database (Denmark)

Chouin, Nicolas; Lindegren, Sture; Frost, Sofia H L

2013-01-01

Targeted α-therapy (TAT) appears to be an ideal therapeutic technique for eliminating malignant circulating, minimal residual, or micrometastatic cells. These types of malignancies are typically infraclinical, complicating the evaluation of potential treatments. This study presents a method of ex...... vivo activity quantification with an α-camera device, allowing measurement of the activity taken up by tumor cells in biologic structures a few tens of microns....

Wavelets in quantification of liver tumors in contrasted computed tomography images

International Nuclear Information System (INIS)

Rodrigues, Bruna T.; Alvarez, Matheus; Souza, Rafael T.F.; Miranda, Jose R.A.; Romeiro, Fernando G.; Pina, Diana R. de; Trindade, Andre Petean

2012-01-01

This paper presents an original methodology of liver tumors segmentation, based on wavelet transform. A virtual phantom was constructed with the same mean and standard deviation of the intensity of gray presented by the measured liver tissue. The optimized algorithm had a sensitivity ranging from 0.81 to 0.83, with a specificity of 0.95 for differentiation of hepatic tumors from normal tissues. We obtained a 96% agreement between the pixels segmented by an experienced radiologist and the algorithm presented here. According to the results shown in this work, the algorithm is optimal for the beginning of the tests for quantification of liver tumors in retrospective surveys. (author)

Exploiting multicompartment effects in triple-echo steady-state T2 mapping for fat fraction quantification.

Science.gov (United States)

Liu, Dian; Steingoetter, Andreas; Curcic, Jelena; Kozerke, Sebastian

2018-01-01

To investigate and exploit the effect of intravoxel off-resonance compartments in the triple-echo steady-state (TESS) sequence without fat suppression for T 2 mapping and to leverage the results for fat fraction quantification. In multicompartment tissue, where at least one compartment is excited off-resonance, the total signal exhibits periodic modulations as a function of echo time (TE). Simulated multicompartment TESS signals were synthesized at various TEs. Fat emulsion phantoms were prepared and scanned at the same TE combinations using TESS. In vivo knee data were obtained with TESS to validate the simulations. The multicompartment effect was exploited for fat fraction quantification in the stomach by acquiring TESS signals at two TE combinations. Simulated and measured multicompartment signal intensities were in good agreement. Multicompartment effects caused erroneous T 2 offsets, even at low water-fat ratios. The choice of TE caused T 2 variations of as much as 28% in cartilage. The feasibility of fat fraction quantification to monitor the decrease of fat content in the stomach during digestion is demonstrated. Intravoxel off-resonance compartments are a confounding factor for T 2 quantification using TESS, causing errors that are dependent on the TE. At the same time, off-resonance effects may allow for efficient fat fraction mapping using steady-state imaging. Magn Reson Med 79:423-429, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Quantification of the Pyrrolizidine Alkaloid Jacobine in Crassocephalum crepidioides by Cation Exchange High-Performance Liquid Chromatography.

Science.gov (United States)

Rozhon, Wilfried; Kammermeier, Lukas; Schramm, Sebastian; Towfique, Nayeem; Adebimpe Adedeji, N; Adesola Ajayi, S; Poppenberger, Brigitte

2018-01-01

Pyrrolizidine alkaloids (PAs) are secondary plant metabolites with considerable hepatoxic, tumorigenic and genotoxic potential. For separation, reversed phase chromatography is commonly used because of its excellent compatibility with detection by mass spectrometry. However, reversed phase chromatography has a low selectivity for PAs. The objective of this work was to investigate the suitability of cation exchange chromatography for separation of PAs and to develop a rapid method for quantification of jacobine in Crassocephalum crepidioides that is suitable for analysis of huge sample numbers as required for mutant screening procedures. We demonstrate that cation exchange chromatography offers excellent selectivity for PAs allowing their separation from most other plant metabolites. Due to the high selectivity, plant extracts can be directly analysed after simple sample preparation. Detection with UV at 200 nm instead of mass spectrometry can be applied, which makes the method very simple and cost-effective. The recovery rate of the method exceeded 95%, the intra-day and inter-day standard deviations were below 7% and the limit of detection and quantification were 1 mg/kg and 3 mg/kg, respectively. The developed method is sufficiently sensitive for reproducible detection of jacobine in C. crepidioides. Simple sample preparation and rapid separation allows for quantification of jacobine in plant material in a high-throughput manner. Thus, the method is suitable for genetic screenings and may be applicable for other plant species, for instance Jacobaea maritima. In addition, our results show that C. crepidioides cannot be considered safe for human consumption. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The quantification of risk and tourism

Directory of Open Access Journals (Sweden)

Piet Croucamp

2014-01-01

Full Text Available Tourism in South Africa comprises 9.5% of Gross Domestic Product (GDP, but remains an underresearched industry, especially regarding the quantification of the risks prevailing in the social, political and economic environment in which the industry operates. Risk prediction, extrapolation forecasting is conducted largely in the context of a qualitative methodology. This article reflects on the quantification of social constructs as variables of risk in the tourism industry with reference to South Africa. The theory and methodology of quantification is briefly reviewed and the indicators of risk are conceptualized and operationalized. The identified indicators are scaled in indices for purposes of quantification. Risk assessments and the quantification of constructs rely heavily on the experience - often personal - of the researcher and this scholarly endeavour is, therefore, not inclusive of all possible identified indicators of risk. It is accepted that tourism in South Africa is an industry comprising of a large diversity of sectors, each with a different set of risk indicators and risk profiles. The emphasis of this article is thus on the methodology to be applied to a risk profile. A secondary endeavour is to provide for clarity about the conceptual and operational confines of risk in general, as well as how quantified risk relates to the tourism industry. The indices provided include both domesticand international risk indicators. The motivation for the article is to encourage a greater emphasis on quantitative research in our efforts to understand and manage a risk profile for the tourist industry.

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

International Nuclear Information System (INIS)

Jackson, Christopher B.; Gallati, Sabina; Schaller, André

2012-01-01

Highlights: ► Serial qPCR accurately determines fragmentation state of any given DNA sample. ► Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. ► Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. ► Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze–thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA (λ nDNA ) and mtDNA (λ mtDNA ) we present an approach to possibly correct measurements in degraded samples in the future. To our knowledge this is the first time different degradation impact of the two

qPCR-based mitochondrial DNA quantification: Influence of template DNA fragmentation on accuracy

Energy Technology Data Exchange (ETDEWEB)

Jackson, Christopher B., E-mail: Christopher.jackson@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Gallati, Sabina, E-mail: sabina.gallati@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland); Schaller, Andre, E-mail: andre.schaller@insel.ch [Division of Human Genetics, Departements of Pediatrics and Clinical Research, Inselspital, University of Berne, Freiburgstrasse, CH-3010 Berne (Switzerland)

2012-07-06

Highlights: Black-Right-Pointing-Pointer Serial qPCR accurately determines fragmentation state of any given DNA sample. Black-Right-Pointing-Pointer Serial qPCR demonstrates different preservation of the nuclear and mitochondrial genome. Black-Right-Pointing-Pointer Serial qPCR provides a diagnostic tool to validate the integrity of bioptic material. Black-Right-Pointing-Pointer Serial qPCR excludes degradation-induced erroneous quantification. -- Abstract: Real-time PCR (qPCR) is the method of choice for quantification of mitochondrial DNA (mtDNA) by relative comparison of a nuclear to a mitochondrial locus. Quantitative abnormal mtDNA content is indicative of mitochondrial disorders and mostly confines in a tissue-specific manner. Thus handling of degradation-prone bioptic material is inevitable. We established a serial qPCR assay based on increasing amplicon size to measure degradation status of any DNA sample. Using this approach we can exclude erroneous mtDNA quantification due to degraded samples (e.g. long post-exicision time, autolytic processus, freeze-thaw cycles) and ensure abnormal DNA content measurements (e.g. depletion) in non-degraded patient material. By preparation of degraded DNA under controlled conditions using sonification and DNaseI digestion we show that erroneous quantification is due to the different preservation qualities of the nuclear and the mitochondrial genome. This disparate degradation of the two genomes results in over- or underestimation of mtDNA copy number in degraded samples. Moreover, as analysis of defined archival tissue would allow to precise the molecular pathomechanism of mitochondrial disorders presenting with abnormal mtDNA content, we compared fresh frozen (FF) with formalin-fixed paraffin-embedded (FFPE) skeletal muscle tissue of the same sample. By extrapolation of measured decay constants for nuclear DNA ({lambda}{sub nDNA}) and mtDNA ({lambda}{sub mtDNA}) we present an approach to possibly correct measurements in

Quantification accuracy and partial volume effect in dependence of the attenuation correction of a state-of-the-art small animal PET scanner

International Nuclear Information System (INIS)

Mannheim, Julia G; Judenhofer, Martin S; Schmid, Andreas; Pichler, Bernd J; Tillmanns, Julia; Stiller, Detlef; Sossi, Vesna

2012-01-01

Quantification accuracy and partial volume effect (PVE) of the Siemens Inveon PET scanner were evaluated. The influence of transmission source activities (40 and 160 MBq) on the quantification accuracy and the PVE were determined. Dynamic range, object size and PVE for different sphere sizes, contrast ratios and positions in the field of view (FOV) were evaluated. The acquired data were reconstructed using different algorithms and correction methods. The activity level of the transmission source and the total emission activity in the FOV strongly influenced the attenuation maps. Reconstruction algorithms, correction methods, object size and location within the FOV had a strong influence on the PVE in all configurations. All evaluated parameters potentially influence the quantification accuracy. Hence, all protocols should be kept constant during a study to allow a comparison between different scans. (paper)

Furan quantification in bread crust: development of a simple and sensitive method using headspace-trap GC-MS.

Science.gov (United States)

Huault, Lucie; Descharles, Nicolas; Rega, Barbara; Bistac, Sophie; Bosc, Véronique; Giampaoli, Pierre

2016-01-01

To study reactivity in bread crust during the baking process in the pan, we followed furan mainly resulting from Maillard and caramelisation reactions in cereal products. Furan quantification is commonly performed with automatic HS-static GC-MS. However, we showed that the automatic HS-trap GC-MS method can improve the sensitivity of the furan quantification. Indeed, this method allowed the LOD to be decreased from 0.3 ng g(-1) with HS-static mode to 0.03 ng g(-1) with HS-trap mode under these conditions. After validation of this method for furan quantification in bread crust, a difference between the crust extracted from the bottom and from the sides of the bread was evident. The quantity of furan in the bottom crust was five times lower than in the side crust, revealing less reactivity on the bottom than on the sides of the bread during the baking process in the pan. Differences in water content may explain these variations in reactivity.

Rapid capillary electrophoresis approach for the quantification of ewe milk adulteration with cow milk.

Science.gov (United States)

Trimboli, Francesca; Morittu, Valeria Maria; Cicino, Caterina; Palmieri, Camillo; Britti, Domenico

2017-10-13

The substitution of ewe milk with more economic cow milk is a common fraud. Here we present a capillary electrophoresis method for the quantification of ewe milk in ovine/bovine milk mixtures, which allows for the rapid and inexpensive recognition of ewe milk adulteration with cow milk. We utilized a routine CE method for human blood and urine proteins analysis, which fulfilled the separation of skimmed milk proteins in alkaline buffer. Under this condition, ovine and bovine milk exhibited a recognizable and distinct CE protein profiles, with a specific ewe peak showing a reproducible migration zone in ovine/bovine mixtures. Based on ewe specific CE peak, we developed a method for ewe milk quantification in ovine/bovine skimmed milk mixtures, which showed good linearity, precision and accuracy, and a minimum amount of detectable fraudulent cow milk equal to 5%. Copyright © 2017 Elsevier B.V. All rights reserved.

High performance liquid chromatography-charged aerosol detection applying an inverse gradient for quantification of rhamnolipid biosurfactants.

Science.gov (United States)

Behrens, Beate; Baune, Matthias; Jungkeit, Janek; Tiso, Till; Blank, Lars M; Hayen, Heiko

2016-07-15

A method using high performance liquid chromatography coupled to charged-aerosol detection (HPLC-CAD) was developed for the quantification of rhamnolipid biosurfactants. Qualitative sample composition was determined by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The relative quantification of different derivatives of rhamnolipids including di-rhamnolipids, mono-rhamnolipids, and their precursors 3-(3-hydroxyalkanoyloxy)alkanoic acids (HAAs) differed for two compared LC-MS instruments and revealed instrument dependent responses. Our here reported HPLC-CAD method provides uniform response. An inverse gradient was applied for the absolute quantification of rhamnolipid congeners to account for the detector's dependency on the solvent composition. The CAD produces a uniform response not only for the analytes but also for structurally different (nonvolatile) compounds. It was demonstrated that n-dodecyl-β-d-maltoside or deoxycholic acid can be used as alternative standards. The method of HPLC-ultra violet (UV) detection after a derivatization of rhamnolipids and HAAs to their corresponding phenacyl esters confirmed the obtained results but required additional, laborious sample preparation steps. Sensitivity determined as limit of detection and limit of quantification for four mono-rhamnolipids was in the range of 0.3-1.0 and 1.2-2.0μg/mL, respectively, for HPLC-CAD and 0.4 and 1.5μg/mL, respectively, for HPLC-UV. Linearity for HPLC-CAD was at least 0.996 (R(2)) in the calibrated range of about 1-200μg/mL. Hence, the here presented HPLC-CAD method allows absolute quantification of rhamnolipids and derivatives. Copyright © 2016 Elsevier B.V. All rights reserved.

Targeting a polyketide synthase gene for Aspergillus carbonarius quantification and ochratoxin A assessment in grapes using real-time PCR

International Nuclear Information System (INIS)

Atoui, A.; Mathieu, F.; Lebrihi, A.

2007-01-01

Aspergillus carbonarius is an ochratoxin producing fungus that has been considered to be responsible of the ochratoxin A (OTA) contamination in grapes and wine. In order to monitor and quantify A. carbonarius, a specific primer pair Ac12RL O TAF/Ac12RL O TAR has been designed from the acyltransferase (AT) domain of the polyketide synthase sequence Ac12RL3 to amplify 141 bp PCR product. Among the mycotoxigenic fungi tested, only A. carbonarius gave a positive result. This specific primer pair was also successfully employed in real-time PCR conjugated with SYBR Green I dye for the direct quantification of this fungus in grape samples. A positive correlation (R2 = 0.81) was found between A. carbonarius DNA content and OTA concentration in 72 grape samples, allowing for the estimation of the potential risk from OTA contamination. Consequently, this work offers a quick alternative to conventional methods of OTA quantification and mycological detection and quantification of A. carbonarius in grapes. (author)

(1) H-MRS processing parameters affect metabolite quantification

DEFF Research Database (Denmark)

Bhogal, Alex A; Schür, Remmelt R; Houtepen, Lotte C

2017-01-01

investigated the influence of model parameters and spectral quantification software on fitted metabolite concentration values. Sixty spectra in 30 individuals (repeated measures) were acquired using a 7-T MRI scanner. Data were processed by four independent research groups with the freedom to choose their own...... + NAAG/Cr + PCr and Glu/Cr + PCr, respectively. Metabolite quantification using identical (1) H-MRS data was influenced by processing parameters, basis sets and software choice. Locally preferred processing choices affected metabolite quantification, even when using identical software. Our results......Proton magnetic resonance spectroscopy ((1) H-MRS) can be used to quantify in vivo metabolite levels, such as lactate, γ-aminobutyric acid (GABA) and glutamate (Glu). However, there are considerable analysis choices which can alter the accuracy or precision of (1) H-MRS metabolite quantification...

Identification and Quantification of Celery Allergens Using Fiber Optic Surface Plasmon Resonance PCR

Directory of Open Access Journals (Sweden)

Devin Daems

2017-07-01

Full Text Available Abstract: Accurate identification and quantification of allergens is key in healthcare, biotechnology and food quality and safety. Celery (Apium graveolens is one of the most important elicitors of food allergic reactions in Europe. Currently, the golden standards to identify, quantify and discriminate celery in a biological sample are immunoassays and two-step molecular detection assays in which quantitative PCR (qPCR is followed by a high-resolution melting analysis (HRM. In order to provide a DNA-based, rapid and simple detection method suitable for one-step quantification, a fiber optic PCR melting assay (FO-PCR-MA was developed to determine different concentrations of celery DNA (1 pM–0.1 fM. The presented method is based on the hybridization and melting of DNA-coated gold nanoparticles to the FO sensor surface in the presence of the target gene (mannitol dehydrogenase, Mtd. The concept was not only able to reveal the presence of celery DNA, but also allowed for the cycle-to-cycle quantification of the target sequence through melting analysis. Furthermore, the developed bioassay was benchmarked against qPCR followed by HRM, showing excellent agreement (R2 = 0.96. In conclusion, this innovative and sensitive diagnostic test could further improve food quality control and thus have a large impact on allergen induced healthcare problems.

Multi-tissue partial volume quantification in multi-contrast MRI using an optimised spectral unmixing approach.

Science.gov (United States)

Collewet, Guylaine; Moussaoui, Saïd; Deligny, Cécile; Lucas, Tiphaine; Idier, Jérôme

2018-06-01

Multi-tissue partial volume estimation in MRI images is investigated with a viewpoint related to spectral unmixing as used in hyperspectral imaging. The main contribution of this paper is twofold. It firstly proposes a theoretical analysis of the statistical optimality conditions of the proportion estimation problem, which in the context of multi-contrast MRI data acquisition allows to appropriately set the imaging sequence parameters. Secondly, an efficient proportion quantification algorithm based on the minimisation of a penalised least-square criterion incorporating a regularity constraint on the spatial distribution of the proportions is proposed. Furthermore, the resulting developments are discussed using empirical simulations. The practical usefulness of the spectral unmixing approach for partial volume quantification in MRI is illustrated through an application to food analysis on the proving of a Danish pastry. Copyright © 2018 Elsevier Inc. All rights reserved.

Benchmarking common quantification strategies for large-scale phosphoproteomics

DEFF Research Database (Denmark)

Hogrebe, Alexander; von Stechow, Louise; Bekker-Jensen, Dorte B

2018-01-01

Comprehensive mass spectrometry (MS)-based proteomics is now feasible, but reproducible quantification remains challenging, especially for post-translational modifications such as phosphorylation. Here, we compare the most popular quantification techniques for global phosphoproteomics: label-free...

Quantification of analytes affected by relevant interfering signals under quality controlled conditions

International Nuclear Information System (INIS)

Bettencourt da Silva, Ricardo J.N.; Santos, Julia R.; Camoes, M. Filomena G.F.C.

2006-01-01

The analysis of organic contaminants or residues in biological samples is frequently affected by the presence of compounds producing interfering instrumental signals. This feature is responsible for the higher complexity and cost of these analyses and/or by a significant reduction of the number of studied analytes in a multi-analyte method. This work presents a methodology to estimate the impact of the interfering compounds on the quality of the analysis of complex samples, based on separative instrumental methods of analysis, aiming at supporting the inclusion of analytes affected by interfering compounds in the list of compounds analysed in the studied samples. The proposed methodology involves the study of the magnitude of the signal produced by the interfering compounds in the analysed matrix, and is applicable to analytical systems affected by interfering compounds with varying concentration in the studied matrix. The proposed methodology is based on the comparison of the signals from a representative number of examples of the studied matrix, in order to estimate the impact of the presence of such compounds on the measurement quality. The treatment of the chromatographic signals necessary to collect these data can be easily performed considering algorithms of subtraction of chromatographic signals available in most of the analytical instrumentation software. The subtraction of the interfering compounds signal from the sample signal allows the compensation of the interfering effect irrespective of the relative magnitude of the interfering and analyte signals, supporting the applicability of the same model of the method performance for a broader concentration range. The quantification of the measurement uncertainty was performed using the differential approach, which allows the estimation of the contribution of the presence of the interfering compounds to the quality of the measurement. The proposed methodology was successfully applied to the analysis of

Multiple headspace-solid-phase microextraction: An application to quantification of mushroom volatiles

Energy Technology Data Exchange (ETDEWEB)

Costa, Rosaria; Tedone, Laura; De Grazia, Selenia [Dipartimento Farmaco-chimico, University of Messina, viale Annunziata, 98168 Messina (Italy); Dugo, Paola [Dipartimento Farmaco-chimico, University of Messina, viale Annunziata, 98168 Messina (Italy); Centro Integrato di Ricerca (C.I.R.), Università Campus-Biomedico, Via Álvaro del Portillo, 21, 00128 Roma (Italy); Mondello, Luigi, E-mail: lmondello@unime.it [Dipartimento Farmaco-chimico, University of Messina, viale Annunziata, 98168 Messina (Italy); Centro Integrato di Ricerca (C.I.R.), Università Campus-Biomedico, Via Álvaro del Portillo, 21, 00128 Roma (Italy)

2013-04-03

Highlights: ► Multiple headspace extraction-solid phase microextraction (MHS-SPME) has been applied to the analysis of Agaricus bisporus. ► Mushroom flavor is characterized by the presence of compounds with a 8-carbon atoms skeleton. ► Formation of 8-carbon compounds involves a unique fungal biochemical pathway. ► The MHS-SPME allowed to determine quantitatively 5 target analytes of A. bisporus for the first time. -- Abstract: Multiple headspace-solid phase microextraction (MHS-SPME) followed by gas chromatography/mass spectrometry (GC–MS) and flame ionization detection (GC–FID) was applied to the identification and quantification of volatiles released by the mushroom Agaricus bisporus, also known as champignon. MHS-SPME allows to perform quantitative analysis of volatiles from solid matrices, free of matrix interferences. Samples analyzed were fresh mushrooms (chopped and homogenized) and mushroom-containing food dressings. 1-Octen-3-ol, 3-octanol, 3-octanone, 1-octen-3-one and benzaldehyde were common constituents of the samples analyzed. Method performance has been tested through the evaluation of limit of detection (LoD, range 0.033–0.078 ng), limit of quantification (LoQ, range 0.111–0.259 ng) and analyte recovery (92.3–108.5%). The results obtained showed quantitative differences among the samples, which can be attributed to critical factors, such as the degree of cell damage upon sample preparation, that are here discussed. Considerations on the mushrooms biochemistry and on the basic principles of MHS analysis are also presented.

Multiple headspace-solid-phase microextraction: An application to quantification of mushroom volatiles

International Nuclear Information System (INIS)

Costa, Rosaria; Tedone, Laura; De Grazia, Selenia; Dugo, Paola; Mondello, Luigi

2013-01-01

Highlights: ► Multiple headspace extraction-solid phase microextraction (MHS-SPME) has been applied to the analysis of Agaricus bisporus. ► Mushroom flavor is characterized by the presence of compounds with a 8-carbon atoms skeleton. ► Formation of 8-carbon compounds involves a unique fungal biochemical pathway. ► The MHS-SPME allowed to determine quantitatively 5 target analytes of A. bisporus for the first time. -- Abstract: Multiple headspace-solid phase microextraction (MHS-SPME) followed by gas chromatography/mass spectrometry (GC–MS) and flame ionization detection (GC–FID) was applied to the identification and quantification of volatiles released by the mushroom Agaricus bisporus, also known as champignon. MHS-SPME allows to perform quantitative analysis of volatiles from solid matrices, free of matrix interferences. Samples analyzed were fresh mushrooms (chopped and homogenized) and mushroom-containing food dressings. 1-Octen-3-ol, 3-octanol, 3-octanone, 1-octen-3-one and benzaldehyde were common constituents of the samples analyzed. Method performance has been tested through the evaluation of limit of detection (LoD, range 0.033–0.078 ng), limit of quantification (LoQ, range 0.111–0.259 ng) and analyte recovery (92.3–108.5%). The results obtained showed quantitative differences among the samples, which can be attributed to critical factors, such as the degree of cell damage upon sample preparation, that are here discussed. Considerations on the mushrooms biochemistry and on the basic principles of MHS analysis are also presented

Quantification of Cannabinoid Content in Cannabis

Science.gov (United States)

Tian, Y.; Zhang, F.; Jia, K.; Wen, M.; Yuan, Ch.

2015-09-01

Cannabis is an economically important plant that is used in many fields, in addition to being the most commonly consumed illicit drug worldwide. Monitoring the spatial distribution of cannabis cultivation and judging whether it is drug- or fiber-type cannabis is critical for governments and international communities to understand the scale of the illegal drug trade. The aim of this study was to investigate whether the cannabinoids content in cannabis could be spectrally quantified using a spectrometer and to identify the optimal wavebands for quantifying the cannabinoid content. Spectral reflectance data of dried cannabis leaf samples and the cannabis canopy were measured in the laboratory and in the field, respectively. Correlation analysis and the stepwise multivariate regression method were used to select the optimal wavebands for cannabinoid content quantification based on the laboratory-measured spectral data. The results indicated that the delta-9-tetrahydrocannabinol (THC) content in cannabis leaves could be quantified using laboratory-measured spectral reflectance data and that the 695 nm band is the optimal band for THC content quantification. This study provides prerequisite information for designing spectral equipment to enable immediate quantification of THC content in cannabis and to discriminate drug- from fiber-type cannabis based on THC content quantification in the field.

Quantification of discreteness effects in cosmological N-body simulations: Initial conditions

International Nuclear Information System (INIS)

Joyce, M.; Marcos, B.

2007-01-01

The relation between the results of cosmological N-body simulations, and the continuum theoretical models they simulate, is currently not understood in a way which allows a quantification of N dependent effects. In this first of a series of papers on this issue, we consider the quantification of such effects in the initial conditions of such simulations. A general formalism developed in [A. Gabrielli, Phys. Rev. E 70, 066131 (2004).] allows us to write down an exact expression for the power spectrum of the point distributions generated by the standard algorithm for generating such initial conditions. Expanded perturbatively in the amplitude of the input (i.e. theoretical, continuum) power spectrum, we obtain at linear order the input power spectrum, plus two terms which arise from discreteness and contribute at large wave numbers. For cosmological type power spectra, one obtains as expected, the input spectrum for wave numbers k smaller than that characteristic of the discreteness. The comparison of real space correlation properties is more subtle because the discreteness corrections are not as strongly localized in real space. For cosmological type spectra the theoretical mass variance in spheres and two-point correlation function are well approximated above a finite distance. For typical initial amplitudes this distance is a few times the interparticle distance, but it diverges as this amplitude (or, equivalently, the initial redshift of the cosmological simulation) goes to zero, at fixed particle density. We discuss briefly the physical significance of these discreteness terms in the initial conditions, in particular, with respect to the definition of the continuum limit of N-body simulations

The quantification of free Amadori compounds and amino acids allows to model the bound Maillard reaction products formation in soybean products.

Science.gov (United States)

Troise, Antonio Dario; Wiltafsky, Markus; Fogliano, Vincenzo; Vitaglione, Paola

2018-05-01

The quantification of protein bound Maillard reaction products (MRPs) is still a challenge in food chemistry. Protein hydrolysis is the bottleneck step: it is time consuming and the protein degradation is not always complete. In this study, the quantitation of free amino acids and Amadori products (APs) was compared to the percentage of blocked lysine by using chemometric tools. Eighty thermally treated soybean samples were analyzed by mass spectrometry to measure the concentration of free amino acids, free APs and the protein-bound markers of the Maillard reaction (furosine, Nε-(carboxymethyl)-l-lysine, Nε-(carboxyethyl)-l-lysine, total lysine). Results demonstrated that Discriminant Analysis (DA) and Correlated Component Regression (CCR) correctly estimated the percent of blocked lysine in a validation and prediction set. These findings indicate that the measure of free markers reflects the extent of protein damage in soybean samples and it suggests the possibility to obtain rapid information on the quality of the industrial processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

A simple method of digitizing analog scintigrams for quantification and digital archiving

International Nuclear Information System (INIS)

Schramm, M.; Kaempfer, B.; Wolf, H.; Clausen, M.; Wendhausen, H.; Henze, E.

1993-01-01

This study was undertaken to evaluate a quick, reliable and cheap method of digitizing analog scintigrams. 40 whole-body bone scintigrams were obtained simultaneously in analog and genuine digital format. The analog scans on X-ray film were then digitized seecondarily by three different methods: 300 dpi flatbed scanning, high-resolution camera scanning and camcorder recording. A simple exposure approach using a light box, a cheap camcorder, a PC and image grabber hard- and software proved to be optimal. Visual interpretation showed no differences in clinical findings when comparing the analog images with their secondarily digitized counterparts. To test the possibility of quantification, 126 equivalent ROIs were drawn both in the genuine digital and the secondarily digitized images. Comparing the ROI count to whole-body count percentage of the corresponding ROIs showed the correlation to be linear. The evaluation of phantom studies showed the linear correlation to be true within a wide activity range. Thus, secondary digitalization of analog scintigrams is an easy, cheap and reliable method of archiving images and allows secondary digital quantification. (orig.) [de

Multiple headspace-solid-phase microextraction: an application to quantification of mushroom volatiles.

Science.gov (United States)

Costa, Rosaria; Tedone, Laura; De Grazia, Selenia; Dugo, Paola; Mondello, Luigi

2013-04-03

Multiple headspace-solid phase microextraction (MHS-SPME) followed by gas chromatography/mass spectrometry (GC-MS) and flame ionization detection (GC-FID) was applied to the identification and quantification of volatiles released by the mushroom Agaricus bisporus, also known as champignon. MHS-SPME allows to perform quantitative analysis of volatiles from solid matrices, free of matrix interferences. Samples analyzed were fresh mushrooms (chopped and homogenized) and mushroom-containing food dressings. 1-Octen-3-ol, 3-octanol, 3-octanone, 1-octen-3-one and benzaldehyde were common constituents of the samples analyzed. Method performance has been tested through the evaluation of limit of detection (LoD, range 0.033-0.078 ng), limit of quantification (LoQ, range 0.111-0.259 ng) and analyte recovery (92.3-108.5%). The results obtained showed quantitative differences among the samples, which can be attributed to critical factors, such as the degree of cell damage upon sample preparation, that are here discussed. Considerations on the mushrooms biochemistry and on the basic principles of MHS analysis are also presented. Copyright © 2013 Elsevier B.V. All rights reserved.

[A simple method of digitizing analog scintigrams for quantification and digital archiving].

Science.gov (United States)

Schramm, M; Kämpfer, B; Wolf, H; Clausen, M; Wendhausen, H; Henze, E

1993-02-01

This study was undertaken to evaluate a quick, reliable and cheap method of digitizing analog scintigrams. 40 whole-body bone scintigrams were obtained simultaneously in analog and genuine digital format. The analog scans on x-ray film were then digitized secondarily by three different methods: 300 dpi flat-bed scanning, high-resolution camera scanning and camcorder recording. A simple exposure approach using a light box, a cheap camcorder, a PC and image grabber hard- and software proved to be optimal. Visual interpretation showed no differences in clinical findings when comparing the analog images with their secondarily digitized counterparts. To test the possibility of quantification, 126 equivalent ROIs were drawn both in the genuine digital and the secondarily digitized images. Comparing the ROI count to whole-body count percentage of the corresponding ROIs showed the correlation to be linear. The evaluation of phantom studies showed the linear correlation to be true within a wide activity range. Thus, secondary digitalization of analog scintigrams is an easy, cheap and reliable method of archiving images and allows secondary digital quantification.

VizieR Online Data Catalog: VIMOS Public Extragalactic Survey (VIPERS) DR1 (Garilli+, 2014)

Science.gov (United States)

Garilli, B.; Guzzo, L.; Scodeggio, M.; Bolzonella, M.; Abbas, U.; Adami, C.; Arnouts, S.; Bel, J.; Bottini, D.; Branchini, E.; Cappi, A.; Coupon, J.; Cucciati, O.; Davidzon, I.; de Lucia, G.; de la Torre, S.; Franzetti, P.; Fritz, A.; Fumana, M.; Granett, B. R.; Ilbert, O.; Iovino, A.; Krywult, J.; Le Brun, V.; Le Fevre, O.; Maccagni, D.; Malek, K.; Marulli, F.; McCracken, H. J.; Paioro, L.; Polletta, M.; Pollo, A.; Schlagenhaufer, H.; Tasca, L. A. M.; Tojeiro, R.; Vergani, D.; Zamorani, G.; Zanichelli, A.; Burden, A.; di Porto, C.; Marchetti, A.; Marinoni, C.; Mellier, Y.; Moscardini, L.; Nichol, R. C.; Peacock, J. A.; Percival, W. J.; Phleps, S.; Wolk, M.

2014-09-01

We present the first Public Data Release (PDR-1) of the VIMOS Public Extragalactic Survey (VIPERS). It comprises 57204 spectroscopic measurements together with all additional information necessary for optimal scientific exploitation of the data, in particular the associated photometric measurements and quantification of the photometric and survey completeness. VIPERS is an ESO Large Programme designed to build a spectroscopic sample of =~100000 galaxies with iABaccessing the data through the survey database (http://vipers.inaf.it) where all information can be queried interactively. (4 data files).

Dermatologic radiotherapy and thyroid cancer. Dose measurements and risk quantification

International Nuclear Information System (INIS)

Goldschmidt, H.; Gorson, R.O.; Lassen, M.

1983-01-01

Thyroid doses for various dermatologic radiation techniques were measured with thermoluminescent dosimeters and ionization rate meters in an Alderson-Rando anthropomorphic phantom. The effects of changes in radiation quality and of the use or nonuse of treatment cones and thyroid shields were evaluated in detail. The results indicate that the potential risk of radiogenic thyroid cancer is very small when proper radiation protection measures are used. The probability of radiogenic thyroid cancer developing and the potential mortality risk were assessed quantitatively for each measurement. The quantification of radiation risks allows comparisons with risks of other therapeutic modalities and the common hazards of daily life

Colour thresholding and objective quantification in bioimaging

Science.gov (United States)

Fermin, C. D.; Gerber, M. A.; Torre-Bueno, J. R.

1992-01-01

Computer imaging is rapidly becoming an indispensable tool for the quantification of variables in research and medicine. Whilst its use in medicine has largely been limited to qualitative observations, imaging in applied basic sciences, medical research and biotechnology demands objective quantification of the variables in question. In black and white densitometry (0-256 levels of intensity) the separation of subtle differences between closely related hues from stains is sometimes very difficult. True-colour and real-time video microscopy analysis offer choices not previously available with monochrome systems. In this paper we demonstrate the usefulness of colour thresholding, which has so far proven indispensable for proper objective quantification of the products of histochemical reactions and/or subtle differences in tissue and cells. In addition, we provide interested, but untrained readers with basic information that may assist decisions regarding the most suitable set-up for a project under consideration. Data from projects in progress at Tulane are shown to illustrate the advantage of colour thresholding over monochrome densitometry and for objective quantification of subtle colour differences between experimental and control samples.

Quantification analysis of CT for aphasic patients

International Nuclear Information System (INIS)

Watanabe, Shunzo; Ooyama, Hiroshi; Hojo, Kei; Tasaki, Hiroichi; Hanazono, Toshihide; Sato, Tokijiro; Metoki, Hirobumi; Totsuka, Motokichi; Oosumi, Noboru.

1987-01-01

Using a microcomputer, the locus and extent of the lesions, as demonstrated by computed tomography, for 44 aphasic patients with various types of aphasia were superimposed onto standardized matrices, composed of 10 slices with 3000 points (50 by 60). The relationships between the foci of the lesions and types of aphasia were investigated on the slices numbered 3, 4, 5, and 6 using a quantification theory, Type 3 (pattern analysis). Some types of regularities were observed on Slices 3, 4, 5, and 6. The group of patients with Broca's aphasia and the group with Wernicke's aphasia were generally separated on the 1st component and the 2nd component of the quantification theory, Type 3. On the other hand, the group with global aphasia existed between the group with Broca's aphasia and that with Wernicke's aphasia. The group of patients with amnestic aphasia had no specific findings, and the group with conduction aphasia existed near those with Wernicke's aphasia. The above results serve to establish the quantification theory, Type 2 (discrimination analysis) and the quantification theory, Type 1 (regression analysis). (author)

Cues, quantification, and agreement in language comprehension.

Science.gov (United States)

Tanner, Darren; Bulkes, Nyssa Z

2015-12-01

We investigated factors that affect the comprehension of subject-verb agreement in English, using quantification as a window into the relationship between morphosyntactic processes in language production and comprehension. Event-related brain potentials (ERPs) were recorded while participants read sentences with grammatical and ungrammatical verbs, in which the plurality of the subject noun phrase was either doubly marked (via overt plural quantification and morphological marking on the noun) or singly marked (via only plural morphology on the noun). Both acceptability judgments and the ERP data showed heightened sensitivity to agreement violations when quantification provided an additional cue to the grammatical number of the subject noun phrase, over and above plural morphology. This is consistent with models of grammatical comprehension that emphasize feature prediction in tandem with cue-based memory retrieval. Our results additionally contrast with those of prior studies that showed no effects of plural quantification on agreement in language production. These findings therefore highlight some nontrivial divergences in the cues and mechanisms supporting morphosyntactic processing in language production and comprehension.

Performance of the Real-Q EBV Quantification Kit for Epstein-Barr Virus DNA Quantification in Whole Blood.

Science.gov (United States)

Huh, Hee Jae; Park, Jong Eun; Kim, Ji Youn; Yun, Sun Ae; Lee, Myoung Keun; Lee, Nam Yong; Kim, Jong Won; Ki, Chang Seok

2017-03-01

There has been increasing interest in standardized and quantitative Epstein-Barr virus (EBV) DNA testing for the management of EBV disease. We evaluated the performance of the Real-Q EBV Quantification Kit (BioSewoom, Korea) in whole blood (WB). Nucleic acid extraction and real-time PCR were performed by using the MagNA Pure 96 (Roche Diagnostics, Germany) and 7500 Fast real-time PCR system (Applied Biosystems, USA), respectively. Assay sensitivity, linearity, and conversion factor were determined by using the World Health Organization international standard diluted in EBV-negative WB. We used 81 WB clinical specimens to compare performance of the Real-Q EBV Quantification Kit and artus EBV RG PCR Kit (Qiagen, Germany). The limit of detection (LOD) and limit of quantification (LOQ) for the Real-Q kit were 453 and 750 IU/mL, respectively. The conversion factor from EBV genomic copies to IU was 0.62. The linear range of the assay was from 750 to 10⁶ IU/mL. Viral load values measured with the Real-Q assay were on average 0.54 log₁₀ copies/mL higher than those measured with the artus assay. The Real-Q assay offered good analytical performance for EBV DNA quantification in WB.

Perfusion quantification in contrast-enhanced ultrasound (CEUS)--ready for research projects and routine clinical use.

Science.gov (United States)

Tranquart, F; Mercier, L; Frinking, P; Gaud, E; Arditi, M

2012-07-01

With contrast-enhanced ultrasound (CEUS) now established as a valuable imaging modality for many applications, a more specific demand has recently emerged for quantifying perfusion and using measured parameters as objective indicators for various disease states. However, CEUS perfusion quantification remains challenging and is not well integrated in daily clinical practice. The development of VueBox™ alleviates existing limitations and enables quantification in a standardized way. VueBox™ operates as an off-line software application, after dynamic contrast-enhanced ultrasound (DCE-US) is performed. It enables linearization of DICOM clips, assessment of perfusion using patented curve-fitting models, and generation of parametric images by synthesizing perfusion information at the pixel level using color coding. VueBox™ is compatible with most of the available ultrasound platforms (nonlinear contrast-enabled), has the ability to process both bolus and disruption-replenishment kinetics loops, allows analysis results and their context to be saved, and generates analysis reports automatically. Specific features have been added to VueBox™, such as fully automatic in-plane motion compensation and an easy-to-use clip editor. Processing time has been reduced as a result of parallel programming optimized for multi-core processors. A long list of perfusion parameters is available for each of the two administration modes to address all possible demands currently reported in the literature for diagnosis or treatment monitoring. In conclusion, VueBox™ is a valid and robust quantification tool to be used for standardizing perfusion quantification and to improve the reproducibility of results across centers. © Georg Thieme Verlag KG Stuttgart · New York.

Application of adaptive hierarchical sparse grid collocation to the uncertainty quantification of nuclear reactor simulators

Energy Technology Data Exchange (ETDEWEB)

Yankov, A.; Downar, T. [University of Michigan, 2355 Bonisteel Blvd, Ann Arbor, MI 48109 (United States)

2013-07-01

Recent efforts in the application of uncertainty quantification to nuclear systems have utilized methods based on generalized perturbation theory and stochastic sampling. While these methods have proven to be effective they both have major drawbacks that may impede further progress. A relatively new approach based on spectral elements for uncertainty quantification is applied in this paper to several problems in reactor simulation. Spectral methods based on collocation attempt to couple the approximation free nature of stochastic sampling methods with the determinism of generalized perturbation theory. The specific spectral method used in this paper employs both the Smolyak algorithm and adaptivity by using Newton-Cotes collocation points along with linear hat basis functions. Using this approach, a surrogate model for the outputs of a computer code is constructed hierarchically by adaptively refining the collocation grid until the interpolant is converged to a user-defined threshold. The method inherently fits into the framework of parallel computing and allows for the extraction of meaningful statistics and data that are not within reach of stochastic sampling and generalized perturbation theory. This paper aims to demonstrate the advantages of spectral methods-especially when compared to current methods used in reactor physics for uncertainty quantification-and to illustrate their full potential. (authors)

A Simple and Effective Isocratic HPLC Method for Fast Identification and Quantification of Surfactin

International Nuclear Information System (INIS)

Muhammad Qadri Effendy Mubarak; Abdul Rahman Hassan; Aidil Abdul Hamid; Sahaid Khalil; Mohd Hafez Mohd Isa

2015-01-01

The aim of this study was to establish a simple, accurate and reproducible method for the identification and quantification of surfactin using high-performance liquid chromatography (HPLC). Previously reported method of identification and quantification of surfactin were time consuming and requires a large quantity of mobile phase. The new method was achieved by application of Chromolith® high performance RP-18 (100 x 4.6 mm, 5 μm) as the stationary phase and optimization of mobile phase ratio and flow rate. Mobile phase consisted of acetonitrile (ACN) and 3.8 mM trifluroacetic acid (TFA) solution of 80:20 ratio at flow rate of 2.2 mL/ min was obtained as the optimal conditions. Total elution time of the obtained surfactin peaks was four times quicker than various methods previously reported in the literature. The method described here allowed for fine separation of surfactin in standard sample (98 % purity) and surfactin in fermentation broth. (author)

Synthesis and Review: Advancing agricultural greenhouse gas quantification

International Nuclear Information System (INIS)

Olander, Lydia P; Wollenberg, Eva; Tubiello, Francesco N; Herold, Martin

2014-01-01

Reducing emissions of agricultural greenhouse gases (GHGs), such as methane and nitrous oxide, and sequestering carbon in the soil or in living biomass can help reduce the impact of agriculture on climate change while improving productivity and reducing resource use. There is an increasing demand for improved, low cost quantification of GHGs in agriculture, whether for national reporting to the United Nations Framework Convention on Climate Change (UNFCCC), underpinning and stimulating improved practices, establishing crediting mechanisms, or supporting green products. This ERL focus issue highlights GHG quantification to call attention to our existing knowledge and opportunities for further progress. In this article we synthesize the findings of 21 papers on the current state of global capability for agricultural GHG quantification and visions for its improvement. We conclude that strategic investment in quantification can lead to significant global improvement in agricultural GHG estimation in the near term. (paper)

Allowing Physicians to Choose the Value of Compensation for Participation in a Web-Based Survey: Randomized Controlled Trial.

Science.gov (United States)

Turnbull, Alison E; O'Connor, Cristi L; Lau, Bryan; Halpern, Scott D; Needham, Dale M

2015-07-29

Survey response rates among physicians are declining, and determining an appropriate level of compensation to motivate participation poses a major challenge. To estimate the effect of permitting intensive care physicians to select their preferred level of compensation for completing a short Web-based survey on physician (1) response rate, (2) survey completion rate, (3) time to response, and (4) time spent completing the survey. A total of 1850 US intensivists from an existing database were randomized to receive a survey invitation email with or without an Amazon.com incentive available to the first 100 respondents. The incentive could be instantly redeemed for an amount chosen by the respondent, up to a maximum of US $50. The overall response rate was 35.90% (630/1755). Among the 35.4% (111/314) of eligible participants choosing the incentive, 80.2% (89/111) selected the maximum value. Among intensivists offered an incentive, the response was 6.0% higher (95% CI 1.5-10.5, P=.01), survey completion was marginally greater (807/859, 94.0% vs 892/991, 90.0%; P=.06), and the median number of days to survey response was shorter (0.8, interquartile range [IQR] 0.2-14.4 vs 6.6, IQR 0.3-22.3; P=.001), with no difference in time spent completing the survey. Permitting intensive care physicians to determine compensation level for completing a short Web-based survey modestly increased response rate and substantially decreased response time without decreasing the time spent on survey completion.

Online updating and uncertainty quantification using nonstationary output-only measurement

Science.gov (United States)

Yuen, Ka-Veng; Kuok, Sin-Chi

2016-01-01

Extended Kalman filter (EKF) is widely adopted for state estimation and parametric identification of dynamical systems. In this algorithm, it is required to specify the covariance matrices of the process noise and measurement noise based on prior knowledge. However, improper assignment of these noise covariance matrices leads to unreliable estimation and misleading uncertainty estimation on the system state and model parameters. Furthermore, it may induce diverging estimation. To resolve these problems, we propose a Bayesian probabilistic algorithm for online estimation of the noise parameters which are used to characterize the noise covariance matrices. There are three major appealing features of the proposed approach. First, it resolves the divergence problem in the conventional usage of EKF due to improper choice of the noise covariance matrices. Second, the proposed approach ensures the reliability of the uncertainty quantification. Finally, since the noise parameters are allowed to be time-varying, nonstationary process noise and/or measurement noise are explicitly taken into account. Examples using stationary/nonstationary response of linear/nonlinear time-varying dynamical systems are presented to demonstrate the efficacy of the proposed approach. Furthermore, comparison with the conventional usage of EKF will be provided to reveal the necessity of the proposed approach for reliable model updating and uncertainty quantification.

40 CFR 35.2025 - Allowance and advance of allowance.

Science.gov (United States)

2010-07-01

... advance of allowance. (a) Allowance. Step 2+3 and Step 3 grant agreements will include an allowance for facilities planning and design of the project and Step 7 agreements will include an allowance for facility... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Allowance and advance of allowance. 35...

Critical points of DNA quantification by real-time PCR--effects of DNA extraction method and sample matrix on quantification of genetically modified organisms.

Science.gov (United States)

Cankar, Katarina; Stebih, Dejan; Dreo, Tanja; Zel, Jana; Gruden, Kristina

2006-08-14

Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary criterion by which to

La quantification en Kabiye: une approche linguistique | Pali ...

African Journals Online (AJOL)

... which is denoted by lexical quantifiers. Quantification with specific reference is provided by different types of linguistic units (nouns, numerals, adjectives, adverbs, ideophones and verbs) in arguments/noun phrases and in the predicative phrase in the sense of Chomsky. Keywords: quantification, class, number, reference, ...

Novel isotopic N, N-Dimethyl Leucine (iDiLeu) Reagents Enable Absolute Quantification of Peptides and Proteins Using a Standard Curve Approach

Science.gov (United States)

Greer, Tyler; Lietz, Christopher B.; Xiang, Feng; Li, Lingjun

2015-01-01

Absolute quantification of protein targets using liquid chromatography-mass spectrometry (LC-MS) is a key component of candidate biomarker validation. One popular method combines multiple reaction monitoring (MRM) using a triple quadrupole instrument with stable isotope-labeled standards (SIS) for absolute quantification (AQUA). LC-MRM AQUA assays are sensitive and specific, but they are also expensive because of the cost of synthesizing stable isotope peptide standards. While the chemical modification approach using mass differential tags for relative and absolute quantification (mTRAQ) represents a more economical approach when quantifying large numbers of peptides, these reagents are costly and still suffer from lower throughput because only two concentration values per peptide can be obtained in a single LC-MS run. Here, we have developed and applied a set of five novel mass difference reagents, isotopic N, N-dimethyl leucine (iDiLeu). These labels contain an amine reactive group, triazine ester, are cost effective because of their synthetic simplicity, and have increased throughput compared with previous LC-MS quantification methods by allowing construction of a four-point standard curve in one run. iDiLeu-labeled peptides show remarkably similar retention time shifts, slightly lower energy thresholds for higher-energy collisional dissociation (HCD) fragmentation, and high quantification accuracy for trypsin-digested protein samples (median errors <15%). By spiking in an iDiLeu-labeled neuropeptide, allatostatin, into mouse urine matrix, two quantification methods are validated. The first uses one labeled peptide as an internal standard to normalize labeled peptide peak areas across runs (<19% error), whereas the second enables standard curve creation and analyte quantification in one run (<8% error).

Quantification analysis of CT for aphasic patients

Energy Technology Data Exchange (ETDEWEB)

Watanabe, S.; Ooyama, H.; Hojo, K.; Tasaki, H.; Hanazono, T.; Sato, T.; Metoki, H.; Totsuka, M.; Oosumi, N.

1987-02-01

Using a microcomputer, the locus and extent of the lesions, as demonstrated by computed tomography, for 44 aphasic patients with various types of aphasia were superimposed onto standardized matrices, composed of 10 slices with 3000 points (50 by 60). The relationships between the foci of the lesions and types of aphasia were investigated on the slices numbered 3, 4, 5, and 6 using a quantification theory, Type 3 (pattern analysis). Some types of regularities were observed on slices 3, 4, 5, and 6. The group of patients with Broca's aphasia and the group with Wernicke's aphasia were generally separated on the 1st component and the 2nd component of the quantification theory, Type 3. On the other hand, the group with global aphasia existed between the group with Broca's aphasia and that with Wernicke's aphasia. The group of patients with amnestic aphasia had no specific findings, and the group with conduction aphasia existed near those with Wernicke's aphasia. The above results serve to establish the quantification theory, Type 2 (discrimination analysis) and the quantification theory, Type 1 (regression analysis).

Development of a software of quantification of tumour density from images of biopsies from caner of head and neck

International Nuclear Information System (INIS)

Fernandez, J. M.; Alba, J. L.; Mera, M.; Lorenzo, Y.; Iglesias, M. B.; Lopez Medina, A.; Munoz, A.

2013-01-01

It has developed a software for automatic quantification of tumoral tissues biopsied density and tinted with Cytokeratin, using information colorimetric and morphologic, that also allows to distinguish between malignant cells and healthy cells. The software allows you to find, within the area biopsied, the area 1 mm 2 with higher tumor density, which in the future may be associated with ADC minimum of the number of patients included in the ARTFIBio project and be able to check the inverse correlation between the two measures. (Author)

Rapid quantification of plant-powdery mildew interactions by qPCR and conidiospore counts.

Science.gov (United States)

Weßling, Ralf; Panstruga, Ralph

2012-08-31

The powdery mildew disease represents a valuable patho-system to study the interaction between plant hosts and obligate biotrophic fungal pathogens. Numerous discoveries have been made on the basis of the quantitative evaluation of plant-powdery mildew interactions, especially in the context of hyper-susceptible and/or resistant plant mutants. However, the presently available methods to score the pathogenic success of powdery mildew fungi are laborious and thus not well suited for medium- to high-throughput analysis. Here we present two new protocols that allow the rapid quantitative assessment of powdery mildew disease development. One procedure depends on quantitative polymerase chain reaction (qPCR)-based evaluation of fungal biomass, while the other relies on the quantification of fungal conidiospores. We validated both techniques using the powdery mildew pathogen Golovinomyces orontii on a set of hyper-susceptible and resistant Arabidopsis thaliana mutants and found that both cover a wide dynamic range of one to two (qPCR) and four to five (quantification of conidia) orders of magnitude, respectively. The two approaches yield reproducible results and are easy to perform without specialized equipment. The qPCR and spore count assays rapidly and reproducibly quantify powdery mildew pathogenesis. Our methods are performed at later stages of infection and discern mutant phenotypes accurately. The assays therefore complement currently used procedures of powdery mildew quantification and can overcome some of their limitations. In addition, they can easily be adapted to other plant-powdery mildew patho-systems.

Strategy study of quantification harmonization of SUV in PET/CT images; Estudo da estrategia de harmonizacao da quantificacao do SUV em imagens de PET/CT

Energy Technology Data Exchange (ETDEWEB)

Fischer, Andreia Caroline Fischer da Silveira

2014-07-01

In clinical practice, PET/CT images are often analyzed qualitatively by visual comparison of tumor lesions and normal tissues uptake; and semi-quantitatively by means of a parameter called SUV (Standardized Uptake Value). To ensure that longitudinal studies acquired on different scanners are interchangeable, and information of quantification is comparable, it is necessary to establish a strategy to harmonize the quantification of SUV. The aim of this study is to evaluate the strategy to harmonize the quantification of PET/CT images, performed with different scanner models and manufacturers. For this purpose, a survey of the technical characteristics of equipment and acquisition protocols of clinical images of different services of PET/CT in the state of Rio Grande do Sul was conducted. For each scanner, the accuracy of SUV quantification, and the Recovery Coefficient (RC) curves were determined, using the reconstruction parameters clinically relevant and available. From these data, harmonized performance specifications among the evaluated scanners were identified, as well as the algorithm that produces, for each one, the most accurate quantification. Finally, the most appropriate reconstruction parameters to harmonize the SUV quantification in each scanner, either regionally or internationally were identified. It was found that the RC values of the analyzed scanners proved to be overestimated by up to 38%, particularly for objects larger than 17mm. These results demonstrate the need for further optimization, through the reconstruction parameters modification, and even the change of the reconstruction algorithm used in each scanner. It was observed that there is a decoupling between the best image for PET/CT qualitative analysis and the best image for quantification studies. Thus, the choice of reconstruction method should be tied to the purpose of the PET/CT study in question, since the same reconstruction algorithm is not adequate, in one scanner, for qualitative

Real-time PCR for the quantification of fungi in planta.

Science.gov (United States)

Klosterman, Steven J

2012-01-01

Methods enabling quantification of fungi in planta can be useful for a variety of applications. In combination with information on plant disease severity, indirect quantification of fungi in planta offers an additional tool in the screening of plants that are resistant to fungal diseases. In this chapter, a method is described for the quantification of DNA from a fungus in plant leaves using real-time PCR (qPCR). Although the method described entails quantification of the fungus Verticillium dahliae in lettuce leaves, the methodology described would be useful for other pathosystems as well. The method utilizes primers that are specific for amplification of a β-tubulin sequence from V. dahliae and a lettuce actin gene sequence as a reference for normalization. This approach enabled quantification of V. dahliae in the amount of 2.5 fg/ng of lettuce leaf DNA at 21 days following plant inoculation.

Methods for modeling and quantification in functional imaging by positron emissions tomography and magnetic resonance imaging

International Nuclear Information System (INIS)

Costes, Nicolas

2017-01-01

This report presents experiences and researches in the field of in vivo medical imaging by positron emission tomography (PET) and magnetic resonance imaging (MRI). In particular, advances in terms of reconstruction, quantification and modeling in PET are described. The validation of processing and analysis methods is supported by the creation of data by simulation of the imaging process in PET. The recent advances of combined PET/MRI clinical cameras, allowing simultaneous acquisition of molecular/metabolic PET information, and functional/structural MRI information opens the door to unique methodological innovations, exploiting spatial alignment and simultaneity of the PET and MRI signals. It will lead to an increase in accuracy and sensitivity in the measurement of biological phenomena. In this context, the developed projects address new methodological issues related to quantification, and to the respective contributions of MRI or PET information for a reciprocal improvement of the signals of the two modalities. They open perspectives for combined analysis of the two imaging techniques, allowing optimal use of synchronous, anatomical, molecular and functional information for brain imaging. These innovative concepts, as well as data correction and analysis methods, will be easily translated into other areas of investigation using combined PET/MRI. (author) [fr

Two-stream Convolutional Neural Network for Methane Emissions Quantification

Science.gov (United States)

Wang, J.; Ravikumar, A. P.; McGuire, M.; Bell, C.; Tchapmi, L. P.; Brandt, A. R.

2017-12-01

Methane, a key component of natural gas, has a 25x higher global warming potential than carbon dioxide on a 100-year basis. Accurately monitoring and mitigating methane emissions require cost-effective detection and quantification technologies. Optical gas imaging, one of the most commonly used leak detection technology, adopted by Environmental Protection Agency, cannot estimate leak-sizes. In this work, we harness advances in computer science to allow for rapid and automatic leak quantification. Particularly, we utilize two-stream deep Convolutional Networks (ConvNets) to estimate leak-size by capturing complementary spatial information from still plume frames, and temporal information from plume motion between frames. We build large leak datasets for training and evaluating purposes by collecting about 20 videos (i.e. 397,400 frames) of leaks. The videos were recorded at six distances from the source, covering 10 -60 ft. Leak sources included natural gas well-heads, separators, and tanks. All frames were labeled with a true leak size, which has eight levels ranging from 0 to 140 MCFH. Preliminary analysis shows that two-stream ConvNets provides significant accuracy advantage over single steam ConvNets. Spatial stream ConvNet can achieve an accuracy of 65.2%, by extracting important features, including texture, plume area, and pattern. Temporal stream, fed by the results of optical flow analysis, results in an accuracy of 58.3%. The integration of the two-stream ConvNets gives a combined accuracy of 77.6%. For future work, we will split the training and testing datasets in distinct ways in order to test the generalization of the algorithm for different leak sources. Several analytic metrics, including confusion matrix and visualization of key features, will be used to understand accuracy rates and occurrences of false positives. The quantification algorithm can help to find and fix super-emitters, and improve the cost-effectiveness of leak detection and repair

Accurate quantification of mouse mitochondrial DNA without co-amplification of nuclear mitochondrial insertion sequences.

Science.gov (United States)

Malik, Afshan N; Czajka, Anna; Cunningham, Phil

2016-07-01

Mitochondria contain an extra-nuclear genome in the form of mitochondrial DNA (MtDNA), damage to which can lead to inflammation and bioenergetic deficit. Changes in MtDNA levels are increasingly used as a biomarker of mitochondrial dysfunction. We previously reported that in humans, fragments in the nuclear genome known as nuclear mitochondrial insertion sequences (NumtS) affect accurate quantification of MtDNA. In the current paper our aim was to determine whether mouse NumtS affect the quantification of MtDNA and to establish a method designed to avoid this. The existence of NumtS in the mouse genome was confirmed using blast N, unique MtDNA regions were identified using FASTA, and MtDNA primers which do not co-amplify NumtS were designed and tested. MtDNA copy numbers were determined in a range of mouse tissues as the ratio of the mitochondrial and nuclear genome using real time qPCR and absolute quantification. Approximately 95% of mouse MtDNA was duplicated in the nuclear genome as NumtS which were located in 15 out of 21 chromosomes. A unique region was identified and primers flanking this region were used. MtDNA levels differed significantly in mouse tissues being the highest in the heart, with levels in descending order (highest to lowest) in kidney, liver, blood, brain, islets and lung. The presence of NumtS in the nuclear genome of mouse could lead to erroneous data when studying MtDNA content or mutation. The unique primers described here will allow accurate quantification of MtDNA content in mouse models without co-amplification of NumtS. Copyright © 2016 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Sensitive targeted multiple protein quantification based on elemental detection of Quantum Dots

Energy Technology Data Exchange (ETDEWEB)

Montoro Bustos, Antonio R.; Garcia-Cortes, Marta [Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, Oviedo 33006 (Spain); González-Iglesias, Hector [Fundación de Investigación Oftalmológica, Instituto Oftalmológico Fernandez-Vega, Avenida Doctores Fernández-Vega, 34, Oviedo 33012 (Spain); Ruiz Encinar, Jorge, E-mail: ruizjorge@uniovi.es [Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, Oviedo 33006 (Spain); Costa-Fernández, José M. [Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, Oviedo 33006 (Spain); Coca-Prados, Miguel [Fundación de Investigación Oftalmológica, Instituto Oftalmológico Fernandez-Vega, Avenida Doctores Fernández-Vega, 34, Oviedo 33012 (Spain); Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT 06510 (United States); Sanz-Medel, Alfredo, E-mail: asm@uniovi.es [Department of Physical and Analytical Chemistry, University of Oviedo, Julián Clavería 8, Oviedo 33006 (Spain)

2015-06-16

Highlights: • Novel generic platform for multiparametric quantification of proteins. • QDs labeling and ICP-MS detection allow significant analytical signal amplification. • ICP-MS mass balances information provided an internal validation of the immunoassay. • Multiparametric determination of 5 proteins in human serum samples. • ICP-MS reduced matrix effects as compared to other conventional detection techniques. - Abstract: A generic strategy based on the use of CdSe/ZnS Quantum Dots (QDs) as elemental labels for protein quantification, using immunoassays with elemental mass spectrometry (ICP-MS), detection is presented. In this strategy, streptavidin modified QDs (QDs-SA) are bioconjugated to a biotinylated secondary antibody (b-Ab{sub 2}). After a multi-technique characterization of the synthesized generic platform (QDs-SA-b-Ab{sub 2}) it was applied to the sequential quantification of five proteins (transferrin, complement C3, apolipoprotein A1, transthyretin and apolipoprotein A4) at different concentration levels in human serum samples. It is shown how this generic strategy does only require the appropriate unlabeled primary antibody for each protein to be detected. Therefore, it introduces a way out to the need for the cumbersome and specific bioconjugation of the QDs to the corresponding specific recognition antibody for every target analyte (protein). Results obtained were validated with those obtained using UV–vis spectrophotometry and commercial ELISA Kits. As expected, ICP-MS offered one order of magnitude lower DL (0.23 fmol absolute for transferrin) than the classical spectrophotometric detection (3.2 fmol absolute). ICP-MS precision and detection limits, however turned out to be compromised by procedural blanks. The full analytical performance of the ICP-MS-based immunoassay proposed was assessed for detection of transferrin (Tf), present at the low ng mL{sup −1} range in a complex “model” synthetic matrix, where the total protein

Detection and Quantification of Viable and Nonviable Trypanosoma cruzi Parasites by a Propidium Monoazide Real-Time Polymerase Chain Reaction Assay

Science.gov (United States)

Cancino-Faure, Beatriz; Fisa, Roser; Alcover, M. Magdalena; Jimenez-Marco, Teresa; Riera, Cristina

2016-01-01

Molecular techniques based on real-time polymerase chain reaction (qPCR) allow the detection and quantification of DNA but are unable to distinguish between signals from dead or live cells. Because of the lack of simple techniques to differentiate between viable and nonviable cells, the aim of this study was to optimize and evaluate a straightforward test based on propidium monoazide (PMA) dye action combined with a qPCR assay (PMA-qPCR) for the selective quantification of viable/nonviable epimastigotes of Trypanosoma cruzi. PMA has the ability to penetrate the plasma membrane of dead cells and covalently cross-link to the DNA during exposure to bright visible light, thereby inhibiting PCR amplification. Different concentrations of PMA (50–200 μM) and epimastigotes of the Maracay strain of T. cruzi (1 × 105–10 parasites/mL) were assayed; viable and nonviable parasites were tested and quantified by qPCR with a TaqMan probe specific for T. cruzi. In the PMA-qPCR assay optimized at 100 μM PMA, a significant qPCR signal reduction was observed in the nonviable versus viable epimastigotes treated with PMA, with a mean signal reduction of 2.5 logarithm units and a percentage of signal reduction > 98%, in all concentrations of parasites assayed. This signal reduction was also observed when PMA-qPCR was applied to a mixture of live/dead parasites, which allowed the detection of live cells, except when the concentration of live parasites was low (10 parasites/mL). The PMA-qPCR developed allows differentiation between viable and nonviable epimastigotes of T. cruzi and could thus be a potential method of parasite viability assessment and quantification. PMID:27139452

Quantification of transformation products of rocket fuel unsymmetrical dimethylhydrazine in soils using SPME and GC-MS.

Science.gov (United States)

Bakaikina, Nadezhda V; Kenessov, Bulat; Ul'yanovskii, Nikolay V; Kosyakov, Dmitry S

2018-07-01

Determination of transformation products (TPs) of rocket fuel unsymmetrical dimethylhydrazine (UDMH) in soil is highly important for environmental impact assessment of the launches of heavy space rockets from Kazakhstan, Russia, China and India. The method based on headspace solid-phase microextraction (HS SPME) and gas chromatography-mass spectrometry is advantageous over other known methods due to greater simplicity and cost efficiency. However, accurate quantification of these analytes using HS SPME is limited by the matrix effect. In this research, we proposed using internal standard and standard addition calibrations to achieve proper combination of accuracies of the quantification of key TPs of UDMH and cost efficiency. 1-Trideuteromethyl-1H-1,2,4-triazole (MTA-d3) was used as the internal standard. Internal standard calibration allowed controlling matrix effects during quantification of 1-methyl-1H-1,2,4-triazole (MTA), N,N-dimethylformamide (DMF), and N-nitrosodimethylamine (NDMA) in soils with humus content < 1%. Using SPME at 60 °C for 15 min by 65 µm Carboxen/polydimethylsiloxane fiber, recoveries of MTA, DMF and NDMA for sandy and loamy soil samples were 91-117, 85-123 and 64-132%, respectively. For improving the method accuracy and widening the range of analytes, standard addition and its combination with internal standard calibration were tested and compared on real soil samples. The combined calibration approach provided greatest accuracies for NDMA, DMF, N-methylformamide, formamide, 1H-pyrazole, 3-methyl-1H-pyrazole and 1H-pyrazole. For determination of 1-formyl-2,2-dimethylhydrazine, 3,5-dimethylpyrazole, 2-ethyl-1H-imidazole, 1H-imidazole, 1H-1,2,4-triazole, pyrazines and pyridines, standard addition calibration is more suitable. However, the proposed approach and collected data allow using both approaches simultaneously. Copyright © 2018 Elsevier B.V. All rights reserved.

DAG expression: high-throughput gene expression analysis of real-time PCR data using standard curves for relative quantification.

Directory of Open Access Journals (Sweden)

María Ballester

Full Text Available BACKGROUND: Real-time quantitative PCR (qPCR is still the gold-standard technique for gene-expression quantification. Recent technological advances of this method allow for the high-throughput gene-expression analysis, without the limitations of sample space and reagent used. However, non-commercial and user-friendly software for the management and analysis of these data is not available. RESULTS: The recently developed commercial microarrays allow for the drawing of standard curves of multiple assays using the same n-fold diluted samples. Data Analysis Gene (DAG Expression software has been developed to perform high-throughput gene-expression data analysis using standard curves for relative quantification and one or multiple reference genes for sample normalization. We discuss the application of DAG Expression in the analysis of data from an experiment performed with Fluidigm technology, in which 48 genes and 115 samples were measured. Furthermore, the quality of our analysis was tested and compared with other available methods. CONCLUSIONS: DAG Expression is a freely available software that permits the automated analysis and visualization of high-throughput qPCR. A detailed manual and a demo-experiment are provided within the DAG Expression software at http://www.dagexpression.com/dage.zip.

Application of Fuzzy Comprehensive Evaluation Method in Trust Quantification

Directory of Open Access Journals (Sweden)

Shunan Ma

2011-10-01

Full Text Available Trust can play an important role for the sharing of resources and information in open network environments. Trust quantification is thus an important issue in dynamic trust management. By considering the fuzziness and uncertainty of trust, in this paper, we propose a fuzzy comprehensive evaluation method to quantify trust along with a trust quantification algorithm. Simulation results show that the trust quantification algorithm that we propose can effectively quantify trust and the quantified value of an entity's trust is consistent with the behavior of the entity.

Survey and analysis of deep water mineral deposits using nuclear methods

International Nuclear Information System (INIS)

Staehle, C.M.; Noakes, J.E.; Spaulding, J.

1991-01-01

Present knowledge of the location, quality, quantity and recoverability of sea floor minerals is severely limited, particularly in the abyssal depths and deep water within the 200 mile Exclusion Economic Zone (EEZ) surrounding the U.S. Pacific Islands. To improve this understanding and permit exploitation of these mineral reserves much additional data is needed. This paper will discuss a sponsored program for extending existing proven nuclear survey methods currently used on the shallow continental margins of the Atlantic and Gulf of Mexico into the deeper waters of the Pacific. This nuclear technology can be readily integrated and extended to depths of 2000 m using the existing RCV-150 remotely operated vehicle (ROV) and the PISCESE V manned deep submersible vehicle (DSV) operated by The University of Hawaii's, Hawaii Underseas Research Laboratory (HURL). Previous papers by the authors have also proposed incorporating these nuclear analytical methods for survey of the deep ocean through the use of Autonomous Underwater Vehicle (AUX). Such a vehicle could extend the use of passive nuclear instrument operation, in addition to conventional analytical methods, into the abyssal depths and do so with speed and economy not otherwise possible. The natural radioactivity associated with manganese nodules and crustal deposits is sufficiently above normal background levels to allow discrimination and quantification in near real time

Droplet digital PCR improves absolute quantification of viable lactic acid bacteria in faecal samples.

Science.gov (United States)

Gobert, Guillaume; Cotillard, Aurélie; Fourmestraux, Candice; Pruvost, Laurence; Miguet, Jean; Boyer, Mickaël

2018-03-14

Analysing correlations between the observed health effects of ingested probiotics and their survival in digestive tract allows adapting their preparations for food. Tracking ingested probiotic in faecal samples requires accurate and specific tools to quantify live vs dead cells at strain level. Traditional culture-based methods are simpler to use but they do not allow quantifying viable but non-cultivable (VBNC) cells and they are poorly discriminant below the species level. We have set up a viable PCR (vPCR) assay combining propidium monoazide (PMA) treatment and either real time quantitative PCR (qPCR) or droplet digital PCR (ddPCR) to quantify a Lactobacillus rhamnosus and two Lactobacillus paracasei subsp. paracasei strains in piglet faeces. Adjustments of the PMA treatment conditions and reduction of the faecal sample size were necessary to obtain accurate discrimination between dead and live cells. The study also revealed differences of PMA efficiency among the two L. paracasei strains. Both PCR methods were able to specifically quantify each strain and provided comparable total bacterial counts. However, quantification of lower numbers of viable cells was best achieved with ddPCR, which was characterized by a reduced lower limit of quantification (improvement of up to 1.76 log 10 compared to qPCR). All three strains were able to survive in the piglets' gut with viability losses between 0.78 and 1.59 log 10 /g faeces. This study shows the applicability of PMA-ddPCR to specific quantification of small numbers of viable bacterial cells in the presence of an important background of unwanted microorganisms, and without the need to set up standard curves. It also illustrates the need to adapt PMA protocols according to the final matrix and target strain, even for closely related strains. The PMA-ddPCR approach provides a new tool to quantify bacterial survival in faecal samples from a preclinical and clinical trial. Copyright © 2018 The Authors. Published by

Iron overload in the liver diagnostic and quantification

Energy Technology Data Exchange (ETDEWEB)

Alustiza, Jose M. [Osatek SA, P Dr. Beguiristain 109, 20014, San Sebastian, Guipuzcoa (Spain)]. E-mail: jmalustiza@osatek.es; Castiella, Agustin [Osatek SA, P Dr. Beguiristain 109, 20014, San Sebastian, Guipuzcoa (Spain); Juan, Maria D. de [Osatek SA, P Dr. Beguiristain 109, 20014, San Sebastian, Guipuzcoa (Spain); Emparanza, Jose I. [Osatek SA, P Dr. Beguiristain 109, 20014, San Sebastian, Guipuzcoa (Spain); Artetxe, Jose [Osatek SA, P Dr. Beguiristain 109, 20014, San Sebastian, Guipuzcoa (Spain); Uranga, Maite [Osatek SA, P Dr. Beguiristain 109, 20014, San Sebastian, Guipuzcoa (Spain)

2007-03-15

Hereditary Hemochromatosis is the most frequent modality of iron overload. Since 1996 genetic tests have facilitated significantly the non-invasive diagnosis of the disease. There are however many cases of negative genetic tests that require confirmation by hepatic iron quantification which is traditionally performed by hepatic biopsy. There are many studies that have demonstrated the possibility of performing hepatic iron quantification with Magnetic Resonance. However, a consensus has not been reached yet regarding the technique or the possibility to reproduce the same method of calculus in different machines. This article reviews the state of the art of the question and delineates possible future lines to standardise this non-invasive method of hepatic iron quantification.

Iron overload in the liver diagnostic and quantification

International Nuclear Information System (INIS)

Alustiza, Jose M.; Castiella, Agustin; Juan, Maria D. de; Emparanza, Jose I.; Artetxe, Jose; Uranga, Maite

2007-01-01

Hereditary Hemochromatosis is the most frequent modality of iron overload. Since 1996 genetic tests have facilitated significantly the non-invasive diagnosis of the disease. There are however many cases of negative genetic tests that require confirmation by hepatic iron quantification which is traditionally performed by hepatic biopsy. There are many studies that have demonstrated the possibility of performing hepatic iron quantification with Magnetic Resonance. However, a consensus has not been reached yet regarding the technique or the possibility to reproduce the same method of calculus in different machines. This article reviews the state of the art of the question and delineates possible future lines to standardise this non-invasive method of hepatic iron quantification

Quantification and Sequencing of Crossover Recombinant Molecules from Arabidopsis Pollen DNA.

Science.gov (United States)

Choi, Kyuha; Yelina, Nataliya E; Serra, Heïdi; Henderson, Ian R

2017-01-01

During meiosis, homologous chromosomes undergo recombination, which can result in formation of reciprocal crossover molecules. Crossover frequency is highly variable across the genome, typically occurring in narrow hotspots, which has a significant effect on patterns of genetic diversity. Here we describe methods to measure crossover frequency in plants at the hotspot scale (bp-kb), using allele-specific PCR amplification from genomic DNA extracted from the pollen of F 1 heterozygous plants. We describe (1) titration methods that allow amplification, quantification and sequencing of single crossover molecules, (2) quantitative PCR methods to more rapidly measure crossover frequency, and (3) application of high-throughput sequencing for study of crossover distributions within hotspots. We provide detailed descriptions of key steps including pollen DNA extraction, prior identification of hotspot locations, allele-specific oligonucleotide design, and sequence analysis approaches. Together, these methods allow the rate and recombination topology of plant hotspots to be robustly measured and compared between varied genetic backgrounds and environmental conditions.

Disease quantification in dermatology

DEFF Research Database (Denmark)

Greve, Tanja Maria; Kamp, Søren; Jemec, Gregor B E

2013-01-01

Accurate documentation of disease severity is a prerequisite for clinical research and the practice of evidence-based medicine. The quantification of skin diseases such as psoriasis currently relies heavily on clinical scores. Although these clinical scoring methods are well established and very ...

Dual-energy CT with iodine quantification in distinguishing between bland and neoplastic portal vein thrombosis in patients with hepatocellular carcinoma

International Nuclear Information System (INIS)

Ascenti, G.; Sofia, C.; Mazziotti, S.; Silipigni, S.; D'Angelo, T.; Pergolizzi, S.; Scribano, E.

2016-01-01

hepatic arterial phase in patients with hepatocellular carcinoma. - Highlights: • Dual-energy MDCT allows the characterization of portal vein thrombosis. • Iodine quantification tool is more accurate than standard enhancement measurements. • Improved thrombus characterization can substantially affect patients' management.

A facile and sensitive method for quantification of cyclic nucleotide monophosphates in mammalian organs: basal levels of eight cNMPs and identification of 2',3'-cIMP.

Science.gov (United States)

Jia, Xin; Fontaine, Benjamin M; Strobel, Fred; Weinert, Emily E

2014-12-12

A sensitive, versatile and economical method to extract and quantify cyclic nucleotide monophosphates (cNMPs) using LC-MS/MS, including both 3',5'-cNMPs and 2',3'-cNMPs, in mammalian tissues and cellular systems has been developed. Problems, such as matrix effects from complex biological samples, are addressed and have been optimized. This protocol allows for comparison of multiple cNMPs in the same system and was used to examine the relationship between tissue levels of cNMPs in a panel of rat organs. In addition, the study reports the first identification and quantification of 2',3'-cIMP. The developed method will allow for quantification of cNMPs levels in cells and tissues with varying disease states, which will provide insight into the role(s) and interplay of cNMP signalling pathways.

An architectural model for software reliability quantification: sources of data

International Nuclear Information System (INIS)

Smidts, C.; Sova, D.

1999-01-01

Software reliability assessment models in use today treat software as a monolithic block. An aversion towards 'atomic' models seems to exist. These models appear to add complexity to the modeling, to the data collection and seem intrinsically difficult to generalize. In 1997, we introduced an architecturally based software reliability model called FASRE. The model is based on an architecture derived from the requirements which captures both functional and nonfunctional requirements and on a generic classification of functions, attributes and failure modes. The model focuses on evaluation of failure mode probabilities and uses a Bayesian quantification framework. Failure mode probabilities of functions and attributes are propagated to the system level using fault trees. It can incorporate any type of prior information such as results of developers' testing, historical information on a specific functionality and its attributes, and, is ideally suited for reusable software. By building an architecture and deriving its potential failure modes, the model forces early appraisal and understanding of the weaknesses of the software, allows reliability analysis of the structure of the system, provides assessments at a functional level as well as at a systems' level. In order to quantify the probability of failure (or the probability of success) of a specific element of our architecture, data are needed. The term element of the architecture is used here in its broadest sense to mean a single failure mode or a higher level of abstraction such as a function. The paper surveys the potential sources of software reliability data available during software development. Next the mechanisms for incorporating these sources of relevant data to the FASRE model are identified

Guided Wave Delamination Detection and Quantification With Wavefield Data Analysis

Science.gov (United States)

Tian, Zhenhua; Campbell Leckey, Cara A.; Seebo, Jeffrey P.; Yu, Lingyu

2014-01-01

Unexpected damage can occur in aerospace composites due to impact events or material stress during off-nominal loading events. In particular, laminated composites are susceptible to delamination damage due to weak transverse tensile and inter-laminar shear strengths. Developments of reliable and quantitative techniques to detect delamination damage in laminated composites are imperative for safe and functional optimally-designed next-generation composite structures. In this paper, we investigate guided wave interactions with delamination damage and develop quantification algorithms by using wavefield data analysis. The trapped guided waves in the delamination region are observed from the wavefield data and further quantitatively interpreted by using different wavenumber analysis methods. The frequency-wavenumber representation of the wavefield shows that new wavenumbers are present and correlate to trapped waves in the damage region. These new wavenumbers are used to detect and quantify the delamination damage through the wavenumber analysis, which can show how the wavenumber changes as a function of wave propagation distance. The location and spatial duration of the new wavenumbers can be identified, providing a useful means not only for detecting the presence of delamination damage but also allowing for estimation of the delamination size. Our method has been applied to detect and quantify real delamination damage with complex geometry (grown using a quasi-static indentation technique). The detection and quantification results show the location, size, and shape of the delamination damage.

Quantification of pelvic floor muscle strength in female urinary incontinence: A systematic review and comparison of contemporary methodologies.

Science.gov (United States)

Deegan, Emily G; Stothers, Lynn; Kavanagh, Alex; Macnab, Andrew J

2018-01-01

There remains no gold standard for quantification of voluntary pelvic floor muscle (PFM) strength, despite international guidelines that recommend PFM assessment in females with urinary incontinence (UI). Methods currently reported for quantification of skeletal muscle strength across disciplines are systematically reviewed and their relevance for clinical and academic use related to the pelvic floor are described. A systematic review via Medline, PubMed, CINHAL, and the Cochrane database using key terms for pelvic floor anatomy and function were cross referenced with skeletal muscle strength quantification from 1946 to 2016. Full text peer-reviewed articles in English having female subjects with incontinence were identified. Each study was analyzed for use of controls, type of methodology as direct or indirect measures, benefits, and limitations of the technique. A total of 1586 articles were identified of which 50 met the inclusion criteria. Nine methodologies of determining PFM strength were described including: digital palpation, perineometer, dynamometry, EMG, vaginal cones, ultrasonography, magnetic resonance imaging, urine stream interruption test, and the Colpexin pull test. Thirty-two percent lacked a control group. Technical refinements in both direct and indirect instrumentation for PFM strength measurement are allowing for sensitivity. However, the most common methods of quantification remain digital palpation and perineometry; techniques that pose limitations and yield subjective or indirect measures of muscular strength. Dynamometry has potential as an accurate and sensitive tool, but is limited by inability to assess PFM strength during dynamic movements. © 2017 Wiley Periodicals, Inc.

Direct quantification of lipopeptide biosurfactants in biological samples via HPLC and UPLC-MS requires sample modification with an organic solvent.

Science.gov (United States)

Biniarz, Piotr; Łukaszewicz, Marcin

2017-06-01

The rapid and accurate quantification of biosurfactants in biological samples is challenging. In contrast to the orcinol method for rhamnolipids, no simple biochemical method is available for the rapid quantification of lipopeptides. Various liquid chromatography (LC) methods are promising tools for relatively fast and exact quantification of lipopeptides. Here, we report strategies for the quantification of the lipopeptides pseudofactin and surfactin in bacterial cultures using different high- (HPLC) and ultra-performance liquid chromatography (UPLC) systems. We tested three strategies for sample pretreatment prior to LC analysis. In direct analysis (DA), bacterial cultures were injected directly and analyzed via LC. As a modification, we diluted the samples with methanol and detected an increase in lipopeptide recovery in the presence of methanol. Therefore, we suggest this simple modification as a tool for increasing the accuracy of LC methods. We also tested freeze-drying followed by solvent extraction (FDSE) as an alternative for the analysis of "heavy" samples. In FDSE, the bacterial cultures were freeze-dried, and the resulting powder was extracted with different solvents. Then, the organic extracts were analyzed via LC. Here, we determined the influence of the extracting solvent on lipopeptide recovery. HPLC methods allowed us to quantify pseudofactin and surfactin with run times of 15 and 20 min per sample, respectively, whereas UPLC quantification was as fast as 4 and 5.5 min per sample, respectively. Our methods provide highly accurate measurements and high recovery levels for lipopeptides. At the same time, UPLC-MS provides the possibility to identify lipopeptides and their structural isoforms.

Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

Directory of Open Access Journals (Sweden)

Žel Jana

2006-08-01

Full Text Available Abstract Background Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Results Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was

Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

Science.gov (United States)

Cankar, Katarina; Štebih, Dejan; Dreo, Tanja; Žel, Jana; Gruden, Kristina

2006-01-01

Background Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Results Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary

Factors controlling volume errors through 2D gully erosion assessment: guidelines for optimal survey design

Science.gov (United States)

Castillo, Carlos; Pérez, Rafael

2017-04-01

The assessment of gully erosion volumes is essential for the quantification of soil losses derived from this relevant degradation process. Traditionally, 2D and 3D approaches has been applied for this purpose (Casalí et al., 2006). Although innovative 3D approaches have recently been proposed for gully volume quantification, a renewed interest can be found in literature regarding the useful information that cross-section analysis still provides in gully erosion research. Moreover, the application of methods based on 2D approaches can be the most cost-effective approach in many situations such as preliminary studies with low accuracy requirements or surveys under time or budget constraints. The main aim of this work is to examine the key factors controlling volume error variability in 2D gully assessment by means of a stochastic experiment involving a Monte Carlo analysis over synthetic gully profiles in order to 1) contribute to a better understanding of the drivers and magnitude of gully erosion 2D-surveys uncertainty and 2) provide guidelines for optimal survey designs. Owing to the stochastic properties of error generation in 2D volume assessment, a statistical approach was followed to generate a large and significant set of gully reach configurations to evaluate quantitatively the influence of the main factors controlling the uncertainty of the volume assessment. For this purpose, a simulation algorithm in Matlab® code was written, involving the following stages: - Generation of synthetic gully area profiles with different degrees of complexity (characterized by the cross-section variability) - Simulation of field measurements characterised by a survey intensity and the precision of the measurement method - Quantification of the volume error uncertainty as a function of the key factors In this communication we will present the relationships between volume error and the studied factors and propose guidelines for 2D field surveys based on the minimal survey

42 CFR 61.9 - Payments: Stipends; dependency allowances; travel allowances.

Science.gov (United States)

2010-10-01

... 42 Public Health 1 2010-10-01 2010-10-01 false Payments: Stipends; dependency allowances; travel... FELLOWSHIPS, INTERNSHIPS, TRAINING FELLOWSHIPS Regular Fellowships § 61.9 Payments: Stipends; dependency allowances; travel allowances. Payments for stipends, dependency allowances, and the travel allowances...

Methods for the physical characterization and quantification of extracellular vesicles in biological samples.

Science.gov (United States)

Rupert, Déborah L M; Claudio, Virginia; Lässer, Cecilia; Bally, Marta

2017-01-01

Our body fluids contain a multitude of cell-derived vesicles, secreted by most cell types, commonly referred to as extracellular vesicles. They have attracted considerable attention for their function as intercellular communication vehicles in a broad range of physiological processes and pathological conditions. Extracellular vesicles and especially the smallest type, exosomes, have also generated a lot of excitement in view of their potential as disease biomarkers or as carriers for drug delivery. In this context, state-of-the-art techniques capable of comprehensively characterizing vesicles in biological fluids are urgently needed. This review presents the arsenal of techniques available for quantification and characterization of physical properties of extracellular vesicles, summarizes their working principles, discusses their advantages and limitations and further illustrates their implementation in extracellular vesicle research. The small size and physicochemical heterogeneity of extracellular vesicles make their physical characterization and quantification an extremely challenging task. Currently, structure, size, buoyant density, optical properties and zeta potential have most commonly been studied. The concentration of vesicles in suspension can be expressed in terms of biomolecular or particle content depending on the method at hand. In addition, common quantification methods may either provide a direct quantitative measurement of vesicle concentration or solely allow for relative comparison between samples. The combination of complementary methods capable of detecting, characterizing and quantifying extracellular vesicles at a single particle level promises to provide new exciting insights into their modes of action and to reveal the existence of vesicle subpopulations fulfilling key biological tasks. Copyright © 2016 Elsevier B.V. All rights reserved.

Exploring Heterogeneous Multicore Architectures for Advanced Embedded Uncertainty Quantification.

Energy Technology Data Exchange (ETDEWEB)

Phipps, Eric T.; Edwards, Harold C.; Hu, Jonathan J.

2014-09-01

We explore rearrangements of classical uncertainty quantification methods with the aim of achieving higher aggregate performance for uncertainty quantification calculations on emerging multicore and manycore architectures. We show a rearrangement of the stochastic Galerkin method leads to improved performance and scalability on several computational architectures whereby un- certainty information is propagated at the lowest levels of the simulation code improving memory access patterns, exposing new dimensions of fine grained parallelism, and reducing communica- tion. We also develop a general framework for implementing such rearrangements for a diverse set of uncertainty quantification algorithms as well as computational simulation codes to which they are applied.

GMO quantification: valuable experience and insights for the future.

Science.gov (United States)

Milavec, Mojca; Dobnik, David; Yang, Litao; Zhang, Dabing; Gruden, Kristina; Zel, Jana

2014-10-01

Cultivation and marketing of genetically modified organisms (GMOs) have been unevenly adopted worldwide. To facilitate international trade and to provide information to consumers, labelling requirements have been set up in many countries. Quantitative real-time polymerase chain reaction (qPCR) is currently the method of choice for detection, identification and quantification of GMOs. This has been critically assessed and the requirements for the method performance have been set. Nevertheless, there are challenges that should still be highlighted, such as measuring the quantity and quality of DNA, and determining the qPCR efficiency, possible sequence mismatches, characteristics of taxon-specific genes and appropriate units of measurement, as these remain potential sources of measurement uncertainty. To overcome these problems and to cope with the continuous increase in the number and variety of GMOs, new approaches are needed. Statistical strategies of quantification have already been proposed and expanded with the development of digital PCR. The first attempts have been made to use new generation sequencing also for quantitative purposes, although accurate quantification of the contents of GMOs using this technology is still a challenge for the future, and especially for mixed samples. New approaches are needed also for the quantification of stacks, and for potential quantification of organisms produced by new plant breeding techniques.

A new analytical method for quantification of olive and palm oil in blends with other vegetable edible oils based on the chromatographic fingerprints from the methyl-transesterified fraction.

Science.gov (United States)

Jiménez-Carvelo, Ana M; González-Casado, Antonio; Cuadros-Rodríguez, Luis

2017-03-01

A new analytical method for the quantification of olive oil and palm oil in blends with other vegetable edible oils (canola, safflower, corn, peanut, seeds, grapeseed, linseed, sesame and soybean) using normal phase liquid chromatography, and applying chemometric tools was developed. The procedure for obtaining of chromatographic fingerprint from the methyl-transesterified fraction from each blend is described. The multivariate quantification methods used were Partial Least Square-Regression (PLS-R) and Support Vector Regression (SVR). The quantification results were evaluated by several parameters as the Root Mean Square Error of Validation (RMSEV), Mean Absolute Error of Validation (MAEV) and Median Absolute Error of Validation (MdAEV). It has to be highlighted that the new proposed analytical method, the chromatographic analysis takes only eight minutes and the results obtained showed the potential of this method and allowed quantification of mixtures of olive oil and palm oil with other vegetable oils. Copyright © 2016 Elsevier B.V. All rights reserved.

The Quantification Process for the PRiME-U34i

International Nuclear Information System (INIS)

Hwang, Mee-Jeong; Han, Sang-Hoon; Yang, Joon-Eon

2006-01-01

In this paper, we introduce the quantification process for the PRIME-U34i, which is the merged model of ETs (Event Trees) and FTs (Fault Trees) for the level 1 internal PSA of UCN 3 and 4. PRiME-U34i has one top event. Therefore, the quantification process is changed to a simplified method when compared to the past one. In the past, we used the text file called a user file to control the quantification process. However, this user file is so complicated that it is difficult for a non-expert to understand it. Moreover, in the past PSA, ET and FT were separated but in PRiMEU34i, ET and FT were merged together. Thus, the quantification process is different. This paper is composed of five sections. In section 2, we introduce the construction of the one top model. Section 3 shows the quantification process used in the PRiME-U34i. Section 4 describes the post processing. Last section is the conclusions

Validation and evaluation of an HPLC methodology for the quantification of the potent antimitotic compound (+)-discodermolide in the Caribbean marine sponge Discodermia dissoluta.

Science.gov (United States)

Valderrama, Katherine; Castellanos, Leonardo; Zea, Sven

2010-08-01

The sponge Discodermia dissoluta is the source of the potent antimitotic compound (+)-discodermolide. The relatively abundant and shallow populations of this sponge in Santa Marta, Colombia, allow for studies to evaluate the natural and biotechnological supply options of (+)-discodermolide. In this work, an RP-HPLC-UV methodology for the quantification of (+)-discodermolide from sponge samples was tested and validated. Our protocol for extracting this compound from the sponge included lyophilization, exhaustive methanol extraction, partitioning using water and dichloromethane, purification of the organic fraction in RP-18 cartridges and then finally retrieving the (+)-discodermolide in the methanol-water (80:20 v/v) fraction. This fraction was injected into an HPLC system with an Xterra RP-18 column and a detection wavelength of 235 nm. The calibration curve was linear, making it possible to calculate the LODs and quantification in these experiments. The intra-day and inter-day precision showed relative standard deviations lower than 5%. The accuracy, determined as the percentage recovery, was 99.4%. Nine samples of the sponge from the Bahamas, Bonaire, Curaçao and Santa Marta had concentrations of (+)-discodermolide ranging from 5.3 to 29.3 microg/g(-1) of wet sponge. This methodology is quick and simple, allowing for the quantification in sponges from natural environments, in situ cultures or dissociated cells.

Quantification of Fusarium graminearum and Fusarium culmorum by real-time PCR system and zearalenone assessment in maize

International Nuclear Information System (INIS)

Atoui, A.; El Khoury, A.; Kallassy, M.; Lebrihi, A.

2012-01-01

Zearalenone (ZEA) is a mycotoxin produced by some species of Fusarium, especially by Fusarium grami- nearum and F. culmorum. ZEA induces hyperoestrogenic responses in mammals and can result in reproductive disorders in farm animals. In the present study, a real-time PCR (qPCR) assay has been successfully developed for the detection and quantification of Fusarium graminearum based on primers targeting the gene PKS13 involved in ZEA biosynthesis. A standard curve was developed by plotting the logarithm of known concentrations of F. graminearum DNA against the cycle threshold (Ct) value. The developed real time PCR system was also used to analyze the occurrence of zearalenone producing F. graminearum strains on maize. In this context, DNA extractions were performed from thirty-two maize samples, and subjected to real time PCR. Maize samples also were analyzed for zearalenone content by HPLC. F. graminearum DNA content (pg DNA/ mg of maize) was then plotted against ZEA content (ppb) in maize samples. The regression curve showed a positive and good correlation (R2 = 0.760) allowing for the estimation of the potential risk from ZEA contamination. Consequently, this work offers a quick alternative to conventional methods of ZEA quantification and mycological detection and quantification of F. graminearum in maize. (author)

Validation of a food quantification picture book targeting children of 0-10 years of age for pan-European and national dietary surveys.

Science.gov (United States)

Trolle, Ellen; Vandevijvere, Stefanie; Ruprich, Jiří; Ege, Majken; Dofková, Marcela; de Boer, Evelien; Ocké, Marga

2013-12-01

The aim of the present study was to validate thirty-eight picture series of six pictures each developed within the PANCAKE (Pilot study for the Assessment of Nutrient intake and food Consumption Among Kids in Europe) project for portion size estimation of foods consumed by infants, toddlers and children for future pan-European and national dietary surveys. Identical validation sessions were conducted in three European countries. In each country, forty-five foods were evaluated; thirty-eight foods were the same as the depicted foods, and seven foods were different, but meant to be quantified by the use of one of the thirty-eight picture series. Each single picture within a picture series was evaluated six times by means of predefined portions. Therefore, thirty-six pre-weighed portions of each food were evaluated by convenience samples of parents having children aged from 3 months to 10 years. The percentages of participants choosing the correct picture, the picture adjacent to the correct picture or a distant picture were calculated, and the performance of individual pictures within the series was assessed. For twenty foods, the picture series performed acceptably (mean difference between the estimated portion number and the served portion number less than 0.4 (SD picture series were acceptable for inclusion in the PANCAKE picture book. However, the picture series of baby food, salads and cakes either can only be used for foods that are very similar to those depicted or need to be substituted by another quantification tool.

Does zero really mean nothing?-first experiences with the new PowerQuant(TM) system in comparison to established real-time quantification kits.

Science.gov (United States)

Poetsch, Micaela; Konrad, Helen; Helmus, Janine; Bajanowski, Thomas; von Wurmb-Schwark, Nicole

2016-07-01

DNA quantification is an important step in the molecular genetic analysis of a forensic sample, hopefully providing reliable data on DNA content for a subsequent generation of reproducible STR profiles for identification. For several years, this quantification has usually been done by real-time PCR protocols and meanwhile a variety of assays are commercially available from different companies. The newest one is the PowerQuant(TM) assay by Promega Inc. which is advertised with the promise that a determined DNA concentration of 0 ng/μl in a forensic sample guarantees the impossibility to achieve true STR results, thus allowing to exclude such samples from STR analysis to save time and money. Thus, the goal of this study was to thoroughly verify the quantification step with regard to its suitability as a screening method. We have evaluated the precision and reliability of four different real-time PCR quantification assays by systematically testing DNA dilutions and forensic samples with various DNA contents. Subsequently, each sample was subjected to the Powerplex® ESX 17 fast kit to determine a reliable cutoff level for exclusion of definitely negative samples from STR analysis. An accurate quantification of different cell line DNA dilutions was not possible with any kit. However, at least the PowerQuant(TM) assay provided suitable data analyzing forensic samples, whereas in other systems up to 46 % of negative samples still displayed reliable STR analysis results. All in all, the PowerQuant(TM) assay represents a big step forward, but the evaluation of real-time PCR quantification results has still to be done with great care.

A HPLC method for the quantification of butyramide and acetamide at ppb levels in hydrogeothermal waters

Energy Technology Data Exchange (ETDEWEB)

Gracy Elias; Earl D. Mattson; Jessica E. Little

2012-01-01

A quantitative analytical method to determine butyramide and acetamide concentrations at the low ppb levels in geothermal waters has been developed. The analytes are concentrated in a preparation step by evaporation and analyzed using HPLC-UV. Chromatographic separation is achieved isocratically with a RP C-18 column using a 30 mM phosphate buffer solution with 5 mM heptane sulfonic acid and methanol (98:2 ratio) as the mobile phase. Absorbance is measured at 200 nm. The limit of detection (LOD) for BA and AA were 2.0 {mu}g L{sup -1} and 2.5 {mu}g L{sup -1}, respectively. The limit of quantification (LOQ) for BA and AA were 5.7 {mu}g L{sup -1} and 7.7 {mu}g L{sup -1}, respectively, at the detection wavelength of 200 nm. Attaining these levels of quantification better allows these amides to be used as thermally reactive tracers in low-temperature hydrogeothermal systems.

Evaluation of uncertainties in the calibration of radiation survey meter

International Nuclear Information System (INIS)

Potiens, M.P.A.; Santos, G.P.

2006-01-01

In order to meet the requirements of ISO 17025, the quantification of the expanded uncertainties of experimental data in the calibration of survey meters must be carried out using well defined concepts, like those expressed in the 'ISO-Guide to the Expression of Uncertainty in Measurement'. The calibration procedure of gamma ray survey meters involves two values that have to get their uncertainties clearly known: measurements of the instrument under calibration and the conventional true values of a quantity. Considering the continuous improvement of the calibration methods and set-ups, it is necessary to evaluate periodically the involved uncertainties in the procedures. In this work it is shown how the measurement uncertainties of an individual calibration can be estimated and how it can be generalized to be valid for others radiation survey meters. (authors)

Quantification of extra virgin olive oil in dressing and edible oil blends using the representative TMS-4,4'-desmethylsterols gas-chromatographic-normalized fingerprint.

Science.gov (United States)

Pérez-Castaño, Estefanía; Sánchez-Viñas, Mercedes; Gázquez-Evangelista, Domingo; Bagur-González, M Gracia

2018-01-15

This paper describes and discusses the application of trimethylsilyl (TMS)-4,4'-desmethylsterols derivatives chromatographic fingerprints (obtained from an off-line HPLC-GC-FID system) for the quantification of extra virgin olive oil in commercial vinaigrettes, dressing salad and in-house reference materials (i-HRM) using two different Partial Least Square-Regression (PLS-R) multivariate quantification methods. Different data pre-processing strategies were carried out being the whole one: (i) internal normalization; (ii) sampling based on The Nyquist Theorem; (iii) internal correlation optimized shifting, icoshift; (iv) baseline correction (v) mean centering and (vi) selecting zones. The first model corresponds to a matrix of dimensions 'n×911' variables and the second one to a matrix of dimensions 'n×431' variables. It has to be highlighted that the proposed two PLS-R models allow the quantification of extra virgin olive oil in binary blends, foodstuffs, etc., when the provided percentage is greater than 25%. Copyright © 2017 Elsevier Ltd. All rights reserved.

Artifacts Quantification of Metal Implants in MRI

Science.gov (United States)

Vrachnis, I. N.; Vlachopoulos, G. F.; Maris, T. G.; Costaridou, L. I.

2017-11-01

The presence of materials with different magnetic properties, such as metal implants, causes distortion of the magnetic field locally, resulting in signal voids and pile ups, i.e. susceptibility artifacts in MRI. Quantitative and unbiased measurement of the artifact is prerequisite for optimization of acquisition parameters. In this study an image gradient based segmentation method is proposed for susceptibility artifact quantification. The method captures abrupt signal alterations by calculation of the image gradient. Then the artifact is quantified in terms of its extent by an automated cross entropy thresholding method as image area percentage. The proposed method for artifact quantification was tested in phantoms containing two orthopedic implants with significantly different magnetic permeabilities. The method was compared against a method proposed in the literature, considered as a reference, demonstrating moderate to good correlation (Spearman’s rho = 0.62 and 0.802 in case of titanium and stainless steel implants). The automated character of the proposed quantification method seems promising towards MRI acquisition parameter optimization.

Mapping in vivo target interaction profiles of covalent inhibitors using chemical proteomics with label-free quantification.

Science.gov (United States)

van Rooden, Eva J; Florea, Bogdan I; Deng, Hui; Baggelaar, Marc P; van Esbroeck, Annelot C M; Zhou, Juan; Overkleeft, Herman S; van der Stelt, Mario

2018-04-01

Activity-based protein profiling (ABPP) has emerged as a valuable chemical proteomics method to guide the therapeutic development of covalent drugs by assessing their on-target engagement and off-target activity. We recently used ABPP to determine the serine hydrolase interaction landscape of the experimental drug BIA 10-2474, thereby providing a potential explanation for the adverse side effects observed with this compound. ABPP allows mapping of protein interaction landscapes of inhibitors in cells, tissues and animal models. Whereas our previous protocol described quantification of proteasome activity using stable-isotope labeling, this protocol describes the procedures for identifying the in vivo selectivity profile of covalent inhibitors with label-free quantitative proteomics. The optimization of our protocol for label-free quantification methods results in high proteome coverage and allows the comparison of multiple biological samples. We demonstrate our protocol by assessing the protein interaction landscape of the diacylglycerol lipase inhibitor DH376 in mouse brain, liver, kidney and testes. The stages of the protocol include tissue lysis, probe incubation, target enrichment, sample preparation, liquid chromatography-mass spectrometry (LC-MS) measurement, data processing and analysis. This approach can be used to study target engagement in a native proteome and to identify potential off targets for the inhibitor under investigation. The entire protocol takes at least 4 d, depending on the number of samples.

Quantification of trace-level DNA by real-time whole genome amplification.

Science.gov (United States)

Kang, Min-Jung; Yu, Hannah; Kim, Sook-Kyung; Park, Sang-Ryoul; Yang, Inchul

2011-01-01

Quantification of trace amounts of DNA is a challenge in analytical applications where the concentration of a target DNA is very low or only limited amounts of samples are available for analysis. PCR-based methods including real-time PCR are highly sensitive and widely used for quantification of low-level DNA samples. However, ordinary PCR methods require at least one copy of a specific gene sequence for amplification and may not work for a sub-genomic amount of DNA. We suggest a real-time whole genome amplification method adopting the degenerate oligonucleotide primed PCR (DOP-PCR) for quantification of sub-genomic amounts of DNA. This approach enabled quantification of sub-picogram amounts of DNA independently of their sequences. When the method was applied to the human placental DNA of which amount was accurately determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES), an accurate and stable quantification capability for DNA samples ranging from 80 fg to 8 ng was obtained. In blind tests of laboratory-prepared DNA samples, measurement accuracies of 7.4%, -2.1%, and -13.9% with analytical precisions around 15% were achieved for 400-pg, 4-pg, and 400-fg DNA samples, respectively. A similar quantification capability was also observed for other DNA species from calf, E. coli, and lambda phage. Therefore, when provided with an appropriate standard DNA, the suggested real-time DOP-PCR method can be used as a universal method for quantification of trace amounts of DNA.

NGS Survey Control Map

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Survey Control Map provides a map of the US which allows you to find and display geodetic survey control points stored in the database of the National...

Collagen Quantification in Tissue Specimens.

Science.gov (United States)

Coentro, João Quintas; Capella-Monsonís, Héctor; Graceffa, Valeria; Wu, Zhuning; Mullen, Anne Maria; Raghunath, Michael; Zeugolis, Dimitrios I

2017-01-01

Collagen is the major extracellular protein in mammals. Accurate quantification of collagen is essential in the biomaterials (e.g., reproducible collagen scaffold fabrication), drug discovery (e.g., assessment of collagen in pathophysiologies, such as fibrosis), and tissue engineering (e.g., quantification of cell-synthesized collagen) fields. Although measuring hydroxyproline content is the most widely used method to quantify collagen in biological specimens, the process is very laborious. To this end, the Sircol™ Collagen Assay is widely used due to its inherent simplicity and convenience. However, this method leads to overestimation of collagen content due to the interaction of Sirius red with basic amino acids of non-collagenous proteins. Herein, we describe the addition of an ultrafiltration purification step in the process to accurately determine collagen content in tissues.

A Facile and Sensitive Method for Quantification of Cyclic Nucleotide Monophosphates in Mammalian Organs: Basal Levels of Eight cNMPs and Identification of 2',3'-cIMP

Directory of Open Access Journals (Sweden)

Xin Jia

2014-12-01

Full Text Available A sensitive, versatile and economical method to extract and quantify cyclic nucleotide monophosphates (cNMPs using LC-MS/MS, including both 3',5'-cNMPs and 2',3'-cNMPs, in mammalian tissues and cellular systems has been developed. Problems, such as matrix effects from complex biological samples, are addressed and have been optimized. This protocol allows for comparison of multiple cNMPs in the same system and was used to examine the relationship between tissue levels of cNMPs in a panel of rat organs. In addition, the study reports the first identification and quantification of 2',3'-cIMP. The developed method will allow for quantification of cNMPs levels in cells and tissues with varying disease states, which will provide insight into the role(s and interplay of cNMP signalling pathways.

Cutset Quantification Error Evaluation for Shin-Kori 1 and 2 PSA model

International Nuclear Information System (INIS)

Choi, Jong Soo

2009-01-01

Probabilistic safety assessments (PSA) for nuclear power plants (NPPs) are based on the minimal cut set (MCS) quantification method. In PSAs, the risk and importance measures are computed from a cutset equation mainly by using approximations. The conservatism of the approximations is also a source of quantification uncertainty. In this paper, exact MCS quantification methods which are based on the 'sum of disjoint products (SDP)' logic and Inclusion-exclusion formula are applied and the conservatism of the MCS quantification results in Shin-Kori 1 and 2 PSA is evaluated

A simplified method for rapid quantification of intracellular nucleoside triphosphates by one-dimensional thin-layer chromatography

DEFF Research Database (Denmark)

Jendresen, Christian Bille; Kilstrup, Mogens; Martinussen, Jan

2011-01-01

-pyrophosphate (PRPP), and inorganic pyrophosphate (PPi) in cell extracts. The method uses one-dimensional thin-layer chromatography (TLC) and radiolabeled biological samples. Nucleotides are resolved at the level of ionic charge in an optimized acidic ammonium formate and chloride solvent, permitting...... quantification of NTPs. The method is significantly simpler and faster than both current two-dimensional methods and high-performance liquid chromatography (HPLC)-based procedures, allowing a higher throughput while common sources of inaccuracies and technical problems are avoided. For determination of PPi...

Quantification of localized vertebral deformities using a sparse wavelet-based shape model.

Science.gov (United States)

Zewail, R; Elsafi, A; Durdle, N

2008-01-01

Medical experts often examine hundreds of spine x-ray images to determine existence of various pathologies. Common pathologies of interest are anterior osteophites, disc space narrowing, and wedging. By careful inspection of the outline shapes of the vertebral bodies, experts are able to identify and assess vertebral abnormalities with respect to the pathology under investigation. In this paper, we present a novel method for quantification of vertebral deformation using a sparse shape model. Using wavelets and Independent component analysis (ICA), we construct a sparse shape model that benefits from the approximation power of wavelets and the capability of ICA to capture higher order statistics in wavelet space. The new model is able to capture localized pathology-related shape deformations, hence it allows for quantification of vertebral shape variations. We investigate the capability of the model to predict localized pathology related deformations. Next, using support-vector machines, we demonstrate the diagnostic capabilities of the method through the discrimination of anterior osteophites in lumbar vertebrae. Experiments were conducted using a set of 150 contours from digital x-ray images of lumbar spine. Each vertebra is labeled as normal or abnormal. Results reported in this work focus on anterior osteophites as the pathology of interest.

Electrical detection and quantification of single and mixed DNA nucleotides in suspension

Science.gov (United States)

Ahmad, Mahmoud Al; Panicker, Neena G.; Rizvi, Tahir A.; Mustafa, Farah

2016-09-01

High speed sequential identification of the building blocks of DNA, (deoxyribonucleotides or nucleotides for short) without labeling or processing in long reads of DNA is the need of the hour. This can be accomplished through exploiting their unique electrical properties. In this study, the four different types of nucleotides that constitute a DNA molecule were suspended in a buffer followed by performing several types of electrical measurements. These electrical parameters were then used to quantify the suspended DNA nucleotides. Thus, we present a purely electrical counting scheme based on the semiconductor theory that allows one to determine the number of nucleotides in a solution by measuring their capacitance-voltage dependency. The nucleotide count was observed to be similar to the multiplication of the corresponding dopant concentration and debye volume after de-embedding the buffer contribution. The presented approach allows for a fast and label-free quantification of single and mixed nucleotides in a solution.

Combination of pentafluorophenylhydrazine derivatization and isotope dilution LC-MS/MS techniques for the quantification of apurinic/apyrimidinic sites in cellular DNA.

Science.gov (United States)

Li, Jie; Leung, Elvis M K; Choi, Martin M F; Chan, Wan

2013-05-01

Apurinic/apyrimidinic (AP) sites are common DNA lesions arising from spontaneous hydrolysis of the N-glycosidic bond and base-excision repair mechanisms of the modified bases. Due to the strong association of AP site formation with physically/chemically induced DNA damage, quantifying AP sites provides important information for risk assessment of exposure to genotoxins and oxidative stress. However, rigorous quantification of AP sites in DNA has been hampered by technical problems relating to the sensitivity and selectivity of existing analytical methods. We have developed a new isotope dilution liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) method for the rigorous quantification of AP sites in genomic DNA. The method entails enzymatic digestion of AP site-containing DNA by endo- and exonucleases, derivatization with pentafluorophenylhydrazine (PFPH), addition of an isotopically labeled PFPH derivative as internal standard, and quantification by LC-MS/MS. The combination of PFPH derivatization with LC-MS/MS analysis on a triple quadrupole mass spectrometer allows for sensitive and selective quantification of AP sites in DNA at a detection limit of 6.5 fmol, corresponding to 4 AP sites/10(9) nt in 5 μg of DNA, which is at least ten times more sensitive than existing analytical methods. The protocol was validated by AP site-containing oligonucleotides and applied in quantifying methyl methanesulfonate-induced formation of AP sites in cellular DNA.

Stereological quantification of mast cells in human synovium

DEFF Research Database (Denmark)

Damsgaard, T E; Sørensen, Flemming Brandt; Herlin, T

1999-01-01

Mast cells participate in both the acute allergic reaction as well as in chronic inflammatory diseases. Earlier studies have revealed divergent results regarding the quantification of mast cells in the human synovium. The aim of the present study was therefore to quantify these cells in the human...... synovium, using stereological techniques. Different methods of staining and quantification have previously been used for mast cell quantification in human synovium. Stereological techniques provide precise and unbiased information on the number of cell profiles in two-dimensional tissue sections of......, in this case, human synovium. In 10 patients suffering from osteoarthritis a median of 3.6 mast cells/mm2 synovial membrane was found. The total number of cells (synoviocytes, fibroblasts, lymphocytes, leukocytes) present was 395.9 cells/mm2 (median). The mast cells constituted 0.8% of all the cell profiles...

Complex Empiricism and the Quantification of Uncertainty in Paleoclimate Reconstructions

Science.gov (United States)

Brumble, K. C.

2014-12-01

Because the global climate cannot be observed directly, and because of vast and noisy data sets, climate science is a rich field to study how computational statistics informs what it means to do empirical science. Traditionally held virtues of empirical science and empirical methods like reproducibility, independence, and straightforward observation are complicated by representational choices involved in statistical modeling and data handling. Examining how climate reconstructions instantiate complicated empirical relationships between model, data, and predictions reveals that the path from data to prediction does not match traditional conceptions of empirical inference either. Rather, the empirical inferences involved are "complex" in that they require articulation of a good deal of statistical processing wherein assumptions are adopted and representational decisions made, often in the face of substantial uncertainties. Proxy reconstructions are both statistical and paleoclimate science activities aimed at using a variety of proxies to reconstruct past climate behavior. Paleoclimate proxy reconstructions also involve complex data handling and statistical refinement, leading to the current emphasis in the field on the quantification of uncertainty in reconstructions. In this presentation I explore how the processing needed for the correlation of diverse, large, and messy data sets necessitate the explicit quantification of the uncertainties stemming from wrangling proxies into manageable suites. I also address how semi-empirical pseudo-proxy methods allow for the exploration of signal detection in data sets, and as intermediary steps for statistical experimentation.

Quantification of methionine and selenomethionine in biological samples using multiple reaction monitoring high performance liquid chromatography tandem mass spectrometry (MRM-HPLC-MS/MS).

Science.gov (United States)

Vu, Dai Long; Ranglová, Karolína; Hájek, Jan; Hrouzek, Pavel

2018-05-01

Quantification of selenated amino-acids currently relies on methods employing inductively coupled plasma mass spectrometry (ICP-MS). Although very accurate, these methods do not allow the simultaneous determination of standard amino-acids, hampering the comparison of the content of selenated versus non-selenated species such as methionine (Met) and selenomethionine (SeMet). This paper reports two approaches for the simultaneous quantification of Met and SeMet. In the first approach, standard enzymatic hydrolysis employing Protease XIV was applied for the preparation of samples. The second approach utilized methanesulfonic acid (MA) for the hydrolysis of samples, either in a reflux system or in a microwave oven, followed by derivatization with diethyl ethoxymethylenemalonate. The prepared samples were then analyzed by multiple reaction monitoring high performance liquid chromatography tandem mass spectrometry (MRM-HPLC-MS/MS). Both approaches provided platforms for the accurate determination of selenium/sulfur substitution rate in Met. Moreover the second approach also provided accurate simultaneous quantification of Met and SeMet with a low limit of detection, low limit of quantification and wide linearity range, comparable to the commonly used gas chromatography mass spectrometry (GC-MS) method or ICP-MS. The novel method was validated using certified reference material in conjunction with the GC-MS reference method. Copyright © 2018. Published by Elsevier B.V.

A simple fluorescence based assay for quantification of human immunodeficiency virus particle release

Directory of Open Access Journals (Sweden)

Heuser Anke-Mareil

2010-04-01

Full Text Available Abstract Background The assembly and release of human immunodeficiency virus (HIV particles from infected cells represent attractive, but not yet exploited targets for antiretroviral therapy. The availability of simple methods to measure the efficiency of these replication steps in tissue culture would facilitate the identification of host factors essential for these processes as well as the screening for lead compounds acting as specific inhibitors of particle formation. We describe here the development of a rapid cell based assay for quantification of human immunodeficiency virus type 1 (HIV-1 particle assembly and/or release. Results Using a fluorescently labelled HIV-derivative, which carries an eYFP domain within the main viral structural protein Gag in the complete viral protein context, the release of virus like particles could be monitored by directly measuring the fluorescence intensity of the tissue culture supernatant. Intracellular Gag was quantitated in parallel by direct fluorescence analysis of cell lysates, allowing us to normalize for Gag expression efficiency. The assay was validated by comparison with p24 capsid ELISA measurements, a standard method for quantifying HIV-1 particles. Optimization of conditions allowed the robust detection of particle amounts corresponding to 50 ng p24/ml in medium by fluorescence spectroscopy. Further adaptation to a multi-well format rendered the assay suitable for medium or high throughput screening of siRNA libraries to identify host cell factors involved in late stages of HIV replication, as well as for random screening approaches to search for potential inhibitors of HIV-1 assembly or release. Conclusions The fast and simple fluorescence based quantification of HIV particle release yielded reproducible results which were comparable to the well established ELISA measurements, while in addition allowing the parallel determination of intracellular Gag expression. The protocols described here

Physical Characterisation and Quantification of Total Above Ground Biomass Derived from First Thinnings for Wood Fuel Consumption in Ireland

OpenAIRE

Mockler, Nicholas

2013-01-01

Comprehensive knowledge of wood fuel properties assists in the optimisation of operations concerned with the harvesting, seasoning, processing and conversion of wood to energy. This study investigated the physical properties of wood fuel. These properties included moisture content and basic density. The field work also allowed for the quantification of above ground biomass partitions. The species investigated were alder (Alnus glutinosa), ash (Fraxinus excelsior L.), birch (Betula spp.), lodg...

42 CFR 61.8 - Benefits: Stipends; dependency allowances; travel allowances; vacation.

Science.gov (United States)

2010-10-01

... 42 Public Health 1 2010-10-01 2010-10-01 false Benefits: Stipends; dependency allowances; travel...; dependency allowances; travel allowances; vacation. Individuals awarded regular fellowships shall be entitled...) Stipend. (b) Dependency allowances. (c) When authorized in advance, separate allowances for travel. Such...

Quantification of cellular uptake of DNA nanostructures by qPCR

DEFF Research Database (Denmark)

Okholm, Anders Hauge; Nielsen, Jesper Sejrup; Vinther, Mathias

2014-01-01

interactions and structural and functional features of the DNA delivery device must be thoroughly investigated. Here, we present a rapid and robust method for the precise quantification of the component materials of DNA origami structures capable of entering cells in vitro. The quantification is performed...

A Subaru galaxy redshift survey: WFMOS survey

International Nuclear Information System (INIS)

Takada, M

2008-01-01

A planned galaxy redshift survey with the Subaru 8.2m telescope, the WFMOS survey, offers a unique opportunity for probing detailed properties of large-scale structure formation in the expanding universe by measuring clustering strength of galaxy distribution as a function of distance scale and redshift. In particular, the precise measurement of the galaxy power spectrum, combined with the cosmic microwave background experiments, allows us to obtain stringent constraints on or even determine absolute mass scales of the Big-Bang relic neutrinos as the neutrinos imprint characteristic scale- and redshift-dependent modifications onto the galaxy power spectrum shape. Here we describe the basic concept of how the galaxy clustering measurement can be used to explore the neutrino masses, with particular emphasis on advantages of the WFMOS survey over the existing low-redshift surveys such as SDSS

Quantification of the radio-metabolites of the serotonin-1A receptor radioligand [carbonyl-11C]WAY-100635 in human plasma: An HPLC-assay which enables measurement of two patients in parallel

International Nuclear Information System (INIS)

Nics, L.; Hahn, A.; Zeilinger, M.; Vraka, C.; Ungersboeck, J.; Haeusler, D.; Hartmann, S.; Wagner, K-H.; Lanzenberger, R.; Wadsak, W.; Mitterhauser, M.

2012-01-01

[Carbonyl- 11 C]WAY-100635 is a potent and effective antagonist for the 5-HT 1A receptor subtype. We aimed to assess the status of [carbonyl- 11 C]WAY-100635 and its main radio-metabolites, [carbonyl- 11 C]desmethyl-WAY-100635 and [carbonyl- 11 C]cyclohexanecarboxylic acid, on the basis of an improved radio-HPLC method. Common methods were characterized by preparative HPLC columns with long runtimes and/or high flow rates. Considering the short half-life of C-11, we developed a more rapid and solvent saving HPLC assay, allowing a fast, efficient and reliable quantification of these major metabolites. - Highlights: ► We developed a HPLC assay which allows the measurement of two patients in parallel. ► It allows a fast and efficient quantification of WAY-100635 and its metabolites. ► Better counting statistics with late samples for modeling the input function is achieved. ► The fastest assay so far is about 40% slower in comparison to the presented method.

High-throughput telomere length quantification by FISH and its application to human population studies.

Science.gov (United States)

Canela, Andrés; Vera, Elsa; Klatt, Peter; Blasco, María A

2007-03-27

A major limitation of studies of the relevance of telomere length to cancer and age-related diseases in human populations and to the development of telomere-based therapies has been the lack of suitable high-throughput (HT) assays to measure telomere length. We have developed an automated HT quantitative telomere FISH platform, HT quantitative FISH (Q-FISH), which allows the quantification of telomere length as well as percentage of short telomeres in large human sample sets. We show here that this technique provides the accuracy and sensitivity to uncover associations between telomere length and human disease.

Use of cesium 137 as a radiotracer in the quantification of tropical soil erosion

International Nuclear Information System (INIS)

Sibello Hernandez, Rita Y.; Cartas Aguila, Hector; Martin Perez, Jorge

2005-01-01

The main objective of this work was to evaluate the applicability of this technique to quantify the soil erosion in the tropical region. With this purpose the technique was applied in the tropical soils belonging to a glide parcel, in Cienfuegos province, in Cuba, in the Caribbean area. This allowed us to compare and to demonstrate the good agreement of the results of the soil loss quantification obtained using the 137 Cs technique: 37.00 + - 0.80 t.ha -1 . year -1 with the obtained using erosion plots in the Soil Experimental Station in Barajagua: 40 t.ha -1 . year -1

Photoacoustic-fluorescence in vitro flow cytometry for quantification of absorption, scattering and fluorescence properties of the cells

Science.gov (United States)

Nedosekin, D. A.; Sarimollaoglu, M.; Foster, S.; Galanzha, E. I.; Zharov, V. P.

2013-03-01

Fluorescence flow cytometry is a well-established analytical tool that provides quantification of multiple biological parameters of cells at molecular levels, including their functional states, morphology, composition, proliferation, and protein expression. However, only the fluorescence and scattering parameters of the cells or labels are available for detection. Cell pigmentation, presence of non-fluorescent dyes or nanoparticles cannot be reliably quantified. Herewith, we present a novel photoacoustic (PA) flow cytometry design for simple integration of absorbance measurements into schematics of conventional in vitro flow cytometers. The integrated system allow simultaneous measurements of light absorbance, scattering and of multicolor fluorescence from single cells in the flow at rates up to 2 m/s. We compared various combinations of excitation laser sources for multicolor detection, including simultaneous excitation of PA and fluorescence using a single 500 kHz pulsed nanosecond laser. Multichannel detection scheme allows simultaneous detection of up to 8 labels, including 4 fluorescent tags and 4 PA colors. In vitro PA-fluorescence flow cytometer was used for studies of nanoparticles uptake and for the analysis of cell line pigmentation, including genetically encoded melanin expression in breast cancer cell line. We demonstrate that this system can be used for direct nanotoxicity studies with simultaneous quantification of nanoparticles content and assessment of cell viability using a conventional fluorescent apoptosis assays.

Uncertainty Quantification given Discontinuous Climate Model Response and a Limited Number of Model Runs

Science.gov (United States)

Sargsyan, K.; Safta, C.; Debusschere, B.; Najm, H.

2010-12-01

Uncertainty quantification in complex climate models is challenged by the sparsity of available climate model predictions due to the high computational cost of model runs. Another feature that prevents classical uncertainty analysis from being readily applicable is bifurcative behavior in climate model response with respect to certain input parameters. A typical example is the Atlantic Meridional Overturning Circulation. The predicted maximum overturning stream function exhibits discontinuity across a curve in the space of two uncertain parameters, namely climate sensitivity and CO2 forcing. We outline a methodology for uncertainty quantification given discontinuous model response and a limited number of model runs. Our approach is two-fold. First we detect the discontinuity with Bayesian inference, thus obtaining a probabilistic representation of the discontinuity curve shape and location for arbitrarily distributed input parameter values. Then, we construct spectral representations of uncertainty, using Polynomial Chaos (PC) expansions on either side of the discontinuity curve, leading to an averaged-PC representation of the forward model that allows efficient uncertainty quantification. The approach is enabled by a Rosenblatt transformation that maps each side of the discontinuity to regular domains where desirable orthogonality properties for the spectral bases hold. We obtain PC modes by either orthogonal projection or Bayesian inference, and argue for a hybrid approach that targets a balance between the accuracy provided by the orthogonal projection and the flexibility provided by the Bayesian inference - where the latter allows obtaining reasonable expansions without extra forward model runs. The model output, and its associated uncertainty at specific design points, are then computed by taking an ensemble average over PC expansions corresponding to possible realizations of the discontinuity curve. The methodology is tested on synthetic examples of

Molecular quantification of genes encoding for green-fluorescent proteins

DEFF Research Database (Denmark)

Felske, A; Vandieken, V; Pauling, B V

2003-01-01

A quantitative PCR approach is presented to analyze the amount of recombinant green fluorescent protein (gfp) genes in environmental DNA samples. The quantification assay is a combination of specific PCR amplification and temperature gradient gel electrophoresis (TGGE). Gene quantification...... PCR strategy is a highly specific and sensitive way to monitor recombinant DNA in environments like the efflux of a biotechnological plant....

A highly sensitive method for quantification of iohexol

DEFF Research Database (Denmark)

Schulz, A.; Boeringer, F.; Swifka, J.

2014-01-01

-chromatography-electrospray-massspectrometry (LC-ESI-MS) approach using the multiple reaction monitoring mode for iohexol quantification. In order to test whether a significantly decreased amount of iohexol is sufficient for reliable quantification, a LC-ESI-MS approach was assessed. We analyzed the kinetics of iohexol in rats after application...... of different amounts of iohexol (15 mg to 150 1.tg per rat). Blood sampling was conducted at four time points, at 15, 30, 60, and 90 min, after iohexol injection. The analyte (iohexol) and the internal standard (iotha(amic acid) were separated from serum proteins using a centrifugal filtration device...... with a cut-off of 3 kDa. The chromatographic separation was achieved on an analytical Zorbax SB C18 column. The detection and quantification were performed on a high capacity trap mass spectrometer using positive ion ESI in the multiple reaction monitoring (MRM) mode. Furthermore, using real-time polymerase...

Terahertz identification and quantification of penicillamine enantiomers

International Nuclear Information System (INIS)

Ji Te; Zhao Hongwei; Chen Min; Xiao Tiqiao; Han Pengyu

2013-01-01

Identification and characterization of L-, D- and DL- penicillamine were demonstrated by Terahertz time-domain spectroscopy (THz-TDS). To understand the physical origins of the low frequency resonant modes, the density functional theory (DFT) was adopted for theoretical calculation. It was found that the collective THz frequency motions were decided by the intramolecular and intermolecular hydrogen bond interactions. Moreover, the quantification of penicillamine enantiomers mixture was demonstrated by a THz spectra fitting method with a relative error of less than 3.5%. This technique can be a valuable tool for the discrimination and quantification of chiral drugs in pharmaceutical industry. (authors)

Quantification of rat brain SPECT with 123I-ioflupane: evaluation of different reconstruction methods and image degradation compensations using Monte Carlo simulation

International Nuclear Information System (INIS)

Roé-Vellvé, N; Pino, F; Cot, A; Ros, D; Falcon, C; Gispert, J D; Pavía, J; Marin, C

2014-01-01

SPECT studies with 123 I-ioflupane facilitate the diagnosis of Parkinson’s disease (PD). The effect on quantification of image degradations has been extensively evaluated in human studies but their impact on studies of experimental PD models is still unclear. The aim of this work was to assess the effect of compensating for the degrading phenomena on the quantification of small animal SPECT studies using 123 I-ioflupane. This assessment enabled us to evaluate the feasibility of quantitatively detecting small pathological changes using different reconstruction methods and levels of compensation for the image degrading phenomena. Monte Carlo simulated studies of a rat phantom were reconstructed and quantified. Compensations for point spread function (PSF), scattering, attenuation and partial volume effect were progressively included in the quantification protocol. A linear relationship was found between calculated and simulated specific uptake ratio (SUR) in all cases. In order to significantly distinguish disease stages, noise-reduction during the reconstruction process was the most relevant factor, followed by PSF compensation. The smallest detectable SUR interval was determined by biological variability rather than by image degradations or coregistration errors. The quantification methods that gave the best results allowed us to distinguish PD stages with SUR values that are as close as 0.5 using groups of six rats to represent each stage. (paper)

Tool for objective quantification of pulmonary sequelae in monitoring of patients with tuberculosis; Ferramenta para quantificacao objetiva de sequelas pulmonares no acompanhamento de pacientes com tuberculose

Energy Technology Data Exchange (ETDEWEB)

Giacomini, Guilherme; Alvarez, Matheus; Pina, Diana R. de; Bacchim Neto, Fernando A.; Pereira, Paulo C.M.; Ribeiro, Sergio M.; Miranda, Jose Ricardo de A., E-mail: guigiacomini92@aluno.ibb.unesp.br [Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Botucaru, SP (Brazil)

2014-07-01

Tuberculosis (TB), caused by Mycobacterium tuberculosis, is an ancient infectious disease that remains a global health problem. Chest radiography is the method commonly employed in assessing the evolution of TB. However, lung damage quantification methods are usually performed on a computerized tomography (CT). This objective quantification is important in the radiological monitoring of the patient by assessing the progression and treatment of TB. However, precise quantification is not feasible by the number of CT examinations necessary due to the high dose subjected to the patient and high cost to the institution. The purpose of this work is to develop a tool to quantify pulmonary sequelae caused by TB through chest X-rays. Aiming the proposed objective, a computational algorithm was developed, creating a three-dimensional representation of the lungs, with regions of dilated sequelae inside. It also made the quantification of pulmonary sequelae of these patients through CT scans performed in upcoming dates, minimizing the differences in disease progression. The measurements from the two methods were compared with results suggest that the effectiveness and applicability of the developed tool, allowing lower doses radiological monitoring of the patient during treatment.

SPECT quantification of regional radionuclide distributions

International Nuclear Information System (INIS)

Jaszczak, R.J.; Greer, K.L.; Coleman, R.E.

1986-01-01

SPECT quantification of regional radionuclide activities within the human body is affected by several physical and instrumental factors including attenuation of photons within the patient, Compton scattered events, the system's finite spatial resolution and object size, finite number of detected events, partial volume effects, the radiopharmaceutical biokinetics, and patient and/or organ motion. Furthermore, other instrumentation factors such as calibration of the center-of-rotation, sampling, and detector nonuniformities will affect the SPECT measurement process. These factors are described, together with examples of compensation methods that are currently available for improving SPECT quantification. SPECT offers the potential to improve in vivo estimates of absorbed dose, provided the acquisition, reconstruction, and compensation procedures are adequately implemented and utilized. 53 references, 2 figures

Quantification of normal vaginal constituents using a new wet preparation technique.

Science.gov (United States)

Fowler, R Stuart

2012-10-01

This study aimed to evaluate a new method for preparing vaginal wet preparations to enable quantification of cells and lactobacilli. The current nonstandardized technique allows for a variable amount of vaginal fluid collected, diluted by a variable amount of saline/KOH, and no quantification of constituents. The vaginal fluids from 100 randomly selected women without vulvovaginitis symptoms presenting to the author's practice at Mayo Clinic underwent analysis by the quantification technique. Women were excluded if they were younger than 18 years, had antibiotics within the past 2 months, currently on their period, had placed anything in the vagina for the past 24 hours, used Depo-Provera, or were lactating. All the wet preparations were made by mixing the natural vaginal fluids with 3 mL of sterile normal saline. Spinal diluting fluid was added to the saline preparation. The saline and KOH mixtures were injected into separate wells of KOVA Glasstic Grid Slide and analyzed with a phase-contrast microscope at 40× and 60×. The concentration of leukocytes, lactobacilli, and squamous cells and the degree of maturation of the majority (>50%) of squamous cells were assessed, and it was determined whether there was excessive non-lactobacilli bacteria (EB) as evident by clumps of bacteria in the background fluid and speckling on the squamous cells. The 3 most common patterns to occur were as follows: First, 51% (95% confidence interval [CI] = 41%-60%) of the total specimens had abundant lactobacilli, no leukocytes, more than 50% fully maturated squamous cells, and no EB. Second, 22% (95% CI = 14%-32%) of the total specimens had low lactobacilli counts, no leukocytes, more than 50% undermaturated squamous cells, and no EB. Third, 12% (95% CI = 6%-20%) of the total specimens had abundant lactobacilli, leukocytes, more than 50% fully maturated squamous cells, and no EB. It is imperative to be able to objectively quantify normal vaginal secretion constituents so that (1) the

Decision peptide-driven: a free software tool for accurate protein quantification using gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry.

Science.gov (United States)

Santos, Hugo M; Reboiro-Jato, Miguel; Glez-Peña, Daniel; Nunes-Miranda, J D; Fdez-Riverola, Florentino; Carvallo, R; Capelo, J L

2010-09-15

The decision peptide-driven tool implements a software application for assisting the user in a protocol for accurate protein quantification based on the following steps: (1) protein separation through gel electrophoresis; (2) in-gel protein digestion; (3) direct and inverse (18)O-labeling and (4) matrix assisted laser desorption ionization time of flight mass spectrometry, MALDI analysis. The DPD software compares the MALDI results of the direct and inverse (18)O-labeling experiments and quickly identifies those peptides with paralleled loses in different sets of a typical proteomic workflow. Those peptides are used for subsequent accurate protein quantification. The interpretation of the MALDI data from direct and inverse labeling experiments is time-consuming requiring a significant amount of time to do all comparisons manually. The DPD software shortens and simplifies the searching of the peptides that must be used for quantification from a week to just some minutes. To do so, it takes as input several MALDI spectra and aids the researcher in an automatic mode (i) to compare data from direct and inverse (18)O-labeling experiments, calculating the corresponding ratios to determine those peptides with paralleled losses throughout different sets of experiments; and (ii) allow to use those peptides as internal standards for subsequent accurate protein quantification using (18)O-labeling. In this work the DPD software is presented and explained with the quantification of protein carbonic anhydrase. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Two-Phase Microfluidic Systems for High Throughput Quantification of Agglutination Assays

KAUST Repository

Castro, David

2018-01-01

assay, with a minimum detection limit of 50 ng/mL using optical image analysis. We compare optical image analysis and light scattering as quantification methods, and demonstrate the first light scattering quantification of agglutination assays in a two

Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization

Science.gov (United States)

Ullrich, Thomas; Ermantraut, Eugen; Schulz, Torsten; Steinmetzer, Katrin

2012-01-01

Background State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. Methodology and Principal Findings The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. Conclusions and Significance The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a

Competitive reporter monitored amplification (CMA--quantification of molecular targets by real time monitoring of competitive reporter hybridization.

Directory of Open Access Journals (Sweden)

Thomas Ullrich

Full Text Available BACKGROUND: State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. METHODOLOGY AND PRINCIPAL FINDINGS: The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. CONCLUSIONS AND SIGNIFICANCE: The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2, we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls

Assessment of probiotic viability during Cheddar cheese manufacture and ripening using propidium monoazide-PCR quantification

Directory of Open Access Journals (Sweden)

Emilie eDesfossés-Foucault

2012-10-01

Full Text Available The use of a suitable food carrier such as cheese could significantly enhance probiotic viability during storage. The main goal of this study was to assess viability of commercial probiotic strains during Cheddar cheesemaking and ripening (four to six months by comparing the efficiency of microbiological and molecular approaches. Molecular methods such as quantitative PCR (qPCR allow bacterial quantification, and DNA-blocking molecules such as propidium monoazide (PMA select only the living cells’ DNA. Cheese samples were manufactured with a lactococci starter and with one of three probiotic strains (Bifidobacterium animalis subsp. lactis BB-12, Lactobacillus rhamnosus RO011 or Lactobacillus helveticus RO052 or a mixed culture containing B. animalis subsp. lactis BB-12 and L. helveticus RO052 (MC1, both lactobacilli strains (MC2 or all three strains (MC3. DNA extractions were then carried out on PMA-treated and non-treated cell pellets in order to assess PMA treatment efficiency, followed by quantification using the 16S rRNA gene, the elongation factor Tu gene (tuf or the transaldolase gene (tal. Results with intact/dead ratios of bacteria showed that PMA-treated cheese samples had a significantly lower bacterial count than non-treated DNA samples (P<0.005, confirming that PMA did eliminate dead bacteria from PCR quantification. For both quantification methods, the addition of probiotic strains seemed to accelerate the loss of lactococci viability in comparison to control cheese samples, especially when L. helveticus RO052 was added. Viability of all three probiotic strains was also significantly reduced in mixed culture cheese samples (P<0.0001, B. animalis subsp. lactis BB-12 being the most sensitive to the presence of other strains. However, all probiotic strains did retain their viability (log nine cfu/g of cheese throughout ripening. This study was successful in monitoring living probiotic species in Cheddar cheese samples through PMA-qPCR.

Radiation dose determines the method for quantification of DNA double strand breaks

International Nuclear Information System (INIS)

Bulat, Tanja; Keta, Olitija; Korićanac, Lela; Žakula, Jelena; Petrović, Ivan; Ristić-Fira, Aleksandra; Todorović, Danijela

2016-01-01

Ionizing radiation induces DNA double strand breaks (DSBs) that trigger phosphorylation of the histone protein H2AX (γH2AX). Immunofluorescent staining visualizes formation of γH2AX foci, allowing their quantification. This method, as opposed to Western blot assay and Flow cytometry, provides more accurate analysis, by showing exact position and intensity of fluorescent signal in each single cell. In practice there are problems in quantification of γH2AX. This paper is based on two issues: the determination of which technique should be applied concerning the radiation dose, and how to analyze fluorescent microscopy images obtained by different microscopes. HTB140 melanoma cells were exposed to γ-rays, in the dose range from 1 to 16 Gy. Radiation effects on the DNA level were analyzed at different time intervals after irradiation by Western blot analysis and immunofluorescence microscopy. Immunochemically stained cells were visualized with two types of microscopes: AxioVision (Zeiss, Germany) microscope, comprising an ApoTome software, and AxioImagerA1 microscope (Zeiss, Germany). Obtained results show that the level of γH2AX is time and dose dependent. Immunofluorescence microscopy provided better detection of DSBs for lower irradiation doses, while Western blot analysis was more reliable for higher irradiation doses. AxioVision microscope containing ApoTome software was more suitable for the detection of γH2AX foci. (author)

Radiation dose determines the method for quantification of DNA double strand breaks

Energy Technology Data Exchange (ETDEWEB)

Bulat, Tanja; Keta, Olitija; Korićanac, Lela; Žakula, Jelena; Petrović, Ivan; Ristić-Fira, Aleksandra [University of Belgrade, Vinča Institute of Nuclear Sciences, Belgrade (Serbia); Todorović, Danijela, E-mail: dtodorovic@medf.kg.ac.rs [University of Kragujevac, Faculty of Medical Sciences, Kragujevac (Serbia)

2016-03-15

Ionizing radiation induces DNA double strand breaks (DSBs) that trigger phosphorylation of the histone protein H2AX (γH2AX). Immunofluorescent staining visualizes formation of γH2AX foci, allowing their quantification. This method, as opposed to Western blot assay and Flow cytometry, provides more accurate analysis, by showing exact position and intensity of fluorescent signal in each single cell. In practice there are problems in quantification of γH2AX. This paper is based on two issues: the determination of which technique should be applied concerning the radiation dose, and how to analyze fluorescent microscopy images obtained by different microscopes. HTB140 melanoma cells were exposed to γ-rays, in the dose range from 1 to 16 Gy. Radiation effects on the DNA level were analyzed at different time intervals after irradiation by Western blot analysis and immunofluorescence microscopy. Immunochemically stained cells were visualized with two types of microscopes: AxioVision (Zeiss, Germany) microscope, comprising an ApoTome software, and AxioImagerA1 microscope (Zeiss, Germany). Obtained results show that the level of γH2AX is time and dose dependent. Immunofluorescence microscopy provided better detection of DSBs for lower irradiation doses, while Western blot analysis was more reliable for higher irradiation doses. AxioVision microscope containing ApoTome software was more suitable for the detection of γH2AX foci. (author)

Low cost high performance uncertainty quantification

KAUST Repository

Bekas, C.; Curioni, A.; Fedulova, I.

2009-01-01

Uncertainty quantification in risk analysis has become a key application. In this context, computing the diagonal of inverse covariance matrices is of paramount importance. Standard techniques, that employ matrix factorizations, incur a cubic cost

AVQS: Attack Route-Based Vulnerability Quantification Scheme for Smart Grid

Directory of Open Access Journals (Sweden)

Jongbin Ko

2014-01-01

Full Text Available A smart grid is a large, consolidated electrical grid system that includes heterogeneous networks and systems. Based on the data, a smart grid system has a potential security threat in its network connectivity. To solve this problem, we develop and apply a novel scheme to measure the vulnerability in a smart grid domain. Vulnerability quantification can be the first step in security analysis because it can help prioritize the security problems. However, existing vulnerability quantification schemes are not suitable for smart grid because they do not consider network vulnerabilities. We propose a novel attack route-based vulnerability quantification scheme using a network vulnerability score and an end-to-end security score, depending on the specific smart grid network environment to calculate the vulnerability score for a particular attack route. To evaluate the proposed approach, we derive several attack scenarios from the advanced metering infrastructure domain. The experimental results of the proposed approach and the existing common vulnerability scoring system clearly show that we need to consider network connectivity for more optimized vulnerability quantification.

AVQS: attack route-based vulnerability quantification scheme for smart grid.

Science.gov (United States)

Ko, Jongbin; Lim, Hyunwoo; Lee, Seokjun; Shon, Taeshik

2014-01-01

A smart grid is a large, consolidated electrical grid system that includes heterogeneous networks and systems. Based on the data, a smart grid system has a potential security threat in its network connectivity. To solve this problem, we develop and apply a novel scheme to measure the vulnerability in a smart grid domain. Vulnerability quantification can be the first step in security analysis because it can help prioritize the security problems. However, existing vulnerability quantification schemes are not suitable for smart grid because they do not consider network vulnerabilities. We propose a novel attack route-based vulnerability quantification scheme using a network vulnerability score and an end-to-end security score, depending on the specific smart grid network environment to calculate the vulnerability score for a particular attack route. To evaluate the proposed approach, we derive several attack scenarios from the advanced metering infrastructure domain. The experimental results of the proposed approach and the existing common vulnerability scoring system clearly show that we need to consider network connectivity for more optimized vulnerability quantification.

Comparison of machine learning and semi-quantification algorithms for (I123)FP-CIT classification: the beginning of the end for semi-quantification?

Science.gov (United States)

Taylor, Jonathan Christopher; Fenner, John Wesley

2017-11-29

Semi-quantification methods are well established in the clinic for assisted reporting of (I123) Ioflupane images. Arguably, these are limited diagnostic tools. Recent research has demonstrated the potential for improved classification performance offered by machine learning algorithms. A direct comparison between methods is required to establish whether a move towards widespread clinical adoption of machine learning algorithms is justified. This study compared three machine learning algorithms with that of a range of semi-quantification methods, using the Parkinson's Progression Markers Initiative (PPMI) research database and a locally derived clinical database for validation. Machine learning algorithms were based on support vector machine classifiers with three different sets of features: Voxel intensities Principal components of image voxel intensities Striatal binding radios from the putamen and caudate. Semi-quantification methods were based on striatal binding ratios (SBRs) from both putamina, with and without consideration of the caudates. Normal limits for the SBRs were defined through four different methods: Minimum of age-matched controls Mean minus 1/1.5/2 standard deviations from age-matched controls Linear regression of normal patient data against age (minus 1/1.5/2 standard errors) Selection of the optimum operating point on the receiver operator characteristic curve from normal and abnormal training data Each machine learning and semi-quantification technique was evaluated with stratified, nested 10-fold cross-validation, repeated 10 times. The mean accuracy of the semi-quantitative methods for classification of local data into Parkinsonian and non-Parkinsonian groups varied from 0.78 to 0.87, contrasting with 0.89 to 0.95 for classifying PPMI data into healthy controls and Parkinson's disease groups. The machine learning algorithms gave mean accuracies between 0.88 to 0.92 and 0.95 to 0.97 for local and PPMI data respectively. Classification

Quantification of underivatised amino acids on dry blood spot, plasma, and urine by HPLC-ESI-MS/MS.

Science.gov (United States)

Giordano, Giuseppe; Di Gangi, Iole Maria; Gucciardi, Antonina; Naturale, Mauro

2012-01-01

Enzyme deficiencies in amino acid (AA) metabolism affecting the levels of amino acids and their derivatives in physiological fluids may serve as diagnostically significant biomarkers for one or a group of metabolic disorders. Therefore, it is important to monitor a wide range of free amino acids simultaneously and to quantify them. This is time consuming if we use the classical methods and more than ever now that many laboratories have introduced Newborn Screening Programs for the semiquantitative analysis, detection, and quantification of some amino acids needed to be performed in a short time to reduce the rate of false positives.We have modified the stable isotope dilution HPLC-electrospray ionization (ESI)-MS/MS method previously described by Qu et al. (Anal Chem 74: 2034-2040, 2002) for a more rapid, robust, sensitive, and specific detection and quantification of underivatised amino acids. The modified method reduces the time of analysis to 10 min with very good reproducibility of retention times and a better separation of the metabolites and their isomers.The omission of the derivatization step allowed us to achieve some important advantages: fast and simple sample preparation and exclusion of artefacts and interferences. The use of this technique is highly sensitive, specific, and allows monitoring of 40 underivatized amino acids, including the key isomers and quantification of some of them, in order to cover many diagnostically important intermediates of metabolic pathways.We propose this HPLC-ESI-MS/MS method for underivatized amino acids as a support for the Newborn Screening as secondary test using the same dried blood spots for a more accurate and specific examination in case of suspected metabolic diseases. In this way, we avoid plasma collection from the patient as it normally occurs, reducing anxiety for the parents and further costs for analysis.The same method was validated and applied also to plasma and urine samples with good reproducibility

Quantification of Iodine-123-FP-CIT SPECT with a resolution-independent method

International Nuclear Information System (INIS)

Dobbeleir, A.A.; Ham, H.R.; Hambye, A.E.; Vervaet, A.M.

2005-01-01

quantification in % of the injected activity was well correlated with both the striatal- to-occipital and the resolution-independent ratios. It is concluded that the partial volume effect severely affects the quantification of FP-CIT uptake and results in a rather large inter-observer variability. Measurement of striatal and non-specific activity in large regions of interest circumvents this problem and provides stable and reproducible resolution-independent results, allowing a direct comparison between data acquired with different imaging systems or even in different hospitals. (author)

Superlattice band structure: New and simple energy quantification condition

Energy Technology Data Exchange (ETDEWEB)

Maiz, F., E-mail: fethimaiz@gmail.com [University of Cartage, Nabeul Engineering Preparatory Institute, Merazka, 8000 Nabeul (Tunisia); King Khalid University, Faculty of Science, Physics Department, P.O. Box 9004, Abha 61413 (Saudi Arabia)

2014-10-01

Assuming an approximated effective mass and using Bastard's boundary conditions, a simple method is used to calculate the subband structure for periodic semiconducting heterostructures. Our method consists to derive and solve the energy quantification condition (EQC), this is a simple real equation, composed of trigonometric and hyperbolic functions, and does not need any programming effort or sophistic machine to solve it. For less than ten wells heterostructures, we have derived and simplified the energy quantification conditions. The subband is build point by point; each point presents an energy level. Our simple energy quantification condition is used to calculate the subband structure of the GaAs/Ga{sub 0.5}Al{sub 0.5}As heterostructures, and build its subband point by point for 4 and 20 wells. Our finding shows a good agreement with previously published results.

High-performance liquid chromatographic quantification of rifampicin in human plasma: method for Therapecutic drug monitoring

International Nuclear Information System (INIS)

Sameh, T.; Hanene, E.; Jebali, N.

2013-01-01

A high performance liquid chromatography (HPLC) method has been developed that allows quantification of Rifampicin in human plasma. The method is based on the precipitation of proteins in human plasma with methanol. Optimal assay conditions were found with a C18 column and a simple mobile phase consisting of 0.05 M dipotassic hydrogen phosphate buffer and acetonitrile (53/47, V/V) with 0.086 % diethylamin, pH = 4.46. The flow-rate was 0.6 ml /mm and the drug was monitored at 340 nm. Results from the HPLC analyses showed that the assay method is linear in the concentration range of 1-40 micro g/ml, (r2 >0.99). The limit of quantification and limit of detection of Rifampicin were 0.632 micro g/ml and 0.208 micro g/ml, respectively. Intraday and interday coefficient of variation and bias were below 10% for all samples, suggesting good precision and accuracy of the method. Recoveries were greater than 90% in a plasma sample volume of 100 micro l. The method is being successfully applied to therapeutic drug monitoring of Rifapicin in plasma samples of tuberculosis and staphylococcal infections patients. (author)

Quantification bias caused by plasmid DNA conformation in quantitative real-time PCR assay.

Science.gov (United States)

Lin, Chih-Hui; Chen, Yu-Chieh; Pan, Tzu-Ming

2011-01-01

Quantitative real-time PCR (qPCR) is the gold standard for the quantification of specific nucleic acid sequences. However, a serious concern has been revealed in a recent report: supercoiled plasmid standards cause significant over-estimation in qPCR quantification. In this study, we investigated the effect of plasmid DNA conformation on the quantification of DNA and the efficiency of qPCR. Our results suggest that plasmid DNA conformation has significant impact on the accuracy of absolute quantification by qPCR. DNA standard curves shifted significantly among plasmid standards with different DNA conformations. Moreover, the choice of DNA measurement method and plasmid DNA conformation may also contribute to the measurement error of DNA standard curves. Due to the multiple effects of plasmid DNA conformation on the accuracy of qPCR, efforts should be made to assure the highest consistency of plasmid standards for qPCR. Thus, we suggest that the conformation, preparation, quantification, purification, handling, and storage of standard plasmid DNA should be described and defined in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) to assure the reproducibility and accuracy of qPCR absolute quantification.

HCV-RNA quantification in liver bioptic samples and extrahepatic compartments, using the abbott RealTime HCV assay.

Science.gov (United States)

Antonucci, FrancescoPaolo; Cento, Valeria; Sorbo, Maria Chiara; Manuelli, Matteo Ciancio; Lenci, Ilaria; Sforza, Daniele; Di Carlo, Domenico; Milana, Martina; Manzia, Tommaso Maria; Angelico, Mario; Tisone, Giuseppe; Perno, Carlo Federico; Ceccherini-Silberstein, Francesca

2017-08-01

We evaluated the performance of a rapid method to quantify HCV-RNA in the hepatic and extrahepatic compartments, by using for the first time the Abbott RealTime HCV-assay. Non-tumoral (NT), tumoral (TT) liver samples, lymph nodes and ascitic fluid from patients undergoing orthotopic-liver-transplantation (N=18) or liver resection (N=4) were used for the HCV-RNA quantification; 5/22 patients were tested after or during direct acting antivirals (DAA) treatment. Total RNA and DNA quantification from tissue-biopsies allowed normalization of HCV-RNA concentrations in IU/μg of total RNA and IU/10 6 liver-cells, respectively. HCV-RNA was successfully quantified with high reliability in liver biopsies, lymph nodes and ascitic fluid samples. Among the 17 untreated patients, a positive and significant HCV-RNA correlation between serum and NT liver-samples was observed (Pearson: rho=0.544, p=0.024). Three DAA-treated patients were HCV-RNA "undetectable" in serum, but still "detectable" in all tested liver-tissues. Differently, only one DAA-treated patient, tested after sustained-virological-response, showed HCV-RNA "undetectability" in liver-tissue. HCV-RNA was successfully quantified with high reliability in liver bioptic samples and extrahepatic compartments, even when HCV-RNA was "undetectable" in serum. Abbott RealTime HCV-assay is a good diagnostic tool for HCV quantification in intra- and extra-hepatic compartments, whenever a bioptic sample is available. Copyright © 2017 Elsevier B.V. All rights reserved.

Experimental design for TBT quantification by isotope dilution SPE-GC-ICP-MS under the European water framework directive.

Science.gov (United States)

Alasonati, Enrica; Fabbri, Barbara; Fettig, Ina; Yardin, Catherine; Del Castillo Busto, Maria Estela; Richter, Janine; Philipp, Rosemarie; Fisicaro, Paola

2015-03-01

In Europe the maximum allowable concentration for tributyltin (TBT) compounds in surface water has been regulated by the water framework directive (WFD) and daughter directive that impose a limit of 0.2 ng L(-1) in whole water (as tributyltin cation). Despite the large number of different methodologies for the quantification of organotin species developed in the last two decades, standardised analytical methods at required concentration level do not exist. TBT quantification at picogram level requires efficient and accurate sample preparation and preconcentration, and maximum care to avoid blank contamination. To meet the WFD requirement, a method for the quantification of TBT in mineral water at environmental quality standard (EQS) level, based on solid phase extraction (SPE), was developed and optimised. The quantification was done using species-specific isotope dilution (SSID) followed by gas chromatography (GC) coupled to inductively coupled plasma mass spectrometry (ICP-MS). The analytical process was optimised using a design of experiment (DOE) based on a factorial fractionary plan. The DOE allowed to evaluate 3 qualitative factors (type of stationary phase and eluent, phase mass and eluent volume, pH and analyte ethylation procedure) for a total of 13 levels studied, and a sample volume in the range of 250-1000 mL. Four different models fitting the results were defined and evaluated with statistic tools: one of them was selected and optimised to find the best procedural conditions. C18 phase was found to be the best stationary phase for SPE experiments. The 4 solvents tested with C18, the pH and ethylation conditions, the mass of the phases, the volume of the eluents and the sample volume can all be optimal, but depending on their respective combination. For that reason, the equation of the model conceived in this work is a useful decisional tool for the planning of experiments, because it can be applied to predict the TBT mass fraction recovery when the

Integration of ground-based laser scanner and aerial digital photogrammetry for topographic modelling of Vesuvio volcano

Science.gov (United States)

Pesci, Arianna; Fabris, Massimo; Conforti, Dario; Loddo, Fabiana; Baldi, Paolo; Anzidei, Marco

2007-05-01

This work deals with the integration of different surveying methodologies for the definition of very accurate Digital Terrain Models (DTM) and/or Digital Surface Models (DSM): in particular, the aerial digital photogrammetry and the terrestrial laser scanning were used to survey the Vesuvio volcano, allowing the total coverage of the internal cone and surroundings (the whole surveyed area was about 3 km × 3 km). The possibility to reach a very high precision, especially from the laser scanner data set, allowed a detailed description of the morphology of the volcano. The comparisons of models obtained in repeated surveys allow a detailed map of residuals providing a data set that can be used for detailed studies of the morphological evolution. Moreover, the reflectivity information, highly correlated to materials properties, allows for the measurement and quantification of some morphological variations in areas where structural discontinuities and displacements are present.

PET Quantification of the Norepinephrine Transporter in Human Brain with (S,S)-18F-FMeNER-D2.

Science.gov (United States)

Moriguchi, Sho; Kimura, Yasuyuki; Ichise, Masanori; Arakawa, Ryosuke; Takano, Harumasa; Seki, Chie; Ikoma, Yoko; Takahata, Keisuke; Nagashima, Tomohisa; Yamada, Makiko; Mimura, Masaru; Suhara, Tetsuya

2017-07-01

Norepinephrine transporter (NET) in the brain plays important roles in human cognition and the pathophysiology of psychiatric disorders. Two radioligands, ( S , S )- 11 C-MRB and ( S , S )- 18 F-FMeNER-D 2 , have been used for imaging NETs in the thalamus and midbrain (including locus coeruleus) using PET in humans. However, NET density in the equally important cerebral cortex has not been well quantified because of unfavorable kinetics with ( S , S )- 11 C-MRB and defluorination with ( S , S )- 18 F-FMeNER-D 2 , which can complicate NET quantification in the cerebral cortex adjacent to the skull containing defluorinated 18 F radioactivity. In this study, we have established analysis methods of quantification of NET density in the brain including the cerebral cortex using ( S , S )- 18 F-FMeNER-D 2 PET. Methods: We analyzed our previous ( S , S )- 18 F-FMeNER-D 2 PET data of 10 healthy volunteers dynamically acquired for 240 min with arterial blood sampling. The effects of defluorination on the NET quantification in the superficial cerebral cortex was evaluated by establishing a time stability of NET density estimations with an arterial input 2-tissue-compartment model, which guided the less-invasive reference tissue model and area under the time-activity curve methods to accurately quantify NET density in all brain regions including the cerebral cortex. Results: Defluorination of ( S , S )- 18 F-FMeNER-D 2 became prominent toward the latter half of the 240-min scan. Total distribution volumes in the superficial cerebral cortex increased with the scan duration beyond 120 min. We verified that 90-min dynamic scans provided a sufficient amount of data for quantification of NET density unaffected by defluorination. Reference tissue model binding potential values from the 90-min scan data and area under the time-activity curve ratios of 70- to 90-min data allowed for the accurate quantification of NET density in the cerebral cortex. Conclusion: We have established

Ultra-Sensitive NT-proBNP Quantification for Early Detection of Risk Factors Leading to Heart Failure

Directory of Open Access Journals (Sweden)

Keum-Soo Song

2017-09-01

Full Text Available Cardiovascular diseases such as acute myocardial infarction and heart failure accounted for the death of 17.5 million people (31% of all global deaths in 2015. Monitoring the level of circulating N-terminal proBNP (NT-proBNP is crucial for the detection of people at risk of heart failure. In this article, we describe a novel ultra-sensitive NT-proBNP test (us-NT-proBNP that allows the quantification of circulating NT-proBNP in 30 min at 25 °C in the linear detection range of 7.0–600 pg/mL. It is a first report on the application of a fluorescence bead labeled detection antibody, DNA-guided detection method, and glass fiber membrane platform for the quantification of NT-proBNP in clinical samples. Limit of blank, limit of detection, and limit of quantification were 2.0 pg/mL, 3.7 pg/mL, and 7 pg/mL, respectively. The coefficient of variation was found to be less than 10% in the entire detection range of 7–600 pg/mL. The test demonstrated specificity for NT-proBNP without interferences from bilirubin, intra-lipid, biotin, and hemoglobin. The serial dilution test for plasma samples containing various NT-proBNP levels showed the linear decrement in concentration with the regression coefficient of 0.980–0.998. These results indicate that us-NT-proBNP test does not suffer from the interference of the plasma components for the measurement of NT-proBNP in clinical samples.

Cyclewise Operation of Printed MoS2 Transistor Biosensors for Rapid Biomolecule Quantification at Femtomolar Levels.

Science.gov (United States)

Ryu, Byunghoon; Nam, Hongsuk; Oh, Bo-Ram; Song, Yujing; Chen, Pengyu; Park, Younggeun; Wan, Wenjie; Kurabayashi, Katsuo; Liang, Xiaogan

2017-02-24

Field-effect transistors made from MoS 2 and other emerging layered semiconductors have been demonstrated to be able to serve as ultrasensitive biosensors. However, such nanoelectronic sensors still suffer seriously from a series of challenges associated with the poor compatibility between electronic structures and liquid analytes. These challenges hinder the practical biosensing applications that demand rapid, low-noise, highly specific biomolecule quantification at femtomolar levels. To address such challenges, we study a cyclewise process for operating MoS 2 transistor biosensors, in which a series of reagent fluids are delivered to the sensor in a time-sequenced manner and periodically set the sensor into four assay-cycle stages, including incubation, flushing, drying, and electrical measurement. Running multiple cycles of such an assay can acquire a time-dependent sensor response signal quantifying the reaction kinetics of analyte-receptor binding. This cyclewise detection approach can avoid the liquid-solution-induced electrochemical damage, screening, and nonspecific adsorption to the sensor and therefore improves the transistor sensor's durability, sensitivity, specificity, and signal-to-noise ratio. These advantages in combination with the inherent high sensitivity of MoS 2 biosensors allow for rapid biomolecule quantification at femtomolar levels. We have demonstrated the cyclewise quantification of Interleukin-1β in pure and complex solutions (e.g., serum and saliva) with a detection limit of ∼1 fM and a total detection time ∼23 min. This work leverages the superior properties of layered semiconductors for biosensing applications and advances the techniques toward realizing fast real-time immunoassay for low-abundance biomolecule detection.

Phytochemical analysis of Vernonanthura tweedieana and a validated UPLC-PDA method for the quantification of eriodictyol

Directory of Open Access Journals (Sweden)

Layzon Antonio Lemos da Silva

Full Text Available AbstractVernonanthura tweedieana (Baker H. Rob., Asteraceae, is used in the Brazilian folk medicine for the treatment of respiratory diseases. In this work the phytochemical investigation of its ethanol extracts as well as the development and validation of an UPLC-PDA method for the quantification of the eriodictyol from the leaves were performed. The phytochemical study for this species lead to the identification of ethyl caffeate, naringenin and chrysoeriol in mixture, eriodictyol from leaves, and the mixture of 3-hydroxy-1-(4-hydroxy-3,5-dimethoxyphenyl-propan-1-one and evofolin B, apigenin, the mixture of caffeic and protocatechuic acid and luteolin from stems with roots, being reported for the first time for V. tweedieana, except for eriodictyol. The structural elucidation of all isolated compounds was achieved by 1H and 2D NMR spectroscopy, and in comparison with published data. An UPLC-PDA method for quantification of the eriodictyol in leaves of V. tweedieana was developed and validated for specificity, linearity, precision (repeatability and intermediate precision, limit of detection (LOD and limit of quantification (LOQ, accuracy and robustness. In this study, an excellent linearity was obtained (r2 = 0.9999, good precision (repeatability RSD = 2% and intermediate precision RSD = 8% and accuracy (average recovery from 98.6% to 99.7%. The content of eriodictyol in the extract of leaves of V. tweedieana was 41.40 ± 0.13 mg/g. Thus, this study allowed the optimization of a simple, fast and validated UPLC-PDA method which can be used to support the quality assessment of this herbal material.

Low cost high performance uncertainty quantification

KAUST Repository

Bekas, C.

2009-01-01

Uncertainty quantification in risk analysis has become a key application. In this context, computing the diagonal of inverse covariance matrices is of paramount importance. Standard techniques, that employ matrix factorizations, incur a cubic cost which quickly becomes intractable with the current explosion of data sizes. In this work we reduce this complexity to quadratic with the synergy of two algorithms that gracefully complement each other and lead to a radically different approach. First, we turned to stochastic estimation of the diagonal. This allowed us to cast the problem as a linear system with a relatively small number of multiple right hand sides. Second, for this linear system we developed a novel, mixed precision, iterative refinement scheme, which uses iterative solvers instead of matrix factorizations. We demonstrate that the new framework not only achieves the much needed quadratic cost but in addition offers excellent opportunities for scaling at massively parallel environments. We based our implementation on BLAS 3 kernels that ensure very high processor performance. We achieved a peak performance of 730 TFlops on 72 BG/P racks, with a sustained performance 73% of theoretical peak. We stress that the techniques presented in this work are quite general and applicable to several other important applications. Copyright © 2009 ACM.

Automated processing of zebrafish imaging data: a survey.

Science.gov (United States)

Mikut, Ralf; Dickmeis, Thomas; Driever, Wolfgang; Geurts, Pierre; Hamprecht, Fred A; Kausler, Bernhard X; Ledesma-Carbayo, María J; Marée, Raphaël; Mikula, Karol; Pantazis, Periklis; Ronneberger, Olaf; Santos, Andres; Stotzka, Rainer; Strähle, Uwe; Peyriéras, Nadine

2013-09-01

Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines.

Automated Processing of Zebrafish Imaging Data: A Survey

Science.gov (United States)

Dickmeis, Thomas; Driever, Wolfgang; Geurts, Pierre; Hamprecht, Fred A.; Kausler, Bernhard X.; Ledesma-Carbayo, María J.; Marée, Raphaël; Mikula, Karol; Pantazis, Periklis; Ronneberger, Olaf; Santos, Andres; Stotzka, Rainer; Strähle, Uwe; Peyriéras, Nadine

2013-01-01

Abstract Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines. PMID:23758125

Quantification of structural uncertainties in multi-scale models; case study of the Lublin Basin, Poland

Science.gov (United States)

Małolepszy, Zbigniew; Szynkaruk, Ewa

2015-04-01

The multiscale static modeling of regional structure of the Lublin Basin is carried on in the Polish Geological Institute, in accordance with principles of integrated 3D geological modelling. The model is based on all available geospatial data from Polish digital databases and analogue archives. Mapped regional structure covers the area of 260x80 km located between Warsaw and Polish-Ukrainian border, along NW-SE-trending margin of the East European Craton. Within the basin, the Paleozoic beds with coalbearing Carboniferous and older formations containing hydrocarbons and unconventional prospects are covered unconformably by Permo-Mesozoic and younger rocks. Vertical extent of the regional model is set from topographic surface to 6000 m ssl and at the bottom includes some Proterozoic crystalline formations of the craton. The project focuses on internal consistency of the models built at different scales - from basin (small) scale to field-scale (large-scale). The models, nested in the common structural framework, are being constructed with regional geological knowledge, ensuring smooth transition in the 3D model resolution and amount of geological detail. Major challenge of the multiscale approach to subsurface modelling is the assessment and consistent quantification of various types of geological uncertainties tied to those various scale sub-models. Decreasing amount of information with depth and, particularly, very limited data collected below exploration targets, as well as accuracy and quality of data, all have the most critical impact on the modelled structure. In deeper levels of the Lublin Basin model, seismic interpretation of 2D surveys is sparsely tied to well data. Therefore time-to-depth conversion carries one of the major uncertainties in the modeling of structures, especially below 3000 m ssl. Furthermore, as all models at different scales are based on the same dataset, we must deal with different levels of generalization of geological structures. The

Preclinical imaging characteristics and quantification of Platinum-195m SPECT

Energy Technology Data Exchange (ETDEWEB)

Aalbersberg, E.A.; Wit-van der Veen, B.J. de; Vegt, E.; Vogel, Wouter V. [The Netherlands Cancer Institute (NKI-AVL), Department of Nuclear Medicine, Amsterdam (Netherlands); Zwaagstra, O.; Codee-van der Schilden, K. [Nuclear Research and Consultancy Group (NRG), Petten (Netherlands)

2017-08-15

In vivo biodistribution imaging of platinum-based compounds may allow better patient selection for treatment with chemo(radio)therapy. Radiolabeling with Platinum-195m ({sup 195m}Pt) allows SPECT imaging, without altering the chemical structure or biological activity of the compound. We have assessed the feasibility of {sup 195m}Pt SPECT imaging in mice, with the aim to determine the image quality and accuracy of quantification for current preclinical imaging equipment. Enriched (>96%) {sup 194}Pt was irradiated in the High Flux Reactor (HFR) in Petten, The Netherlands (NRG). A 0.05 M HCl {sup 195m}Pt-solution with a specific activity of 33 MBq/mg was obtained. Image quality was assessed for the NanoSPECT/CT (Bioscan Inc., Washington DC, USA) and U-SPECT{sup +}/CT (MILabs BV, Utrecht, the Netherlands) scanners. A radioactivity-filled rod phantom (rod diameter 0.85-1.7 mm) filled with 1 MBq {sup 195m}Pt was scanned with different acquisition durations (10-120 min). Four healthy mice were injected intravenously with 3-4 MBq {sup 195m}Pt. Mouse images were acquired with the NanoSPECT for 120 min at 0, 2, 4, or 24 h after injection. Organs were delineated to quantify {sup 195m}Pt concentrations. Immediately after scanning, the mice were sacrificed, and the platinum concentration was determined in organs using a gamma counter and graphite furnace - atomic absorption spectroscopy (GF-AAS) as reference standards. A 30-min acquisition of the phantom provided visually adequate image quality for both scanners. The smallest visible rods were 0.95 mm in diameter on the NanoSPECT and 0.85 mm in diameter on the U-SPECT{sup +}. The image quality in mice was visually adequate. Uptake was seen in the kidneys with excretion to the bladder, and in the liver, blood, and intestine. No uptake was seen in the brain. The Spearman correlation between SPECT and gamma counter was 0.92, between SPECT and GF-AAS it was 0.84, and between GF-AAS and gamma counter it was0.97 (all p < 0

Molecular Approaches for High Throughput Detection and Quantification of Genetically Modified Crops: A Review

Directory of Open Access Journals (Sweden)

Ibrahim B. Salisu

2017-10-01

Full Text Available As long as the genetically modified crops are gaining attention globally, their proper approval and commercialization need accurate and reliable diagnostic methods for the transgenic content. These diagnostic techniques are mainly divided into two major groups, i.e., identification of transgenic (1 DNA and (2 proteins from GMOs and their products. Conventional methods such as PCR (polymerase chain reaction and enzyme-linked immunosorbent assay (ELISA were routinely employed for DNA and protein based quantification respectively. Although, these Techniques (PCR and ELISA are considered as significantly convenient and productive, but there is need for more advance technologies that allow for high throughput detection and the quantification of GM event as the production of more complex GMO is increasing day by day. Therefore, recent approaches like microarray, capillary gel electrophoresis, digital PCR and next generation sequencing are more promising due to their accuracy and precise detection of transgenic contents. The present article is a brief comparative study of all such detection techniques on the basis of their advent, feasibility, accuracy, and cost effectiveness. However, these emerging technologies have a lot to do with detection of a specific event, contamination of different events and determination of fusion as well as stacked gene protein are the critical issues to be addressed in future.

Fibrin-Targeted Magnetic Resonance Imaging Allows In Vivo Quantification of Thrombus Fibrin Content and Identifies Thrombi Amenable for Thrombolysis

Science.gov (United States)

Jenkins, Julia; Modarai, Bijan; Wiethoff, Andrea J.; Phinikaridou, Alkystis; Grover, Steven P.; Patel, Ashish S.; Schaeffter, Tobias; Smith, Alberto; Botnar, Rene M.

2014-01-01

Objective Deep venous thrombosis is a major health problem. Thrombolytic therapies are effective in recanalizing the veins and preventing post-thrombotic complications, but there is no consensus on selection criteria. The aim of this study was to investigate a fibrin-specific MRI contrast agent (EP-2104R) for the accurate quantification of thrombus’ fibrin content in vivo and for the identification of thrombus suitable for thrombolysis. Approach and Results Venous thrombosis was induced in the inferior vena cava of 8- to 10-week-old male BALB/C mice and MRI performed 2, 4, 7, 10, 14, and 21 days later. Eighteen mice were scanned at each time point pre and 2 hours post injection of EP-2104R (8.0 μmol/kg) with 12 mice at each time point used to correlate fibrin contrast uptake with thrombus’ histological stage and fibrin content. Six mice at each time point were immediately subjected to intravascular thrombolytic therapy (10 mg/kg of tissue-type plasminogen activator). Mice were imaged to assess response to lytic therapy 24 hours after thrombolytic treatment. Two mice at each time point were scanned post injection of 0.2 mmol/kg of Gd-DTPA (gadolinium with diethylenetriaminepentacetate, Magnevist, Schering AG, Berlin, Germany) for control purpose. Contrast uptake was correlated positively with the fibrin content of the thrombus measured by Western blotting (R2=0.889; PThrombus relaxation rate (R1) post contrast and the change in visualized thrombus size on late gadolinium enhancement inversion recovery MRI pre–EP-2104R and post–EP-2104R injection were the best predictors for successful thrombolysis (area under the curve, 0.989 [95% confidence interval, 0.97–1.00] and 0.994 [95% confidence interval, 0.98–1.00] respectively). Conclusions MRI with a fibrin-specific contrast agent accurately estimates thrombus fibrin content in vivo and identifies thrombi that are amenable for thrombolysis. PMID:24723557

Simultaneous quantification of carotenoids, retinol, and tocopherols in forage, bovine plasma, and milk: validation of a novel UPLC method

Energy Technology Data Exchange (ETDEWEB)

Chauveau-Duriot, B.; Doreau, M.; Noziere, P.; Graulet, B. [UR1213 Research Unit on Herbivores, INRA, Saint Genes Champanelle (France)

2010-05-15

Simultaneous quantification of various liposoluble micronutrients is not a new area of interest since these compounds participate in the nutritional quality of feeds that is largely explored in human, and also in animal diet. However, the development of related methods is still under concern, especially when the carotenoid composition is complex such as in forage given to ruminants or in lipid-rich matrices like milk. In this paper, an original method for simultaneous extraction and quantification of all carotenoids, vitamins E, and A in milk was proposed. Moreover, a new UPLC method allowing simultaneous determination of carotenoids and vitamins A and E in forage, plasma and milk, and separation of 23 peaks of carotenoids in forage was described. This UPLC method using a HSS T3 column and a gradient solvent system was compared to a previously published reverse-phase HPLC using two C18 columns in series and an isocratic solvent system. The UPLC method gave similar concentrations of carotenoids and vitamins A and E than the HPLC method. Moreover, UPLC allowed a better resolution for xanthophylls, especially lutein and zeaxanthin, for the three isomers of {beta}-carotene (all-E-, 9Z- and 13Z-) and for vitamins A, an equal or better sensitivity according to gradient, and a better reproducibility of peak areas and retention times, but did not reduce the time required for analysis. (orig.)

Simultaneous quantification of carotenoids, retinol, and tocopherols in forages, bovine plasma, and milk: validation of a novel UPLC method.

Science.gov (United States)

Chauveau-Duriot, B; Doreau, M; Nozière, P; Graulet, B

2010-05-01

Simultaneous quantification of various liposoluble micronutrients is not a new area of interest since these compounds participate in the nutritional quality of feeds that is largely explored in human, and also in animal diet. However, the development of related methods is still under concern, especially when the carotenoid composition is complex such as in forages given to ruminants or in lipid-rich matrices like milk. In this paper, an original method for simultaneous extraction and quantification of all carotenoids, vitamins E, and A in milk was proposed. Moreover, a new UPLC method allowing simultaneous determination of carotenoids and vitamins A and E in forage, plasma and milk, and separation of 23 peaks of carotenoids in forages was described. This UPLC method using a HSS T3 column and a gradient solvent system was compared to a previously published reverse-phase HPLC using two C18 columns in series and an isocratic solvent system. The UPLC method gave similar concentrations of carotenoids and vitamins A and E than the HPLC method. Moreover, UPLC allowed a better resolution for xanthophylls, especially lutein and zeaxanthin, for the three isomers of beta-carotene (all-E-, 9Z- and 13Z-) and for vitamins A, an equal or better sensitivity according to gradient, and a better reproducibility of peak areas and retention times, but did not reduce the time required for analysis.

Towards an uncertainty quantification methodology with CASMO-5

International Nuclear Information System (INIS)

Wieselquist, W.; Vasiliev, A.; Ferroukhi, H.

2011-01-01

We present the development of an uncertainty quantification (UQ) methodology for the CASMO-5 lattice physics code, used extensively at the Paul Scherrer Institut for standalone neutronics calculations, as well as the generation of nuclear fuel segment libraries for the downstream core simulator, SIMULATE-3. We focus here on propagation of nuclear data uncertainties and describe the framework required for 'black box' UQ--in this case minor modifications of the code are necessary to allow perturbation of the CASMO-5 nuclear data library. We then implement a basic rst-order UQ method, direct perturbation, which directly produces sensitivity coefficients and when folded with the input nuclear data variance-covariance matrix (VCM) yields output uncertainties in the form of an output VCM. We discuss the implementation, including how to map the VCMs of a different group structure to the code library group structure (in our case the ENDF/B-VII-based 586-group library in CASMO-5), present some results for pin cell calculations, and conclude with future work. (author)

freeQuant: A Mass Spectrometry Label-Free Quantification Software Tool for Complex Proteome Analysis.

Science.gov (United States)

Deng, Ning; Li, Zhenye; Pan, Chao; Duan, Huilong

2015-01-01

Study of complex proteome brings forward higher request for the quantification method using mass spectrometry technology. In this paper, we present a mass spectrometry label-free quantification tool for complex proteomes, called freeQuant, which integrated quantification with functional analysis effectively. freeQuant consists of two well-integrated modules: label-free quantification and functional analysis with biomedical knowledge. freeQuant supports label-free quantitative analysis which makes full use of tandem mass spectrometry (MS/MS) spectral count, protein sequence length, shared peptides, and ion intensity. It adopts spectral count for quantitative analysis and builds a new method for shared peptides to accurately evaluate abundance of isoforms. For proteins with low abundance, MS/MS total ion count coupled with spectral count is included to ensure accurate protein quantification. Furthermore, freeQuant supports the large-scale functional annotations for complex proteomes. Mitochondrial proteomes from the mouse heart, the mouse liver, and the human heart were used to evaluate the usability and performance of freeQuant. The evaluation showed that the quantitative algorithms implemented in freeQuant can improve accuracy of quantification with better dynamic range.

Pore space quantification of carbonate rocks before-after supercritical CO2 interaction by optical image analysis

Science.gov (United States)

Berrezueta, Edgar; José Domínguez-Cuesta, María

2017-04-01

The aim of this research is to show an experimental application of an automated quantification process of optical porosity in thin sections. Petrographic studies using scanning electronic microscopy, optical microscopy (OpM) and optical image analysis (OIA) could provide a reproducible pore characterization of carbonate rocks in applications related to the geological storage of CO2. This research is focused on i) the quantification of optical pores in a carbonate rock before and after supercritical CO2-rich brine (P ≈ 7.5 MPa and T ≈ 35 °C) and ii) the description of the process followed to guarantee the reproducibility of the OIA method on images acquired with high-resolution scanner. Mineral images were acquired from thin sections using a high-resolution scanner (HRS). Digital images were geo-referenced by using geographic information system to ensure correct spatial correlation and superposition. The optical measures of porosity by image analysis on the carbonates thin sections showed an effective pore segmentation considering different cross-polarized light conditions (90°/0°; 120°/30°) and plane-polarized light conditions (90°/-) of the same petrographic scene. The pore characterization by OpM and OIA-HRS has allowed a preliminary approximation of pore evolution in carbonate rocks under the supercritical CO2-rich brine. This study shows a fast, effective and reproducible methodology that allowed a preliminary characterization (changes in the pore network) of the samples studied. The procedure carried out could be applied to similar experimental injection tests.

Cross recurrence quantification for cover song identification

Energy Technology Data Exchange (ETDEWEB)

Serra, Joan; Serra, Xavier; Andrzejak, Ralph G [Department of Information and Communication Technologies, Universitat Pompeu Fabra, Roc Boronat 138, 08018 Barcelona (Spain)], E-mail: joan.serraj@upf.edu

2009-09-15

There is growing evidence that nonlinear time series analysis techniques can be used to successfully characterize, classify, or process signals derived from real-world dynamics even though these are not necessarily deterministic and stationary. In the present study, we proceed in this direction by addressing an important problem our modern society is facing, the automatic classification of digital information. In particular, we address the automatic identification of cover songs, i.e. alternative renditions of a previously recorded musical piece. For this purpose, we here propose a recurrence quantification analysis measure that allows the tracking of potentially curved and disrupted traces in cross recurrence plots (CRPs). We apply this measure to CRPs constructed from the state space representation of musical descriptor time series extracted from the raw audio signal. We show that our method identifies cover songs with a higher accuracy as compared to previously published techniques. Beyond the particular application proposed here, we discuss how our approach can be useful for the characterization of a variety of signals from different scientific disciplines. We study coupled Roessler dynamics with stochastically modulated mean frequencies as one concrete example to illustrate this point.

Cross recurrence quantification for cover song identification

International Nuclear Information System (INIS)

Serra, Joan; Serra, Xavier; Andrzejak, Ralph G

2009-01-01

There is growing evidence that nonlinear time series analysis techniques can be used to successfully characterize, classify, or process signals derived from real-world dynamics even though these are not necessarily deterministic and stationary. In the present study, we proceed in this direction by addressing an important problem our modern society is facing, the automatic classification of digital information. In particular, we address the automatic identification of cover songs, i.e. alternative renditions of a previously recorded musical piece. For this purpose, we here propose a recurrence quantification analysis measure that allows the tracking of potentially curved and disrupted traces in cross recurrence plots (CRPs). We apply this measure to CRPs constructed from the state space representation of musical descriptor time series extracted from the raw audio signal. We show that our method identifies cover songs with a higher accuracy as compared to previously published techniques. Beyond the particular application proposed here, we discuss how our approach can be useful for the characterization of a variety of signals from different scientific disciplines. We study coupled Roessler dynamics with stochastically modulated mean frequencies as one concrete example to illustrate this point.

First discoveries of z ˜ 6 quasars with the Kilo-Degree Survey and VISTA Kilo-Degree Infrared Galaxy survey

NARCIS (Netherlands)

Venemans, B. P.; Verdoes Kleijn, G. A.; Mwebaze, J.; Valentijn, E. A.; Bañados, E.; Decarli, R.; de Jong, J. T. A.; Findlay, J. R.; Kuijken, K. H.; Barbera, F. La; Mc Farland, John; McMahon, R. G.; Napolitano, N.; Sikkema, G.; Sutherland, W. J.

2015-01-01

We present the results of our first year of quasar search in the ongoing ESO public Kilo-Degree Survey (KiDS) and VISTA Kilo-Degree Infrared Galaxy (VIKING) surveys. These surveys are among the deeper wide-field surveys that can be used to uncover large numbers of z ˜ 6 quasars. This allows us to

Culture-independent identification and quantification of Gallibacterium anatis (G. anatis) by real-time quantitative PCR

DEFF Research Database (Denmark)

Wang, Chong; Robles, Francisco; Ramirez, Saul

2016-01-01

Gallibacterium is a genus within the family Pasteurellaceae characterized by a high level of phenotypic and genetic diversity. No diagnostic method has yet been described, which allows species-specific identification of Gallibacterium anatis. The aim of this study was to develop a real...... published conventional PCR method and culture-based identification, respectively. The detection rates were 97%, 78% and 34% for the current qPCR, the conventional PCR and the culture-based identification method, respectively. The qPCR assay was able to detect the gene gyrB in serial dilutions of 10......-time quantitative PCR (qPCR) method allowing species-specific identification and quantification of G. anatis. A G. anatis specific DNA sequence was identified in the gyrase subunit B gene (gyrB) and used to design a TaqMan probe and corresponding primers. The specificity of the assay was tested on 52 bacterial...

Quantification of N-acetyl- and N-glycolylneuraminic acids by a stable isotope dilution assay using high-performance liquid chromatography-tandem mass spectrometry.

Science.gov (United States)

Allevi, Pietro; Femia, Eti Alessandra; Costa, Maria Letizia; Cazzola, Roberta; Anastasia, Mario

2008-11-28

The present report describes a method for the quantification of N-acetyl- and N-glycolylneuraminic acids without any derivatization, using their (13)C(3)-isotopologues as internal standards and a C(18) reversed-phase column modified by decylboronic acid which allows for the first time a complete chromatographic separation between the two analytes. The method is based on high-performance liquid chromatographic coupled with electrospray ion-trap mass spectrometry. The limit of quantification of the method is 0.1mg/L (2.0ng on column) for both analytes. The calibration curves are linear for both sialic acids over the range of 0.1-80mg/L (2.0-1600ng on column) with a correlation coefficient greater than 0.997. The proposed method was applied to the quantitative determination of sialic acids released from fetuin as a model of glycoproteins.

Quantification of aortic regurgitation by magnetic resonance velocity mapping

DEFF Research Database (Denmark)

Søndergaard, Lise; Lindvig, K; Hildebrandt, P

1993-01-01

The use of magnetic resonance (MR) velocity mapping in the quantification of aortic valvular blood flow was examined in 10 patients with angiographically verified aortic regurgitation. MR velocity mapping succeeded in identifying and quantifying the regurgitation in all patients, and the regurgit......The use of magnetic resonance (MR) velocity mapping in the quantification of aortic valvular blood flow was examined in 10 patients with angiographically verified aortic regurgitation. MR velocity mapping succeeded in identifying and quantifying the regurgitation in all patients...

Itô-SDE MCMC method for Bayesian characterization of errors associated with data limitations in stochastic expansion methods for uncertainty quantification

Science.gov (United States)

Arnst, M.; Abello Álvarez, B.; Ponthot, J.-P.; Boman, R.

2017-11-01

This paper is concerned with the characterization and the propagation of errors associated with data limitations in polynomial-chaos-based stochastic methods for uncertainty quantification. Such an issue can arise in uncertainty quantification when only a limited amount of data is available. When the available information does not suffice to accurately determine the probability distributions that must be assigned to the uncertain variables, the Bayesian method for assigning these probability distributions becomes attractive because it allows the stochastic model to account explicitly for insufficiency of the available information. In previous work, such applications of the Bayesian method had already been implemented by using the Metropolis-Hastings and Gibbs Markov Chain Monte Carlo (MCMC) methods. In this paper, we present an alternative implementation, which uses an alternative MCMC method built around an Itô stochastic differential equation (SDE) that is ergodic for the Bayesian posterior. We draw together from the mathematics literature a number of formal properties of this Itô SDE that lend support to its use in the implementation of the Bayesian method, and we describe its discretization, including the choice of the free parameters, by using the implicit Euler method. We demonstrate the proposed methodology on a problem of uncertainty quantification in a complex nonlinear engineering application relevant to metal forming.

Quantification of rutile in anatase by X-ray diffraction

International Nuclear Information System (INIS)

Chavez R, A.

2001-01-01

Nowadays the discovering of new and better materials required in all areas of the industry has been lead to the human being to introduce him to this small and great world. The crystalline materials, have properties markedly directional. When it is necessary to realize a quantitative analysis to these materials the task is not easy. The main objective of this work is the research of a real problem, its solution and perfecting of a technique involving the theoretical and experimental principles which allow the quantification of crystalline phases. The chapter 1 treats about the study of crystalline state during the last century, by means of the X-ray diffraction technique. The chapter 2 studies the nature and production of X-rays, the chapter 3 expounds the principles of the diffraction technique which to carry out when it is satisfied the Bragg law studying the powder diffraction method and its applications. In the chapter 4 it is explained how the intensities of the beams diffracted are determined by the atoms positions inside of the elemental cell of the crystal. The properties of the crystalline samples of anatase and rutile are described in the chapter 5. The results of this last analysis are the information which will be processed by means of the auxiliary software: Diffrac AT, Axum and Peakfit as well as the TAFOR and CUANTI software describing this part with more detail in the chapters 6 and 7 where it is mentioned step by step the function of each software until to reach the quantification of crystalline phases, objective of this work. Finally, in the chapter 8 there are a results analysis and conclusions. The contribution of this work is for those learned institutions of limited resources which can tackle in this way the characterization of materials. (Author)

Note: Electrical detection and quantification of spin rectification effect enabled by shorted microstrip transmission line technique

International Nuclear Information System (INIS)

Soh, Wee Tee; Ong, C. K.; Peng, Bin; Chai, Guozhi

2014-01-01

We describe a shorted microstrip method for the sensitive quantification of Spin Rectification Effect (SRE). SRE for a Permalloy (Ni 80 Fe 20 ) thin film strip sputtered onto SiO 2 substrate is demonstrated. Our method obviates the need for simultaneous lithographic patterning of the sample and transmission line, therefore greatly simplifying the SRE measurement process. Such a shorted microstrip method can allow different contributions to SRE (anisotropic magnetoresistance, Hall effect, and anomalous Hall effect) to be simultaneously determined. Furthermore, SRE signals from unpatterned 50 nm thick Permalloy films of area dimensions 5 mm × 10 mm can even be detected

Quantification by aberration corrected (S)TEM of boundaries formed by symmetry breaking phase transformations

Energy Technology Data Exchange (ETDEWEB)

Schryvers, D., E-mail: nick.schryvers@uantwerpen.be [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Salje, E.K.H. [Department of Earth Sciences, University of Cambridge, Cambridge CB2 3EQ (United Kingdom); Nishida, M. [Department of Engineering Sciences for Electronics and Materials, Faculty of Engineering Sciences, Kyushu University, Kasuga, Fukuoka 816-8580 (Japan); De Backer, A. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Idrissi, H. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Institute of Mechanics, Materials and Civil Engineering, Université Catholique de Louvain, Place Sainte Barbe, 2, B-1348, Louvain-la-Neuve (Belgium); Van Aert, S. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium)

2017-05-15

The present contribution gives a review of recent quantification work of atom displacements, atom site occupations and level of crystallinity in various systems and based on aberration corrected HR(S)TEM images. Depending on the case studied, picometer range precisions for individual distances can be obtained, boundary widths at the unit cell level determined or statistical evolutions of fractions of the ordered areas calculated. In all of these cases, these quantitative measures imply new routes for the applications of the respective materials. - Highlights: • Quantification of picometer displacements at ferroelastic twin boundary in CaTiO{sub 3.} • Quantification of kinks in meandering ferroelectric domain wall in LiNbO{sub 3}. • Quantification of column occupation in anti-phase boundary in Co-Pt. • Quantification of atom displacements at twin boundary in Ni-Ti B19′ martensite.

Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients.

Science.gov (United States)

de Vos, Luka; Gevensleben, Heidrun; Schröck, Andreas; Franzen, Alina; Kristiansen, Glen; Bootz, Friedrich; Dietrich, Dimo

2017-01-01

.81-0.84, AUC testing  = 0.80). The accurate prediction of overall survival was possible with all three algorithms (training cohort: HR SEPT9  = 1.23-1.90, HR SHOX2  = 1.14-1.85, HR mean SEPT9 / SHOX2  =1.19-1.89 ; testing cohort: HR SEPT9  =1.22-1.67, HR SHOX2  = 1.15-1.71, HR mean SEPT9 / SHOX2  = 1.12-1.77). The concordant clinical performance based on different quantification algorithms allows for the application of various diagnostic platforms for the analysis of ccfDNA methylation biomarkers.

Tannin quantification in red grapes and wine: comparison of polysaccharide- and protein-based tannin precipitation techniques and their ability to model wine astringency.

Science.gov (United States)

Mercurio, Meagan D; Smith, Paul A

2008-07-23

Quantification of red grape tannin and red wine tannin using the methyl cellulose precipitable (MCP) tannin assay and the Adams-Harbertson (A-H) tannin assay were investigated. The study allowed for direct comparison between the repeatability of the assays and for the assessment of other practical considerations such as time efficiency, ease of practice, and throughput, and assessed the relationships between tannin quantification by both analytical techniques. A strong correlation between the two analytical techniques was observed when quantifying grape tannin (r(2) = 0.96), and a good correlation was observed for wine tannins (r(2) = 0.80). However, significant differences in the reported tannin values for the analytical techniques were observed (approximately 3-fold). To explore potential reasons for the difference, investigations were undertaken to determine how several variables influenced the final tannin quantification for both assays. These variables included differences in the amount of tannin precipitated (monitored by HPLC), assay matrix variables, and the monomers used to report the final values. The relationship between tannin quantification and wine astringency was assessed for the MCP and A-H tannin assays, and both showed strong correlations with perceived wine astringency (r(2) = 0.83 and r(2) = 0.90, respectively). The work described here gives guidance to those wanting to understand how the values between the two assays relate; however, a conclusive explanation for the differences in values between the MCP and A-H tannin assays remains unclear, and further work in this area is required.

The use of self-quantification systems for personal health information: big data management activities and prospects.

Science.gov (United States)

Almalki, Manal; Gray, Kathleen; Sanchez, Fernando Martin

2015-01-01

Self-quantification is seen as an emerging paradigm for health care self-management. Self-quantification systems (SQS) can be used for tracking, monitoring, and quantifying health aspects including mental, emotional, physical, and social aspects in order to gain self-knowledge. However, there has been a lack of a systematic approach for conceptualising and mapping the essential activities that are undertaken by individuals who are using SQS in order to improve health outcomes. In this paper, we propose a new model of personal health information self-quantification systems (PHI-SQS). PHI-SQS model describes two types of activities that individuals go through during their journey of health self-managed practice, which are 'self-quantification' and 'self-activation'. In this paper, we aimed to examine thoroughly the first type of activity in PHI-SQS which is 'self-quantification'. Our objectives were to review the data management processes currently supported in a representative set of self-quantification tools and ancillary applications, and provide a systematic approach for conceptualising and mapping these processes with the individuals' activities. We reviewed and compared eleven self-quantification tools and applications (Zeo Sleep Manager, Fitbit, Actipressure, MoodPanda, iBGStar, Sensaris Senspod, 23andMe, uBiome, Digifit, BodyTrack, and Wikilife), that collect three key health data types (Environmental exposure, Physiological patterns, Genetic traits). We investigated the interaction taking place at different data flow stages between the individual user and the self-quantification technology used. We found that these eleven self-quantification tools and applications represent two major tool types (primary and secondary self-quantification systems). In each type, the individuals experience different processes and activities which are substantially influenced by the technologies' data management capabilities. Self-quantification in personal health maintenance

Clinical applications of MS-based protein quantification.

Science.gov (United States)

Sabbagh, Bassel; Mindt, Sonani; Neumaier, Michael; Findeisen, Peter

2016-04-01

Mass spectrometry-based assays are increasingly important in clinical laboratory medicine and nowadays are already commonly used in several areas of routine diagnostics. These include therapeutic drug monitoring, toxicology, endocrinology, pediatrics, and microbiology. Accordingly, some of the most common analyses are therapeutic drug monitoring of immunosuppressants, vitamin D, steroids, newborn screening, and bacterial identification. However, MS-based quantification of peptides and proteins for routine diagnostic use is rather rare up to now despite excellent analytical specificity and good sensitivity. Here, we want to give an overview over current fit-for-purpose assays for MS-based protein quantification. Advantages as well as challenges of this approach will be discussed with focus on feasibility for routine diagnostic use. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Survey: interpolation methods for whole slide image processing.

Science.gov (United States)

Roszkowiak, L; Korzynska, A; Zak, J; Pijanowska, D; Swiderska-Chadaj, Z; Markiewicz, T

2017-02-01

Evaluating whole slide images of histological and cytological samples is used in pathology for diagnostics, grading and prognosis . It is often necessary to rescale whole slide images of a very large size. Image resizing is one of the most common applications of interpolation. We collect the advantages and drawbacks of nine interpolation methods, and as a result of our analysis, we try to select one interpolation method as the preferred solution. To compare the performance of interpolation methods, test images were scaled and then rescaled to the original size using the same algorithm. The modified image was compared to the original image in various aspects. The time needed for calculations and results of quantification performance on modified images were also compared. For evaluation purposes, we used four general test images and 12 specialized biological immunohistochemically stained tissue sample images. The purpose of this survey is to determine which method of interpolation is the best to resize whole slide images, so they can be further processed using quantification methods. As a result, the interpolation method has to be selected depending on the task involving whole slide images. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Uncertainty Quantification in Aerodynamics Simulations, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — The objective of the proposed work (Phases I and II) is to develop uncertainty quantification methodologies and software suitable for use in CFD simulations of...

Quantification Model for Estimating Temperature Field Distributions of Apple Fruit

OpenAIRE

Zhang , Min; Yang , Le; Zhao , Huizhong; Zhang , Leijie; Zhong , Zhiyou; Liu , Yanling; Chen , Jianhua

2009-01-01

International audience; A quantification model of transient heat conduction was provided to simulate apple fruit temperature distribution in the cooling process. The model was based on the energy variation of apple fruit of different points. It took into account, heat exchange of representative elemental volume, metabolism heat and external heat. The following conclusions could be obtained: first, the quantification model can satisfactorily describe the tendency of apple fruit temperature dis...

Initial water quantification results using neutron computed tomography

Science.gov (United States)

Heller, A. K.; Shi, L.; Brenizer, J. S.; Mench, M. M.

2009-06-01

Neutron computed tomography is an important imaging tool in the field of non-destructive testing and in fundamental research for many engineering applications. Contrary to X-rays, neutrons can be attenuated by some light materials, such as hydrogen, but can penetrate many heavy materials. Thus, neutron computed tomography is useful in obtaining important three-dimensional information about a sample's interior structure and material properties that other traditional methods cannot provide. The neutron computed tomography system at the Pennsylvania State University's Radiation Science and Engineering Center is being utilized to develop a water quantification technique for investigation of water distribution in fuel cells under normal conditions. A hollow aluminum cylinder test sample filled with a known volume of water was constructed for purposes of testing the quantification technique. Transmission images of the test sample at different angles were easily acquired through the synthesis of a dedicated image acquisition computer driving a rotary table controller and an in-house developed synchronization software package. After data acquisition, Octopus (version 8.2) and VGStudio Max (version 1.2) were used to perform cross-sectional and three-dimensional reconstructions of the sample, respectively. The initial reconstructions and water quantification results are presented.

Perfusion Quantification Using Gaussian Process Deconvolution

DEFF Research Database (Denmark)

Andersen, Irene Klærke; Have, Anna Szynkowiak; Rasmussen, Carl Edward

2002-01-01

The quantification of perfusion using dynamic susceptibility contrast MRI (DSC-MRI) requires deconvolution to obtain the residual impulse response function (IRF). In this work, a method using the Gaussian process for deconvolution (GPD) is proposed. The fact that the IRF is smooth is incorporated...

Uncertainty Quantification Bayesian Framework for Porous Media Flows

Science.gov (United States)

Demyanov, V.; Christie, M.; Erbas, D.

2005-12-01

Uncertainty quantification is an increasingly important aspect of many areas of applied science, where the challenge is to make reliable predictions about the performance of complex physical systems in the absence of complete or reliable data. Predicting flows of fluids through undersurface reservoirs is an example of a complex system where accuracy in prediction is needed (e.g. in oil industry it is essential for financial reasons). Simulation of fluid flow in oil reservoirs is usually carried out using large commercially written finite difference simulators solving conservation equations describing the multi-phase flow through the porous reservoir rocks, which is a highly computationally expensive task. This work examines a Bayesian Framework for uncertainty quantification in porous media flows that uses a stochastic sampling algorithm to generate models that match observed time series data. The framework is flexible for a wide range of general physical/statistical parametric models, which are used to describe the underlying hydro-geological process in its temporal dynamics. The approach is based on exploration of the parameter space and update of the prior beliefs about what the most likely model definitions are. Optimization problem for a highly parametric physical model usually have multiple solutions, which impact the uncertainty of the made predictions. Stochastic search algorithm (e.g. genetic algorithm) allows to identify multiple "good enough" models in the parameter space. Furthermore, inference of the generated model ensemble via MCMC based algorithm evaluates the posterior probability of the generated models and quantifies uncertainty of the predictions. Machine learning algorithm - Artificial Neural Networks - are used to speed up the identification of regions in parameter space where good matches to observed data can be found. Adaptive nature of ANN allows to develop different ways of integrating them into the Bayesian framework: as direct time

Microwave-assisted extraction of green coffee oil and quantification of diterpenes by HPLC.

Science.gov (United States)

Tsukui, A; Santos Júnior, H M; Oigman, S S; de Souza, R O M A; Bizzo, H R; Rezende, C M

2014-12-01

The microwave-assisted extraction (MAE) of 13 different green coffee beans (Coffea arabica L.) was compared to Soxhlet extraction for oil obtention. The full factorial design applied to the microwave-assisted extraction (MAE), related to time and temperature parameters, allowed to develop a powerful fast and smooth methodology (10 min at 45°C) compared to a 4h Soxhlet extraction. The quantification of cafestol and kahweol diterpenes present in the coffee oil was monitored by HPLC/UV and showed satisfactory linearity (R(2)=0.9979), precision (CV 3.7%), recovery (yield calculated on the diterpenes content for sample AT1 (Arabica green coffee) showed a six times higher value compared to the traditional Soxhlet method. Copyright © 2014 Elsevier Ltd. All rights reserved.

Temperature dependence of postmortem MR quantification for soft tissue discrimination

Energy Technology Data Exchange (ETDEWEB)

Zech, Wolf-Dieter; Schwendener, Nicole; Jackowski, Christian [University of Bern, From the Institute of Forensic Medicine, Bern (Switzerland); Persson, Anders; Warntjes, Marcel J. [University of Linkoeping, The Center for Medical Image Science and Visualization (CMIV), Linkoeping (Sweden)

2015-08-15

To investigate and correct the temperature dependence of postmortem MR quantification used for soft tissue characterization and differentiation in thoraco-abdominal organs. Thirty-five postmortem short axis cardiac 3-T MR examinations were quantified using a quantification sequence. Liver, spleen, left ventricular myocardium, pectoralis muscle and subcutaneous fat were analysed in cardiac short axis images to obtain mean T1, T2 and PD tissue values. The core body temperature was measured using a rectally inserted thermometer. The tissue-specific quantitative values were related to the body core temperature. Equations to correct for temperature differences were generated. In a 3D plot comprising the combined data of T1, T2 and PD, different organs/tissues could be well differentiated from each other. The quantitative values were influenced by the temperature. T1 in particular exhibited strong temperature dependence. The correction of quantitative values to a temperature of 37 C resulted in better tissue discrimination. Postmortem MR quantification is feasible for soft tissue discrimination and characterization of thoraco-abdominal organs. This provides a base for computer-aided diagnosis and detection of tissue lesions. The temperature dependence of the T1 values challenges postmortem MR quantification. Equations to correct for the temperature dependence are provided. (orig.)

Temperature dependence of postmortem MR quantification for soft tissue discrimination

International Nuclear Information System (INIS)

Zech, Wolf-Dieter; Schwendener, Nicole; Jackowski, Christian; Persson, Anders; Warntjes, Marcel J.

2015-01-01

To investigate and correct the temperature dependence of postmortem MR quantification used for soft tissue characterization and differentiation in thoraco-abdominal organs. Thirty-five postmortem short axis cardiac 3-T MR examinations were quantified using a quantification sequence. Liver, spleen, left ventricular myocardium, pectoralis muscle and subcutaneous fat were analysed in cardiac short axis images to obtain mean T1, T2 and PD tissue values. The core body temperature was measured using a rectally inserted thermometer. The tissue-specific quantitative values were related to the body core temperature. Equations to correct for temperature differences were generated. In a 3D plot comprising the combined data of T1, T2 and PD, different organs/tissues could be well differentiated from each other. The quantitative values were influenced by the temperature. T1 in particular exhibited strong temperature dependence. The correction of quantitative values to a temperature of 37 C resulted in better tissue discrimination. Postmortem MR quantification is feasible for soft tissue discrimination and characterization of thoraco-abdominal organs. This provides a base for computer-aided diagnosis and detection of tissue lesions. The temperature dependence of the T1 values challenges postmortem MR quantification. Equations to correct for the temperature dependence are provided. (orig.)

Quantification is Neither Necessary Nor Sufficient for Measurement

International Nuclear Information System (INIS)

Mari, Luca; Maul, Andrew; Torres Irribarra, David; Wilson, Mark

2013-01-01

Being an infrastructural, widespread activity, measurement is laden with stereotypes. Some of these concern the role of measurement in the relation between quality and quantity. In particular, it is sometimes argued or assumed that quantification is necessary for measurement; it is also sometimes argued or assumed that quantification is sufficient for or synonymous with measurement. To assess the validity of these positions the concepts of measurement and quantitative evaluation should be independently defined and their relationship analyzed. We contend that the defining characteristic of measurement should be the structure of the process, not a feature of its results. Under this perspective, quantitative evaluation is neither sufficient nor necessary for measurement

Detection and quantification of proteins and cells by use of elemental mass spectrometry: progress and challenges.

Science.gov (United States)

Yan, Xiaowen; Yang, Limin; Wang, Qiuquan

2013-07-01

Much progress has been made in identification of the proteins in proteomes, and quantification of these proteins has attracted much interest. In addition to popular tandem mass spectrometric methods based on soft ionization, inductively coupled plasma mass spectrometry (ICPMS), a typical example of mass spectrometry based on hard ionization, usually used for analysis of elements, has unique advantages in absolute quantification of proteins by determination of an element with a definite stoichiometry in a protein or attached to the protein. In this Trends article, we briefly describe state-of-the-art ICPMS-based methods for quantification of proteins, emphasizing protein-labeling and element-tagging strategies developed on the basis of chemically selective reactions and/or biospecific interactions. Recent progress from protein to cell quantification by use of ICPMS is also discussed, and the possibilities and challenges of ICPMS-based protein quantification for universal, selective, or targeted quantification of proteins and cells in a biological sample are also discussed critically. We believe ICPMS-based protein quantification will become ever more important in targeted quantitative proteomics and bioanalysis in the near future.

Automation of a Nile red staining assay enables high throughput quantification of microalgal lipid production.

Science.gov (United States)

Morschett, Holger; Wiechert, Wolfgang; Oldiges, Marco

2016-02-09

Within the context of microalgal lipid production for biofuels and bulk chemical applications, specialized higher throughput devices for small scale parallelized cultivation are expected to boost the time efficiency of phototrophic bioprocess development. However, the increasing number of possible experiments is directly coupled to the demand for lipid quantification protocols that enable reliably measuring large sets of samples within short time and that can deal with the reduced sample volume typically generated at screening scale. To meet these demands, a dye based assay was established using a liquid handling robot to provide reproducible high throughput quantification of lipids with minimized hands-on-time. Lipid production was monitored using the fluorescent dye Nile red with dimethyl sulfoxide as solvent facilitating dye permeation. The staining kinetics of cells at different concentrations and physiological states were investigated to successfully down-scale the assay to 96 well microtiter plates. Gravimetric calibration against a well-established extractive protocol enabled absolute quantification of intracellular lipids improving precision from ±8 to ±2 % on average. Implementation into an automated liquid handling platform allows for measuring up to 48 samples within 6.5 h, reducing hands-on-time to a third compared to manual operation. Moreover, it was shown that automation enhances accuracy and precision compared to manual preparation. It was revealed that established protocols relying on optical density or cell number for biomass adjustion prior to staining may suffer from errors due to significant changes of the cells' optical and physiological properties during cultivation. Alternatively, the biovolume was used as a measure for biomass concentration so that errors from morphological changes can be excluded. The newly established assay proved to be applicable for absolute quantification of algal lipids avoiding limitations of currently established

Quantification of fossil fuel CO2 at the building/street level for large US cities

Science.gov (United States)

Gurney, K. R.; Razlivanov, I. N.; Song, Y.

2012-12-01

Quantification of fossil fuel CO2 emissions from the bottom-up perspective is a critical element in emerging plans on a global, integrated, carbon monitoring system (CMS). A space/time explicit emissions data product can act as both a verification and planning system. It can verify atmospheric CO2 measurements (in situ and remote) and offer detailed mitigation information to management authorities in order to optimize the mix of mitigation efforts. Here, we present the Hestia Project, an effort aimed at building a high resolution (eg. building and road link-specific, hourly) fossil fuel CO2 emissions data product for the urban domain as a pilot effort to a CMS. A complete data product has been built for the city of Indianapolis and preliminary quantification has been completed for Los Angeles and Phoenix (see figure). The effort in Indianapolis is now part of a larger effort aimed at a convergent top-down/bottom-up assessment of greenhouse gas emissions, called INFLUX. Our urban-level quantification relies on a mixture of data and modeling structures. We start with the sector-specific Vulcan Project estimate at the mix of geocoded and county-wide levels. The Hestia aim is to distribute the Vulcan result in space and time. Two components take the majority of effort: buildings and onroad emissions. In collaboration with our INFLUX colleagues, we are transporting these high resolution emissions through an atmospheric transport model for a forward comparison of the Hestia data product with atmospheric measurements, collected on aircraft and cell towers. In preparation for a formal urban-scale inversion, these forward comparisons offer insights into both improving our emissions data product and measurement strategies. A key benefit of the approach taken in this study is the tracking and archiving of fuel and process-level detail (eg. combustion process, other pollutants), allowing for a more thorough understanding and analysis of energy throughputs in the urban

The NASA Langley Multidisciplinary Uncertainty Quantification Challenge

Science.gov (United States)

Crespo, Luis G.; Kenny, Sean P.; Giesy, Daniel P.

2014-01-01

This paper presents the formulation of an uncertainty quantification challenge problem consisting of five subproblems. These problems focus on key aspects of uncertainty characterization, sensitivity analysis, uncertainty propagation, extreme-case analysis, and robust design.

Computer-assisted imaging algorithms facilitate histomorphometric quantification of kidney damage in rodent renal failure models

Directory of Open Access Journals (Sweden)

Marcin Klapczynski

2012-01-01

Full Text Available Introduction: Surgical 5/6 nephrectomy and adenine-induced kidney failure in rats are frequently used models of progressive renal failure. In both models, rats develop significant morphological changes in the kidneys and quantification of these changes can be used to measure the efficacy of prophylactic or therapeutic approaches. In this study, the Aperio Genie Pattern Recognition technology, along with the Positive Pixel Count, Nuclear and Rare Event algorithms were used to quantify histological changes in both rat renal failure models. Methods: Analysis was performed on digitized slides of whole kidney sagittal sections stained with either hematoxylin and eosin or immunohistochemistry with an anti-nestin antibody to identify glomeruli, regenerating tubular epithelium, and tubulointerstitial myofibroblasts. An anti-polymorphonuclear neutrophil (PMN antibody was also used to investigate neutrophil tissue infiltration. Results: Image analysis allowed for rapid and accurate quantification of relevant histopathologic changes such as increased cellularity and expansion of glomeruli, renal tubular dilatation, and degeneration, tissue inflammation, and mineral aggregation. The algorithms provided reliable and consistent results in both control and experimental groups and presented a quantifiable degree of damage associated with each model. Conclusion: These algorithms represent useful tools for the uniform and reproducible characterization of common histomorphologic features of renal injury in rats.

Quantification of regional cerebral blood flow and volume with dynamic susceptibility contrast-enhanced MR imaging.

Science.gov (United States)

Rempp, K A; Brix, G; Wenz, F; Becker, C R; Gückel, F; Lorenz, W J

1994-12-01

Quantification of regional cerebral blood flow (rCBF) and volume (rCBV) with dynamic magnetic resonance (MR) imaging. After bolus administration of a paramagnetic contrast medium, rapid T2*-weighted gradient-echo images of two sections were acquired for the simultaneous creation of concentration-time curves in the brain-feeding arteries and in brain tissue. Absolute rCBF and rCBV values were determined for gray and white brain matter in 12 subjects with use of principles of the indicator dilution theory. The mean rCBF value in gray matter was 69.7 mL/min +/- 29.7 per 100 g tissue and in white matter, 33.6 mL/min +/- 11.5 per 100 g tissue; the average rCBV was 8.0 mL +/- 3.1 per 100 g tissue and 4.2 mL +/- 1.0 per 100 g tissue, respectively. An age-related decrease in rCBF and rCBV for gray and white matter was observed. Preliminary data demonstrate that the proposed technique allows the quantification of rCBF and rCBV. Although the results are in good agreement with data from positron emission tomography studies, further evaluation is needed to establish the validity of method.

Uncertainty Quantification with Applications to Engineering Problems

DEFF Research Database (Denmark)

Bigoni, Daniele

in measurements, predictions and manufacturing, and we can say that any dynamical system used in engineering is subject to some of these uncertainties. The first part of this work presents an overview of the mathematical framework used in Uncertainty Quantification (UQ) analysis and introduces the spectral tensor...... and thus the UQ analysis of the associated systems will benefit greatly from the application of methods which require few function evaluations. We first consider the propagation of the uncertainty and the sensitivity analysis of the non-linear dynamics of railway vehicles with suspension components whose......-scale problems, where efficient methods are necessary with today’s computational resources. The outcome of this work was also the creation of several freely available Python modules for Uncertainty Quantification, which are listed and described in the appendix....

The Southern H ii Region Discovery Survey (SHRDS): Pilot Survey

Energy Technology Data Exchange (ETDEWEB)

Brown, C.; Dickey, John M. [School of Physical Sciences, Private Bag 37, University of Tasmania, Hobart, TAS, 7001 (Australia); Jordan, C. [International Centre for Radio Astronomy Research, Curtin University, Perth, WA, 6845 (Australia); Anderson, L. D.; Armentrout, W. P. [Department of Physics and Astronomy, West Virginia University, P.O. Box 6315, Morgantown, WV 26506 (United States); Balser, Dana S.; Wenger, Trey V. [National Radio Astronomy Observatory, 520 Edgemont Road, Charlottesville, VA 22904 (United States); Bania, T. M. [Institute for Astrophysical Research, Department of Astronomy, Boston University, 725 Commonwealth Avenue, Boston, MA 02215 (United States); Dawson, J. R. [Department of Physics and Astronomy and MQ Research Centre in Astronomy, Astrophysics and Astrophotonics, Macquarie University, NSW, 2109 (Australia); Mc Clure-Griffiths, N. M. [Research School of Astronomy and Astrophysics, The Australian National University, Canberra ACT 2611 (Australia)

2017-07-01

The Southern H ii Region Discovery Survey is a survey of the third and fourth quadrants of the Galactic plane that will detect radio recombination line (RRL) and continuum emission at cm-wavelengths from several hundred H ii region candidates using the Australia Telescope Compact Array. The targets for this survey come from the WISE Catalog of Galactic H ii Regions and were identified based on mid-infrared and radio continuum emission. In this pilot project, two different configurations of the Compact Array Broad Band receiver and spectrometer system were used for short test observations. The pilot surveys detected RRL emission from 36 of 53 H ii region candidates, as well as seven known H ii regions that were included for calibration. These 36 recombination line detections confirm that the candidates are true H ii regions and allow us to estimate their distances.

The Southern H ii Region Discovery Survey (SHRDS): Pilot Survey

International Nuclear Information System (INIS)

Brown, C.; Dickey, John M.; Jordan, C.; Anderson, L. D.; Armentrout, W. P.; Balser, Dana S.; Wenger, Trey V.; Bania, T. M.; Dawson, J. R.; Mc Clure-Griffiths, N. M.

2017-01-01

The Southern H ii Region Discovery Survey is a survey of the third and fourth quadrants of the Galactic plane that will detect radio recombination line (RRL) and continuum emission at cm-wavelengths from several hundred H ii region candidates using the Australia Telescope Compact Array. The targets for this survey come from the WISE Catalog of Galactic H ii Regions and were identified based on mid-infrared and radio continuum emission. In this pilot project, two different configurations of the Compact Array Broad Band receiver and spectrometer system were used for short test observations. The pilot surveys detected RRL emission from 36 of 53 H ii region candidates, as well as seven known H ii regions that were included for calibration. These 36 recombination line detections confirm that the candidates are true H ii regions and allow us to estimate their distances.

Microplastics in Baltic bottom sediments: Quantification procedures and first results.

Science.gov (United States)

Zobkov, M; Esiukova, E

2017-01-30

Microplastics in the marine environment are known as a global ecological problem but there are still no standardized analysis procedures for their quantification. The first breakthrough in this direction was the NOAA Laboratory Methods for quantifying synthetic particles in water and sediments, but fibers numbers have been found to be underestimated with this approach. We propose modifications for these methods that will allow us to analyze microplastics in bottom sediments, including small fibers. Addition of an internal standard to sediment samples and occasional empty runs are advised for analysis quality control. The microplastics extraction efficiency using the proposed modifications is 92±7%. Distribution of microplastics in bottom sediments of the Russian part of the Baltic Sea is presented. Microplastic particles were found in all of the samples with an average concentration of 34±10 items/kg DW and have the same order of magnitude as neighbor studies reported. Copyright © 2016 Elsevier Ltd. All rights reserved.

Uncertainty quantification in Eulerian-Lagrangian models for particle-laden flows

Science.gov (United States)

Fountoulakis, Vasileios; Jacobs, Gustaaf; Udaykumar, Hs

2017-11-01

A common approach to ameliorate the computational burden in simulations of particle-laden flows is to use a point-particle based Eulerian-Lagrangian model, which traces individual particles in their Lagrangian frame and models particles as mathematical points. The particle motion is determined by Stokes drag law, which is empirically corrected for Reynolds number, Mach number and other parameters. The empirical corrections are subject to uncertainty. Treating them as random variables renders the coupled system of PDEs and ODEs stochastic. An approach to quantify the propagation of this parametric uncertainty to the particle solution variables is proposed. The approach is based on averaging of the governing equations and allows for estimation of the first moments of the quantities of interest. We demonstrate the feasibility of our proposed methodology of uncertainty quantification of particle-laden flows on one-dimensional linear and nonlinear Eulerian-Lagrangian systems. This research is supported by AFOSR under Grant FA9550-16-1-0008.

Gamma camera based Positron Emission Tomography: a study of the viability on quantification

International Nuclear Information System (INIS)

Pozzo, Lorena

2005-01-01

Positron Emission Tomography (PET) is a Nuclear Medicine imaging modality for diagnostic purposes. Pharmaceuticals labeled with positron emitters are used and images which represent the in vivo biochemical process within tissues can be obtained. The positron/electron annihilation photons are detected in coincidence and this information is used for object reconstruction. Presently, there are two types of systems available for this imaging modality: the dedicated systems and those based on gamma camera technology. In this work, we utilized PET/SPECT systems, which also allows for the traditional Nuclear Medicine studies based on single photon emitters. There are inherent difficulties which affect quantification of activity and other indices. They are related to the Poisson nature of radioactivity, to radiation interactions with patient body and detector, noise due to statistical nature of these interactions and to all the detection processes, as well as the patient acquisition protocols. Corrections are described in the literature and not all of them are implemented by the manufacturers: scatter, attenuation, random, decay, dead time, spatial resolution, and others related to the properties of each equipment. The goal of this work was to assess these methods adopted by two manufacturers, as well as the influence of some technical characteristics of PET/SPECT systems on the estimation of SUV. Data from a set of phantoms were collected in 3D mode by one camera and 2D, by the other. We concluded that quantification is viable in PET/SPECT systems, including the estimation of SUVs. This is only possible if, apart from the above mentioned corrections, the camera is well tuned and coefficients for sensitivity normalization and partial volume corrections are applied. We also verified that the shapes of the sources used for obtaining these factors play a role on the final results and should be delt with carefully in clinical quantification. Finally, the choice of the region

Allowable Pressure In Soils and Rocks by Seismic Wave Velocities

International Nuclear Information System (INIS)

Tezcan, S.; Keceli, A.; Oezdemir, Z.

2007-01-01

Firstly, the historical background is presented for the determination of ultimate bearing capacity of shallow foundations. The principles of plastic equilibrium used in the classical formulation of the ultimate bearing capacity are reviewed, followed by a discussion about the sources of approximations inherent in the classical theory. Secondly, based on a variety of case histories of site investigations, including extensive bore hole data, laboratory testing and geophysical prospecting, an empirical formulation is proposed for the determination of allowable bearing capacity of shallow foundations. The proposed expression corroborates consistently with the results of the classical theory and is proven to be reliable and safe, also from the view point of maximum allowable settlements. It consists of only two soil parameters, namely, the Institut measured shear wave velocity, and the unit weight. The unit weight may be also determined with sufficient accuracy, by means of another empirical expression, using the P-wave velocity. It is indicated that once the shear and P-wave velocities are measured Institut by an appropriate geophysical survey, the allowable bearing capacity is determined reliably through a single step operation. Such an approach, is considerably cost and time-saving, in practice

Lung involvement quantification in chest radiographs; Quantificacao de comprometimento pulmonar em radiografias de torax

Energy Technology Data Exchange (ETDEWEB)

Giacomini, Guilherme; Alvarez, Matheus; Oliveira, Marcela de; Miranda, Jose Ricardo A. [Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Botucatu, SP (Brazil). Instituto de Biociencias. Departamento de Fisica e Biofisica; Pina, Diana R.; Pereira, Paulo C.M.; Ribeiro, Sergio M., E-mail: giacomini@ibb.unesp.br [Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Botucatu, SP (Brazil). Faculdade de Medicina. Departamento de Doencas Tropicais e Diagnostico por Imagem

2014-12-15

Tuberculosis (TB) caused by Mycobacterium tuberculosis, is an infectious disease which remains a global health problem. The chest radiography is the commonly method employed to assess the TB's evolution. The methods for quantification of abnormalities of chest are usually performed on CT scans (CT). This quantification is important to assess the TB evolution and treatment and comparing different treatments. However, precise quantification is not feasible for the amount of CT scans required. The purpose of this work is to develop a methodology for quantification of lung damage caused by TB through chest radiographs. It was developed an algorithm for computational processing of exams in Matlab, which creates a lungs' 3D representation, with compromised dilated regions inside. The quantification of lung lesions was also made for the same patients through CT scans. The measurements from the two methods were compared and resulting in strong correlation. Applying statistical Bland and Altman, all samples were within the limits of agreement, with a confidence interval of 95%. The results showed an average variation of around 13% between the two quantification methods. The results suggest the effectiveness and applicability of the method developed, providing better risk-benefit to the patient and cost-benefit ratio for the institution. (author)

Quantification of virus syndrome in chili peppers

African Journals Online (AJOL)

Jane

2011-06-15

Jun 15, 2011 ... alternative for the quantification of the disease' syndromes in regards to this crop. The result of these ..... parison of treatments such as cultivars or control measures and ..... Vascular discoloration and stem necrosis. 2.

New LightCycler PCR for Rapid and Sensitive Quantification of Parvovirus B19 DNA Guides Therapeutic Decision-Making in Relapsing Infections

Science.gov (United States)

Harder, Timm C.; Hufnagel, Markus; Zahn, Katrin; Beutel, Karin; Schmitt, Heinz-Josef; Ullmann, Uwe; Rautenberg, Peter

2001-01-01

Detection of parvovirus B19 DNA offers diagnostic advantages over serology, particularly in persistent infections of immunocompromised patients. A rapid, novel method of B19 DNA detection and quantification is introduced. This method, a quantitative PCR assay, is based on real-time glass capillary thermocycling (LightCycler [LC]) and fluorescence resonance energy transfer (FRET). The PCR assay allowed quantification over a dynamic range of over 7 logs and could quantify as little as 250 B19 genome equivalents (geq) per ml as calculated for plasmid DNA (i.e., theoretically ≥5 geq per assay). Interrater agreement analysis demonstrated equivalence of LC-FRET PCR and conventional nested PCR in the diagnosis of an active B19 infection (kappa coefficient = 0.83). The benefit of the new method was demonstrated in an immunocompromised child with a relapsing infection, who required an attenuation of the immunosuppressive therapy in addition to repeated doses of immunoglobulin to eliminate the virus. PMID:11724854

Lamb Wave Damage Quantification Using GA-Based LS-SVM

Directory of Open Access Journals (Sweden)

Fuqiang Sun

2017-06-01

Full Text Available Lamb waves have been reported to be an efficient tool for non-destructive evaluations (NDE for various application scenarios. However, accurate and reliable damage quantification using the Lamb wave method is still a practical challenge, due to the complex underlying mechanism of Lamb wave propagation and damage detection. This paper presents a Lamb wave damage quantification method using a least square support vector machine (LS-SVM and a genetic algorithm (GA. Three damage sensitive features, namely, normalized amplitude, phase change, and correlation coefficient, were proposed to describe changes of Lamb wave characteristics caused by damage. In view of commonly used data-driven methods, the GA-based LS-SVM model using the proposed three damage sensitive features was implemented to evaluate the crack size. The GA method was adopted to optimize the model parameters. The results of GA-based LS-SVM were validated using coupon test data and lap joint component test data with naturally developed fatigue cracks. Cases of different loading and manufacturer were also included to further verify the robustness of the proposed method for crack quantification.

Lamb Wave Damage Quantification Using GA-Based LS-SVM.

Science.gov (United States)

Sun, Fuqiang; Wang, Ning; He, Jingjing; Guan, Xuefei; Yang, Jinsong

2017-06-12

Lamb waves have been reported to be an efficient tool for non-destructive evaluations (NDE) for various application scenarios. However, accurate and reliable damage quantification using the Lamb wave method is still a practical challenge, due to the complex underlying mechanism of Lamb wave propagation and damage detection. This paper presents a Lamb wave damage quantification method using a least square support vector machine (LS-SVM) and a genetic algorithm (GA). Three damage sensitive features, namely, normalized amplitude, phase change, and correlation coefficient, were proposed to describe changes of Lamb wave characteristics caused by damage. In view of commonly used data-driven methods, the GA-based LS-SVM model using the proposed three damage sensitive features was implemented to evaluate the crack size. The GA method was adopted to optimize the model parameters. The results of GA-based LS-SVM were validated using coupon test data and lap joint component test data with naturally developed fatigue cracks. Cases of different loading and manufacturer were also included to further verify the robustness of the proposed method for crack quantification.

[DNA quantification of blood samples pre-treated with pyramidon].

Science.gov (United States)

Zhu, Chuan-Hong; Zheng, Dao-Li; Ni, Rao-Zhi; Wang, Hai-Sheng; Ning, Ping; Fang, Hui; Liu, Yan

2014-06-01

To study DNA quantification and STR typing of samples pre-treated with pyramidon. The blood samples of ten unrelated individuals were anticoagulated in EDTA. The blood stains were made on the filter paper. The experimental groups were divided into six groups in accordance with the storage time, 30 min, 1 h, 3 h, 6 h, 12 h and 24h after pre-treated with pyramidon. DNA was extracted by three methods: magnetic bead-based extraction, QIAcube DNA purification method and Chelex-100 method. The quantification of DNA was made by fluorescent quantitative PCR. STR typing was detected by PCR-STR fluorescent technology. In the same DNA extraction method, the sample DNA decreased gradually with times after pre-treatment with pyramidon. In the same storage time, the DNA quantification in different extraction methods had significant differences. Sixteen loci DNA typing were detected in 90.56% of samples. Pyramidon pre-treatment could cause DNA degradation, but effective STR typing can be achieved within 24 h. The magnetic bead-based extraction is the best method for STR profiling and DNA extraction.

Real-Time PCR Quantification of Chloroplast DNA Supports DNA Barcoding of Plant Species.

Science.gov (United States)

Kikkawa, Hitomi S; Tsuge, Kouichiro; Sugita, Ritsuko

2016-03-01

Species identification from extracted DNA is sometimes needed for botanical samples. DNA quantification is required for an accurate and effective examination. If a quantitative assay provides unreliable estimates, a higher quantity of DNA than the estimated amount may be used in additional analyses to avoid failure to analyze samples from which extracting DNA is difficult. Compared with conventional methods, real-time quantitative PCR (qPCR) requires a low amount of DNA and enables quantification of dilute DNA solutions accurately. The aim of this study was to develop a qPCR assay for quantification of chloroplast DNA from taxonomically diverse plant species. An absolute quantification method was developed using primers targeting the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene using SYBR Green I-based qPCR. The calibration curve was generated using the PCR amplicon as the template. DNA extracts from representatives of 13 plant families common in Japan. This demonstrates that qPCR analysis is an effective method for quantification of DNA from plant samples. The results of qPCR assist in the decision-making will determine the success or failure of DNA analysis, indicating the possibility of optimization of the procedure for downstream reactions.

Stereo-particle image velocimetry uncertainty quantification

International Nuclear Information System (INIS)

Bhattacharya, Sayantan; Vlachos, Pavlos P; Charonko, John J

2017-01-01

Particle image velocimetry (PIV) measurements are subject to multiple elemental error sources and thus estimating overall measurement uncertainty is challenging. Recent advances have led to a posteriori uncertainty estimation methods for planar two-component PIV. However, no complete methodology exists for uncertainty quantification in stereo PIV. In the current work, a comprehensive framework is presented to quantify the uncertainty stemming from stereo registration error and combine it with the underlying planar velocity uncertainties. The disparity in particle locations of the dewarped images is used to estimate the positional uncertainty of the world coordinate system, which is then propagated to the uncertainty in the calibration mapping function coefficients. Next, the calibration uncertainty is combined with the planar uncertainty fields of the individual cameras through an uncertainty propagation equation and uncertainty estimates are obtained for all three velocity components. The methodology was tested with synthetic stereo PIV data for different light sheet thicknesses, with and without registration error, and also validated with an experimental vortex ring case from 2014 PIV challenge. Thorough sensitivity analysis was performed to assess the relative impact of the various parameters to the overall uncertainty. The results suggest that in absence of any disparity, the stereo PIV uncertainty prediction method is more sensitive to the planar uncertainty estimates than to the angle uncertainty, although the latter is not negligible for non-zero disparity. Overall the presented uncertainty quantification framework showed excellent agreement between the error and uncertainty RMS values for both the synthetic and the experimental data and demonstrated reliable uncertainty prediction coverage. This stereo PIV uncertainty quantification framework provides the first comprehensive treatment on the subject and potentially lays foundations applicable to volumetric

Activity quantification of phantom using dual-head SPECT with two-view planar image

International Nuclear Information System (INIS)

Guo Leiming; Chen Tao; Sun Xiaoguang; Huang Gang

2005-01-01

The absorbed radiation dose from internally deposited radionuclide is a major factor in assessing risk and therapeutic utility in nuclear medicine diagnosis or treatment. The quantification of absolute activity in vivo is necessary procedure of estimating the absorbed dose of organ or tissue. To understand accuracy in the determination of organ activity, the experiments on 99 Tc m activity quantification were made for a body phantom using dual-heat SPECT with the two-view counting technique. Accuracy in the activity quantification is credible and is not affected by depth of source organ in vivo. When diameter of the radiation source is ≤2 cm, the most accurate activity quantification result can be obtained on the basis of establishing the system calibration factor and transmission factor. The use of Buijs's method is preferable, especially at very low source-to-background activity concentration rations. (authors)

A new clinical tool for the quantification of myocardial CT perfusion imaging in patients with suspected Ischemic Heart Disease

Energy Technology Data Exchange (ETDEWEB)

Ruiz Muñoz, A.; Dux-Santoy Hurtado, L.; Rodriguez Palomares, J.L.; Piella Fenoy, G.

2016-07-01

In the clinical practice, the evaluation of myocardial perfusion by using Computed Tomography (CT) Imaging is usually performed visually or semi-quantitatively. The scarcity of quantitative perfusion data not always allows a proper diagnose of patients which are suspected of suffering from some diseases, such as Ischemic Heart Disease (IHD). In this work, a clinical tool for the automatic quantification of myocardial perfusion in patients with suspected IHD is proposed. Myocardial perfusion is assessed based on a combined diagnosis protocol (CT/CTP protocol) which involves the acquisition of two contrastenhanced CT images, one obtained at rest and another acquired under pharmacological stress. The clinical tool allows the automatic quantification of perfusion in different myocardial segments defined according to the 16-AHA-segmentation model of the left ventricle, by providing the mean of Hounsfield Units in those regions. Based on this analysis, the clinicians can compare the values at baseline and at hyperemia, and they can better determine hypoperfusion defects in patients with IHD. The validation of the clinical tool was performed by comparing automatic and manual perfusion measurements of 10 patients with suspected IHD who were previously assessed with Single Photon Emission Computed Tomography (SPECT) for perfusion analysis. A strong linear correlation was found between the automatic and manual results. Afterwards, perfusion defects obtained from CT/CTP protocol were compared to perfusion defects from SPECT, to assess the applicability of this clinical tool for the diagnosis of IHD. (Author)

Improved Strategies and Optimization of Calibration Models for Real-time PCR Absolute Quantification

Science.gov (United States)

Real-time PCR absolute quantification applications rely on the use of standard curves to make estimates of DNA target concentrations in unknown samples. Traditional absolute quantification approaches dictate that a standard curve must accompany each experimental run. However, t...

Quantification of uranyl in presence of citric acid

International Nuclear Information System (INIS)

Garcia G, N.; Barrera D, C.E.; Ordonez R, E.

2007-01-01

To determine the influence that has the organic matter of the soil on the uranyl sorption on some solids is necessary to have a detection technique and quantification of uranyl that it is reliable and sufficiently quick in the obtaining of results. For that in this work, it intends to carry out the uranyl quantification in presence of citric acid modifying the Fluorescence induced by UV-Vis radiation technique. Since the uranyl ion is very sensitive to the medium that contains it, (speciation, pH, ionic forces, etc.) it was necessary to develop an analysis technique that stands out the fluorescence of uranyl ion avoiding the out one that produce the organic acids. (Author)

Automated quantification of renal interstitial fibrosis for computer-aided diagnosis: A comprehensive tissue structure segmentation method.

Science.gov (United States)

Tey, Wei Keat; Kuang, Ye Chow; Ooi, Melanie Po-Leen; Khoo, Joon Joon

2018-03-01

Interstitial fibrosis in renal biopsy samples is a scarring tissue structure that may be visually quantified by pathologists as an indicator to the presence and extent of chronic kidney disease. The standard method of quantification by visual evaluation presents reproducibility issues in the diagnoses. This study proposes an automated quantification system for measuring the amount of interstitial fibrosis in renal biopsy images as a consistent basis of comparison among pathologists. The system extracts and segments the renal tissue structures based on colour information and structural assumptions of the tissue structures. The regions in the biopsy representing the interstitial fibrosis are deduced through the elimination of non-interstitial fibrosis structures from the biopsy area and quantified as a percentage of the total area of the biopsy sample. A ground truth image dataset has been manually prepared by consulting an experienced pathologist for the validation of the segmentation algorithms. The results from experiments involving experienced pathologists have demonstrated a good correlation in quantification result between the automated system and the pathologists' visual evaluation. Experiments investigating the variability in pathologists also proved the automated quantification error rate to be on par with the average intra-observer variability in pathologists' quantification. Interstitial fibrosis in renal biopsy samples is a scarring tissue structure that may be visually quantified by pathologists as an indicator to the presence and extent of chronic kidney disease. The standard method of quantification by visual evaluation presents reproducibility issues in the diagnoses due to the uncertainties in human judgement. An automated quantification system for accurately measuring the amount of interstitial fibrosis in renal biopsy images is presented as a consistent basis of comparison among pathologists. The system identifies the renal tissue structures

On the Confounding Effect of Temperature on Chemical Shift-Encoded Fat Quantification

Science.gov (United States)

Hernando, Diego; Sharma, Samir D.; Kramer, Harald; Reeder, Scott B.

2014-01-01

Purpose To characterize the confounding effect of temperature on chemical shift-encoded (CSE) fat quantification. Methods The proton resonance frequency of water, unlike triglycerides, depends on temperature. This leads to a temperature dependence of the spectral models of fat (relative to water) that are commonly used by CSE-MRI methods. Simulation analysis was performed for 1.5 Tesla CSE fat–water signals at various temperatures and echo time combinations. Oil–water phantoms were constructed and scanned at temperatures between 0 and 40°C using spectroscopy and CSE imaging at three echo time combinations. An explanted human liver, rejected for transplantation due to steatosis, was scanned using spectroscopy and CSE imaging. Fat–water reconstructions were performed using four different techniques: magnitude and complex fitting, with standard or temperature-corrected signal modeling. Results In all experiments, magnitude fitting with standard signal modeling resulted in large fat quantification errors. Errors were largest for echo time combinations near TEinit ≈ 1.3 ms, ΔTE ≈ 2.2 ms. Errors in fat quantification caused by temperature-related frequency shifts were smaller with complex fitting, and were avoided using a temperature-corrected signal model. Conclusion Temperature is a confounding factor for fat quantification. If not accounted for, it can result in large errors in fat quantifications in phantom and ex vivo acquisitions. PMID:24123362

Re-evaluation of thin layer chromatography as an alternative method for the quantification of prostaglandins from rat Kupffer cells.

Science.gov (United States)

Pestel, Sabine; Jungermann, Kurt; Schieferdecker, Henrike L

2005-01-01

In contrast to conventionally used immunoassays, thin layer chromatography (TLC)--by prelabeling of cells with radioactive arachidonic acid (AA)--allows to differentiate between cellularly built and added prostanoids and thus to investigate feedback effects of prostanoids on their own release. PGD2, TXB2 and PGE2 released from zymosan-stimulated Kupffer cells were separated with distinct RF-values, corresponding to those of the pure substances. Quantification of PGD2 and PGE2 gave comparable results with TLC and immunoassays, but measurement in the presence of added prostanoids was only possible with TLC. Moreover TLC was superior to immunoassays in having a longer linear range while being comparably sensitive. Cellularly built TXB2 in its radioactively labeled form was not detectable by TLC. Inhibition of TXB2 release by externally added AA or technical artifacts were excluded, suggesting that the cellular AA-pools used for prostaglandin and thromboxane synthesis differ in their accessibility for added AA. Thus, TLC is a simple, sensitive and precise method for the quantification of cellularly built prostaglandins but not of thromboxane even in the presence of added prostanoids.

Quantification of taurine in energy drinks using ¹H NMR.

Science.gov (United States)

Hohmann, Monika; Felbinger, Christine; Christoph, Norbert; Wachter, Helmut; Wiest, Johannes; Holzgrabe, Ulrike

2014-05-01

The consumption of so called energy drinks is increasing, especially among adolescents. These beverages commonly contain considerable amounts of the amino sulfonic acid taurine, which is related to a magnitude of various physiological effects. The customary method to control the legal limit of taurine in energy drinks is LC-UV/vis with postcolumn derivatization using ninhydrin. In this paper we describe the quantification of taurine in energy drinks by (1)H NMR as an alternative to existing methods of quantification. Variation of pH values revealed the separation of a distinct taurine signal in (1)H NMR spectra, which was applied for integration and quantification. Quantification was performed using external calibration (R(2)>0.9999; linearity verified by Mandel's fitting test with a 95% confidence level) and PULCON. Taurine concentrations in 20 different energy drinks were analyzed by both using (1)H NMR and LC-UV/vis. The deviation between (1)H NMR and LC-UV/vis results was always below the expanded measurement uncertainty of 12.2% for the LC-UV/vis method (95% confidence level) and at worst 10.4%. Due to the high accordance to LC-UV/vis data and adequate recovery rates (ranging between 97.1% and 108.2%), (1)H NMR measurement presents a suitable method to quantify taurine in energy drinks. Copyright © 2013 Elsevier B.V. All rights reserved.

Initial water quantification results using neutron computed tomography

Energy Technology Data Exchange (ETDEWEB)

Heller, A.K. [Department of Mechanical and Nuclear Engineering, Pennsylvania State University (United States)], E-mail: axh174@psu.edu; Shi, L.; Brenizer, J.S.; Mench, M.M. [Department of Mechanical and Nuclear Engineering, Pennsylvania State University (United States)

2009-06-21

Neutron computed tomography is an important imaging tool in the field of non-destructive testing and in fundamental research for many engineering applications. Contrary to X-rays, neutrons can be attenuated by some light materials, such as hydrogen, but can penetrate many heavy materials. Thus, neutron computed tomography is useful in obtaining important three-dimensional information about a sample's interior structure and material properties that other traditional methods cannot provide. The neutron computed tomography system at Pennsylvania State University's Radiation Science and Engineering Center is being utilized to develop a water quantification technique for investigation of water distribution in fuel cells under normal conditions. A hollow aluminum cylinder test sample filled with a known volume of water was constructed for purposes of testing the quantification technique. Transmission images of the test sample at different angles were easily acquired through the synthesis of a dedicated image acquisition computer driving a rotary table controller and an in-house developed synchronization software package. After data acquisition, Octopus (version 8.2) and VGStudio Max (version 1.2) were used to perform cross-sectional and three-dimensional reconstructions of the sample, respectively. The initial reconstructions and water quantification results are presented.

Follow-up skeletal surveys for nonaccidental trauma: can a more limited survey be performed?

Energy Technology Data Exchange (ETDEWEB)

Harlan, Susan R. [University of Utah School of Medicine, Department of Radiology, Salt Lake City, UT (United States); Nixon, G.W.; Prince, Jeffrey S. [Primary Children' s Medical Center, Department of Medical Imaging, Salt Lake City, UT (United States); Campbell, Kristine A.; Hansen, Karen [University of Utah School of Medicine, Department of Pediatrics, Salt Lake City, UT (United States)

2009-09-15

Studies have demonstrated the value of the follow-up skeletal survey in identifying additional fractures, clarifying indeterminate findings, and improving dating of skeletal injuries in victims of physical abuse. To determine whether a more limited follow-up survey could yield the same radiologic data as a full follow-up survey. The study cohort comprised 101 children who had follow-up surveys that met our inclusion criteria. Consensus readings of both original and follow-up surveys were performed by two pediatric radiologists. These results were compared to determine additional findings from the follow-up surveys. Limited skeletal survey protocols were evaluated to determine whether they would detect the same fractures seen with a complete osseous survey. In the 101 children 244 fractures were identified on the initial osseous survey. Follow-up surveys demonstrated new information in 38 children (37.6%). A 15-view limited follow-up survey identified all additional information seen on the complete follow-up survey. Our data demonstrate that a 15-view limited follow-up skeletal survey could be performed without missing clinically significant new fractures and still allow proper identification of confirmed fractures or normal findings. A limited survey would decrease radiation dose in children. (orig.)

Follow-up skeletal surveys for nonaccidental trauma: can a more limited survey be performed?

International Nuclear Information System (INIS)

Harlan, Susan R.; Nixon, G.W.; Prince, Jeffrey S.; Campbell, Kristine A.; Hansen, Karen

2009-01-01

Studies have demonstrated the value of the follow-up skeletal survey in identifying additional fractures, clarifying indeterminate findings, and improving dating of skeletal injuries in victims of physical abuse. To determine whether a more limited follow-up survey could yield the same radiologic data as a full follow-up survey. The study cohort comprised 101 children who had follow-up surveys that met our inclusion criteria. Consensus readings of both original and follow-up surveys were performed by two pediatric radiologists. These results were compared to determine additional findings from the follow-up surveys. Limited skeletal survey protocols were evaluated to determine whether they would detect the same fractures seen with a complete osseous survey. In the 101 children 244 fractures were identified on the initial osseous survey. Follow-up surveys demonstrated new information in 38 children (37.6%). A 15-view limited follow-up survey identified all additional information seen on the complete follow-up survey. Our data demonstrate that a 15-view limited follow-up skeletal survey could be performed without missing clinically significant new fractures and still allow proper identification of confirmed fractures or normal findings. A limited survey would decrease radiation dose in children. (orig.)

Optimizing total reflection X-ray fluorescence for direct trace element quantification in proteins I: Influence of sample homogeneity and reflector type

Science.gov (United States)

Wellenreuther, G.; Fittschen, U. E. A.; Achard, M. E. S.; Faust, A.; Kreplin, X.; Meyer-Klaucke, W.

2008-12-01

Total reflection X-ray fluorescence (TXRF) is a very promising method for the direct, quick and reliable multi-elemental quantification of trace elements in protein samples. With the introduction of an internal standard consisting of two reference elements, scandium and gallium, a wide range of proteins can be analyzed, regardless of their salt content, buffer composition, additives and amino acid composition. This strategy also enables quantification of matrix effects. Two potential issues associated with drying have been considered in this study: (1) Formation of heterogeneous residues of varying thickness and/or density; and (2) separation of the internal standard and protein during drying (which has to be prevented to allow accurate quantification). These issues were investigated by microbeam X-ray fluorescence (μXRF) with special emphasis on (I) the influence of sample support and (II) the protein / buffer system used. In the first part, a model protein was studied on well established sample supports used in TXRF, PIXE and XRF (Mylar, siliconized quartz, Plexiglas and silicon). In the second part we imaged proteins of different molecular weight, oligomerization state, bound metals and solubility. A partial separation of protein and internal standard was only observed with untreated silicon, suggesting it may not be an adequate support material. Siliconized quartz proved to be the least prone to heterogeneous drying of the sample and yielded the most reliable results.

Overall Key Performance Indicator to Optimizing Operation of High-Pressure Homogenizers for a Reliable Quantification of Intracellular Components in Pichia pastoris.

Science.gov (United States)

Garcia-Ortega, Xavier; Reyes, Cecilia; Montesinos, José Luis; Valero, Francisco

2015-01-01

The most commonly used cell disruption procedures may present lack of reproducibility, which introduces significant errors in the quantification of intracellular components. In this work, an approach consisting in the definition of an overall key performance indicator (KPI) was implemented for a lab scale high-pressure homogenizer (HPH) in order to determine the disruption settings that allow the reliable quantification of a wide sort of intracellular components. This innovative KPI was based on the combination of three independent reporting indicators: decrease of absorbance, release of total protein, and release of alkaline phosphatase activity. The yeast Pichia pastoris growing on methanol was selected as model microorganism due to it presents an important widening of the cell wall needing more severe methods and operating conditions than Escherichia coli and Saccharomyces cerevisiae. From the outcome of the reporting indicators, the cell disruption efficiency achieved using HPH was about fourfold higher than other lab standard cell disruption methodologies, such bead milling cell permeabilization. This approach was also applied to a pilot plant scale HPH validating the methodology in a scale-up of the disruption process. This innovative non-complex approach developed to evaluate the efficacy of a disruption procedure or equipment can be easily applied to optimize the most common disruption processes, in order to reach not only reliable quantification but also recovery of intracellular components from cell factories of interest.

Optimizing total reflection X-ray fluorescence for direct trace element quantification in proteins I: Influence of sample homogeneity and reflector type

Energy Technology Data Exchange (ETDEWEB)

Wellenreuther, G. [European Molecular Biology Laboratory, Notkestr. 85, 22603 Hamburg (Germany); Fittschen, U.E.A. [Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg (Germany); Achard, M.E.S.; Faust, A.; Kreplin, X. [European Molecular Biology Laboratory, Notkestr. 85, 22603 Hamburg (Germany); Meyer-Klaucke, W. [European Molecular Biology Laboratory, Notkestr. 85, 22603 Hamburg (Germany)], E-mail: Wolfram@embl-hamburg.de

2008-12-15

Total reflection X-ray fluorescence (TXRF) is a very promising method for the direct, quick and reliable multi-elemental quantification of trace elements in protein samples. With the introduction of an internal standard consisting of two reference elements, scandium and gallium, a wide range of proteins can be analyzed, regardless of their salt content, buffer composition, additives and amino acid composition. This strategy also enables quantification of matrix effects. Two potential issues associated with drying have been considered in this study: (1) Formation of heterogeneous residues of varying thickness and/or density; and (2) separation of the internal standard and protein during drying (which has to be prevented to allow accurate quantification). These issues were investigated by microbeam X-ray fluorescence ({mu}XRF) with special emphasis on (I) the influence of sample support and (II) the protein / buffer system used. In the first part, a model protein was studied on well established sample supports used in TXRF, PIXE and XRF (Mylar, siliconized quartz, Plexiglas and silicon). In the second part we imaged proteins of different molecular weight, oligomerization state, bound metals and solubility. A partial separation of protein and internal standard was only observed with untreated silicon, suggesting it may not be an adequate support material. Siliconized quartz proved to be the least prone to heterogeneous drying of the sample and yielded the most reliable results.

Techniques for quantification of liver fat in risk stratification of diabetics

International Nuclear Information System (INIS)

Kuehn, J.P.; Spoerl, M.C.; Mahlke, C.; Hegenscheid, K.

2015-01-01

Fatty liver disease plays an important role in the development of type 2 diabetes. Accurate techniques for detection and quantification of liver fat are essential for clinical diagnostics. Chemical shift-encoded magnetic resonance imaging (MRI) is a simple approach to quantify liver fat content. Liver fat quantification using chemical shift-encoded MRI is influenced by several bias factors, such as T2* decay, T1 recovery and the multispectral complexity of fat. The confounder corrected proton density fat fraction is a simple approach to quantify liver fat with comparable results independent of the software and hardware used. The proton density fat fraction is an accurate biomarker for assessment of liver fat. An accurate and reproducible quantification of liver fat using chemical shift-encoded MRI requires a calculation of the proton density fat fraction. (orig.) [de

An external standard method for quantification of human cytomegalovirus by PCR

International Nuclear Information System (INIS)

Rongsen, Shen; Liren, Ma; Fengqi, Zhou; Qingliang, Luo

1997-01-01

An external standard method for PCR quantification of HCMV was reported. [α- 32 P]dATP was used as a tracer. 32 P-labelled specific amplification product was separated by agarose gel electrophoresis. A gel piece containing the specific product band was excised and counted in a plastic scintillation counter. Distribution of [α- 32 P]dATP in the electrophoretic gel plate and effect of separation between the 32 P-labelled specific product and free [α- 32 P]dATP were observed. A standard curve for quantification of HCMV by PCR was established and detective results of quality control templets were presented. The external standard method and the electrophoresis separation effect were appraised. The results showed that the method could be used for relative quantification of HCMV. (author)

High temperature liquid chromatography hyphenated with ESI-MS and ICP-MS detection for the structural characterization and quantification of halogen containing drug metabolites

International Nuclear Information System (INIS)

Vlieger, Jon S.B. de; Giezen, Mark J.N.; Falck, David; Tump, Cornelis; Heuveln, Fred van; Giera, Martin; Kool, Jeroen; Lingeman, Henk; Wieling, Jaap; Honing, Maarten; Irth, Hubertus; Niessen, Wilfried M.A.

2011-01-01

Highlights: → Hyphenation of high temperature liquid chromatography to ICP-MS and ESI-MS. → Structural characterization of kinase inhibitor metabolites with high resolution MS n experiments. → Quantification of drug metabolites with ICP-MS based on Iodine detection. → Significant changes in ESI-MS response after small structural changes. - Abstract: In this paper we describe the hyphenation of high temperature liquid chromatography with ICP-MS and ESI-MS for the characterization of halogen containing drug metabolites. The use of temperature gradients up to 200 deg. C enabled the separation of metabolites with low organic modifier content. This specific property allowed the use of detection methods that suffer from (significant) changes in analyte response factors as a function of the organic modifier content such as ICP-MS. Metabolites of two kinase inhibitors (SB-203580-Iodo and MAPK inhibitor VIII) produced by bacterial cytochrome P450 BM3 mutants and human liver microsomes were identified based on high resolution MS n data. Quantification was done using their normalized and elemental specific response in the ICP-MS. The importance of these kinds of quantification strategies is stressed by the observation that the difference of the position of one oxygen atom in a structure can greatly affect its response in ESI-MS and UV detection.

Generation of structural MR images from amyloid PET: Application to MR-less quantification.

Science.gov (United States)

Choi, Hongyoon; Lee, Dong Soo

2017-12-07

Structural magnetic resonance (MR) images concomitantly acquired with PET images can provide crucial anatomical information for precise quantitative analysis. However, in the clinical setting, not all the subjects have corresponding MR. Here, we developed a model to generate structural MR images from amyloid PET using deep generative networks. We applied our model to quantification of cortical amyloid load without structural MR. Methods: We used florbetapir PET and structural MR data of Alzheimer's Disease Neuroimaging Initiative database. The generative network was trained to generate realistic structural MR images from florbetapir PET images. After the training, the model was applied to the quantification of cortical amyloid load. PET images were spatially normalized to the template space using the generated MR and then standardized uptake value ratio (SUVR) of the target regions was measured by predefined regions-of-interests. A real MR-based quantification was used as the gold standard to measure the accuracy of our approach. Other MR-less methods, a normal PET template-based, multi-atlas PET template-based and PET segmentation-based normalization/quantification methods, were also tested. We compared performance of quantification methods using generated MR with that of MR-based and MR-less quantification methods. Results: Generated MR images from florbetapir PET showed visually similar signal patterns to the real MR. The structural similarity index between real and generated MR was 0.91 ± 0.04. Mean absolute error of SUVR of cortical composite regions estimated by the generated MR-based method was 0.04±0.03, which was significantly smaller than other MR-less methods (0.29±0.12 for the normal PET-template, 0.12±0.07 for multiatlas PET-template and 0.08±0.06 for PET segmentation-based methods). Bland-Altman plots revealed that the generated MR-based SUVR quantification was the closest to the SUVR values estimated by the real MR-based method. Conclusion

Authentication of Piper betle L. folium and quantification of their antifungal-activity

Directory of Open Access Journals (Sweden)

I Made Agus Gelgel Wirasuta

2017-07-01

The NCPs profiles of intra- and inter-day precision results offered multi-dimensional chromatogram fingerprints for better marker peak pattern recognition and identification. Using the r-value fingerprints data series generated with this method allowed more precise discrimination the PBL. from other Piper species compared to the marker peak area fingerprint method. The cosine pair comparison was a simple method for authentication of two different fingerprints. The ward linkage clustering and the pair cross-correlation comparison were better chemometric methods to determine the consistency peak area ratio between fingerprints. The first component PCA-loading values of peak marker area fingerprints were correlated linearly to both the bio-marker concentration as well as the antifungal activity. This relationship could be used to control the quality and pharmacological potency. This simple method was developed for the authentication and quantification of herbal medicine.

Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN.

Science.gov (United States)

Hao, Jie; Liebeke, Manuel; Astle, William; De Iorio, Maria; Bundy, Jacob G; Ebbels, Timothy M D

2014-01-01

Data processing for 1D NMR spectra is a key bottleneck for metabolomic and other complex-mixture studies, particularly where quantitative data on individual metabolites are required. We present a protocol for automated metabolite deconvolution and quantification from complex NMR spectra by using the Bayesian automated metabolite analyzer for NMR (BATMAN) R package. BATMAN models resonances on the basis of a user-controllable set of templates, each of which specifies the chemical shifts, J-couplings and relative peak intensities for a single metabolite. Peaks are allowed to shift position slightly between spectra, and peak widths are allowed to vary by user-specified amounts. NMR signals not captured by the templates are modeled non-parametrically by using wavelets. The protocol covers setting up user template libraries, optimizing algorithmic input parameters, improving prior information on peak positions, quality control and evaluation of outputs. The outputs include relative concentration estimates for named metabolites together with associated Bayesian uncertainty estimates, as well as the fit of the remainder of the spectrum using wavelets. Graphical diagnostics allow the user to examine the quality of the fit for multiple spectra simultaneously. This approach offers a workflow to analyze large numbers of spectra and is expected to be useful in a wide range of metabolomics studies.

The Parallel C++ Statistical Library ‘QUESO’: Quantification of Uncertainty for Estimation, Simulation and Optimization

KAUST Repository

Prudencio, Ernesto E.

2012-01-01

QUESO is a collection of statistical algorithms and programming constructs supporting research into the uncertainty quantification (UQ) of models and their predictions. It has been designed with three objectives: it should (a) be sufficiently abstract in order to handle a large spectrum of models, (b) be algorithmically extensible, allowing an easy insertion of new and improved algorithms, and (c) take advantage of parallel computing, in order to handle realistic models. Such objectives demand a combination of an object-oriented design with robust software engineering practices. QUESO is written in C++, uses MPI, and leverages libraries already available to the scientific community. We describe some UQ concepts, present QUESO, and list planned enhancements.

Characterising non-linear dynamics in nocturnal breathing patterns of healthy infants using recurrence quantification analysis.

Science.gov (United States)

Terrill, Philip I; Wilson, Stephen J; Suresh, Sadasivam; Cooper, David M; Dakin, Carolyn

2013-05-01

Breathing dynamics vary between infant sleep states, and are likely to exhibit non-linear behaviour. This study applied the non-linear analytical tool recurrence quantification analysis (RQA) to 400 breath interval periods of REM and N-REM sleep, and then using an overlapping moving window. The RQA variables were different between sleep states, with REM radius 150% greater than N-REM radius, and REM laminarity 79% greater than N-REM laminarity. RQA allowed the observation of temporal variations in non-linear breathing dynamics across a night's sleep at 30s resolution, and provides a basis for quantifying changes in complex breathing dynamics with physiology and pathology. Copyright © 2013 Elsevier Ltd. All rights reserved.

A real-time reverse transcriptase polymerase chain reaction for detection and quantification of Vesiculovirus

Directory of Open Access Journals (Sweden)

Aline Lavado Tolardo

2016-06-01

Full Text Available Vesiculoviruses (VSV are zoonotic viruses that cause vesicular stomatitis disease in cattle, horses and pigs, as well as sporadic human cases of acute febrile illness. Therefore, diagnosis of VSV infections by reliable laboratory techniques is important to allow a proper case management and implementation of strategies for the containment of virus spread. We show here a sensitive and reproducible real-time reverse transcriptase polymerase chain reaction (RT-PCR for detection and quantification of VSV. The assay was evaluated with arthropods and serum samples obtained from horses, cattle and patients with acute febrile disease. The real-time RT-PCR amplified the Piry, Carajas, Alagoas and Indiana Vesiculovirus at a melting temperature 81.02 ± 0.8ºC, and the sensitivity of assay was estimated in 10 RNA copies/mL to the Piry Vesiculovirus. The viral genome has been detected in samples of horses and cattle, but not detected in human sera or arthropods. Thus, this assay allows a preliminary differential diagnosis of VSV infections.

CHILD ALLOWANCE

CERN Multimedia

Human Resources Division

2001-01-01

HR Division wishes to clarify to members of the personnel that the allowance for a dependent child continues to be paid during all training courses ('stages'), apprenticeships, 'contrats de qualification', sandwich courses or other courses of similar nature. Any payment received for these training courses, including apprenticeships, is however deducted from the amount reimbursable as school fees. HR Division would also like to draw the attention of members of the personnel to the fact that any contract of employment will lead to the suppression of the child allowance and of the right to reimbursement of school fees.

Comparative quantification of alcohol exposure as risk factor for global burden of disease.

Science.gov (United States)

Rehm, Jürgen; Klotsche, Jens; Patra, Jayadeep

2007-01-01

Alcohol has been identified as one of the most important risk factors in the burden experienced as a result of disease. The objective of the present contribution is to establish a framework to comparatively quantify alcohol exposure as it is relevant for burden of disease. Different key indicators are combined to derive this quantification. First, adult per capita consumption, composed of recorded and unrecorded consumption, yields the best overall estimate of alcohol exposure for a country or region. Second, survey information is used to allocate the per capita consumption into sex and age groups. Third, an index for detrimental patterns of drinking is used to determine the additional impact on injury and cardiovascular burden. The methodology is applied to estimate global alcohol exposure for the year 2002. Finally, assumptions and potential problems of the approach are discussed. Copyright (c) 2007 John Wiley & Sons, Ltd.

MR Spectroscopy: Real-Time Quantification of in-vivo MR Spectroscopic data

OpenAIRE

Massé, Kunal

2009-01-01

In the last two decades, magnetic resonance spectroscopy (MRS) has had an increasing success in biomedical research. This technique has the faculty of discerning several metabolites in human tissue non-invasively and thus offers a multitude of medical applications. In clinical routine, quantification plays a key role in the evaluation of the different chemical elements. The quantification of metabolites characterizing specific pathologies helps physicians establish the patient's diagnosis. E...

Improving allowed outage time and surveillance test interval requirements: a study of their interactions using probabilistic methods

International Nuclear Information System (INIS)

Martorell, S.A.; Serradell, V.G.; Samanta, P.K.

1995-01-01

Technical Specifications (TS) define the limits and conditions for operating nuclear plants safely. We selected the Limiting Conditions for Operations (LCO) and Surveillance Requirements (SR), both within TS, as the main items to be evaluated using probabilistic methods. In particular, we focused on the Allowed Outage Time (AOT) and Surveillance Test Interval (STI) requirements in LCO and SR, respectively. Already, significant operating and design experience has accumulated revealing several problems which require modifications in some TS rules. Developments in Probabilistic Safety Assessment (PSA) allow the evaluation of effects due to such modifications in AOT and STI from a risk point of view. Thus, some changes have already been adopted in some plants. However, the combined effect of several changes in AOT and STI, i.e. through their interactions, is not addressed. This paper presents a methodology which encompasses, along with the definition of AOT and STI interactions, the quantification of interactions in terms of risk using PSA methods, an approach for evaluating simultaneous AOT and STI modifications, and an assessment of strategies for giving flexibility to plant operation through simultaneous changes on AOT and STI using trade-off-based risk criteria

cGAMP Quantification in Virus-Infected Human Monocyte-Derived Cells by HPLC-Coupled Tandem Mass Spectrometry.

Science.gov (United States)

Paijo, Jennifer; Kaever, Volkhard; Kalinke, Ulrich

2017-01-01

Upon virus infection, cells of the innate immune system such as dendritic cells and macrophages can mount type I interferon (IFN-I) responses that restrict viral dissemination. To inform host cells of virus infection, detection of cytosolic DNA is one important mechanism. Inappropriate sensing of endogenous DNA and subsequent induction of IFN-I responses can also cause autoimmunity, highlighting the need to tightly regulate DNA sensing. The cyclic GMP-AMP synthase (cGAS) was recently identified to be the major sensor of cytosolic DNA that triggers IFN-I expression. Upon DNA binding, cGAS synthesizes the second messenger cyclic guanosine-adenosine monophosphate (cGAMP) that induces IFN-I expression by the activation of the stimulator of interferon genes (STING). Notably, cGAMP does not only act in infected cells, but can also be relocated to noninfected bystander cells to there trigger IFN-I expression. Thus, direct quantification of cGAMP in cells of the innate immune system is an important approach to study where, when, and how DNA is sensed and IFN-I responses are induced. Here, we describe a method that allows specific quantification of cGAMP from extracts of virus-infected human myeloid cells by HPLC-coupled tandem mass spectrometry.

Rapid and sensitive Nitrosomonas europaea biosensor assay for quantification of bioavailable ammonium sensu strictu in soil.

Science.gov (United States)

Nguyen, Minh Dong; Risgaard-Petersen, Nils; Sørensen, Jan; Brandt, Kristian K

2011-02-01

Knowledge on bioavailable ammonium sensu strictu (i.e., immediately available for cellular uptake) in soil is required to understand nutrient uptake processes in microorganisms and thus of vital importance for plant production. We here present a novel ammonium biosensor approach based on the lithoautotrophic ammonia-oxidizing bacterium Nitrosomonas europaea transformed with a luxAB sensor plasmid. Bioluminescence-based ammonium detection was achieved within 10 min with a quantification limit in liquid samples of ∼20 μM and a linear response range up to 400 μM. Biosensor and conventional chemical quantification of ammonium in soil solutions agreed well across a range of sample and assay conditions. The biosensor was subsequently applied for a solid phase-contact assay allowing for direct interaction of biosensor cells with soil particle-associated (i.e., exchangeable plus fixed) ammonium. The assay successfully quantified bioavailable ammonium even in unfertilized soil and demonstrated markedly higher ratios of bioavailable ammonium to water- or 2 M KCl-exchangeable ammonium in anoxic soil than in corresponding oxic soil. Particle-associated ammonium contributed by at least 74% and 93% of the total bioavailable pool in oxic and anoxic soil, respectively. The N. europaea biosensor should have broad relevance for environmental monitoring of bioavailable ammonium and processes depending on ammonium bioavailability.

Virtual quantification of metabolites by capillary electrophoresis-electrospray ionization-mass spectrometry: predicting ionization efficiency without chemical standards.

Science.gov (United States)

Chalcraft, Kenneth R; Lee, Richard; Mills, Casandra; Britz-McKibbin, Philip

2009-04-01

A major obstacle in metabolomics remains the identification and quantification of a large fraction of unknown metabolites in complex biological samples when purified standards are unavailable. Herein we introduce a multivariate strategy for de novo quantification of cationic/zwitterionic metabolites using capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) based on fundamental molecular, thermodynamic, and electrokinetic properties of an ion. Multivariate calibration was used to derive a quantitative relationship between the measured relative response factor (RRF) of polar metabolites with respect to four physicochemical properties associated with ion evaporation in ESI-MS, namely, molecular volume (MV), octanol-water distribution coefficient (log D), absolute mobility (mu(o)), and effective charge (z(eff)). Our studies revealed that a limited set of intrinsic solute properties can be used to predict the RRF of various classes of metabolites (e.g., amino acids, amines, peptides, acylcarnitines, nucleosides, etc.) with reasonable accuracy and robustness provided that an appropriate training set is validated and ion responses are normalized to an internal standard(s). The applicability of the multivariate model to quantify micromolar levels of metabolites spiked in red blood cell (RBC) lysates was also examined by CE-ESI-MS without significant matrix effects caused by involatile salts and/or major co-ion interferences. This work demonstrates the feasibility for virtual quantification of low-abundance metabolites and their isomers in real-world samples using physicochemical properties estimated by computer modeling, while providing deeper insight into the wide disparity of solute responses in ESI-MS. New strategies for predicting ionization efficiency in silico allow for rapid and semiquantitative analysis of newly discovered biomarkers and/or drug metabolites in metabolomics research when chemical standards do not exist.

Uncertainty Quantification for Large-Scale Ice Sheet Modeling

Energy Technology Data Exchange (ETDEWEB)

Ghattas, Omar [Univ. of Texas, Austin, TX (United States)

2016-02-05

This report summarizes our work to develop advanced forward and inverse solvers and uncertainty quantification capabilities for a nonlinear 3D full Stokes continental-scale ice sheet flow model. The components include: (1) forward solver: a new state-of-the-art parallel adaptive scalable high-order-accurate mass-conservative Newton-based 3D nonlinear full Stokes ice sheet flow simulator; (2) inverse solver: a new adjoint-based inexact Newton method for solution of deterministic inverse problems governed by the above 3D nonlinear full Stokes ice flow model; and (3) uncertainty quantification: a novel Hessian-based Bayesian method for quantifying uncertainties in the inverse ice sheet flow solution and propagating them forward into predictions of quantities of interest such as ice mass flux to the ocean.

Swift Quantification of Fenofibrate and Tiemonium methylsulfate Active Ingredients in Solid Drugs Using Particle Induced X-Ray Emission

International Nuclear Information System (INIS)

Bejjani, A.; Nsouli, B.; Zahraman, K.; Assi, S.; Younes, Gh.; Yazbi, F.

2011-01-01

The quantification of active ingredients (AI) in drugs is a crucial and important step in the drug quality control process. This is usually performed by using wet chemical techniques like LC-MS, UV spectrophotometry and other appropriate organic analytical methods. However, if the active ingredient contains specific heteroatoms (F, S, Cl), elemental IBA like PIXE and PIGE techniques, using small tandem accelerator of 1-2 MV, can be explored for molecular quantification. IBA techniques permit the analysis of the sample under solid form, without any laborious sample preparations. In this work, we demonstrate the ability of the Thick Target PIXE technique for rapid and accurate quantification of both low and high concentrations of active ingredients in different commercial drugs. Fenofibrate, a chlorinated active ingredient, is present in high amounts in two different commercial drugs, its quantification was done using the relative approach to an external standard. On the other hand, Tiemonium methylsulfate which exists in relatively low amount in commercial drugs, its quantification was done using GUPIX simulation code (absolute quantification). The experimental aspects related to the quantification validity (use of external standards, absolute quantification, matrix effect,...) are presented and discussed. (author)

Superposition Quantification

Science.gov (United States)

Chang, Li-Na; Luo, Shun-Long; Sun, Yuan

2017-11-01

The principle of superposition is universal and lies at the heart of quantum theory. Although ever since the inception of quantum mechanics a century ago, superposition has occupied a central and pivotal place, rigorous and systematic studies of the quantification issue have attracted significant interests only in recent years, and many related problems remain to be investigated. In this work we introduce a figure of merit which quantifies superposition from an intuitive and direct perspective, investigate its fundamental properties, connect it to some coherence measures, illustrate it through several examples, and apply it to analyze wave-particle duality. Supported by Science Challenge Project under Grant No. TZ2016002, Laboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Beijing, Key Laboratory of Random Complex Structures and Data Science, Chinese Academy of Sciences, Grant under No. 2008DP173182

Spectrometric aerial survey as a new tool for geological survey and mining prospecting

International Nuclear Information System (INIS)

Cambon, R.

1997-01-01

Airborne survey for radioactive minerals started around 1945. The limited sensitivity of the tools used, the difficulties found for the topographic and training effect corrections, made difficult the evaluation of the results. The technical progresses realized in the recent past years in electronic and computer sciences allowed to overcome these difficulties and gave to the method all its potentialities. With the aerial spectrometric survey, a new step was made, because this method can be used for other topics than radioactive prospection such as geological survey and mining prospection for metallic and industrial minerals. The spectrometric method is based on the possibility to measure photopeak energies (gamma radiation) emitted by radioactive minerals and discriminate between them those emitted by U238, TI 208 and K40 respectively daughter products of uranium, thorium and potassium. For airborne survey, one consider that measuring instruments will allow to pick-up 80% of the radioactive emission concerning the first 15 to 30 centimetres of ground (1 metre maximum). The use of this method for geological and mineral exploration is based on the assumption that different rock types or ore bearing rock types are composed of certain amounts of rock forming minerals which comprise specific quantities of radioactive elements such as potassium, uranium and thorium (cf: Gabelman 77). To be able to evaluate the results of the spectrometric survey it will be necessary to know roughly the behaviour of the different radioactive elements through a complete geological cycle. (author)

Noninvasive Quantification of Pancreatic Fat in Humans

OpenAIRE

Lingvay, Ildiko; Esser, Victoria; Legendre, Jaime L.; Price, Angela L.; Wertz, Kristen M.; Adams-Huet, Beverley; Zhang, Song; Unger, Roger H.; Szczepaniak, Lidia S.

2009-01-01

Objective: To validate magnetic resonance spectroscopy (MRS) as a tool for non-invasive quantification of pancreatic triglyceride (TG) content and to measure the pancreatic TG content in a diverse human population with a wide range of body mass index (BMI) and glucose control.

15 CFR 990.52 - Injury assessment-quantification.

Science.gov (United States)

2010-01-01

... (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE OIL POLLUTION ACT..., trustees must quantify the degree, and spatial and temporal extent of such injuries relative to baseline. (b) Quantification approaches. Trustees may quantify injuries in terms of: (1) The degree, and...

Design and Use of a Full Flow Sampling System (FFS) for the Quantification of Methane Emissions.

Science.gov (United States)

Johnson, Derek R; Covington, April N; Clark, Nigel N

2016-06-12

The use of natural gas continues to grow with increased discovery and production of unconventional shale resources. At the same time, the natural gas industry faces continued scrutiny for methane emissions from across the supply chain, due to methane's relatively high global warming potential (25-84x that of carbon dioxide, according to the Energy Information Administration). Currently, a variety of techniques of varied uncertainties exists to measure or estimate methane emissions from components or facilities. Currently, only one commercial system is available for quantification of component level emissions and recent reports have highlighted its weaknesses. In order to improve accuracy and increase measurement flexibility, we have designed, developed, and implemented a novel full flow sampling system (FFS) for quantification of methane emissions and greenhouse gases based on transportation emissions measurement principles. The FFS is a modular system that consists of an explosive-proof blower(s), mass airflow sensor(s) (MAF), thermocouple, sample probe, constant volume sampling pump, laser based greenhouse gas sensor, data acquisition device, and analysis software. Dependent upon the blower and hose configuration employed, the current FFS is able to achieve a flow rate ranging from 40 to 1,500 standard cubic feet per minute (SCFM). Utilization of laser-based sensors mitigates interference from higher hydrocarbons (C2+). Co-measurement of water vapor allows for humidity correction. The system is portable, with multiple configurations for a variety of applications ranging from being carried by a person to being mounted in a hand drawn cart, on-road vehicle bed, or from the bed of utility terrain vehicles (UTVs). The FFS is able to quantify methane emission rates with a relative uncertainty of ± 4.4%. The FFS has proven, real world operation for the quantification of methane emissions occurring in conventional and remote facilities.

Design and Use of a Full Flow Sampling System (FFS) for the Quantification of Methane Emissions

Science.gov (United States)

Johnson, Derek R.; Covington, April N.; Clark, Nigel N.

2016-01-01

The use of natural gas continues to grow with increased discovery and production of unconventional shale resources. At the same time, the natural gas industry faces continued scrutiny for methane emissions from across the supply chain, due to methane's relatively high global warming potential (25-84x that of carbon dioxide, according to the Energy Information Administration). Currently, a variety of techniques of varied uncertainties exists to measure or estimate methane emissions from components or facilities. Currently, only one commercial system is available for quantification of component level emissions and recent reports have highlighted its weaknesses. In order to improve accuracy and increase measurement flexibility, we have designed, developed, and implemented a novel full flow sampling system (FFS) for quantification of methane emissions and greenhouse gases based on transportation emissions measurement principles. The FFS is a modular system that consists of an explosive-proof blower(s), mass airflow sensor(s) (MAF), thermocouple, sample probe, constant volume sampling pump, laser based greenhouse gas sensor, data acquisition device, and analysis software. Dependent upon the blower and hose configuration employed, the current FFS is able to achieve a flow rate ranging from 40 to 1,500 standard cubic feet per minute (SCFM). Utilization of laser-based sensors mitigates interference from higher hydrocarbons (C2+). Co-measurement of water vapor allows for humidity correction. The system is portable, with multiple configurations for a variety of applications ranging from being carried by a person to being mounted in a hand drawn cart, on-road vehicle bed, or from the bed of utility terrain vehicles (UTVs). The FFS is able to quantify methane emission rates with a relative uncertainty of ± 4.4%. The FFS has proven, real world operation for the quantification of methane emissions occurring in conventional and remote facilities. PMID:27341646

Voltammetric Quantification of Paraquat and Glyphosate in Surface Waters

Directory of Open Access Journals (Sweden)

William Roberto Alza-Camacho

2016-09-01

Full Text Available The indiscriminate use of pesticides on crops has a negative environmental impact that affects organisms, soil and water resources, essential for life. Therefore, it is necessary to evaluate the residual effect of these substances in water sources. A simple, affordable and accessible electrochemical method for Paraquat and Glyphosate quantification in water was developed. The study was conducted using as supporting electrolyte Britton-Robinson buffer solution, working electrode of glassy carbon, Ag/AgCl as the reference electrode, and platinum as auxiliary electrode. Differential pulse voltammetry (VDP method for both compounds were validated. Linearity of the methods presented a correlation coefficient of 0.9949 and 0.9919 and the limits of detection and quantification were 130 and 190 mg/L for Paraquat and 40 and 50 mg/L for glyphosate. Comparison with the reference method showed that the electrochemical method provides superior results in quantification of analytes. Of the samples tested, a value of Paraquat was between 0,011 to 1,572 mg/L and for glyphosate it was between 0.201 to 2.777 mg/L, indicating that these compounds are present in water sources and that those may be causing serious problems to human health.

HPLC Quantification of astaxanthin and canthaxanthin in Salmonidae eggs.

Science.gov (United States)

Tzanova, Milena; Argirova, Mariana; Atanasov, Vasil

2017-04-01

Astaxanthin and canthaxanthin are naturally occurring antioxidants referred to as xanthophylls. They are used as food additives in fish farms to improve the organoleptic qualities of salmonid products and to prevent reproductive diseases. This study reports the development and single-laboratory validation of a rapid method for quantification of astaxanthin and canthaxanthin in eggs of rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis М.). An advantage of the proposed method is the perfect combination of selective extraction of the xanthophylls and analysis of the extract by high-performance liquid chromatography and photodiode array detection. The method validation was carried out in terms of linearity, accuracy, precision, recovery and limits of detection and quantification. The method was applied for simultaneous quantification of the two xanthophylls in eggs of rainbow trout and brook trout after their selective extraction. The results show that astaxanthin accumulations in salmonid fish eggs are larger than those of canthaxanthin. As the levels of these two xanthophylls affect fish fertility, this method can be used to improve the nutritional quality and to minimize the occurrence of the M74 syndrome in fish populations. Copyright © 2016 John Wiley & Sons, Ltd.

Nuclear and mitochondrial DNA quantification of various forensic materials.

Science.gov (United States)

Andréasson, H; Nilsson, M; Budowle, B; Lundberg, H; Allen, M

2006-12-01

Due to the different types and quality of forensic evidence materials, their DNA content can vary substantially, and particularly low quantities can impact the results in an identification analysis. In this study, the quantity of mitochondrial and nuclear DNA was determined in a variety of materials using a previously described real-time PCR method. DNA quantification in the roots and distal sections of plucked and shed head hairs revealed large variations in DNA content particularly between the root and the shaft of plucked hairs. Also large intra- and inter-individual variations were found among hairs. In addition, DNA content was estimated in samples collected from fingerprints and accessories. The quantification of DNA on various items also displayed large variations, with some materials containing large amounts of nuclear DNA while no detectable nuclear DNA and only limited amounts of mitochondrial DNA were seen in others. Using this sensitive real-time PCR quantification assay, a better understanding was obtained regarding DNA content and variation in commonly analysed forensic evidence materials and this may guide the forensic scientist as to the best molecular biology approach for analysing various forensic evidence materials.

Development of a Taqman real-time PCR assay for rapid detection and quantification of Vibrio tapetis in extrapallial fluids of clams

Directory of Open Access Journals (Sweden)

Adeline Bidault

2015-12-01

Full Text Available The Gram-negative bacterium Vibrio tapetis is known as the causative agent of Brown Ring Disease (BRD in the Manila clam Venerupis (=Ruditapes philippinarum. This bivalve is the second most important species produced in aquaculture and has a high commercial value. In spite of the development of several molecular methods, no survey has been yet achieved to rapidly quantify the bacterium in the clam. In this study, we developed a Taqman real-time PCR assay targeting virB4 gene for accurate and quantitative identification of V. tapetis strains pathogenic to clams. Sensitivity and reproducibility of the method were assessed using either filtered sea water or extrapallial fluids of clam injected with the CECT4600T V. tapetis strain. Quantification curves of V. tapetis strain seeded in filtered seawater (FSW or extrapallial fluids (EF samples were equivalent showing reliable qPCR efficacies. With this protocol, we were able to specifically detect V. tapetis strains down to 1.125 101 bacteria per mL of EF or FSW, taking into account the dilution factor used for appropriate template DNA preparation. This qPCR assay allowed us to monitor V. tapetis load both experimentally or naturally infected Manila clams. This technique will be particularly useful for monitoring the kinetics of massive infections by V. tapetis and for designing appropriate control measures for aquaculture purposes.

Model Uncertainty Quantification Methods In Data Assimilation

Science.gov (United States)

Pathiraja, S. D.; Marshall, L. A.; Sharma, A.; Moradkhani, H.

2017-12-01

Data Assimilation involves utilising observations to improve model predictions in a seamless and statistically optimal fashion. Its applications are wide-ranging; from improving weather forecasts to tracking targets such as in the Apollo 11 mission. The use of Data Assimilation methods in high dimensional complex geophysical systems is an active area of research, where there exists many opportunities to enhance existing methodologies. One of the central challenges is in model uncertainty quantification; the outcome of any Data Assimilation study is strongly dependent on the uncertainties assigned to both observations and models. I focus on developing improved model uncertainty quantification methods that are applicable to challenging real world scenarios. These include developing methods for cases where the system states are only partially observed, where there is little prior knowledge of the model errors, and where the model error statistics are likely to be highly non-Gaussian.

Real-time quantitative PCR for retrovirus-like particle quantification in CHO cell culture.

Science.gov (United States)

de Wit, C; Fautz, C; Xu, Y

2000-09-01

Chinese hamster ovary (CHO) cells have been widely used to manufacture recombinant proteins intended for human therapeutic uses. Retrovirus-like particles, which are apparently defective and non-infectious, have been detected in all CHO cells by electron microscopy (EM). To assure viral safety of CHO cell-derived biologicals, quantification of retrovirus-like particles in production cell culture and demonstration of sufficient elimination of such retrovirus-like particles by the down-stream purification process are required for product market registration worldwide. EM, with a detection limit of 1x10(6) particles/ml, is the standard retrovirus-like particle quantification method. The whole process, which requires a large amount of sample (3-6 litres), is labour intensive, time consuming, expensive, and subject to significant assay variability. In this paper, a novel real-time quantitative PCR assay (TaqMan assay) has been developed for the quantification of retrovirus-like particles. Each retrovirus particle contains two copies of the viral genomic particle RNA (pRNA) molecule. Therefore, quantification of retrovirus particles can be achieved by quantifying the pRNA copy number, i.e. every two copies of retroviral pRNA is equivalent to one retrovirus-like particle. The TaqMan assay takes advantage of the 5'-->3' exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 Sequence Detection System of PE Applied Biosystems (Foster City, CA, U.S.A.) for automated pRNA quantification through a dual-labelled fluorogenic probe. The TaqMan quantification technique is highly comparable to the EM analysis. In addition, it offers significant advantages over the EM analysis, such as a higher sensitivity of less than 600 particles/ml, greater accuracy and reliability, higher sample throughput, more flexibility and lower cost. Therefore, the TaqMan assay should be used as a substitute for EM analysis for retrovirus-like particle quantification in CHO cell

Inference of pain stimulus level from stereotypical behavioral response of C.elegans allows quantification of effects of anesthesia and mutation

Science.gov (United States)

Leung, Kawai; Mohammadi, Aylia; Ryu, William; Nemenman, Ilya

In animals, we must infer the pain level from experimental characterization of behavior. This is not trivial since behaviors are very complex and multidimensional. To establish C.elegans as a model for pain research, we propose for the first time a quantitative model that allows inference of a thermal nociceptive stimulus level from the behavior of an individual worm. We apply controlled levels of pain by locally heating worms with an infrared laser and capturing the subsequent behavior. We discover that the behavioral response is a product of stereotypical behavior and a nonlinear function of the strength of stimulus. The same stereotypical behavior is observed in normal, anesthetized and mutated worms. From this result we build a Bayesian model to infer the strength of laser stimulus from the behavior. This model allows us to measure the efficacy of anaesthetization and mutation by comparing the inferred strength of stimulus. Based on the measured nociceptive escape of over 200 worms, our model is able to significantly differentiate normal, anaesthetized and mutated worms with 40 worm samples. This work was partially supported by NSF Grant No. IOS/1208126 and HFSP Grant No. RGY0084/.

Validation of tumor protein marker quantification by two independent automated immunofluorescence image analysis platforms

Science.gov (United States)

Peck, Amy R; Girondo, Melanie A; Liu, Chengbao; Kovatich, Albert J; Hooke, Jeffrey A; Shriver, Craig D; Hu, Hai; Mitchell, Edith P; Freydin, Boris; Hyslop, Terry; Chervoneva, Inna; Rui, Hallgeir

2016-01-01

Protein marker levels in formalin-fixed, paraffin-embedded tissue sections traditionally have been assayed by chromogenic immunohistochemistry and evaluated visually by pathologists. Pathologist scoring of chromogen staining intensity is subjective and generates low-resolution ordinal or nominal data rather than continuous data. Emerging digital pathology platforms now allow quantification of chromogen or fluorescence signals by computer-assisted image analysis, providing continuous immunohistochemistry values. Fluorescence immunohistochemistry offers greater dynamic signal range than chromogen immunohistochemistry, and combined with image analysis holds the promise of enhanced sensitivity and analytic resolution, and consequently more robust quantification. However, commercial fluorescence scanners and image analysis software differ in features and capabilities, and claims of objective quantitative immunohistochemistry are difficult to validate as pathologist scoring is subjective and there is no accepted gold standard. Here we provide the first side-by-side validation of two technologically distinct commercial fluorescence immunohistochemistry analysis platforms. We document highly consistent results by (1) concordance analysis of fluorescence immunohistochemistry values and (2) agreement in outcome predictions both for objective, data-driven cutpoint dichotomization with Kaplan–Meier analyses or employment of continuous marker values to compute receiver-operating curves. The two platforms examined rely on distinct fluorescence immunohistochemistry imaging hardware, microscopy vs line scanning, and functionally distinct image analysis software. Fluorescence immunohistochemistry values for nuclear-localized and tyrosine-phosphorylated Stat5a/b computed by each platform on a cohort of 323 breast cancer cases revealed high concordance after linear calibration, a finding confirmed on an independent 382 case cohort, with concordance correlation coefficients >0

Literature survey: health effects of radiation

International Nuclear Information System (INIS)

Tveten, U.; Garder, K.

This report was originally written as a chapter of a report entitled 'Air pollution effects of electric power generation, a literature survey', written jointly by the Norwegian Institute for Air Research (NILU) and the Institutt for Atomenergi (IFA). (INIS RN242406). A survey is presented of the health effects of radiation. It has not, however, been the intention of the authors to make a complete list of all the literature relevant to this subject. The NILU/IFA report was meant as a first step towards a method of comparing the health effects of electric power generation by fission, gas and oil. Consequently information relevant to quantification of the health effects on humans has been selected. It is pointed out that quantitative information on the health effects of low radiation and dose rates, as are relevant to routine releases, does not exist for humans. The convention of linear extrapolation from higher doses and dose rates is used worldwide, but it is felt by most that the estimates are conservative. As an example of the use of the current best estimates, a calculation of normal release radiation doses is performed. (Auth.)

2D histomorphometric quantification from 3D computerized tomography

International Nuclear Information System (INIS)

Lima, Inaya; Oliveira, Luis Fernando de; Lopes, Ricardo T.; Jesus, Edgar Francisco O. de; Alves, Jose Marcos

2002-01-01

In the present article, preliminary results are presented showing the application of the tridimensional computerized microtomographic technique (3D-μCT) to bone tissue characterization, through histomorphometric quantification which are based on stereologic concepts. Two samples of human bone were correctly prepared to be submitted to the tomographic system. The system used to realize that process were a radiographic system with a microfocus X-ray tube. Through these three processes, acquisition, reconstruction and quantification, it was possible to get the good results and coherent to the literature data. From this point, it is intended to compare these results with the information due the conventional method, that is, conventional histomorphometry. (author)

Advances in forensic DNA quantification: a review.

Science.gov (United States)

Lee, Steven B; McCord, Bruce; Buel, Eric

2014-11-01

This review focuses upon a critical step in forensic biology: detection and quantification of human DNA from biological samples. Determination of the quantity and quality of human DNA extracted from biological evidence is important for several reasons. Firstly, depending on the source and extraction method, the quality (purity and length), and quantity of the resultant DNA extract can vary greatly. This affects the downstream method as the quantity of input DNA and its relative length can determine which genotyping procedure to use-standard short-tandem repeat (STR) typing, mini-STR typing or mitochondrial DNA sequencing. Secondly, because it is important in forensic analysis to preserve as much of the evidence as possible for retesting, it is important to determine the total DNA amount available prior to utilizing any destructive analytical method. Lastly, results from initial quantitative and qualitative evaluations permit a more informed interpretation of downstream analytical results. Newer quantitative techniques involving real-time PCR can reveal the presence of degraded DNA and PCR inhibitors, that provide potential reasons for poor genotyping results and may indicate methods to use for downstream typing success. In general, the more information available, the easier it is to interpret and process the sample resulting in a higher likelihood of successful DNA typing. The history of the development of quantitative methods has involved two main goals-improving precision of the analysis and increasing the information content of the result. This review covers advances in forensic DNA quantification methods and recent developments in RNA quantification. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advancing agricultural greenhouse gas quantification*

Science.gov (United States)

Olander, Lydia; Wollenberg, Eva; Tubiello, Francesco; Herold, Martin

2013-03-01

descriptive trends are sufficient or an understanding of drivers and causes are needed. While there are certainly similar needs across uses and users, the necessary methods, data, and models for quantifying GHGs may vary. Common challenges for quantification noted in an informal survey of users of GHG information by Olander et al (2013) include the following. 3.1. Need for user-friendly methods that work across scales, regions, and systems Much of the data gathered and models developed by the research community provide high confidence in data or indicators computed at one place or for one issue, thus they are relevant for only specific uses, not transparent, or not comparable. These research approaches need to be translated to practitioners though the development of farmer friendly, transparent, comparable, and broadly applicable methods. Many users noted the need for quantification data and methods that work and are accurate across region and scales. One of the interviewed users, Charlotte Streck, summed it up nicely: 'A priority would be to produce comparable datasets for agricultural GHG emissions of particular agricultural practices for a broad set of countries ... with a gradual increase in accuracy'. 3.2. Need for lower cost, feasible approaches Concerns about cost and complexity of existing quantification methods were raised by a number of users interviewed in the survey. In the field it is difficult to measure changes in GHGs from agricultural management due to spatial and temporal variability, and the scale of the management-induced changes relative to background pools and fluxes. Many users noted data gaps and inconsistencies and insufficient technical capacity and infrastructure to generate necessary information, particularly in developing countries. The need for creative approaches for data collection and analysis, such as crowd sourcing and mobile technology, were noted. 3.3. Need for methods that can crosswalk between emission-reduction strategy and inventories

Quantification of rice bran oil in oil blends

Energy Technology Data Exchange (ETDEWEB)

Mishra, R.; Sharma, H. K.; Sengar, G.

2012-11-01

Blends consisting of physically refined rice bran oil (PRBO): sunflower oil (SnF) and PRBO: safflower oil (SAF) in different proportions were analyzed for various physicochemical parameters. The quantification of pure rice bran oil in the blended oils was carried out using different methods including gas chromatographic, HPLC, ultrasonic velocity and methods based on physico-chemical parameters. The physicochemical parameters such as ultrasonic velocity, relative association and acoustic impedance at 2 MHz, iodine value, palmitic acid content and oryzanol content reflected significant changes with increased proportions of PRBO in the blended oils. These parameters were selected as dependent parameters and % PRBO proportion was selected as independent parameters. The study revealed that regression equations based on the oryzanol content, palmitic acid composition, ultrasonic velocity, relative association, acoustic impedance, and iodine value can be used for the quantification of rice bran oil in blended oils. The rice bran oil can easily be quantified in the blended oils based on the oryzanol content by HPLC even at a 1% level. The palmitic acid content in blended oils can also be used as an indicator to quantify rice bran oil at or above the 20% level in blended oils whereas the method based on ultrasonic velocity, acoustic impedance and relative association showed initial promise in the quantification of rice bran oil. (Author) 23 refs.

HPLC for simultaneous quantification of total ceramide, glucosylceramide, and ceramide trihexoside concentrations in plasma

NARCIS (Netherlands)

Groener, Johanna E. M.; Poorthuis, Ben J. H. M.; Kuiper, Sijmen; Helmond, Mariette T. J.; Hollak, Carla E. M.; Aerts, Johannes M. F. G.

2007-01-01

BACKGROUND: Simple, reproducible assays are needed for the quantification of sphingolipids, ceramide (Cer), and sphingoid bases. We developed an HPLC method for simultaneous quantification of total plasma concentrations of Cer, glucosylceramide (GlcCer), and ceramide trihexoside (CTH). METHODS:

Aerosol-type retrieval and uncertainty quantification from OMI data

Science.gov (United States)

Kauppi, Anu; Kolmonen, Pekka; Laine, Marko; Tamminen, Johanna

2017-11-01

We discuss uncertainty quantification for aerosol-type selection in satellite-based atmospheric aerosol retrieval. The retrieval procedure uses precalculated aerosol microphysical models stored in look-up tables (LUTs) and top-of-atmosphere (TOA) spectral reflectance measurements to solve the aerosol characteristics. The forward model approximations cause systematic differences between the modelled and observed reflectance. Acknowledging this model discrepancy as a source of uncertainty allows us to produce more realistic uncertainty estimates and assists the selection of the most appropriate LUTs for each individual retrieval.This paper focuses on the aerosol microphysical model selection and characterisation of uncertainty in the retrieved aerosol type and aerosol optical depth (AOD). The concept of model evidence is used as a tool for model comparison. The method is based on Bayesian inference approach, in which all uncertainties are described as a posterior probability distribution. When there is no single best-matching aerosol microphysical model, we use a statistical technique based on Bayesian model averaging to combine AOD posterior probability densities of the best-fitting models to obtain an averaged AOD estimate. We also determine the shared evidence of the best-matching models of a certain main aerosol type in order to quantify how plausible it is that it represents the underlying atmospheric aerosol conditions.The developed method is applied to Ozone Monitoring Instrument (OMI) measurements using a multiwavelength approach for retrieving the aerosol type and AOD estimate with uncertainty quantification for cloud-free over-land pixels. Several larger pixel set areas were studied in order to investigate the robustness of the developed method. We evaluated the retrieved AOD by comparison with ground-based measurements at example sites. We found that the uncertainty of AOD expressed by posterior probability distribution reflects the difficulty in model

Aerosol-type retrieval and uncertainty quantification from OMI data

Directory of Open Access Journals (Sweden)

A. Kauppi

2017-11-01

Full Text Available We discuss uncertainty quantification for aerosol-type selection in satellite-based atmospheric aerosol retrieval. The retrieval procedure uses precalculated aerosol microphysical models stored in look-up tables (LUTs and top-of-atmosphere (TOA spectral reflectance measurements to solve the aerosol characteristics. The forward model approximations cause systematic differences between the modelled and observed reflectance. Acknowledging this model discrepancy as a source of uncertainty allows us to produce more realistic uncertainty estimates and assists the selection of the most appropriate LUTs for each individual retrieval.This paper focuses on the aerosol microphysical model selection and characterisation of uncertainty in the retrieved aerosol type and aerosol optical depth (AOD. The concept of model evidence is used as a tool for model comparison. The method is based on Bayesian inference approach, in which all uncertainties are described as a posterior probability distribution. When there is no single best-matching aerosol microphysical model, we use a statistical technique based on Bayesian model averaging to combine AOD posterior probability densities of the best-fitting models to obtain an averaged AOD estimate. We also determine the shared evidence of the best-matching models of a certain main aerosol type in order to quantify how plausible it is that it represents the underlying atmospheric aerosol conditions.The developed method is applied to Ozone Monitoring Instrument (OMI measurements using a multiwavelength approach for retrieving the aerosol type and AOD estimate with uncertainty quantification for cloud-free over-land pixels. Several larger pixel set areas were studied in order to investigate the robustness of the developed method. We evaluated the retrieved AOD by comparison with ground-based measurements at example sites. We found that the uncertainty of AOD expressed by posterior probability distribution reflects the

Quantification of coating aging using impedance measurements

NARCIS (Netherlands)

Westing, E.P.M. van; Weijde, D.H. van der; Vreijling, M.P.W.; Ferrari, G.M.; Wit, J.H.W. de

1998-01-01

This chapter shows the application results of a novel approach to quantify the ageing of organic coatings using impedance measurements. The ageing quantification is based on the typical impedance behaviour of barrier coatings in immersion. This immersion behaviour is used to determine the limiting

A reduction approach to improve the quantification of linked fault trees through binary decision diagrams

International Nuclear Information System (INIS)

Ibanez-Llano, Cristina; Rauzy, Antoine; Melendez, Enrique; Nieto, Francisco

2010-01-01

Over the last two decades binary decision diagrams have been applied successfully to improve Boolean reliability models. Conversely to the classical approach based on the computation of the MCS, the BDD approach involves no approximation in the quantification of the model and is able to handle correctly negative logic. However, when models are sufficiently large and complex, as for example the ones coming from the PSA studies of the nuclear industry, it begins to be unfeasible to compute the BDD within a reasonable amount of time and computer memory. Therefore, simplification or reduction of the full model has to be considered in some way to adapt the application of the BDD technology to the assessment of such models in practice. This paper proposes a reduction process based on using information provided by the set of the most relevant minimal cutsets of the model in order to perform the reduction directly on it. This allows controlling the degree of reduction and therefore the impact of such simplification on the final quantification results. This reduction is integrated in an incremental procedure that is compatible with the dynamic generation of the event trees and therefore adaptable to the recent dynamic developments and extensions of the PSA studies. The proposed method has been applied to a real case study, and the results obtained confirm that the reduction enables the BDD computation while maintaining accuracy.

A reduction approach to improve the quantification of linked fault trees through binary decision diagrams

Energy Technology Data Exchange (ETDEWEB)

Ibanez-Llano, Cristina, E-mail: cristina.ibanez@iit.upcomillas.e [Instituto de Investigacion Tecnologica (IIT), Escuela Tecnica Superior de Ingenieria ICAI, Universidad Pontificia Comillas, C/Santa Cruz de Marcenado 26, 28015 Madrid (Spain); Rauzy, Antoine, E-mail: Antoine.RAUZY@3ds.co [Dassault Systemes, 10 rue Marcel Dassault CS 40501, 78946 Velizy Villacoublay, Cedex (France); Melendez, Enrique, E-mail: ema@csn.e [Consejo de Seguridad Nuclear (CSN), C/Justo Dorado 11, 28040 Madrid (Spain); Nieto, Francisco, E-mail: nieto@iit.upcomillas.e [Instituto de Investigacion Tecnologica (IIT), Escuela Tecnica Superior de Ingenieria ICAI, Universidad Pontificia Comillas, C/Santa Cruz de Marcenado 26, 28015 Madrid (Spain)

2010-12-15

Over the last two decades binary decision diagrams have been applied successfully to improve Boolean reliability models. Conversely to the classical approach based on the computation of the MCS, the BDD approach involves no approximation in the quantification of the model and is able to handle correctly negative logic. However, when models are sufficiently large and complex, as for example the ones coming from the PSA studies of the nuclear industry, it begins to be unfeasible to compute the BDD within a reasonable amount of time and computer memory. Therefore, simplification or reduction of the full model has to be considered in some way to adapt the application of the BDD technology to the assessment of such models in practice. This paper proposes a reduction process based on using information provided by the set of the most relevant minimal cutsets of the model in order to perform the reduction directly on it. This allows controlling the degree of reduction and therefore the impact of such simplification on the final quantification results. This reduction is integrated in an incremental procedure that is compatible with the dynamic generation of the event trees and therefore adaptable to the recent dynamic developments and extensions of the PSA studies. The proposed method has been applied to a real case study, and the results obtained confirm that the reduction enables the BDD computation while maintaining accuracy.

Quantification of character-impacting compounds in Ocimum basilicum and 'Pesto alla Genovese' with selected ion flow tube mass spectrometry.

Science.gov (United States)

Amadei, Gianluca; Ross, Brian M

2012-02-15

Basil (Ocimum basilicum) is an important flavourant plant which constitutes the major ingredient of the pasta sauce 'Pesto alla Genovese'. The characteristic smell of basil stems mainly from a handful of terpenoids (methyl cinnamate, eucalyptol, linalool and estragole), the concentration of which varies according to basil cultivars. The simple and rapid analysis of the terpenoid constituents of basil would be useful as a means to optimise harvesting times and to act as a quality control process for basil-containing foodstuffs. Classical analytical techniques such as gas chromatography/mass spectrometry (GC/MS) are, however, slow, technically demanding and therefore less suitable for routine analysis. A new chemical ionisation technique which allows real-time quantification of traces gases, Selected Ion Flow Tube Mass Spectrometry (SIFT-MS), was therefore utilised to determine its usefulness for the assay of terpenoid concentrations in basil and pesto sauce headspace. Trace gas analysis was performed using the NO(+) precursor ion which minimised interference from other compounds. Character-impacting compound concentration was measured in basil headspace with good reproducibility and statistically significant differences were observed between cultivars. Quantification of linalool in pesto sauce headspace proved more difficult due to the presence of interfering compounds. This was resolved by careful selection of reaction product ions which allowed us to detect differences between various commercial brands of pesto. We conclude that SIFT-MS may be a valid tool for the fast and reproducible analysis of flavourant terpenoids in basil and basil-derived foodstuffs. Copyright © 2011 John Wiley & Sons, Ltd.

Parsing and Quantification of Raw Orbitrap Mass Spectrometer Data Using RawQuant.

Science.gov (United States)

Kovalchik, Kevin A; Moggridge, Sophie; Chen, David D Y; Morin, Gregg B; Hughes, Christopher S

2018-06-01

Effective analysis of protein samples by mass spectrometry (MS) requires careful selection and optimization of a range of experimental parameters. As the output from the primary detection device, the "raw" MS data file can be used to gauge the success of a given sample analysis. However, the closed-source nature of the standard raw MS file can complicate effective parsing of the data contained within. To ease and increase the range of analyses possible, the RawQuant tool was developed to enable parsing of raw MS files derived from Thermo Orbitrap instruments to yield meta and scan data in an openly readable text format. RawQuant can be commanded to export user-friendly files containing MS 1 , MS 2 , and MS 3 metadata as well as matrices of quantification values based on isobaric tagging approaches. In this study, the utility of RawQuant is demonstrated in several scenarios: (1) reanalysis of shotgun proteomics data for the identification of the human proteome, (2) reanalysis of experiments utilizing isobaric tagging for whole-proteome quantification, and (3) analysis of a novel bacterial proteome and synthetic peptide mixture for assessing quantification accuracy when using isobaric tags. Together, these analyses successfully demonstrate RawQuant for the efficient parsing and quantification of data from raw Thermo Orbitrap MS files acquired in a range of common proteomics experiments. In addition, the individual analyses using RawQuant highlights parametric considerations in the different experimental sets and suggests targetable areas to improve depth of coverage in identification-focused studies and quantification accuracy when using isobaric tags.

Quantification of glycyrrhizin biomarker in Glycyrrhiza glabra ...

African Journals Online (AJOL)

Background: A simple and sensitive thin-layer chromatographic method has been established for quantification of glycyrrhizin in Glycyrrhiza glabra rhizome and baby herbal formulations by validated Reverse Phase HPTLC method. Materials and Methods: RP-HPTLC Method was carried out using glass coated with RP-18 ...

Data-driven Demand Response Characterization and Quantification

DEFF Research Database (Denmark)

Le Ray, Guillaume; Pinson, Pierre; Larsen, Emil Mahler

2017-01-01

Analysis of load behavior in demand response (DR) schemes is important to evaluate the performance of participants. Very few real-world experiments have been carried out and quantification and characterization of the response is a difficult task. Nevertheless it will be a necessary tool for portf...

Uncertainty Quantification in Alchemical Free Energy Methods.

Science.gov (United States)

Bhati, Agastya P; Wan, Shunzhou; Hu, Yuan; Sherborne, Brad; Coveney, Peter V

2018-05-02

Alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulations. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and quantification of associated uncertainties in such methods have barely been discussed. Here, we apply a systematic protocol for uncertainty quantification to a number of popular alchemical free energy methods, covering both absolute and relative free energy predictions. We show that a reliable measure of error estimation is provided by ensemble simulation-an ensemble of independent MD simulations-which applies irrespective of the free energy method. The need to use ensemble methods is fundamental and holds regardless of the duration of time of the molecular dynamics simulations performed.

Level 2 probabilistic event analyses and quantification

International Nuclear Information System (INIS)

Boneham, P.

2003-01-01

In this paper an example of quantification of a severe accident phenomenological event is given. The performed analysis for assessment of the probability that the debris released from the reactor vessel was in a coolable configuration in the lower drywell is presented. It is also analysed the assessment of the type of core/concrete attack that would occur. The coolability of the debris ex-vessel evaluation by an event in the Simplified Boiling Water Reactor (SBWR) Containment Event Tree (CET) and a detailed Decomposition Event Tree (DET) developed to aid in the quantification of this CET event are considered. The headings in the DET selected to represent plant physical states (e.g., reactor vessel pressure at the time of vessel failure) and the uncertainties associated with the occurrence of critical physical phenomena (e.g., debris configuration in the lower drywell) considered important to assessing whether the debris was coolable or not coolable ex-vessel are also discussed

Seed shape quantification in the order Cucurbitales

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Emilio Cervantes

2018-02-01

Full Text Available Seed shape quantification in diverse species of the families belonging to the order Cucurbitales is done based on the comparison of seed images with geometric figures. Quantification of seed shape is a useful tool in plant description for phenotypic characterization and taxonomic analysis. J index gives the percent of similarity of the image of a seed with a geometric figure and it is useful in taxonomy for the study of relationships between plant groups. Geometric figures used as models in the Cucurbitales are the ovoid, two ellipses with different x/y ratios and the outline of the Fibonacci spiral. The images of seeds have been compared with these figures and values of J index obtained. The results obtained for 29 species in the family Cucurbitaceae support a relationship between seed shape and species ecology. Simple seed shape, with images resembling simple geometric figures like the ovoid, ellipse or the Fibonacci spiral, may be a feature in the basal clades of taxonomic groups.

Perfect additivity of microinterface arrays for liquid-liquid measurements: Application to cadmium ions quantification

International Nuclear Information System (INIS)

Mastouri, A.; Peulon, S.; Farcage, D.; Bellakhal, N.; Chaussé, A.

2014-01-01

Graphical abstract: - Highlights: • Confirmation of the perfect additivity of micropores independently of the geometry of arrays. • Study of assisted transfer of cadmium ions by 8-HQ at water/1,2-DCE. • Validation by cyclic and square wave voltammetry measurements for high and low concentrations. • Quantification of Cd(II) ions until 11 ppb in very simple conditions. • Highlighting of the very interesting use of arrays in a classical liquid-liquid microinterface device. - Abstract: For the first time, experimental measurements confirm the real additivity of the currents with micropore arrays, independently of the geometry (square, circular or in crosswise), from one single micropore until 256 micropores, in the case of the assisted transfer of cadmium ions by 8-hydroxyquinolinol (8-HQ). This result was obtained for measurements made by cyclic voltammetry at high concentration of cadmium ions (10 −4 M). At lower concentrations (until 10 −6 M), measurements performed by square wave voltammetry confirm also this additivity until 64 micropores. A calibration curve performed with a 64 micropores array allows us, in very simple conditions, the quantification of cadmium ions until 11 ppb (100 nM), which is lower than to the imposed limit for this specie in various fields, and in industrial effluents, in particular. The gain of sensitivity is close to 170 compared to measurements performed with one single micropore, illustrating the real interest of these arrays

A Survey of FDG- and Amyloid-PET Imaging in Dementia and GRADE Analysis

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Perani Daniela

2014-01-01

Full Text Available PET based tools can improve the early diagnosis of Alzheimer’s disease (AD and differential diagnosis of dementia. The importance of identifying individuals at risk of developing dementia among people with subjective cognitive complaints or mild cognitive impairment has clinical, social, and therapeutic implications. Within the two major classes of AD biomarkers currently identified, that is, markers of pathology and neurodegeneration, amyloid- and FDG-PET imaging represent decisive tools for their measurement. As a consequence, the PET tools have been recognized to be of crucial value in the recent guidelines for the early diagnosis of AD and other dementia conditions. The references based recommendations, however, include large PET imaging literature based on visual methods that greatly reduces sensitivity and specificity and lacks a clear cut-off between normal and pathological findings. PET imaging can be assessed using parametric or voxel-wise analyses by comparing the subject’s scan with a normative data set, significantly increasing the diagnostic accuracy. This paper is a survey of the relevant literature on FDG and amyloid-PET imaging aimed at providing the value of quantification for the early and differential diagnosis of AD. This allowed a meta-analysis and GRADE analysis revealing high values for PET imaging that might be useful in considering recommendations.

Modeling qRT-PCR dynamics with application to cancer biomarker quantification.

Science.gov (United States)

Chervoneva, Inna; Freydin, Boris; Hyslop, Terry; Waldman, Scott A

2017-01-01

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used for molecular diagnostics and evaluating prognosis in cancer. The utility of mRNA expression biomarkers relies heavily on the accuracy and precision of quantification, which is still challenging for low abundance transcripts. The critical step for quantification is accurate estimation of efficiency needed for computing a relative qRT-PCR expression. We propose a new approach to estimating qRT-PCR efficiency based on modeling dynamics of polymerase chain reaction amplification. In contrast, only models for fluorescence intensity as a function of polymerase chain reaction cycle have been used so far for quantification. The dynamics of qRT-PCR efficiency is modeled using an ordinary differential equation model, and the fitted ordinary differential equation model is used to obtain effective polymerase chain reaction efficiency estimates needed for efficiency-adjusted quantification. The proposed new qRT-PCR efficiency estimates were used to quantify GUCY2C (Guanylate Cyclase 2C) mRNA expression in the blood of colorectal cancer patients. Time to recurrence and GUCY2C expression ratios were analyzed in a joint model for survival and longitudinal outcomes. The joint model with GUCY2C quantified using the proposed polymerase chain reaction efficiency estimates provided clinically meaningful results for association between time to recurrence and longitudinal trends in GUCY2C expression.

Recurrence quantification analysis in Liu's attractor

International Nuclear Information System (INIS)

Balibrea, Francisco; Caballero, M. Victoria; Molera, Lourdes

2008-01-01

Recurrence Quantification Analysis is used to detect transitions chaos to periodical states or chaos to chaos in a new dynamical system proposed by Liu et al. This system contains a control parameter in the second equation and was originally introduced to investigate the forming mechanism of the compound structure of the chaotic attractor which exists when the control parameter is zero

MEG evidence for conceptual combination but not numeral quantification in the left anterior temporal lobe during language production

Directory of Open Access Journals (Sweden)

Paul eDel Prato

2014-06-01

Full Text Available The left anterior temporal lobe (LATL has risen as a leading candidate for a brain locus of composition in language; yet the computational details of its function are unknown. Although most literature discusses it as a combinatory region in very general terms, it has also been proposed to reflect the more specific function of conceptual combination, which in the classic use of this term mainly pertains to the combination of open class words with obvious conceptual contributions. We aimed to distinguish between these two possibilities by contrasting plural nouns in contexts where they were either preceded by a color modifier (red cups, eliciting conceptual combination, or by a number word (two cups, eliciting numeral quantification but no conceptual combination. This contrast was chosen because within a production task, it allows the manipulation of composition type while keeping the physical stimulus constant: a display of two red cups can be named as two cups or red cups depending on the task instruction. These utterances were compared to productions of two-word number and color lists, intended as noncombinatory control conditions. MEG activity was recorded during the planning for production, prior to motion artifacts. As expected on the basis of comprehension studies, color modification elicited increased LATL activity as compared to color lists, demonstrating that this basic combinatory effect is strongly crossmodal. However, numeral quantification did not elicit a parallel effect, suggesting that the function of the LATL is (i semantic and not syntactic (given that both color modification and numeral quantification involve syntactic composition and (ii corresponds more closely to the classical psychological notion of conceptual combination as opposed to a more general semantic combinatory function.

Genomic DNA-based absolute quantification of gene expression in Vitis.

Science.gov (United States)

Gambetta, Gregory A; McElrone, Andrew J; Matthews, Mark A

2013-07-01

Many studies in which gene expression is quantified by polymerase chain reaction represent the expression of a gene of interest (GOI) relative to that of a reference gene (RG). Relative expression is founded on the assumptions that RG expression is stable across samples, treatments, organs, etc., and that reaction efficiencies of the GOI and RG are equal; assumptions which are often faulty. The true variability in RG expression and actual reaction efficiencies are seldom determined experimentally. Here we present a rapid and robust method for absolute quantification of expression in Vitis where varying concentrations of genomic DNA were used to construct GOI standard curves. This methodology was utilized to absolutely quantify and determine the variability of the previously validated RG ubiquitin (VvUbi) across three test studies in three different tissues (roots, leaves and berries). In addition, in each study a GOI was absolutely quantified. Data sets resulting from relative and absolute methods of quantification were compared and the differences were striking. VvUbi expression was significantly different in magnitude between test studies and variable among individual samples. Absolute quantification consistently reduced the coefficients of variation of the GOIs by more than half, often resulting in differences in statistical significance and in some cases even changing the fundamental nature of the result. Utilizing genomic DNA-based absolute quantification is fast and efficient. Through eliminating error introduced by assuming RG stability and equal reaction efficiencies between the RG and GOI this methodology produces less variation, increased accuracy and greater statistical power. © 2012 Scandinavian Plant Physiology Society.

A refined methodology for modeling volume quantification performance in CT

Science.gov (United States)

Chen, Baiyu; Wilson, Joshua; Samei, Ehsan

2014-03-01

The utility of CT lung nodule volume quantification technique depends on the precision of the quantification. To enable the evaluation of quantification precision, we previously developed a mathematical model that related precision to image resolution and noise properties in uniform backgrounds in terms of an estimability index (e'). The e' was shown to predict empirical precision across 54 imaging and reconstruction protocols, but with different correlation qualities for FBP and iterative reconstruction (IR) due to the non-linearity of IR impacted by anatomical structure. To better account for the non-linearity of IR, this study aimed to refine the noise characterization of the model in the presence of textured backgrounds. Repeated scans of an anthropomorphic lung phantom were acquired. Subtracted images were used to measure the image quantum noise, which was then used to adjust the noise component of the e' calculation measured from a uniform region. In addition to the model refinement, the validation of the model was further extended to 2 nodule sizes (5 and 10 mm) and 2 segmentation algorithms. Results showed that the magnitude of IR's quantum noise was significantly higher in structured backgrounds than in uniform backgrounds (ASiR, 30-50%; MBIR, 100-200%). With the refined model, the correlation between e' values and empirical precision no longer depended on reconstruction algorithm. In conclusion, the model with refined noise characterization relfected the nonlinearity of iterative reconstruction in structured background, and further showed successful prediction of quantification precision across a variety of nodule sizes, dose levels, slice thickness, reconstruction algorithms, and segmentation software.

UPLC TOF MS for sensitive quantification of naturally occurring pyrrolizidine alkaloids in Petasites hybridus extract (Ze 339).

Science.gov (United States)

Schenk, Alexander; Siewert, Beate; Toff, Stephan; Drewe, Jürgen

2015-08-01

Due to increasing regulatory awareness of their hepatotoxic, genotoxic and possibly carcinogenic potential, pyrrolizidine alkaloid (PA) content has to be thoroughly monitored in herbal medicinal preparations. Recently, new very low PA regulatory threshold concentrations have been requested by the authorities. Therefore, a highly sensitive and reproducible UPLC TOF MS method for the quantification of the PAs senkirkine, senecionine, seneciphylline, senecionine-N-oxide and seneciphylline-N-oxide in a CO2-extract of Petasites hybridus leaves (Ze 339) has been developed. The limit of quantification (LOQ) was 2ppb for all PAs. Recovery at the LOQ was between 88.9 and 141.9%, the repeatability precision between 3.5 and 13.6%. Linearity of the five PAs showed correlation coefficients between 0.9995 and 0.9998 and coefficients of variation between 7.44 and 8.56%. A working range between 2 ppb and 200 ppb could be fixed. In the tested batches of the P. hybridus extract Ze 339, the absence of PAs could be demonstrated. In conclusion, this assay allows to determine trace PA concentrations in P. hybridus extract Ze 339, making it suitable for analytical PA monitoring in accordance with regulatory requirements. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Techniques of biomolecular quantification through AMS detection of radiocarbon

International Nuclear Information System (INIS)

Vogel, S.J.; Turteltaub, K.W.; Frantz, C.; Felton, J.S.; Gledhill, B.L.

1992-01-01

Accelerator mass spectrometry offers a large gain over scintillation counting in sensitivity for detecting radiocarbon in biomolecular tracing. Application of this sensitivity requires new considerations of procedures to extract or isolate the carbon fraction to be quantified, to inventory all carbon in the sample, to prepare graphite from the sample for use in the spectrometer, and to derive a meaningful quantification from the measured isotope ratio. These procedures need to be accomplished without contaminating the sample with radiocarbon, which may be ubiquitous in laboratories and on equipment previously used for higher dose, scintillation experiments. Disposable equipment, materials and surfaces are used to control these contaminations. Quantification of attomole amounts of labeled substances are possible through these techniques

Imaging-based quantification of hepatic fat: methods and clinical applications.

Science.gov (United States)

Ma, Xiaozhou; Holalkere, Nagaraj-Setty; Kambadakone R, Avinash; Mino-Kenudson, Mari; Hahn, Peter F; Sahani, Dushyant V

2009-01-01

Fatty liver disease comprises a spectrum of conditions (simple hepatic steatosis, steatohepatitis with inflammatory changes, and end-stage liver disease with fibrosis and cirrhosis). Hepatic steatosis is often associated with diabetes and obesity and may be secondary to alcohol and drug use, toxins, viral infections, and metabolic diseases. Detection and quantification of liver fat have many clinical applications, and early recognition is crucial to institute appropriate management and prevent progression. Histopathologic analysis is the reference standard to detect and quantify fat in the liver, but results are vulnerable to sampling error. Moreover, it can cause morbidity and complications and cannot be repeated often enough to monitor treatment response. Imaging can be repeated regularly and allows assessment of the entire liver, thus avoiding sampling error. Selection of appropriate imaging methods demands understanding of their advantages and limitations and the suitable clinical setting. Ultrasonography is effective for detecting moderate or severe fatty infiltration but is limited by lack of interobserver reliability and intraobserver reproducibility. Computed tomography allows quantitative and qualitative evaluation and is generally highly accurate and reliable; however, the results may be confounded by hepatic parenchymal changes due to cirrhosis or depositional diseases. Magnetic resonance (MR) imaging with appropriate sequences (eg, chemical shift techniques) has similarly high sensitivity, and MR spectroscopy provides unique advantages for some applications. However, both are expensive and too complex to be used to monitor steatosis. (c) RSNA, 2009.

Uncertainty Quantification of Fork Detector Measurements from Spent Fuel Loading Campaigns

International Nuclear Information System (INIS)

Vaccaro, S.; De Baere, P.; Schwalbach, P.; Gauld, I.; Hu, J.

2015-01-01

With increasing activities at the end of the fuel cycle, the requirements for the verification of spent nuclear fuel for safeguards purposes are continuously growing. In the European Union we are experiencing a dramatic increase in the number of cask loadings for interim dry storage. This is caused by the progressive shut-down of reactors, related to facility ageing but also due to politically motivated phase-out of nuclear power. On the other hand there are advanced plans for the construction of encapsulation plants and geological repositories. The cask loading or the encapsulation process will provide the last occasion to verify the spent fuel assemblies. In this context, Euratom and the US DOE have carried out a critical review of the widely used Fork measurements method of irradiated assemblies. The Nuclear Safeguards directorates of the European Commission's Directorate General for Energy and Oak Ridge National Laboratory have collaborated to improve the Fork data evaluation process and simplify its use for inspection applications. Within the Commission's standard data evaluation package CRISP, we included a SCALE/ORIGEN-based irradiation and depletion simulation of the measured assembly and modelled the fork transfer function to calculate expected count rates based on operator's declarations. The complete acquisition and evaluation process has been automated to compare expected (calculated) with measured count rates. This approach allows a physics-based improvement of the data review and evaluation process. At the same time the new method provides the means for better measurement uncertainty quantification. The present paper will address the implications of the combined approach involving measured and simulated data to the quantification of measurement uncertainty and the consequences of these uncertainties in the possible use of the Fork detector as a partial defect detection method. (author)

Pore network quantification of sandstones under experimental CO2 injection using image analysis

Science.gov (United States)

Berrezueta, Edgar; González-Menéndez, Luís; Ordóñez-Casado, Berta; Olaya, Peter

2015-04-01

Automated-image identification and quantification of minerals, pores and textures together with petrographic analysis can be applied to improve pore system characterization in sedimentary rocks. Our case study is focused on the application of these techniques to study the evolution of rock pore network subjected to super critical CO2-injection. We have proposed a Digital Image Analysis (DIA) protocol that guarantees measurement reproducibility and reliability. This can be summarized in the following stages: (i) detailed description of mineralogy and texture (before and after CO2-injection) by optical and scanning electron microscopy (SEM) techniques using thin sections; (ii) adjustment and calibration of DIA tools; (iii) data acquisition protocol based on image capture with different polarization conditions (synchronized movement of polarizers); (iv) study and quantification by DIA that allow (a) identification and isolation of pixels that belong to the same category: minerals vs. pores in each sample and (b) measurement of changes in pore network, after the samples have been exposed to new conditions (in our case: SC-CO2-injection). Finally, interpretation of the petrography and the measured data by an automated approach were done. In our applied study, the DIA results highlight the changes observed by SEM and microscopic techniques, which consisted in a porosity increase when CO2 treatment occurs. Other additional changes were minor: variations in the roughness and roundness of pore edges, and pore aspect ratio, shown in the bigger pore population. Additionally, statistic tests of pore parameters measured were applied to verify that the differences observed between samples before and after CO2-injection were significant.

A non-invasive modality: the US virtual touch tissue quantification (VTTQ) for evaluation of breast cancer.

Science.gov (United States)

Tamaki, Kentaro; Tamaki, Nobumitsu; Kamada, Yoshihiko; Uehara, Kano; Miyashita, Minoru; Ishida, Takanori; Sasano, Hironobu

2013-09-01

We evaluated the biologic features of breast tissues using a newly developed non-invasive diagnostic system, named virtual touch tissue quantification. A total of 180 patients including 115 invasive ductal carcinoma, 30 ductal carcinoma in situ, 4 mucinous carcinoma, 7 invasive lobular carcinoma, 8 fibroadenoma, 12 fibrocystic change and 4 intraductal papilloma were studied at Nahanishi Clinic, Okinawa. We first compared the results of virtual touch tissue quantification according to each histologic subtype and determined the optimal cutoff values for virtual touch tissue quantification to distinguish benign from malignant tissues, using the receiver operating characteristic method. In addition, we also examined the correlation between virtual touch tissue quantification velocities and Ki-67, estrogen receptor, progesterone receptor or human epidermal growth factor receptor 2 in cases of invasive ductal carcinoma using linear regression analyses and Student's t-test. Virtual touch tissue quantification velocities were statistically higher in malignant cases than in benign cases (P breast cancer pathology in a non-invasive fashion.

Survey of seismic fragilities used in PRA studies of nuclear power plants

International Nuclear Information System (INIS)

Park, Y.J.; Hofmayer, C.H.; Chokshi, N.C.

1998-01-01

In recent years, seismic PRA studies have been performed on a large number of nuclear power plants in the USA. This paper presents a summary of a survey on fragility databases and the range of evaluated fragility values of various equipment categories based on past PRAs. The survey includes the use of experience data, the interpretations of available test data, and the quantification of uncertainties. The surveyed fragility databases are limited to data available in the public domain such as NUREG reports, conference proceedings and other publicly available reports. The extent of the availability of data as well as limitations are studied and tabulated for various equipment categories. The survey of the fragility values in past PRA studies includes not only the best estimate values, but also the dominant failure modes and the estimated uncertainty levels for each equipment category. The engineering judgments employed in estimating the uncertainty in the fragility values are also studied. This paper provides a perspective on the seismic fragility evaluation procedures for equipment in order to clearly identify the engineering analysis and judgment used in past seismic PRA studies

RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods

KAUST Repository

Germain, Pierre-Luc

2016-06-20

RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet no consensus exists as to the most appropriate pipeline for its analysis, with current benchmarks suffering important limitations. Here, we address these challenges through a rich benchmarking resource harnessing (i) two RNAseq datasets including ERCC ExFold spike-ins; (ii) Nanostring measurements of a panel of 150 genes on the same samples; (iii) a set of internal, genetically-determined controls; (iv) a reanalysis of the SEQC dataset; and (v) a focus on relative quantification (i.e. across-samples). We use this resource to compare different approaches to each step of RNAseq analysis, from alignment to differential expression testing. We show that methods providing the best absolute quantification do not necessarily provide good relative quantification across samples, that count-based methods are superior for gene-level relative quantification, and that the new generation of pseudo-alignment-based software performs as well as established methods, at a fraction of the computing time. We also assess the impact of library type and size on quantification and differential expression analysis. Finally, we have created a R package and a web platform to enable the simple and streamlined application of this resource to the benchmarking of future methods.

RNAontheBENCH: computational and empirical resources for benchmarking RNAseq quantification and differential expression methods

KAUST Repository

Germain, Pierre-Luc; Vitriolo, Alessandro; Adamo, Antonio; Laise, Pasquale; Das, Vivek; Testa, Giuseppe

2016-01-01

RNA sequencing (RNAseq) has become the method of choice for transcriptome analysis, yet no consensus exists as to the most appropriate pipeline for its analysis, with current benchmarks suffering important limitations. Here, we address these challenges through a rich benchmarking resource harnessing (i) two RNAseq datasets including ERCC ExFold spike-ins; (ii) Nanostring measurements of a panel of 150 genes on the same samples; (iii) a set of internal, genetically-determined controls; (iv) a reanalysis of the SEQC dataset; and (v) a focus on relative quantification (i.e. across-samples). We use this resource to compare different approaches to each step of RNAseq analysis, from alignment to differential expression testing. We show that methods providing the best absolute quantification do not necessarily provide good relative quantification across samples, that count-based methods are superior for gene-level relative quantification, and that the new generation of pseudo-alignment-based software performs as well as established methods, at a fraction of the computing time. We also assess the impact of library type and size on quantification and differential expression analysis. Finally, we have created a R package and a web platform to enable the simple and streamlined application of this resource to the benchmarking of future methods.

[Real-time quantification to analyze historical Colombian samples detecting a short fragment of hypervariable region II of mitochondrial DNA].

Science.gov (United States)

Pérez, Luz Adriana; Rodríguez, Freddy; Langebaek, Carl Henrik; Groot, Helena

2016-09-01

Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples. Materials and methods: The proposed method is based on the use of mini-primers for the specific amplification of short fragments of mitochondrial DNA. The subsequent purification of these amplified fragments allows a standard curve to be constructed with concentrations in accordance to the state of degradation of the samples. Results: The proposed method successfully detected DNA from ancient samples including bone remains and mummified tissue. DNA inhibitory substances were also detected. Conclusion: The proposed method represents a simpler and cost-effective way to detect low amounts of aDNA, and a tool to differentiate DNA-free samples from samples with inhibitory substances.

Identification and quantification of genipin and geniposide from Genipa americana L. by HPLC-DAD using a fused-core column

Directory of Open Access Journals (Sweden)

Grazielle NÁTHIA-NEVES

2018-01-01

Full Text Available Abstract In this work, it was developed a fast, simple and selective method for quantification of genipin and geniposide from unripe fruits of genipap, which are known as natural colorants, blue and yellow, respectively. The compounds separation was performed in a fused-core C18 column using as mobile phase water (A and acetonitrile (B both acidified with 0.1% formic acid, with the following gradient: 0 min, 99% A; 9 min, 75% A; 10 min, 99% A and 13 min, 99% A. The temperature and flow rate that allowed the best chromatographic performance were 35 °C and 1.5 mL/min, respectively, resulting a total run time of 13 min, including column clean-up and re-equilibration. This short analysis time represents an advantage compared to the methods reported in the literature where the running times are 2-5 times greater. The detection wavelength was set at 240 nm. The method validation was performed based on specificity, linearity, detection and quantification limits, precision and accuracy, according to ICH methodology. Finally, the developed method was suitable for monitoring analysis of those compounds content in vegetable samples.

Estimation of the quantification uncertainty from flow injection and liquid chromatography transient signals in inductively coupled plasma mass spectrometry

International Nuclear Information System (INIS)

Laborda, Francisco; Medrano, Jesus; Castillo, Juan R.

2004-01-01

The quality of the quantitative results obtained from transient signals in high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICPMS) and flow injection-inductively coupled plasma mass spectrometry (FI-ICPMS) was investigated under multielement conditions. Quantification methods were based on multiple-point calibration by simple and weighted linear regression, and double-point calibration (measurement of the baseline and one standard). An uncertainty model, which includes the main sources of uncertainty from FI-ICPMS and HPLC-ICPMS (signal measurement, sample flow rate and injection volume), was developed to estimate peak area uncertainties and statistical weights used in weighted linear regression. The behaviour of the ICPMS instrument was characterized in order to be considered in the model, concluding that the instrument works as a concentration detector when it is used to monitorize transient signals from flow injection or chromatographic separations. Proper quantification by the three calibration methods was achieved when compared to reference materials, although the double-point calibration allowed to obtain results of the same quality as the multiple-point calibration, shortening the calibration time. Relative expanded uncertainties ranged from 10-20% for concentrations around the LOQ to 5% for concentrations higher than 100 times the LOQ

A multicenter study benchmarks software tools for label-free proteome quantification.

Science.gov (United States)

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I; Aebersold, Ruedi; Tenzer, Stefan

2016-11-01

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

Predicting survey responses: how and why semantics shape survey statistics on organizational behaviour.

Directory of Open Access Journals (Sweden)

Jan Ketil Arnulf

Full Text Available Some disciplines in the social sciences rely heavily on collecting survey responses to detect empirical relationships among variables. We explored whether these relationships were a priori predictable from the semantic properties of the survey items, using language processing algorithms which are now available as new research methods. Language processing algorithms were used to calculate the semantic similarity among all items in state-of-the-art surveys from Organisational Behaviour research. These surveys covered areas such as transformational leadership, work motivation and work outcomes. This information was used to explain and predict the response patterns from real subjects. Semantic algorithms explained 60-86% of the variance in the response patterns and allowed remarkably precise prediction of survey responses from humans, except in a personality test. Even the relationships between independent and their purported dependent variables were accurately predicted. This raises concern about the empirical nature of data collected through some surveys if results are already given a priori through the way subjects are being asked. Survey response patterns seem heavily determined by semantics. Language algorithms may suggest these prior to administering a survey. This study suggests that semantic algorithms are becoming new tools for the social sciences, opening perspectives on survey responses that prevalent psychometric theory cannot explain.

Volumetric adsorptive microsampling-liquid chromatography tandem mass spectrometry assay for the simultaneous quantification of four antibiotics in human blood: Method development, validation and comparison with dried blood spot.

Science.gov (United States)

Barco, Sebastiano; Castagnola, Elio; Moscatelli, Andrea; Rudge, James; Tripodi, Gino; Cangemi, Giuliana

2017-10-25

In this paper we show the development and validation of a volumetric absorptive microsampling (VAMS™)-LC-MS/MS method for the simultaneous quantification of four antibiotics: piperacillin-tazobactam, meropenem, linezolid and ceftazidime in 10μL human blood. The novel VAMS-LC-MS/MS method has been compared with a dried blood spot (DBS)-based method in terms of impact of hematocrit (HCT) on accuracy, reproducibility, recovery and matrix effect. Antibiotics were extracted from VAMS and DBS by protein precipitation with methanol after a re-hydration step at 37°C for 10min. LC-MS/MS was carried out on a Thermo Scientific™ TSQ Quantum™ Access MAX triple quadrupole coupled to an Accela ™UHPLC system. The VAMS-LC-MS/MS method is selective, precise and reproducible. In contrast to DBS, it allows an accurate quantification without any HCT influence. It has been applied to samples derived from pediatric patients under therapy. VAMS is a valid alternative sampling strategy for the quantification of antibiotics and is valuable in support of clinical PK/PD studies and consequently therapeutic drug monitoring (TDM) in pediatrics. Copyright © 2017 Elsevier B.V. All rights reserved.

Pore REconstruction and Segmentation (PORES) method for improved porosity quantification of nanoporous materials

Energy Technology Data Exchange (ETDEWEB)

Van Eyndhoven, G., E-mail: geert.vaneyndhoven@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Kurttepeli, M. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Van Oers, C.J.; Cool, P. [Laboratory of Adsorption and Catalysis, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Bals, S. [EMAT, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp (Belgium); Batenburg, K.J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde and Informatica, Science Park 123, NL-1090 GB Amsterdam (Netherlands); Mathematical Institute, Universiteit Leiden, Niels Bohrweg 1, NL-2333 CA Leiden (Netherlands); Sijbers, J. [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium)

2015-01-15

Electron tomography is currently a versatile tool to investigate the connection between the structure and properties of nanomaterials. However, a quantitative interpretation of electron tomography results is still far from straightforward. Especially accurate quantification of pore-space is hampered by artifacts introduced in all steps of the processing chain, i.e., acquisition, reconstruction, segmentation and quantification. Furthermore, most common approaches require subjective manual user input. In this paper, the PORES algorithm “POre REconstruction and Segmentation” is introduced; it is a tailor-made, integral approach, for the reconstruction, segmentation, and quantification of porous nanomaterials. The PORES processing chain starts by calculating a reconstruction with a nanoporous-specific reconstruction algorithm: the Simultaneous Update of Pore Pixels by iterative REconstruction and Simple Segmentation algorithm (SUPPRESS). It classifies the interior region to the pores during reconstruction, while reconstructing the remaining region by reducing the error with respect to the acquired electron microscopy data. The SUPPRESS reconstruction can be directly plugged into the remaining processing chain of the PORES algorithm, resulting in accurate individual pore quantification and full sample pore statistics. The proposed approach was extensively validated on both simulated and experimental data, indicating its ability to generate accurate statistics of nanoporous materials. - Highlights: • An electron tomography reconstruction/segmentation method for nanoporous materials. • The method exploits the porous nature of the scanned material. • Validated extensively on both simulation and real data experiments. • Results in increased image resolution and improved porosity quantification.

Improved quantification of farnesene during microbial production from Saccharomyces cerevisiae in two-liquid-phase fermentations

DEFF Research Database (Denmark)

Tippmann, Stefan; Nielsen, Jens; Khoomrung, Sakda

2016-01-01

Organic solvents are widely used in microbial fermentations to reduce gas stripping effects and capture hydrophobic or toxic compounds. Reliable quantification of biochemical products in these overlays is highly challenging and practically difficult. Here, we present a significant improvement...... carryover could be minimized. Direct quantification of farnesene in dodecane was achieved by GC-FID whereas GC-MS demonstrated to be an excellent technique for identification of known and unknown metabolites. The GC-FID is a suitable technique for direct quantification of farnesene in complex matrices...

Prospective comparison of liver stiffness measurements between two point wave elastography methods: Virtual ouch quantification and elastography point quantification

Energy Technology Data Exchange (ETDEWEB)

Yoo, Hyun Suk; Lee, Jeong Min; Yoon, Jeong Hee; Lee, Dong Ho; Chang, Won; Han, Joon Koo [Seoul National University Hospital, Seoul (Korea, Republic of)

2016-09-15

To prospectively compare technical success rate and reliable measurements of virtual touch quantification (VTQ) elastography and elastography point quantification (ElastPQ), and to correlate liver stiffness (LS) measurements obtained by the two elastography techniques. Our study included 85 patients, 80 of whom were previously diagnosed with chronic liver disease. The technical success rate and reliable measurements of the two kinds of point shear wave elastography (pSWE) techniques were compared by χ{sup 2} analysis. LS values measured using the two techniques were compared and correlated via Wilcoxon signed-rank test, Spearman correlation coefficient, and 95% Bland-Altman limit of agreement. The intraobserver reproducibility of ElastPQ was determined by 95% Bland-Altman limit of agreement and intraclass correlation coefficient (ICC). The two pSWE techniques showed similar technical success rate (98.8% for VTQ vs. 95.3% for ElastPQ, p = 0.823) and reliable LS measurements (95.3% for VTQ vs. 90.6% for ElastPQ, p = 0.509). The mean LS measurements obtained by VTQ (1.71 ± 0.47 m/s) and ElastPQ (1.66 ± 0.41 m/s) were not significantly different (p = 0.209). The LS measurements obtained by the two techniques showed strong correlation (r = 0.820); in addition, the 95% limit of agreement of the two methods was 27.5% of the mean. Finally, the ICC of repeat ElastPQ measurements was 0.991. Virtual touch quantification and ElastPQ showed similar technical success rate and reliable measurements, with strongly correlated LS measurements. However, the two methods are not interchangeable due to the large limit of agreement.

A single-beam titration method for the quantification of open-path Fourier transform infrared spectroscopy

International Nuclear Information System (INIS)

Sung, Lung-Yu; Lu, Chia-Jung

2014-01-01

This study introduced a quantitative method that can be used to measure the concentration of analytes directly from a single-beam spectrum of open-path Fourier Transform Infrared Spectroscopy (OP-FTIR). The peak shapes of the analytes in a single-beam spectrum were gradually canceled (i.e., “titrated”) by dividing an aliquot of a standard transmittance spectrum with a known concentration, and the sum of the squared differential synthetic spectrum was calculated as an indicator for the end point of this titration. The quantity of a standard transmittance spectrum that is needed to reach the end point can be used to calculate the concentrations of the analytes. A NIST traceable gas standard containing six known compounds was used to compare the quantitative accuracy of both this titration method and that of a classic least square (CLS) using a closed-cell FTIR spectrum. The continuous FTIR analysis of industrial exhausting stack showed that concentration trends were consistent between the CLS and titration methods. The titration method allowed the quantification to be performed without the need of a clean single-beam background spectrum, which was beneficial for the field measurement of OP-FTIR. Persistent constituents of the atmosphere, such as NH 3 , CH 4 and CO, were successfully quantified using the single-beam titration method with OP-FTIR data that is normally inaccurate when using the CLS method due to the lack of a suitable background spectrum. Also, the synthetic spectrum at the titration end point contained virtually no peaks of analytes, but it did contain the remaining information needed to provide an alternative means of obtaining an ideal single-beam background for OP-FTIR. - Highlights: • Establish single beam titration quantification method for OP-FTIR. • Define the indicator for the end-point of spectrum titration. • An ideal background spectrum can be obtained using single beam titration. • Compare the quantification between titration

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis.

Directory of Open Access Journals (Sweden)

Wei Zhang

2015-12-01

Full Text Available High-throughput mRNA sequencing (RNA-Seq is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-Seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA, the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification. Net-RSTQ toolbox is available at http://compbio.cs.umn.edu/Net-RSTQ/.

WE-AB-204-05: Harmonizing PET/CT Quantification in Multicenter Studies: A Case Study

International Nuclear Information System (INIS)

Marques da Silva, A; Fischer, A

2015-01-01

Purpose: To present the implementation of a strategy to harmonize FDG PET/CT quantification (SUV), performed with different scanner models and manufacturers. Methods: The strategy was based on Boellaard (2011) and EARL FDG-PET/CT accreditation program, that propose quality control measurements for harmonizing scanner performance. A NEMA IEC Body phantom study was performed using four different devices: PHP-1 (Gemini TF Base, Philips); PHP-2 (Gemini GXL, Philips); GEH (Discovery 600, General Electric); SMS (Biograph Hi-Rez 16, Siemens). The SUV Recovery Coefficient (RC) was calculated using the clinical protocol and other clinically relevant reconstruction parameters. The most appropriate reconstruction parameters (MARP) for SUV harmonization, in each scanner, are those which achieve EARL harmonizing standards. They were identified using the lowest root mean square errors (RMSE). To evaluate the strategy’s effectiveness, the Maximum Differences (MD) between the clinical and MARP RC values were calculated. Results: The reconstructions parameters that obtained the lowest RMSE are: FBP 5mm (PHP-1); LOR-RAMLA 2i0.008l (PHP-2); VuePointHD 2i32s10mm (GEH); and FORE+OSEM 4i8s6mm (SMS). Thus, to ensure that quantitative PET image measurements are interchangeable between these sites, images must be reconstructed with the above-mentioned parameters. Although, a decoupling between the best image for PET/CT qualitative analysis and the best image for quantification studies was observed. The MD showed that the strategy was effective in reducing the variability of SUV quantification for small structures (<17mm). Conclusion: The harmonization strategy of the SUV quantification implemented with these devices was effective in reducing the variability of small structures quantification, minimizing the inter-scanner and inter-institution differences in quantification. However, it is essential that, in addition to the harmonization of quantification, the standardization of the

Absolute quantification by droplet digital PCR versus analog real-time PCR

Science.gov (United States)

Hindson, Christopher M; Chevillet, John R; Briggs, Hilary A; Gallichotte, Emily N; Ruf, Ingrid K; Hindson, Benjamin J; Vessella, Robert L; Tewari, Muneesh

2014-01-01

Nanoliter-sized droplet technology paired with digital PCR (ddPCR) holds promise for highly precise, absolute nucleic acid quantification. Our comparison of microRNA quantification by ddPCR and real-time PCR revealed greater precision (coefficients of variation decreased by 37–86%) and improved day-to-day reproducibility (by a factor of seven) of ddPCR but with comparable sensitivity. When we applied ddPCR to serum microRNA biomarker analysis, this translated to superior diagnostic performance for identifying individuals with cancer. PMID:23995387

Development of an indirect competitive enzyme-linked immunosorbent assay applied to the Botrytis cinerea quantification in tissues of postharvest fruits

Directory of Open Access Journals (Sweden)

Raba Julio

2011-10-01

Full Text Available Abstract Background Botrytis cinerea is a phytopathogenic fungus responsible for the disease known as gray mold, which causes substantial losses of fruits at postharvest. This fungus is present often as latent infection and an apparently healthy fruit can deteriorate suddenly due to the development of this infection. For this reason, rapid and sensitive methods are necessary for its detection and quantification. This article describes the development of an indirect competitive enzyme-linked immunosorbent assay (ELISA for quantification of B. cinerea in apple (Red Delicious, table grape (pink Moscatel, and pear (William's tissues. Results The method was based in the competition for the binding site of monoclonal antibodies between B. cinerea antigens present in fruit tissues and B. cinerea purified antigens immobilized by a crosslinking agent onto the surface of the microtiter plates. The method was validated considering parameters such as selectivity, linearity, precision, accuracy and sensibility. The calculated detection limit was 0.97 μg mL-1 B. cinerea antigens. The immobilized antigen was perfectly stable for at least 4 months assuring the reproducibility of the assay. The fungus was detected and quantified in any of the fruits tested when the rot was not visible yet. Results were compared with a DNA quantification method and these studies showed good correlation. Conclusions The developed method allowed detects the presence of B. cinerea in asymptomatic fruits and provides the advantages of low cost, easy operation, and short analysis time determination for its possible application in the phytosanitary programs of the fruit industry worldwide.

A Micropillar Compression Methodology for Ductile Damage Quantification

NARCIS (Netherlands)

Tasan, C.C.; Hoefnagels, J.P.M.; Geers, M.G.D.

2012-01-01

Microstructural damage evolution is reported to influence significantly the failures of new high-strength alloys. Its accurate quantification is, therefore, critical for (1) microstructure optimization and (2) continuum damage models to predict failures of these materials. As existing methodologies

A micropillar compression methodology for ductile damage quantification

NARCIS (Netherlands)

Tasan, C.C.; Hoefnagels, J.P.M.; Geers, M.G.D.

2012-01-01

Microstructural damage evolution is reported to influence significantly the failures of new high-strength alloys. Its accurate quantification is, therefore, critical for (1) microstructure optimization and (2) continuum damage models to predict failures of these materials. As existing methodologies

Geotechnical survey procedures for a repository mine

International Nuclear Information System (INIS)

Walther, C.

1993-01-01

The approach to the survey involves the operational realisation of an information process beginning with the definition of the survey programme and ending with the presentation of the survey results in the form of planning and assessment documents. - The survey methods must conform with the mine regulations, provide reliable predictions and produce the maximum possible salient information. The recording of large and varied amounts of data, and the complex interpretation procedures that follow require effective data and information management to allow the presentation of the results in accordance with the planning specifications. (orig.) [de

Quantification of competitive value of documents

Directory of Open Access Journals (Sweden)

Pavel Šimek

2009-01-01

Full Text Available The majority of Internet users use the global network to search for different information using fulltext search engines such as Google, Yahoo!, or Seznam. The web presentation operators are trying, with the help of different optimization techniques, to get to the top places in the results of fulltext search engines. Right there is a great importance of Search Engine Optimization and Search Engine Marketing, because normal users usually try links only on the first few pages of the fulltext search engines results on certain keywords and in catalogs they use primarily hierarchically higher placed links in each category. Key to success is the application of optimization methods which deal with the issue of keywords, structure and quality of content, domain names, individual sites and quantity and reliability of backward links. The process is demanding, long-lasting and without a guaranteed outcome. A website operator without advanced analytical tools do not identify the contribution of individual documents from which the entire web site consists. If the web presentation operators want to have an overview of their documents and web site in global, it is appropriate to quantify these positions in a specific way, depending on specific key words. For this purpose serves the quantification of competitive value of documents, which consequently sets global competitive value of a web site. Quantification of competitive values is performed on a specific full-text search engine. For each full-text search engine can be and often are, different results. According to published reports of ClickZ agency or Market Share is according to the number of searches by English-speaking users most widely used Google search engine, which has a market share of more than 80%. The whole procedure of quantification of competitive values is common, however, the initial step which is the analysis of keywords depends on a choice of the fulltext search engine.

Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis

KAUST Repository

Emwas, Abdul-Hamid M.

2016-01-08

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment.

Recommendations and Standardization of Biomarker Quantification Using NMR-based Metabolomics with Particular Focus on Urinary Analysis

KAUST Repository

Emwas, Abdul-Hamid M.; Roy, Raja; McKay, Ryan T.; Ryan, Danielle; Brennan, Lorraine; Tenori, Leonardo; Luchinat, Claudio; Gao, Xin; Zeri, Ana Carolina; Gowda, G. A. Nagana; Raftery, Daniel; Steinbeck, Christoph; Salek, Reza M; Wishart, David S.

2016-01-01

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to non-destructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Indeed, precise metabolite quantification is a necessary prerequisite to move any chemical biomarker or biomarker panel from the lab into the clinic. Among the many biofluids (urine, serum, plasma, cerebrospinal fluid and saliva) commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, easily obtained, needs little sample preparation and does not require any invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, thereby providing a rich source of potentially useful disease biomarkers. However, the incredible variation in urine chemical concentrations due to effects such as gender, age, diet, life style, health conditions, and physical activity make the analysis of urine and the identification of useful urinary biomarkers by NMR quite challenging. In this review, we discuss a number of the most significant issues regarding NMR-based urinary metabolomics with a specific emphasis on metabolite quantification for disease biomarker applications. We also propose a number of data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, as well as recommendations regarding sample preparation and biomarker assessment.

A phase quantification method based on EBSD data for a continuously cooled microalloyed steel

Energy Technology Data Exchange (ETDEWEB)

Zhao, H.; Wynne, B.P.; Palmiere, E.J., E-mail: e.j.palmiere@sheffield.ac.uk

2017-01-15

Mechanical properties of steels depend on the phase constitutions of the final microstructures which can be related to the processing parameters. Therefore, accurate quantification of different phases is necessary to investigate the relationships between processing parameters, final microstructures and mechanical properties. Point counting on micrographs observed by optical or scanning electron microscopy is widely used as a phase quantification method, and different phases are discriminated according to their morphological characteristics. However, it is difficult to differentiate some of the phase constituents with similar morphology. Differently, for EBSD based phase quantification methods, besides morphological characteristics, other parameters derived from the orientation information can also be used for discrimination. In this research, a phase quantification method based on EBSD data in the unit of grains was proposed to identify and quantify the complex phase constitutions of a microalloyed steel subjected to accelerated coolings. Characteristics of polygonal ferrite/quasi-polygonal ferrite, acicular ferrite and bainitic ferrite on grain averaged misorientation angles, aspect ratios, high angle grain boundary fractions and grain sizes were analysed and used to develop the identification criteria for each phase. Comparing the results obtained by this EBSD based method and point counting, it was found that this EBSD based method can provide accurate and reliable phase quantification results for microstructures with relatively slow cooling rates. - Highlights: •A phase quantification method based on EBSD data in the unit of grains was proposed. •The critical grain area above which GAM angles are valid parameters was obtained. •Grain size and grain boundary misorientation were used to identify acicular ferrite. •High cooling rates deteriorate the accuracy of this EBSD based method.

GC-MS quantification of suspected volatile allergens in fragrances. 2. Data treatment strategies and method performances.

Science.gov (United States)

Bassereau, Maud; Chaintreau, Alain; Duperrex, Stéphanie; Joulain, Daniel; Leijs, Hans; Loesing, Gerd; Owen, Neil; Sherlock, Alan; Schippa, Christine; Thorel, Pierre-Jean; Vey, Matthias

2007-01-10

The performances of the GC-MS determination of suspected allergens in fragrance concentrates have been investigated. The limit of quantification was experimentally determined (10 mg/L), and the variability was investigated for three different data treatment strategies: (1) two columns and three quantification ions; (2) two columns and one quantification ion; and (3) one column and three quantification ions. The first strategy best minimizes the risk of determination bias due to coelutions. This risk was evaluated by calculating the probability of coeluting a suspected allergen with perfume constituents exhibiting ions in common. For hydroxycitronellal, when using a two-column strategy, this may statistically occur more than once every 36 analyses for one ion or once every 144 analyses for three ions in common.

Within-day repeatability for absolute quantification of Lawsonia intracellularis bacteria in feces from growing pigs

DEFF Research Database (Denmark)

Pedersen, Ken Steen; Pedersen, Klaus H.; Hjulsager, Charlotte Kristiane

2012-01-01

Absolute quantification of Lawsonia intracellularis by real-time polymerase chain reaction (PCR) is now possible on a routine basis. Poor repeatability of quantification can result in disease status misclassification of individual pigs when a single fecal sample is obtained. The objective...

Multi data reservior history matching and uncertainty quantification framework

KAUST Repository

Katterbauer, Klemens; Hoteit, Ibrahim; Sun, Shuyu

2015-01-01

A multi-data reservoir history matching and uncertainty quantification framework is provided. The framework can utilize multiple data sets such as production, seismic, electromagnetic, gravimetric and surface deformation data for improving

Quantification of intraventricular hemorrhage is consistent using a spherical sensitivity matrix

Science.gov (United States)

Tang, Te; Sadleir, Rosalind

2010-04-01

We have developed a robust current pattern for detection of intraventricular hemorrhage (IVH). In this study, the current pattern was applied on two realistic shaped neonatal head models and one head-shaped phantom. We found that a sensitivity matrix calculated from a spherical model gave us satisfactory reconstructions in terms of both image quality and quantification. Incorporating correct geometry information into the forward model improved image quality. However, it did not improve quantification accuracy. The results indicate that using a spherical matrix may be a more practical choice for monitoring IVH volumes in neonates.

Recent advances in hopanoids analysis: Quantification protocols overview, main research targets and selected problems of complex data exploration.

Science.gov (United States)

Zarzycki, Paweł K; Portka, Joanna K

2015-09-01

Pentacyclic triterpenoids, particularly hopanoids, are organism-specific compounds and are generally considered as useful biomarkers that allow fingerprinting and classification of biological, environmental and geological samples. Simultaneous quantification of various hopanoids together with battery of related non-polar and low-molecular mass compounds may provide principal information for geochemical and environmental research focusing on both modern and ancient investigations. Target compounds can be derived from microbial biomass, water columns, sediments, coals, crude fossils or rocks. This create number of analytical problems due to different composition of the analytical matrix and interfering compounds and therefore, proper optimization of quantification protocols for such biomarkers is still the challenge. In this work we summarizing typical analytical protocols that were recently applied for quantification of hopanoids like compounds from different samples. Main steps including components of interest extraction, pre-purification, fractionation, derivatization and quantification involving gas (1D and 2D) as well as liquid separation techniques (liquid-liquid extraction, solid-phase extraction, planar and low resolution column chromatography, high-performance liquid chromatography) are described and discussed from practical point of view, mainly based on the experimental papers that were published within last two years, where significant increase in hopanoids research was noticed. The second aim of this review is to describe the latest research trends concerning determination of hopanoids and related low-molecular mass lipids analyzed in various samples including sediments, rocks, coals, crude oils and plant fossils as well as stromatolites and microbial biomass cultivated under different conditions. It has been found that majority of the most recent papers are based on uni- or bivariate approach for complex data analysis. Data interpretation involves

Quantification of Structural Isomers via Mode-Selective Irmpd

Science.gov (United States)

Polfer, Nicolas C.

2016-06-01

Mixtures of structural isomers can pose a challenge for vibrational ion spectroscopy. In cases where particular structures display diagnostic vibrations, these structures can be selectively "burned away". In ion traps, the ion population can be subjected to multiple laser shots, in order to fully deplete a particular structure, in effect allowing a quantification of this structure. Protonated para-amino benzoic acid (PABA) serves as an illustrative example. PABA is known to preferentially exist in the N-protonated (N-prot) form in solution, but in the gas phase it is energetically favorable in the O-protonated (O-prot) form. As shown in Figure 1, the N-prot structure can be kinetically trapped in the gas phase when sprayed from non-protic solvent, whereas the O-prot structure is obtained when sprayed from protic solvents, analogous to results by others [1,2]. y parking the light source on the diagnostic 3440 wn mode, the percentage of the O-prot structure can be determined, and by default the remainder is assumed to adopt the N-prot structure. It will be shown that the relative percentages of O-prot vs N-prot are highly dependent on the solvent mixture, going from close to 0% O-prot in non-protic solvents, to 99% in protic solvents. Surprisingly, water behaves much more like a non-protic solvent than methanol. It is observed that the capillary temperature, which aids droplet desolvation by black-body radiation in the ESI source, is critical to promote the appearance of O-prot structures. These results are consistent with the picture that a protic bridge mechanism is at play to facilitate proton transfer, and thus allow conversion from N-prot to O-prot, but that this mechanism is subject to appreciable kinetic barriers on the timescale of solvent evaporation. 1. J. Phys. Chem. A 2011, 115, 7625. 2. Anal. Chem. 2012, 84, 7857.

Rapid in Vitro Quantification of S. aureus Biofilms on Vascular Graft Surfaces

Directory of Open Access Journals (Sweden)

Monika Herten

2017-12-01

reproducibility of the ATP-assay presented as inter-assay-variance of 2.1 and as intra-assay variance of 8.1 on polystyrene.Conclusion: The in-vitro model reproducibly quantifies biofilm on standardized vascular graft surfaces with ATP assay as detection system. The ATP assay allows accelerated microbial quantification, however the correlation with the CFU assay may be strain- and surface-dependent.

Quantification of Human Fecal Bifidobacterium Species by Use of Quantitative Real-Time PCR Analysis Targeting the groEL Gene

Science.gov (United States)

Junick, Jana

2012-01-01

Quantitative real-time PCR assays targeting the groEL gene for the specific enumeration of 12 human fecal Bifidobacterium species were developed. The housekeeping gene groEL (HSP60 in eukaryotes) was used as a discriminative marker for the differentiation of Bifidobacterium adolescentis, B. angulatum, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. gallicum, B. longum, B. pseudocatenulatum, B. pseudolongum, and B. thermophilum. The bifidobacterial chromosome contains a single copy of the groEL gene, allowing the determination of the cell number by quantification of the groEL copy number. Real-time PCR assays were validated by comparing fecal samples spiked with known numbers of a given Bifidobacterium species. Independent of the Bifidobacterium species tested, the proportion of groEL copies recovered from fecal samples spiked with 5 to 9 log10 cells/g feces was approximately 50%. The quantification limit was 5 to 6 log10 groEL copies/g feces. The interassay variability was less than 10%, and variability between different DNA extractions was less than 23%. The method developed was applied to fecal samples from healthy adults and full-term breast-fed infants. Bifidobacterial diversity in both adults and infants was low, with mostly ≤3 Bifidobacterium species and B. longum frequently detected. The predominant species in infant and adult fecal samples were B. breve and B. adolescentis, respectively. It was possible to distinguish B. catenulatum and B. pseudocatenulatum. We conclude that the groEL gene is a suitable molecular marker for the specific and accurate quantification of human fecal Bifidobacterium species by real-time PCR. PMID:22307308

Data-independent MS/MS quantification of neuropeptides for determination of putative feeding-related neurohormones in microdialysate.

Science.gov (United States)

Schmerberg, Claire M; Liang, Zhidan; Li, Lingjun

2015-01-21

Food consumption is an important behavior that is regulated by an intricate array of neuropeptides (NPs). Although many feeding-related NPs have been identified in mammals, precise mechanisms are unclear and difficult to study in mammals, as current methods are not highly multiplexed and require extensive a priori knowledge about analytes. New advances in data-independent acquisition (DIA) MS/MS and the open-source quantification software Skyline have opened up the possibility to identify hundreds of compounds and quantify them from a single DIA MS/MS run. An untargeted DIA MS(E) quantification method using Skyline software for multiplexed, discovery-driven quantification was developed and found to produce linear calibration curves for peptides at physiologically relevant concentrations using a protein digest as internal standard. By using this method, preliminary relative quantification of the crab Cancer borealis neuropeptidome (winnowing candidate NPs related to a behavior of interest in a functionally relevant manner, and demonstrates the success of such a UPLC-MS(E) quantification method using the open source software Skyline.

Identification of flow paths and quantification of return flow volumes and timing at field scale

Science.gov (United States)

Claes, N.; Paige, G. B.; Parsekian, A.

2017-12-01

Flood irrigation, which constitutes a large part of agricultural water use, accounts for a significant amount of the water that is diverted from western streams. Return flow, the portion of the water applied to irrigated areas that returns to the stream, is important for maintaining base flows in streams and ecological function of riparian zones and wetlands hydrologically linked with streams. Prediction of timing and volumes of return flow during and after flood irrigation pose a challenge due to the heterogeneity of pedogenic and soil physical factors that influence vadose zone processes. In this study, we quantify volumes of return flow and potential pathways in the subsurface through a vadose zone flow model that is informed by both hydrological and geophysical observations in a Bayesian setting. We couple a two-dimensional vadose zone flow model through a Bayesian Markov Chain Monte Carlo approach with time lapse ERT, borehole NMR datasets that are collected during and after flood irrigation experiments, and soil physical lab analysis. The combination of both synthetic models and field observations leads to flow path identification and allows for quantification of volumes and timing and associated uncertainties of subsurface return that stems from flood irrigation. The quantification of the impact of soil heterogeneity enables us to translate these results to other sites and predict return flow under different soil physical settings. This is key when managing irrigation water resources and predictions of outcomes of different scenarios have to be evaluated.

Accuracy of bone mineral density quantification using dual-layer spectral detector CT: a phantom study

Energy Technology Data Exchange (ETDEWEB)

Hamersvelt, Robbert W. van; Schilham, Arnold M.R.; Harder, Annemarie M. den; Leiner, Tim; Jong, Pim A. de; Willemink, Martin J. [University Medical Centre Utrecht, Department of Radiology, P.O. Box 85500, Utrecht (Netherlands); Engelke, Klaus [University of Erlangen-Nuernberg, Institute of Medical Physics, Erlangen (Germany); Keizer, Bart de [University Medical Centre Utrecht, Department of Nuclear Medicine, Utrecht (Netherlands); Verhaar, Harald J. [University Medical Centre Utrecht, Department of Geriatric Medicine, Utrecht (Netherlands)

2017-10-15

To investigate the accuracy of bone mineral density (BMD) quantification using dual-layer spectral detector CT (SDCT) at various scan protocols. Two validated anthropomorphic phantoms containing inserts of 50-200 mg/cm{sup 3} calcium hydroxyapatite (HA) were scanned using a 64-slice SDCT scanner at various acquisition protocols (120 and 140 kVp, and 50, 100 and 200 mAs). Regions of interest (ROIs) were placed in each insert and mean attenuation profiles at monochromatic energy levels (90-200 keV) were constructed. These profiles were fitted to attenuation profiles of pure HA and water to calculate HA concentrations. For comparison, one phantom was scanned using dual energy X-ray absorptiometry (DXA). At both 120 and 140 kVp, excellent correlations (R = 0.97, P < 0.001) were found between true and measured HA concentrations. Mean error for all measurements at 120 kVp was -5.6 ± 5.7 mg/cm{sup 3} (-3.6 ± 3.2%) and at 140 kVp -2.4 ± 3.7 mg/cm{sup 3} (-0.8 ± 2.8%). Mean measurement errors were smaller than 6% for all acquisition protocols. Strong linear correlations (R{sup 2} ≥ 0.970, P < 0.001) with DXA were found. SDCT allows for accurate BMD quantification and potentially opens up the possibility for osteoporosis evaluation and opportunistic screening in patients undergoing SDCT for other clinical indications. However, patient studies are needed to extend and translate our findings. (orig.)

Compositional Solution Space Quantification for Probabilistic Software Analysis

Science.gov (United States)

Borges, Mateus; Pasareanu, Corina S.; Filieri, Antonio; d'Amorim, Marcelo; Visser, Willem

2014-01-01

Probabilistic software analysis aims at quantifying how likely a target event is to occur during program execution. Current approaches rely on symbolic execution to identify the conditions to reach the target event and try to quantify the fraction of the input domain satisfying these conditions. Precise quantification is usually limited to linear constraints, while only approximate solutions can be provided in general through statistical approaches. However, statistical approaches may fail to converge to an acceptable accuracy within a reasonable time. We present a compositional statistical approach for the efficient quantification of solution spaces for arbitrarily complex constraints over bounded floating-point domains. The approach leverages interval constraint propagation to improve the accuracy of the estimation by focusing the sampling on the regions of the input domain containing the sought solutions. Preliminary experiments show significant improvement on previous approaches both in results accuracy and analysis time.

Method for indirect quantification of CH4 production via H2O production using hydrogenotrophic methanogens

Directory of Open Access Journals (Sweden)

Ruth-Sophie eTaubner

2016-04-01

Full Text Available ydrogenotrophic methanogens are an intriguing group of microorganisms from the domain Archaea. They exhibit extraordinary ecological, biochemical, physiological characteristics colorbox{yellow}{and have a huge biotechnological potential}. Yet, the only possibility to assess the methane (CH$_4$ production potential of hydrogenotrophic methanogens is to apply gas chromatographic quantification of CH$_4$.In order to be able to effectively screen pure cultures of hydrogenotrophic methanogens regarding their CH$_4$ production potential we developed a novel method for indirect quantification of colorbox{yellow}{the} volumetric CH$_4$ production rate by measuring colorbox{yellow}{the} volumetric water production rate. This colorbox{yellow}{ } method was established in serum bottles for cultivation of methanogens in closed batch cultivation mode. Water production was colorbox{yellow}{estimated} by determining the difference in mass increase in an isobaric setting.This novel CH$_4$ quantification method is an accurate and precise analytical technique, colorbox{yellow}{which can be used} to rapidly screen pure cultures of methanogens regarding colorbox{yellow}{their} volumetric CH$_{4}$ evolution rate. colorbox{yellow}{It} is a cost effective alternative colorbox{yellow}{determining} CH$_4$ production of methanogens over CH$_4$ quantification by using gas chromatography, especially if colorbox{yellow}{ } applied as a high throughput quantification method. colorbox{yellow}{Eventually, the} method can be universally applied for quantification of CH$_4$ production from psychrophilic, thermophilic and hyperthermophilic hydrogenotrophic methanogens.

Attitude changes toward nuclear power generation. Analysis of data from a longitudinal survey

International Nuclear Information System (INIS)

Matsuda, Toshihiro

1998-01-01

The Attitude changes toward nuclear power generation in response to incidents/accidents at the nuclear facilities were examined, using a longitudinal survey. A replicated survey was conducted in Kansai area following the incidents in 1995 and 1997, and a panel survey was conducted in 1997, using the same subjects as those in the survey conducted by C. Hayashi in 1993 about the attitude toward nuclear power generation. The results of the panel survey showed that an anxiety about a nuclear incident/accident tended to increase and that the number of those who decreased an anxiety about a nuclear incident/accident was relatively small, compared to an anxiety about other incidents/accidents. Using the quantification theory to analyze the group that showed changes in attitude toward nuclear power generation, it was suggested that the increase or decrease in the level of anxiety about a nuclear power incident/accident had an influence on the changes in attitude. However, the influence was not the most significant one compared to other factors. With the inclusion of the group that showed no change in attitude, the general population structure that the approval for nuclear power generation because of inevitable use of nuclear energy accounted for sixty percent remained with no significant change. (author)

A data fusion approach for progressive damage quantification in reinforced concrete masonry walls

International Nuclear Information System (INIS)

Vanniamparambil, Prashanth Abraham; Carmi, Rami; Kontsos, Antonios; Bolhassani, Mohammad; Khan, Fuad; Bartoli, Ivan; Moon, Franklin L; Hamid, Ahmad

2014-01-01

This paper presents a data fusion approach based on digital image correlation (DIC) and acoustic emission (AE) to detect, monitor and quantify progressive damage development in reinforced concrete masonry walls (CMW) with varying types of reinforcements. CMW were tested to evaluate their structural behavior under cyclic loading. The combination of DIC with AE provided a framework for the cross-correlation of full field strain maps on the surface of CMW with volume-inspecting acoustic activity. AE allowed in situ monitoring of damage progression which was correlated with the DIC through quantification of strain concentrations and by tracking crack evolution, visually verified. The presented results further demonstrate the relationships between the onset and development of cracking with changes in energy dissipation at each loading cycle, measured principal strains and computed AE energy, providing a promising paradigm for structural health monitoring applications on full-scale concrete masonry buildings. (paper)

Quantification of Sediment Transport During Glacier Surges and its Impact on Landform Architecture

DEFF Research Database (Denmark)

Kjær, Kurt H.; Schomacker, Anders; Korsgaard, Niels Jákup

) for 1945, prior to the last surge in 1964, and for 2003 in order to assess the effect of the surge on the sediment architecture in the forefield. The pre- and post-surge DEMs allow direct quantification of the sediment volumes that were re-distributed in the forefield by the surging ice mass in 1964...... or glaciofluvial outwash fans. Mapping of the sediment thickness in the glacier forefield shows higher accumulation along ice marginal positions related to wedge formation during extremely rapid ice flow. Fast flow was sustained by overpressurized water causing sediment-bedrock decoupling beneath a thick sediment...... architecture occurs distal to the 1810 ice margin, where the 1890 surge advanced over hitherto undeformed sediments. Proximal to the 1810 ice margin, the landscape have been transgressed by either one or two glaciers (in 1890 and 1964). The most complex landscape architecture is found proximal to the 1964 ice...

Outcome quantification using SPHARM-PDM toolbox in orthognathic surgery

Science.gov (United States)

Cevidanes, Lucia; Zhu, HongTu; Styner, Martin

2011-01-01

Purpose Quantification of surgical outcomes in longitudinal studies has led to significant progress in the treatment of dentofacial deformity, both by offering options to patients who might not otherwise have been recommended for treatment and by clarifying the selection of appropriate treatment methods. Most existing surgical treatments have not been assessed in a systematic way. This paper presents the quantification of surgical outcomes in orthognathic surgery via our localized shape analysis framework. Methods In our setting, planning and surgical simulation is performed using the surgery planning software CMFapp. We then employ the SPHARM-PDM to measure the difference between pre-surgery and virtually simulated post-surgery models. This SPHARM-PDM shape framework is validated for use with craniofacial structures via simulating known 3D surgical changes within CMFapp. Results Our results show that SPHARM-PDM analysis accurately measures surgical displacements, compared with known displacement values. Visualization of color maps of virtually simulated surgical displacements describe corresponding surface distances that precisely describe location of changes, and difference vectors indicate directionality and magnitude of changes. Conclusions SPHARM-PDM-based quantification of surgical outcome is feasible. When compared to prior solutions, our method has the potential to make the surgical planning process more flexible, increase the level of detail and accuracy of the plan, yield higher operative precision and control and enhance the follow-up and documentation of clinical cases. PMID:21161693

Impact of muscular uptake and statistical noise on tumor quantification based on simulated FDG-PET studies

International Nuclear Information System (INIS)

Silva-Rodríguez, Jesús; Domínguez-Prado, Inés; Pardo-Montero, Juan; Ruibal, Álvaro

2017-01-01

Purpose: The aim of this work is to study the effect of physiological muscular uptake variations and statistical noise on tumor quantification in FDG-PET studies. Methods: We designed a realistic framework based on simulated FDG-PET acquisitions from an anthropomorphic phantom that included different muscular uptake levels and three spherical lung lesions with diameters of 31, 21 and 9 mm. A distribution of muscular uptake levels was obtained from 136 patients remitted to our center for whole-body FDG-PET. Simulated FDG-PET acquisitions were obtained by using the Simulation System for Emission Tomography package (SimSET) Monte Carlo package. Simulated data was reconstructed by using an iterative Ordered Subset Expectation Maximization (OSEM) algorithm implemented in the Software for Tomographic Image Reconstruction (STIR) library. Tumor quantification was carried out by using estimations of SUV max , SUV 50 and SUV mean from different noise realizations, lung lesions and multiple muscular uptakes. Results: Our analysis provided quantification variability values of 17–22% (SUV max ), 11–19% (SUV 50 ) and 8–10% (SUV mean ) when muscular uptake variations and statistical noise were included. Meanwhile, quantification variability due only to statistical noise was 7–8% (SUV max ), 3–7% (SUV 50 ) and 1–2% (SUV mean ) for large tumors (>20 mm) and 13% (SUV max ), 16% (SUV 50 ) and 8% (SUV mean ) for small tumors (<10 mm), thus showing that the variability in tumor quantification is mainly affected by muscular uptake variations when large enough tumors are considered. In addition, our results showed that quantification variability is strongly dominated by statistical noise when the injected dose decreases below 222 MBq. Conclusions: Our study revealed that muscular uptake variations between patients who are totally relaxed should be considered as an uncertainty source of tumor quantification values. - Highlights: • Distribution of muscular uptake from 136 PET

an expansion of the aboveground biomass quantification model for ...

African Journals Online (AJOL)

Research Note BECVOL 3: an expansion of the aboveground biomass quantification model for ... African Journal of Range and Forage Science ... encroachment and estimation of food to browser herbivore species, was proposed during 1989.

Cytochrome c oxidase subunit 1-based human RNA quantification to enhance mRNA profiling in forensic biology

Directory of Open Access Journals (Sweden)

Dong Zhao

2017-01-01

Full Text Available RNA analysis offers many potential applications in forensic science, and molecular identification of body fluids by analysis of cell-specific RNA markers represents a new technique for use in forensic cases. However, due to the nature of forensic materials that often admixed with nonhuman cellular components, human-specific RNA quantification is required for the forensic RNA assays. Quantification assay for human RNA has been developed in the present study with respect to body fluid samples in forensic biology. The quantitative assay is based on real-time reverse transcription-polymerase chain reaction of mitochondrial RNA cytochrome c oxidase subunit I and capable of RNA quantification with high reproducibility and a wide dynamic range. The human RNA quantification improves the quality of mRNA profiling in the identification of body fluids of saliva and semen because the quantification assay can exclude the influence of nonhuman components and reduce the adverse affection from degraded RNA fragments.

Image analysis for the detection and quantification of concrete bugholes in a tunnel lining

Directory of Open Access Journals (Sweden)

Isamu Yoshitake

2018-06-01

Full Text Available A measurement and quantification system for concrete bugholes (surface air voids on sidewalls was developed to quantify the surface quality of tunnel-lining concrete. The developed system uses and evaluates red/green/blue values of color images taken by a commercial digital still camera. A comparative test shows that the developed system has higher accuracy than image analyses using thresholding and can estimate bugholes with accuracy almost equal to that of a detailed visual inspection. The results confirm that even small bugholes (<1 mm can be detected in color image analysis, whereas such bugholes are hardly detected in the detailed visual survey. In addition, color image analysis improves the calculations of the area of multiple bugholes distributed randomly over a concrete surface. Fundamental tests employing image analysis demonstrate that the prevalence of bugholes increases with an increase in the negative angle of the concrete form and a decrease in concrete workability. The system is applicable to the quantitative evaluation of a concrete surface having visible and invisible bugholes. Results indicate that the developed color image analysis can contribute to the reasonable and appropriate evaluation of bugholes and replace a detailed survey that requires much human resource and has a long inspection time. Keywords: Bughole, Image analysis, Surface quality, Tunnel lining concrete, Laboratory test, Inspection

Uncertainty quantification and sensitivity analysis with CASL Core Simulator VERA-CS

International Nuclear Information System (INIS)

Brown, C.S.; Zhang, Hongbin

2016-01-01

VERA-CS (Virtual Environment for Reactor Applications, Core Simulator) is a coupled neutron transport and thermal-hydraulics code under development by the Consortium for Advanced Simulation of Light Water Reactors (CASL). An approach to uncertainty quantification and sensitivity analysis with VERA-CS was developed and a new toolkit was created to perform uncertainty quantification and sensitivity analysis. A 2 × 2 fuel assembly model was developed and simulated by VERA-CS, and uncertainty quantification and sensitivity analysis were performed with fourteen uncertain input parameters. The minimum departure from nucleate boiling ratio (MDNBR), maximum fuel center-line temperature, and maximum outer clad surface temperature were chosen as the selected figures of merit. Pearson, Spearman, and partial correlation coefficients were considered for all of the figures of merit in sensitivity analysis and coolant inlet temperature was consistently the most influential parameter. Parameters used as inputs to the critical heat flux calculation with the W-3 correlation were shown to be the most influential on the MDNBR, maximum fuel center-line temperature, and maximum outer clad surface temperature.

Ochratoxin A in raisins and currants: basic extraction procedure used in two small marketing surveys of the occurrence and control of the heterogeneity of the toxins in samples.

Science.gov (United States)

Möller, T E; Nyberg, M

2003-11-01

A basic extraction procedure for analysis of ochratoxin A (OTA) in currants and raisins is described, as well as the occurrence of OTA and a control of heterogeneity of the toxin in samples bought for two small marketing surveys 1999/2000 and 2001/02. Most samples in the surveys were divided into two subsamples that were individually prepared as slurries and analysed separately. The limit of quantification for the method was estimated as 0.1 microg kg(-1) and recoveries of 85, 90 and 115% were achieved in recovery experiments at 10, 5 and 0.1 microg kg(-1), respectively. Of all 118 subsamples analysed in the surveys, 96 (84%) contained ochratoxin A at levels above the quantification level and five samples (4%) contained more than the European Community legislation of 10 microg kg(-1). The OTA concentrations found in the first survey were in the range Big differences were often achieved between individual subsamples of the original sample, which indicate a wide heterogeneous distribution of the toxin. Data from the repeatability test as well as recovery experiments from the same slurries showed that preparation of slurries as described here seemed to give a homogeneous and representative sample. The extraction with the basic sodium bicarbonate-methanol mixture used in the surveys gave similar or somewhat higher OTA values on some samples tested in a comparison with a weak phosphoric acid water-methanol extraction mixture.

A nuclear DNA-based species determination and DNA quantification assay for common poultry species.

Science.gov (United States)

Ng, J; Satkoski, J; Premasuthan, A; Kanthaswamy, S

2014-12-01

DNA testing for food authentication and quality control requires sensitive species-specific quantification of nuclear DNA from complex and unknown biological sources. We have developed a multiplex assay based on TaqMan® real-time quantitative PCR (qPCR) for species-specific detection and quantification of chicken (Gallus gallus), duck (Anas platyrhynchos), and turkey (Meleagris gallopavo) nuclear DNA. The multiplex assay is able to accurately detect very low quantities of species-specific DNA from single or multispecies sample mixtures; its minimum effective quantification range is 5 to 50 pg of starting DNA material. In addition to its use in food fraudulence cases, we have validated the assay using simulated forensic sample conditions to demonstrate its utility in forensic investigations. Despite treatment with potent inhibitors such as hematin and humic acid, and degradation of template DNA by DNase, the assay was still able to robustly detect and quantify DNA from each of the three poultry species in mixed samples. The efficient species determination and accurate DNA quantification will help reduce fraudulent food labeling and facilitate downstream DNA analysis for genetic identification and traceability.

FIM imaging and FIMtrack: two new tools allowing high-throughput and cost effective locomotion analysis.

Science.gov (United States)

Risse, Benjamin; Otto, Nils; Berh, Dimitri; Jiang, Xiaoyi; Klämbt, Christian

2014-12-24

The analysis of neuronal network function requires a reliable measurement of behavioral traits. Since the behavior of freely moving animals is variable to a certain degree, many animals have to be analyzed, to obtain statistically significant data. This in turn requires a computer assisted automated quantification of locomotion patterns. To obtain high contrast images of almost translucent and small moving objects, a novel imaging technique based on frustrated total internal reflection called FIM was developed. In this setup, animals are only illuminated with infrared light at the very specific position of contact with the underlying crawling surface. This methodology results in very high contrast images. Subsequently, these high contrast images are processed using established contour tracking algorithms. Based on this, we developed the FIMTrack software, which serves to extract a number of features needed to quantitatively describe a large variety of locomotion characteristics. During the development of this software package, we focused our efforts on an open source architecture allowing the easy addition of further modules. The program operates platform independent and is accompanied by an intuitive GUI guiding the user through data analysis. All locomotion parameter values are given in form of csv files allowing further data analyses. In addition, a Results Viewer integrated into the tracking software provides the opportunity to interactively review and adjust the output, as might be needed during stimulus integration. The power of FIM and FIMTrack is demonstrated by studying the locomotion of Drosophila larvae.

UV-Vis as quantification tool for solubilized lignin following a single-shot steam process.

Science.gov (United States)

Lee, Roland A; Bédard, Charles; Berberi, Véronique; Beauchet, Romain; Lavoie, Jean-Michel

2013-09-01

In this short communication, UV/Vis was used as an analytical tool for the quantification of lignin concentrations in aqueous mediums. A significant correlation was determined between absorbance and concentration of lignin in solution. For this study, lignin was produced from different types of biomasses (willow, aspen, softwood, canary grass and hemp) using steam processes. Quantification was performed at 212, 225, 237, 270, 280 and 287 nm. UV-Vis quantification of lignin was found suitable for different types of biomass making this a timesaving analytical system that could lead to uses as Process Analytical Tool (PAT) in biorefineries utilizing steam processes or comparable approaches. Copyright © 2013 Elsevier Ltd. All rights reserved.

Near-Earth Object Survey Simulation Software

Science.gov (United States)

Naidu, Shantanu P.; Chesley, Steven R.; Farnocchia, Davide

2017-10-01

There is a significant interest in Near-Earth objects (NEOs) because they pose an impact threat to Earth, offer valuable scientific information, and are potential targets for robotic and human exploration. The number of NEO discoveries has been rising rapidly over the last two decades with over 1800 being discovered last year, making the total number of known NEOs >16000. Pan-STARRS and the Catalina Sky Survey are currently the most prolific NEO surveys, having discovered >1600 NEOs between them in 2016. As next generation surveys such as Large Synoptic Survey Telescope (LSST) and the proposed Near-Earth Object Camera (NEOCam) become operational in the next decade, the discovery rate is expected to increase tremendously. Coordination between various survey telescopes will be necessary in order to optimize NEO discoveries and create a unified global NEO discovery network. We are collaborating on a community-based, open-source software project to simulate asteroid surveys to facilitate such coordination and develop strategies for improving discovery efficiency. Our effort so far has focused on development of a fast and efficient tool capable of accepting user-defined asteroid population models and telescope parameters such as a list of pointing angles and camera field-of-view, and generating an output list of detectable asteroids. The software takes advantage of the widely used and tested SPICE library and architecture developed by NASA’s Navigation and Ancillary Information Facility (Acton, 1996) for saving and retrieving asteroid trajectories and camera pointing. Orbit propagation is done using OpenOrb (Granvik et al. 2009) but future versions will allow the user to plug in a propagator of their choice. The software allows the simulation of both ground-based and space-based surveys. Performance is being tested using the Grav et al. (2011) asteroid population model and the LSST simulated survey “enigma_1189”.

Metering error quantification under voltage and current waveform distortion

Science.gov (United States)

Wang, Tao; Wang, Jia; Xie, Zhi; Zhang, Ran

2017-09-01

With integration of more and more renewable energies and distortion loads into power grid, the voltage and current waveform distortion results in metering error in the smart meters. Because of the negative effects on the metering accuracy and fairness, it is an important subject to study energy metering combined error. In this paper, after the comparing between metering theoretical value and real recorded value under different meter modes for linear and nonlinear loads, a quantification method of metering mode error is proposed under waveform distortion. Based on the metering and time-division multiplier principles, a quantification method of metering accuracy error is proposed also. Analyzing the mode error and accuracy error, a comprehensive error analysis method is presented which is suitable for new energy and nonlinear loads. The proposed method has been proved by simulation.

Quantification of Na+,K+ pumps and their transport rate in skeletal muscle: Functional significance

Science.gov (United States)

2013-01-01

During excitation, muscle cells gain Na+ and lose K+, leading to a rise in extracellular K+ ([K+]o), depolarization, and loss of excitability. Recent studies support the idea that these events are important causes of muscle fatigue and that full use of the Na+,K+-ATPase (also known as the Na+,K+ pump) is often essential for adequate clearance of extracellular K+. As a result of their electrogenic action, Na+,K+ pumps also help reverse depolarization arising during excitation, hyperkalemia, and anoxia, or from cell damage resulting from exercise, rhabdomyolysis, or muscle diseases. The ability to evaluate Na+,K+-pump function and the capacity of the Na+,K+ pumps to fill these needs require quantification of the total content of Na+,K+ pumps in skeletal muscle. Inhibition of Na+,K+-pump activity, or a decrease in their content, reduces muscle contractility. Conversely, stimulation of the Na+,K+-pump transport rate or increasing the content of Na+,K+ pumps enhances muscle excitability and contractility. Measurements of [3H]ouabain binding to skeletal muscle in vivo or in vitro have enabled the reproducible quantification of the total content of Na+,K+ pumps in molar units in various animal species, and in both healthy people and individuals with various diseases. In contrast, measurements of 3-O-methylfluorescein phosphatase activity associated with the Na+,K+-ATPase may show inconsistent results. Measurements of Na+ and K+ fluxes in intact isolated muscles show that, after Na+ loading or intense excitation, all the Na+,K+ pumps are functional, allowing calculation of the maximum Na+,K+-pumping capacity, expressed in molar units/g muscle/min. The activity and content of Na+,K+ pumps are regulated by exercise, inactivity, K+ deficiency, fasting, age, and several hormones and pharmaceuticals. Studies on the α-subunit isoforms of the Na+,K+-ATPase have detected a relative increase in their number in response to exercise and the glucocorticoid dexamethasone but have not

Quantification of Na+,K+ pumps and their transport rate in skeletal muscle: functional significance.

Science.gov (United States)

Clausen, Torben

2013-10-01

During excitation, muscle cells gain Na(+) and lose K(+), leading to a rise in extracellular K(+) ([K(+)]o), depolarization, and loss of excitability. Recent studies support the idea that these events are important causes of muscle fatigue and that full use of the Na(+),K(+)-ATPase (also known as the Na(+),K(+) pump) is often essential for adequate clearance of extracellular K(+). As a result of their electrogenic action, Na(+),K(+) pumps also help reverse depolarization arising during excitation, hyperkalemia, and anoxia, or from cell damage resulting from exercise, rhabdomyolysis, or muscle diseases. The ability to evaluate Na(+),K(+)-pump function and the capacity of the Na(+),K(+) pumps to fill these needs require quantification of the total content of Na(+),K(+) pumps in skeletal muscle. Inhibition of Na(+),K(+)-pump activity, or a decrease in their content, reduces muscle contractility. Conversely, stimulation of the Na(+),K(+)-pump transport rate or increasing the content of Na(+),K(+) pumps enhances muscle excitability and contractility. Measurements of [(3)H]ouabain binding to skeletal muscle in vivo or in vitro have enabled the reproducible quantification of the total content of Na(+),K(+) pumps in molar units in various animal species, and in both healthy people and individuals with various diseases. In contrast, measurements of 3-O-methylfluorescein phosphatase activity associated with the Na(+),K(+)-ATPase may show inconsistent results. Measurements of Na(+) and K(+) fluxes in intact isolated muscles show that, after Na(+) loading or intense excitation, all the Na(+),K(+) pumps are functional, allowing calculation of the maximum Na(+),K(+)-pumping capacity, expressed in molar units/g muscle/min. The activity and content of Na(+),K(+) pumps are regulated by exercise, inactivity, K(+) deficiency, fasting, age, and several hormones and pharmaceuticals. Studies on the α-subunit isoforms of the Na(+),K(+)-ATPase have detected a relative increase in their

An investigation of natural genetic variation in the circadian system of Drosophila melanogaster: rhythm characteristics and methods of quantification.

Science.gov (United States)

Emery, P T; Morgan, E; Birley, A J

1994-04-01

Variation in four characteristics of the circadian locomotor activity rhythm was investigated in 24 true-breeding strains of Drosophila melanogaster with a view to establishing methods of phenotypic measurement sufficiently robust to allow subsequent biometric analysis. Between them, these strains formed a representative sample of the genetic variability of a natural population. Period, phase, definition (the degree to which a rhythmic signal was obscured by noise), and rhythm waveform were all found to vary continuously among the strains, although within each strain the rhythm phenotype was remarkably consistent. Each characteristic was found to be sufficiently robust to permit objective measurement using several different methods of quantification, which were then compared.

Distinguishing enhancing from nonenhancing renal masses with dual-source dual-energy CT: iodine quantification versus standard enhancement measurements.

Science.gov (United States)

Ascenti, Giorgio; Mileto, Achille; Krauss, Bernhard; Gaeta, Michele; Blandino, Alfredo; Scribano, Emanuele; Settineri, Nicola; Mazziotti, Silvio

2013-08-01

To compare the diagnostic accuracy of iodine quantification and standard enhancement measurements in distinguishing enhancing from nonenhancing renal masses. The Institutional Review Board approved this retrospective study conducted from data found in institutional patient databases and archives. Seventy-two renal masses were characterised as enhancing or nonenhancing using standard enhancement measurements (in HU) and iodine quantification (in mg/ml). Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of standard enhancement measurements and iodine quantification were calculated from χ (2) tests of contingency with histopathology or imaging follow-up as the reference standard. Difference in accuracy was assessed by means of McNemar analysis. Sensitivity, specificity, PPV, NPV and diagnostic accuracy for standard enhancement measurements and iodine quantification were 77.7 %, 100 %, 100 %, 81.8 %, 89 % and 100 %, 94.4 %, 94.7, 100 % and 97 %, respectively. The McNemar analysis showed that the accuracy of iodine quantification was significantly better (P < 0.001) than that of standard enhancement measurements. Compared with standard enhancement measurements, whole-tumour iodine quantification is more accurate in distinguishing enhancing from nonenhancing renal masses. • Enhancement of renal lesions is important when differentiating benign from malignant tumours. • Dual-energy CT offers measurement of iodine uptake rather than mere enhancement values. • Whole-tumour iodine quantification seems more accurate than standard CT enhancement measurements.

Detection and quantification of Leveillula taurica growth in pepper leaves.

Science.gov (United States)

Zheng, Zheng; Nonomura, Teruo; Bóka, Károly; Matsuda, Yoshinori; Visser, Richard G F; Toyoda, Hideyoshi; Kiss, Levente; Bai, Yuling

2013-06-01

Leveillula taurica is an obligate fungal pathogen that causes powdery mildew disease on a broad range of plants, including important crops such as pepper, tomato, eggplant, onion, cotton, and so on. The early stage of this disease is difficult to diagnose and the disease can easily spread unobserved; for example, in pepper and tomato production fields and greenhouses. The objective of this study was to develop a detection and quantification method of L. taurica biomass in pepper leaves with special regard to the early stages of infection. We monitored the development of the disease to time the infection process on the leaf surface as well as inside the pepper leaves. The initial and final steps of the infection taking place on the leaf surface were consecutively observed using a dissecting microscope and a scanning electron microscope. The development of the intercellular mycelium in the mesophyll was followed by light and transmission electron microscopy. A pair of L. taurica-specific primers was designed based on the internal transcribed spacer sequence of L. taurica and used in real-time polymerase chain reaction (PCR) assay to quantify the fungal DNA during infection. The specificity of this assay was confirmed by testing the primer pair with DNA from host plants and also from another powdery mildew species, Oidium neolycopersici, infecting tomato. A standard curve was obtained for absolute quantification of L. taurica biomass. In addition, we tested a relative quantification method by using a plant gene as reference and the obtained results were compared with the visual disease index scoring. The real-time PCR assay for L. taurica provides a valuable tool for detection and quantification of this pathogen in breeding activities as well in plant-microbe interaction studies.

Comparison of DNA quantification methodology used in the DNA extraction protocol for the UK Biobank cohort.

Science.gov (United States)

Welsh, Samantha; Peakman, Tim; Sheard, Simon; Almond, Rachael

2017-01-05

UK Biobank is a large prospective cohort study in the UK established by the Medical Research Council (MRC) and the Wellcome Trust to enable approved researchers to investigate the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. A wide range of phenotypic data has been collected at recruitment and has recently been enhanced by the UK Biobank Genotyping Project. All UK Biobank participants (500,000) have been genotyped on either the UK Biobank Axiom® Array or the Affymetrix UK BiLEVE Axiom® Array and the workflow for preparing samples for genotyping is described. The genetic data is hoped to provide further insight into the genetics of disease. All data, including the genetic data, is available for access to approved researchers. Data for two methods of DNA quantification (ultraviolet-visible spectroscopy [UV/Vis]) measured on the Trinean DropSense™ 96 and PicoGreen®) were compared by two laboratories (UK Biobank and Affymetrix). The sample processing workflow established at UK Biobank, for genotyping on the custom Affymetrix Axiom® array, resulted in high quality DNA (average DNA concentration 38.13 ng/μL, average 260/280 absorbance 1.91). The DNA generated high quality genotype data (average call rate 99.48% and pass rate 99.45%). The DNA concentration measured on the Trinean DropSense™ 96 at UK Biobank correlated well with DNA concentration measured by PicoGreen® at Affymetrix (r = 0.85). The UK Biobank Genotyping Project demonstrated that the high throughput DNA extraction protocol described generates high quality DNA suitable for genotyping on the Affymetrix Axiom array. The correlation between DNA concentration derived from UV/Vis and PicoGreen® quantification methods suggests, in large-scale genetic studies involving two laboratories, it may be possible to remove the DNA quantification step in one laboratory without affecting downstream analyses. This would result in

Adaptive multiscale MCMC algorithm for uncertainty quantification in seismic parameter estimation

KAUST Repository

Tan, Xiaosi

2014-08-05

Formulating an inverse problem in a Bayesian framework has several major advantages (Sen and Stoffa, 1996). It allows finding multiple solutions subject to flexible a priori information and performing uncertainty quantification in the inverse problem. In this paper, we consider Bayesian inversion for the parameter estimation in seismic wave propagation. The Bayes\\' theorem allows writing the posterior distribution via the likelihood function and the prior distribution where the latter represents our prior knowledge about physical properties. One of the popular algorithms for sampling this posterior distribution is Markov chain Monte Carlo (MCMC), which involves making proposals and calculating their acceptance probabilities. However, for large-scale problems, MCMC is prohibitevely expensive as it requires many forward runs. In this paper, we propose a multilevel MCMC algorithm that employs multilevel forward simulations. Multilevel forward simulations are derived using Generalized Multiscale Finite Element Methods that we have proposed earlier (Efendiev et al., 2013a; Chung et al., 2013). Our overall Bayesian inversion approach provides a substantial speed-up both in the process of the sampling via preconditioning using approximate posteriors and the computation of the forward problems for different proposals by using the adaptive nature of multiscale methods. These aspects of the method are discussed n the paper. This paper is motivated by earlier work of M. Sen and his collaborators (Hong and Sen, 2007; Hong, 2008) who proposed the development of efficient MCMC techniques for seismic applications. In the paper, we present some preliminary numerical results.

Quantification of serial changes in cerebral blood volume and metabolism in patients with recurrent glioblastoma undergoing antiangiogenic therapy

Energy Technology Data Exchange (ETDEWEB)

Stadlbauer, Andreas, E-mail: andi@nmr.at [Institute of Medical Radiology, University Clinic of St. Pölten, Propst Führer-Straße 4, A-3100 St. Pölten (Austria); Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen (Germany); Department of Radiology and Nuclear Medicine, Medical University Vienna, Währinger Gürtel 18-20, A-1097 Vienna (Austria); Pichler, Petra [First Department of Internal Medicine, University Clinic of St. Pölten, Propst Führer-Straße 4, A-3100 St. Poelten (Austria); Karl, Marianne [Institute of Medical Radiology, University Clinic of St. Pölten, Propst Führer-Straße 4, A-3100 St. Pölten (Austria); Brandner, Sebastian [Department of Neurosurgery, University of Erlangen-Nuremberg, Schwabachanlage 6, D-91054 Erlangen (Germany); Lerch, Claudia [Institute of Medical Radiology, University Clinic of St. Pölten, Propst Führer-Straße 4, A-3100 St. Pölten (Austria); Renner, Bertold [Institute of Experimental and Clinical Pharmacology and Toxicology, University of Erlangen-Nürnberg, Erlangen (Germany); Heinz, Gertraud [Institute of Medical Radiology, University Clinic of St. Pölten, Propst Führer-Straße 4, A-3100 St. Pölten (Austria)

2015-06-15

Highlights: • Antiangiogenic therapy can lead to a decreased in CBV in normal brain tissue. • Responding and pseudoresponding lesions to AAT showed a similar CBV decrease. • Cho and NAA allowed for a distinction of responding and pseudoresponding lesions. • Cr ratios are not suited for evaluation of antiangiogenic therapy response. • Responders to AAT may have an increased risk for remote progression of the GBM. - Abstract: Objectives: To evaluate the usefulness of quantitative advanced magnetic resonance imaging (MRI) methods for assessment of antiangiogenic therapy (AAT) response in recurrent glioblastoma multiforme (GBM). Methods: Eighteen patients with recurrent GBM received bevacizumab and 18 patients served as control group. Baseline MRI and two follow-up examinations were acquired every 3–5 months using dynamic susceptibility-weighted contrast (DSC) perfusion MRI and {sup 1}H-MR spectroscopic imaging ({sup 1}H-MRSI). Maps of absolute cerebral blood volume (aCBV) were coregistered with choline (Cho) and N-acetyl-aspartate (NAA) concentrations and compared to usually used relative parameters as well as controls. Results: Perfusion significantly decreased in responding and pseudoresponding GBMs but also in normal appearing brain after AAT onset. Cho and NAA concentrations were superior to Cr-ratios in lesion differentiation and showed a clear gap between responding and pseudoresponding lesions. Responders to AAT exceptionally frequently (6 out of 8 patients) showed remote GBM progression. Conclusions: Quantification of CBV reveals changes in normal brain perfusion due to AAT, which were not described so far. DSC perfusion MRI seems not to be suitable for differentiation between response and pseudoresponse to AAT. However, absolute quantification of brain metabolites may allow for distinction due to a clear gap at 6–9 months after therapy onset.

Species identification and quantification in meat and meat products using droplet digital PCR (ddPCR).

Science.gov (United States)

Floren, C; Wiedemann, I; Brenig, B; Schütz, E; Beck, J

2015-04-15

Species fraud and product mislabelling in processed food, albeit not being a direct health issue, often results in consumer distrust. Therefore methods for quantification of undeclared species are needed. Targeting mitochondrial DNA, e.g. CYTB gene, for species quantification is unsuitable, due to a fivefold inter-tissue variation in mtDNA content per cell resulting in either an under- (-70%) or overestimation (+160%) of species DNA contents. Here, we describe a reliable two-step droplet digital PCR (ddPCR) assay targeting the nuclear F2 gene for precise quantification of cattle, horse, and pig in processed meat products. The ddPCR assay is advantageous over qPCR showing a limit of quantification (LOQ) and detection (LOD) in different meat products of 0.01% and 0.001%, respectively. The specificity was verified in 14 different species. Hence, determining F2 in food by ddPCR can be recommended for quality assurance and control in production systems. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Comparison of Survey Data Collection Methods

Directory of Open Access Journals (Sweden)

VIDAL DÍAZ DE RADA

2017-01-01

Full Text Available This paper presents the results of a mixed-mode survey of the general population using a combination of postal, telephone, and Internet survey protocols. Potential respondents were invited to participate by ordinary mail and were allowed to choose their preferred response mode. The paper focuses on response quality (taking non-responses into consideration, fieldwork time and data collection cost. The results reveal that the Internet survey produces the lowest rate of non-responses and requires significantly less fieldwork time, although it is slightly more costly than the postal survey. However, when differences in cost structure are taken into account, we find that the same number of completed questionnaires could have been obtained through the Internet alone at a cost that is 18.2% lower than the mixed-mode survey.

Investigation on feasibility of recurrence quantification analysis for ...

African Journals Online (AJOL)

The RQA parameters such as percent recurrence (REC), trapping time (TT), percent laminarity (LAM) and entropy (ENT), and also the recurrence plots color patterns for different flank wear, can be used in detecting insert wear in face milling. Keywords: milling, flank wear, recurrence plot, recurrence quantification analysis.

Automatic quantification of subarachnoid hemorrhage on noncontrast CT

NARCIS (Netherlands)

Boers, Anna Maria Merel; Zijlstra, I.A.; Gathier, C.S.; van den Berg, R.; Slump, Cornelis H.; Marquering, H.A.; Majoie, C.B.

2014-01-01

Quantification of blood after SAH on initial NCCT is an important radiologic measure to predict patient outcome and guide treatment decisions. In current scales, hemorrhage volume and density are not accounted for. The purpose of this study was to develop and validate a fully automatic method for

Double-layer Tablets of Lornoxicam: Validation of Quantification ...

African Journals Online (AJOL)

Double-layer Tablets of Lornoxicam: Validation of Quantification Method, In vitro Dissolution and Kinetic Modelling. ... Satisfactory results were obtained from all the tablet formulations met compendial requirements. The slowest drug release rate was obtained with tablet cores based on PVP K90 (1.21 mg%.h-1).

Direct quantification of airborne nanoparticles composition by TXRF after collection on filters

Energy Technology Data Exchange (ETDEWEB)

Motellier, S; Lhaute, K; Guiot, A; Golanski, L; Tardif, F [CEA Grenoble, DRT, LITEN, DTNM, Laboratory of Nanochemistry and Nanosafety, 17 Avenue des Martyrs, Cedex 9, F-38054 Grenoble (France); Geoffroy, C, E-mail: sylvie.motellier@cea.fr [Elexience, 9 rue des petits ruisseaux, BP 61, 91371 Verrieres-le-Buisson Cedex (France)

2011-07-06

Direct TXRF analysis of nanoparticles deposited on filters was evaluated. Standard filters spiked with known amounts of NP were produced using an atomizer which generates an aerosol from a NP containing-liquid suspension. Polycarbonate filters provided the highest fluorescence signals and black polycarbonate filters containing chromium were further selected, Cr being used as internal standard for elemental quantification of the filter contaminants. Calibration curves were established for various NP (TiO{sub 2}, ZnO, CeO{sub 2}, Al{sub 2}O{sub 3}). Good linearity was observed. Low limits of detection were in the tens to the hundreds of ngs per filter, the method being less adapted to Al{sub 2}O{sub 3} due to the poor TXRF sensitivity for light elements. The analysis of MW-CNTs was attempted by quantification of their metal (Fe) catalyst impurities. Problems like CNT dispersion in liquids, quantification of the deposited quantity and high Fe-background contamination.

A Constrained Genetic Algorithm with Adaptively Defined Fitness Function in MRS Quantification

Science.gov (United States)

Papakostas, G. A.; Karras, D. A.; Mertzios, B. G.; Graveron-Demilly, D.; van Ormondt, D.

MRS Signal quantification is a rather involved procedure and has attracted the interest of the medical engineering community, regarding the development of computationally efficient methodologies. Significant contributions based on Computational Intelligence tools, such as Neural Networks (NNs), demonstrated a good performance but not without drawbacks already discussed by the authors. On the other hand preliminary application of Genetic Algorithms (GA) has already been reported in the literature by the authors regarding the peak detection problem encountered in MRS quantification using the Voigt line shape model. This paper investigates a novel constrained genetic algorithm involving a generic and adaptively defined fitness function which extends the simple genetic algorithm methodology in case of noisy signals. The applicability of this new algorithm is scrutinized through experimentation in artificial MRS signals interleaved with noise, regarding its signal fitting capabilities. Although extensive experiments with real world MRS signals are necessary, the herein shown performance illustrates the method's potential to be established as a generic MRS metabolites quantification procedure.

Quaternary ammonium isobaric tag for a relative and absolute quantification of peptides.

Science.gov (United States)

Setner, Bartosz; Stefanowicz, Piotr; Szewczuk, Zbigniew

2018-02-01

Isobaric labeling quantification of peptides has become a method of choice for mass spectrometry-based proteomics studies. However, despite of wide variety of commercially available isobaric tags, none of the currently available methods offers significant improvement of sensitivity of detection during MS experiment. Recently, many strategies were applied to increase the ionization efficiency of peptides involving chemical modifications introducing quaternary ammonium fixed charge. Here, we present a novel quaternary ammonium-based isobaric tag for relative and absolute quantification of peptides (QAS-iTRAQ 2-plex). Upon collisional activation, the new stable benzylic-type cationic reporter ion is liberated from the tag. Deuterium atoms were used to offset the differential masses of a reporter group. We tested the applicability of QAS-iTRAQ 2-plex reagent on a series of model peptides as well as bovine serum albumin tryptic digest. Obtained results suggest usefulness of this isobaric ionization tag for relative and absolute quantification of peptides. Copyright © 2017 John Wiley & Sons, Ltd.

Lowering the quantification limit of the QubitTM RNA HS assay using RNA spike-in.

Science.gov (United States)

Li, Xin; Ben-Dov, Iddo Z; Mauro, Maurizio; Williams, Zev

2015-05-06

RNA quantification is often a prerequisite for most RNA analyses such as RNA sequencing. However, the relatively low sensitivity and large sample consumption of traditional RNA quantification methods such as UV spectrophotometry and even the much more sensitive fluorescence-based RNA quantification assays, such as the Qubit™ RNA HS Assay, are often inadequate for measuring minute levels of RNA isolated from limited cell and tissue samples and biofluids. Thus, there is a pressing need for a more sensitive method to reliably and robustly detect trace levels of RNA without interference from DNA. To improve the quantification limit of the Qubit™ RNA HS Assay, we spiked-in a known quantity of RNA to achieve the minimum reading required by the assay. Samples containing trace amounts of RNA were then added to the spike-in and measured as a reading increase over RNA spike-in baseline. We determined the accuracy and precision of reading increases between 1 and 20 pg/μL as well as RNA-specificity in this range, and compared to those of RiboGreen(®), another sensitive fluorescence-based RNA quantification assay. We then applied Qubit™ Assay with RNA spike-in to quantify plasma RNA samples. RNA spike-in improved the quantification limit of the Qubit™ RNA HS Assay 5-fold, from 25 pg/μL down to 5 pg/μL while maintaining high specificity to RNA. This enabled quantification of RNA with original concentration as low as 55.6 pg/μL compared to 250 pg/μL for the standard assay and decreased sample consumption from 5 to 1 ng. Plasma RNA samples that were not measurable by the Qubit™ RNA HS Assay were measurable by our modified method. The Qubit™ RNA HS Assay with RNA spike-in is able to quantify RNA with high specificity at 5-fold lower concentration and uses 5-fold less sample quantity than the standard Qubit™ Assay.

Hepatic Iron Quantification on 3 Tesla (3 T Magnetic Resonance (MR: Technical Challenges and Solutions

Directory of Open Access Journals (Sweden)

Muhammad Anwar

2013-01-01

Full Text Available MR has become a reliable and noninvasive method of hepatic iron quantification. Currently, most of the hepatic iron quantification is performed on 1.5 T MR, and the biopsy measurements have been paired with R2 and R2* values for 1.5 T MR. As the use of 3 T MR scanners is steadily increasing in clinical practice, it has become important to evaluate the practicality of calculating iron burden at 3 T MR. Hepatic iron quantification on 3 T MR requires a better understanding of the process and more stringent technical considerations. The purpose of this work is to focus on the technical challenges in establishing a relationship between T2* values at 1.5 T MR and 3 T MR for hepatic iron concentration (HIC and to develop an appropriately optimized MR protocol for the evaluation of T2* values in the liver at 3 T magnetic field strength. We studied 22 sickle cell patients using multiecho fast gradient-echo sequence (MFGRE 3 T MR and compared the results with serum ferritin and liver biopsy results. Our study showed that the quantification of hepatic iron on 3 T MRI in sickle cell disease patients correlates well with clinical blood test results and biopsy results. 3 T MR liver iron quantification based on MFGRE can be used for hepatic iron quantification in transfused patients.

5 CFR 591.224 - How does OPM adjust price indexes between surveys?

Science.gov (United States)

2010-01-01

... REGULATIONS ALLOWANCES AND DIFFERENTIALS Cost-of-Living Allowance and Post Differential-Nonforeign Areas Cost-Of-Living Allowances § 591.224 How does OPM adjust price indexes between surveys? (a) OPM adjusts...

Development of Accident Scenarios and Quantification Methodology for RAON Accelerator

International Nuclear Information System (INIS)

Lee, Yongjin; Jae, Moosung

2014-01-01

The RIsp (Rare Isotope Science Project) plans to provide neutron-rich isotopes (RIs) and stable heavy ion beams. The accelerator is defined as radiation production system according to Nuclear Safety Law. Therefore, it needs strict operate procedures and safety assurance to prevent radiation exposure. In order to satisfy this condition, there is a need for evaluating potential risk of accelerator from the design stage itself. Though some of PSA researches have been conducted for accelerator, most of them focus on not general accident sequence but simple explanation of accident. In this paper, general accident scenarios are developed by Event Tree and deduce new quantification methodology of Event Tree. In this study, some initial events, which may occur in the accelerator, are selected. Using selected initial events, the accident scenarios of accelerator facility are developed with Event Tree. These results can be used as basic data of the accelerator for future risk assessments. After analyzing the probability of each heading, it is possible to conduct quantification and evaluate the significance of the accident result. If there is a development of the accident scenario for external events, risk assessment of entire accelerator facility will be completed. To reduce the uncertainty of the Event Tree, it is possible to produce a reliable data via the presented quantification techniques

Use of quantification in cardiac reporting: How does it change the clinical result?

International Nuclear Information System (INIS)

Gnanasegaran, G.; Hilson, A.J.W.; Buscombe, J.R.

2005-01-01

Many gamma camera systems are now sold with cardiac quantification packages. These are said to increase the accuracy of reporting. However the use of such quantification packages may change the clinical report as read from the tomographic slices. The aim of this study was to quantify the differences between qualitative visual reporting and quantification. The stress and rest myocardial perfusion studies were quantitatively reported in 37 patients comprising 333 segments of the heart (9 segments/patient). A defect was defined by a reduction in activity of >50% in each of the segments. For the tomographic qualitative reporting the data was reconstructed using iterative reconstruction with a Wiener smoothing filter. Quantification used an Emory bull's eye system with gender and age matched normal controls. Number of abnormal segments noted by qualitative reading of data were 119 at stress and 79 at rest. For the bull's eye plot 98 abnormal segments were seen at stress and 76 at rest. Thirty-three segments (10%) were abnormal on the qualitative reading of data alone and 7 (2%) were abnormal on bull's eye alone. Of the 55 segments reported as ischaemic qualitative reading of data, 26 (48%) were normal on bull's eye, 13 of these in the right coronary artery (RCA) territory segments. Of the 67 segments reported on the qualitative reading of data as infarct, 10 (13%) were normal on bull's eye, 7 of these in the territory of the RCA segments. There are significant differences in the results of reporting scans using a bull's eye plot especially in identifying inferior wall ischaemia. Therefore before using such a quantification method a full assessment of the accuracy of each method should be performed. (author)

DNA imaging and quantification using chemi-luminescent probes; Imagerie et quantification d`ADN par chimiluminescence

Energy Technology Data Exchange (ETDEWEB)

Dorner, G; Redjdal, N; Laniece, P; Siebert, R; Tricoire, H; Valentin, L [Groupe I.P.B., Experimental Research Division, Inst. de Physique Nucleaire, Paris-11 Univ., 91 - Orsay (France)

1999-11-01

During this interdisciplinary study we have developed an ultra sensitive and reliable imaging system of DNA labelled by chemiluminescence. Based on a liquid nitrogen cooled CCD, the system achieves sensitivities down to 10 fg/mm{sup 2} labelled DNA over a surface area of 25 x 25 cm{sup 2} with a sub-millimeter resolution. Commercially available chemi-luminescent - and enhancer molecules are compared and their reaction conditions optimized for best signal-to-noise ratios. Double labelling was performed to verify quantification with radioactive probes. (authors) 1 fig.

Quantification of arbuscular mycorrhizal fungal DNA in roots: how important is material preservation?

Science.gov (United States)

Janoušková, Martina; Püschel, David; Hujslová, Martina; Slavíková, Renata; Jansa, Jan

2015-04-01

Monitoring populations of arbuscular mycorrhizal fungi (AMF) in roots is a pre-requisite for improving our understanding of AMF ecology and functioning of the symbiosis in natural conditions. Among other approaches, quantification of fungal DNA in plant tissues by quantitative real-time PCR is one of the advanced techniques with a great potential to process large numbers of samples and to deliver truly quantitative information. Its application potential would greatly increase if the samples could be preserved by drying, but little is currently known about the feasibility and reliability of fungal DNA quantification from dry plant material. We addressed this question by comparing quantification results based on dry root material to those obtained from deep-frozen roots of Medicago truncatula colonized with Rhizophagus sp. The fungal DNA was well conserved in the dry root samples with overall fungal DNA levels in the extracts comparable with those determined in extracts of frozen roots. There was, however, no correlation between the quantitative data sets obtained from the two types of material, and data from dry roots were more variable. Based on these results, we recommend dry material for qualitative screenings but advocate using frozen root materials if precise quantification of fungal DNA is required.

Forest Carbon Leakage Quantification Methods and Their Suitability for Assessing Leakage in REDD

Directory of Open Access Journals (Sweden)

Sabine Henders

2012-01-01

Full Text Available This paper assesses quantification methods for carbon leakage from forestry activities for their suitability in leakage accounting in a future Reducing Emissions from Deforestation and Forest Degradation (REDD mechanism. To that end, we first conducted a literature review to identify specific pre-requisites for leakage assessment in REDD. We then analyzed a total of 34 quantification methods for leakage emissions from the Clean Development Mechanism (CDM, the Verified Carbon Standard (VCS, the Climate Action Reserve (CAR, the CarbonFix Standard (CFS, and from scientific literature sources. We screened these methods for the leakage aspects they address in terms of leakage type, tools used for quantification and the geographical scale covered. Results show that leakage methods can be grouped into nine main methodological approaches, six of which could fulfill the recommended REDD leakage requirements if approaches for primary and secondary leakage are combined. The majority of methods assessed, address either primary or secondary leakage; the former mostly on a local or regional and the latter on national scale. The VCS is found to be the only carbon accounting standard at present to fulfill all leakage quantification requisites in REDD. However, a lack of accounting methods was identified for international leakage, which was addressed by only two methods, both from scientific literature.

Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

Science.gov (United States)

Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

2013-08-01

Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

Application of the third theory of quantification in coal and gas outburst forecast

Energy Technology Data Exchange (ETDEWEB)

Wu, C.; Qin, Y.; Zhang, X. [China University of Mining and Technology, Xuzhou (China). School of Resource and Geoscience Engineering

2004-12-01

The essential principles of the third theory of quantification are discussed. The concept and calculated method of reaction degree are put forward which extend the applying range and scientificalness of the primary reaction. Taking the Zhongmacun mine as example, on the base of analyzing the rules of gas geology synthetically and traversing the geological factors affecting coal and gas outburst. The paper adopts the method of combining statistical units with the third theory of quantification, screens out 8 sensitive geological factors from 11 geological indexes and carries through the work of gas geology regionalism to the exploited area of Zhongmacun according to the research result. The practice shows that it is feasible to apply the third theory of quantification to gas geology, which offers a new thought to screen the sensitive geological factors of gas outburst forecast. 3 refs., 3 figs., 3 tabs.

Bayesian adaptive survey protocols for resource management

Science.gov (United States)

Halstead, Brian J.; Wylie, Glenn D.; Coates, Peter S.; Casazza, Michael L.

2011-01-01

Transparency in resource management decisions requires a proper accounting of uncertainty at multiple stages of the decision-making process. As information becomes available, periodic review and updating of resource management protocols reduces uncertainty and improves management decisions. One of the most basic steps to mitigating anthropogenic effects on populations is determining if a population of a species occurs in an area that will be affected by human activity. Species are rarely detected with certainty, however, and falsely declaring a species absent can cause improper conservation decisions or even extirpation of populations. We propose a method to design survey protocols for imperfectly detected species that accounts for multiple sources of uncertainty in the detection process, is capable of quantitatively incorporating expert opinion into the decision-making process, allows periodic updates to the protocol, and permits resource managers to weigh the severity of consequences if the species is falsely declared absent. We developed our method using the giant gartersnake (Thamnophis gigas), a threatened species precinctive to the Central Valley of California, as a case study. Survey date was negatively related to the probability of detecting the giant gartersnake, and water temperature was positively related to the probability of detecting the giant gartersnake at a sampled location. Reporting sampling effort, timing and duration of surveys, and water temperatures would allow resource managers to evaluate the probability that the giant gartersnake occurs at sampled sites where it is not detected. This information would also allow periodic updates and quantitative evaluation of changes to the giant gartersnake survey protocol. Because it naturally allows multiple sources of information and is predicated upon the idea of updating information, Bayesian analysis is well-suited to solving the problem of developing efficient sampling protocols for species of

Quantification of Uncertainties in Integrated Spacecraft System Models, Phase I

Data.gov (United States)

National Aeronautics and Space Administration — The proposed effort is to investigate a novel uncertainty quantification (UQ) approach based on non-intrusive polynomial chaos (NIPC) for computationally efficient...

Automated image analysis for quantification of filamentous bacteria

DEFF Research Database (Denmark)

Fredborg, Marlene; Rosenvinge, Flemming Schønning; Spillum, Erik

2015-01-01

in systems relying on colorimetry or turbidometry (such as Vitek-2, Phoenix, MicroScan WalkAway). The objective was to examine an automated image analysis algorithm for quantification of filamentous bacteria using the 3D digital microscopy imaging system, oCelloScope. Results Three E. coli strains displaying...

The Search for Symbiotic Stars in the IPHAS Survey

Directory of Open Access Journals (Sweden)

Corradi R. L. M.

2012-06-01

Full Text Available We have started a project to search for symbiotic stars using the data from IPHAS, the Hα survey of the Northern Galactic plane. Candidates are selected from the IPHAS photometric catalogue based on their colors, combined with the information in the near-infrared from 2MASS. So far, follow-up spectroscopy allowed us to discover 14 new symbiotic stars, compared to the 10 systems previously known in the IPHAS survey area. Their general characteristics and the most notable cases are briefly presented. the spectroscopic campaign also allowed us to refine the selection criteria for symbiotic stars in IPHAS. Perspectives, which include the extension of the survey in the Southern Galactic plane and a portion of the bulge (VPHAS+, are discussed.

Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals

Science.gov (United States)

Crooks, Kevin R.; Burdett, Christopher L.; Theobald, David M.; King, Sarah R. B.; Rondinini, Carlo; Boitani, Luigi

2017-01-01

Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world’s terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world’s terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation. PMID:28673992

Quantification of deep medullary veins at 7 T brain MRI

Energy Technology Data Exchange (ETDEWEB)

Kuijf, Hugo J.; Viergever, Max A.; Vincken, Koen L. [University Medical Center Utrecht, Image Sciences Institute, Utrecht (Netherlands); Bouvy, Willem H.; Razoux Schultz, Tom B.; Biessels, Geert Jan [University Medical Center Utrecht, Department of Neurology, Brain Center Rudolf Magnus, Utrecht (Netherlands); Zwanenburg, Jaco J.M. [University Medical Center Utrecht, Image Sciences Institute, Utrecht (Netherlands); University Medical Center Utrecht, Department of Radiology, Utrecht (Netherlands)

2016-10-15

Deep medullary veins support the venous drainage of the brain and may display abnormalities in the context of different cerebrovascular diseases. We present and evaluate a method to automatically detect and quantify deep medullary veins at 7 T. Five participants were scanned twice, to assess the robustness and reproducibility of manual and automated vein detection. Additionally, the method was evaluated on 24 participants to demonstrate its application. Deep medullary veins were assessed within an automatically created region-of-interest around the lateral ventricles, defined such that all veins must intersect it. A combination of vesselness, tubular tracking, and hysteresis thresholding located individual veins, which were quantified by counting and computing (3-D) density maps. Visual assessment was time-consuming (2 h/scan), with an intra-/inter-observer agreement on absolute vein count of ICC = 0.76 and 0.60, respectively. The automated vein detection showed excellent inter-scan reproducibility before (ICC = 0.79) and after (ICC = 0.88) visually censoring false positives. It had a positive predictive value of 71.6 %. Imaging at 7 T allows visualization and quantification of deep medullary veins. The presented method offers fast and reliable automated assessment of deep medullary veins. (orig.)

LORD-Q: a long-run real-time PCR-based DNA-damage quantification method for nuclear and mitochondrial genome analysis

Science.gov (United States)

Lehle, Simon; Hildebrand, Dominic G.; Merz, Britta; Malak, Peter N.; Becker, Michael S.; Schmezer, Peter; Essmann, Frank; Schulze-Osthoff, Klaus; Rothfuss, Oliver

2014-01-01

DNA damage is tightly associated with various biological and pathological processes, such as aging and tumorigenesis. Although detection of DNA damage is attracting increasing attention, only a limited number of methods are available to quantify DNA lesions, and these techniques are tedious or only detect global DNA damage. In this study, we present a high-sensitivity long-run real-time PCR technique for DNA-damage quantification (LORD-Q) in both the mitochondrial and nuclear genome. While most conventional methods are of low-sensitivity or restricted to abundant mitochondrial DNA samples, we established a protocol that enables the accurate sequence-specific quantification of DNA damage in >3-kb probes for any mitochondrial or nuclear DNA sequence. In order to validate the sensitivity of this method, we compared LORD-Q with a previously published qPCR-based method and the standard single-cell gel electrophoresis assay, demonstrating a superior performance of LORD-Q. Exemplarily, we monitored induction of DNA damage and repair processes in human induced pluripotent stem cells and isogenic fibroblasts. Our results suggest that LORD-Q provides a sequence-specific and precise method to quantify DNA damage, thereby allowing the high-throughput assessment of DNA repair, genotoxicity screening and various other processes for a wide range of life science applications. PMID:24371283

Preliminary study on computer automatic quantification of brain atrophy

International Nuclear Information System (INIS)

Li Chuanfu; Zhou Kangyuan

2006-01-01

Objective: To study the variability of normal brain volume with the sex and age, and put forward an objective standard for computer automatic quantification of brain atrophy. Methods: The cranial volume, brain volume and brain parenchymal fraction (BPF) of 487 cases of brain atrophy (310 males, 177 females) and 1901 cases of normal subjects (993 males, 908 females) were calculated with the newly developed algorithm of automatic quantification for brain atrophy. With the technique of polynomial curve fitting, the mathematical relationship of BPF with age in normal subjects was analyzed. Results: The cranial volume, brain volume and BPF of normal subjects were (1 271 322 ± 128 699) mm 3 , (1 211 725 ± 122 077) mm 3 and (95.3471 ± 2.3453)%, respectively, and those of atrophy subjects were (1 276 900 ± 125 180) mm 3 , (1 203 400 ± 117 760) mm 3 and BPF(91.8115 ± 2.3035)% respectively. The difference of BPF between the two groups was extremely significant (P 0.05). The expression P(x)=-0.0008x 2 + 0.0193x + 96.9999 could accurately describe the mathematical relationship between BPF and age in normal subject (lower limit of 95% CI y=-0.0008x 2 +0.0184x+95.1090). Conclusion: The lower limit of 95% confidence interval mathematical relationship between BPF and age could be used as an objective criteria for automatic quantification of brain atrophy with computer. (authors)

40 CFR 82.8 - Grant of essential use allowances and critical use allowances.

Science.gov (United States)

2010-07-01

... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Grant of essential use allowances and critical use allowances. 82.8 Section 82.8 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Albemarle Bill Clark Pest Control, Inc. Burnside Services, Inc. Cardinal Professional Products Chemtura Corp...

Simultaneous quantification of protein phosphorylation sites using liquid chromatography-tandem mass spectrometry-based targeted proteomics: a linear algebra approach for isobaric phosphopeptides.

Science.gov (United States)

Xu, Feifei; Yang, Ting; Sheng, Yuan; Zhong, Ting; Yang, Mi; Chen, Yun

2014-12-05

As one of the most studied post-translational modifications (PTM), protein phosphorylation plays an essential role in almost all cellular processes. Current methods are able to predict and determine thousands of phosphorylation sites, whereas stoichiometric quantification of these sites is still challenging. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based targeted proteomics is emerging as a promising technique for site-specific quantification of protein phosphorylation using proteolytic peptides as surrogates of proteins. However, several issues may limit its application, one of which relates to the phosphopeptides with different phosphorylation sites and the same mass (i.e., isobaric phosphopeptides). While employment of site-specific product ions allows for these isobaric phosphopeptides to be distinguished and quantified, site-specific product ions are often absent or weak in tandem mass spectra. In this study, linear algebra algorithms were employed as an add-on to targeted proteomics to retrieve information on individual phosphopeptides from their common spectra. To achieve this simultaneous quantification, a LC-MS/MS-based targeted proteomics assay was first developed and validated for each phosphopeptide. Given the slope and intercept of calibration curves of phosphopeptides in each transition, linear algebraic equations were developed. Using a series of mock mixtures prepared with varying concentrations of each phosphopeptide, the reliability of the approach to quantify isobaric phosphopeptides containing multiple phosphorylation sites (≥ 2) was discussed. Finally, we applied this approach to determine the phosphorylation stoichiometry of heat shock protein 27 (HSP27) at Ser78 and Ser82 in breast cancer cells and tissue samples.

MMT hypervelocity star survey. III. The complete survey

Energy Technology Data Exchange (ETDEWEB)

Brown, Warren R.; Geller, Margaret J.; Kenyon, Scott J., E-mail: wbrown@cfa.harvard.edu, E-mail: mgeller@cfa.harvard.edu, E-mail: skenyon@cfa.harvard.edu [Smithsonian Astrophysical Observatory, 60 Garden Street, Cambridge, MA 02138 (United States)

2014-05-20

We describe our completed spectroscopic survey for unbound hypervelocity stars (HVSs) ejected from the Milky Way. Three new discoveries bring the total number of unbound late B-type stars to 21. We place new constraints on the nature of the stars and on their distances using moderate resolution MMT spectroscopy. Half of the stars are fast rotators; they are certain 2.5-4 M {sub ☉} main sequence stars at 50-120 kpc distances. Correcting for stellar lifetime, our survey implies that unbound 2.5-4 M {sub ☉} stars are ejected from the Milky Way at a rate of 1.5 × 10{sup –6} yr{sup –1}. These unbound HVSs are likely ejected continuously over the past 200 Myr and do not share a common flight time. The anisotropic spatial distribution of HVSs on the sky remains puzzling. Southern hemisphere surveys like SkyMapper will soon allow us to map the all-sky distribution of HVSs. Future proper motion measurements with Hubble Space Telescope and Gaia will provide strong constraints on origin. Existing observations are all consistent with HVS ejections from encounters with the massive black hole in the Galactic center.

MMT hypervelocity star survey. III. The complete survey

International Nuclear Information System (INIS)

Brown, Warren R.; Geller, Margaret J.; Kenyon, Scott J.

2014-01-01

We describe our completed spectroscopic survey for unbound hypervelocity stars (HVSs) ejected from the Milky Way. Three new discoveries bring the total number of unbound late B-type stars to 21. We place new constraints on the nature of the stars and on their distances using moderate resolution MMT spectroscopy. Half of the stars are fast rotators; they are certain 2.5-4 M ☉ main sequence stars at 50-120 kpc distances. Correcting for stellar lifetime, our survey implies that unbound 2.5-4 M ☉ stars are ejected from the Milky Way at a rate of 1.5 × 10 –6 yr –1 . These unbound HVSs are likely ejected continuously over the past 200 Myr and do not share a common flight time. The anisotropic spatial distribution of HVSs on the sky remains puzzling. Southern hemisphere surveys like SkyMapper will soon allow us to map the all-sky distribution of HVSs. Future proper motion measurements with Hubble Space Telescope and Gaia will provide strong constraints on origin. Existing observations are all consistent with HVS ejections from encounters with the massive black hole in the Galactic center.

Quantification of physical activity using the QAPACE Questionnaire: a two stage cluster sample design survey of children and adolescents attending urban school.

Science.gov (United States)

Barbosa, Nicolas; Sanchez, Carlos E; Patino, Efrain; Lozano, Benigno; Thalabard, Jean C; LE Bozec, Serge; Rieu, Michel

2016-05-01

Quantification of physical activity as energy expenditure is important since youth for the prevention of chronic non communicable diseases in adulthood. It is necessary to quantify physical activity expressed in daily energy expenditure (DEE) in school children and adolescents between 8-16 years, by age, gender and socioeconomic level (SEL) in Bogotá. This is a Two Stage Cluster Survey Sample. From a universe of 4700 schools and 760000 students from three existing socioeconomic levels in Bogotá (low, medium and high). The random sample was 20 schools and 1840 students (904 boys and 936 girls). Foreshadowing desertion of participants and inconsistency in the questionnaire responses, the sample size was increased. Thus, 6 individuals of each gender for each of the nine age groups were selected, resulting in a total sample of 2160 individuals. Selected students filled the QAPACE questionnaire under supervision. The data was analyzed comparing means with multivariate general linear model. Fixed factors used were: gender (boys and girls), age (8 to 16 years old) and tri-strata SEL (low, medium and high); as independent variables were assessed: height, weight, leisure time, expressed in hours/day and dependent variable: daily energy expenditure DEE (kJ.kg-1.day-1): during leisure time (DEE-LT), during school time (DEE-ST), during vacation time (DEE-VT), and total mean DEE per year (DEEm-TY) RESULTS: Differences in DEE by gender, in boys, LT and all DEE, with the SEL all variables were significant; but age-SEL was only significant in DEE-VT. In girls, with the SEL all variables were significant. The post hoc multiple comparisons tests were significant with age using Fisher's Least Significant Difference (LSD) test in all variables. For both genders and for all SELs the values in girls had the higher value except SEL high (5-6) The boys have higher values in DEE-LT, DEE-ST, DEE-VT; except in DEEm-TY in SEL (5-6) In SEL (5-6) all DEEs for both genders are highest. For SEL

Global Sensitivity Analysis and Estimation of Model Error, Toward Uncertainty Quantification in Scramjet Computations

Science.gov (United States)

Huan, Xun; Safta, Cosmin; Sargsyan, Khachik; Geraci, Gianluca; Eldred, Michael S.; Vane, Zachary P.; Lacaze, Guilhem; Oefelein, Joseph C.; Najm, Habib N.

2018-03-01

The development of scramjet engines is an important research area for advancing hypersonic and orbital flights. Progress toward optimal engine designs requires accurate flow simulations together with uncertainty quantification. However, performing uncertainty quantification for scramjet simulations is challenging due to the large number of uncertain parameters involved and the high computational cost of flow simulations. These difficulties are addressed in this paper by developing practical uncertainty quantification algorithms and computational methods, and deploying them in the current study to large-eddy simulations of a jet in crossflow inside a simplified HIFiRE Direct Connect Rig scramjet combustor. First, global sensitivity analysis is conducted to identify influential uncertain input parameters, which can help reduce the systems stochastic dimension. Second, because models of different fidelity are used in the overall uncertainty quantification assessment, a framework for quantifying and propagating the uncertainty due to model error is presented. These methods are demonstrated on a nonreacting jet-in-crossflow test problem in a simplified scramjet geometry, with parameter space up to 24 dimensions, using static and dynamic treatments of the turbulence subgrid model, and with two-dimensional and three-dimensional geometries.

Global Sensitivity Analysis and Estimation of Model Error, Toward Uncertainty Quantification in Scramjet Computations

Energy Technology Data Exchange (ETDEWEB)

Huan, Xun [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Safta, Cosmin [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Sargsyan, Khachik [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Geraci, Gianluca [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Eldred, Michael S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Vane, Zachary P. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Lacaze, Guilhem [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Oefelein, Joseph C. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Najm, Habib N. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

2018-02-09

The development of scramjet engines is an important research area for advancing hypersonic and orbital flights. Progress toward optimal engine designs requires accurate flow simulations together with uncertainty quantification. However, performing uncertainty quantification for scramjet simulations is challenging due to the large number of uncertain parameters involved and the high computational cost of flow simulations. These difficulties are addressed in this paper by developing practical uncertainty quantification algorithms and computational methods, and deploying them in the current study to large-eddy simulations of a jet in crossflow inside a simplified HIFiRE Direct Connect Rig scramjet combustor. First, global sensitivity analysis is conducted to identify influential uncertain input parameters, which can help reduce the system’s stochastic dimension. Second, because models of different fidelity are used in the overall uncertainty quantification assessment, a framework for quantifying and propagating the uncertainty due to model error is presented. Finally, these methods are demonstrated on a nonreacting jet-in-crossflow test problem in a simplified scramjet geometry, with parameter space up to 24 dimensions, using static and dynamic treatments of the turbulence subgrid model, and with two-dimensional and three-dimensional geometries.

The need for clinical quantification of combined PET/MRI data in pediatric epilepsy

International Nuclear Information System (INIS)

Muzik, Otto; Pai, Darshan; Juhasz, Csaba; Hua, Jing

2013-01-01

In the past, multimodality integrative analysis of image data has been used to obtain a better understanding of underlying mechanisms of seizure generation and propagation in children with extratemporal lobe epilepsy. However, despite important advances in the combined analysis of PET, MRI, DTI and EEG data, successful surgical outcome is only achieved in about 2/3 of patients undergoing resective surgery. The advent of simultaneous PET/MR data acquisition promises an important advance in neuroimaging through clinical quantification, which will finally translate the strength of PET (which is the ability to absolutely quantify physiological parameters such as metabolic rates and receptor densities) into clinical work. Taking advantage of recently developed integrated PET/MR devices, absolute physiological values will be available in clinical routine, replacing currently used visual assessment of relative tissue tracer uptake. This will allow assessment of global increases/decreases of brain function during critical phases of development and is likely to have a significant impact on patient management in pediatric epilepsy

The need for clinical quantification of combined PET/MRI data in pediatric epilepsy

Energy Technology Data Exchange (ETDEWEB)

Muzik, Otto, E-mail: otto@pet.wayne.edu [Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI (United States); Department of Radiology, Wayne State University School of Medicine, Detroit, MI (United States); Pai, Darshan [Department of Computer Science, Wayne State University School of Medicine, Detroit, MI (United States); Juhasz, Csaba [Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI (United States); Hua, Jing [Department of Computer Science, Wayne State University School of Medicine, Detroit, MI (United States)

2013-02-21

In the past, multimodality integrative analysis of image data has been used to obtain a better understanding of underlying mechanisms of seizure generation and propagation in children with extratemporal lobe epilepsy. However, despite important advances in the combined analysis of PET, MRI, DTI and EEG data, successful surgical outcome is only achieved in about 2/3 of patients undergoing resective surgery. The advent of simultaneous PET/MR data acquisition promises an important advance in neuroimaging through clinical quantification, which will finally translate the strength of PET (which is the ability to absolutely quantify physiological parameters such as metabolic rates and receptor densities) into clinical work. Taking advantage of recently developed integrated PET/MR devices, absolute physiological values will be available in clinical routine, replacing currently used visual assessment of relative tissue tracer uptake. This will allow assessment of global increases/decreases of brain function during critical phases of development and is likely to have a significant impact on patient management in pediatric epilepsy.

Electronic cigarette use in restaurants and workplaces where combustible tobacco smoking is not allowed: an Internet survey in Japan.

Science.gov (United States)

Kiyohara, Kosuke; Tabuchi, Takahiro

2018-05-01

The present study aimed to examine the experience of actual electronic cigarette (e-cigarette) use in smoke-free areas of restaurants and workplaces and to explore the determinants associated with such use among Japanese adults who reported any experience using e-cigarettes (e-cigarette ever-users). An Internet-based self-reported questionnaire survey was conducted in 2015 on Japanese e-cigarette ever-users. The proportion of the respondents who had ever used or frequently used e-cigarettes in smoke-free restaurants and/or workplaces was calculated. Potential factors associated with e-cigarette use in those smoke-free areas were also examined by using multivariable logistic regression analyses. In total, 1243 e-cigarette ever-users (662 current and 581 former e-cigarette users) were analysed. The majority of them (1020/1243, 82.1%) were male and their mean age ± SD was 47.0±10.4 years. The proportion of those who had ever used e-cigarettes in smoke-free restaurants was 28.8% (358/1243) and that in smoke-free workplaces was 25.5% (317/1243), respectively. The proportion of those who had frequently used e-cigarettes in smoke-free restaurants was 18.5% (230/1243) and that in smoke-free workplaces was 16.3% (202/1243), respectively. In general, the proportion of e-cigarette use in those smoke-free areas was higher among those having a higher educational level than those having a lower educational level. Among adult Japanese e-cigarette ever-users, approximately 26%-29% had ever used and 16%-19% had frequently used e-cigarettes in restaurants and/or workplaces where combustible tobacco smoking is not allowed. Policy-makers may need to establish explicit rules as to e-cigarette use in smoke-free environments. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Error quantification of abnormal extreme high waves in Operational Oceanographic System in Korea

Science.gov (United States)

Jeong, Sang-Hun; Kim, Jinah; Heo, Ki-Young; Park, Kwang-Soon

2017-04-01

In winter season, large-height swell-like waves have occurred on the East coast of Korea, causing property damages and loss of human life. It is known that those waves are generated by a local strong wind made by temperate cyclone moving to eastward in the East Sea of Korean peninsula. Because the waves are often occurred in the clear weather, in particular, the damages are to be maximized. Therefore, it is necessary to predict and forecast large-height swell-like waves to prevent and correspond to the coastal damages. In Korea, an operational oceanographic system (KOOS) has been developed by the Korea institute of ocean science and technology (KIOST) and KOOS provides daily basis 72-hours' ocean forecasts such as wind, water elevation, sea currents, water temperature, salinity, and waves which are computed from not only meteorological and hydrodynamic model (WRF, ROMS, MOM, and MOHID) but also wave models (WW-III and SWAN). In order to evaluate the model performance and guarantee a certain level of accuracy of ocean forecasts, a Skill Assessment (SA) system was established as a one of module in KOOS. It has been performed through comparison of model results with in-situ observation data and model errors have been quantified with skill scores. Statistics which are used in skill assessment are including a measure of both errors and correlations such as root-mean-square-error (RMSE), root-mean-square-error percentage (RMSE%), mean bias (MB), correlation coefficient (R), scatter index (SI), circular correlation (CC) and central frequency (CF) that is a frequency with which errors lie within acceptable error criteria. It should be utilized simultaneously not only to quantify an error but also to improve an accuracy of forecasts by providing a feedback interactively. However, in an abnormal phenomena such as high-height swell-like waves in the East coast of Korea, it requires more advanced and optimized error quantification method that allows to predict the abnormal