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Sample records for dot-based quantification revealed

  1. Quantum dot-based quantification revealed differences in subcellular localization of EGFR and E-cadherin between EGFR-TKI sensitive and insensitive cancer cells

    NASA Astrophysics Data System (ADS)

    Huang, Dong-hai; Su, Ling; Peng, Xiang-hong; Zhang, Hongzheng; Khuri, Fadlo R.; Shin, Dong M.; Chen, Zhuo

    2009-06-01

    Nanoparticle quantum dots (QDs) provide sharper and more photostable fluorescent signals than organic dyes, allowing quantification of multiple biomarkers simultaneously. In this study, we quantified the expression of epidermal growth factor receptor (EGFR) and E-cadherin (E-cad) in the same cells simultaneously by using secondary antibody-conjugated QDs with two different emission wavelengths (QD605 and QD565) and compared the cellular distribution of EGFR and E-cad between EGFR-tyrosine kinase inhibitor (TKI)-insensitive and -sensitive lung and head and neck cancer cell lines. Relocalization of EGFR and E-cad upon treatment with the EGFR-TKI erlotinib in the presence of EGF was visualized and analyzed quantitatively. Our results showed that QD-immunocytochemistry (ICC)-based technology can not only quantify basal levels of multiple biomarkers but also track the localization of the biomarkers upon biostimulation. With this new technology we found that in EGFR-TKI-insensitive cells, EGFR and E-cad were located mainly in the cytoplasm; while in sensitive cells, they were found mainly on the cell membrane. After induction with EGF, both EGFR and E-cad internalized to the cytoplasm, but the internalization capability in sensitive cells was greater than that in insensitive cells. Quantification also showed that inhibition of EGF-induced EGFR and E-cad internalization by erlotinib in the sensitive cells was stronger than that in the insensitive cells. These studies demonstrate substantial differences between EGFR-TKI-insensitive and -sensitive cancer cells in EGFR and E-cad expression and localization both at the basal level and in response to EGF and erlotinib. QD-based analysis facilitates the understanding of the features of EGFR-TKI-insensitive versus -sensitive cancer cells and may be used in the prediction of patient response to EGFR-targeted therapy.

  2. In vivo behavior of NTBI revealed by automated quantification system.

    PubMed

    Ito, Satoshi; Ikuta, Katsuya; Kato, Daisuke; Lynda, Addo; Shibusa, Kotoe; Niizeki, Noriyasu; Toki, Yasumichi; Hatayama, Mayumi; Yamamoto, Masayo; Shindo, Motohiro; Iizuka, Naomi; Kohgo, Yutaka; Fujiya, Mikihiro

    2016-08-01

    Non-Tf-bound iron (NTBI), which appears in serum in iron overload, is thought to contribute to organ damage; the monitoring of serum NTBI levels may therefore be clinically useful in iron-overloaded patients. However, NTBI quantification methods remain complex, limiting their use in clinical practice. To overcome the technical difficulties often encountered, we recently developed a novel automated NTBI quantification system capable of measuring large numbers of samples. In the present study, we investigated the in vivo behavior of NTBI in human and animal serum using this newly established automated system. Average NTBI in healthy volunteers was 0.44 ± 0.076 μM (median 0.45 μM, range 0.28-0.66 μM), with no significant difference between sexes. Additionally, serum NTBI rapidly increased after iron loading, followed by a sudden disappearance. NTBI levels also decreased in inflammation. The results indicate that NTBI is a unique marker of iron metabolism, unlike other markers of iron metabolism, such as serum ferritin. Our new automated NTBI quantification method may help to reveal the clinical significance of NTBI and contribute to our understanding of iron overload. PMID:27086349

  3. Quantification of the stapedial reflex reveals delayed responses in autism.

    PubMed

    Lukose, Richard; Brown, Kevin; Barber, Carol M; Kulesza, Randy Joseph

    2013-10-01

    Autism is a developmental disorder characterized, in part, by sensory abnormalities. It is well established that most if not all patients with autism have problems with auditory processing, ranging from deafness to hyperacusis, and physiological testing of auditory function (i.e. auditory brain stem responses) implicates brain stem dysfunction in autism. Additionally, previous research from this lab has revealed significantly fewer auditory brain stem neurons in autistic subjects as young as 2 years of age. These observations have led us to hypothesize that objective, noninvasive measures of auditory function can be used as an early screening tool to identify neonates with an elevated risk of carrying a diagnosis of autism. Here, we provide a detailed quantitative investigation of the acoustic stapedial reflex (ASR), a three- or four-neuron brain stem circuit, in young autistic subjects and normal developing controls. Indeed, we find significantly lower thresholds, responses occurring at significantly longer latency and right-left asymmetry in autistic subjects. The results from this investigation support deficits in auditory function as a cardinal feature of autism and suggest that individuals with autism can be identified by their ASR responses. PMID:23825093

  4. Competitive hybridization in quantum dot-based nanodevices

    NASA Astrophysics Data System (ADS)

    Beltako, Katawoura; Cavassilas, Nicolas; Michelini, Fabienne

    2016-03-01

    By means of nonequilibrium Green's functions using the Born approximation to treat the light-matter coupling, we numerically investigate impacts of competitive hybridization on the photocurrent of a quantum dot based optoelectronic device. The model of device is an absorbing quantum dot connected to two semiconducting electrodes through energy filtering quantum dots. Hybridization occurs between the absorber and the filter, via the inter-dot coupling β, and between the filter and the electrode, via the dot-lead coupling Γ. At the tunnel resonance between the absorber and the filter, the investigation reveals the existence of two operating regimes in the nanodevice characterized by opposite variations of the photocurrent depending on ratio β/ Γ.

  5. Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

    PubMed Central

    Smits, Arne H.; Lindeboom, Rik G.H.; Perino, Matteo; van Heeringen, Simon J.; Veenstra, Gert Jan C.; Vermeulen, Michiel

    2014-01-01

    While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass spectrometry-based proteomics, quantifying over 5800 proteins in the largest single cell proteome characterized to date. Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance. Protein copy numbers in single eggs range from tens of thousands to ten trillion copies per cell. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identify 439 proteins that significantly change in abundance during early embryogenesis. Downregulated proteins include ribosomal proteins and upregulated proteins include basal transcription factors, among others. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in X. laevis eggs. PMID:25056316

  6. A six-plex proteome quantification strategy reveals the dynamics of protein turnover.

    PubMed

    Wang, Fangjun; Cheng, Kai; Wei, Xiaoluan; Qin, Hongqiang; Chen, Rui; Liu, Jing; Zou, Hanfa

    2013-01-01

    MS1 full scan based quantification is one of the most popular approaches for large-scale proteome quantification. Typically only three different samples can be differentially labeled and quantified in a single experiment. Here we present a two stages stable isotope labeling strategy which allows six different protein samples (six-plex) to be reliably labeled and simultaneously quantified at MS1 level. Briefly in the first stage, isotope lysine-d0 (K0) and lysine-d4 (K4) are in vivo incorporated into different protein samples during cell culture. Then in the second stage, three of K0 and K4 labeled protein samples are digested by lysine C and in vitro labeled with light (2CH3), medium (2CD2H), and heavy (2(13)CD3) dimethyl groups, respectively. We demonstrated that this six-plex isotope labeling strategy could successfully investigate the dynamics of protein turnover in a high throughput manner. PMID:23661174

  7. Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins.

    PubMed

    Narumi, Ryohei; Shimizu, Yoshihiro; Ukai-Tadenuma, Maki; Ode, Koji L; Kanda, Genki N; Shinohara, Yuta; Sato, Aya; Matsumoto, Katsuhiko; Ueda, Hiroki R

    2016-06-14

    Absolute values of protein expression levels in cells are crucial information for understanding cellular biological systems. Precise quantification of proteins can be achieved by liquid chromatography (LC)-mass spectrometry (MS) analysis of enzymatic digests of proteins in the presence of isotope-labeled internal standards. Thus, development of a simple and easy way for the preparation of internal standards is advantageous for the analyses of multiple target proteins, which will allow systems-level studies. Here we describe a method, termed MS-based Quantification By isotope-labeled Cell-free products (MS-QBiC), which provides the simple and high-throughput preparation of internal standards by using a reconstituted cell-free protein synthesis system, and thereby facilitates both multiplexed and sensitive quantification of absolute amounts of target proteins. This method was applied to a systems-level dynamic analysis of mammalian circadian clock proteins, which consist of transcription factors and protein kinases that govern central and peripheral circadian clocks in mammals. Sixteen proteins from 20 selected circadian clock proteins were successfully quantified from mouse liver over a 24-h time series, and 14 proteins had circadian variations. Quantified values were applied to detect internal body time using a previously developed molecular timetable method. The analyses showed that single time-point data from wild-type mice can predict the endogenous state of the circadian clock, whereas data from clock mutant mice are not applicable because of the disappearance of circadian variation. PMID:27247408

  8. Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis.

    PubMed

    Akama, Satoru; Shimizu-Inatsugi, Rie; Shimizu, Kentaro K; Sese, Jun

    2014-04-01

    Genome duplication with hybridization, or allopolyploidization, occurs commonly in plants, and is considered to be a strong force for generating new species. However, genome-wide quantification of homeolog expression ratios was technically hindered because of the high homology between homeologous gene pairs. To quantify the homeolog expression ratio using RNA-seq obtained from polyploids, a new method named HomeoRoq was developed, in which the genomic origin of sequencing reads was estimated using mismatches between the read and each parental genome. To verify this method, we first assembled the two diploid parental genomes of Arabidopsis halleri subsp. gemmifera and Arabidopsis lyrata subsp. petraea (Arabidopsis petraea subsp. umbrosa), then generated a synthetic allotetraploid, mimicking the natural allopolyploid Arabidopsis kamchatica. The quantified ratios corresponded well to those obtained by Pyrosequencing. We found that the ratios of homeologs before and after cold stress treatment were highly correlated (r = 0.870). This highlights the presence of nonstochastic polyploid gene regulation despite previous research identifying stochastic variation in expression. Moreover, our new statistical test incorporating overdispersion identified 226 homeologs (1.11% of 20 369 expressed homeologs) with significant ratio changes, many of which were related to stress responses. HomeoRoq would contribute to the study of the genes responsible for polyploid-specific environmental responses. PMID:24423873

  9. Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism.

    PubMed

    Chen, Walter W; Freinkman, Elizaveta; Wang, Tim; Birsoy, Kıvanç; Sabatini, David M

    2016-08-25

    Mitochondria house metabolic pathways that impact most aspects of cellular physiology. While metabolite profiling by mass spectrometry is widely applied at the whole-cell level, it is not routinely possible to measure the concentrations of small molecules in mammalian organelles. We describe a method for the rapid and specific isolation of mitochondria and use it in tandem with a database of predicted mitochondrial metabolites ("MITObolome") to measure the matrix concentrations of more than 100 metabolites across various states of respiratory chain (RC) function. Disruption of the RC reveals extensive compartmentalization of mitochondrial metabolism and signatures unique to the inhibition of each RC complex. Pyruvate enables the proliferation of RC-deficient cells but has surprisingly limited effects on matrix contents. Interestingly, despite failing to restore matrix NADH/NAD balance, pyruvate does increase aspartate, likely through the exchange of matrix glutamate for cytosolic aspartate. We demonstrate the value of mitochondrial metabolite profiling and describe a strategy applicable to other organelles. PMID:27565352

  10. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

    DOE PAGES

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-10-13

    Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test thismore » strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.« less

  11. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

    SciTech Connect

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-10-13

    Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.

  12. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.

    PubMed

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-10-28

    Reengineering protein-protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of "second-site suppressors," where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein-protein interfaces. To extend this approach, it would be advantageous to be able to "transplant" existing engineered and experimentally validated specificity changes to other homologous protein-protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain-peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein-protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. Although the context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein-protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.

  13. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition.

    PubMed

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-10-28

    Reengineering protein-protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of "second-site suppressors," where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein-protein interfaces. To extend this approach, it would be advantageous to be able to "transplant" existing engineered and experimentally validated specificity changes to other homologous protein-protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain-peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein-protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. Although the context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein-protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context. PMID:25313039

  14. Quantum Dots-based Reverse Phase Protein Microarray

    SciTech Connect

    Shingyoji, Masato; Gerion, Daniele; Pinkel, Dan; Gray, Joe W.; Chen, Fanqing

    2005-07-15

    CdSe nanocrystals, also called quantum dots (Qdots) are a novel class of fluorophores, which have a diameter of a few nanometers and possess high quantum yield, tunable emission wavelength and photostability. They are an attractive alternative to conventional fluorescent dyes. Quantum dots can be silanized to be soluble in aqueous solution under biological conditions, and thus be used in bio-detection. In this study, we established a novel Qdot-based technology platform that can perform accurate and reproducible quantification of protein concentration in a crude cell lysate background. Protein lysates have been spiked with a target protein, and a dilution series of the cell lysate with a dynamic range of three orders of magnitude has been used for this proof-of-concept study. The dilution series has been spotted in microarray format, and protein detection has been achieved with a sensitivity that is at least comparable to standard commercial assays, which are based on horseradish peroxidase (HRP) catalyzed diaminobenzidine (DAB) chromogenesis. The data obtained through the Qdot method has shown a close linear correlation between relative fluorescence unit and relative protein concentration. The Qdot results are in almost complete agreement with data we obtained with the well-established HRP-DAB colorimetric array (R{sup 2} = 0.986). This suggests that Qdots can be used for protein quantification in microarray format, using the platform presented here.

  15. Quantum dot-based microfluidic biosensor for cancer detection

    NASA Astrophysics Data System (ADS)

    Ghrera, Aditya Sharma; Pandey, Chandra Mouli; Ali, Md. Azahar; Malhotra, Bansi Dhar

    2015-05-01

    We report results of the studies relating to fabrication of an impedimetric microfluidic-based nucleic acid sensor for quantification of DNA sequences specific to chronic myelogenous leukemia (CML). The sensor chip is prepared by patterning an indium-tin-oxide (ITO) coated glass substrate via wet chemical etching method followed by sealing with polydimethylsiloxane (PDMS) microchannel for fluid control. The fabricated microfluidic chip comprising of a patterned ITO substrate is modified by depositing cadmium selenide quantum dots (QCdSe) via Langmuir-Blodgett technique. Further, the QCdSe surface has been functionalized with specific DNA probe for CML detection. The probe DNA functionalized QCdSe integrated miniaturized system has been used to monitor target complementary DNA concentration by measuring the interfacial charge transfer resistance via hybridization. The presence of complementary DNA in buffer solution significantly results in decreased electro-conductivity of the interface due to presence of a charge barrier for transport of the redox probe ions. The microfluidic DNA biosensor exhibits improved linearity in the concentration range of 10-15 M to 10-11 M.

  16. Quantum dot-based microfluidic biosensor for cancer detection

    SciTech Connect

    Ghrera, Aditya Sharma; Pandey, Chandra Mouli; Ali, Md. Azahar; Malhotra, Bansi Dhar

    2015-05-11

    We report results of the studies relating to fabrication of an impedimetric microfluidic–based nucleic acid sensor for quantification of DNA sequences specific to chronic myelogenous leukemia (CML). The sensor chip is prepared by patterning an indium–tin–oxide (ITO) coated glass substrate via wet chemical etching method followed by sealing with polydimethylsiloxane (PDMS) microchannel for fluid control. The fabricated microfluidic chip comprising of a patterned ITO substrate is modified by depositing cadmium selenide quantum dots (QCdSe) via Langmuir–Blodgett technique. Further, the QCdSe surface has been functionalized with specific DNA probe for CML detection. The probe DNA functionalized QCdSe integrated miniaturized system has been used to monitor target complementary DNA concentration by measuring the interfacial charge transfer resistance via hybridization. The presence of complementary DNA in buffer solution significantly results in decreased electro-conductivity of the interface due to presence of a charge barrier for transport of the redox probe ions. The microfluidic DNA biosensor exhibits improved linearity in the concentration range of 10{sup −15} M to 10{sup −11} M.

  17. Quantum-dot based nanothermometry in optical plasmonic recording media

    SciTech Connect

    Maestro, Laura Martinez; Zhang, Qiming; Li, Xiangping; Gu, Min; Jaque, Daniel

    2014-11-03

    We report on the direct experimental determination of the temperature increment caused by laser irradiation in a optical recording media constituted by a polymeric film in which gold nanorods have been incorporated. The incorporation of CdSe quantum dots in the recording media allowed for single beam thermal reading of the on-focus temperature from a simple analysis of the two-photon excited fluorescence of quantum dots. Experimental results have been compared with numerical simulations revealing an excellent agreement and opening a promising avenue for further understanding and optimization of optical writing processes and media.

  18. A triple quantum dot based nano-electromechanical memory device

    SciTech Connect

    Pozner, R.; Lifshitz, E.; Peskin, U.

    2015-09-14

    Colloidal quantum dots (CQDs) are free-standing nano-structures with chemically tunable electronic properties. This tunability offers intriguing possibilities for nano-electromechanical devices. In this work, we consider a nano-electromechanical nonvolatile memory (NVM) device incorporating a triple quantum dot (TQD) cluster. The device operation is based on a bias induced motion of a floating quantum dot (FQD) located between two bound quantum dots (BQDs). The mechanical motion is used for switching between two stable states, “ON” and “OFF” states, where ligand-mediated effective interdot forces between the BQDs and the FQD serve to hold the FQD in each stable position under zero bias. Considering realistic microscopic parameters, our quantum-classical theoretical treatment of the TQD reveals the characteristics of the NVM.

  19. Quantification of immunogold labelling reveals enrichment of glutamate in mossy and parallel fibre terminals in cat cerebellum.

    PubMed

    Somogyi, P; Halasy, K; Somogyi, J; Storm-Mathisen, J; Ottersen, O P

    1986-12-01

    The glutamate immunoreactivity of different cell populations was compared quantitatively in the cerebellar cortex of cat, using an antiserum raised against glutamate coupled to bovine serum albumin by glutaraldehyde. Neuronal and glial processes were identified on serial electron microscopic sections which were processed by a postembedding immunogold procedure. The surface density of colloidal gold particles was used for statistical comparison of the relative levels of glutamate in cell populations, or in different parts of the same population. The terminals of mossy and parallel fibres had significantly higher levels of glutamate immunoreactivity than Golgi cell terminals, granule cell dendritic digits, Purkinje cell dendrites or dendritic spines. Golgi cell terminals were identified by their position and GABA immunoreactivity as revealed by immunogold in serial sections. The dendritic digits of the putative glutamatergic granule cells had significantly higher glutamate immunoreactivity than did Purkinje cell dendrites and dendritic spines. Glial cell processes in the molecular layer had lower level of glutamate immunoreactivity than any of the neuronal processes. The results demonstrate that the highest levels of glutamate immunoreactivity occur in mossy and parallel fibre presynaptic terminals that are known to have an excitatory effect. This supports previous suggestions that glutamate may be a transmitter at these synapses. The measurement of the levels of putative amino acid transmitters in identified neuronal populations, or in different parts of the same population, could have wide applications in studies on the chemical neuroanatomy of the nervous system.

  20. Single-cell quantification of IL-2 response by effector and regulatory T cells reveals critical plasticity in immune response

    PubMed Central

    Feinerman, Ofer; Jentsch, Garrit; Tkach, Karen E; Coward, Jesse W; Hathorn, Matthew M; Sneddon, Michael W; Emonet, Thierry; Smith, Kendall A; Altan-Bonnet, Grégoire

    2010-01-01

    Understanding how the immune system decides between tolerance and activation by antigens requires addressing cytokine regulation as a highly dynamic process. We quantified the dynamics of interleukin-2 (IL-2) signaling in a population of T cells during an immune response by combining in silico modeling and single-cell measurements in vitro. We demonstrate that IL-2 receptor expression levels vary widely among T cells creating a large variability in the ability of the individual cells to consume, produce and participate in IL-2 signaling within the population. Our model reveals that at the population level, these heterogeneous cells are engaged in a tug-of-war for IL-2 between regulatory (Treg) and effector (Teff) T cells, whereby access to IL-2 can either increase the survival of Teff cells or the suppressive capacity of Treg cells. This tug-of-war is the mechanism enforcing, at the systems level, a core function of Treg cells, namely the specific suppression of survival signals for weakly activated Teff cells but not for strongly activated cells. Our integrated model yields quantitative, experimentally validated predictions for the manipulation of Treg suppression. PMID:21119631

  1. Quantification of human-associated fecal indicators reveal sewage from urban watersheds as a source of pollution to Lake Michigan.

    PubMed

    Templar, Hayley A; Dila, Deborah K; Bootsma, Melinda J; Corsi, Steven R; McLellan, Sandra L

    2016-09-01

    Sewage contamination of urban waterways from sewer overflows and failing infrastructure is a major environmental and public health concern. Fecal coliforms (FC) are commonly employed as fecal indicator bacteria, but do not distinguish between human and non-human sources of fecal contamination. Human Bacteroides and human Lachnospiraceae, two genetic markers for human-associated indicator bacteria, were used to identify sewage signals in two urban rivers and the estuary that drains to Lake Michigan. Grab samples were collected from the rivers throughout 2012 and 2013 and hourly samples were collected in the estuary across the hydrograph during summer 2013. Human Bacteroides and human Lachnospiraceae were highly correlated with each other in river samples (Pearson's r = 0.86), with average concentrations at most sites elevated during wet weather. These human indicators were found during baseflow, indicating that sewage contamination is chronic in these waterways. FC are used for determining total maximum daily loads (TMDLs) in management plans; however, FC concentrations alone failed to prioritize river reaches with potential health risks. While 84% of samples with >1000 CFU/100 ml FC had sewage contamination, 52% of samples with moderate (200-1000 CFU/100 ml) and 46% of samples with low (<200 CFU/100 ml) FC levels also had evidence of human sewage. Load calculations in the in the Milwaukee estuary revealed storm-driven sewage contamination varied greatly among events and was highest during an event with a short duration of intense rain. This work demonstrates urban areas have unrecognized sewage inputs that may not be adequately prioritized for remediation by the TMDL process. Further analysis using these approaches could determine relationships between land use, storm characteristics, and other factors that drive sewage contamination in urban waterways. PMID:27236594

  2. Quantification of human-associated fecal indicators reveal sewage from urban watersheds as a source of pollution to Lake Michigan.

    PubMed

    Templar, Hayley A; Dila, Deborah K; Bootsma, Melinda J; Corsi, Steven R; McLellan, Sandra L

    2016-09-01

    Sewage contamination of urban waterways from sewer overflows and failing infrastructure is a major environmental and public health concern. Fecal coliforms (FC) are commonly employed as fecal indicator bacteria, but do not distinguish between human and non-human sources of fecal contamination. Human Bacteroides and human Lachnospiraceae, two genetic markers for human-associated indicator bacteria, were used to identify sewage signals in two urban rivers and the estuary that drains to Lake Michigan. Grab samples were collected from the rivers throughout 2012 and 2013 and hourly samples were collected in the estuary across the hydrograph during summer 2013. Human Bacteroides and human Lachnospiraceae were highly correlated with each other in river samples (Pearson's r = 0.86), with average concentrations at most sites elevated during wet weather. These human indicators were found during baseflow, indicating that sewage contamination is chronic in these waterways. FC are used for determining total maximum daily loads (TMDLs) in management plans; however, FC concentrations alone failed to prioritize river reaches with potential health risks. While 84% of samples with >1000 CFU/100 ml FC had sewage contamination, 52% of samples with moderate (200-1000 CFU/100 ml) and 46% of samples with low (<200 CFU/100 ml) FC levels also had evidence of human sewage. Load calculations in the in the Milwaukee estuary revealed storm-driven sewage contamination varied greatly among events and was highest during an event with a short duration of intense rain. This work demonstrates urban areas have unrecognized sewage inputs that may not be adequately prioritized for remediation by the TMDL process. Further analysis using these approaches could determine relationships between land use, storm characteristics, and other factors that drive sewage contamination in urban waterways.

  3. Quantification of human-associated fecal indicators reveal sewage from urban watersheds as a source of pollution to Lake Michigan

    USGS Publications Warehouse

    Templar, Hayley A.; Dila, Deborah K.; Bootsma, Melinda J.; Corsi, Steven; McLellan, Sandra L.

    2016-01-01

    Sewage contamination of urban waterways from sewer overflows and failing infrastructure is a major environmental and public health concern. Fecal coliforms (FC) are commonly employed as fecal indicator bacteria, but do not distinguish between human and non-human sources of fecal contamination. Human Bacteroides and humanLachnospiraceae, two genetic markers for human-associated indicator bacteria, were used to identify sewage signals in two urban rivers and the estuary that drains to Lake Michigan. Grab samples were collected from the rivers throughout 2012 and 2013 and hourly samples were collected in the estuary across the hydrograph during summer 2013. Human Bacteroides and human Lachnospiraceae were highly correlated with each other in river samples (Pearson’s r = 0.86), with average concentrations at most sites elevated during wet weather. These human indicators were found during baseflow, indicating that sewage contamination is chronic in these waterways. FC are used for determining total maximum daily loads (TMDLs) in management plans; however, FC concentrations alone failed to prioritize river reaches with potential health risks. While 84% of samples with >1000 CFU/100 ml FC had sewage contamination, 52% of samples with moderate (200–1000 CFU/100 ml) and 46% of samples with low (<200 CFU/100 ml) FC levels also had evidence of human sewage. Load calculations in the in the Milwaukee estuary revealed storm-driven sewage contamination varied greatly among events and was highest during an event with a short duration of intense rain. This work demonstrates urban areas have unrecognized sewage inputs that may not be adequately prioritized for remediation by the TMDL process. Further analysis using these approaches could determine relationships between land use, storm characteristics, and other factors that drive sewage contamination in urban waterways.

  4. Semi-automated quantification of C9orf72 expansion size reveals inverse correlation between hexanucleotide repeat number and disease duration in frontotemporal degeneration.

    PubMed

    Suh, EunRan; Lee, Edward B; Neal, Donald; Wood, Elisabeth M; Toledo, Jon B; Rennert, Lior; Irwin, David J; McMillan, Corey T; Krock, Bryan; Elman, Lauren B; McCluskey, Leo F; Grossman, Murray; Xie, Sharon X; Trojanowski, John Q; Van Deerlin, Vivianna M

    2015-09-01

    We investigated whether chromosome 9 open reading frame 72 hexanucleotide repeat expansion (C9orf72 expansion) size in peripheral DNA was associated with clinical differences in frontotemporal degeneration (FTD) and amyotrophic lateral sclerosis (ALS) linked to C9orf72 repeat expansion mutations. A novel quantification workflow was developed to measure C9orf72 expansion size by Southern blot densitometry in a cross-sectional cohort of C9orf72 expansion carriers with FTD (n = 39), ALS (n = 33), both (n = 35), or who are unaffected (n = 21). Multivariate linear regressions were performed to assess whether C9orf72 expansion size from peripheral DNA was associated with clinical phenotype, age of disease onset, disease duration and age at death. Mode values of C9orf72 expansion size were significantly shorter in FTD compared to ALS (p = 0.0001) but were not associated with age at onset in either FTD or ALS. A multivariate regression model correcting for patient's age at DNA collection and disease phenotype revealed that C9orf72 expansion size is significantly associated with shorter disease duration (p = 0.0107) for individuals with FTD, but not with ALS. Despite considerable somatic instability of the C9orf72 expansion, semi-automated expansion size measurements demonstrated an inverse relationship between C9orf72 expansion size and disease duration in patients with FTD. Our finding suggests that C9orf72 repeat size may be a molecular disease modifier in FTD linked to hexanucleotide repeat expansion.

  5. Single Cell Quantification of Reporter Gene Expression in Live Adult Caenorhabditis elegans Reveals Reproducible Cell-Specific Expression Patterns and Underlying Biological Variation.

    PubMed

    Mendenhall, Alexander R; Tedesco, Patricia M; Sands, Bryan; Johnson, Thomas E; Brent, Roger

    2015-01-01

    In multicellular organisms such as Caenorhabditis elegans, differences in complex phenotypes such as lifespan correlate with the level of expression of particular engineered reporter genes. In single celled organisms, quantitative understanding of responses to extracellular signals and of cell-to-cell variation in responses has depended on precise measurement of reporter gene expression. Here, we developed microscope-based methods to quantify reporter gene expression in cells of Caenorhabditis elegans with low measurement error. We then quantified expression in strains that carried different configurations of Phsp-16.2-fluorescent-protein reporters, in whole animals, and in all 20 cells of the intestine tissue, which is responsible for most of the fluorescent signal. Some animals bore more recently developed single copy Phsp-16.2 reporters integrated at defined chromosomal sites, others, "classical" multicopy reporter gene arrays integrated at random sites. At the level of whole animals, variation in gene expression was similar: strains with single copy reporters showed the same amount of animal-to-animal variation as strains with multicopy reporters. At the level of cells, in animals with single copy reporters, the pattern of expression in cells within the tissue was highly stereotyped. In animals with multicopy reporters, the cell-specific expression pattern was also stereotyped, but distinct, and somewhat more variable. Our methods are rapid and gentle enough to allow quantification of expression in the same cells of an animal at different times during adult life. They should allow investigators to use changes in reporter expression in single cells in tissues as quantitative phenotypes, and link those to molecular differences. Moreover, by diminishing measurement error, they should make possible dissection of the causes of the remaining, real, variation in expression. Understanding such variation should help reveal its contribution to differences in complex

  6. Pump dependence of the dynamics of quantum dot based waveguide absorbers

    NASA Astrophysics Data System (ADS)

    Viktorov, Evgeny A.; Erneux, Thomas; Piwonski, Tomasz; Pulka, Jaroslaw; Huyet, Guillaume; Houlihan, John

    2012-06-01

    The nonlinear two stage recovery of quantum dot based reverse-biased waveguide absorbers is investigated experimentally and analytically as a function of the initial ground state occupation probability of the dot. The latter is controlled experimentally by the pump pulse power. The slow stage of the recovery is exponential and its basic timescale is independent of pump power. The fast stage of the recovery is a logistic function which we analyze in detail. The relative strength of slow to fast components is highlighted and the importance of higher order absorption processes at the highest pump level is demonstrated.

  7. A Novel Quantum Dots-Based Point of Care Test for Syphilis

    NASA Astrophysics Data System (ADS)

    Yang, Hao; Li, Ding; He, Rong; Guo, Qin; Wang, Kan; Zhang, Xueqing; Huang, Peng; Cui, Daxiang

    2010-05-01

    One-step lateral flow test is recommended as the first line screening of syphilis for primary healthcare settings in developing countries. However, it generally shows low sensitivity. We describe here the development of a novel fluorescent POC (Point Of Care) test method to be used for screening for syphilis. The method was designed to combine the rapidness of lateral flow test and sensitiveness of fluorescent method. 50 syphilis-positive specimens and 50 healthy specimens conformed by Treponema pallidum particle agglutination (TPPA) were tested with Quantum Dot-labeled and colloidal gold-labeled lateral flow test strips, respectively. The results showed that both sensitivity and specificity of the quantum dots-based method reached up to 100% (95% confidence interval [CI], 91-100%), while those of the colloidal gold-based method were 82% (95% CI, 68-91%) and 100% (95% CI, 91-100%), respectively. In addition, the naked-eye detection limit of quantum dot-based method could achieve 2 ng/ml of anti-TP47 polyclonal antibodies purified by affinity chromatography with TP47 antigen, which was tenfold higher than that of colloidal gold-based method. In conclusion, the quantum dots were found to be suitable for labels of lateral flow test strip. Its ease of use, sensitiveness and low cost make it well-suited for population-based on-the-site syphilis screening.

  8. Quantum-dot based ultrafast photoconductive antennae for efficient THz radiation

    NASA Astrophysics Data System (ADS)

    Gorodetsky, Andrei; Bazieva, Natalia; Rafailov, Edik U.

    2016-03-01

    Here we overview our work on quantum dot based THz photoconductive antennae, capable of being pumped at very high optical intensities of higher than 1W optical mean power, i.e. about 50 times higher than the conventional LT-GaAs based antennae. Apart from high thermal tolerance, defect-free GaAs crystal layers in an InAs:GaAs quantum dot structure allow high carrier mobility and ultra-short photo carrier lifetimes simultaneously. Thus, they combine the advantages and lacking the disadvantages of GaAs and LT-GaAs, which are the most popular materials so far, and thus can be used for both CW and pulsed THz generation. By changing quantum dot size, composition, density of dots and number of quantum dot layers, the optoelectronic properties of the overall structure can be set over a reasonable range-compact semiconductor pump lasers that operate at wavelengths in the region of 1.0 μm to 1.3 μm can be used. InAs:GaAs quantum dot-based antennae samples show no saturation in pulsed THz generation for all average pump powers up to 1W focused into 30 μm spot. Generated THz power is super-linearly proportional to laser pump power. The generated THz spectrum depends on antenna design and can cover from 150 GHz up to 1.5 THz.

  9. Quantum dot-based molecular imaging of cancer cell growth using a clone formation assay

    PubMed Central

    Geng, Xia-Fei; Fang, Min; Liu, Shao-Ping; Li, Yan

    2016-01-01

    This aim of the present study was to investigate clonal growth behavior and analyze the proliferation characteristics of cancer cells. The MCF-7 human breast cancer cell line, SW480 human colon cancer cell line and SGC7901 human gastric cancer cell line were selected to investigate the morphology of cell clones. Quantum dot-based molecular targeted imaging techniques (which stained pan-cytokeratin in the cytoplasm green and Ki67 in the cell nucleus yellow or red) were used to investigate the clone formation rate, cell morphology, discrete tendency, and Ki67 expression and distribution in clones. From the cell clone formation assay, the MCF-7, SW480 and SGC7901 cells were observed to form clones on days 6, 8 and 12 of cell culture, respectively. These three types of cells had heterogeneous morphology, large nuclear:cytoplasmic ratios, and conspicuous pathological mitotic features. The cells at the clone periphery formed multiple pseudopodium. In certain clones, cancer cells at the borderline were separated from the central cell clusters or presented a discrete tendency. With quantum dot-based molecular targeted imaging techniques, cells with strong Ki67 expression were predominantly shown to be distributed at the clone periphery, or concentrated on one side of the clones. In conclusion, cancer cell clones showed asymmetric growth behavior, and Ki67 was widely expressed in clones of these three cell lines, with strong expression around the clones, or aggregated at one side. Cell clone formation assay based on quantum dots molecular imaging offered a novel method to study the proliferative features of cancer cells, thus providing a further insight into tumor biology. PMID:27572664

  10. Specific detection of the cleavage activity of mycobacterial enzymes using a quantum dot based DNA nanosensor

    NASA Astrophysics Data System (ADS)

    Jepsen, Morten Leth; Harmsen, Charlotte; Godbole, Adwait Anand; Nagaraja, Valakunja; Knudsen, Birgitta R.; Ho, Yi-Ping

    2015-12-01

    We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes.We present a quantum dot based DNA nanosensor specifically targeting the cleavage step in the reaction cycle of the essential DNA-modifying enzyme, mycobacterial topoisomerase I. The design takes advantages of the unique photophysical properties of quantum dots to generate visible fluorescence recovery upon specific cleavage by mycobacterial topoisomerase I. This report, for the first time, demonstrates the possibility to quantify the cleavage activity of the mycobacterial enzyme without the pre-processing sample purification or post-processing signal amplification. The cleavage induced signal response has also proven reliable in biological matrices, such as whole cell extracts prepared from Escherichia coli and human Caco-2 cells. It is expected that the assay may contribute to the clinical diagnostics of bacterial diseases, as well as the evaluation of treatment outcomes. Electronic supplementary information (ESI) available: Characterization of the QD-based DNA Nanosensor. See DOI: 10.1039/c5nr06326d

  11. A novel method for high-throughput detection and quantification of neutrophil extracellular traps reveals ROS-independent NET release with immune complexes.

    PubMed

    Kraaij, Tineke; Tengström, Fredrik C; Kamerling, Sylvia W A; Pusey, Charles D; Scherer, H Ulrich; Toes, Rene E M; Rabelink, Ton J; van Kooten, Cees; Teng, Y K Onno

    2016-06-01

    A newly-described first-line immune defence mechanism of neutrophils is the release of neutrophil extracellular traps (NETs). Immune complexes (ICxs) induce low level NET release. As such, the in vitro quantification of NETs is challenging with current methodologies. In order to investigate the role of NET release in ICx-mediated autoimmune diseases, we developed a highly sensitive and automated method for quantification of NETs. After labelling human neutrophils with PKH26 and extracellular DNA with Sytox green, cells are fixed and automatically imaged with 3-dimensional confocal laser scanning microscopy (3D-CLSM). NET release is then quantified with digital image analysis whereby the NET amount (Sytox green area) is corrected for the number of imaged neutrophils (PKH26 area). A high sensitivity of the assay is achieved by a) significantly augmenting the area of the well imaged (11%) as compared to conventional assays (0.5%) and b) using a 3D imaging technique for optimal capture of NETs, which are topologically superimposed on neutrophils. In this assay, we confirmed low levels of NET release upon human ICx stimulation which were positive for citrullinated histones and neutrophil elastase. In contrast to PMA-induced NET release, ICx-induced NET release was unchanged when co-incubated with diphenyleneiodonium (DPI). We were able to quantify NET release upon stimulation with serum from RA and SLE patients, which was not observed with normal human serum. To our knowledge, this is the first semi-automated assay capable of sensitive detection and quantification of NET release at a low threshold by using 3D CLSM. The assay is applicable in a high-throughput manner and allows the in vitro analysis of NET release in ICx-mediated autoimmune diseases.

  12. Quantum Dot-Based Luminescent Oxygen Channeling Assay for Potential Application in Homogeneous Bioassays.

    PubMed

    Zhuang, Si-Hui; Guo, Xin-Xin; Wu, Ying-Song; Chen, Zhen-Hua; Chen, Yao; Ren, Zhi-Qi; Liu, Tian-Cai

    2016-01-01

    The unique photoproperties of quantum dots are promising for potential application in bioassays. In the present study, quantum dots were applied to a luminescent oxygen channeling assay. The reaction system developed in this study was based on interaction of biotin with streptavidin. Carboxyl-modified polystyrene microspheres doped with quantum dots were biotinylated and used as acceptors. Photosensitizer-doped carboxyl-modified polystyrene microspheres were conjugated with streptavidin and used as donors. The results indicated that the singlet oxygen that was released from the donor beads diffused into the acceptor beads. The acceptor beads were then exited via thioxene, and were subsequently fluoresced. To avoid generating false positives, a high concentration (0.01 mg/mL) of quantum dots is required for application in homogeneous immunoassays. Compared to a conventional luminescent oxygen channeling assay, this quantum dots-based technique requires less time, and would be easier to automate and miniaturize because it requires no washing to remove excess labels.

  13. Quantification of sphingosine 1-phosphate by validated LC-MS/MS method revealing strong correlation with apolipoprotein M in plasma but not in serum due to platelet activation during blood coagulation.

    PubMed

    Frej, Cecilia; Andersson, Anders; Larsson, Benny; Guo, Li Jun; Norström, Eva; Happonen, Kaisa E; Dahlbäck, Björn

    2015-11-01

    Sphingosine 1-phosphate (S1P) is a signalling sphingolipid affecting multiple cellular functions of vascular and immune systems. It circulates at submicromolar levels bound to HDL-associated apolipoprotein M (apoM) or to albumin. S1P in blood is mainly produced by platelets and erythrocytes, making blood sampling for S1P quantification delicate. Standardisation of sampling is thereby of great importance to obtain robust data. By optimising and characterising the extraction procedure and the LC-MS/MS analysis, we have developed and validated a highly specific and sensitive method for S1P quantification. Blood was collected from healthy individuals (n = 15) to evaluate the effects of differential blood sampling on S1P levels. To evaluate correlation between S1P and apoM in different types of plasma and serum, apoM was measured by ELISA. The method showed good accuracy and precision in the range of 0.011 to 0.9 μM with less than 0.07 % carryover. We found that the methanol precipitation used to extract S1P co-extracted apoM and several other HDL-proteins from plasma. The platelet-associated S1P was released during coagulation, thus increasing the S1P concentration to double in serum as compared to that in plasma. Gel filtration chromatography revealed that the platelet-released S1P was mainly bound to albumin. This explains why the strong correlation between S1P and apoM levels in plasma is lost upon the clotting process and hence not observed in serum. We have developed, characterised and validated an efficient, highly sensitive and specific method for the quantification of S1P in biological material.

  14. Role of gibberellins during arbuscular mycorrhizal formation in tomato: new insights revealed by endogenous quantification and genetic analysis of their metabolism in mycorrhizal roots.

    PubMed

    Martín-Rodríguez, José Ángel; Ocampo, Juan Antonio; Molinero-Rosales, Nuria; Tarkowská, Danuše; Ruíz-Rivero, Omar; García-Garrido, José Manuel

    2015-05-01

    Gibberellins (GAs) are key regulators of plant growth and development and recent studies suggest also a role during arbuscular mycorrhizal (AM) formation. Here, complementary approaches have been used to obtain a clearer picture that correlates AM fungal development inside roots with GA metabolism. An extensive analysis of genes associated with GA metabolism as well as a quantification of GA content in roots was made. Application of GA3 and its biosynthesis inhibitor prohexadione calcium (PrCa) combined with a GA-constitutive response mutant (procera) were used to determine whether fungal colonization is altered by the level of these hormones or by changes in the GA-signaling pathway. The increased levels of specific GAs from the 13-hydroxylation pathway in mycorrhizal roots correlate closely with the increased expression of genes coding enzymes from the GA biosynthetic trail. The imbalance of GAs in tomato roots caused by exogenous applications of GA3 or PrCa affects arbuscules in both negative and positive ways, respectively. In addition, procera plants were adversely affected by the mycorrhization process. Our findings demonstrate that an imbalance in favor of an increased amount of GAs negatively affects the frequency of mycorrhization and particularly the arbuscular abundance in tomato mycorrhizal roots and the results point out that AM formation is associated with a change in the 13-hydroxylation pathway of GAs.

  15. Role of gibberellins during arbuscular mycorrhizal formation in tomato: new insights revealed by endogenous quantification and genetic analysis of their metabolism in mycorrhizal roots.

    PubMed

    Martín-Rodríguez, José Ángel; Ocampo, Juan Antonio; Molinero-Rosales, Nuria; Tarkowská, Danuše; Ruíz-Rivero, Omar; García-Garrido, José Manuel

    2015-05-01

    Gibberellins (GAs) are key regulators of plant growth and development and recent studies suggest also a role during arbuscular mycorrhizal (AM) formation. Here, complementary approaches have been used to obtain a clearer picture that correlates AM fungal development inside roots with GA metabolism. An extensive analysis of genes associated with GA metabolism as well as a quantification of GA content in roots was made. Application of GA3 and its biosynthesis inhibitor prohexadione calcium (PrCa) combined with a GA-constitutive response mutant (procera) were used to determine whether fungal colonization is altered by the level of these hormones or by changes in the GA-signaling pathway. The increased levels of specific GAs from the 13-hydroxylation pathway in mycorrhizal roots correlate closely with the increased expression of genes coding enzymes from the GA biosynthetic trail. The imbalance of GAs in tomato roots caused by exogenous applications of GA3 or PrCa affects arbuscules in both negative and positive ways, respectively. In addition, procera plants were adversely affected by the mycorrhization process. Our findings demonstrate that an imbalance in favor of an increased amount of GAs negatively affects the frequency of mycorrhization and particularly the arbuscular abundance in tomato mycorrhizal roots and the results point out that AM formation is associated with a change in the 13-hydroxylation pathway of GAs. PMID:25186107

  16. Highly sensitive detection of DNA methylation levels by using a quantum dot-based FRET method

    NASA Astrophysics Data System (ADS)

    Ma, Yunfei; Zhang, Honglian; Liu, Fangming; Wu, Zhenhua; Lu, Shaohua; Jin, Qinghui; Zhao, Jianlong; Zhong, Xinhua; Mao, Hongju

    2015-10-01

    DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR amplification for the incorporation of Alexa Fluor-647 (A647) fluorophores. DNA methylation levels can be detected qualitatively through gel analysis and quantitatively by the signal amplification from QDs to A647 during FRET. Furthermore, the methylation levels of three tumor suppressor genes, PCDHGB6, HOXA9 and RASSF1A, in 20 lung adenocarcinoma and 20 corresponding adjacent nontumorous tissue (NT) samples were measured to verify the feasibility of the QD-based FRET method and a high sensitivity for cancer detection (up to 90%) was achieved. Our QD-based FRET method is a convenient, continuous and high-throughput method, and is expected to be an alternative for detecting DNA methylation as a biomarker for certain human cancers.DNA methylation is the most frequently studied epigenetic modification that is strongly involved in genomic stability and cellular plasticity. Aberrant changes in DNA methylation status are ubiquitous in human cancer and the detection of these changes can be informative for cancer diagnosis. Herein, we reported a facile quantum dot-based (QD-based) fluorescence resonance energy transfer (FRET) technique for the detection of DNA methylation. The method relies on methylation-sensitive restriction enzymes for the differential digestion of genomic DNA based on its methylation status. Digested DNA is then subjected to PCR

  17. Quantum dot-based molecular beacon to monitor intracellular microRNAs.

    PubMed

    Lee, Jonghwan; Moon, Sung Ung; Lee, Yong Seung; Ali, Bahy A; Al-Khedhairy, Abdulaziz A; Ali, Daoud; Ahmed, Javed; Al Salem, Abdullah M; Kim, Soonhag

    2015-06-02

    Fluorescence monitoring of endogenous microRNA (miRNA or miR) activity related to neuronal development using nano-sized materials provides crucial information on miRNA expression patterns in a noninvasive manner. In this study, we report a new method to monitor intracellular miRNA124a using quantum dot-based molecular beacon (R9-QD-miR124a beacon). The R9-QD-miR124a beacon was constructed using QDs and two probes, miR124a-targeting oligomer and arginine rich cell-penetrating peptide (R9 peptide). The miR124a-targeting oligomer contains a miR124a binging sequence and a black hole quencher 1 (BHQ1). In the absence of target miR124a, the R9-QD-miR124a beacon forms a partial duplex beacon and remained in quenched state because the BHQ1 quenches the fluorescence signal of the R9-QD-miR124a beacon. The binding of miR124a to the miR124a binding sequence of the miR124a-targeting oligomer triggered the separation of the BHQ1 quencher and subsequent signal-on of a red fluorescence signal. Moreover, enhanced cellular uptake was achieved by conjugation with the R9 peptide, which resulted in increased fluorescent signal of the R9-QD-miR124a beacons in P19 cells during neurogenesis due to the endogenous expression of miR124a.

  18. Absolute quantification of acetylation and phosphorylation of the histone variant H2AX upon ionizing radiation reveals distinct cellular responses in two cancer cell lines.

    PubMed

    Matsuda, Shun; Furuya, Kanji; Ikura, Masae; Matsuda, Tomonari; Ikura, Tsuyoshi

    2015-11-01

    Histone modifications change upon the cellular response to ionizing radiation, and their cellular amounts could reflect the DNA damage response activity. We previously reported a sensitive and reliable method for the absolute quantification of γH2AX within cells, using liquid chromatography-tandem mass spectrometry (LC/MS/MS). The technique has broad adaptability to a variety of biological systems and can quantitate different modifications of histones. In this study, we applied it to quantitate the levels of γH2AX and K5-acetylated H2AX, and to compare the radiation responses between two cancer cell lines: HeLa and U-2 OS. The two cell lines have distinct properties in terms of their H2AX modifications. HeLa cells have relatively high γH2AX (3.1 %) against the total H2AX even in un-irradiated cells, while U-2 OS cells have an essentially undetectable level (nearly 0 %) of γH2AX. In contrast, the amounts of acetylated histones are lower in HeLa cells (9.3 %) and higher in U-2 OS cells (24.2 %) under un-irradiated conditions. Furthermore, after ionizing radiation exposure, the time-dependent increases and decreases in the amounts of histone modifications differed between the two cell lines, especially at the early time points. These results suggest that each biological system has distinct kinase/phosphatase and/or acetylase/deacetylase activities. In conclusion, for the first time, we have succeeded in simultaneously monitoring the absolute amounts of phosphorylated and acetylated cellular H2AX after ionizing radiation exposure. This multi-criteria assessment enables precise comparisons of the effects of radiation between any biological systems.

  19. Abundance of four sulfur mustard-DNA adducts ex vivo and in vivo revealed by simultaneous quantification in stable isotope dilution-ultrahigh performance liquid chromatography-tandem mass spectrometry.

    PubMed

    Yue, Lijun; Wei, Yuxia; Chen, Jia; Shi, Huiqin; Liu, Qin; Zhang, Yajiao; He, Jun; Guo, Lei; Zhang, Tingfen; Xie, Jianwei; Peng, Shuangqing

    2014-04-21

    Sulfur mustard (SM) is a highly reactive alkylating vesicant and causes blisters upon contact with skin, eyes, and respiratory organs. It covalently links with DNAs by forming four mono- or cross-link adducts. In this article, the reference standards of SM-DNA adducts and deuterated analogues were first synthesized with simplified procedures containing only one or two steps and using less toxic chemical 2-(2-chloroethylthio)ethanol or nontoxic chemical thiodiglycol as starting materials. A sensitive and high-throughput simultaneous quantification method of N(7)-[2-[(2-hydroxyethyl)thio]-ethyl]guanine (N(7)-HETEG), O(6)-[2-[(2-hydroxyethyl)thio]-ethyl]guanine (O(6)-HETEG), N(3)-[2-[(2-hydroxyethyl)thio]-ethyl]adenine (N(3)-HETEA), and bis[2-(guanin-7-yl)ethyl]sulfide (Bis-G) in the Sprague-Dawley rat derma samples was developed by stable isotope dilution-ultrahigh performance liquid chromatography-tandem mass spectrometry (ID-UPLC-MS/MS) with the aim of revealing the real metabolic behaviors of four adducts. The method was validated, the limit of detection (S/N ratio greater than 10) was 0.01, 0.002, 0.04, and 0.11 fmol on column for N(7)-HETEG, O(6)-HETEG, Bis-G, and N(3)-HETEA, respectively, and the lower limit of quantification (S/N ratio greater than 20) was 0.04, 0.01, 0.12, and 0.33 fmol on column for N(7)-HETEG, O(6)-HETEG, Bis-G, and N(3)-HETEA, respectively. The accuracy of this method was determined to be 76% to 129% (n = 3), and both the interday (n = 6) and intraday (n = 7) precisions were less than 10%. The method was further applied for the quantifications of four adducts in the derma of adult male Sprague-Dawley rats exposed to SM ex vivo and in vivo, and all adducts had time- and dose-effect relationships. To the best of our knowledge, this is the first time that the real presented status of four DNA adducts was simultaneously revealed by the MS-based method, in which Bis-G showed much higher abundance than the result previously reported and N(3

  20. Quantification of Leishmania (Viannia) Kinetoplast DNA in Ulcers of Cutaneous Leishmaniasis Reveals Inter-site and Inter-sampling Variability in Parasite Load

    PubMed Central

    Suárez, Milagros; Valencia, Braulio M.; Jara, Marlene; Alba, Milena; Boggild, Andrea K.; Dujardin, Jean-Claude; Llanos-Cuentas, Alejandro; Arevalo, Jorge; Adaui, Vanessa

    2015-01-01

    Background Cutaneous leishmaniasis (CL) is a skin disease caused by the protozoan parasite Leishmania. Few studies have assessed the influence of the sample collection site within the ulcer and the sampling method on the sensitivity of parasitological and molecular diagnostic techniques for CL. Sensitivity of the technique can be dependent upon the load and distribution of Leishmania amastigotes in the lesion. Methodology/Principal Findings We applied a quantitative real-time PCR (qPCR) assay for Leishmania (Viannia) minicircle kinetoplast DNA (kDNA) detection and parasite load quantification in biopsy and scraping samples obtained from 3 sites within each ulcer (border, base, and center) as well as in cytology brush specimens taken from the ulcer base and center. A total of 248 lesion samples from 31 patients with laboratory confirmed CL of recent onset (≤3 months) were evaluated. The kDNA-qPCR detected Leishmania DNA in 97.6% (242/248) of the examined samples. Median parasite loads were significantly higher in the ulcer base and center than in the border in biopsies (P<0.0001) and scrapings (P = 0.0002). There was no significant difference in parasite load between the ulcer base and center (P = 0.80, 0.43, and 0.07 for biopsy, scraping, and cytology brush specimens, respectively). The parasite load varied significantly by sampling method: in the ulcer base and center, the descending order for the parasite load levels in samples was: cytology brushes, scrapings, and biopsies (P<0.0001); in the ulcer border, scrapings had higher parasite load than biopsies (P<0.0001). There was no difference in parasite load according to L. braziliensis and L. peruviana infections (P = 0.4). Conclusion/Significance Our results suggest an uneven distribution of Leishmania amastigotes in acute CL ulcers, with higher parasite loads in the ulcer base and center, which has implications for bedside collection of diagnostic specimens. The use of scrapings and cytology brushes is

  1. Simultaneous quantification of methane and carbon dioxide fluxes reveals that a shallow arctic methane seep is a net sink for greenhouse gases

    NASA Astrophysics Data System (ADS)

    Pohlman, J.; Greinert, J.; Ruppel, C. D.; Silyakova, A.; Vielstädte, L.; Magen, C.; Casso, M.; Bunz, S.; Mienert, J.

    2015-12-01

    Warming of high-latitude continental-margin oceans has the potential to release large quantities of carbon from gas hydrate and other sedimentary reservoirs. To assess how carbon mobilized from the seafloor might amplify global warming or alter ocean chemistry, a robust analysis of the concentrations and isotopic content of methane and carbon dioxide (CO2) in the water column and atmosphere is required. To this effect, a gas analysis system consisting of three cavity ring-down spectrometers was developed to obtain a real-time, three-dimensional characterization of the distribution and isotopic variability of methane and CO2 at a shallow (<100 m water depth) bubbling methane seep offshore of western Svalbard. Surface water methane concentrations from the continuous-flow CRDS system agreed remarkably well with discrete samples analyzed by the GC-based headspace analysis technique and with a CRDS-based discrete sample analysis module. Reliable carbon isotope data were also obtained from the CRDSs once an isotopic calibration routine was applied. The resulting data revealed that CO2 uptake from the atmosphere within the surface water methane plume overlying the gas seep was elevated by 36-45% relative to surrounding waters. In comparison to the positive radiative forcing effect expected from the methane emissions, the negative radiative forcing potential from CO2 uptake was 32-43 times greater. Lower water temperatures, elevated chlorophyll-fluorescence and 13C-enriched CO2 within the surface methane plume suggest that bubble-driven upwelling of cold, nutrient-rich water stimulated CO2 uptake by phytoplankton. The observation that a shallow methane seep has a net negative radiative forcing effect challenges the widely-held perception that methane seeps contribute to the global atmospheric greenhouse gas burden.

  2. Carbon-dot-based ratiometric fluorescent probe for imaging and biosensing of superoxide anion in live cells.

    PubMed

    Gao, Xiang; Ding, Changqin; Zhu, Anwei; Tian, Yang

    2014-07-15

    In this article, a ratiometric fluorescent biosensor for O2(•-) was developed, by employing carbon dots (C-Dots) as the reference fluorophore and hydroethidine (HE), a specific organic molecule toward O2(•-), playing the role as both specific recognition element and response signal. The hybrid fluorescent probe CD-HE only emitted at 525 nm is ascribed to C-Dots, while HE was almost nonfluorescent, upon excitation at 488 nm. However, after reaction with O2(•-), a new emission peak ascribed to the reaction products of HE and O2(•-) was clearly observed at 610 nm. Meanwhile, this peak gradually increased with the increasing concentration of O2(•-) but the emission peak at 525 nm stayed constant, leading to a ratiometric detection of O2(•-). The inorganic-organic fluorescent sensor exhibited high sensitivity, a broad dynamic linear range of ~5 × 10(-7)-1.4 × 10(-4) M, and low detection limit down to 100 nM. The present probe also showed high accuracy and excellent selectivity for O2(•-) over other reactive oxygen species (ROS), metal ions, and so on. Moreover, the C-Dot-based inorganic-organic probe demonstrated long-term stability against pH changes and continuous light illumination, good cell-permeability, and low cytotoxicity. Accordingly, the developed fluorescent biosensor was eventually applied for intracellular bioimaging and biosensing of O2(•-) changes upon oxidative stress.

  3. A Modified Quantum Dot-Based Dot Blot Assay for Rapid Detection of Fish Pathogen Vibrio anguillarum.

    PubMed

    Zhang, Yang; Xiao, Jingfan; Wang, Qiyao; Zhang, Yuanxing

    2016-08-28

    Vibrio anguillarum, a devastating pathogen causing vibriosis among marine fish, is prevailing in worldwide fishery industries and accounts for grievous economic losses. Therefore, a rapid on-site detection and diagnostic technique for this pathogen is in urgent need. In this study, two mouse monoclonal antibodies (MAbs) against V. anguillarum, 6B3-C5 and 8G3-B5, were generated by using hybridoma technology and their isotypes were characterized. MAb 6B3-C5 was chosen as the detector antibody and conjugated with quantum dots. Based on MAb 6B3- C5 labeled with quantum dots, a modified dot blot assay was developed for the on-site determination of V. anguillarum. It was found that the method had no cross-reactivity with other than V. anguillarum bacteria. The detection limit (LOD) for V. anguillarum was 1 × 10(3) CFU/ml in cultured bacterial suspension samples, which was a 100-fold higher sensitivity than the reported colloidal gold immunochromatographic test strip. When V. anguillarum was mixed with turbot tissue homogenates, the LOD was 1 × 10(3) CFU/ml, suggesting that tissue homogenates did not influence the detection capabilities. Preenrichment with the tissue homogenates for 12 h could raise the LOD up to 1 × 10(2) CFU/ml, confirming the reliability of the method.

  4. A Modified Quantum Dot-Based Dot Blot Assay for Rapid Detection of Fish Pathogen Vibrio anguillarum.

    PubMed

    Zhang, Yang; Xiao, Jingfan; Wang, Qiyao; Zhang, Yuanxing

    2016-08-28

    Vibrio anguillarum, a devastating pathogen causing vibriosis among marine fish, is prevailing in worldwide fishery industries and accounts for grievous economic losses. Therefore, a rapid on-site detection and diagnostic technique for this pathogen is in urgent need. In this study, two mouse monoclonal antibodies (MAbs) against V. anguillarum, 6B3-C5 and 8G3-B5, were generated by using hybridoma technology and their isotypes were characterized. MAb 6B3-C5 was chosen as the detector antibody and conjugated with quantum dots. Based on MAb 6B3- C5 labeled with quantum dots, a modified dot blot assay was developed for the on-site determination of V. anguillarum. It was found that the method had no cross-reactivity with other than V. anguillarum bacteria. The detection limit (LOD) for V. anguillarum was 1 × 10(3) CFU/ml in cultured bacterial suspension samples, which was a 100-fold higher sensitivity than the reported colloidal gold immunochromatographic test strip. When V. anguillarum was mixed with turbot tissue homogenates, the LOD was 1 × 10(3) CFU/ml, suggesting that tissue homogenates did not influence the detection capabilities. Preenrichment with the tissue homogenates for 12 h could raise the LOD up to 1 × 10(2) CFU/ml, confirming the reliability of the method. PMID:27116991

  5. Enhanced Performance of Quantum Dot-Based Light-Emitting Diodes with Gold Nanoparticle-Doped Hole Injection Layer

    NASA Astrophysics Data System (ADS)

    Chen, Fei; Lin, Qingli; Wang, Hongzhe; Wang, Lei; Zhang, Fengjuan; Du, Zuliang; Shen, Huaibin; Li, Lin Song

    2016-08-01

    In this paper, the performance of quantum dot-based light-emitting diodes (QLEDs) comprising ZnCdSe/ZnS core-shell QDs as an emitting layer were enhanced by employing Au-doped poly(3,4-ethylenedioxythiophene)/polystyrene sulfonate (PEDOT:PSS) hole injection layer (HIL). By varying the concentration and dimension of Au nanoparticle (NP) dopants in PEDOT:PSS, the optimal devices were obtained with ~22-nm-sized Au NP dopant at the concentration with an optical density (OD) of 0.21. Highly bright green QLEDs with a maximum external quantum efficiency (EQE) of 8.2 % and a current efficiency of 29.1 cd/A exhibit 80 % improvement compared with devices without Au NP dopants. The improved performance may be attributed to the significant increase in the hole injection rate as a result of the introduction of Au NPs and the good matching between the resonance frequency of the localized surface plasmon resonance (LSPR) generated by the Au NPs and the emission band of QD layer, as well as the suppressed Auger recombination of QD layer due to the LSPR-induced near-field enhanced radiative recombination rate of excitons. These results are helpful for fabricating high-performance QD-based applications, such as full-color displays and solid-state lighting.

  6. Direct fluorescence in situ hybridization (FISH) in Escherichia coli with a target-specific quantum dot-based molecular beacon.

    PubMed

    Wu, Sheng-Mei; Tian, Zhi-Quan; Zhang, Zhi-Ling; Huang, Bi-Hai; Jiang, Peng; Xie, Zhi-Xiong; Pang, Dai-Wen

    2010-10-15

    Quantum dots (QDs) are inorganic fluorescent nanocrystals with excellent properties such as tunable emission spectra and photo-bleaching resistance compared with organic dyes, which make them appropriate for applications in molecular beacons. In this work, quantum dot-based molecular beacons (QD-based MBs) were fabricated to specifically detect β-lactamase genes located in pUC18 which were responsible for antibiotic resistance in bacteria Escherichia coli (E. coli) DH5α. QD-based MBs were constructed by conjugating mercaptoacetic acid-quantum dots (MAA-QDs) with black hole quencher 2 (BHQ2) labeled thiol DNA vial metal-thiol bonds. Two types of molecular beacons, double-strands beacons and hairpin beacons, were observed in product characterization by gel electrophoresis. Using QD-based MBs, one-step FISH in tiny bacteria DH5α was realized for the first time. QD-based MBs retained their bioactivity when hybridizing with complementary target DNA, which showed excellent advantages of eliminating background noise caused by adsorption of non-specific bioprobes and achieving clearer focus of genes in plasmids pUC18, and capability of bacterial cell penetration and signal specificity in one-step in situ hybridization.

  7. Label-Free Carbon-Dots-Based Ratiometric Fluorescence pH Nanoprobes for Intracellular pH Sensing.

    PubMed

    Shangguan, Jingfang; He, Dinggeng; He, Xiaoxiao; Wang, Kemin; Xu, Fengzhou; Liu, Jinquan; Tang, Jinlu; Yang, Xue; Huang, Jin

    2016-08-01

    Measuring pH in living cells is of great importance for better understanding cellular functions as well as providing pivotal assistance for early diagnosis of diseases. In this work, we report the first use of a novel kind of label-free carbon dots for intracellular ratiometric fluorescence pH sensing. By simple one-pot hydrothermal treatment of citric acid and basic fuchsin, the carbon dots showing dual emission bands at 475 and 545 nm under single-wavelength excitation were synthesized. It is demonstrated that the fluorescence intensities of the as-synthesized carbon dots at the two emissions are pH-sensitive simultaneously. The intensity ratio (I475 nm/I545 nm) is linear against pH values from 5.2 to 8.8 in buffer solution, affording the capability as ratiometric probes for intracellular pH sensing. It also displays that the carbon dots show excellent reversibility and photostability in pH measurements. With this nanoprobe, quantitative fluorescence imaging using the ratio of two emissions (I475 nm/I545 nm) for the detection of intracellular pH were successfully applied in HeLa cells. In contrast to most of the reported nanomaterials-based ratiometric pH sensors which rely on the attachment of additional dyes, these carbon-dots-based ratiometric probes are low in toxicity, easy to synthesize, and free from labels. PMID:27334762

  8. Quantum dots-based double-color imaging of HER2 positive breast cancer invasion

    SciTech Connect

    Liu, Xiu-Li; Peng, Chun-Wei; Chen, Chuang; Yang, Xue-Qin; Hu, Ming-Bai; Xia, He-Shun; Liu, Shao-Ping; and others

    2011-06-10

    Highlights: {yields} HER2 level is closely related to the biologic behaviors of breast cancer cells. {yields} A new method to simultaneously image HER2 and type IV collagen was established. {yields} HER2 status and type IV collagen degradation predict breast cancer invasion. {yields} The complex interactions between tumor and its environment were revealed. -- Abstract: It has been well recognized that human epidermal growth factor receptor 2 (HER2) level in breast cancer (BC) is closely related to the malignant biologic behaviors of the tumor, including invasion and metastasis. Yet, there has been a lack of directly observable evidence to support such notion. Here we report a quantum dots (QDs)-based double-color imaging technique to simultaneously show the HER2 level on BC cells and the type IV collagen in the tumor matrix. In benign breast tumor, the type IV collagen was intact. With the increasing of HER2 expression level, there has been a progressive decrease in type IV collagen around the cancer nest. At HER2 (3+) expression level, there has virtually been a total destruction of type IV collagen. Moreover, HER2 (3+) BC cells also show direct invasion into the blood vessels. This novel imaging method provides direct observable evidence to support the theory that the HER2 expression level is directly related to BC invasion.

  9. Simple and accurate quantification of quantum dots via single-particle counting.

    PubMed

    Zhang, Chun-yang; Johnson, Lawrence W

    2008-03-26

    Quantification of quantum dots (QDs) is essential to the quality control of QD synthesis, development of QD-based LEDs and lasers, functionalizing of QDs with biomolecules, and engineering of QDs for biological applications. However, simple and accurate quantification of QD concentration in a variety of buffer solutions and in complex mixtures still remains a critical technological challenge. Here, we introduce a new methodology for quantification of QDs via single-particle counting, which is conceptually different from established UV-vis absorption and fluorescence spectrum techniques where large amounts of purified QDs are needed and specific absorption coefficient or quantum yield values are necessary for measurements. We demonstrate that single-particle counting allows us to nondiscriminately quantify different kinds of QDs by their distinct fluorescence burst counts in a variety of buffer solutions regardless of their composition, structure, and surface modifications, and without the necessity of absorption coefficient and quantum yield values. This single-particle counting can also unambiguously quantify individual QDs in a complex mixture, which is practically impossible for both UV-vis absorption and fluorescence spectrum measurements. Importantly, the application of this single-particle counting is not just limited to QDs but also can be extended to fluorescent microspheres, quantum dot-based microbeads, and fluorescent nano rods, some of which currently lack efficient quantification methods.

  10. Quantification of Endogenous Retinoids

    PubMed Central

    Kane, Maureen A.; Napoli, Joseph L.

    2014-01-01

    Numerous physiological processes require retinoids, including development, nervous system function, immune responsiveness, proliferation, differentiation, and all aspects of reproduction. Reliable retinoid quantification requires suitable handling and, in some cases, resolution of geometric isomers that have different biological activities. Here we describe procedures for reliable and accurate quantification of retinoids, including detailed descriptions for handling retinoids, preparing standard solutions, collecting samples and harvesting tissues, extracting samples, resolving isomers, and detecting with high sensitivity. Sample-specific strategies are provided for optimizing quantification. Approaches to evaluate assay performance also are provided. Retinoid assays described here for mice also are applicable to other organisms including zebrafish, rat, rabbit, and human and for cells in culture. Retinoid quantification, especially that of retinoic acid, should provide insight into many diseases, including Alzheimer’s disease, type 2 diabetes, obesity, and cancer. PMID:20552420

  11. Quantification of Secondary Metabolites.

    PubMed

    2016-01-01

    Plants are a rich source of secondary metabolites that have medicinal and aromatic properties. Secondary metabolites such as alkaloids, iridoids and phenolics generally produced by plants for their defence mechanisms have been implicated in the therapeutic properties of most medicinal plants. Hence, quantification of these metabolites will aid to discover new and effective drugs from plant sources and also to scientifically validate the existing traditional practices. Quantification of large group of phytochemicals such as phenolics and flavonoids is quantified in this context.

  12. Rapid and Automated Quantification of Microalgal Lipids on a Spinning Disc.

    PubMed

    Kim, Yubin; Jeong, Su-Nam; Kim, Bolam; Kim, Dong-Pyo; Cho, Yoon-Kyoung

    2015-08-01

    We have developed a fully integrated centrifugal microfluidic device for rapid on-site quantification of lipids from microalgal samples. The fully automated serial process involving cell sedimentation and lysis, liquid-liquid extraction, and colorimetric detection of lipid contents was accomplished within 13 min using a lab-on-a-disc. The presented organic solvent-tolerable (for n-hexane, ethanol) microfluidic disc was newly fabricated by combining thermal fusion bonding and carbon dot-based valving techniques. It is expected that this novel platform will possibly contribute toward sustainable biofuel applications by providing a practical solution for on-site monitoring of lipid accumulation in microalgal samples, thus providing imperative contribution toward energy and environmental purposes of centrifugal microfluidic technology.

  13. Quantification of nonclassicality

    NASA Astrophysics Data System (ADS)

    Gehrke, C.; Sperling, J.; Vogel, W.

    2012-11-01

    To quantify single-mode nonclassicality, we start from an operational approach. A positive semidefinite observable is introduced to describe a measurement setup. The quantification is based on the negativity of the normally ordered version of this observable. Perfect operational quantumness corresponds to the quantum-noise-free measurement of the chosen observable. Surprisingly, even moderately squeezed states may exhibit perfect quantumness for a properly designed measurement. The quantification is also considered from an axiomatic viewpoint, based on the algebraic structure of the quantum states and the quantum superposition principle. Basic conclusions from both approaches are consistent with this fundamental principle of the quantum world.

  14. Quantification of Secondary Metabolites.

    PubMed

    2016-01-01

    Plants are a rich source of secondary metabolites that have medicinal and aromatic properties. Secondary metabolites such as alkaloids, iridoids and phenolics generally produced by plants for their defence mechanisms have been implicated in the therapeutic properties of most medicinal plants. Hence, quantification of these metabolites will aid to discover new and effective drugs from plant sources and also to scientifically validate the existing traditional practices. Quantification of large group of phytochemicals such as phenolics and flavonoids is quantified in this context. PMID:26939265

  15. Quantificational logic of context

    SciTech Connect

    Buvac, Sasa

    1996-12-31

    In this paper we extend the Propositional Logic of Context, to the quantificational (predicate calculus) case. This extension is important in the declarative representation of knowledge for two reasons. Firstly, since contexts are objects in the semantics which can be denoted by terms in the language and which can be quantified over, the extension enables us to express arbitrary first-order properties of contexts. Secondly, since the extended language is no longer only propositional, we can express that an arbitrary predicate calculus formula is true in a context. The paper describes the syntax and the semantics of a quantificational language of context, gives a Hilbert style formal system, and outlines a proof of the system`s completeness.

  16. The proteomics quantification dilemma.

    PubMed

    Jungblut, Peter R

    2014-07-31

    Proteomics is dominated today by the protein expression discourse, which favorites the bottom-up approach because of its high throughput and its high sensitivity. For quantification this proceeding is misleading, if a protein is present with more than one protein species in the sample to be analyzed. The protein speciation discourse considers this more realistic situation and affords the top-down procedures or at least a separation of the protein species in advance to identification and quantification. Today all of the top-down procedures are one order of magnitude less sensitive than the bottom-up ones. To increase sensitivity and to increase throughput are major challenges for proteomics of the next years. This article is part of a Special Issue entitled: 20years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini, Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez. PMID:24681132

  17. SERS Quantification of Entacapone Isomers

    NASA Astrophysics Data System (ADS)

    Marković, Marina; Biljan, Tomislav

    2010-08-01

    Raman spectroscopy, due to its non-destructive character and speed, has found widespread use in pharmaceutical applications [1]. It is also being used for quantifying various isomer mixtures, best known being the quantification of xylene isomers [2-3]. Solid-state isomer quantification of entacapone was earlier reported [4]. Here, we report quantification of isomer mixture of an active pharmaceutical substance, in solution, by SERS.

  18. Quantum dot-based immunofluorescent imaging and quantitative detection of TOP2A and prognostic value in triple-negative breast cancer

    PubMed Central

    Zheng, Hongmei; Li, Xiang; Chen, Chuang; Chen, Jian; Sun, Jinzhong; Sun, Si; Jin, Liting; Li, Juanjuan; Sun, Shengrong; Wu, Xinhong

    2016-01-01

    Background Topoisomerase 2 alpha (TOP2A) is a key enzyme in DNA replication and a target of various cytotoxic agents including anthracyclines. Previous studies evaluating the predictive and prognostic values of TOP2A in breast cancer are contradictory, likely secondary to the use of both different detection methods and different cutoff thresholds for positive status. Our own studies have previously confirmed the advantages of quantum dot-based nanotechnology for quantitative analysis of biomarkers relative to conventional immunohistochemistry (IHC). This study was designed to 1) assess the expression of TOP2A, 2) investigate the relationship between TOP2A expression and major clinical pathological parameters, and 3) evaluate the prognostic value of TOP2A by quantum dot-based immunofluorescent imaging and quantitative analytical system (QD-IIQAS) in triple-negative breast cancer (TNBC). Patients and methods TOP2A expression in 145 TNBC specimens was detected using IHC and QD-IIQAS, and a comparative analysis of the two methods was conducted, including an exploration of the relationship between TOP2A expression and major clinical pathological parameters in TNBC. The prognostic value of TOP2A in TNBC was assessed. Results A similar antigen localization, a high correlation of staining rates (r=0.79), and a high agreement of measurements (κ=0.763) of TOP2A expression in TNBC were found by QD-IIQAS and conventional IHC (cutoff: 45.0 and 0.45, respectively). TOP2A was significantly higher in larger tumors (P=0.002), higher grade tumors (P=0.005), and lymph node positive patients (P<0.001). The 5-year disease-free survival (5-DFS) of the high and low TOP2A subgroups was significantly different for both QD-IIQAS and IHC (P<0.001, log-rank test for both). TOP2A expression was an independent predictor of survival in TNBC (P=0.001). Conclusion QD-IIQAS was an easy and accurate method for detecting and assessing TOP2A. The TOP2A expression was an independent prognostic

  19. Novel magnetic Fe3O4@CdSe composite quantum dot-based electrochemiluminescence detection of thrombin by a multiple DNA cycle amplification strategy.

    PubMed

    Jie, Guifen; Yuan, Jinxin

    2012-03-20

    A novel small magnetic electrochemiluminescent Fe(3)O(4)@CdSe composite quantum dot (QD) was facilely prepared and successfully applied to sensitive electrochemiluminescence (ECL) detection of thrombin by a multiple DNA cycle amplification strategy for the first time. The as-prepared composite QDs feature intense ECL, excellent magnetism, strong fluorescence, and favorable biocompatibility, which offers promising advantages for ECL biosensing. ECL of the composite QDs was efficiently quenched by gold nanoparticles (NPs). Taking advantages of the unique and attractive ECL and magnetic characteristics of the composite QDs, a novel DNA-amplified detection method based on ECL quenching was thus developed for a sensitive assay of thrombin. More importantly, the DNA devices by cleavage reaction were cycled multiple rounds, which greatly amplified the ECL signal and much improve the detection sensitivity. This flexible biosensing system exhibits not only high sensitivity and specificity but also excellent performance in real human serum assay. The present work opens a promising approach to develop magnetic quantum dot-based amplified ECL bioassays, which has wider potential application with more favorable analytical performances than other ECL reagent-based systems. Moreover, the composite QDs are suitable for long-term fluorescent cellular imaging, which also highlights the promising directions for further development of QD-based in vitro and in vivo imaging materials.

  20. ZnCuInS/ZnSe/ZnS Quantum Dot-Based Downconversion Light-Emitting Diodes and Their Thermal Effect

    DOE PAGES

    Liu, Wenyan; Zhang, Yu; Ruan, Cheng; Wang, Dan; Zhang, Tieqiang; Feng, Yi; Gao, Wenzhu; Yin, Jingzhi; Wang, Yiding; Riley, Alexis P.; et al

    2015-01-01

    The quantum dot-based light-emitting diodes (QD-LEDs) were fabricated using blue GaN chips and red-, yellow-, and green-emitting ZnCuInS/ZnSe/ZnS QDs. The power efficiencies were measured as 14.0 lm/W for red, 47.1 lm/W for yellow, and 62.4 lm/W for green LEDs at 2.6 V. The temperature effect of ZnCuInS/ZnSe/ZnS QDs on these LEDs was investigated using CIE chromaticity coordinates, spectral wavelength, full width at half maximum (FWHM), and power efficiency (PE). The thermal quenching induced by the increased surface temperature of the device was confirmed to be one of the important factors to decrease power efficiencies while the CIE chromaticity coordinates changed little due to themore » low emission temperature coefficients of 0.022, 0.050, and 0.068 nm/°C for red-, yellow-, and green-emitting ZnCuInS/ZnSe/ZnS QDs. These indicate that ZnCuInS/ZnSe/ZnS QDs are more suitable for downconversion LEDs compared to CdSe QDs.« less

  1. Efficient in vitro and in vivo pulmonary delivery of nucleic acid by carbon dot-based nanocarriers.

    PubMed

    Pierrat, Philippe; Wang, Rongrong; Kereselidze, Dimitri; Lux, Marie; Didier, Pascal; Kichler, Antoine; Pons, Françoise; Lebeau, Luc

    2015-05-01

    Cationic carbon dots were fabricated by pyrolysis of citric acid and bPEI25k under microwave radiation. Various nanoparticles were produced in a 20-30% yield through straightforward modifications of the reaction parameters (stoichiometry of the reactants and energy supply regime). Particular attention was paid to the purification of the reaction products to ensure satisfactory elimination of the residual starting polyamine. Intrinsic properties of the particles (size, surface charge, photoluminescence and quantum yield) were measured and their ability to form stable complexes with nucleic acid was determined. Their potential to deliver plasmid DNA or small interfering RNA to various cell lines was investigated and compared to that of bPEI25k. The pDNA in vitro transfection efficiency of these carbon dots was similar to that of the parent PEI, as was their cytotoxicity. The higher cytotoxicity of bPEI25k/siRNA complexes when compared to that of the CD/siRNA complexes however had marked consequences on the gene silencing efficiency of the two carriers. These results are not fully consistent with those in some earlier reports on similar nanoparticles, revealing that toxicity of the carbon dots strongly depends on their protocol of fabrication. Finally, these carriers were evaluated for in vivo gene delivery through the non-invasive pulmonary route in mice. High transgene expression was obtained in the lung that was similar to that obtained with the golden standard formulation GL67A, but was associated with significantly lower toxicity. Post-functionalization of these carbon dots with PEG or targeting moieties should significantly broaden their scope and practical implications in improving their in vivo transfection efficiency and biocompatibility. PMID:25771019

  2. Rapid screening and identification of dominant B cell epitopes of HBV surface antigen by quantum dot-based fluorescence polarization assay

    NASA Astrophysics Data System (ADS)

    Meng, Zhongji; Song, Ruihua; Chen, Yue; Zhu, Yang; Tian, Yanhui; Li, Ding; Cui, Daxiang

    2013-03-01

    A method for quickly screening and identifying dominant B cell epitopes was developed using hepatitis B virus (HBV) surface antigen as a target. Eleven amino acid fragments from HBV surface antigen were synthesized by 9-fluorenylmethoxy carbonyl solid-phase peptide synthesis strategy, and then CdTe quantum dots were used to label the N-terminals of all peptides. After optimizing the factors for fluorescence polarization (FP) immunoassay, the antigenicities of synthetic peptides were determined by analyzing the recognition and combination of peptides and standard antibody samples. The results of FP assays confirmed that 10 of 11 synthetic peptides have distinct antigenicities. In order to screen dominant antigenic peptides, the FP assays were carried out to investigate the antibodies against the 10 synthetic peptides of HBV surface antigen respectively in 159 samples of anti-HBV surface antigen-positive antiserum. The results showed that 3 of the 10 antigenic peptides may be immunodominant because the antibodies against them existed more widely among the samples and their antibody titers were higher than those of other peptides. Using three dominant antigenic peptides, 293 serum samples were detected for HBV infection by FP assays; the results showed that the antibody-positive ratio was 51.9% and the sensitivity and specificity were 84.3% and 98.2%, respectively. In conclusion, a quantum dot-based FP assay is a very simple, rapid, and convenient method for determining immunodominant antigenic peptides and has great potential in applications such as epitope mapping, vaccine designing, or clinical disease diagnosis in the future.

  3. Influence of the active layer nanomorphology on device performance for ternary PbS x Se1-x quantum dots based solution-processed infrared photodetector

    NASA Astrophysics Data System (ADS)

    Song, Taojian; Cheng, Haijuan; Fu, Chunjie; He, Bo; Li, Weile; Xu, Junfeng; Tang, Yi; Yang, Shengyi; Zou, Bingsuo

    2016-04-01

    In this paper, the influence of the active layer nanomorphology on device performance for ternary PbS x Se1-x quantum dot-based solution-processed infrared photodetector is presented. Firstly, ternary PbS x Se1-x quantum dots (QDs) in various chemical composition were synthesized and the bandgap of the ternary PbS x Se1-x QDs can be controlled by the component ratio of S/(S + Se), and then field-effect transistor (FET) based photodetectors Au/PbS0.4Se0.6:P3HT/PMMA/Al, in which ternary PbS0.4Se0.6 QDs doped with poly(3-hexylthiophene) (P3HT) act as the active layer and poly(methyl methacrylate) (PMMA) as the dielectric layer, were presented. By changing the weight ratio of P3HT to PbS0.4Se0.6 QDs (K = MP3HT:MQDs) in dichlorobenzene solution, we found that the device with K = 2:1 shows optimal electrical property in dark; however, the device with K = 1:2 demonstrated optimal performance under illumination, showing a maximum responsivity and specific detectivity of 55.98 mA W-1 and 1.02 × 1010 Jones, respectively, at low V DS = -10 V and V G = 3 V under 980 nm laser with an illumination intensity of 0.1 mW cm-2. By measuring the atomic force microscopy phase images of PbS0.4Se0.6:P3HT films in different weight ratio K, our experimental data show that the active layer nanomorphology has a great influence on the device performance. Also, it provides an easy way to fabricate high performance solution-processed infrared photodetector.

  4. Influence of the active layer nanomorphology on device performance for ternary PbS(x)Se(1-x) quantum dots based solution-processed infrared photodetector.

    PubMed

    Song, Taojian; Cheng, Haijuan; Fu, Chunjie; He, Bo; Li, Weile; Xu, Junfeng; Tang, Yi; Yang, Shengyi; Zou, Bingsuo

    2016-04-22

    In this paper, the influence of the active layer nanomorphology on device performance for ternary PbS(x)Se(1-x) quantum dot-based solution-processed infrared photodetector is presented. Firstly, ternary PbS(x)Se(1-x) quantum dots (QDs) in various chemical composition were synthesized and the bandgap of the ternary PbS(x)Se(1-x) QDs can be controlled by the component ratio of S/(S + Se), and then field-effect transistor (FET) based photodetectors Au/PbS0.4Se0.6:P3HT/PMMA/Al, in which ternary PbS0.4Se0.6 QDs doped with poly(3-hexylthiophene) (P3HT) act as the active layer and poly(methyl methacrylate) (PMMA) as the dielectric layer, were presented. By changing the weight ratio of P3HT to PbS0.4Se0.6 QDs (K = M(P3HT):M(QDs)) in dichlorobenzene solution, we found that the device with K = 2:1 shows optimal electrical property in dark; however, the device with K = 1:2 demonstrated optimal performance under illumination, showing a maximum responsivity and specific detectivity of 55.98 mA W(-1) and 1.02 × 10(10) Jones, respectively, at low V(DS) = -10 V and V(G) = 3 V under 980 nm laser with an illumination intensity of 0.1 mW cm(-2). By measuring the atomic force microscopy phase images of PbS0.4Se0.6:P3HT films in different weight ratio K, our experimental data show that the active layer nanomorphology has a great influence on the device performance. Also, it provides an easy way to fabricate high performance solution-processed infrared photodetector. PMID:26963474

  5. Influence of the active layer nanomorphology on device performance for ternary PbS(x)Se(1-x) quantum dots based solution-processed infrared photodetector.

    PubMed

    Song, Taojian; Cheng, Haijuan; Fu, Chunjie; He, Bo; Li, Weile; Xu, Junfeng; Tang, Yi; Yang, Shengyi; Zou, Bingsuo

    2016-04-22

    In this paper, the influence of the active layer nanomorphology on device performance for ternary PbS(x)Se(1-x) quantum dot-based solution-processed infrared photodetector is presented. Firstly, ternary PbS(x)Se(1-x) quantum dots (QDs) in various chemical composition were synthesized and the bandgap of the ternary PbS(x)Se(1-x) QDs can be controlled by the component ratio of S/(S + Se), and then field-effect transistor (FET) based photodetectors Au/PbS0.4Se0.6:P3HT/PMMA/Al, in which ternary PbS0.4Se0.6 QDs doped with poly(3-hexylthiophene) (P3HT) act as the active layer and poly(methyl methacrylate) (PMMA) as the dielectric layer, were presented. By changing the weight ratio of P3HT to PbS0.4Se0.6 QDs (K = M(P3HT):M(QDs)) in dichlorobenzene solution, we found that the device with K = 2:1 shows optimal electrical property in dark; however, the device with K = 1:2 demonstrated optimal performance under illumination, showing a maximum responsivity and specific detectivity of 55.98 mA W(-1) and 1.02 × 10(10) Jones, respectively, at low V(DS) = -10 V and V(G) = 3 V under 980 nm laser with an illumination intensity of 0.1 mW cm(-2). By measuring the atomic force microscopy phase images of PbS0.4Se0.6:P3HT films in different weight ratio K, our experimental data show that the active layer nanomorphology has a great influence on the device performance. Also, it provides an easy way to fabricate high performance solution-processed infrared photodetector.

  6. Quantification of human responses

    NASA Technical Reports Server (NTRS)

    Steinlage, R. C.; Gantner, T. E.; Lim, P. Y. W.

    1992-01-01

    Human perception is a complex phenomenon which is difficult to quantify with instruments. For this reason, large panels of people are often used to elicit and aggregate subjective judgments. Print quality, taste, smell, sound quality of a stereo system, softness, and grading Olympic divers and skaters are some examples of situations where subjective measurements or judgments are paramount. We usually express what is in our mind through language as a medium but languages are limited in available choices of vocabularies, and as a result, our verbalizations are only approximate expressions of what we really have in mind. For lack of better methods to quantify subjective judgments, it is customary to set up a numerical scale such as 1, 2, 3, 4, 5 or 1, 2, 3, ..., 9, 10 for characterizing human responses and subjective judgments with no valid justification except that these scales are easy to understand and convenient to use. But these numerical scales are arbitrary simplifications of the complex human mind; the human mind is not restricted to such simple numerical variations. In fact, human responses and subjective judgments are psychophysical phenomena that are fuzzy entities and therefore difficult to handle by conventional mathematics and probability theory. The fuzzy mathematical approach provides a more realistic insight into understanding and quantifying human responses. This paper presents a method for quantifying human responses and subjective judgments without assuming a pattern of linear or numerical variation for human responses. In particular, quantification and evaluation of linguistic judgments was investigated.

  7. Chiral quantum dot based materials

    NASA Astrophysics Data System (ADS)

    Govan, Joseph; Loudon, Alexander; Baranov, Alexander V.; Fedorov, Anatoly V.; Gun'ko, Yurii

    2014-05-01

    Recently, the use of stereospecific chiral stabilising molecules has also opened another avenue of interest in the area of quantum dot (QD) research. The main goal of our research is to develop new types of technologically important quantum dot materials containing chiral defects, study their properties and explore their applications. The utilisation of chiral penicillamine stabilisers allowed the preparation of new water soluble white emitting CdS quantum nanostructures which demonstrated circular dichroism in the band-edge region of the spectrum. It was also demonstrated that all three types of QDs (D-, L-, and Rac penicillamine stabilised) show very broad emission bands between 400 and 700 nm due to defects or trap states on the surfaces of the nanocrystals. In this work the chiral CdS based quantum nanostructures have also been doped by copper metal ions and new chiral penicilamine stabilized CuS nanoparticles have been prepared and investigated. It was found that copper doping had a strong effect at low levels in the synthesis of chiral CdS nanostructures. We expect that this research will open new horizons in the chemistry of chiral nanomaterials and their application in biotechnology, sensing and asymmetric synthesis.

  8. MAMA Software Features: Quantification Verification Documentation-1

    SciTech Connect

    Ruggiero, Christy E.; Porter, Reid B.

    2014-05-21

    This document reviews the verification of the basic shape quantification attributes in the MAMA software against hand calculations in order to show that the calculations are implemented mathematically correctly and give the expected quantification results.

  9. Proteomics of Microparticles with SILAC Quantification (PROMIS-Quan): A Novel Proteomic Method for Plasma Biomarker Quantification*

    PubMed Central

    Harel, Michal; Oren-Giladi, Pazit; Kaidar-Person, Orit; Shaked, Yuval; Geiger, Tamar

    2015-01-01

    Unbiased proteomic analysis of plasma samples holds the promise to reveal clinically invaluable disease biomarkers. However, the tremendous dynamic range of the plasma proteome has so far hampered the identification of such low abundant markers. To overcome this challenge we analyzed the plasma microparticle proteome, and reached an unprecedented depth of over 3000 plasma proteins in single runs. To add a quantitative dimension, we developed PROMIS-Quan—PROteomics of MIcroparticles with Super-Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) Quantification, a novel mass spectrometry-based technology for plasma microparticle proteome quantification. PROMIS-Quan enables a two-step relative and absolute SILAC quantification. First, plasma microparticle proteomes are quantified relative to a super-SILAC mix composed of cell lines from distinct origins. Next, the absolute amounts of selected proteins of interest are quantified relative to the super-SILAC mix. We applied PROMIS-Quan to prostate cancer and compared plasma microparticle samples of healthy individuals and prostate cancer patients. We identified in total 5374 plasma-microparticle proteins, and revealed a predictive signature of three proteins that were elevated in the patient-derived plasma microparticles. Finally, PROMIS-Quan enabled determination of the absolute quantitative changes in prostate specific antigen (PSA) upon treatment. We propose PROMIS-Quan as an innovative platform for biomarker discovery, validation, and quantification in both the biomedical research and in the clinical worlds. PMID:25624350

  10. Selective and absolute quantification of endogenous hypochlorous acid with quantum-dot conjugated microbeads.

    PubMed

    Yang, Yi-Cyun; Lu, Hsueh-Han; Wang, Wei-Ti; Liau, Ian

    2011-11-01

    Endogenous hypochlorous acid (HOCl) secreted by leukocytes plays a critical role in both the immune defense of mammalians and the pathogenesis of various diseases intimately related to inflammation. We report the first selective and absolute quantification of endogenous HOCl produced by leukocytes in vitro and in vivo with a novel quantum dot-based sensor. An activated human neutrophil secreted 6.5 ± 0.9 × 10(8) HOCl molecules into its phagosome, and kinetic measurement for the secretions showed that the extracellular generation of HOCl was temporally retarded, but the quantity eventually attained a level comparable with its intraphagosomal counterpart with a delay of about 1.5 h. The quantity of HOCl secreted from the hepatic leukocytes of rats with or without stimulation of lipopolysaccharide was also determined. These results indicate a possibility to extend our approach to not only clinical settings for quantitative assessment of the bactericidal capability of isolated leukocytes of patients but also fundamental biomedical research that requires critical evaluation of the inflammatory response of animals. PMID:21950322

  11. Quantification of Condylar Resorption in TMJ Osteoarthritis

    PubMed Central

    Cevidanes, LHS; Hajati, A-K; Paniagua, B; Lim, PF; Walker, DG; Palconet, G; Nackley, AG; Styner, M; Ludlow, JB; Zhu, H; Phillips, C

    2010-01-01

    OBJECTIVE This study was performed to determine the condylar morphological variation of osteoarthritic (OA) and asymptomatic temporomandibular joints (TMJ) and to determine its correlation with pain intensity and duration. STUDY DESIGN Three dimensional surface models of mandibular condyles were constructed from Cone-Beam CT images of 29 female patients with TMJ OA (Research Diagnostic Criteria for Temporomandibular Disorders Group III) and 36 female asymptomatic subjects. Shape Correspondence was used to localize and quantify the condylar morphology. Statistical analysis was performed with MANCOVA analysis using Hotelling T2 metric based on covariance matrices, and Pearson correlation. RESULTS OA condylar morphology was statistically significantly different from the asymptomatic condyles (p<0.05). 3D morphological variation of the OA condyles was significantly correlated with pain intensity and duration. CONCLUSION 3D quantification of condylar morphology revealed profound differences between OA and asymptomatic condyles and the extent of the resorptive changes paralleled pain severity and duration. PMID:20382043

  12. Preparation of graphene quantum dots based core-satellite hybrid spheres and their use as the ratiometric fluorescence probe for visual determination of mercury(II) ions.

    PubMed

    Hua, Mengjuan; Wang, Chengquan; Qian, Jing; Wang, Kan; Yang, Zhenting; Liu, Qian; Mao, Hanping; Wang, Kun

    2015-08-12

    We herein proposed a simple and effective strategy for preparing graphene quantum dots (GQDs)-based core-satellite hybrid spheres and further explored the feasibility of using such spheres as the ratiometric fluorescence probe for the visual determination of Hg(2+). The red-emitting CdTe QDs were firstly entrapped in the silica nanosphere to reduce their toxicity and improve their photo and chemical stabilities, thus providing a built-in correction for environmental effects, while the GQDs possessing good biocompatibility and low toxicity were electrostatic self-assembly on the silica surface acting as reaction sites. Upon exposure to the increasing contents of Hg(2+), the blue fluorescence of GQDs can be gradually quenched presumably due to facilitating nonradiative electron/hole recombination annihilation. With the embedded CdTe QDs as the internal standard, the variations of the tested solution display continuous fluorescence color changes from blue to red, which can be easily observed by the naked eye without any sophisticated instrumentations and specially equipped laboratories. This sensor exhibits high sensitivity and selectivity toward Hg(2+) in a broad linear range of 10 nM-22 μM with a low detection limit of 3.3 nM (S/N = 3), much lower than the allowable Hg(2+) contents in drinking water set by U.S. Environmental Protection Agency. This prototype ratiometric probe is of good simplicity, low toxicity, excellent stabilities, and thus potentially attractive for Hg(2+) quantification related biological systems. PMID:26320973

  13. 3D-printed biosensor with poly(dimethylsiloxane) reservoir for magnetic separation and quantum dots-based immunolabeling of metallothionein.

    PubMed

    Heger, Zbynek; Zitka, Jan; Cernei, Natalia; Krizkova, Sona; Sztalmachova, Marketa; Kopel, Pavel; Masarik, Michal; Hodek, Petr; Zitka, Ondrej; Adam, Vojtech; Kizek, Rene

    2015-06-01

    Currently, metallothioneins (MTs) are extensively investigated as the molecular biomarkers and the significant positive association of the MT amount was observed in tumorous versus healthy tissue of various types of malignant tumors, including head and neck cancer. Thus, we proposed a biosensor with fluorescence detection, comprising paramagnetic nanoparticles (nanomaghemite core with gold nanoparticles containing shell) for the magnetic separation of MT, based on affinity of its sulfhydryl groups toward gold. Biosensor was crafted from PDMS combined with technology of 3D printing and contained reservoir with volume of 50 μL linked to input (sample/detection components and washing/immunobuffer) and output (waste). For the immunolabeling of immobilized MT anti-MT antibodies conjugated to CdTe quantum dots through synthetic heptapeptide were employed. After optimization of fundamental conditions of the immunolabeling (120 min, 20°C, and 1250 rpm) we performed it on a surface of paramagnetic nanoparticles in the biosensor reservoir, with evaluation of fluorescence of quantum dots (λexc 400 nm, and λem 555 nm). The developed biosensor was applied for quantification of MT in cell lines derived from spinocellular carcinoma (cell line 122P-N) and fibroblasts (122P-F) and levels of the biomarker were found to be about 90 nM in tumor cells and 37 nM in fibroblasts. The proposed system is able to work with low volumes (< 100 μL), with low acquisition costs and high portability. PMID:25735231

  14. Disposable integrated bismuth citrate-modified screen-printed immunosensor for ultrasensitive quantum dot-based electrochemical assay of C-reactive protein in human serum.

    PubMed

    Kokkinos, Christos; Prodromidis, Mamas; Economou, Anastasios; Petrou, Panagiota; Kakabakos, Sotirios

    2015-07-30

    A novel immunosensor based on graphite screen-printed electrodes (SPEs) modified with bismuth citrate was developed for the voltammetric determination of C-reactive protein (CRP) in human serum using quantum dots (QDs) labels. The sandwich-type immunoassay involved physisorption of CRP capture antibody on the surface of the sensor, sequential immunoreactions with CRP and biotinylated CRP reporter antibody and finally reaction with streptavidin-conjugated PbS QDs. The quantification of the target protein was performed with acidic dissolution of the PbS QDs and anodic stripping voltammetric detection of the Pb(II) released. Detection was performed at bismuth nanodomains formed on the sensor surface during the electrolytic preconcentration step, as bismuth citrate was reduced to metallic bismuth simultaneously with the deposition of Pb on the surface of the immunosensor. Under optimal conditions, the response was linear over the range 0.2-100 ng mL(-1) CRP and the limit of detection was 0.05 ng mL(-1) CRP. Since the modified SPE serves as both the biorecognition element and the QDs reader, the analytical procedure is simplified, the drawbacks of existing electroplated immunosensors are minimized while the proposed disposable sensing platform provides convenient, low-cost and ultrasensitive detection of proteins and wider scope for mass-production. PMID:26320633

  15. Detection and Quantification of Neurotransmitters in Dialysates

    PubMed Central

    Zapata, Agustin; Chefer, Vladimir I.; Shippenberg, Toni S.; Denoroy, Luc

    2010-01-01

    Sensitive analytical methods are needed for the separation and quantification of neurotransmitters obtained in microdialysate studies. This unit describes methods that permit quantification of nanomolar concentrations of monoamines and their metabolites (high-pressure liquid chromatography electrochemical detection), acetylcholine (HPLC-coupled to an enzyme reactor), and amino acids (HPLC-fluorescence detection; capillary electrophoresis with laser-induced fluorescence detection). PMID:19575473

  16. Classification and quantification of leaf curvature

    PubMed Central

    Liu, Zhongyuan; Jia, Liguo; Mao, Yanfei; He, Yuke

    2010-01-01

    Various mutants of Arabidopsis thaliana deficient in polarity, cell division, and auxin response are characterized by certain types of leaf curvature. However, comparison of curvature for clarification of gene function can be difficult without a quantitative measurement of curvature. Here, a novel method for classification and quantification of leaf curvature is reported. Twenty-two mutant alleles from Arabidopsis mutants and transgenic lines deficient in leaf flatness were selected. The mutants were classified according to the direction, axis, position, and extent of leaf curvature. Based on a global measure of whole leaves and a local measure of four regions in the leaves, the curvature index (CI) was proposed to quantify the leaf curvature. The CI values accounted for the direction, axis, position, and extent of leaf curvature in all of the Arabidopsis mutants grown in growth chambers. Comparison of CI values between mutants reveals the spatial and temporal variations of leaf curvature, indicating the strength of the mutant alleles and the activities of the corresponding genes. Using the curvature indices, the extent of curvature in a complicated genetic background becomes quantitative and comparable, thus providing a useful tool for defining the genetic components of leaf development and to breed new varieties with leaf curvature desirable for the efficient capture of sunlight for photosynthesis and high yields. PMID:20400533

  17. Simultaneous quantification of sialyloligosaccharides from human milk by capillary electrophoresis

    PubMed Central

    Bao, Yuanwu; Zhu, Libin; Newburg, David S.

    2007-01-01

    The acidic oligosaccharides of human milk are predominantly sialyloligosaccharides. Pathogens that bind sialic acid-containing glycans on their host mucosal surfaces may be inhibited by human milk sialyloligosaccharides, but testing this hypothesis requires their reliable quantification in milk. Sialyloligosaccharides have been quantified by anion exchange HPLC, reverse or normal phase HPLC, and capillary electrophoresis (CE) of fluorescent derivatives; in milk, these oligosaccharides have been analyzed by high pH anion exchange chromatography with pulsed amperometric detection, and, in our laboratory, by CE with detection at 205 nm. The novel method described herein uses a running buffer of aqueous 200 mM NaH2PO4 at pH 7.05 containing 100 mM SDS made 45% (v/v) with methanol to baseline resolve five oligosaccharides, and separate all 12. This allows automated simultaneous quantification of the 12 major sialyloligosaccharides of human milk in a single 35-minute run. This method revealed differences in sialyloligosaccharide concentrations between less and more mature milk from the same donors. Individual donors also varied in expression of sialyloligosaccharides in their milk. Thus, the facile quantification of sialyloligosaccharides by this method is suitable for measuring variation in expression of specific sialyloligosaccharides in milk and their relationship to decreased risk of specific diseases in infants. PMID:17761135

  18. Quantification Bias Caused by Plasmid DNA Conformation in Quantitative Real-Time PCR Assay

    PubMed Central

    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. PMID:22194997

  19. Processing and domain selection: Quantificational variability effects

    PubMed Central

    Harris, Jesse A.; Clifton, Charles; Frazier, Lyn

    2014-01-01

    Three studies investigated how readers interpret sentences with variable quantificational domains, e.g., The army was mostly in the capital, where mostly may quantify over individuals or parts (Most of the army was in the capital) or over times (The army was in the capital most of the time). It is proposed that a general conceptual economy principle, No Extra Times (Majewski 2006, in preparation), discourages the postulation of potentially unnecessary times, and thus favors the interpretation quantifying over parts. Disambiguating an ambiguously quantified sentence to a quantification over times interpretation was rated as less natural than disambiguating it to a quantification over parts interpretation (Experiment 1). In an interpretation questionnaire, sentences with similar quantificational variability were constructed so that both interpretations of the sentence would require postulating multiple times; this resulted in the elimination of the preference for a quantification over parts interpretation, suggesting the parts preference observed in Experiment 1 is not reducible to a lexical bias of the adverb mostly (Experiment 2). An eye movement recording study showed that, in the absence of prior evidence for multiple times, readers exhibit greater difficulty when reading material that forces a quantification over times interpretation than when reading material that allows a quantification over parts interpretation (Experiment 3). These experiments contribute to understanding readers’ default assumptions about the temporal properties of sentences, which is essential for understanding the selection of a domain for adverbial quantifiers and, more generally, for understanding how situational constraints influence sentence processing. PMID:25328262

  20. Advancing agricultural greenhouse gas quantification*

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    1. Introduction Better information on greenhouse gas (GHG) emissions and mitigation potential in the agricultural sector is necessary to manage these emissions and identify responses that are consistent with the food security and economic development priorities of countries. Critical activity data (what crops or livestock are managed in what way) are poor or lacking for many agricultural systems, especially in developing countries. In addition, the currently available methods for quantifying emissions and mitigation are often too expensive or complex or not sufficiently user friendly for widespread use. The purpose of this focus issue is to capture the state of the art in quantifying greenhouse gases from agricultural systems, with the goal of better understanding our current capabilities and near-term potential for improvement, with particular attention to quantification issues relevant to smallholders in developing countries. This work is timely in light of international discussions and negotiations around how agriculture should be included in efforts to reduce and adapt to climate change impacts, and considering that significant climate financing to developing countries in post-2012 agreements may be linked to their increased ability to identify and report GHG emissions (Murphy et al 2010, CCAFS 2011, FAO 2011). 2. Agriculture and climate change mitigation The main agricultural GHGs—methane and nitrous oxide—account for 10%-12% of anthropogenic emissions globally (Smith et al 2008), or around 50% and 60% of total anthropogenic methane and nitrous oxide emissions, respectively, in 2005. Net carbon dioxide fluxes between agricultural land and the atmosphere linked to food production are relatively small, although significant carbon emissions are associated with degradation of organic soils for plantations in tropical regions (Smith et al 2007, FAO 2012). Population growth and shifts in dietary patterns toward more meat and dairy consumption will lead to

  1. Revealing Mercury

    NASA Astrophysics Data System (ADS)

    Prockter, L. M.; Solomon, S. C.; Head, J. W.; Watters, T. R.; Murchie, S. L.; Robinson, M. S.; Chapman, C. R.; McNutt, R. L.

    2009-04-01

    The MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft, developed under NASA's Discovery Program, launched in August 2004. En route to insertion into orbit about Mercury in 2011, MESSENGER flies by Mercury three times. The first and second of these encounters were accomplished in January and October of 2008. These flybys viewed portions of Mercury's surface that were not observed by Mariner 10 during its reconnaissance of somewhat less than half of the planet in 1974-1975. All MESSENGER instruments operated during each flyby and returned a wealth of new data. Many of the new observations were focused on the planet's geology, including monochrome imaging at resolutions as high as 100 m/pixel, multispectral imaging in 11 filters at resolutions as high as 500 m/pixel, laser altimetry tracks extending over several thousands of kilometers, and high-resolution spectral measurements of several types of terrain. Here we present an overview of the first inferences on the global geology of Mercury from the MESSENGER observations. Whereas evidence for volcanism was equivocal from Mariner 10 data, the new MESSENGER images and altimetry provide compelling evidence that volcanism was widespread and protracted on Mercury. Color imaging reveals three common spectral units on the surface: a higher-reflectance, relatively red material occurring as a distinct class of smooth plains, typically with distinct embayment relationships interpreted to indicate volcanic emplacement; a lower-reflectance, relatively blue material typically excavated by impact craters and therefore inferred to be more common at depth; and a spectrally intermediate terrain that constitutes much of the uppermost crust. Three more minor spectral units are also seen: fresh crater ejecta, reddish material associated with rimless depressions interpreted to be volcanic centers, and high-reflectance deposits seen in some crater floors. Preliminary measurements of crater size

  2. The NASA Langley Multidisciplinary Uncertainty Quantification Challenge

    NASA Technical Reports Server (NTRS)

    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.

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

    PubMed

    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.

  4. MAMA Software Features: Visual Examples of Quantification

    SciTech Connect

    Ruggiero, Christy E.; Porter, Reid B.

    2014-05-20

    This document shows examples of the results from quantifying objects of certain sizes and types in the software. It is intended to give users a better feel for some of the quantification calculations, and, more importantly, to help users understand the challenges with using a small set of ‘shape’ quantification calculations for objects that can vary widely in shapes and features. We will add more examples to this in the coming year.

  5. Quantification of gap junction selectivity.

    PubMed

    Ek-Vitorín, Jose F; Burt, Janis M

    2005-12-01

    Gap junctions, which are essential for functional coordination and homeostasis within tissues, permit the direct intercellular exchange of small molecules. The abundance and diversity of this exchange depends on the number and selectivity of the comprising channels and on the transjunctional gradient for and chemical character of the permeant molecules. Limited knowledge of functionally significant permeants and poor detectability of those few that are known have made it difficult to define channel selectivity. Presented herein is a multifaceted approach to the quantification of gap junction selectivity that includes determination of the rate constant for intercellular diffusion of a fluorescent probe (k2-DYE) and junctional conductance (gj) for each junction studied, such that the selective permeability (k2-DYE/gj) for dyes with differing chemical characteristics or junctions with differing connexin (Cx) compositions (or treatment conditions) can be compared. In addition, selective permeability can be correlated using single-channel conductance when this parameter is also measured. Our measurement strategy is capable of detecting 1) rate constants and selective permeabilities that differ across three orders of magnitude and 2) acute changes in that rate constant. Using this strategy, we have shown that 1) the selective permeability of Cx43 junctions to a small cationic dye varied across two orders of magnitude, consistent with the hypothesis that the various channel configurations adopted by Cx43 display different selective permeabilities; and 2) the selective permeability of Cx37 vs. Cx43 junctions was consistently and significantly lower. PMID:16093281

  6. Stirling Convertor Fasteners Reliability Quantification

    NASA Technical Reports Server (NTRS)

    Shah, Ashwin R.; Korovaichuk, Igor; Kovacevich, Tiodor; Schreiber, Jeffrey G.

    2006-01-01

    Onboard Radioisotope Power Systems (RPS) being developed for NASA s deep-space science and exploration missions require reliable operation for up to 14 years and beyond. Stirling power conversion is a candidate for use in an RPS because it offers a multifold increase in the conversion efficiency of heat to electric power and reduced inventory of radioactive material. Structural fasteners are responsible to maintain structural integrity of the Stirling power convertor, which is critical to ensure reliable performance during the entire mission. Design of fasteners involve variables related to the fabrication, manufacturing, behavior of fasteners and joining parts material, structural geometry of the joining components, size and spacing of fasteners, mission loads, boundary conditions, etc. These variables have inherent uncertainties, which need to be accounted for in the reliability assessment. This paper describes these uncertainties along with a methodology to quantify the reliability, and provides results of the analysis in terms of quantified reliability and sensitivity of Stirling power conversion reliability to the design variables. Quantification of the reliability includes both structural and functional aspects of the joining components. Based on the results, the paper also describes guidelines to improve the reliability and verification testing.

  7. Cell-based quantification of molecular biomarkers in histopathology specimens

    PubMed Central

    Al-Kofahi, Yousef; Lassoued, Wiem; Grama, Kedar; Nath, Sumit K; Zhu, Jianliang; Oueslati, Ridha; Feldman, Michael; Lee, William M F; Roysam, Badrinath

    2011-01-01

    Aims To investigate the use of a computer-assisted technology for objective, cell-based quantification of molecular biomarkers in specified cell types in histopathology specimens, with the aim of advancing current visual estimation or pixel-level (rather than cell-based) quantification methods. Methods and results Tissue specimens were multiplex-immunostained to reveal cell structures, cell type markers, and analytes, and imaged with multispectral microscopy. The image data were processed with novel software that automatically delineates and types each cell in the field, measures morphological features, and quantifies analytes in different subcellular compartments of specified cells. The methodology was validated with the use of cell blocks composed of differentially labelled cultured cells mixed in known proportions, and evaluated on human breast carcinoma specimens for quantifying human epidermal growth factor receptor 2, oestrogen receptor, progesterone receptor, Ki67, phospho-extracellular signal-related kinase, and phospho-S6. Automated cell-level analyses closely matched human assessments, but, predictably, differed from pixel-level analyses of the same images. Conclusions Our method reveals the type, distribution, morphology and biomarker state of each cell in the field, and allows multiple biomarkers to be quantified over specified cell types, regardless of abundance. It is ideal for studying specimens from patients in clinical trials of targeted therapeutic agents, for investigating minority stromal cell subpopulations, and for phenotypic characterization to personalize therapy and prognosis. PMID:21771025

  8. Rapid digital quantification of microfracture populations

    NASA Astrophysics Data System (ADS)

    Gomez, Leonel A.; Laubach, Stephen E.

    2006-03-01

    Populations of microfractures are a structural fabric in many rocks deformed at upper crustal conditions. In some cases these fractures are visible in transmitted-light microscopy as fluid-inclusion planes or cement filled microfractures, but because SEM-based cathodoluminescence (CL) reveals more fractures and delineates their shapes, sizes, and crosscutting relations, it is a more effective structural tool. Yet at magnifications of 150-300×, at which many microfractures are visible, SEM-CL detectors image only small sample areas (0.5-0.1 mm 2) relative to fracture population patterns. The substantial effort required to image and measure centimeter-size areas at high-magnification has impeded quantitative study of microfractures. We present a method for efficient collection of mosaics of high-resolution CL imagery, a preparation method that allows samples to be any size while retaining continuous imagery of rock (no gaps), and software that facilitates fracture mapping and data reduction. Although the method introduced here was developed for CL imagery, it can be used with any other kind of images, including mosaics from petrographic microscopes. Compared with manual measurements, the new method increases several fold the number of microfractures imaged without a proportional increase in level of effort, increases the accuracy and repeatability of fracture measurements, and speeds quantification and display of fracture population attributes. We illustrate the method on microfracture arrays in dolostone from NE Mexico and sandstone from NW Scotland. We show that key aspects of microfracture population attributes are only fully manifest at scales larger than a single thin section.

  9. Optical and electrical characterizations of a single step ion beam milling mesa devices of chloride passivated PbS colloidal quantum dots based film

    NASA Astrophysics Data System (ADS)

    Hechster, Elad; Shapiro, Arthur; Lifshitz, Efrat; Sarusi, Gabby

    2016-07-01

    Colloidal Quantum Dots (CQDs) are of increasing interest, thanks to their quantum size effect that gives rise to their usage in various applications, such as biological tagging, solar cells and as the sensitizing layer of night vision devices. Here, we analyze the optical absorbance of chloride passivated PbS CQDs as well as revealing a correlation between their photoluminescence and sizes distribution, using theoretical models and experimental results from the literature. Next, we calculate the CQDs resistivity as a film. Although resistivity can be calculated from sheet resistance measurement using four point probes, such measurement is usually carried-out on the layer's surface that in most cases has dangling bonds and surface states, which might affect the charges flow and modify the resistivity. Therefore; our approach, which was applied in this work, is to extract the actual resistivity from measurements that are performed along the film's thickness (z-direction). For this intent, we fabricated gold capped PbS mesas devices using a single step Ion Beam Milling (IBM) process where we milled the gold and the PbS film continually, and then measured the vertical resistance. Knowing the mesas' dimensions, we calculate the resistivity. To the best of our knowledge, no previous work has extracted, vertically, the resistivity of chloride passivated PbS CQDs using the above method.

  10. Multimodal optical studies of single and clustered colloidal quantum dots for the long-term optical property evaluation of quantum dot-based molecular imaging phantoms

    PubMed Central

    Kang, HyeongGon; Clarke, Matthew L.; Lacerda, Silvia H. De Paoli; Karim, Alamgir; Pease, Leonard F.; Hwang, Jeeseong

    2012-01-01

    Understanding the optical properties of clustered quantum dots (QDs) is essential to the design of QD-based optical phantoms for molecular imaging. Single and clustered core/shell colloidal QDs of dimers, trimers, and tetramers are self-assembled, separated, and preferentially collected using electrospray differential mobility analysis (ES-DMA) with electrostatic deposition. Multimodal optical characterization and analysis of their dynamical photoluminescence (PL) properties enables the long-term evaluation of the physicochemical and optical properties of QDs in a single or a clustered state. A multimodal time-correlated spectroscopic confocal microscope capable of simultaneously measuring the time evolution of PL intensity fluctuation, PL lifetime, and emission spectra reveals the long-term dynamic optical properties of interacting QDs in individual dimeric clusters of QDs. This new method will benefit research into the quantitative interpretation of fluorescence intensity and lifetime results in QD-based molecular imaging techniques. The process of photooxidation leads to coupling of the QDs in a dimer, leading to unique optical properties when compared to an isolated QD. These results guide the design and evaluation of QD-based phantom materials for the validation of the PL measurements for quantitative molecular imaging of biological samples labeled with QD probes. PMID:22741078

  11. In-Gel Stable-Isotope Labeling (ISIL): a strategy for mass spectrometry-based relative quantification.

    PubMed

    Asara, John M; Zhang, Xiang; Zheng, Bin; Christofk, Heather H; Wu, Ning; Cantley, Lewis C

    2006-01-01

    Most proteomics approaches for relative quantification of protein expression use a combination of stable-isotope labeling and mass spectrometry. Traditionally, researchers have used difference gel electrophoresis (DIGE) from stained 1D and 2D gels for relative quantification. While differences in protein staining intensity can often be visualized, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. A method is presented for quantifying changes in the abundance of a specific protein or changes in specific modifications of a protein using In-gel Stable-Isotope Labeling (ISIL). Proteins extracted from any source (tissue, cell line, immunoprecipitate, etc.), treated under two experimental conditions, are resolved in separate lanes by gel electrophoresis. The regions of interest (visualized by staining) are reacted separately with light versus heavy isotope-labeled reagents, and the gel slices are then mixed and digested with proteases. The resulting peptides are then analyzed by LC-MS to determine relative abundance of light/heavy isotope pairs and analyzed by LC-MS/MS for identification of sequence and modifications. The strategy compares well with other relative quantification strategies, and in silico calculations reveal its effectiveness as a global relative quantification strategy. An advantage of ISIL is that visualization of gel differences can be used as a first quantification step followed by accurate and sensitive protein level stable-isotope labeling and mass spectrometry-based relative quantification.

  12. Antioxidant Activity and Validation of Quantification Method for Lycopene Extracted from Tomato.

    PubMed

    Cefali, Letícia Caramori; Cazedey, Edith Cristina Laignier; Souza-Moreira, Tatiana Maria; Correa, Marcos Antônio; Salgado, Hérida Regina Nunes; Isaac, Vera Lucia Borges

    2015-01-01

    Lycopene is a carotenoid found in tomatoes with potent antioxidant activity. The aim of the study was to obtain an extract containing lycopene from four types of tomatoes, validate a quantification method for the extracts by HPLC, and assess its antioxidant activity. Results revealed that the tomatoes analyzed contained lycopene and antioxidant activity. Salad tomato presented the highest concentration of this carotenoid and antioxidant activity. The quantification method exhibited linearity with a correlation coefficient of 0.9992. Tests for the assessment of precision, accuracy, and robustness achieved coefficients with variation of less than 5%. The LOD and LOQ were 0.0012 and 0.0039 μg/mL, respectively. Salad tomato can be used as a source of lycopene for the development of topical formulations, and based on performed tests, the chosen method for the identification and quantification of lycopene was considered to be linear, precise, exact, selective, and robust. PMID:26525253

  13. Separation and quantification of microalgal carbohydrates.

    PubMed

    Templeton, David W; Quinn, Matthew; Van Wychen, Stefanie; Hyman, Deborah; Laurens, Lieve M L

    2012-12-28

    Structural carbohydrates can constitute a large fraction of the dry weight of algal biomass and thus accurate identification and quantification is important for summative mass closure. Two limitations to the accurate characterization of microalgal carbohydrates are the lack of a robust analytical procedure to hydrolyze polymeric carbohydrates to their respective monomers and the subsequent identification and quantification of those monosaccharides. We address the second limitation, chromatographic separation of monosaccharides, here by identifying optimum conditions for the resolution of a synthetic mixture of 13 microalgae-specific monosaccharides, comprised of 8 neutral, 2 amino sugars, 2 uronic acids and 1 alditol (myo-inositol as an internal standard). The synthetic 13-carbohydrate mix showed incomplete resolution across 11 traditional high performance liquid chromatography (HPLC) methods, but showed improved resolution and accurate quantification using anion exchange chromatography (HPAEC) as well as alditol acetate derivatization followed by gas chromatography (for the neutral- and amino-sugars only). We demonstrate the application of monosaccharide quantification using optimized chromatography conditions after sulfuric acid analytical hydrolysis for three model algae strains and compare the quantification and complexity of monosaccharides in analytical hydrolysates relative to a typical terrestrial feedstock, sugarcane bagasse.

  14. Carotid intraplaque neovascularization quantification software (CINQS).

    PubMed

    Akkus, Zeynettin; van Burken, Gerard; van den Oord, Stijn C H; Schinkel, Arend F L; de Jong, Nico; van der Steen, Antonius F W; Bosch, Johan G

    2015-01-01

    Intraplaque neovascularization (IPN) is an important biomarker of atherosclerotic plaque vulnerability. As IPN can be detected by contrast enhanced ultrasound (CEUS), imaging-biomarkers derived from CEUS may allow early prediction of plaque vulnerability. To select the best quantitative imaging-biomarkers for prediction of plaque vulnerability, a systematic analysis of IPN with existing and new analysis algorithms is necessary. Currently available commercial contrast quantification tools are not applicable for quantitative analysis of carotid IPN due to substantial motion of the carotid artery, artifacts, and intermittent perfusion of plaques. We therefore developed a specialized software package called Carotid intraplaque neovascularization quantification software (CINQS). It was designed for effective and systematic comparison of sets of quantitative imaging biomarkers. CINQS includes several analysis algorithms for carotid IPN quantification and overcomes the limitations of current contrast quantification tools and existing carotid IPN quantification approaches. CINQS has a modular design which allows integrating new analysis tools. Wizard-like analysis tools and its graphical-user-interface facilitate its usage. In this paper, we describe the concept, analysis tools, and performance of CINQS and present analysis results of 45 plaques of 23 patients. The results in 45 plaques showed excellent agreement with visual IPN scores for two quantitative imaging-biomarkers (The area under the receiver operating characteristic curve was 0.92 and 0.93). PMID:25561454

  15. Quantification of isotopic turnover in agricultural systems

    NASA Astrophysics Data System (ADS)

    Braun, A.; Auerswald, K.; Schnyder, H.

    2012-04-01

    The isotopic turnover, which is a proxy for the metabolic rate, is gaining scientific importance. It is quantified for an increasing range of organisms, from microorganisms over plants to animals including agricultural livestock. Additionally, the isotopic turnover is analyzed on different scales, from organs to organisms to ecosystems and even to the biosphere. In particular, the quantification of the isotopic turnover of specific tissues within the same organism, e.g. organs like liver and muscle and products like milk and faeces, has brought new insights to improve understanding of nutrient cycles and fluxes, respectively. Thus, the knowledge of isotopic turnover is important in many areas, including physiology, e.g. milk synthesis, ecology, e.g. soil retention time of water, and medical science, e.g. cancer diagnosis. So far, the isotopic turnover is quantified by applying time, cost and expertise intensive tracer experiments. Usually, this comprises two isotopic equilibration periods. A first equilibration period with a constant isotopic input signal is followed by a second equilibration period with a distinct constant isotopic input signal. This yields a smooth signal change from the first to the second signal in the object under consideration. This approach reveals at least three major problems. (i) The input signals must be controlled isotopically, which is almost impossible in many realistic cases like free ranging animals. (ii) Both equilibration periods may be very long, especially when the turnover rate of the object under consideration is very slow, which aggravates the first problem. (iii) The detection of small or slow pools is improved by large isotopic signal changes, but large isotopic changes also involve a considerable change in the input material; e.g. animal studies are usually carried out as diet-switch experiments, where the diet is switched between C3 and C4 plants, since C3 and C4 plants differ strongly in their isotopic signal. The

  16. Carbon Nanotubes Released from an Epoxy-Based Nanocomposite: Quantification and Particle Toxicity.

    PubMed

    Schlagenhauf, Lukas; Buerki-Thurnherr, Tina; Kuo, Yu-Ying; Wichser, Adrian; Nüesch, Frank; Wick, Peter; Wang, Jing

    2015-09-01

    Studies combining both the quantification of free nanoparticle release and the toxicological investigations of the released particles from actual nanoproducts in a real-life exposure scenario are urgently needed, yet very rare. Here, a new measurement method was established to quantify the amount of free-standing and protruding multiwalled carbon nanotubes (MWCNTs) in the respirable fraction of particles abraded from a MWCNT-epoxy nanocomposite. The quantification approach involves the prelabeling of MWCNTs with lead ions, nanocomposite production, abrasion and collection of the inhalable particle fraction, and quantification of free-standing and protruding MWCNTs by measuring the concentration of released lead ions. In vitro toxicity studies for genotoxicity, reactive oxygen species formation, and cell viability were performed using A549 human alveolar epithelial cells and THP-1 monocyte-derived macrophages. The quantification experiment revealed that in the respirable fraction of the abraded particles, approximately 4000 ppm of the MWCNTs were released as exposed MWCNTs (which could contact lung cells upon inhalation) and approximately 40 ppm as free-standing MWCNTs in the worst-case scenario. The release of exposed MWCNTs was lower for nanocomposites containing agglomerated MWCNTs. The toxicity tests revealed that the abraded particles did not induce any acute cytotoxic effects.

  17. Advancing agricultural greenhouse gas quantification*

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    1. Introduction Better information on greenhouse gas (GHG) emissions and mitigation potential in the agricultural sector is necessary to manage these emissions and identify responses that are consistent with the food security and economic development priorities of countries. Critical activity data (what crops or livestock are managed in what way) are poor or lacking for many agricultural systems, especially in developing countries. In addition, the currently available methods for quantifying emissions and mitigation are often too expensive or complex or not sufficiently user friendly for widespread use. The purpose of this focus issue is to capture the state of the art in quantifying greenhouse gases from agricultural systems, with the goal of better understanding our current capabilities and near-term potential for improvement, with particular attention to quantification issues relevant to smallholders in developing countries. This work is timely in light of international discussions and negotiations around how agriculture should be included in efforts to reduce and adapt to climate change impacts, and considering that significant climate financing to developing countries in post-2012 agreements may be linked to their increased ability to identify and report GHG emissions (Murphy et al 2010, CCAFS 2011, FAO 2011). 2. Agriculture and climate change mitigation The main agricultural GHGs—methane and nitrous oxide—account for 10%-12% of anthropogenic emissions globally (Smith et al 2008), or around 50% and 60% of total anthropogenic methane and nitrous oxide emissions, respectively, in 2005. Net carbon dioxide fluxes between agricultural land and the atmosphere linked to food production are relatively small, although significant carbon emissions are associated with degradation of organic soils for plantations in tropical regions (Smith et al 2007, FAO 2012). Population growth and shifts in dietary patterns toward more meat and dairy consumption will lead to

  18. Quantification of carbon nanomaterials in vivo.

    PubMed

    Wang, Haifang; Yang, Sheng-Tao; Cao, Aoneng; Liu, Yuanfang

    2013-03-19

    A diverse array of carbon nanomaterials (NMs), including fullerene, carbon nanotubes (CNTs), graphene, nanodiamonds, and carbon nanoparticles, have been discovered and widely applied in a variety of industries. Carbon NMs have been detected in the environment and have a strong possibility of entering the human body. The safety of carbon NMs has thus become a serious concern in academia and society. To achieve strict biosafety assessments, researchers need to fully understand the effects and fates of NMs in the human body, including information about absorption, distribution, metabolism, excretion, and toxicity (ADME/T). To acquire the ADME data, researchers must quantify NMs, but carbon NMs are very difficult to quantify in vivo. The carbon background in a typical biological system is high, particularly compared with the much lower concentration of carbon NMs. Moreover, carbon NMs lack a specific detection signal. Therefore, isotopic labeling, with its high sensitivity and specificity, is the first choice to quantify carbon NMs in vivo. Previously, researchers have used many isotopes, including ¹³C, ¹⁴C, ¹²⁵I, ¹³¹I, ³H, ⁶⁴Cu, ¹¹¹In, ⁸⁶Y, 99mTc, and ⁶⁷Ga, to label carbon NMs. We used these isotopic labeling methods to study the ADME of carbon NMs via different exposure pathways in animal models. Except for the metabolism of carbon NMs, which has seldom been investigated, significant amounts of data have been reported on the in vivo absorption, distribution, excretion, and toxicity of carbon NMs, which have revealed characteristic behaviors of carbon NMs, such as reticuloendothelial system (RES) capture. However, the complexity of the biological systems and diverse preparation and functionalization of the same carbon NMs have led to inconsistent results across different studies. Therefore, the data obtained so far have not provided a compatible and systematic profile of biosafety. Further efforts are needed to address these problems. In

  19. The quantification of hydrogen and methane in contaminated groundwater: validation of robust procedures for sampling and quantification.

    PubMed

    Dorgerloh, Ute; Becker, Roland; Theissen, Hubert; Nehls, Irene

    2010-10-01

    A number of currently recommended sampling techniques for the determination of hydrogen in contaminated groundwater were compared regarding the practical proficiency in field campaigns. Key characteristics of appropriate sampling procedures are reproducibility of results, robustness against varying field conditions such as hydrostatic pressure, aquifer flow, and biological activity. Laboratory set-ups were used to investigate the most promising techniques. Bubble stripping with gas sampling bulbs yielded reproducible recovery of hydrogen and methane which could be verified for groundwater sampled in two field campaigns. The methane content of the groundwater was confirmed by analysis of directly pumped samples thus supporting the trueness of the stripping results. Laboratory set-ups and field campaigns revealed that bubble stripping of hydrogen may be restricted to the type of used pump. Concentrations of dissolved hydrogen after bubble stripping with an electrically driven submersible pump were about one order of magnitude higher than those obtained from diffusion sampling. The gas chromatographic determination for hydrogen and methane requires manual injection of gas samples and detection by a pulsed discharge detector (PDD) and allows limits of quantification of 3 nM dissolved hydrogen and 1 µg L⁻¹ dissolved methane in groundwater. The combined standard uncertainty of the bubble stripping and GC/PDD quantification of hydrogen in field samples was 7% at 7.8 nM and 18% for 78 nM. PMID:20730246

  20. Quantum Dot-Based Cell Motility Assay

    SciTech Connect

    Gu, Weiwei; Pellegrino, Teresa; Parak Wolfgang J; Boudreau,Rosanne; Le Gros, Mark A.; Gerion, Daniele; Alivisatos, A. Paul; Larabell, Carolyn A.

    2005-06-06

    Because of their favorable physical and photochemical properties, colloidal CdSe/ZnS-semiconductor nanocrystals (commonly known as quantum dots) have enormous potential for use in biological imaging. In this report, we present an assay that uses quantum dots as markers to quantify cell motility. Cells that are seeded onto a homogeneous layer of quantum dots engulf and absorb the nanocrystals and, as a consequence, leave behind a fluorescence-free trail. By subsequently determining the ratio of cell area to fluorescence-free track area, we show that it is possible to differentiate between invasive and noninvasive cancer cells. Because this assay uses simple fluorescence detection, requires no significant data processing, and can be used in live-cell studies, it has the potential to be a powerful new tool for discriminating between invasive and noninvasive cancer cell lines or for studying cell signaling events involved in migration.

  1. Quantification of Cannabinoid Content in Cannabis

    NASA Astrophysics Data System (ADS)

    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.

  2. Colour thresholding and objective quantification in bioimaging

    NASA Technical Reports Server (NTRS)

    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.

  3. HPC Analytics Support. Requirements for Uncertainty Quantification Benchmarks

    SciTech Connect

    Paulson, Patrick R.; Purohit, Sumit; Rodriguez, Luke R.

    2015-05-01

    This report outlines techniques for extending benchmark generation products so they support uncertainty quantification by benchmarked systems. We describe how uncertainty quantification requirements can be presented to candidate analytical tools supporting SPARQL. We describe benchmark data sets for evaluating uncertainty quantification, as well as an approach for using our benchmark generator to produce data sets for generating benchmark data sets.

  4. Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy.

    PubMed

    Laux, Eva-Maria; Knigge, Xenia; Bier, Frank F; Wenger, Christian; Hölzel, Ralph

    2015-09-01

    The combination of alternating electric fields with nanometer-sized electrodes allows the permanent immobilization of proteins by dielectrophoretic force. Here, atomic force microscopy is introduced as a quantification method, and results are compared with fluorescence microscopy. Experimental parameters, for example the applied voltage and duration of field application, are varied systematically, and the influence on the amount of immobilized proteins is investigated. A linear correlation to the duration of field application was found by atomic force microscopy, and both microscopical methods yield a square dependence of the amount of immobilized proteins on the applied voltage. While fluorescence microscopy allows real-time imaging, atomic force microscopy reveals immobilized proteins obscured in fluorescence images due to low S/N. Furthermore, the higher spatial resolution of the atomic force microscope enables the visualization of the protein distribution on single nanoelectrodes. The electric field distribution is calculated and compared to experimental results with very good agreement to atomic force microscopy measurements.

  5. Experimental investigations for uncertainty quantification in brake squeal analysis

    NASA Astrophysics Data System (ADS)

    Renault, A.; Massa, F.; Lallemand, B.; Tison, T.

    2016-04-01

    The aim of this paper is to improve the correlation between the experimental and the numerical prediction of unstable frequencies for automotive brake systems considering uncertainty. First, an experimental quantification of uncertainty and a discussion analysing the contributions of uncertainty to a numerical squeal simulation are proposed. Frequency and transient simulations are performed considering nominal values of model parameters, determined experimentally. The obtained results are compared with those derived from experimental tests to highlight the limitation of deterministic simulations. The effects of the different kinds of uncertainty detected in working conditions of brake system, the pad boundary condition, the brake system material properties and the pad surface topography are discussed by defining different unstable mode classes. Finally, a correlation between experimental and numerical results considering uncertainty is successfully proposed for an industrial brake system. Results from the different comparisons reveal also a major influence of the pad topography and consequently the contact distribution.

  6. Performance and Limitations of Phosphate Quantification: Guidelines for Plant Biologists.

    PubMed

    Kanno, Satomi; Cuyas, Laura; Javot, Hélène; Bligny, Richard; Gout, Elisabeth; Dartevelle, Thibault; Hanchi, Mohamed; Nakanishi, Tomoko M; Thibaud, Marie-Christine; Nussaume, Laurent

    2016-04-01

    Phosphate (Pi) is a macronutrient that is essential for plant life. Several regulatory components involved in Pi homeostasis have been identified, revealing a very high complexity at the cellular and subcellular levels. Determining the Pi content in plants is crucial to understanding this regulation, and short real-time(33)Pi uptake imaging experiments have shown Pi movement to be highly dynamic. Furthermore, gene modulation by Pi is finely controlled by localization of this ion at the tissue as well as the cellular and subcellular levels. Deciphering these regulations requires access to and quantification of the Pi pool in the various plant compartments. This review presents the different techniques available to measure, visualize and trace Pi in plants, with a discussion of the future prospects. PMID:26865660

  7. Quantification of plasma exosome is a potential prognostic marker for esophageal squamous cell carcinoma

    PubMed Central

    Matsumoto, Yasunori; Kano, Masayuki; Akutsu, Yasunori; Hanari, Naoyuki; Hoshino, Isamu; Murakami, Kentaro; Usui, Akihiro; Suito, Hiroshi; Takahashi, Masahiko; Otsuka, Ryota; Xin, Hu; Komatsu, Aki; Iida, Keiko; Matsubara, Hisahiro

    2016-01-01

    Exosomes play important roles in cancer progression. Although its contents (e.g., proteins and microRNAs) have been focused on in cancer research, particularly as potential diagnostic markers, the exosome behavior and methods for exosome quantification remain unclear. In the present study, we analyzed the tumor-derived exosome behavior and assessed the quantification of exosomes in patient plasma as a biomarker for esophageal squamous cell carcinoma (ESCC). A CD63-GFP expressing human ESCC cell line (TE2-CD63-GFP) was made by transfection, and mouse subcutaneous tumor models were established. Fluorescence imaging was performed on tumors and plasma exosomes harvested from mice. GFP-positive small vesicles were confirmed in the plasma obtained from TE2-CD63-GFP tumor-bearing mice. Patient plasma was collected in Chiba University Hospital (n=86). Exosomes were extracted from 100 µl of the plasma and quantified by acetylcholinesterase (AChE) activity. The relationship between exosome quantification and the patient clinical characteristics was assessed. The quantification of exosomes isolated from the patient plasma revealed that esophageal cancer patients (n=66) expressed higher exosome levels than non-malignant patients (n=20) (P=0.0002). Although there was no correlation between the tumor progression and the exosome levels, exosome number was the independent prognostic marker and low levels of exosome predicted a poor prognosis (P=0.03). In conclusion, exosome levels may be useful as an independent prognostic factor for ESCC patients. PMID:27599779

  8. Quantification of taurine in energy drinks using ¹H NMR.

    PubMed

    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.

  9. Sulphite quantification on damaged stones and mortars

    NASA Astrophysics Data System (ADS)

    Gobbi, G.; Zappia, G.; Sabbioni, C.

    An analytical procedure was developed for the simultaneous identification and quantification of the sulphite and main anions found in degradation patinas on historic buildings and monuments, as well as on stones and mortars exposed in simulation chamber and field tests. The quantification of anions was performed by means of ion chromatography (IC), after the stabilisation of sulphite with a D(-) fructose solution. The utilisation of two different chromatographic columns, connected in series, allowed the simultaneous determination of fluoride, acetate, formate, chloride, nitrite, bromide, iodide, oxyhalides, nitrate, phosphate, sulphite, sulphate and oxalate, in a time of approximately 25 min, without interference and with high reproducibility. Finally, the results show how in the majority of cases the formation of sulphite is an intermediate stage in the sulphation process affecting building materials exposed to the environment and needs to be measured together with sulphate, in order to obtain a correct interpretation of degradation mechanisms on such materials.

  10. Whitepaper on Uncertainty Quantification for MPACT

    SciTech Connect

    Williams, Mark L.

    2015-12-17

    The MPACT code provides the ability to perform high-fidelity deterministic calculations to obtain a wide variety of detailed results for very complex reactor core models. However MPACT currently does not have the capability to propagate the effects of input data uncertainties to provide uncertainties in the calculated results. This white paper discusses a potential method for MPACT uncertainty quantification (UQ) based on stochastic sampling.

  11. Automated quantification of synapses by fluorescence microscopy.

    PubMed

    Schätzle, Philipp; Wuttke, René; Ziegler, Urs; Sonderegger, Peter

    2012-02-15

    The quantification of synapses in neuronal cultures is essential in studies of the molecular mechanisms underlying synaptogenesis and synaptic plasticity. Conventional counting of synapses based on morphological or immunocytochemical criteria is extremely work-intensive. We developed a fully automated method which quantifies synaptic elements and complete synapses based on immunocytochemistry. Pre- and postsynaptic elements are detected by their corresponding fluorescence signals and their proximity to dendrites. Synapses are defined as the combination of a pre- and postsynaptic element within a given distance. The analysis is performed in three dimensions and all parameters required for quantification can be easily adjusted by a graphical user interface. The integrated batch processing enables the analysis of large datasets without any further user interaction and is therefore efficient and timesaving. The potential of this method was demonstrated by an extensive quantification of synapses in neuronal cultures from DIV 7 to DIV 21. The method can be applied to all datasets containing a pre- and postsynaptic labeling plus a dendritic or cell surface marker.

  12. Protein quantification using a cleavable reporter peptide.

    PubMed

    Duriez, Elodie; Trevisiol, Stephane; Domon, Bruno

    2015-02-01

    Peptide and protein quantification based on isotope dilution and mass spectrometry analysis are widely employed for the measurement of biomarkers and in system biology applications. The accuracy and reliability of such quantitative assays depend on the quality of the stable-isotope labeled standards. Although the quantification using stable-isotope labeled peptides is precise, the accuracy of the results can be severely biased by the purity of the internal standards, their stability and formulation, and the determination of their concentration. Here we describe a rapid and cost-efficient method to recalibrate stable isotope labeled peptides in a single LC-MS analysis. The method is based on the equimolar release of a protein reference peptide (used as surrogate for the protein of interest) and a universal reporter peptide during the trypsinization of a concatenated polypeptide standard. The quality and accuracy of data generated with such concatenated polypeptide standards are highlighted by the quantification of two clinically important proteins in urine samples and compared with results obtained with conventional stable isotope labeled reference peptides. Furthermore, the application of the UCRP standards in complex samples is described.

  13. Protein quantification using a cleavable reporter peptide.

    PubMed

    Duriez, Elodie; Trevisiol, Stephane; Domon, Bruno

    2015-02-01

    Peptide and protein quantification based on isotope dilution and mass spectrometry analysis are widely employed for the measurement of biomarkers and in system biology applications. The accuracy and reliability of such quantitative assays depend on the quality of the stable-isotope labeled standards. Although the quantification using stable-isotope labeled peptides is precise, the accuracy of the results can be severely biased by the purity of the internal standards, their stability and formulation, and the determination of their concentration. Here we describe a rapid and cost-efficient method to recalibrate stable isotope labeled peptides in a single LC-MS analysis. The method is based on the equimolar release of a protein reference peptide (used as surrogate for the protein of interest) and a universal reporter peptide during the trypsinization of a concatenated polypeptide standard. The quality and accuracy of data generated with such concatenated polypeptide standards are highlighted by the quantification of two clinically important proteins in urine samples and compared with results obtained with conventional stable isotope labeled reference peptides. Furthermore, the application of the UCRP standards in complex samples is described. PMID:25411902

  14. Numerical approach for quantification of epistemic uncertainty

    NASA Astrophysics Data System (ADS)

    Jakeman, John; Eldred, Michael; Xiu, Dongbin

    2010-06-01

    In the field of uncertainty quantification, uncertainty in the governing equations may assume two forms: aleatory uncertainty and epistemic uncertainty. Aleatory uncertainty can be characterised by known probability distributions whilst epistemic uncertainty arises from a lack of knowledge of probabilistic information. While extensive research efforts have been devoted to the numerical treatment of aleatory uncertainty, little attention has been given to the quantification of epistemic uncertainty. In this paper, we propose a numerical framework for quantification of epistemic uncertainty. The proposed methodology does not require any probabilistic information on uncertain input parameters. The method only necessitates an estimate of the range of the uncertain variables that encapsulates the true range of the input variables with overwhelming probability. To quantify the epistemic uncertainty, we solve an encapsulation problem, which is a solution to the original governing equations defined on the estimated range of the input variables. We discuss solution strategies for solving the encapsulation problem and the sufficient conditions under which the numerical solution can serve as a good estimator for capturing the effects of the epistemic uncertainty. In the case where probability distributions of the epistemic variables become known a posteriori, we can use the information to post-process the solution and evaluate solution statistics. Convergence results are also established for such cases, along with strategies for dealing with mixed aleatory and epistemic uncertainty. Several numerical examples are presented to demonstrate the procedure and properties of the proposed methodology.

  15. Automated Template Quantification for DNA Sequencing Facilities

    PubMed Central

    Ivanetich, Kathryn M.; Yan, Wilson; Wunderlich, Kathleen M.; Weston, Jennifer; Walkup, Ward G.; Simeon, Christian

    2005-01-01

    The quantification of plasmid DNA by the PicoGreen dye binding assay has been automated, and the effect of quantification of user-submitted templates on DNA sequence quality in a core laboratory has been assessed. The protocol pipets, mixes and reads standards, blanks and up to 88 unknowns, generates a standard curve, and calculates template concentrations. For pUC19 replicates at five concentrations, coefficients of variance were 0.1, and percent errors were from 1% to 7% (n = 198). Standard curves with pUC19 DNA were nonlinear over the 1 to 1733 ng/μL concentration range required to assay the majority (98.7%) of user-submitted templates. Over 35,000 templates have been quantified using the protocol. For 1350 user-submitted plasmids, 87% deviated by ≥ 20% from the requested concentration (500 ng/μL). Based on data from 418 sequencing reactions, quantification of user-submitted templates was shown to significantly improve DNA sequence quality. The protocol is applicable to all types of double-stranded DNA, is unaffected by primer (1 pmol/μL), and is user modifiable. The protocol takes 30 min, saves 1 h of technical time, and costs approximately $0.20 per unknown. PMID:16461949

  16. Quantification in MALDI-TOF mass spectrometry of modified polymers.

    PubMed

    Walterová, Zuzana; Horský, Jiří

    2011-05-01

    MALDI-TOF mass spectrometry quantification is hampered by the poor reproducibility of the signal intensity and by molecular-mass and compositional discrimination. The addition of a suitable compound as an internal standard increases reproducibility and allows a calibration curve to be constructed. The concept was also verified with synthetic polymers but no instructions for practical implementation were given [H. Chen, M. He, J. Pei, H. He, Anal. Chem. 75 (2003) 6531-6535.], even though synthetic polymers are generally non-uniform with respect to molecular mass and composition and access to the polymer of the same molecular mass distribution and composition as that of the quantified one is thus the exception rather than rule. On the other hand, relative quantification of polymers e.g., the content of the precursor polymer in a batch of a modified polymer, is usually sought. In this particular case, the pure precursor is usually available and the modified polymer can serve as an internal standard. However, the calibration curve still cannot be constructed and the use of the internal standard has to be combined with the method of standard addition in which the precursor polymer is added directly to the analyzed sample. The experiments with simulated modified polymers, mixtures of poly(ethylene glycol) (PEG) and poly(ethylene glycol) monomethyl ether (MPEG) of similar molecular-mass distribution, revealed a power dependence of the PEG/MPEG signal-intensity ratio (MS ratio) on the PEG/MPEG concentrations ratio in the mixture (gravimetric ratio). The result was obtained using standard procedures and instrumentation, which means that the basic assumption of the standard-addition method, i.e., the proportionality of the MS and gravimetric ratios, generally cannot be taken for granted. Therefore, the multi-point combined internal-standard standard-addition method was developed and experimentally verified for the quantification of the precursor in modified polymers. In this

  17. Tissue elasticity quantification by acoustic radiation force impulse for the assessment of renal allograft function.

    PubMed

    He, Wan-Yuan; Jin, Yun-Jie; Wang, Wen-Ping; Li, Chao-Lun; Ji, Zheng-Biao; Yang, Cheng

    2014-02-01

    Acoustic radiation force impulse (ARFI) quantification, a novel ultrasound-based elastography method, has been used to measure liver fibrosis. However, few studies have been performed on the use of ARFI quantification in kidney examinations. We evaluated renal allograft stiffness using ARFI quantification in patients with stable renal function (n = 52) and those with biopsy-proven allograft dysfunction (n = 50). ARFI quantification, given as shear wave velocity (SWV), was performed. The resistance index (RI) was calculated by pulsed-wave Doppler ultrasound, and clinical and laboratory data were collected. Morphologic changes in transplanted kidneys were diagnosed by an independent pathologist. Mean SWV was more significantly negatively correlated with estimated glomerular filtration rate (eGFR) (r = -0.657, p < 0.0001) than was RI (r = -0.429, p = 0.0004) in transplanted kidneys. Receiver operating characteristic curve analysis revealed that the sensitivity and specificity of quantitative ultrasound in the diagnosis of renal allograft dysfunction were 72.0% and 86.5% (cutoff value = 2.625), respectively. The latter values were better than those of RI, which were 62.0% and 69.2% (cutoff value = 0.625), respectively. The coefficient of variation for repeat SWV measurements of the middle part of transplanted kidney was 8.64%, and inter-observer agreement on SWV was good (Bland-Altman method, ICC = 0.890). In conclusion, tissue elasticity quantification by ARFI is more accurate than the RI in diagnosing renal allograft function.

  18. Comparative study between extraction techniques and column separation for the quantification of sinigrin and total isothiocyanates in mustard seed.

    PubMed

    Cools, Katherine; Terry, Leon A

    2012-07-15

    Glucosinolates are β-thioglycosides which are found naturally in Cruciferae including the genus Brassica. When enzymatically hydrolysed, glucosinolates yield isothiocyanates and give a pungent taste. Both glucosinolates and isothiocyanates have been linked with anticancer activity as well as antifungal and antibacterial properties and therefore the quantification of these compounds is scientifically important. A wide range of literature exists on glucosinolates, however the extraction and quantification procedures differ greatly resulting in discrepancies between studies. The aim of this study was therefore to compare the most popular extraction procedures to identify the most efficacious method and whether each extraction can also be used for the quantification of total isothiocyanates. Four extraction techniques were compared for the quantification of sinigrin from mustard cv. Centennial (Brassica juncea L.) seed; boiling water, boiling 50% (v/v) aqueous acetonitrile, boiling 100% methanol and 70% (v/v) aqueous methanol at 70 °C. Prior to injection into the HPLC, the extractions which involved solvents (acetonitrile or methanol) were freeze-dried and resuspended in water. To identify whether the same extract could be used to measure total isothiocyanates, a dichloromethane extraction was carried out on the sinigrin extracts. For the quantification of sinigrin alone, boiling 50% (v/v) acetonitrile was found to be the most efficacious extraction solvent of the four tested yielding 15% more sinigrin than the water extraction. However, the removal of the acetonitrile by freeze-drying had a negative impact on the isothiocyanate content. Quantification of both sinigrin and total isothiocyanates was possible when the sinigrin was extracted using boiling water. Two columns were compared for the quantification of sinigrin revealing the Zorbax Eclipse to be the best column using this particular method. PMID:22743340

  19. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.

    PubMed

    Äijö, Tarmo; Huang, Yun; Mannerström, Henrik; Chavez, Lukas; Tsagaratou, Ageliki; Rao, Anjana; Lähdesmäki, Harri

    2016-03-14

    We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.

  20. QUANTIFICATION OF TISSUE PROPERTIES IN SMALL VOLUMES

    SciTech Connect

    J. MOURANT; ET AL

    2000-12-01

    The quantification of tissue properties by optical measurements will facilitate the development of noninvasive methods of cancer diagnosis and detection. Optical measurements are sensitive to tissue structure which is known to change during tumorigenesis. The goals of the work presented in this paper were to verify that the primary scatterers of light in cells are structures much smaller than the nucleus and then to develop an optical technique that can quantify parameters of structures the same size as the scattering features in cells. Polarized, elastic back-scattering was found to be able to quantify changes in scattering properties for turbid media consisting of scatterers of the size found in tissue.

  1. Tutorial examples for uncertainty quantification methods.

    SciTech Connect

    De Bord, Sarah

    2015-08-01

    This report details the work accomplished during my 2015 SULI summer internship at Sandia National Laboratories in Livermore, CA. During this internship, I worked on multiple tasks with the common goal of making uncertainty quantification (UQ) methods more accessible to the general scientific community. As part of my work, I created a comprehensive numerical integration example to incorporate into the user manual of a UQ software package. Further, I developed examples involving heat transfer through a window to incorporate into tutorial lectures that serve as an introduction to UQ methods.

  2. Adjoint-Based Uncertainty Quantification with MCNP

    SciTech Connect

    Seifried, Jeffrey E.

    2011-09-01

    This work serves to quantify the instantaneous uncertainties in neutron transport simulations born from nuclear data and statistical counting uncertainties. Perturbation and adjoint theories are used to derive implicit sensitivity expressions. These expressions are transformed into forms that are convenient for construction with MCNP6, creating the ability to perform adjoint-based uncertainty quantification with MCNP6. These new tools are exercised on the depleted-uranium hybrid LIFE blanket, quantifying its sensitivities and uncertainties to important figures of merit. Overall, these uncertainty estimates are small (< 2%). Having quantified the sensitivities and uncertainties, physical understanding of the system is gained and some confidence in the simulation is acquired.

  3. Quantification of tsunami-induced flows on a Mediterranean carbonate ramp reveals catastrophic evolution

    NASA Astrophysics Data System (ADS)

    Slootman, Arnoud; Cartigny, Matthieu J. B.; Moscariello, Andrea; Chiaradia, Massimo; de Boer, Poppe L.

    2016-06-01

    Cool-water carbonates are the dominant limestones in the Mediterranean Basin since the Early Pliocene. Their deposition typically resulted in ramp morphologies due to high rates of resedimentation. Several such fossil carbonate ramps are characterised by a bimodal facies stacking pattern, where background deposition of subaqueous dune and/or tempestite deposits is repeatedly interrupted by anomalously thick sedimentary units, dominated by backset-stratification formed by supercritical flows. A multitude of exceptional triggers (e.g. storms, floods, tsunamis) have been invoked to explain the origin of these supercritical flows, which, in the absence of a quantitative analysis, remains speculative as yet. Here, for the first time, the catastrophic evolution of one such Mediterranean carbonate ramp, on Favignana Island (Italy), is quantified by combining 87Sr/86Sr dating, outcrop-based palaeoflow reconstructions and hydraulic calculations. We demonstrate that rare tsunami-induced flows, occurring on average once every 14 to 35 kyr, lasting a few hours only, deposited the anomalously thick backset-bedded units that form half of the sedimentary record. In between such events, cumulative two years of storm-induced flows deposited the remaining half of the succession by the stacking of subaqueous dunes. The two to four orders of magnitude difference in average recurrence period between the two flow types, and their associated sedimentation rates, emphasises the genetic differences between the two styles of deposition. In terms of sediment transport, the studied carbonate ramp was inactive for at least 99% of the time with gradual progradation during decennial to centennial storm activity. Carbonate ramp evolution attained a catastrophic signature by the contribution of rare tsunamis, producing short-lived, high-energy sediment gravity flows.

  4. Precise quantification of silica and ceria nanoparticle uptake revealed by 3D fluorescence microscopy

    PubMed Central

    Torrano, Adriano A

    2014-01-01

    Summary Particle_in_Cell-3D is a powerful method to quantify the cellular uptake of nanoparticles. It combines the advantages of confocal fluorescence microscopy with fast and precise semi-automatic image analysis. In this work we present how this method was applied to investigate the impact of 310 nm silica nanoparticles on human vascular endothelial cells (HUVEC) in comparison to a cancer cell line derived from the cervix carcinoma (HeLa). The absolute number of intracellular silica nanoparticles within the first 24 h was determined and shown to be cell type-dependent. As a second case study, Particle_in_Cell-3D was used to assess the uptake kinetics of 8 nm and 30 nm ceria nanoparticles interacting with human microvascular endothelial cells (HMEC-1). These small nanoparticles formed agglomerates in biological medium, and the particles that were in effective contact with cells had a mean diameter of 417 nm and 316 nm, respectively. A significant particle size-dependent effect was observed after 48 h of interaction, and the number of intracellular particles was more than four times larger for the 316 nm agglomerates. Interestingly, our results show that for both particle sizes there is a maximum dose of intracellular nanoparticles at about 24 h. One of the causes for such an interesting and unusual uptake behavior could be cell division. PMID:25383274

  5. High-throughput optical quantification of mechanosensory habituation reveals neurons encoding memory in Caenorhabditis elegans

    PubMed Central

    Sugi, Takuma; Ohtani, Yasuko; Kumiya, Yuta; Igarashi, Ryuji; Shirakawa, Masahiro

    2014-01-01

    A major goal of neuroscience studies is to identify the neurons and molecules responsible for memory. Mechanosensory habituation in Caenorhabditis elegans is a simple form of learning and memory, in which a circuit of several sensory neurons and interneurons governs behavior. However, despite the usefulness of this paradigm, there are hardly any systems for rapid and accurate behavioral genetic analysis. Here, we developed a multiplexed optical system to genetically analyze C. elegans mechanosensory habituation, and identified two interneurons involved in memory formation. The system automatically trains large populations of animals and simultaneously quantifies the behaviors of various strains by optically discriminating between transgenic and nontransgenic animals. Biochemical and cell-specific behavioral analyses indicated that phosphorylation of cyclic AMP response element-binding protein (CREB), a factor known to regulate memory allocation, was facilitated during training and this phosphorylation in AVA and AVD interneurons was required for habituation. These interneurons are a potential target for cell-specific exploration of the molecular substrates of memory. PMID:25404296

  6. Quantification of intensive hybrid coastal reclamation for revealing its impacts on macrozoobenthos

    NASA Astrophysics Data System (ADS)

    Yan, Jiaguo; Cui, Baoshan; Zheng, Jingjing; Xie, Tian; Wang, Qing; Li, Shanze

    2015-01-01

    Managing and identifying the sources of anthropogenic stress in coastal wetlands requires an in-depth understanding of relationships between species diversity and human activities. Empirical and experimental studies provide clear evidence that coastal reclamation can have profound impacts on marine organisms, but the focus of such studies is generally on comparative or laboratory research. We developed a compound intensity index (reclamation intensity index, RI) on hybrid coastal reclamation, to quantify the impacts of reclamation on coastal ecosystems. We also made use of mean annual absolute changes to a number of biotic variables (biodiversity, species richness, biomass of total macrozoobenthos, and species richness and biomass of Polychaeta, Mollusca, Crustacea, and Echinodermata) to determine Hedges’d index, which is a measure of the potential effects of coastal reclamation. Our results showed that there was significant difference of coastal reclamation intensity between Yellow Sea, East China Sea and South China Sea, the biological changes in effect sizes of the three regions differed greatly over time. Our modelling analyses showed that hybrid coastal reclamation generally had significant negative impacts on species diversity and biomass of macrozoobenthos. These relationships varied among different taxonomic groups and included both linear and nonlinear relationships. The results indicated that a high-intensity of coastal reclamation contributed to a pronounced decline in species diversity and biomass, while lower-intensity reclamation, or reclamation within certain thresholds, resulted in a small increase in species diversity and biomass. These results have important implications for biodiversity conservation and the ecological restoration of coastal wetlands in face of the intensive reclamation activities.

  7. Volumetric quantification of fluid flow reveals fish's use of hydrodynamic stealth to capture evasive prey

    PubMed Central

    Gemmell, Brad J.; Adhikari, Deepak; Longmire, Ellen K.

    2014-01-01

    In aquatic ecosystems, predation on zooplankton by fish provides a major pathway for the transfer of energy to higher trophic levels. Copepods are an abundant zooplankton group that sense hydromechanical disturbances produced by approaching predators and respond with rapid escapes. Despite this capability, fish capture copepods with high success. Previous studies have focused on the predatory strike to elucidate details of this interaction. However, these raptorial strikes and resulting suction are only effective at short range. Thus, small fish must closely approach highly sensitive prey without triggering an escape in order for a strike to be successful. We use a new method, high-speed, infrared, tomographic particle image velocimetry, to investigate three-dimensional fluid patterns around predator and prey during approaches. Our results show that at least one planktivorous fish (Danio rerio) can control the bow wave in front of the head during the approach and consumption of prey (copepod). This alters hydrodynamic profiles at the location of the copepod such that it is below the threshold required to elicit an escape response. We find this behaviour to be mediated by the generation of suction within the buccopharyngeal cavity, where the velocity into the mouth roughly matches the forward speed of the fish. These results provide insight into how animals modulate aspects of fluid motion around their bodies to overcome escape responses and enhance prey capture. PMID:24227312

  8. Quantification of social behavior in D. discoideum reveals complex fixed and facultative strategies.

    PubMed

    Buttery, Neil J; Rozen, Daniel E; Wolf, Jason B; Thompson, Christopher R L

    2009-08-25

    Understanding the maintenance of cooperation requires an understanding of the nature of cheaters and the strategies used to mitigate their effects. However, it is often difficult to determine how cheating or differential social success has arisen. For example, cheaters may employ different strategies (e.g., fixed and facultative), whereas other causes of unequal fitness in social situations can result in winners and losers without cheating. To address these problems, we quantified the social success of naturally occurring genotypes of Dictyostelium discoideum during the formation of chimeric fruiting bodies, consisting of dead stalk cells and viable spores. We demonstrate that an apparent competitive dominance hierarchy of spore formation in chimera is partly due to a fixed strategy where genotypes exhibit dramatically different spore allocations. However, we also find complex, variable facultative strategies, where genotypes change their allocation in chimera. By determining the magnitude and direction of these changes, we partition facultative cheating into two forms: (1) promotion of individual fitness through selfish behaviour ("self-promotion") and (2) coercion of other genotypes to act cooperatively. Our results demonstrate and define social interactions between D. discoideum isolates, thus providing a conceptual framework for the study of the genetic mechanisms that underpin social evolution.

  9. Virus detection and quantification using electrical parameters

    PubMed Central

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

    2014-01-01

    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. PMID:25355078

  10. Quantification of prebiotics in commercial infant formulas.

    PubMed

    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.

  11. Simple quantification of in planta fungal biomass.

    PubMed

    Ayliffe, Michael; Periyannan, Sambasivam K; Feechan, Angela; Dry, Ian; Schumann, Ulrike; Lagudah, Evans; Pryor, Anthony

    2014-01-01

    An accurate assessment of the disease resistance status of plants to fungal pathogens is an essential requirement for the development of resistant crop plants. Many disease resistance phenotypes are partial rather than obvious immunity and are frequently scored using subjective qualitative estimates of pathogen development or plant disease symptoms. Here we report a method for the accurate comparison of total fungal biomass in plant tissues. This method, called the WAC assay, is based upon the specific binding of the plant lectin wheat germ agglutinin to fungal chitin. The assay is simple, high-throughput, and sensitive enough to discriminate between single Puccinia graminis f.sp tritici infection sites on a wheat leaf segment. It greatly lends itself to replication as large volumes of tissue can be pooled from independent experiments and assayed to provide truly representative quantification, or, alternatively, fungal growth on a single, small leaf segment can be quantified. In addition, as the assay is based upon a microscopic technique, pathogen infection sites can also be examined at high magnification prior to quantification if desired and average infection site areas are determined. Previously, we have demonstrated the application of the WAC assay for quantifying the growth of several different pathogen species in both glasshouse grown material and large-scale field plots. Details of this method are provided within.

  12. Virus detection and quantification using electrical parameters

    NASA Astrophysics Data System (ADS)

    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.

  13. Quantification of ontogenetic allometry in ammonoids.

    PubMed

    Korn, Dieter

    2012-01-01

    Ammonoids are well-known objects used for studies on ontogeny and phylogeny, but a quantification of ontogenetic change has not yet been carried out. Their planispirally coiled conchs allow for a study of "longitudinal" ontogenetic data, that is data of ontogenetic trajectories that can be obtained from a single specimen. Therefore, they provide a good model for ontogenetic studies of geometry in other shelled organisms. Using modifications of three cardinal conch dimensions, computer simulations can model artificial conchs. The trajectories of ontogenetic allometry of these simulations can be analyzed in great detail in a theoretical morphospace. A method for the classification of conch ontogeny and quantification of the degree of allometry is proposed. Using high-precision cross-sections, the allometric conch growth of real ammonoids can be documented and compared. The members of the Ammonoidea show a wide variety of allometric growth, ranging from near isometry to monophasic, biphasic, or polyphasic allometry. Selected examples of Palaeozoic and Mesozoic ammonoids are shown with respect to their degree of change during ontogeny of the conch.

  14. Quantification of abdominal aortic deformation after EVAR

    NASA Astrophysics Data System (ADS)

    Demirci, Stefanie; Manstad-Hulaas, Frode; Navab, Nassir

    2009-02-01

    Quantification of abdominal aortic deformation is an important requirement for the evaluation of endovascular stenting procedures and the further refinement of stent graft design. During endovascular aortic repair (EVAR) treatment, the aortic shape is subject to severe deformation that is imposed by medical instruments such as guide wires, catheters, and, the stent graft. This deformation can affect the flow characteristics and morphology of the aorta which have been shown to be elicitors for stent graft failures and be reason for reappearance of aneurysms. We present a method for quantifying the deformation of an aneurysmatic aorta imposed by an inserted stent graft device. The outline of the procedure includes initial rigid alignment of the two abdominal scans, segmentation of abdominal vessel trees, and automatic reduction of their centerline structures to one specified region of interest around the aorta. This is accomplished by preprocessing and remodeling of the pre- and postoperative aortic shapes before performing a non-rigid registration. We further narrow the resulting displacement fields to only include local non-rigid deformation and therefore, eliminate all remaining global rigid transformations. Finally, deformations for specified locations can be calculated from the resulting displacement fields. In order to evaluate our method, experiments for the extraction of aortic deformation fields are conducted on 15 patient datasets from endovascular aortic repair (EVAR) treatment. A visual assessment of the registration results and evaluation of the usage of deformation quantification were performed by two vascular surgeons and one interventional radiologist who are all experts in EVAR procedures.

  15. Quantification of ontogenetic allometry in ammonoids.

    PubMed

    Korn, Dieter

    2012-01-01

    Ammonoids are well-known objects used for studies on ontogeny and phylogeny, but a quantification of ontogenetic change has not yet been carried out. Their planispirally coiled conchs allow for a study of "longitudinal" ontogenetic data, that is data of ontogenetic trajectories that can be obtained from a single specimen. Therefore, they provide a good model for ontogenetic studies of geometry in other shelled organisms. Using modifications of three cardinal conch dimensions, computer simulations can model artificial conchs. The trajectories of ontogenetic allometry of these simulations can be analyzed in great detail in a theoretical morphospace. A method for the classification of conch ontogeny and quantification of the degree of allometry is proposed. Using high-precision cross-sections, the allometric conch growth of real ammonoids can be documented and compared. The members of the Ammonoidea show a wide variety of allometric growth, ranging from near isometry to monophasic, biphasic, or polyphasic allometry. Selected examples of Palaeozoic and Mesozoic ammonoids are shown with respect to their degree of change during ontogeny of the conch. PMID:23134208

  16. An improved competitive inhibition enzymatic immunoassay method for tetrodotoxin quantification.

    PubMed

    Stokes, Amber N; Williams, Becky L; French, Susannah S

    2012-01-01

    Quantifying tetrodotoxin (TTX) has been a challenge in both ecological and medical research due to the cost, time and training required of most quantification techniques. Here we present a modified Competitive Inhibition Enzymatic Immunoassay for the quantification of TTX, and to aid researchers in the optimization of this technique for widespread use with a high degree of accuracy and repeatability.

  17. Accurate episomal HIV 2-LTR circles quantification using optimized DNA isolation and droplet digital PCR

    PubMed Central

    Malatinkova, Eva; Kiselinova, Maja; Bonczkowski, Pawel; Trypsteen, Wim; Messiaen, Peter; Vermeire, Jolien; Verhasselt, Bruno; Vervisch, Karen; Vandekerckhove, Linos; De Spiegelaere, Ward

    2014-01-01

    Introduction In HIV-infected patients on combination antiretroviral therapy (cART), the detection of episomal HIV 2-LTR circles is a potential marker for ongoing viral replication. Quantification of 2-LTR circles is based on quantitative PCR or more recently on digital PCR assessment, but is hampered due to its low abundance. Sample pre-PCR processing is a critical step for 2-LTR circles quantification, which has not yet been sufficiently evaluated in patient derived samples. Materials and Methods We compared two sample processing procedures to more accurately quantify 2-LTR circles using droplet digital PCR (ddPCR). Episomal HIV 2-LTR circles were either isolated by genomic DNA isolation or by a modified plasmid DNA isolation, to separate the small episomal circular DNA from chromosomal DNA. This was performed in a dilution series of HIV-infected cells and HIV-1 infected patient derived samples (n=59). Samples for the plasmid DNA isolation method were spiked with an internal control plasmid. Results Genomic DNA isolation enables robust 2-LTR circles quantification. However, in the lower ranges of detection, PCR inhibition caused by high genomic DNA load substantially limits the amount of sample input and this impacts sensitivity and accuracy. Moreover, total genomic DNA isolation resulted in a lower recovery of 2-LTR templates per isolate, further reducing its sensitivity. The modified plasmid DNA isolation with a spiked reference for normalization was more accurate in these low ranges compared to genomic DNA isolation. A linear correlation of both methods was observed in the dilution series (R2=0.974) and in the patient derived samples with 2-LTR numbers above 10 copies per million peripheral blood mononuclear cells (PBMCs), (R2=0.671). Furthermore, Bland–Altman analysis revealed an average agreement between the methods within the 27 samples in which 2-LTR circles were detectable with both methods (bias: 0.3875±1.2657 log10). Conclusions 2-LTR circles

  18. Survey and Evaluate Uncertainty Quantification Methodologies

    SciTech Connect

    Lin, Guang; Engel, David W.; Eslinger, Paul W.

    2012-02-01

    The Carbon Capture Simulation Initiative (CCSI) is a partnership among national laboratories, industry and academic institutions that will develop and deploy state-of-the-art computational modeling and simulation tools to accelerate the commercialization of carbon capture technologies from discovery to development, demonstration, and ultimately the widespread deployment to hundreds of power plants. The CCSI Toolset will provide end users in industry with a comprehensive, integrated suite of scientifically validated models with uncertainty quantification, optimization, risk analysis and decision making capabilities. The CCSI Toolset will incorporate commercial and open-source software currently in use by industry and will also develop new software tools as necessary to fill technology gaps identified during execution of the project. The CCSI Toolset will (1) enable promising concepts to be more quickly identified through rapid computational screening of devices and processes; (2) reduce the time to design and troubleshoot new devices and processes; (3) quantify the technical risk in taking technology from laboratory-scale to commercial-scale; and (4) stabilize deployment costs more quickly by replacing some of the physical operational tests with virtual power plant simulations. The goal of CCSI is to deliver a toolset that can simulate the scale-up of a broad set of new carbon capture technologies from laboratory scale to full commercial scale. To provide a framework around which the toolset can be developed and demonstrated, we will focus on three Industrial Challenge Problems (ICPs) related to carbon capture technologies relevant to U.S. pulverized coal (PC) power plants. Post combustion capture by solid sorbents is the technology focus of the initial ICP (referred to as ICP A). The goal of the uncertainty quantification (UQ) task (Task 6) is to provide a set of capabilities to the user community for the quantification of uncertainties associated with the carbon

  19. Quantification of acidic compounds in complex biomass-derived streams

    SciTech Connect

    Karp, Eric M.; Nimlos, Claire T.; Deutch, Steve; Salvachúa, Davinia; Cywar, Robin M.; Beckham, Gregg T.

    2016-01-01

    Biomass-derived streams that contain acidic compounds from the degradation of lignin and polysaccharides (e.g. black liquor, pyrolysis oil, pyrolytic lignin, etc.) are chemically complex solutions prone to instability and degradation during analysis, making quantification of compounds within them challenging. Here we present a robust analytical method to quantify acidic compounds in complex biomass-derived mixtures using ion exchange, sample reconstitution in pyridine and derivatization with BSTFA. The procedure is based on an earlier method originally reported for kraft black liquors and, in this work, is applied to identify and quantify a large slate of acidic compounds in corn stover derived alkaline pretreatment liquor (APL) as a function of pretreatment severity. Analysis of the samples is conducted with GCxGC-TOFMS to achieve good resolution of the components within the complex mixture. The results reveal the dominant low molecular weight components and their concentrations as a function of pretreatment severity. Application of this method is also demonstrated in the context of lignin conversion technologies by applying it to track the microbial conversion of an APL substrate. Here too excellent results are achieved, and the appearance and disappearance of compounds is observed in agreement with the known metabolic pathways of two bacteria, indicating the sample integrity was maintained throughout analysis. Finally, it is shown that this method applies more generally to lignin-rich materials by demonstrating its usefulness in analysis of pyrolysis oil and pyrolytic lignin.

  20. Quantification and prediction of rare events in nonlinear waves

    NASA Astrophysics Data System (ADS)

    Sapsis, Themistoklis; Cousins, Will; Mohamad, Mustafa

    2014-11-01

    The scope of this work is the quantification and prediction of rare events characterized by extreme intensity, in nonlinear dispersive models that simulate water waves. In particular we are interested for the understanding and the short-term prediction of rogue waves in the ocean and to this end, we consider 1-dimensional nonlinear models of the NLS type. To understand the energy transfers that occur during the development of an extreme event we perform a spatially localized analysis of the energy distribution along different wavenumbers by means of the Gabor transform. A stochastic analysis of the Gabor coefficients reveals i) the low-dimensionality of the intermittent structures, ii) the interplay between non-Gaussian statistical properties and nonlinear energy transfers between modes, as well as iii) the critical scales (or Gabor coefficients) where a critical energy can trigger the formation of an extreme event. The unstable character of these critical localized modes is analysed directly through the system equation and it is shown that it is defined as the result of the system nonlinearity and the wave dissipation (that mimics wave breaking). These unstable modes are randomly triggered through the dispersive ``heat bath'' of random waves that propagate in the nonlinear medium. Using these properties we formulate low-dimensional functionals of these Gabor coefficients that allow for the prediction of extreme event well before the strongly nonlinear interactions begin to occur. The prediction window is further enhanced by the combination of the developed scheme with traditional filtering schemes.

  1. Quantification of Internalized Silica Nanoparticles via STED Microscopy

    PubMed Central

    Peuschel, Henrike; Ruckelshausen, Thomas; Cavelius, Christian; Kraegeloh, Annette

    2015-01-01

    The development of safe engineered nanoparticles (NPs) requires a detailed understanding of their interaction mechanisms on a cellular level. Therefore, quantification of NP internalization is crucial to predict the potential impact of intracellular NP doses, providing essential information for risk assessment as well as for drug delivery applications. In this study, the internalization of 25 nm and 85 nm silica nanoparticles (SNPs) in alveolar type II cells (A549) was quantified by application of super-resolution STED (stimulated emission depletion) microscopy. Cells were exposed to equal particle number concentrations (9.2 × 1010 particles mL−1) of each particle size and the sedimentation of particles during exposure was taken into account. Microscopy images revealed that particles of both sizes entered the cells after 5 h incubation in serum supplemented and serum-free medium. According to the in vitro sedimentation, diffusion, and dosimetry (ISDD) model 20–27% of the particles sedimented. In comparison, 102-103 NPs per cell were detected intracellularly serum-containing medium. Furthermore, in the presence of serum, no cytotoxicity was induced by the SNPs. In serum-free medium, large agglomerates of both particle sizes covered the cells whereas only high concentrations (≥ 3.8 × 1012 particles mL−1) of the smaller particles induced cytotoxicity. PMID:26125028

  2. Classification and quantification of bacteriophage taxa in human gut metagenomes

    PubMed Central

    Waller, Alison S; Yamada, Takuji; Kristensen, David M; Kultima, Jens Roat; Sunagawa, Shinichi; Koonin, Eugene V; Bork, Peer

    2014-01-01

    Bacteriophages have key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities are scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, five phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to four orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, ‘Group 936 lactococcal phages' are more prevalent and abundant in Danish samples than in samples from Spain or the United States of America. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a 1-year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage–host network of the human gut was established and includes numerous novel host–phage associations. PMID:24621522

  3. Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum.

    PubMed

    Cheng, Dongmei; Hoogenraad, Casper C; Rush, John; Ramm, Elizabeth; Schlager, Max A; Duong, Duc M; Xu, Ping; Wijayawardana, Sameera R; Hanfelt, John; Nakagawa, Terunaga; Sheng, Morgan; Peng, Junmin

    2006-06-01

    The postsynaptic density (PSD) of central excitatory synapses is essential for postsynaptic signaling, and its components are heterogeneous among different neuronal subtypes and brain structures. Here we report large scale relative and absolute quantification of proteins in PSDs purified from adult rat forebrain and cerebellum. PSD protein profiles were determined using the cleavable ICAT strategy and LC-MS/MS. A total of 296 proteins were identified and quantified with 43 proteins exhibiting statistically significant abundance change between forebrain and cerebellum, indicating marked molecular heterogeneity of PSDs between different brain regions. Moreover we utilized absolute quantification strategy, in which synthetic isotope-labeled peptides were used as internal standards, to measure the molar abundance of 32 key PSD proteins in forebrain and cerebellum. These data confirm the abundance of calcium/calmodulin-dependent protein kinase II and PSD-95 and reveal unexpected stoichiometric ratios between glutamate receptors, scaffold proteins, and signaling molecules in the PSD. Our data also demonstrate that the absolute quantification method is well suited for targeted quantitative proteomic analysis. Overall this study delineates a crucial molecular difference between forebrain and cerebellar PSDs and provides a quantitative framework for measuring the molecular stoichiometry of the PSD. PMID:16507876

  4. Comprehensive polar lipid identification and quantification in milk by liquid chromatography-mass spectrometry.

    PubMed

    Liu, Zhiqian; Moate, Peter; Cocks, Ben; Rochfort, Simone

    2015-01-26

    Polar lipids (PLs) are a significant functional component of milk that are difficult to quantitate. A simple method for comprehensive identification and quantitative analysis of all essential PL species using bovine milk is described. The lipid fraction was extracted by a mix of chloroform and methanol and the extract was directly used for PL identification and quantification. PLs were separated by hydrophilic interaction liquid chromatography (HILIC) and detected by an Orbitrap mass analyser in positive mode. The structure of PLs was established or confirmed by tandem MS in both positive and negative modes. The method is sensitive (with a LOD for all PL classes ≤0.1 ng) and reproducible, enabling simultaneous quantification of 70 PL species within a run of 45 min. Application of this method to the quantification of PLs in 32 bovine milk samples revealed the relative abundance of different PL classes, significant variation of PL content between individual samples and the correlation between the major PL classes. The method provides a tool for investigating the variation and metabolism of important PL components in bovine and human milk and in diverse mammalian species.

  5. Fluorometric quantification of polyphosphate in environmental plankton samples: extraction protocols, matrix effects, and nucleic acid interference.

    PubMed

    Martin, Patrick; Van Mooy, Benjamin A S

    2013-01-01

    Polyphosphate (polyP) is a ubiquitous biochemical with many cellular functions and comprises an important environmental phosphorus pool. However, methodological challenges have hampered routine quantification of polyP in environmental samples. We tested 15 protocols to extract inorganic polyphosphate from natural marine samples and cultured cyanobacteria for fluorometric quantification with 4',6-diamidino-2-phenylindole (DAPI) without prior purification. A combination of brief boiling and digestion with proteinase K was superior to all other protocols, including other enzymatic digestions and neutral or alkaline leaches. However, three successive extractions were required to extract all polyP. Standard addition revealed matrix effects that differed between sample types, causing polyP to be over- or underestimated by up to 50% in the samples tested here. Although previous studies judged that the presence of DNA would not complicate fluorometric quantification of polyP with DAPI, we show that RNA can cause significant interference at the wavelengths used to measure polyP. Importantly, treating samples with DNase and RNase before proteinase K digestion reduced fluorescence by up to 57%. We measured particulate polyP along a North Pacific coastal-to-open ocean transect and show that particulate polyP concentrations increased toward the open ocean. While our final method is optimized for marine particulate matter, different environmental sample types may need to be assessed for matrix effects, extraction efficiency, and nucleic acid interference.

  6. Fully automated system for the quantification of human osteoarthritic knee joint effusion volume using magnetic resonance imaging

    PubMed Central

    2010-01-01

    Introduction Joint effusion is frequently associated with osteoarthritis (OA) flare-up and is an important marker of therapeutic response. This study aimed at developing and validating a fully automated system based on magnetic resonance imaging (MRI) for the quantification of joint effusion volume in knee OA patients. Methods MRI examinations consisted of two axial sequences: a T2-weighted true fast imaging with steady-state precession and a T1-weighted gradient echo. An automated joint effusion volume quantification system using MRI was developed and validated (a) with calibrated phantoms (cylinder and sphere) and effusion from knee OA patients; (b) with assessment by manual quantification; and (c) by direct aspiration. Twenty-five knee OA patients with joint effusion were included in the study. Results The automated joint effusion volume quantification was developed as a four stage sequencing process: bone segmentation, filtering of unrelated structures, segmentation of joint effusion, and subvoxel volume calculation. Validation experiments revealed excellent coefficients of variation with the calibrated cylinder (1.4%) and sphere (0.8%) phantoms. Comparison of the OA knee joint effusion volume assessed by the developed automated system and by manual quantification was also excellent (r = 0.98; P < 0.0001), as was the comparison with direct aspiration (r = 0.88; P = 0.0008). Conclusions The newly developed fully automated MRI-based system provided precise quantification of OA knee joint effusion volume with excellent correlation with data from phantoms, a manual system, and joint aspiration. Such an automated system will be instrumental in improving the reproducibility/reliability of the evaluation of this marker in clinical application. PMID:20846392

  7. Feature isolation and quantification of evolving datasets

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Identifying and isolating features is an important part of visualization and a crucial step for the analysis and understanding of large time-dependent data sets (either from observation or simulation). In this proposal, we address these concerns, namely the investigation and implementation of basic 2D and 3D feature based methods to enhance current visualization techniques and provide the building blocks for automatic feature recognition, tracking, and correlation. These methods incorporate ideas from scientific visualization, computer vision, image processing, and mathematical morphology. Our focus is in the area of fluid dynamics, and we show the applicability of these methods to the quantification and tracking of three-dimensional vortex and turbulence bursts.

  8. Poliovirus: Generation, Quantification, Propagation, Purification, and Storage

    PubMed Central

    Burrill, Cecily P.; Strings, Vanessa R.; Andino, Raul

    2016-01-01

    Poliovirus (PV) is the prototypical picornavirus. It is a non-enveloped RNA virus with a small (~7.5 kb) genome of positive polarity. It has long served as a model to study RNA virus biology, pathogenesis, and evolution. cDNA clones of several strains are available, and infectious virus can be produced by the transfection of in vitro transcribed viral genomes into an appropriate host cell. PV infects many human and non-human primate cell lines including HeLa and HeLa S3 cells, and can grow to high titer in culture. Protocols for the production, propagation, quantification, and purification of PV are presented. A separate chapter concerning the generation and characterization of PV mutants will also be presented. PMID:23686830

  9. Uncertainty quantification in DIC with Kriging regression

    NASA Astrophysics Data System (ADS)

    Wang, Dezhi; DiazDelaO, F. A.; Wang, Weizhuo; Lin, Xiaoshan; Patterson, Eann A.; Mottershead, John E.

    2016-03-01

    A Kriging regression model is developed as a post-processing technique for the treatment of measurement uncertainty in classical subset-based Digital Image Correlation (DIC). Regression is achieved by regularising the sample-point correlation matrix using a local, subset-based, assessment of the measurement error with assumed statistical normality and based on the Sum of Squared Differences (SSD) criterion. This leads to a Kriging-regression model in the form of a Gaussian process representing uncertainty on the Kriging estimate of the measured displacement field. The method is demonstrated using numerical and experimental examples. Kriging estimates of displacement fields are shown to be in excellent agreement with 'true' values for the numerical cases and in the experimental example uncertainty quantification is carried out using the Gaussian random process that forms part of the Kriging model. The root mean square error (RMSE) on the estimated displacements is produced and standard deviations on local strain estimates are determined.

  10. Quantification of adipose tissue insulin sensitivity.

    PubMed

    Søndergaard, Esben; Jensen, Michael D

    2016-06-01

    In metabolically healthy humans, adipose tissue is exquisitely sensitive to insulin. Similar to muscle and liver, adipose tissue lipolysis is insulin resistant in adults with central obesity and type 2 diabetes. Perhaps uniquely, however, insulin resistance in adipose tissue may directly contribute to development of insulin resistance in muscle and liver because of the increased delivery of free fatty acids to those tissues. It has been hypothesized that insulin adipose tissue resistance may precede other metabolic defects in obesity and type 2 diabetes. Therefore, precise and reproducible quantification of adipose tissue insulin sensitivity, in vivo, in humans, is an important measure. Unfortunately, no consensus exists on how to determine adipose tissue insulin sensitivity. We review the methods available to quantitate adipose tissue insulin sensitivity and will discuss their strengths and weaknesses.

  11. Recurrence quantification analysis of global stock markets

    NASA Astrophysics Data System (ADS)

    Bastos, João A.; Caiado, Jorge

    2011-04-01

    This study investigates the presence of deterministic dependencies in international stock markets using recurrence plots and recurrence quantification analysis (RQA). The results are based on a large set of free float-adjusted market capitalization stock indices, covering a period of 15 years. The statistical tests suggest that the dynamics of stock prices in emerging markets is characterized by higher values of RQA measures when compared to their developed counterparts. The behavior of stock markets during critical financial events, such as the burst of the technology bubble, the Asian currency crisis, and the recent subprime mortgage crisis, is analyzed by performing RQA in sliding windows. It is shown that during these events stock markets exhibit a distinctive behavior that is characterized by temporary decreases in the fraction of recurrence points contained in diagonal and vertical structures.

  12. Quantification of Glutathione in Caenorhabditis elegans

    PubMed Central

    Caito, Samuel W.; Aschner, Michael

    2015-01-01

    Glutathione (GSH) is the most abundant intracellular thiol with diverse functions from redox signaling, xenobiotic detoxification, and apoptosis. The quantification of GSH is an important measure for redox capacity and oxidative stress. This protocol quantifies total GSH from Caenorhabditis elegans, an emerging model organism for toxicology studies. GSH is measured using the 5,5′-dithiobis-(2-nitrobenzoic acid) (DTNB) cycling method originally created for cell and tissue samples but optimized for whole worm extracts. DTNB reacts with GSH to from a 5′-thio-2-nitrobenzoic acid (TNB) chromophore with maximum absorbance of 412 nm. This method is both rapid and sensitive, making it ideal for studies involving a large number of transgenic nematode strains. PMID:26309452

  13. Carotenoid Extraction and Quantification from Capsicum annuum

    PubMed Central

    Richins, Richard D.; Kilcrease, James; Rodgriguez-Uribe, Laura; O'Connell, Mary A.

    2016-01-01

    Carotenoids are ubiquitous pigments that play key roles in photosynthesis and also accumulate to high levels in fruit and flowers. Specific carotenoids play essential roles in human health as these compounds are precursors for Vitamin A; other specific carotenoids are important sources of macular pigments and all carotenoids are important anti-oxidants. Accurate determination of the composition and concentration of this complex set of natural products is therefore important in many different scientific areas. One of the richest sources of these compounds is the fruit of Capsicum; these red, yellow and orange fruit accumulate multiple carotenes and xanthophylls. This report describes the detailed method for the extraction and quantification of specific carotenes and xanthophylls. PMID:27570797

  14. [Quantification of motor activity in biomedicine].

    PubMed

    Giannazzo, E

    1993-01-01

    A computer-assisted analysis of motor activity was carried out using ultrasound waves, that are not invasive and free from any kind of interference, because of their specific characteristics. We worked out the Doppler's effect which determines a frequency variation on the reflected wave from any body in motion. That variation is linked to the velocity of the moving body and the superimposition of the emitted wave with those reflected, results in beats, which have a frequency proportional to the motor activity velocity. Our research group planned and carried out an electronic quantification apparatus that can be interfaced with a personal computer system by means of an Analog to Digital acquisition card. The performed test on the apparatus confirmed that the theory that the number of antinodes detected was proportional to the space covered by the moving body. The equipment was also tested on several types of animals.

  15. Quantification of uncertainty in geochemical reactions

    NASA Astrophysics Data System (ADS)

    Srinivasan, Gowri; Tartakovsky, Daniel M.; Robinson, Bruce A.; Aceves, Alejandro B.

    2007-12-01

    Predictions of reactive transport in the subsurface are routinely compromised by both model (structural) and parametric uncertainties. We present a set of computational tools for quantifying these two types of uncertainties. The model uncertainty is resolved at the molecular scale where epistemic uncertainty incorporates aleatory uncertainty. The parametric uncertainty is resolved at both molecular and continuum (Darcy) scales. We use the proposed approach to quantify uncertainty in modeling the sorption of neptunium through a competitive ion exchange. This radionuclide is of major concern for various high-level waste storage projects because of its relatively long half-life and its high-solubility and low-sorption properties. We demonstrate how parametric and model uncertainties affect one's ability to estimate the distribution coefficient. The uncertainty quantification tools yield complete probabilistic descriptions of key parameters affecting the fate and migration of neptunium in the subsurface rather than the lower statistical moments. This is important, since these distributions are highly skewed.

  16. Kinetic quantification of plyometric exercise intensity.

    PubMed

    Ebben, William P; Fauth, McKenzie L; Garceau, Luke R; Petushek, Erich J

    2011-12-01

    Ebben, WP, Fauth, ML, Garceau, LR, and Petushek, EJ. Kinetic quantification of plyometric exercise intensity. J Strength Cond Res 25(12): 3288-3298, 2011-Quantification of plyometric exercise intensity is necessary to understand the characteristics of these exercises and the proper progression of this mode of exercise. The purpose of this study was to assess the kinetic characteristics of a variety of plyometric exercises. This study also sought to assess gender differences in these variables. Twenty-six men and 23 women with previous experience in performing plyometric training served as subjects. The subjects performed a variety of plyometric exercises including line hops, 15.24-cm cone hops, squat jumps, tuck jumps, countermovement jumps (CMJs), loaded CMJs equal to 30% of 1 repetition maximum squat, depth jumps normalized to the subject's jump height (JH), and single leg jumps. All plyometric exercises were assessed with a force platform. Outcome variables associated with the takeoff, airborne, and landing phase of each plyometric exercise were evaluated. These variables included the peak vertical ground reaction force (GRF) during takeoff, the time to takeoff, flight time, JH, peak power, landing rate of force development, and peak vertical GRF during landing. A 2-way mixed analysis of variance with repeated measures for plyometric exercise type demonstrated main effects for exercise type and all outcome variables (p ≤ 0.05) and for the interaction between gender and peak vertical GRF during takeoff (p ≤ 0.05). Bonferroni-adjusted pairwise comparisons identified a number of differences between the plyometric exercises for the outcome variables assessed (p ≤ 0.05). These findings can be used to guide the progression of plyometric training by incorporating exercises of increasing intensity over the course of a program. PMID:22080319

  17. Quantification of heterogeneity observed in medical images

    PubMed Central

    2013-01-01

    Background There has been much recent interest in the quantification of visually evident heterogeneity within functional grayscale medical images, such as those obtained via magnetic resonance or positron emission tomography. In the case of images of cancerous tumors, variations in grayscale intensity imply variations in crucial tumor biology. Despite these considerable clinical implications, there is as yet no standardized method for measuring the heterogeneity observed via these imaging modalities. Methods In this work, we motivate and derive a statistical measure of image heterogeneity. This statistic measures the distance-dependent average deviation from the smoothest intensity gradation feasible. We show how this statistic may be used to automatically rank images of in vivo human tumors in order of increasing heterogeneity. We test this method against the current practice of ranking images via expert visual inspection. Results We find that this statistic provides a means of heterogeneity quantification beyond that given by other statistics traditionally used for the same purpose. We demonstrate the effect of tumor shape upon our ranking method and find the method applicable to a wide variety of clinically relevant tumor images. We find that the automated heterogeneity rankings agree very closely with those performed visually by experts. Conclusions These results indicate that our automated method may be used reliably to rank, in order of increasing heterogeneity, tumor images whether or not object shape is considered to contribute to that heterogeneity. Automated heterogeneity ranking yields objective results which are more consistent than visual rankings. Reducing variability in image interpretation will enable more researchers to better study potential clinical implications of observed tumor heterogeneity. PMID:23453000

  18. Uncertainty Quantification of Equilibrium Climate Sensitivity

    NASA Astrophysics Data System (ADS)

    Lucas, D. D.; Brandon, S. T.; Covey, C. C.; Domyancic, D. M.; Johannesson, G.; Klein, R.; Tannahill, J.; Zhang, Y.

    2011-12-01

    Significant uncertainties exist in the temperature response of the climate system to changes in the levels of atmospheric carbon dioxide. We report progress to quantify the uncertainties of equilibrium climate sensitivity using perturbed parameter ensembles of the Community Earth System Model (CESM). Through a strategic initiative at the Lawrence Livermore National Laboratory, we have been developing uncertainty quantification (UQ) methods and incorporating them into a software framework called the UQ Pipeline. We have applied this framework to generate a large number of ensemble simulations using Latin Hypercube and other schemes to sample up to three dozen uncertain parameters in the atmospheric (CAM) and sea ice (CICE) model components of CESM. The parameters sampled are related to many highly uncertain processes, including deep and shallow convection, boundary layer turbulence, cloud optical and microphysical properties, and sea ice albedo. An extensive ensemble database comprised of more than 46,000 simulated climate-model-years of recent climate conditions has been assembled. This database is being used to train surrogate models of CESM responses and to perform statistical calibrations of the CAM and CICE models given observational data constraints. The calibrated models serve as a basis for propagating uncertainties forward through climate change simulations using a slab ocean model configuration of CESM. This procedure is being used to quantify the probability density function of equilibrium climate sensitivity accounting for uncertainties in climate model processes. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and was funded by the Uncertainty Quantification Strategic Initiative Laboratory Directed Research and Development Project at LLNL under project tracking code 10-SI-013. (LLNL-ABS-491765)

  19. Detection and Quantification of Rotenoids from Clitoria fairchildiana and its Lipids Profile.

    PubMed

    Santos, Rauldenis A F; David, Jorge M; David, Juceni P

    2016-05-01

    This work describes the isolation and quantification of rotenoids from crude organic extracts of different parts of Clitoria fairchildiana R. A. Howard (Leguminosae) by HPLC-DAD. The lipid composition and the Artemia salina cytotoxic activities of the isolates were also conducted. Clitoriacetal (1), 6-deoxyclitoriacetal (2), stemonal and stemonone were isolated by chromatographic procedures and identified by usual spectroscopic and spectrometric techniques. Clitoriacetal and 6-deoxyclitoriacetal were not found in all parts of the plant, such as leaves and petals, but in the roots they occur in higher concentration. The activity against brine shrimp revealed that the root extract (LD50 = 158 ppm) was the more active. PMID:27319136

  20. Quantification of uncertainties for application in detonation simulation

    NASA Astrophysics Data System (ADS)

    Zheng, Miao; Ma, Zhibo

    2016-06-01

    Numerical simulation has become an important means in designing detonation systems, and the quantification of its uncertainty is also necessary to reliability certification. As to quantifying the uncertainty, it is the most important to analyze how the uncertainties occur and develop, and how the simulations develop from benchmark models to new models. Based on the practical needs of engineering and the technology of verification & validation, a framework of QU(quantification of uncertainty) is brought forward in the case that simulation is used on detonation system for scientific prediction. An example is offered to describe the general idea of quantification of simulation uncertainties.

  1. HPCE quantification of 5-methyl-2'-deoxycytidine in genomic DNA: methodological optimization for chestnut and other woody species.

    PubMed

    Hasbún, Rodrigo; Valledor, Luís; Rodríguez, José L; Santamaria, Estrella; Ríos, Darcy; Sanchez, Manuel; Cañal, María J; Rodríguez, Roberto

    2008-01-01

    Quantification of deoxynucleosides using micellar high-performance capillary electrophoresis (HPCE) is an efficient, fast and inexpensive evaluation method of genomic DNA methylation. This approach has been demonstrated to be more sensitive and specific than other methods for the quantification of DNA methylation content. However, effective detection and quantification of 5-methyl-2'-deoxycytidine depend of the sample characteristics. Previous works have revealed that in most woody species, the quality and quantity of RNA-free DNA extracted that is suitable for analysis by means of HPCE varies among species of the same gender, among tissues taken from the same tree, and vary in the same tissue depending on the different seasons of the year. The aim of this work is to establish a quantification method of genomic DNA methylation that lends itself to use in different Castanea sativa Mill. materials, and in other angiosperm and gymnosperm woody species. Using a DNA extraction kit based in silica membrane has increased the resolutive capacity of the method. Under these conditions, it can be analyzed different organs or tissues of angiosperms and gymnosperms, regardless of their state of development. We emphasized the importance of samples free of nucleosides, although, in the contrary case, the method ensures the effective separation of deoxynucleosides and identification of 5-methyl-2'-deoxycytidine. PMID:18538578

  2. How Are Preferences Revealed?

    PubMed

    Beshears, John; Choi, James J; Laibson, David; Madrian, Brigitte C

    2008-08-01

    Revealed preferences are tastes that rationalize an economic agent's observed actions. Normative preferences represent the agent's actual interests. It sometimes makes sense to assume that revealed preferences are identical to normative preferences. But there are many cases where this assumption is violated. We identify five factors that increase the likelihood of a disparity between revealed preferences and normative preferences: passive choice, complexity, limited personal experience, third-party marketing, and intertemporal choice. We then discuss six approaches that jointly contribute to the identification of normative preferences: structural estimation, active decisions, asymptotic choice, aggregated revealed preferences, reported preferences, and informed preferences. Each of these approaches uses consumer behavior to infer some property of normative preferences without equating revealed and normative preferences. We illustrate these issues with evidence from savings and investment outcomes. PMID:24761048

  3. How Are Preferences Revealed?

    PubMed Central

    Beshears, John; Choi, James J.; Laibson, David; Madrian, Brigitte C.

    2009-01-01

    Revealed preferences are tastes that rationalize an economic agent’s observed actions. Normative preferences represent the agent’s actual interests. It sometimes makes sense to assume that revealed preferences are identical to normative preferences. But there are many cases where this assumption is violated. We identify five factors that increase the likelihood of a disparity between revealed preferences and normative preferences: passive choice, complexity, limited personal experience, third-party marketing, and intertemporal choice. We then discuss six approaches that jointly contribute to the identification of normative preferences: structural estimation, active decisions, asymptotic choice, aggregated revealed preferences, reported preferences, and informed preferences. Each of these approaches uses consumer behavior to infer some property of normative preferences without equating revealed and normative preferences. We illustrate these issues with evidence from savings and investment outcomes. PMID:24761048

  4. Software-assisted serum metabolite quantification using NMR.

    PubMed

    Jung, Young-Sang; Hyeon, Jin-Seong; Hwang, Geum-Sook

    2016-08-31

    The goal of metabolomics is to analyze a whole metabolome under a given set of conditions, and accurate and reliable quantitation of metabolites is crucial. Absolute concentration is more valuable than relative concentration; however, the most commonly used method in NMR-based serum metabolic profiling, bin-based and full data point peak quantification, provides relative concentration levels of metabolites and are not reliable when metabolite peaks overlap in a spectrum. In this study, we present the software-assisted serum metabolite quantification (SASMeQ) method, which allows us to identify and quantify metabolites in NMR spectra using Chenomx software. This software uses the ERETIC2 utility from TopSpin to add a digitally synthesized peak to a spectrum. The SASMeQ method will advance NMR-based serum metabolic profiling by providing an accurate and reliable method for absolute quantification that is superior to bin-based quantification. PMID:27506360

  5. Quantification of Human Kallikrein-Related Peptidases in Biological Fluids by Multiplatform Targeted Mass Spectrometry Assays.

    PubMed

    Karakosta, Theano D; Soosaipillai, Antoninus; Diamandis, Eleftherios P; Batruch, Ihor; Drabovich, Andrei P

    2016-09-01

    Human kallikrein-related peptidases (KLKs) are a group of 15 secreted serine proteases encoded by the largest contiguous cluster of protease genes in the human genome. KLKs are involved in coordination of numerous physiological functions including regulation of blood pressure, neuronal plasticity, skin desquamation, and semen liquefaction, and thus represent promising diagnostic and therapeutic targets. Until now, quantification of KLKs in biological and clinical samples was accomplished by enzyme-linked immunosorbent assays (ELISA). Here, we developed multiplex targeted mass spectrometry assays for the simultaneous quantification of all 15 KLKs. Proteotypic peptides for each KLK were carefully selected based on experimental data and multiplexed in single assays. Performance of assays was evaluated using three different mass spectrometry platforms including triple quadrupole, quadrupole-ion trap, and quadrupole-orbitrap instruments. Heavy isotope-labeled synthetic peptides with a quantifying tag were used for absolute quantification of KLKs in sweat, cervico-vaginal fluid, seminal plasma, and blood serum, with limits of detection ranging from 5 to 500 ng/ml. Analytical performance of assays was evaluated by measuring endogenous KLKs in relevant biological fluids, and results were compared with selected ELISAs. The multiplex targeted proteomic assays were demonstrated to be accurate, reproducible, sensitive, and specific alternatives to antibody-based assays. Finally, KLK4, a highly prostate-specific protein and a speculated biomarker of prostate cancer, was unambiguously detected and quantified by immunoenrichment-SRM assay in seminal plasma and blood serum samples from individuals with confirmed prostate cancer and negative biopsy. Mass spectrometry revealed exclusively the presence of a secreted isoform and thus unequivocally resolved earlier disputes about KLK4 identity in seminal plasma. Measurements of KLK4 in either 41 seminal plasma or 58 blood serum samples

  6. Uncertainty quantification in reacting flow modeling.

    SciTech Connect

    Le MaÒitre, Olivier P.; Reagan, Matthew T.; Knio, Omar M.; Ghanem, Roger Georges; Najm, Habib N.

    2003-10-01

    Uncertainty quantification (UQ) in the computational modeling of physical systems is important for scientific investigation, engineering design, and model validation. In this work we develop techniques for UQ based on spectral and pseudo-spectral polynomial chaos (PC) expansions, and we apply these constructions in computations of reacting flow. We develop and compare both intrusive and non-intrusive spectral PC techniques. In the intrusive construction, the deterministic model equations are reformulated using Galerkin projection into a set of equations for the time evolution of the field variable PC expansion mode strengths. The mode strengths relate specific parametric uncertainties to their effects on model outputs. The non-intrusive construction uses sampling of many realizations of the original deterministic model, and projects the resulting statistics onto the PC modes, arriving at the PC expansions of the model outputs. We investigate and discuss the strengths and weaknesses of each approach, and identify their utility under different conditions. We also outline areas where ongoing and future research are needed to address challenges with both approaches.

  7. Shape regression for vertebra fracture quantification

    NASA Astrophysics Data System (ADS)

    Lund, Michael Tillge; de Bruijne, Marleen; Tanko, Laszlo B.; Nielsen, Mads

    2005-04-01

    Accurate and reliable identification and quantification of vertebral fractures constitute a challenge both in clinical trials and in diagnosis of osteoporosis. Various efforts have been made to develop reliable, objective, and reproducible methods for assessing vertebral fractures, but at present there is no consensus concerning a universally accepted diagnostic definition of vertebral fractures. In this project we want to investigate whether or not it is possible to accurately reconstruct the shape of a normal vertebra, using a neighbouring vertebra as prior information. The reconstructed shape can then be used to develop a novel vertebra fracture measure, by comparing the segmented vertebra shape with its reconstructed normal shape. The vertebrae in lateral x-rays of the lumbar spine were manually annotated by a medical expert. With this dataset we built a shape model, with equidistant point distribution between the four corner points. Based on the shape model, a multiple linear regression model of a normal vertebra shape was developed for each dataset using leave-one-out cross-validation. The reconstructed shape was calculated for each dataset using these regression models. The average prediction error for the annotated shape was on average 3%.

  8. Quantification of moving target cyber defenses

    NASA Astrophysics Data System (ADS)

    Farris, Katheryn A.; Cybenko, George

    2015-05-01

    Current network and information systems are static, making it simple for attackers to maintain an advantage. Adaptive defenses, such as Moving Target Defenses (MTD) have been developed as potential "game-changers" in an effort to increase the attacker's workload. With many new methods being developed, it is difficult to accurately quantify and compare their overall costs and effectiveness. This paper compares the tradeoffs between current approaches to the quantification of MTDs. We present results from an expert opinion survey on quantifying the overall effectiveness, upfront and operating costs of a select set of MTD techniques. We find that gathering informed scientific opinions can be advantageous for evaluating such new technologies as it offers a more comprehensive assessment. We end by presenting a coarse ordering of a set of MTD techniques from most to least dominant. We found that seven out of 23 methods rank as the more dominant techniques. Five of which are techniques of either address space layout randomization or instruction set randomization. The remaining two techniques are applicable to software and computer platforms. Among the techniques that performed the worst are those primarily aimed at network randomization.

  9. Detection of aneuploidies by paralogous sequence quantification

    PubMed Central

    Deutsch, S; Choudhury, U; Merla, G; Howald, C; Sylvan, A; Antonarakis, S

    2004-01-01

    Background: Chromosomal aneuploidies are a common cause of congenital disorders associated with cognitive impairment and multiple dysmorphic features. Pre-natal diagnosis of aneuploidies is most commonly performed by the karyotyping of fetal cells obtained by amniocentesis or chorionic villus sampling, but this method is labour intensive and requires about 14 days to complete. Methods: We have developed a PCR based method for the detection of targeted chromosome number abnormalities termed paralogous sequence quantification (PSQ), based on the use of paralogous genes. Paralogous sequences have a high degree of sequence identity, but accumulate nucleotide substitutions in a locus specific manner. These sequence differences, which we term paralogous sequence mismatches (PSMs), can be quantified using pyrosequencing technology, to estimate the relative dosage between different chromosomes. We designed 10 assays for the detection of trisomies of chromosomes 13, 18, and 21 and sex chromosome aneuploidies. Results: We evaluated the performance of this method on 175 DNAs, highly enriched for abnormal samples. A correct and unambiguous diagnosis was given for 119 out of 120 aneuploid samples as well as for all the controls. One sample which gave an intermediate value for the chromosome 13 assays could not be diagnosed. Conclusions: Our data suggests that PSQ is a robust, easy to interpret, and easy to set up method for the diagnosis of common aneuploidies, and can be performed in less than 48 h, representing a competitive alternative for widespread use in diagnostic laboratories. PMID:15591276

  10. Quantification of the vocal folds’ dynamic displacements

    NASA Astrophysics Data System (ADS)

    del Socorro Hernández-Montes, María; Muñoz, Silvino; De La Torre, Manuel; Flores, Mauricio; Pérez, Carlos; Mendoza-Santoyo, Fernando

    2016-05-01

    Fast dynamic data acquisition techniques are required to investigate the motional behavior of the vocal folds (VFs) when they are subjected to a steady air-flow through the trachea. High-speed digital holographic interferometry (DHI) is a non-invasive full-field-of-view technique that has proved its usefulness to study rapid and non-repetitive object movements. Hence it is an ideal technique used here to measure VF displacements and vibration patterns at 2000 fps. Analyses from a set of 200 displacement images showed that VFs’ vibration cycles are established along their width (y) and length (x). Furthermore, the maximum deformation for the right and left VFs’ area may be quantified from these images, which in itself represents an important result in the characterization of this structure. At a controlled air pressure, VF displacements fall within the range ~100-1740 nm, with a calculated precision and accuracy that yields a variation coefficient of 1.91%. High-speed acquisition of full-field images of VFs and their displacement quantification are on their own significant data in the study of their functional and physiological behavior since voice quality and production depend on how they vibrate, i.e. their displacement amplitude and frequency. Additionally, the use of high speed DHI avoids prolonged examinations and represents a significant scientific and technological alternative contribution in advancing the knowledge and working mechanisms of these tissues.

  11. Quantification of biological aging in young adults

    PubMed Central

    Belsky, Daniel W.; Caspi, Avshalom; Houts, Renate; Cohen, Harvey J.; Corcoran, David L.; Danese, Andrea; Harrington, HonaLee; Israel, Salomon; Levine, Morgan E.; Schaefer, Jonathan D.; Sugden, Karen; Williams, Ben; Yashin, Anatoli I.; Poulton, Richie; Moffitt, Terrie E.

    2015-01-01

    Antiaging therapies show promise in model organism research. Translation to humans is needed to address the challenges of an aging global population. Interventions to slow human aging will need to be applied to still-young individuals. However, most human aging research examines older adults, many with chronic disease. As a result, little is known about aging in young humans. We studied aging in 954 young humans, the Dunedin Study birth cohort, tracking multiple biomarkers across three time points spanning their third and fourth decades of life. We developed and validated two methods by which aging can be measured in young adults, one cross-sectional and one longitudinal. Our longitudinal measure allows quantification of the pace of coordinated physiological deterioration across multiple organ systems (e.g., pulmonary, periodontal, cardiovascular, renal, hepatic, and immune function). We applied these methods to assess biological aging in young humans who had not yet developed age-related diseases. Young individuals of the same chronological age varied in their “biological aging” (declining integrity of multiple organ systems). Already, before midlife, individuals who were aging more rapidly were less physically able, showed cognitive decline and brain aging, self-reported worse health, and looked older. Measured biological aging in young adults can be used to identify causes of aging and evaluate rejuvenation therapies. PMID:26150497

  12. Comparison of analysis methods for airway quantification

    NASA Astrophysics Data System (ADS)

    Odry, Benjamin L.; Kiraly, Atilla P.; Novak, Carol L.; Naidich, David P.

    2012-03-01

    Diseased airways have been known for several years as a possible contributing factor to airflow limitation in Chronic Obstructive Pulmonary Diseases (COPD). Quantification of disease severity through the evaluation of airway dimensions - wall thickness and lumen diameter - has gained increased attention, thanks to the availability of multi-slice computed tomography (CT). Novel approaches have focused on automated methods of measurement as a faster and more objective means that the visual assessment routinely employed in the clinic. Since the Full-Width Half-Maximum (FWHM) method of airway measurement was introduced two decades ago [1], several new techniques for quantifying airways have been detailed in the literature, but no approach has truly become a standard for such analysis. Our own research group has presented two alternative approaches for determining airway dimensions, one involving a minimum path and the other active contours [2, 3]. With an increasing number of techniques dedicated to the same goal, we decided to take a step back and analyze the differences of these methods. We consequently put to the test our two methods of analysis and the FWHM approach. We first measured a set of 5 airways from a phantom of known dimensions. Then we compared measurements from the three methods to those of two independent readers, performed on 35 airways in 5 patients. We elaborate on the differences of each approach and suggest conclusions on which could be defined as the best one.

  13. Numerical Uncertainty Quantification for Radiation Analysis Tools

    NASA Technical Reports Server (NTRS)

    Anderson, Brooke; Blattnig, Steve; Clowdsley, Martha

    2007-01-01

    Recently a new emphasis has been placed on engineering applications of space radiation analyses and thus a systematic effort of Verification, Validation and Uncertainty Quantification (VV&UQ) of the tools commonly used for radiation analysis for vehicle design and mission planning has begun. There are two sources of uncertainty in geometric discretization addressed in this paper that need to be quantified in order to understand the total uncertainty in estimating space radiation exposures. One source of uncertainty is in ray tracing, as the number of rays increase the associated uncertainty decreases, but the computational expense increases. Thus, a cost benefit analysis optimizing computational time versus uncertainty is needed and is addressed in this paper. The second source of uncertainty results from the interpolation over the dose vs. depth curves that is needed to determine the radiation exposure. The question, then, is what is the number of thicknesses that is needed to get an accurate result. So convergence testing is performed to quantify the uncertainty associated with interpolating over different shield thickness spatial grids.

  14. Quality Quantification of Evaluated Cross Section Covariances

    SciTech Connect

    Varet, S.; Dossantos-Uzarralde, P.

    2015-01-15

    Presently, several methods are used to estimate the covariance matrix of evaluated nuclear cross sections. Because the resulting covariance matrices can be different according to the method used and according to the assumptions of the method, we propose a general and objective approach to quantify the quality of the covariance estimation for evaluated cross sections. The first step consists in defining an objective criterion. The second step is computation of the criterion. In this paper the Kullback-Leibler distance is proposed for the quality quantification of a covariance matrix estimation and its inverse. It is based on the distance to the true covariance matrix. A method based on the bootstrap is presented for the estimation of this criterion, which can be applied with most methods for covariance matrix estimation and without the knowledge of the true covariance matrix. The full approach is illustrated on the {sup 85}Rb nucleus evaluations and the results are then used for a discussion on scoring and Monte Carlo approaches for covariance matrix estimation of the cross section evaluations.

  15. Quantification of perceived macro-uniformity

    NASA Astrophysics Data System (ADS)

    Lee, Ki-Youn; Bang, Yousun; Choh, Heui-Keun

    2011-01-01

    Macro-uniformity refers to the subjective impression of overall uniformity in the print sample. By the efforts of INCITS W1.1 team, macro-uniformity is categorized into five types of attributes: banding, streaks, mottle, gradients, and moiré patterns, and the ruler samples are generated with perceptual scales. W1.1 macro-uniformity ruler is useful for judging the levels of print defect, but it is not an easy task to reproduce the samples having the same perceptual scales at different times in different places. An objective quantification method is more helpful and convenient for developers to analyze print quality and design printing system components. In this paper, we propose a method for measuring perceived macro-uniformity for a given print using a flat-bed scanner. First, banding, 2D noise, and gradients are separately measured, and they are converted to the perceptual scales based on subjective results of each attribute. The correlation coefficients between the measured values of the attributes and the perceptual scales are 0.92, 0.97, and 0.86, respectively. Another subjective test is performed to find the relationship between the overall macro-uniformity and the three attributes. The weighting factors are obtained by the experimental result, and the final macro-uniformity grade is determined by the weighted sums of each attribute.

  16. Quantification of bromophenols in Islay whiskies.

    PubMed

    Bendig, Paul; Lehnert, Katja; Vetter, Walter

    2014-04-01

    Two single malt whiskies from the Scottish island Islay, i.e., Laphroiag and Lagavulin, are characterized by an iodine-like flavor associated with marine environments. In this study we investigated if this flavor impression could be due to bromophenols which are character impact compounds of marine fish and shrimps. In this study we developed a method suited for the determination of dibromo- and tribromophenols in whisky. Aliquots were O-acetylated, and quantification was carried out with gas chromatography with electron-capture negative ion mass spectrometry (GC/ECNI-MS). Both Islay whiskies contained more than 400 ng/L bromophenols with 2,6-dibromophenol being the most relevant homologue (>300 ng/L, respectively). These concentrations are at least 1 order of magnitude higher than the taste threshold of 2,6-dibromophenol in water. A third Islay whisky, Bowmore, contained ∼100 ng/L bromophenols while seventeen other whiskies from other regions in Scotland as well as from the USA, Ireland, and Germany contained at least 1 order of magnitude less than the two whiskies with the marine taste. Accordingly, bromophenols may contribute to the marine flavor and taste of Laphroaig and Lagavulin.

  17. Legionella spp. isolation and quantification from greywater

    PubMed Central

    Rodríguez-Martínez, Sara; Blanky, Marina; Friedler, Eran; Halpern, Malka

    2015-01-01

    Legionella, an opportunistic human pathogen whose natural environment is water, is transmitted to humans through inhalation of contaminated aerosols. Legionella has been isolated from a high diversity of water types. Due its importance as a pathogen, two ISO protocols have been developed for its monitoring. However, these two protocols are not suitable for analyzing Legionella in greywater (GW). GW is domestic wastewater excluding the inputs from toilets and kitchen. It can serve as an alternative water source, mainly for toilet flushing and garden irrigation; both producing aerosols that can cause a risk for Legionella infection. Hence, before reuse, GW has to be treated and its quality needs to be monitored. The difficulty of Legionella isolation from GW strives in the very high load of contaminant bacteria. Here we describe a modification of the ISO protocol 11731:1998 that enables the isolation and quantification of Legionella from GW samples. The following modifications were made:•To enable isolation of Legionella from greywater, a pre-filtration step that removes coarse matter is recommended.•Legionella can be isolated after a combined acid-thermic treatment that eliminates the high load of contaminant bacteria in the sample. PMID:26740925

  18. Legionella spp. isolation and quantification from greywater.

    PubMed

    Rodríguez-Martínez, Sara; Blanky, Marina; Friedler, Eran; Halpern, Malka

    2015-01-01

    Legionella, an opportunistic human pathogen whose natural environment is water, is transmitted to humans through inhalation of contaminated aerosols. Legionella has been isolated from a high diversity of water types. Due its importance as a pathogen, two ISO protocols have been developed for its monitoring. However, these two protocols are not suitable for analyzing Legionella in greywater (GW). GW is domestic wastewater excluding the inputs from toilets and kitchen. It can serve as an alternative water source, mainly for toilet flushing and garden irrigation; both producing aerosols that can cause a risk for Legionella infection. Hence, before reuse, GW has to be treated and its quality needs to be monitored. The difficulty of Legionella isolation from GW strives in the very high load of contaminant bacteria. Here we describe a modification of the ISO protocol 11731:1998 that enables the isolation and quantification of Legionella from GW samples. The following modifications were made:•To enable isolation of Legionella from greywater, a pre-filtration step that removes coarse matter is recommended.•Legionella can be isolated after a combined acid-thermic treatment that eliminates the high load of contaminant bacteria in the sample.

  19. Uncertainty quantification for systems of conservation laws

    SciTech Connect

    Poette, Gael Despres, Bruno Lucor, Didier

    2009-04-20

    Uncertainty quantification through stochastic spectral methods has been recently applied to several kinds of non-linear stochastic PDEs. In this paper, we introduce a formalism based on kinetic theory to tackle uncertain hyperbolic systems of conservation laws with Polynomial Chaos (PC) methods. The idea is to introduce a new variable, the entropic variable, in bijection with our vector of unknowns, which we develop on the polynomial basis: by performing a Galerkin projection, we obtain a deterministic system of conservation laws. We state several properties of this deterministic system in the case of a general uncertain system of conservation laws. We then apply the method to the case of the inviscid Burgers' equation with random initial conditions and we present some preliminary results for the Euler system. We systematically compare results from our new approach to results from the stochastic Galerkin method. In the vicinity of discontinuities, the new method bounds the oscillations due to Gibbs phenomenon to a certain range through the entropy of the system without the use of any adaptative random space discretizations. It is found to be more precise than the stochastic Galerkin method for smooth cases but above all for discontinuous cases.

  20. Uncertainty Quantification of Modelling of Equiaxed Solidification

    NASA Astrophysics Data System (ADS)

    Fezi, K.; Krane, M. J. M.

    2016-07-01

    Numerical simulations of metal alloy solidification are used to gain insight into physical phenomena that cannot be observed experimentally. Often validation of such models has been done through comparison to sparse experimental data, to which agreement can be misinterpreted due to both model and experimental uncertainty. Uncertainty quantification (UQ) and sensitivity analysis are performed on a transient model of solidification of Al-4.5 wt.% Cu in a rectangular cavity, with equiaxed (grain refined) solidification morphology. This model solves equations for momentum, temperature, and species conservation; UQ and sensitivity analysis are performed for the degree of macrosegregation. A Smolyak sparse grid algorithm is used to select input values to construct a response surface fit to model outputs. The response surface is then used as a surrogate for the solidification model to determine the sensitivities and probability density functions of the model outputs. Uncertain model inputs of interest include the secondary dendrite arm spacing, equiaxed particle size, and fraction solid at which the rigid mushy zone forms. Similar analysis was also performed on a transient model of direct chill casting of the same alloy.

  1. Bacterial adhesion force quantification by fluidic force microscopy

    NASA Astrophysics Data System (ADS)

    Potthoff, Eva; Ossola, Dario; Zambelli, Tomaso; Vorholt, Julia A.

    2015-02-01

    Quantification of detachment forces between bacteria and substrates facilitates the understanding of the bacterial adhesion process that affects cell physiology and survival. Here, we present a method that allows for serial, single bacterial cell force spectroscopy by combining the force control of atomic force microscopy with microfluidics. Reversible bacterial cell immobilization under physiological conditions on the pyramidal tip of a microchanneled cantilever is achieved by underpressure. Using the fluidic force microscopy technology (FluidFM), we achieve immobilization forces greater than those of state-of-the-art cell-cantilever binding as demonstrated by the detachment of Escherichia coli from polydopamine with recorded forces between 4 and 8 nN for many cells. The contact time and setpoint dependence of the adhesion forces of E. coli and Streptococcus pyogenes, as well as the sequential detachment of bacteria out of a chain, are shown, revealing distinct force patterns in the detachment curves. This study demonstrates the potential of the FluidFM technology for quantitative bacterial adhesion measurements of cell-substrate and cell-cell interactions that are relevant in biofilms and infection biology.Quantification of detachment forces between bacteria and substrates facilitates the understanding of the bacterial adhesion process that affects cell physiology and survival. Here, we present a method that allows for serial, single bacterial cell force spectroscopy by combining the force control of atomic force microscopy with microfluidics. Reversible bacterial cell immobilization under physiological conditions on the pyramidal tip of a microchanneled cantilever is achieved by underpressure. Using the fluidic force microscopy technology (FluidFM), we achieve immobilization forces greater than those of state-of-the-art cell-cantilever binding as demonstrated by the detachment of Escherichia coli from polydopamine with recorded forces between 4 and 8 nN for many

  2. Quantification of leukocyte migration: improvement of a method.

    PubMed

    Sunder-Plassmann, G; Hofbauer, R; Sengoelge, G; Hörl, W H

    1996-01-01

    Eighteen different permeable membrane supports with and without confluent endothelial cell monolayers were incubated with normal donor derived neutrophils in the upper chambers of a 24 multiwell double chamber system. In order to study transmembrane or transendothelial leukocyte migration leukocytes were stimulated by chemoattractants, or endothelial cells were activated by IL-1. After coincubation the membrane supports building the upper chambers were discarded. Using this technique, leukocytes that had migrated into the lower chamber were exposed to the fluorescent dye calcein AM without additional washing or transfer steps. Absolute cell counts were determined computer assisted using dilution series of calcein AM labeled leukocytes as standards. Serial dilutions of neutrophils exposed to calcein AM showed reproducible linear fluorescence intensity, and relative fluorescence intensity correlated significant with cell counts (r2 = 0.974, p < 0.0001). Out of 18 membrane supports only one was suitable for our assay set up. Best technical and optical performance was achieved with a membrane made of polyethylene terephtalate with a pore size of 3 mm at a pore density of 0.8 x 10(6)/cm2. Stimulation of leukocytes or endothelium by FMLP or IL-1 revealed an increase of transendothelial migration to 7.2 +/- 1.8 x 10(5) PMN and 5.1 +/- 0.7 x 10(5) PMN respectively if compared with medium (0.6 +/- 0.2 x 10(5) PMN). IL-1 induced migration of neutrophils was inhibited by anti IL-1 autoantibodies derived from chronic renal failure patients (IL-1: 100% of PMN migrated, anti IL-1 antibody: 39% of PMN migrated, control antibody: 84% of PMN migrated). In summary, a simple fluorimetric assay was established for the quantification of transmembrane and transendothelial leukocyte migration. PMID:8675234

  3. Quantification and Propagation of Nuclear Data Uncertainties

    NASA Astrophysics Data System (ADS)

    Rising, Michael E.

    The use of several uncertainty quantification and propagation methodologies is investigated in the context of the prompt fission neutron spectrum (PFNS) uncertainties and its impact on critical reactor assemblies. First, the first-order, linear Kalman filter is used as a nuclear data evaluation and uncertainty quantification tool combining available PFNS experimental data and a modified version of the Los Alamos (LA) model. The experimental covariance matrices, not generally given in the EXFOR database, are computed using the GMA methodology used by the IAEA to establish more appropriate correlations within each experiment. Then, using systematics relating the LA model parameters across a suite of isotopes, the PFNS for both the uranium and plutonium actinides are evaluated leading to a new evaluation including cross-isotope correlations. Next, an alternative evaluation approach, the unified Monte Carlo (UMC) method, is studied for the evaluation of the PFNS for the n(0.5 MeV)+Pu-239 fission reaction and compared to the Kalman filter. The UMC approach to nuclear data evaluation is implemented in a variety of ways to test convergence toward the Kalman filter results and to determine the nonlinearities present in the LA model. Ultimately, the UMC approach is shown to be comparable to the Kalman filter for a realistic data evaluation of the PFNS and is capable of capturing the nonlinearities present in the LA model. Next, the impact that the PFNS uncertainties have on important critical assemblies is investigated. Using the PFNS covariance matrices in the ENDF/B-VII.1 nuclear data library, the uncertainties of the effective multiplication factor, leakage, and spectral indices of the Lady Godiva and Jezebel critical assemblies are quantified. Using principal component analysis on the PFNS covariance matrices results in needing only 2-3 principal components to retain the PFNS uncertainties. Then, using the polynomial chaos expansion (PCE) on the uncertain output

  4. Quantification of microvessels in canine lymph nodes.

    PubMed

    Tonar, Zbynĕk; Egger, Gunter F; Witter, Kirsti; Wolfesberger, Birgitt

    2008-10-01

    Quantification of microvessels in tumors is mostly based on counts of vessel profiles in tumor hot spots. Drawbacks of this method include low reproducibility and large interobserver variance, mainly as a result of individual differences in sampling of image fields for analysis. Our aim was to test an unbiased method for quantifying microvessels in healthy and tumorous lymph nodes of dogs. The endothelium of blood vessels was detected in paraffin sections by a combination of immunohistochemistry (von Willebrand factor) and lectin histochemistry (wheat germ agglutinin) in comparison with detection of basal laminae by laminin immunohistochemistry or silver impregnation. Systematic uniform random sampling of 50 image fields was performed during photo-documentation. An unbiased counting frame (area 113,600 microm(2)) was applied to each micrograph. The total area sampled from each node was 5.68 mm(2). Vessel profiles were counted according to stereological counting rules. Inter- and intraobserver variabilities were tested. The application of systematic uniform random sampling was compared with the counting of vessel profiles in hot spots. The unbiased estimate of the number of vessel profiles per unit area ranged from 100.5 +/- 44.0/mm(2) to 442.6 +/- 102.5/mm(2) in contrast to 264 +/- 72.2/mm(2) to 771.0 +/- 108.2/mm(2) in hot spots. The advantage of using systematic uniform random sampling is its reproducibility, with reasonable interobserver and low intraobserver variance. This method also allows for the possibility of using archival material, because staining quality is not limiting as it is for image analysis, and artifacts can easily be excluded. However, this method is comparatively time-consuming.

  5. Fluorometric quantification of natural inorganic polyphosphate.

    PubMed

    Diaz, Julia M; Ingall, Ellery D

    2010-06-15

    Polyphosphate, a linear polymer of orthophosphate, is abundant in the environment and a key component in wastewater treatment and many bioremediation processes. Despite the broad relevance of polyphosphate, current methods to quantify it possess significant disadvantages. Here, we describe a new approach for the direct quantification of inorganic polyphosphate in complex natural samples. The protocol relies on the interaction between the fluorochrome 4',6-diamidino-2-phenylindole (DAPI) and dissolved polyphosphate. With the DAPI-based approach we describe, polyphosphate can be quantified at concentrations ranging from 0.5-3 microM P in a neutral-buffered freshwater matrix with an accuracy of +/-0.03 microM P. The patterns of polyphosphate concentration versus fluorescence yielded by standards exhibit no chain length dependence across polyphosphates ranging from 15-130 phosphorus units in size. Shorter length polyphosphate molecules (e.g., polyphosphate of three and five phosphorus units in length) contribute little to no signal in this approach, as these molecules react only slightly or not at all with DAPI in the concentration range tested. The presence of salt suppresses fluorescence from intermediate polyphosphate chain lengths (e.g., 15 phosphorus units) at polyphosphate concentrations ranging from 0.5-3 microM P. For longer chain lengths (e.g., 45-130 phosphorus units), this salt interference is not evident at conductivities up to approximately 10mS/cm. Our results indicate that standard polyphosphates should be stored frozen for no longer than 10-15 days to avoid inconsistent results associated with standard degradation. We have applied the fluorometric protocol to the analysis of five well-characterized natural samples to demonstrate the use of the method. PMID:20507063

  6. Size-Resolved Identification, Characterization, and Quantification of Primary Biological Organic Aerosol at a European Rural Site.

    PubMed

    Bozzetti, Carlo; Daellenbach, Kaspar R; Hueglin, Christoph; Fermo, Paola; Sciare, Jean; Kasper-Giebl, Anneliese; Mazar, Yinon; Abbaszade, Gülcin; El Kazzi, Mario; Gonzalez, Raquel; Shuster-Meiseles, Timor; Flasch, Mira; Wolf, Robert; Křepelová, Adéla; Canonaco, Francesco; Schnelle-Kreis, Jürgen; Slowik, Jay G; Zimmermann, Ralf; Rudich, Yinon; Baltensperger, Urs; El Haddad, Imad; Prévôt, André S H

    2016-04-01

    Primary biological organic aerosols (PBOA) represent a major component of the coarse organic matter (OMCOARSE, aerodynamic diameter > 2.5 μm). Although this fraction affects human health and the climate, its quantification and chemical characterization currently remain elusive. We present the first quantification of the entire PBOACOARSE mass and its main sources by analyzing size-segregated filter samples collected during the summer and winter at the rural site of Payerne (Switzerland), representing a continental Europe background environment. The size-segregated water-soluble OM was analyzed by a newly developed offline aerosol mass spectrometric technique (AMS). Collected spectra were analyzed by three-dimensional positive matrix factorization (3D-PMF), showing that PBOA represented the main OMCOARSE source during summer and its contribution to PM10 was comparable to that of secondary organic aerosol. We found substantial cellulose contributions to OMCOARSE, which in combination with gas chromatography mass spectrometry molecular markers quantification, underlined the predominance of plant debris. Quantitative polymerase chain reaction (qPCR) analysis instead revealed that the sum of bacterial and fungal spores mass represented only a minor OMCOARSE fraction (<0.1%). X-ray photoelectron spectroscopic (XPS) analysis of C and N binding energies throughout the size fractions revealed an organic N increase in the PM10 compared to PM1 consistent with AMS observations. PMID:26900965

  7. Size-Resolved Identification, Characterization, and Quantification of Primary Biological Organic Aerosol at a European Rural Site.

    PubMed

    Bozzetti, Carlo; Daellenbach, Kaspar R; Hueglin, Christoph; Fermo, Paola; Sciare, Jean; Kasper-Giebl, Anneliese; Mazar, Yinon; Abbaszade, Gülcin; El Kazzi, Mario; Gonzalez, Raquel; Shuster-Meiseles, Timor; Flasch, Mira; Wolf, Robert; Křepelová, Adéla; Canonaco, Francesco; Schnelle-Kreis, Jürgen; Slowik, Jay G; Zimmermann, Ralf; Rudich, Yinon; Baltensperger, Urs; El Haddad, Imad; Prévôt, André S H

    2016-04-01

    Primary biological organic aerosols (PBOA) represent a major component of the coarse organic matter (OMCOARSE, aerodynamic diameter > 2.5 μm). Although this fraction affects human health and the climate, its quantification and chemical characterization currently remain elusive. We present the first quantification of the entire PBOACOARSE mass and its main sources by analyzing size-segregated filter samples collected during the summer and winter at the rural site of Payerne (Switzerland), representing a continental Europe background environment. The size-segregated water-soluble OM was analyzed by a newly developed offline aerosol mass spectrometric technique (AMS). Collected spectra were analyzed by three-dimensional positive matrix factorization (3D-PMF), showing that PBOA represented the main OMCOARSE source during summer and its contribution to PM10 was comparable to that of secondary organic aerosol. We found substantial cellulose contributions to OMCOARSE, which in combination with gas chromatography mass spectrometry molecular markers quantification, underlined the predominance of plant debris. Quantitative polymerase chain reaction (qPCR) analysis instead revealed that the sum of bacterial and fungal spores mass represented only a minor OMCOARSE fraction (<0.1%). X-ray photoelectron spectroscopic (XPS) analysis of C and N binding energies throughout the size fractions revealed an organic N increase in the PM10 compared to PM1 consistent with AMS observations.

  8. Quantification of chemical gaseous plumes on hyperspectral imagery

    NASA Astrophysics Data System (ADS)

    Niu, Sidi

    The passive remote chemical plume quantification problem may be approached from multiple aspects, corresponding to a variety of physical effects that may be exploited. Accordingly, a diversity of statistical quantification algorithms has been proposed in the literature. The ultimate performance and algorithmic complexity of each is influenced by the assumptions made about the scene, which may include the presence of ancillary measurements or particular background/plume features that may or may not be present. In this work, we evaluate and investigate the advantages and limitations of a number of quantification algorithms that span a variety of such assumptions. With these in-depth insights we gain, a new quantification algorithm is proposed for single gas quantification which is superior to all state-of-the-art algorithms in every almost every aspects including applicability, accuracy, and efficiency. The new method, called selected-band algorithm, achieves its superior performance through an accurate estimation of the unobservable off-plume radiance. The reason why off-plume radiance is recoverable relies on a common observation that most chemical gases only exhibit strong absorptive behavior in certain spectral bands. Those spectral bands where the gas absorption is almost zero or small are ideal to carry out background estimation. In this thesis, the new selected-band algorithm is first derived from its favorable narrow-band sharp-featured gas and then extended to an iterative algorithm that suits all kinds of gases. The performance improvement is verified by simulated data for a variety of experimental settings.

  9. GMO quantification: valuable experience and insights for the future.

    PubMed

    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. PMID:25182968

  10. GMO quantification: valuable experience and insights for the future.

    PubMed

    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.

  11. Accurate Peptide Fragment Mass Analysis: Multiplexed Peptide Identification and Quantification

    PubMed Central

    Weisbrod, Chad R.; Eng, Jimmy K.; Hoopmann, Michael R.; Baker, Tahmina; Bruce, James E.

    2012-01-01

    FT All Reaction Monitoring (FT-ARM) is a novel approach for the identification and quantification of peptides that relies upon the selectivity of high mass accuracy data and the specificity of peptide fragmentation patterns. An FT-ARM experiment involves continuous, data-independent, high mass accuracy MS/MS acquisition spanning a defined m/z range. Custom software was developed to search peptides against the multiplexed fragmentation spectra by comparing theoretical or empirical fragment ions against every fragmentation spectrum across the entire acquisition. A dot product score is calculated against each spectrum in order to generate a score chromatogram used for both identification and quantification. Chromatographic elution profile characteristics are not used to cluster precursor peptide signals to their respective fragment ions. FT-ARM identifications are demonstrated to be complementary to conventional data-dependent shotgun analysis, especially in cases where the data-dependent method fails due to fragmenting multiple overlapping precursors. The sensitivity, robustness and specificity of FT-ARM quantification are shown to be analogous to selected reaction monitoring-based peptide quantification with the added benefit of minimal assay development. Thus, FT-ARM is demonstrated to be a novel and complementary data acquisition, identification, and quantification method for the large scale analysis of peptides. PMID:22288382

  12. Rapid and portable electrochemical quantification of phosphorus.

    PubMed

    Kolliopoulos, Athanasios V; Kampouris, Dimitrios K; Banks, Craig E

    2015-04-21

    Phosphorus is one of the key indicators of eutrophication levels in natural waters where it exists mainly as dissolved phosphorus. Various analytical protocols exist to provide an offsite analysis, and a point of site analysis is required. The current standard method recommended by the Environmental Protection Agency (EPA) for the detection of total phosphorus is colorimetric and based upon the color of a phosphomolybdate complex formed as a result of the reaction between orthophosphates and molybdates ions where ascorbic acid and antimony potassium tartrate are added and serve as reducing agents. Prior to the measurements, all forms of phosphorus are converted into orthophosphates via sample digestion (heating and acidifying). The work presented here details an electrochemical adaptation of this EPA recommended colorimetric approach for the measurement of dissolved phosphorus in water samples using screen-printed graphite macroelectrodes for the first time. This novel indirect electrochemical sensing protocol allows the determination of orthophosphates over the range from 0.5 to 20 μg L(-1) in ideal pH 1 solutions utilizing cyclic voltammetry with a limit of detection (3σ) found to correspond to 0.3 μg L(-1) of phosphorus. The reaction time and influence of foreign ions (potential interferents) upon this electroanalytical protocol was also investigated, where it was found that a reaction time of 5 min, which is essential in the standard colorimetric approach, is not required in the new proposed electrochemically adapted protocol. The proposed electrochemical method was independently validated through the quantification of orthophosphates and total dissolved phosphorus in polluted water samples (canal water samples) with ion chromatography and ICP-OES, respectively. This novel electrochemical protocol exhibits advantages over the established EPA recommended colorimetric determination for total phosphorus with lower detection limits and shorter experimental times

  13. Uncertainty Quantification Techniques of SCALE/TSUNAMI

    SciTech Connect

    Rearden, Bradley T; Mueller, Don

    2011-01-01

    The Standardized Computer Analysis for Licensing Evaluation (SCALE) code system developed at Oak Ridge National Laboratory (ORNL) includes Tools for Sensitivity and Uncertainty Analysis Methodology Implementation (TSUNAMI). The TSUNAMI code suite can quantify the predicted change in system responses, such as k{sub eff}, reactivity differences, or ratios of fluxes or reaction rates, due to changes in the energy-dependent, nuclide-reaction-specific cross-section data. Where uncertainties in the neutron cross-section data are available, the sensitivity of the system to the cross-section data can be applied to propagate the uncertainties in the cross-section data to an uncertainty in the system response. Uncertainty quantification is useful for identifying potential sources of computational biases and highlighting parameters important to code validation. Traditional validation techniques often examine one or more average physical parameters to characterize a system and identify applicable benchmark experiments. However, with TSUNAMI correlation coefficients are developed by propagating the uncertainties in neutron cross-section data to uncertainties in the computed responses for experiments and safety applications through sensitivity coefficients. The bias in the experiments, as a function of their correlation coefficient with the intended application, is extrapolated to predict the bias and bias uncertainty in the application through trending analysis or generalized linear least squares techniques, often referred to as 'data adjustment.' Even with advanced tools to identify benchmark experiments, analysts occasionally find that the application models include some feature or material for which adequately similar benchmark experiments do not exist to support validation. For example, a criticality safety analyst may want to take credit for the presence of fission products in spent nuclear fuel. In such cases, analysts sometimes rely on 'expert judgment' to select an

  14. Rapid and portable electrochemical quantification of phosphorus.

    PubMed

    Kolliopoulos, Athanasios V; Kampouris, Dimitrios K; Banks, Craig E

    2015-04-21

    Phosphorus is one of the key indicators of eutrophication levels in natural waters where it exists mainly as dissolved phosphorus. Various analytical protocols exist to provide an offsite analysis, and a point of site analysis is required. The current standard method recommended by the Environmental Protection Agency (EPA) for the detection of total phosphorus is colorimetric and based upon the color of a phosphomolybdate complex formed as a result of the reaction between orthophosphates and molybdates ions where ascorbic acid and antimony potassium tartrate are added and serve as reducing agents. Prior to the measurements, all forms of phosphorus are converted into orthophosphates via sample digestion (heating and acidifying). The work presented here details an electrochemical adaptation of this EPA recommended colorimetric approach for the measurement of dissolved phosphorus in water samples using screen-printed graphite macroelectrodes for the first time. This novel indirect electrochemical sensing protocol allows the determination of orthophosphates over the range from 0.5 to 20 μg L(-1) in ideal pH 1 solutions utilizing cyclic voltammetry with a limit of detection (3σ) found to correspond to 0.3 μg L(-1) of phosphorus. The reaction time and influence of foreign ions (potential interferents) upon this electroanalytical protocol was also investigated, where it was found that a reaction time of 5 min, which is essential in the standard colorimetric approach, is not required in the new proposed electrochemically adapted protocol. The proposed electrochemical method was independently validated through the quantification of orthophosphates and total dissolved phosphorus in polluted water samples (canal water samples) with ion chromatography and ICP-OES, respectively. This novel electrochemical protocol exhibits advantages over the established EPA recommended colorimetric determination for total phosphorus with lower detection limits and shorter experimental times

  15. Symmetry quantification and mapping using convergent beam electron diffraction.

    PubMed

    Kim, Kyou-Hyun; Zuo, Jian-Min

    2013-01-01

    We propose a new algorithm to quantify symmetry recorded in convergent beam electron diffraction (CBED) patterns and use it for symmetry mapping in materials applications. We evaluate the effectiveness of the profile R-factor (R(p)) and the normalized cross-correlation coefficient (γ) for quantifying the amount of symmetry in a CBED pattern. The symmetry quantification procedures are automated and the algorithm is implemented as a DM (Digital Micrograph(©)) script. Experimental and simulated CBED patterns recorded from a Si single crystal are used to calibrate the proposed algorithm for the symmetry quantification. The proposed algorithm is then applied to a Si sample with defects to test the sensitivity of symmetry quantification to defects. Using the mirror symmetry as an example, we demonstrate that the normalized cross-correlation coefficient provides an effective and robust measurement of the symmetry recorded in experimental CBED patterns. PMID:23142747

  16. Real-Time PCR for Gene Expression Quantification in Asthma.

    PubMed

    Segundo-Val, Ignacio San; García-Solaesa, Virginia; García-Sánchez, Asunción

    2016-01-01

    The quantitative real-time PCR (qPCR) has become the reference technique for studying gene expression in recent years. The application of qPCR to the study of asthma provides very useful information regarding the gene expression mechanisms. The quantification of RNA from cDNA can be performed by using fluorescent dyes or specific sequence probes. Here, we describe the protocol to quantify gene expression levels using SYBR Green as fluorescent dye. The protocol starts with the RNA extraction, followed by reverse transcription to obtain cDNA, quantification and finally data analysis.

  17. Real-Time PCR for Gene Expression Quantification in Asthma.

    PubMed

    Segundo-Val, Ignacio San; García-Solaesa, Virginia; García-Sánchez, Asunción

    2016-01-01

    The quantitative real-time PCR (qPCR) has become the reference technique for studying gene expression in recent years. The application of qPCR to the study of asthma provides very useful information regarding the gene expression mechanisms. The quantification of RNA from cDNA can be performed by using fluorescent dyes or specific sequence probes. Here, we describe the protocol to quantify gene expression levels using SYBR Green as fluorescent dye. The protocol starts with the RNA extraction, followed by reverse transcription to obtain cDNA, quantification and finally data analysis. PMID:27300530

  18. Quantification of Line Tracking Solutions for Automotive Applications

    NASA Astrophysics Data System (ADS)

    Shi, Jane; Rourke, Rick F.; Groll, Dave; Tavora, Peter W.

    Unlike line tracking in automotive painting applications, line tracking for automotive general assembly applications requires position tracking in order to perform assembly operations to a required assembly tolerance. Line tracking quantification experiments have been designed and conducted for a total of 16 test cases for two line tracking scenarios with three types of line tracking solutions: encoder based tracking, encoder plus static vision based tracking, and the analog sensor-based tracking for general assembly robotic automation. This chapter presents the quantification results, identifies key performance drivers, and illustrates their implications for automotive assembly applications.

  19. Quantification is Neither Necessary Nor Sufficient for Measurement

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

    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.

  20. Clinical PET Myocardial Perfusion Imaging and Flow Quantification.

    PubMed

    Juneau, Daniel; Erthal, Fernanda; Ohira, Hiroshi; Mc Ardle, Brian; Hessian, Renée; deKemp, Robert A; Beanlands, Rob S B

    2016-02-01

    Cardiac PET imaging is a powerful tool for the assessment of coronary artery disease. Many tracers with different advantages and disadvantages are available. It has several advantages over single photon emission computed tomography, including superior accuracy and lower radiation exposure. It provides powerful prognostic information, which can help to stratify patients and guide clinicians. The addition of flow quantification enables better detection of multivessel disease while providing incremental prognostic information. Flow quantification provides important physiologic information, which may be useful to individualize patient therapy. This approach is being applied in some centers, but requires standardization before it is more widely applied. PMID:26590781

  1. Detection and quantification of chimerism by droplet digital PCR.

    PubMed

    George, David; Czech, Juliann; John, Bobby; Yu, Min; Jennings, Lawrence J

    2013-01-01

    Accurate quantification of chimerism and microchimerism is proving to be increasingly valuable for hematopoietic cell transplantation as well as non-transplant conditions. However, methods that are available to quantify low-level chimerism lack accuracy. Therefore, we developed and validated a method for quantifying chimerism based on digital PCR technology. We demonstrate accurate quantification that far exceeds what is possible with analog qPCR down to 0.01% with the potential to go even lower. Also, this method is inherently more informative than qPCR. We expect the advantages of digital PCR will make it the preferred method for chimerism analysis.

  2. Brief review of uncertainty quantification for particle image velocimetry

    NASA Astrophysics Data System (ADS)

    Farias, M. H.; Teixeira, R. S.; Koiller, J.; Santos, A. M.

    2016-07-01

    Metrological studies for particle image velocimetry (PIV) are recent in literature. An attempt to evaluate the uncertainty quantifications (UQ) of the PIV velocity field are in evidence. Therefore, a short review on main sources of uncertainty in PIV and available methodologies for its quantification are presented. In addition, the potential of some mathematical techniques, coming from the area of geometric mechanics and control, that could interest the fluids UQ community are highlighted as good possibilities. “We must measure what is measurable and make measurable what cannot be measured” (Galileo)

  3. A quick colorimetric method for total lipid quantification in microalgae.

    PubMed

    Byreddy, Avinesh R; Gupta, Adarsha; Barrow, Colin J; Puri, Munish

    2016-06-01

    Discovering microalgae with high lipid productivity are among the key milestones for achieving sustainable biodiesel production. Current methods of lipid quantification are time intensive and costly. A rapid colorimetric method based on sulfo-phospho-vanillin (SPV) reaction was developed for the quantification of microbial lipids to facilitate screening for lipid producing microalgae. This method was successfully tested on marine thraustochytrid strains and vegetable oils. The colorimetric method results correlated well with gravimetric method estimates. The new method was less time consuming than gravimetric analysis and is quantitative for lipid determination, even in the presence of carbohydrates, proteins and glycerol. PMID:27050419

  4. Quantification of toxicological effects for dichloromethane. Draft report (Final)

    SciTech Connect

    Not Available

    1990-04-01

    The source documents for background information used to develop the report on the quantification of toxicological effects for dichloromethane are the health assessment document (HAD) for dichloromethane and a subsequent addendum to the HAD (U.S. EPA, 1985b). In addition, some references published since 1985 are discussed. To summarize the results of the quantification of toxicological effects, a One-day Health Advisory of 10,000 ug/L for a 10-kg child was calculated, based on an acute oral study in rats reported by Kimura et al. (1971). No suitable data for the derivation of a Ten-day Health Advisory were found in the available literature.

  5. Practical quantification of necrosis in histological whole-slide images.

    PubMed

    Homeyer, André; Schenk, Andrea; Arlt, Janine; Dahmen, Uta; Dirsch, Olaf; Hahn, Horst K

    2013-06-01

    Since the histological quantification of necrosis is a common task in medical research and practice, we evaluate different image analysis methods for quantifying necrosis in whole-slide images. In a practical usage scenario, we assess the impact of different classification algorithms and feature sets on both accuracy and computation time. We show how a well-chosen combination of multiresolution features and an efficient postprocessing step enables the accurate quantification necrosis in gigapixel images in less than a minute. The results are general enough to be applied to other areas of histological image analysis as well. PMID:23796718

  6. McKay agar enables routine quantification of the 'Streptococcus milleri' group in cystic fibrosis patients.

    PubMed

    Sibley, Christopher D; Grinwis, Margot E; Field, Tyler R; Parkins, Michael D; Norgaard, Jens C; Gregson, Daniel B; Rabin, Harvey R; Surette, Michael G

    2010-05-01

    The 'Streptococcus milleri' group (SMG) has recently been recognized as a contributor to bronchopulmonary disease in cystic fibrosis (CF). Routine detection and quantification is limited by current CF microbiology protocols. McKay agar was developed previously for the semi-selective isolation of this group. Here, McKay agar was validated against a panel of clinical SMG isolates, which revealed improved SMG recovery compared with Columbia blood agar. The effectiveness of this medium was evaluated by appending it to the standard CF sputum microbiology protocols in a clinical laboratory for a 6-month period. All unique colony types were isolated and identified by 16S rRNA gene sequencing. Whilst a wide variety of organisms were isolated, members of the SMG were the most prevalent bacteria cultured, and McKay agar allowed routine quantification of the SMG from 10(3) to >10(8) c.f.u. ml(-1) directly from sputum. All members of the SMG were detected [Streptococcus anginosus (40.7 %), Streptococcus intermedius (34.3 %) and Streptococcus constellatus (25 %)] with an overall prevalence rate of 40.6 % in our adult CF population. Without exception, samples where SMG isolates were cultured at 10(7) c.f.u. ml(-1) or greater were associated with pulmonary exacerbations. This study demonstrates that McKay agar can be used routinely to quantify the SMG from complex clinical samples.

  7. Biochemical analysis and quantification of hematopoietic stem cells by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Zelig, Udi; Dror, Ziv; Iskovich, Svetlana; Zwielly, Amir; Ben-Harush, Miri; Nathan, Ilana; Mordechai, Shaul; Kapelushnik, Joseph

    2010-05-01

    Identification of hematopoietic stem cells (HSCs) in different stages of maturation is one of the major issues in stem cell research and bone marrow (BM) transplantation. Each stage of maturation of HSCs is characterized by a series of distinct glycoproteins present on the cell plasma membrane surface, named a cluster of differentiation (CD). Currently, complicated and expensive procedures based on CD expression are needed for identification and isolation of HSCs. This method is under dispute, since the correct markers' composition is not strictly clear, thus there is need for a better method for stem cell characterization. In the present study, Fourier transform infrared (FTIR) spectroscopy is employed as a novel optical method for identification and characterization of HSCs based on their entire biochemical features. FTIR spectral analysis of isolated mice HSCs reveals several spectral markers related to lipids, nucleic acids, and carbohydrates, which distinguish HSCs from BM cells. The unique ``open'' conformation of HSC DNA as identified by FTIR is exploited for HSCs quantification in the BM. The proposed method of FTIR spectroscopy for HSC identification and quantification can contribute to stem cell research and BM transplantation.

  8. Online updating and uncertainty quantification using nonstationary output-only measurement

    NASA Astrophysics Data System (ADS)

    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.

  9. Large scale systematic proteomic quantification from non-metastatic to metastatic colorectal cancer

    NASA Astrophysics Data System (ADS)

    Yin, Xuefei; Zhang, Yang; Guo, Shaowen; Jin, Hong; Wang, Wenhai; Yang, Pengyuan

    2015-07-01

    A systematic proteomic quantification of formalin-fixed, paraffin-embedded (FFPE) colorectal cancer tissues from stage I to stage IIIC was performed in large scale. 1017 proteins were identified with 338 proteins in quantitative changes by label free method, while 341 proteins were quantified with significant expression changes among 6294 proteins by iTRAQ method. We found that proteins related to migration expression increased and those for binding and adherent decreased during the colorectal cancer development according to the gene ontology (GO) annotation and ingenuity pathway analysis (IPA). The integrin alpha 5 (ITA5) in integrin family was focused, which was consistent with the metastasis related pathway. The expression level of ITA5 decreased in metastasis tissues and the result has been further verified by Western blotting. Another two cell migration related proteins vitronectin (VTN) and actin-related protein (ARP3) were also proved to be up-regulated by both mass spectrometry (MS) based quantification results and Western blotting. Up to now, our result shows one of the largest dataset in colorectal cancer proteomics research. Our strategy reveals a disease driven omics-pattern for the metastasis colorectal cancer.

  10. Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions

    PubMed Central

    Nakayama, Yuki; Yamaguchi, Hiromi; Einaga, Naoki; Esumi, Mariko

    2016-01-01

    The Qubit fluorometer is a DNA quantification device based on the fluorescence intensity of fluorescent dye binding to double-stranded DNA (dsDNA). Qubit is generally considered useful for checking DNA quality before next-generation sequencing because it measures intact dsDNA. To examine the most accurate and suitable methods for quantifying DNA for quality assessment, we compared three quantification methods: NanoDrop, which measures UV absorbance; Qubit; and quantitative PCR (qPCR), which measures the abundance of a target gene. For the comparison, we used three types of DNA: 1) DNA extracted from fresh frozen liver tissues (Frozen-DNA); 2) DNA extracted from formalin-fixed, paraffin-embedded liver tissues comparable to those used for Frozen-DNA (FFPE-DNA); and 3) DNA extracted from the remaining fractions after RNA extraction with Trizol reagent (Trizol-DNA). These DNAs were serially diluted with distilled water and measured using three quantification methods. For Frozen-DNA, the Qubit values were not proportional to the dilution ratio, in contrast with the NanoDrop and qPCR values. This non-proportional decrease in Qubit values was dependent on a lower salt concentration, and over 1 mM NaCl in the DNA solution was required for the Qubit measurement. For FFPE-DNA, the Qubit values were proportional to the dilution ratio and were lower than the NanoDrop values. However, electrophoresis revealed that qPCR reflected the degree of DNA fragmentation more accurately than Qubit. Thus, qPCR is superior to Qubit for checking the quality of FFPE-DNA. For Trizol-DNA, the Qubit values were proportional to the dilution ratio and were consistently lower than the NanoDrop values, similar to FFPE-DNA. However, the qPCR values were higher than the NanoDrop values. Electrophoresis with SYBR Green I and single-stranded DNA (ssDNA) quantification demonstrated that Trizol-DNA consisted mostly of non-fragmented ssDNA. Therefore, Qubit is not always the most accurate method for

  11. Evaluation of the reliability of maize reference assays for GMO quantification.

    PubMed

    Papazova, Nina; Zhang, David; Gruden, Kristina; Vojvoda, Jana; Yang, Litao; Buh Gasparic, Meti; Blejec, Andrej; Fouilloux, Stephane; De Loose, Marc; Taverniers, Isabel

    2010-03-01

    A reliable PCR reference assay for relative genetically modified organism (GMO) quantification must be specific for the target taxon and amplify uniformly along the commercialised varieties within the considered taxon. Different reference assays for maize (Zea mays L.) are used in official methods for GMO quantification. In this study, we evaluated the reliability of eight existing maize reference assays, four of which are used in combination with an event-specific polymerase chain reaction (PCR) assay validated and published by the Community Reference Laboratory (CRL). We analysed the nucleotide sequence variation in the target genomic regions in a broad range of transgenic and conventional varieties and lines: MON 810 varieties cultivated in Spain and conventional varieties from various geographical origins and breeding history. In addition, the reliability of the assays was evaluated based on their PCR amplification performance. A single base pair substitution, corresponding to a single nucleotide polymorphism (SNP) reported in an earlier study, was observed in the forward primer of one of the studied alcohol dehydrogenase 1 (Adh1) (70) assays in a large number of varieties. The SNP presence is consistent with a poor PCR performance observed for this assay along the tested varieties. The obtained data show that the Adh1 (70) assay used in the official CRL NK603 assay is unreliable. Based on our results from both the nucleotide stability study and the PCR performance test, we can conclude that the Adh1 (136) reference assay (T25 and Bt11 assays) as well as the tested high mobility group protein gene assay, which also form parts of CRL methods for quantification, are highly reliable. Despite the observed uniformity in the nucleotide sequence of the invertase gene assay, the PCR performance test reveals that this target sequence might occur in more than one copy. Finally, although currently not forming a part of official quantification methods, zein and SSIIb

  12. Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions.

    PubMed

    Nakayama, Yuki; Yamaguchi, Hiromi; Einaga, Naoki; Esumi, Mariko

    2016-01-01

    The Qubit fluorometer is a DNA quantification device based on the fluorescence intensity of fluorescent dye binding to double-stranded DNA (dsDNA). Qubit is generally considered useful for checking DNA quality before next-generation sequencing because it measures intact dsDNA. To examine the most accurate and suitable methods for quantifying DNA for quality assessment, we compared three quantification methods: NanoDrop, which measures UV absorbance; Qubit; and quantitative PCR (qPCR), which measures the abundance of a target gene. For the comparison, we used three types of DNA: 1) DNA extracted from fresh frozen liver tissues (Frozen-DNA); 2) DNA extracted from formalin-fixed, paraffin-embedded liver tissues comparable to those used for Frozen-DNA (FFPE-DNA); and 3) DNA extracted from the remaining fractions after RNA extraction with Trizol reagent (Trizol-DNA). These DNAs were serially diluted with distilled water and measured using three quantification methods. For Frozen-DNA, the Qubit values were not proportional to the dilution ratio, in contrast with the NanoDrop and qPCR values. This non-proportional decrease in Qubit values was dependent on a lower salt concentration, and over 1 mM NaCl in the DNA solution was required for the Qubit measurement. For FFPE-DNA, the Qubit values were proportional to the dilution ratio and were lower than the NanoDrop values. However, electrophoresis revealed that qPCR reflected the degree of DNA fragmentation more accurately than Qubit. Thus, qPCR is superior to Qubit for checking the quality of FFPE-DNA. For Trizol-DNA, the Qubit values were proportional to the dilution ratio and were consistently lower than the NanoDrop values, similar to FFPE-DNA. However, the qPCR values were higher than the NanoDrop values. Electrophoresis with SYBR Green I and single-stranded DNA (ssDNA) quantification demonstrated that Trizol-DNA consisted mostly of non-fragmented ssDNA. Therefore, Qubit is not always the most accurate method for

  13. Evaluation of the reliability of maize reference assays for GMO quantification.

    PubMed

    Papazova, Nina; Zhang, David; Gruden, Kristina; Vojvoda, Jana; Yang, Litao; Buh Gasparic, Meti; Blejec, Andrej; Fouilloux, Stephane; De Loose, Marc; Taverniers, Isabel

    2010-03-01

    A reliable PCR reference assay for relative genetically modified organism (GMO) quantification must be specific for the target taxon and amplify uniformly along the commercialised varieties within the considered taxon. Different reference assays for maize (Zea mays L.) are used in official methods for GMO quantification. In this study, we evaluated the reliability of eight existing maize reference assays, four of which are used in combination with an event-specific polymerase chain reaction (PCR) assay validated and published by the Community Reference Laboratory (CRL). We analysed the nucleotide sequence variation in the target genomic regions in a broad range of transgenic and conventional varieties and lines: MON 810 varieties cultivated in Spain and conventional varieties from various geographical origins and breeding history. In addition, the reliability of the assays was evaluated based on their PCR amplification performance. A single base pair substitution, corresponding to a single nucleotide polymorphism (SNP) reported in an earlier study, was observed in the forward primer of one of the studied alcohol dehydrogenase 1 (Adh1) (70) assays in a large number of varieties. The SNP presence is consistent with a poor PCR performance observed for this assay along the tested varieties. The obtained data show that the Adh1 (70) assay used in the official CRL NK603 assay is unreliable. Based on our results from both the nucleotide stability study and the PCR performance test, we can conclude that the Adh1 (136) reference assay (T25 and Bt11 assays) as well as the tested high mobility group protein gene assay, which also form parts of CRL methods for quantification, are highly reliable. Despite the observed uniformity in the nucleotide sequence of the invertase gene assay, the PCR performance test reveals that this target sequence might occur in more than one copy. Finally, although currently not forming a part of official quantification methods, zein and SSIIb

  14. Reliability quantification and visualization for electric microgrids

    NASA Astrophysics Data System (ADS)

    Panwar, Mayank

    and parallel with the area Electric Power Systems (EPS), (3) includes the local EPS and may include portions of the area EPS, and (4) is intentionally planned. A more reliable electric power grid requires microgrids to operate in tandem with the EPS. The reliability can be quantified through various metrics for performance measure. This is done through North American Electric Reliability Corporation (NERC) metrics in North America. The microgrid differs significantly from the traditional EPS, especially at asset level due to heterogeneity in assets. Thus, the performance cannot be quantified by the same metrics as used for EPS. Some of the NERC metrics are calculated and interpreted in this work to quantify performance for a single asset and group of assets in a microgrid. Two more metrics are introduced for system level performance quantification. The next step is a better representation of the large amount of data generated by the microgrid. Visualization is one such form of representation which is explored in detail and a graphical user interface (GUI) is developed as a deliverable tool to the operator for informative decision making and planning. Electronic appendices-I and II contain data and MATLAB© program codes for analysis and visualization for this work.

  15. Remote sensing for quantification of agronomic properties

    NASA Astrophysics Data System (ADS)

    Sullivan, Dana Grace

    Remote sensing (RS) may be used to rapidly assess surface features and facilitate natural resource management, precision agriculture and soil survey. Information obtained in such a way would streamline data collection and improve diagnostic capabilities. Current RS technology has had limited testing, particularly within the Southeast. Our study was designed to evaluate RS as a rapid assessment tool in three different natural resource applications: nitrogen (N) management in a corn crop (Zea mays L.), assessment of in situ crop residue cover, and quantification of near-surface soil properties. In 2000, study sites were established in four physiographic provinces of Alabama: Tennessee Valley, Ridge and Valley, Appalachian Plateau, and Coastal Plain. Spectral measurements were acquired via spectroradiometer (350--1050 nm), airborne ATLAS multispectral scanner (400--12,500 nm), and IKONOS satellite (450--900 nm). Corn plots were established from fresh-tilled ground in a completely randomized design at the Appalachian Plateau and Coastal Plain study sites in 2000. Plots received four N rates (0, 56, 112, and 168 kg N ha-1 ), and were maintained for three consecutive growing seasons. Spectroradiometer data were acquired biweekly from V6-R2 and ATLAS and IKONOS were acquired per availability. Results showed vegetation indices derived from hand-held spectroradiometer measurements as early as V6-V8 were linearly related to yield and tissue N. ATLAS imagery showed promise at the AP site during the V6 stage (r2 = 0.66), but no significant relationships between plant N and IKONOS imagery were observed. Residue plots (15m x 15m) were established at the Appalachian Plateau and Coastal Plain in 2000 and 200. Residue treatments consisted of hand applied wheat straw cover (0, 10 20, 50, or 80%) arranged in a completely randomized design. Spectroradiometer data were acquired monthly and ATLAS and IKONOS were acquired per availability. Residue cover estimates were best with ATLAS

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

    EPA Science Inventory

    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...

  17. Uncertainty Quantification in Ocean State Estimation using Hessian Information

    NASA Astrophysics Data System (ADS)

    Kalmikov, A.; Heimbach, P.

    2012-12-01

    We present a second derivative-based (Hessian) method for Uncertainty Quantification (UQ) in large-scale Ocean State Estimation. Matrix-free Hessian-times-vector code of the MIT General Circulation Model (MITgcm) is generated by means of algorithmic differentiation (AD). Lanczos-type numerical algebra tools are then applied for extracting leading rank eigenvectors and eigenvalues used in the UQ algorithm. Computational complexity is reduced by tangent linear (forward-mode) differentiation of the adjoint code, which preserves the efficiency of the checkpointing schemes. The inverse and forward uncertainty propagation algorithm is designed for assimilating observation and control variable uncertainties, and for projecting these uncertainties onto oceanographically relevant target quantities of interest. The algorithm evaluates both reduction of a priori-assumed uncertainty as well as prior-independent information gain. The inverse propagation maps prior and data uncertainties onto posterior uncertainties in each component of the high-dimensional control space. The forward propagation of the posteriors provides a measure of uncertainties of the target quantity. The time-resolving analysis of uncertainty propagation in the ocean model reveals transient and steady state uncertainty regimes. The system is applied to quantifying uncertainties in Drake Passage transport in a global barotropic configuration of the MITgcm. The model is constrained by synthetic observations of sea surface height and velocities. The control space consists of two-dimensional maps of initial conditions (velocities and sea surface height), surface boundary conditions (wind stress), and model parameters (bottom drag), amounting to a 10^5-dimensional space of uncertain variables. It is demonstrated how the choice of observations and their geographic coverage determines the reduction in uncertainties of the estimated transport. The system also yields information on how well control parameters are

  18. [Sweet syndrome revealing leukemia].

    PubMed

    Elleuch, E; Hammami, B; Smaoui, F; Maaloul, I; Turki, H; Elloumi, M; Ben Jemaa, M

    2011-09-01

    Sweet syndrome is a neutrophilic dermatosis that can lead to various inflammatory and neoplastic pathologies. We report a case of Sweet syndrome revealing acute leukemia at a 13-year-old girl, who had no history of illness. The diagnosis was made in spite of atypical skin lesions and was confirmed by the skin biopsy and the bone marrow examination. In spite of corticosteroid therapy and chemotherapy, the patient died. Sweet syndrome's diagnosis requires an exhaustive etiologic survey. If there is no evidence of underlying disease, patients must be regularly monitored.

  19. Quantification of tocopherols and tocotrienols in soybean oil by supercritical-fluid chromatography coupled to high-resolution mass spectrometry.

    PubMed

    Méjean, Marie; Brunelle, Alain; Touboul, David

    2015-07-01

    For the most effective analytical strategies, development and validation include optimization of such analytical variables as resolution, detectability, sensitivity, simplicity, cost effectiveness, flexibility, and speed. However, other aspects concerning operator safety and environmental impact are not considered at the same level. The result has been many unintended negative effects of analytical methods developed to investigate different kinds of sample, especially hydrophobic compounds that generate a large amount of chemical waste and have a strong negative environmental impact. In this context, quantification of tocopherols and tocotrienols, i.e. the vitamin E family, is usually achieved by normal-phase liquid chromatography using large volumes of toxic organic solvents, or reversed-phase liquid chromatography using a high percentage of methanol for elution. We propose here a "greener" analytical strategy, including the hyphenation of supercritical-fluid chromatography, using CO2 and ethanol as mobile phase, NH2 as stationary phase, and mass spectrometry for the detection and quantification of vitamin E congeners in soybean oil. An atmospheric-pressure photoionization (APPI) source seemed significantly more sensitive and robust than electrospray or atmospheric-pressure chemical ionization (APCI). This method led to shortened analysis time (less than 5 min) and was revealed to be as sensitive as more traditional approaches, with limits of detection and quantification in the tens of μg L(-1).

  20. Rapid Quantification and Validation of Lipid Concentrations within Liposomes.

    PubMed

    Roces, Carla B; Kastner, Elisabeth; Stone, Peter; Lowry, Deborah; Perrie, Yvonne

    2016-01-01

    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. PMID:27649231

  1. Detection and Quantification of Magnetically Labeled Cells by Cellular MRI

    PubMed Central

    Liu, Wei; Frank, Joseph A.

    2008-01-01

    Labeling cells with superparamagnetic iron oxide (SPIO) nanoparticles, paramagnetic contrast agent (gadolinium) or perfluorocarbons allows for the possibility of tracking single or clusters of labeled cells within target tissues following either direct implantation or intravenous injection. This review summarizes the practical issues regarding detection and quantification of magnetically labeled cells with various MRI contrast agents with a focus on SPIO nanoparticles. PMID:18995978

  2. Colorimetric Quantification and in Situ Detection of Collagen

    ERIC Educational Resources Information Center

    Esteban, Francisco J.; del Moral, Maria L.; Sanchez-Lopez, Ana M.; Blanco, Santos; Jimenez, Ana; Hernandez, Raquel; Pedrosa, Juan A.; Peinado, Maria A.

    2005-01-01

    A simple multidisciplinary and inexpensive laboratory exercise is proposed, in which the undergraduate student may correlate biochemical and anatomical findings. The entire practical session can be completed in one 2.5-3 hour laboratory period, and consists of the quantification of collagen and total protein content from tissue sections--without…

  3. Literacy and Language Education: The Quantification of Learning

    ERIC Educational Resources Information Center

    Gibb, Tara

    2015-01-01

    This chapter describes international policy contexts of adult literacy and language assessment and the shift toward standardization through measurement tools. It considers the implications the quantification of learning outcomes has for pedagogy and practice and for the social inclusion of transnational migrants.

  4. The Role of Uncertainty Quantification for Reactor Physics

    SciTech Connect

    Salvatores, Massimo; Palmiotti, Giuseppe; Aliberti, G.

    2015-01-01

    The quantification of uncertainties is a crucial step in design. The comparison of a-priori uncertainties with the target accuracies, allows to define needs and priorities for uncertainty reduction. In view of their impact, the uncertainty analysis requires a reliability assessment of the uncertainty data used. The choice of the appropriate approach and the consistency of different approaches are discussed.

  5. The Role of Uncertainty Quantification for Reactor Physics

    SciTech Connect

    Salvatores, M.; Aliberti, G.; Palmiotti, G.

    2015-01-15

    The quantification of uncertainties is a crucial step in design. The comparison of a-priori uncertainties with the target accuracies, allows to define needs and priorities for uncertainty reduction. In view of their impact, the uncertainty analysis requires a reliability assessment of the uncertainty data used. The choice of the appropriate approach and the consistency of different approaches are discussed.

  6. 15 CFR 990.52 - Injury assessment-quantification.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... incident. (c) Natural recovery. To quantify injury, trustees must estimate, quantitatively or qualitatively, the time for natural recovery without restoration, but including any response actions. The analysis of...—quantification. (a) General. In addition to determining whether injuries have resulted from the...

  7. 15 CFR 990.52 - Injury assessment-quantification.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... incident. (c) Natural recovery. To quantify injury, trustees must estimate, quantitatively or qualitatively, the time for natural recovery without restoration, but including any response actions. The analysis of...—quantification. (a) General. In addition to determining whether injuries have resulted from the...

  8. 15 CFR 990.52 - Injury assessment-quantification.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... incident. (c) Natural recovery. To quantify injury, trustees must estimate, quantitatively or qualitatively, the time for natural recovery without restoration, but including any response actions. The analysis of...—quantification. (a) General. In addition to determining whether injuries have resulted from the...

  9. Infectious Viral Quantification of Chikungunya Virus-Virus Plaque Assay.

    PubMed

    Kaur, Parveen; Lee, Regina Ching Hua; Chu, Justin Jang Hann

    2016-01-01

    The plaque assay is an essential method for quantification of infectious virus titer. Cells infected with virus particles are overlaid with a viscous substrate. A suitable incubation period results in the formation of plaques, which can be fixed and stained for visualization. Here, we describe a method for measuring Chikungunya virus (CHIKV) titers via virus plaque assays.

  10. Rapid Quantification and Validation of Lipid Concentrations within Liposomes

    PubMed Central

    Roces, Carla B.; Kastner, Elisabeth; Stone, Peter; Lowry, Deborah; Perrie, Yvonne

    2016-01-01

    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 d-(+)-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. PMID:27649231

  11. Quantification and Single-Spore Detection of Phakopsora pachyrhizi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The microscopic identification and quantification of Phakopsora pachyrhizi spores from environmental samples, spore traps, and laboratory specimens can represent a challenge. Such reports, especially from passive spore traps, commonly describe the number of “rust-like” spores; for other forensic sa...

  12. Identification and Quantification Soil Redoximorphic Features by Digital Image Processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil redoximorphic features (SRFs) have provided scientists and land managers with insight into relative soil moisture for approximately 60 years. The overall objective of this study was to develop a new method of SRF identification and quantification from soil cores using a digital camera and imag...

  13. Evaluation of Digital PCR for Absolute RNA Quantification

    PubMed Central

    Sanders, Rebecca; Mason, Deborah J.; Foy, Carole A.; Huggett, Jim F.

    2013-01-01

    Gene expression measurements detailing mRNA quantities are widely employed in molecular biology and are increasingly important in diagnostic fields. Reverse transcription (RT), necessary for generating complementary DNA, can be both inefficient and imprecise, but remains a quintessential RNA analysis tool using qPCR. This study developed a Transcriptomic Calibration Material and assessed the RT reaction using digital (d)PCR for RNA measurement. While many studies characterise dPCR capabilities for DNA quantification, less work has been performed investigating similar parameters using RT-dPCR for RNA analysis. RT-dPCR measurement using three, one-step RT-qPCR kits was evaluated using single and multiplex formats when measuring endogenous and synthetic RNAs. The best performing kit was compared to UV quantification and sensitivity and technical reproducibility investigated. Our results demonstrate assay and kit dependent RT-dPCR measurements differed significantly compared to UV quantification. Different values were reported by different kits for each target, despite evaluation of identical samples using the same instrument. RT-dPCR did not display the strong inter-assay agreement previously described when analysing DNA. This study demonstrates that, as with DNA measurement, RT-dPCR is capable of accurate quantification of low copy RNA targets, but the results are both kit and target dependent supporting the need for calibration controls. PMID:24073259

  14. Comparison of DNA Quantification Methods for Next Generation Sequencing

    PubMed Central

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

    2016-01-01

    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. PMID:27048884

  15. Quantification of Wheat Grain Arabinoxylans Using a Phloroglucinol Colorimetric Assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Arabinoxylans (AX) play a critical role in end-use quality and nutrition of wheat (Triticum aestivum L.). An efficient, accurate method of AX quantification is desirable as AX plays an important role in processing, end use quality and human health. The objective of this work was to evaluate a stand...

  16. A Quantification Approach to Popular American Theatre: Outline.

    ERIC Educational Resources Information Center

    Woods, Alan

    A previously relatively unexplored area of theater history studies is the quantification of titles, authors, and locations of productions of plays in Canada and the United States. Little is known, for example, about the number of times any one play was staged, especially in the earlier days of American drama. A project which counts productions on…

  17. The Universe Revealed

    NASA Astrophysics Data System (ADS)

    Spence, Pam

    1998-10-01

    The Universe is a bewildering place to the uninitiated. The concepts and theories that govern space seem complex and often contradictory. The Universe Revealed provides the keys to unlocking the wonders of the cosmos. Elegantly written and lavishly illustrated, it begins with the Sun and stretches through our solar system into deepest space. Lucid prose, written by many of the people who have shaped our current thinking on space, and spectacular photographs make the physics of the Universe accessible and provide a solid background for understanding the most recent astronomical discoveries. Covering the most intriguing features of the cosmos, the topics discussed range from the Earth and global warming to cosmic collisions and the size of the Universe. Major sections examine the Solar System, stars, galaxies, cosmology, and the observational techniques used by astronomers, both amateur and professional. The Universe Revealed represents the collaboration of internationally renowned experts in astronomy and cosmology, with contributions from authors including David Malin, F. Duccio Macchetto, Iain Nicholson, Neil Bone, Ian Ridpath, Seth Shostak, Mike Lancaster, Steve Miller, Ken Croswell, Geoff McNamara, and Steven Young. This extraordinary blend of astronomy, astrophysics, and cosmology, will appeal to amateur and armchair astronomers alike.

  18. Systematic toxicological analysis revealing a rare case of captan ingestion.

    PubMed

    Gottzein, Anne K; Musshoff, Frank; Madea, Burkhard

    2013-07-01

    This article presents a case of suicide by intoxication with various pharmaceuticals, particularly anticonvulsants, combined with the fungicide captan. A cause of death could not be ascertained at autopsy. However, systematic toxicological analysis (STA) including a screening via solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS) for (semi) volatile organic compounds revealed results suggesting a possible cause of death. The effects of captan on the human organism, its metabolism, and distribution will be discussed. Macroscopically, the cause of death was unascertained. STA revealed clonazepam, citalopram, and its metabolites, lamotrigine, levetiracetam, lacosamide, clonazepam, captan, and its metabolite tetrahydrophthalimide (THPI). For the first time, it was detected in human viscera. A quantification of THPI was performed to obtain distribution in the organs. The significance of a complete STA must be emphasized. The presence of THPI would have been missed without previous detection of captan. Consequently, this fatality would not have been investigated satisfactorily.

  19. Rapid screening and quantification of sulfonate derivatives in white peony root by UHPLC-MS-MS.

    PubMed

    Yan, Zhixiang; Chen, Chen; Xie, Xiabing; Fu, Bo; Yang, Xinghao

    2012-02-01

    A rapid ultra-high-performance liquid chromatographic-tandem mass spectrometric (UHPLC-MS-MS) method has been developed for rapid screening and quantitative analysis of sulfonate derivatives (SDs) in commercial white peony root. Separation was performed on an Agilent Zorbax Eclipse Plus-C18 column by gradient elution with acetonitrile-0.1% (v/v) formic acid as the mobile phase. In-source fragmentation was used to generate the characteristic fragment ion at m/z 259 and to screen for nine SDs. Detection of these SDs was further performed in multiple reaction monitoring (MRM) mode to improve sensitivity and to quantify the two SDs paeoniflorin sulfonate and benzoylpaeoniflorin sulfonate. The method was validated for specificity, linearity, limits of detection and quantification, precision, accuracy, and matrix effects. Nine commercial white peony root samples were examined by use of this method, which revealed great variety in the paeoniflorin sulfonate and benzoylpaeoniflorin sulfonate content.

  20. Quantification of female and male Plasmodium falciparum gametocytes by reverse transcriptase quantitative PCR.

    PubMed

    Schneider, Petra; Reece, Sarah E; van Schaijk, Ben C L; Bousema, Teun; Lanke, Kjerstin H W; Meaden, Cora S J; Gadalla, Amal; Ranford-Cartwright, Lisa C; Babiker, Hamza A

    2015-01-01

    The transmission of malaria parasites depends on the presence of sexual stages (gametocytes) in the blood, making the ratio and densities of female and male gametocytes important determinants of parasite fitness. This manuscript describes the development of reverse transcriptase quantitative PCR (RT-qPCR) assays to separately quantify mature female and male gametocytes of the human malaria parasite Plasmodium falciparum, and reveals that Pfs25 mRNA is expressed only in female gametocytes. The female (Pfs25) and male (Pfs230p) gametocyte specific RT-qPCR assays have lower detection limits of 0.3 female and 1.8 male gametocytes per microlitre of blood, respectively, making them more sensitive than microscopy. Accurate quantification of the ratio and densities of female and male gametocytes will increase understanding of P. falciparum transmission and improve the evaluation of transmission blocking interventions.

  1. Quantification of the effect of oil layer thickness on entrainment of surface oil.

    PubMed

    Zeinstra-Helfrich, Marieke; Koops, Wierd; Dijkstra, Klaas; Murk, Albertinka J

    2015-07-15

    This study quantifies the effect of oil layer thickness on entrainment and dispersion of oil into seawater, using a plunging jet with a camera system. In contrast to what is generally assumed, we revealed that for the low viscosity "surrogate MC252 oil" we used, entrainment rate is directly proportional to layer thickness. Furthermore, the volume of stably suspended small oil droplets increases with energy input (plunge height) and is mostly proportional to layer thickness. Oil pre-treated with dispersants (dispersant-oil ratio ranges from 1:50 to 1:300) is greatly entrained in such large amounts of small droplets that quantification was impossible with the camera system. Very low interfacial tension causes entrainment by even minor secondary surface disturbances. Our results indicate that the effect of oil layer thickness should be included in oil entrainment and dispersion modelling. PMID:26002094

  2. In vivo assessment of human burn scars through automated quantification of vascularity using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Liew, Yih Miin; McLaughlin, Robert A.; Gong, Peijun; Wood, Fiona M.; Sampson, David D.

    2013-06-01

    In scars arising from burns, objective assessment of vascularity is important in the early identification of pathological scarring, and in the assessment of progression and treatment response. We demonstrate the first clinical assessment and automated quantification of vascularity in cutaneous burn scars of human patients in vivo that uses optical coherence tomography (OCT). Scar microvasculature was delineated in three-dimensional OCT images using speckle decorrelation. The diameter and area density of blood vessels were automatically quantified. A substantial increase was observed in the measured density of vasculature in hypertrophic scar tissues (38%) when compared against normal, unscarred skin (22%). A proliferation of larger vessels (diameter≥100 μm) was revealed in hypertrophic scarring, which was absent from normal scars and normal skin over the investigated physical depth range of 600 μm. This study establishes the feasibility of this methodology as a means of clinical monitoring of scar progression.

  3. Quantification of total pigments in citrus essential oils by thermal wave resonant cavity photopyroelectric spectroscopy.

    PubMed

    López-Muñoz, Gerardo A; Antonio-Pérez, Aurora; Díaz-Reyes, J

    2015-05-01

    A general theory of thermal wave resonant cavity photopyroelectric spectroscopy (TWRC-PPE) was recently proposed by Balderas-López (2012) for the thermo-optical characterisation of substances in a condensed phase. This theory is used to quantify the total carotenoids and chlorophylls in several folded and un-folded citrus essential oils to demonstrate the viability of using this technique as an alternative analytical method for the quantification of total pigments in citrus oils. An analysis of variance (ANOVA) reveals significant differences (p < 0.05) among the means of optical absorption coefficient data for the folding degree and fruit type in citrus oils. The experimental results show that TWRC-PPE spectroscopy can be used to quantify concentrations up to five times higher of total carotenoids and chlorophylls in citrus oils than UV-Vis spectroscopy without sample preparation or dilution. The optical limits of this technique and possible interference are also described.

  4. Quantification of major allergen parvalbumin in 22 species of fish by SDS-PAGE.

    PubMed

    Kobayashi, Yukihiro; Yang, Tao; Yu, Cheng-Tao; Ume, Chiaki; Kubota, Hiroyuki; Shimakura, Kuniyoshi; Shiomi, Kazuo; Hamada-Sato, Naoko

    2016-03-01

    Fish is an important causative material of food allergy. Although the allergenicity of fish is considered to correlate with the content of parvalbumin, the major fish allergen, available information about the parvalbumin content in fish is limited. In this study, a simple and reliable quantification method for fish parvalbumin by SDS-PAGE was first established. Application of the SDS-PAGE method to 22 species of fish revealed a marked variation in parvalbumin content among fish. Furthermore, the parvalbumin content was found to be higher in dorsal white muscle than in ventral white muscle, in rostral part of white muscle than in caudal part of white muscle and in white muscle than in dark muscle. IgE reactivity of fish was roughly proportional to parvalbumin content. Interestingly, large-sized migratory fish, such as salmon, swordfish and tuna, were commonly very low in both parvalbumin content and IgE reactivity. PMID:26471564

  5. Identification and quantification of stress concentrations in ferroelectrics using Kikuchi pattern indexing

    NASA Astrophysics Data System (ADS)

    MacLaren, I.; Schmitt, L. A.; Fuess, H.; Kungl, H.; Hoffmann, M. J.

    2006-02-01

    Transmission electron microscopy has been used to investigate the junction between two lamellar bands in a tetragonal lead zirconate titanate (PZT) ceramic. It is found that significant bending occurs in the area due to the matching of different domains on <101> planes. Analysis of CBED patterns shows that the orientation relationships between the long boundaries between lamellae is much as expected and allows quantification of local c/a ratios. The short boundaries at the band junction, however, are highly stressed and deviate significantly from ideal misorientation values. This reveals that the areas between the 4- domain junctions in the band junction are highly stressed with peak stresses in the GPa range, which are highly likely to function as the source of microcracks under the additional strains found in device application.

  6. Simple quantification of surface carboxylic acids on chemically oxidized multi-walled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Gong, Hyejin; Kim, Seong-Taek; Lee, Jong Doo; Yim, Sanggyu

    2013-02-01

    The surface of multi-walled carbon nanotube (MWCNT) was chemically oxidized using nitric acid and sulfuric-nitric acid mixtures. Thermogravimetric analysis, transmission electron microscopy and infrared spectroscopy revealed that the use of acid mixtures led to higher degree of oxidation. More quantitative identification of surface carboxylic acids was carried out using X-ray photoelectron spectroscopy (XPS) and acid-base titration. However, these techniques are costly and require very long analysis times to promptly respond to the extent of the reaction. We propose a much simpler method using pH measurements and pre-determined pKa value in order to estimate the concentration of carboxylic acids on the oxidized MWCNT surfaces. The results from this technique were consistent with those obtained from XPS and titration, and it is expected that this simple quantification method can provide a cheap and fast way to monitor and control the oxidation reaction of MWCNT.

  7. Validated LC-MS/MS Method for the Quantification of Ponatinib in Plasma: Application to Metabolic Stability

    PubMed Central

    Kadi, Adnan A.; Darwish, Hany W.; Attwa, Mohamed W.; Amer, Sawsan M.

    2016-01-01

    In the current work, a rapid, specific, sensitive and validated liquid chromatography tandem mass-spectrometric method was developed for the quantification of ponatinib (PNT) in human plasma and rat liver microsomes (RLMs) with its application to metabolic stability. Chromatographic separation of PNT and vandetanib (IS) were accomplished on Agilent eclipse plus C18 analytical column (50 mm × 2.1 mm, 1.8 μm particle size) maintained at 21±2°C. Flow rate was 0.25 mLmin-1 with run time of 4 min. Mobile phase consisted of solvent A (10 mM ammonium formate, pH adjusted to 4.1 with formic acid) and solvent B (acetonitrile). Ions were generated by electrospray (ESI) and multiple reaction monitoring (MRM) was used as basis for quantification. The results revealed a linear calibration curve in the range of 5–400 ngmL-1 (r2 ≥ 0.9998) with lower limit of quantification (LOQ) and lower limit of detection (LOD) of 4.66 and 1.53 ngmL-1 in plasma, 4.19 and 1.38 ngmL-1 in RLMs. The intra- and inter-day precision and accuracy in plasma ranged from1.06 to 2.54% and -1.48 to -0.17, respectively. Whereas in RLMs ranged from 0.97 to 2.31% and -1.65 to -0.3%. The developed procedure was applied for quantification of PNT in human plasma and RLMs for study metabolic stability of PNT. PNT disappeared rapidly in the 1st 10 minutes of RLM incubation and the disappearance plateaued out for the rest of the incubation. In vitro half-life (t1/2) was 6.26 min and intrinsic clearance (CLin) was 15.182± 0.477. PMID:27764191

  8. Gusev's Rim Revealed

    NASA Technical Reports Server (NTRS)

    2004-01-01

    NASA's Mars Exploration Rover Spirit took this panoramic camera image on sol 91 (April 5, 2004). Spirit is looking to the southeast, and through the martian haze has captured the rim of Gusev Crater approximately 80 kilometers (49.7 miles) away on the horizon.

    The right side of this image reveals the portion of the crater edge that descends into the mouth of Ma'adim Vallis, a channel that opens into Gusev Crater. Spirit is currently traveling toward the informally named 'Columbia Hills,' which lie to the left of the region pictured here.

    This image is similar to a panoramic camera image taken on sol 68, but Gusev's ridge is more visible here because the atmospheric dust caused by winter dust storms has settled. Scientists expect to get even clearer images than this one in upcoming sols.

    This image has been modified to make the crater rim more visible.

  9. Quantification of processing artifacts in textile composites

    NASA Technical Reports Server (NTRS)

    Pastore, Christopher M.

    1993-01-01

    One of the greatest difficulties in developing detailed models of the mechanical response of textile reinforced composites is an accurate model of the reinforcing elements. In the case of elastic property prediction, the variation of fiber position may not have a critical role in performance. However, when considering highly localized stress events, such as those associated with cracks and holes, the exact position of the reinforcement probably dominates the failure mode. Models were developed for idealized reinforcements which provide an insight into the local behavior. However, even casual observations of micrographical images reveals that the actual material deviates strongly from the idealized models. Some of the deviations and causes are presented for triaxially braided and three dimensionally woven textile composites. The necessary modeling steps to accommodate these variations are presented with some examples. Some of the ramifications of not accounting for these discrepencies are also addressed.

  10. The Climate Revealed

    NASA Astrophysics Data System (ADS)

    Burroughs, William

    1999-10-01

    El Niño, La Niña, global warming--terms that crop up frequently in current media coverage of anomalous weather conditions: a spring thaw in January in New York City...a snowstorm in Bakersfield, California...winterlike temperatures in Miami. Such phenomena as these and reports of devastating droughts, floods, and storms around the world bring home the fact of how deeply climate affects our daily lives--and of our inability to control the consequences of climatic events. Extraordinarily timely, The Climate Revealed explores the human-climate "relationship" in all its fascinating complexity. Packed with 250 beautiful, full-color photographs, the volume travels the globe to provide a detailed portrait of individual climate zones from the polar icecaps to the fiercest deserts. The expert and highly accessible text uncovers the essential elements--earth, air, fire and water--that make up the world's various climates. William Burroughs reveals the dramatic discoveries and techniques of historians and archaeologists in their search to understand climates of the past. In the book's conclusion he considers the future and presents every facet of the current environmental debate. With its detailed coverage of the past, present, and future, this marvelous work is essential reading for all those who want to understand one of the most critical facets of life, climate. William Burroughs is a well known and successful science author who has written four books on the weather including Does the Weather Really Matter? (1997), Weather Cycles: Real or Imaginary (1992), and Watching the World's Weather (1991), all published by Cambridge University Press.

  11. The therapeutic potential of Berberis darwinii stem-bark: quantification of berberine and in vitro evidence for Alzheimer's disease therapy.

    PubMed

    Habtemariam, Solomon

    2011-08-01

    Berberis darwinii is native to South America but has been widely distributed in Europe and other continents following its discovery by Charles Darwin. Herewith, the therapeutic potential of stem-bark of the plant for treating Alzheimer's disease was studied using an in vitro acetylcholinesterase inhibition assay. It was found that the methanolic extract of the stem-bark was a potent inhibitor of the enzyme with an IC50 value of 1.23 +/- 0.05 microg/mL. An HPLC-based berberine quantification study revealed an astonishing 38% yield of the dried methanolic extract.

  12. Revealing cosmic rotation

    NASA Astrophysics Data System (ADS)

    Yadav, Amit P. S.; Shimon, Meir; Keating, Brian G.

    2012-10-01

    Cosmological Birefringence, a rotation of the polarization plane of radiation coming to us from distant astrophysical sources, may reveal parity violation in either the electromagnetic or gravitational sectors of the fundamental interactions in nature. Until only recently this phenomenon could be probed with only radio observations or observations at UV wavelengths. Recently, there is a substantial effort to constrain such nonstandard models using observations of the rotation of the polarization plane of cosmic microwave background (CMB) radiation. This can be done via measurements of the B-modes of the CMB or by measuring its TB and EB correlations which vanish in the standard model. In this paper we show that EB correlations-based estimator is the best for upcoming polarization experiments. The EB-based estimator surpasses other estimators because it has the smallest noise and of all the estimators is least affected by systematics. Current polarimeters are optimized for the detection of B-mode polarization from either primordial gravitational waves or by large-scale structures via gravitational lensing. In the paper we also study the optimization of CMB experiments for the detection of cosmological birefringence, in the presence of instrumental systematics, which by themselves are capable of producing EB correlations, potentially mimicking cosmological birefringence.

  13. Transparency-based microplates for fluorescence quantification.

    PubMed

    Cheong, Brandon Huey-Ping; Diep, Vu; Ng, Tuck Wah; Liew, Oi Wah

    2012-03-01

    Microplates for use in resource-limited laboratories should ideally not require processes that involve substantial large-scale production in order to be viable. We describe and demonstrate here an approach of using a silicone sheet with holes, conveniently cut out precisely using an inexpensive cutting plotter to correspond with regions where liquid is to be dispensed, and attaching it to a transparency to create very thin well arrays. With this, the contact angle hysteresis behavior of liquid could be harnessed to produce taller drop shapes so that the fiber probe used could read in the emitted light more effectively. Experimentation conducted revealed fluorescence measurements that were significantly more sensitive than standard microplates, notwithstanding that smaller volumes of liquid were needed. This was achieved using both the fiber optic and imaging evaluation modes. The two methods investigated, one with a lid placed and one without, showed the latter to produce marginally more sensitive readings as opposed to improved immunity from the environment with the former. These favorable measurement characteristics were found to be achievable with an estimated production cost of AU $0.40 and fabrication times of 3.5 min (96 wells) and 6.5 min (384 wells) per plate. PMID:22266206

  14. Compositional Solution Space Quantification for Probabilistic Software Analysis

    NASA Technical Reports Server (NTRS)

    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.

  15. An uncertainty inventory demonstration - a primary step in uncertainty quantification

    SciTech Connect

    Langenbrunner, James R.; Booker, Jane M; Hemez, Francois M; Salazar, Issac F; Ross, Timothy J

    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.

  16. Good quantification practices of flavours and fragrances by mass spectrometry

    PubMed Central

    Begnaud, Frédéric

    2016-01-01

    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’. PMID:27644977

  17. Quantification of viable helminth eggs in samples of sewage sludge.

    PubMed

    Rocha, Maria Carolina Vieira da; Barés, Monica Eboly; Braga, Maria Cristina Borba

    2016-10-15

    For the application of sewage sludge as fertilizer, it is of fundamental importance the absence of pathogenic organisms, such as viable helminth eggs. Thus, the quantification of these organisms has to be carried out by means of the application of reliable and accurate methodologies. Nevertheless, until the present date, there is no consensus with regard to the adoption of a universal methodology for the detection and quantification of viable helminth eggs. It is therefore necessary to instigate a debate on the different protocols currently in use, as well as to assemble relevant information in order to assist in the development of a more comprehensive and accurate method to quantify viable helminth eggs in samples of sewage sludge and its derivatives. PMID:27470467

  18. Quantification techniques and biodistribution of semiconductor quantum dots.

    PubMed

    Pic, Emilie; Bezdetnaya, Lina; Guillemin, François; Marchal, Frédéric

    2009-03-01

    Quantum dots (QDs) are fluorescent inorganic nanocrystals with advantageous optical properties, which have been applied for biomedical purposes including imaging, diagnostic, drug delivery or therapy. Potential toxicity of QDs remains the major barrier to clinical translation, and as such the precise analysis of in vivo QDs distribution and pharmacokinetics is of major importance. Biodistribution studies in animal models are, however, sparse. The present review provides in a first lieu a summary of different techniques, which are currently used for relative quantification of QDs in vivo or their absolute quantification ex vivo. Fluorescence and radioactivity based techniques along with mass-spectrometry detection at the elementary level are addressed in this review. We further introduce biodistribution studies in animal models and discuss the possibilities to modify quantum dots biodistribution in function of different injection ways.

  19. Frequency feature based quantification of defect depth and thickness

    NASA Astrophysics Data System (ADS)

    Tian, Shulin; Chen, Kai; Bai, Libing; Cheng, Yuhua; Tian, Lulu; Zhang, Hong

    2014-06-01

    This study develops a frequency feature based pulsed eddy current method. A frequency feature, termed frequency to zero, is proposed for subsurface defects and metal loss quantification in metallic specimens. A curve fitting method is also employed to generate extra frequency components and improve the accuracy of the proposed method. Experimental validation is carried out. Conclusions and further work are derived on the basis of the studies.

  20. Frequency feature based quantification of defect depth and thickness.

    PubMed

    Tian, Shulin; Chen, Kai; Bai, Libing; Cheng, Yuhua; Tian, Lulu; Zhang, Hong

    2014-06-01

    This study develops a frequency feature based pulsed eddy current method. A frequency feature, termed frequency to zero, is proposed for subsurface defects and metal loss quantification in metallic specimens. A curve fitting method is also employed to generate extra frequency components and improve the accuracy of the proposed method. Experimental validation is carried out. Conclusions and further work are derived on the basis of the studies.

  1. Visualization and Quantification of Rotor Tip Vortices in Helicopter Flows

    NASA Technical Reports Server (NTRS)

    Kao, David L.; Ahmad, Jasim U.; Holst, Terry L.

    2015-01-01

    This paper presents an automated approach for effective extraction, visualization, and quantification of vortex core radii from the Navier-Stokes simulations of a UH-60A rotor in forward flight. We adopt a scaled Q-criterion to determine vortex regions and then perform vortex core profiling in these regions to calculate vortex core radii. This method provides an efficient way of visualizing and quantifying the blade tip vortices. Moreover, the vortices radii are displayed graphically in a plane.

  2. Quantification of the Electrophilicity of Benzyne and Related Intermediates.

    PubMed

    Fine Nathel, Noah F; Morrill, Lucas A; Mayr, Herbert; Garg, Neil K

    2016-08-24

    The determination of reactivity parameters for short-lived intermediates provides an indispensable tool for synthetic design. Despite that electrophilicity parameters have now been established for more than 250 reactive species, the corresponding parameters for benzyne and related intermediates have not been uncovered. We report a study that has allowed for the quantification of benzyne's electrophilicity parameter. Our approach relies on the strategic use of the diffusion-clock method and also provides electrophilicity parameters E for other substituted arynes.

  3. The Challenges of Credible Thermal Protection System Reliability Quantification

    NASA Technical Reports Server (NTRS)

    Green, Lawrence L.

    2013-01-01

    The paper discusses several of the challenges associated with developing a credible reliability estimate for a human-rated crew capsule thermal protection system. The process of developing such a credible estimate is subject to the quantification, modeling and propagation of numerous uncertainties within a probabilistic analysis. The development of specific investment recommendations, to improve the reliability prediction, among various potential testing and programmatic options is then accomplished through Bayesian analysis.

  4. Universal Quantification in a Constraint-Based Planner

    NASA Technical Reports Server (NTRS)

    Golden, Keith; Frank, Jeremy; Clancy, Daniel (Technical Monitor)

    2002-01-01

    Constraints and universal quantification are both useful in planning, but handling universally quantified constraints presents some novel challenges. We present a general approach to proving the validity of universally quantified constraints. The approach essentially consists of checking that the constraint is not violated for all members of the universe. We show that this approach can sometimes be applied even when variable domains are infinite, and we present some useful special cases where this can be done efficiently.

  5. Quantification Of Margins And Uncertainties: A Bayesian Approach (full Paper)

    SciTech Connect

    Wallstrom, Timothy C

    2008-01-01

    Quantification of Margins and Uncertainties (QMU) is 'a formalism for dealing with the reliability of complex technical systems, and the confidence which can be placed in estimates of that reliability.' (Eardleyet al, 2005). In this paper, we show how QMU may be interpreted in the framework of Bayesian statistical inference, using a probabilistic network. The Bayesian approach clarifies the probabilistic underpinnings of the formalism, and shows how the formalism can be used for deciSion-making.

  6. Diagnostic utility of droplet digital PCR for HIV reservoir quantification.

    PubMed

    Trypsteen, Wim; Kiselinova, Maja; Vandekerckhove, Linos; De Spiegelaere, Ward

    2016-01-01

    Quantitative real-time PCR (qPCR) is implemented in many molecular laboratories worldwide for the quantification of viral nucleic acids. However, over the last two decades, there has been renewed interest in the concept of digital PCR (dPCR) as this platform offers direct quantification without the need for standard curves, a simplified workflow and the possibility to extend the current detection limit. These benefits are of great interest in terms of the quantification of low viral levels in HIV reservoir research because changes in the dynamics of residual HIV reservoirs will be important to monitor HIV cure efforts. Here, we have implemented a systematic literature screening and text mining approach to map the use of droplet dPCR (ddPCR) in the context of HIV quantification. In addition, several technical aspects of ddPCR were compared with qPCR: accuracy, sensitivity, precision and reproducibility, to determine its diagnostic utility. We have observed that ddPCR was used in different body compartments in multiple HIV-1 and HIV-2 assays, with the majority of reported assays focusing on HIV-1 DNA-based applications (i.e. total HIV DNA). Furthermore, ddPCR showed a higher accuracy, precision and reproducibility, but similar sensitivity when compared to qPCR due to reported false positive droplets in the negative template controls with a need for standardised data analysis (i.e. threshold determination). In the context of a low level of detection and HIV reservoir diagnostics, ddPCR can offer a valid alternative to qPCR-based assays but before this platform can be clinically accredited, some remaining issues need to be resolved. PMID:27482456

  7. Neutron-Encoded Protein Quantification by Peptide Carbamylation

    NASA Astrophysics Data System (ADS)

    Ulbrich, Arne; Merrill, Anna E.; Hebert, Alexander S.; Westphall, Michael S.; Keller, Mark P.; Attie, Alan D.; Coon, Joshua J.

    2014-01-01

    We describe a chemical tag for duplex proteome quantification using neutron encoding (NeuCode). The method utilizes the straightforward, efficient, and inexpensive carbamylation reaction. We demonstrate the utility of NeuCode carbamylation by accurately measuring quantitative ratios from tagged yeast lysates mixed in known ratios and by applying this method to quantify differential protein expression in mice fed a either control or high-fat diet.

  8. Comparison of methods for the quantification of the different carbon fractions in atmospheric aerosol samples

    NASA Astrophysics Data System (ADS)

    Nunes, Teresa; Mirante, Fátima; Almeida, Elza; Pio, Casimiro

    2010-05-01

    to evaluate the possibility of continue using, for trend analysis, the historical data set, we performed an inter-comparison between our method and an adaptation of EUSAAR-2 protocol, taking into account that this last protocol will possibly be recommended for analysing carbonaceous aerosols at European sites. In this inter-comparison we tested different types of samples (PM2,5, PM2,5-10, PM10) with large spectra of carbon loadings, with and without pre-treatment acidification. For a reduced number of samples, five replicates of each one were analysed by each method for statistical purposes. The inter-comparison study revealed that when the sample analysis were performed in similar room conditions, the two thermo-optic methods give similar results for TC, OC and EC, without significant differences at a 95% confidence level. The correlation between the methods, DAO and EUSAAR-2 for EC is smaller than for TC and OC, although showing a coefficient correlation over 0,95, with a slope close to one. For samples performed in different periods, room temperatures seem to have a significant effect over OC quantification. The sample pre-treatment with HCl fumigation tends to decrease TC quantification, mainly due to the more volatile organic fraction release during the first heating step. For a set of 20 domestic biomass burning samples analyzed by the DAO method we observed an average decrease in TC quantification of 3,7 % in relation to non-acidified samples, even though this decrease is accompanied by an average increase in the less volatile organic fraction. The indirect measurement of carbon carbonate, usually a minor carbon component in the carbonaceous aerosol, based on the difference between TC measured by TOM of acidified and non-acidified samples is not a robust measurement, considering the biases affecting his quantification. The present study show that the two thermo-optic temperature program used for OC and EC quantification give similar results, and if in the

  9. Quantification of Efficiency of Beneficiation of Lunar Regolith

    NASA Technical Reports Server (NTRS)

    Trigwell, Steve; Lane, John; Captain, James; Weis, Kyle; Quinn, Jacqueline; Watanabe, Fumiya

    2011-01-01

    Electrostatic beneficiation of lunar regolith is being researched at Kennedy Space Center to enhance the ilmenite concentration of the regolith for the production of oxygen in in-situ resource utilization on the lunar surface. Ilmenite enrichment of up to 200% was achieved using lunar simulants. For the most accurate quantification of the regolith particles, standard petrographic methods are typically followed, but in order to optimize the process, many hundreds of samples were generated in this study that made the standard analysis methods time prohibitive. In the current studies, X-ray photoelectron spectroscopy (XPS) and Secondary Electron microscopy/Energy Dispersive Spectroscopy (SEM/EDS) were used that could automatically, and quickly, analyze many separated fractions of lunar simulant. In order to test the accuracy of the quantification, test mixture samples of known quantities of ilmenite (2, 5, 10, and 20 wt%) in silica (pure quartz powder), were analyzed by XPS and EDS. The results showed that quantification for low concentrations of ilmenite in silica could be accurately achieved by both XPS and EDS, knowing the limitations of the techniques. 1

  10. Initial water quantification results using neutron computed tomography

    NASA Astrophysics Data System (ADS)

    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.

  11. Radio-frequency energy quantification in magnetic resonance imaging

    NASA Astrophysics Data System (ADS)

    Alon, Leeor

    Mapping of radio frequency (RF) energy deposition has been challenging for 50+ years, especially, when scanning patients in the magnetic resonance imaging (MRI) environment. As result, electromagnetic simulation software is often used for estimating the specific absorption rate (SAR), the rate of RF energy deposition in tissue. The thesis work presents challenges associated with aligning information provided by electromagnetic simulation and MRI experiments. As result of the limitations of simulations, experimental methods for the quantification of SAR were established. A system for quantification of the total RF energy deposition was developed for parallel transmit MRI (a system that uses multiple antennas to excite and image the body). The system is capable of monitoring and predicting channel-by-channel RF energy deposition, whole body SAR and capable of tracking potential hardware failures that occur in the transmit chain and may cause the deposition of excessive energy into patients. Similarly, we demonstrated that local RF power deposition can be mapped and predicted for parallel transmit systems based on a series of MRI temperature mapping acquisitions. Resulting from the work, we developed tools for optimal reconstruction temperature maps from MRI acquisitions. The tools developed for temperature mapping paved the way for utilizing MRI as a diagnostic tool for evaluation of RF/microwave emitting device safety. Quantification of the RF energy was demonstrated for both MRI compatible and non-MRI-compatible devices (such as cell phones), while having the advantage of being noninvasive, of providing millimeter resolution and high accuracy.

  12. Zonated quantification of steatosis in an entire mouse liver.

    PubMed

    Schwen, Lars Ole; Homeyer, André; Schwier, Michael; Dahmen, Uta; Dirsch, Olaf; Schenk, Arne; Kuepfer, Lars; Preusser, Tobias; Schenk, Andrea

    2016-06-01

    Many physiological processes and pathological conditions in livers are spatially heterogeneous, forming patterns at the lobular length scale or varying across the organ. Steatosis, a common liver disease characterized by lipids accumulating in hepatocytes, exhibits heterogeneity at both these spatial scales. The main goal of the present study was to provide a method for zonated quantification of the steatosis patterns found in an entire mouse liver. As an example application, the results were employed in a pharmacokinetics simulation. For the analysis, an automatic detection of the lipid vacuoles was used in multiple slides of histological serial sections covering an entire mouse liver. Lobuli were determined semi-automatically and zones were defined within the lobuli. Subsequently, the lipid content of each zone was computed. The steatosis patterns were found to be predominantly periportal, with a notable organ-scale heterogeneity. The analysis provides a quantitative description of the extent of steatosis in unprecedented detail. The resulting steatosis patterns were successfully used as a perturbation to the liver as part of an exemplary whole-body pharmacokinetics simulation for the antitussive drug dextromethorphan. The zonated quantification is also applicable to other pathological conditions that can be detected in histological images. Besides being a descriptive research tool, this quantification could perspectively complement diagnosis based on visual assessment of histological images. PMID:27104496

  13. Gas plume quantification in downlooking hyperspectral longwave infrared images

    NASA Astrophysics Data System (ADS)

    Turcotte, Caroline S.; Davenport, Michael R.

    2010-10-01

    Algorithms have been developed to support quantitative analysis of a gas plume using down-looking airborne hyperspectral long-wave infrared (LWIR) imagery. The resulting gas quantification "GQ" tool estimates the quantity of one or more gases at each pixel, and estimates uncertainty based on factors such as atmospheric transmittance, background clutter, and plume temperature contrast. GQ uses gas-insensitive segmentation algorithms to classify the background very precisely so that it can infer gas quantities from the differences between plume-bearing pixels and similar non-plume pixels. It also includes MODTRAN-based algorithms to iteratively assess various profiles of air temperature, water vapour, and ozone, and select the one that implies smooth emissivity curves for the (unknown) materials on the ground. GQ then uses a generalized least-squares (GLS) algorithm to simultaneously estimate the most likely mixture of background (terrain) material and foreground plume gases. Cross-linking of plume temperature to the estimated gas quantity is very non-linear, so the GLS solution was iteratively assessed over a range of plume temperatures to find the best fit to the observed spectrum. Quantification errors due to local variations in the camera-topixel distance were suppressed using a subspace projection operator. Lacking detailed depth-maps for real plumes, the GQ algorithm was tested on synthetic scenes generated by the Digital Imaging and Remote Sensing Image Generation (DIRSIG) software. Initial results showed pixel-by-pixel gas quantification errors of less than 15% for a Freon 134a plume.

  14. Automatic quantification of neo-vasculature from micro-CT

    NASA Astrophysics Data System (ADS)

    Mallya, Yogish; Narayanan, A. K.; Zagorchev, Lyubomir

    2009-02-01

    Angiogenesis is the process of formation of new blood vessels as outgrowths of pre-existing ones. It occurs naturally during development, tissue repair, and abnormally in pathologic diseases such as cancer. It is associated with proliferation of blood vessels/tubular sprouts that penetrate deep into tissues to supply nutrients and remove waste products. The process starts with migration of endothelial cells. As the cells move towards the target area they form small tubular sprouts recruited from the parent vessel. The sprouts grow in length due to migration, proliferation, and recruitment of new endothelial cells and the process continues until the target area becomes fully vascular. Accurate quantification of sprout formation is very important for evaluation of treatments for ischemia as well as angiogenesis inhibitors and plays a key role in the battle against cancer. This paper presents a technique for automatic quantification of newly formed blood vessels from Micro-CT volumes of tumor samples. A semiautomatic technique based on interpolation of Bezier curves was used to segment out the cancerous growths. Small vessels as determined by their diameter within the segmented tumors were enhanced and quantified with a multi-scale 3-D line detection filter. The same technique can be easily extended for quantification of tubular structures in other 3-D medical imaging modalities. Experimental results are presented and discussed.

  15. Label-Free Identification and Quantification of SUMO Target Proteins.

    PubMed

    Hendriks, Ivo A; Vertegaal, Alfred C O

    2016-01-01

    Mass spectrometry-based approaches are utilized with increasing frequency to facilitate identification of novel SUMO target proteins and to elucidate the dynamics of SUMOylation in response to cellular stresses. Here, we describe a robust method for the identification of SUMO target proteins, and the relative quantification of SUMOylation dynamics, using a label-free approach. The method relies on a decahistidine (His10)-tagged SUMO, which is expressed at a low level in a mammalian cell line or model organism. The His10-tag allows for a single-step, high-yield, and high-purity enrichment of SUMOylated proteins, which are then digested and analyzed by high-resolution mass spectrometry. Matching between runs and label-free quantification integrated in the freely available MaxQuant software allow for a high rate and accuracy of quantification, providing a strong alternative to laborious sample or cell labeling techniques. The method described here allows for identification of >1000 SUMO target proteins, and characterization of their SUMOylation dynamics, without requiring sample fractionation. The purification procedure, starting from total lysate, can be performed in ~4 days. PMID:27631806

  16. Assessment methods for angiogenesis and current approaches for its quantification

    PubMed Central

    AlMalki, Waleed Hassan; Shahid, Imran; Mehdi, Abeer Yousaf; Hafeez, Muhammad Hassan

    2014-01-01

    Angiogenesis is a physiological process which describes the development of new blood vessels from the existing vessels. It is a common and the most important process in the formation and development of blood vessels, so it is supportive in the healing of wounds and granulation of tissues. The different assays for the evaluation of angiogenesis have been described with distinct advantages and some limitations. In order to develop angiogenic and antiangiogenic techniques, continuous efforts have been resulted to give animal models for more quantitative analysis of angiogenesis. Most of the studies on angiogenic inducers and inhibitors rely on various models, both in vitro, in vivo and in ova, as indicators of efficacy. The angiogenesis assays are very much helpful to test efficacy of both pro- and anti- angiogenic agents. The development of non-invasive procedures for quantification of angiogenesis will facilitate this process significantly. The main objective of this review article is to focus on the novel and existing methods of angiogenesis and their quantification techniques. These findings will be helpful to establish the most convenient methods for the detection, quantification of angiogenesis and to develop a novel, well tolerated and cost effective anti-angiogenic treatment in the near future. PMID:24987169

  17. Quantification of splice variants using molecular beacon or scorpion primers.

    PubMed

    Taveau, Mathieu; Stockholm, Daniel; Spencer, Melissa; Richard, Isabelle

    2002-06-15

    Uncovering the relationship between the generation of alternative transcripts and cellular processes is of crucial importance in the exploration of a gene's biology. The description and quantification of the spatiotemporal splicing pattern can be one method to select the most interesting transcripts for future studies. Fluorescence-based real-time quantitative RT-PCR has recently revolutionized the possibilities for transcriptional quantification studies. In this report, Molecular Beacon and Scorpion probes have been tested as new possibilities for determining the expression level of alternative transcripts. We validated these systems by analyzing alternative splicing of exons 6, 15, and 16 of the calpain 3 gene with tissues containing large variation in the ratio of the different transcripts. We determined conditions that demonstrated that boundary probes are useful tools and good alternatives to boundary primers, when developing a system to quantify specific transcripts. We suggest that the choice of a quantification system should depend in part on the structure and base composition of the gene and may have to be determined experimentally.

  18. Photoacoustic sensor system for the quantification of soot aerosols (abstract)

    NASA Astrophysics Data System (ADS)

    Haisch, C.; Beck, H.; Niessner, R.

    2003-01-01

    The influence of soot particles on human health as well as global and local climate is well established by now. Hence, the need for fast and sensitive soot detection in urban and remote areas is obvious. The state of the art thermochemical detection methods for soot analysis is based on filter sampling and subsequent wet chemical analysis and combustion, which requires laborious and time consuming sample preparation. Due to the integration on a filter, a time-resolved analysis is not possible. The presented photoacoustic sensor system is optimized for a highly sensitive and fast on-line and in situ quantification of soot. Soot particles, as classical "black absorbers," absorb electromagnetic radiation over the whole spectrum. Two similar systems are introduced. The first system is designed for the development and testing of combustion engines, mainly the next generation of diesel engines. In the next decade, legal thresholds for extremely low particle emissions are foreseen. Their implementation will be only possible if a time-resolved soot detection with sufficient sensitivity can be realized as the highest particle emissions from diesel engines are generated only for seconds during load changes. During a load change, the emitted soot concentrations can rise several orders of magnitude for only a period of few seconds. The system combines a time resolution of 1 s (sampling rate 1 Hz) with an aerosol mass sensitivity better than 10 μg m-3. Up to a maximum dimension of about 800 nm the signal is independent of the particle size. The systems consist of two photoacoustic cells, which are operated in a differential mode to avoid cross sensitivities. The cells are built as acoustical resonators to increase sensitivity. A diode laser with a wavelength of 810 nm and an output power of 1.1 W is employed for excitation. Its collimated beam passes first through the reference cell and then through the measurement cell. To avoid condensation of water, the cells are heated to

  19. Validation of tumor protein marker quantification by two independent automated immunofluorescence image analysis platforms.

    PubMed

    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

    2016-10-01

    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

  20. Validation of tumor protein marker quantification by two independent automated immunofluorescence image analysis platforms

    PubMed Central

    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

  1. Uniform Doping in Quantum-Dots-Based Dilute Magnetic Semiconductor.

    PubMed

    Saha, Avijit; Shetty, Amitha; Pavan, A R; Chattopadhyay, Soma; Shibata, Tomohiro; Viswanatha, Ranjani

    2016-07-01

    Effective manipulation of magnetic spin within a semiconductor leading to a search for ferromagnets with semiconducting properties has evolved into an important field of dilute magnetic semiconductors (DMS). Although a lot of research is focused on understanding the still controversial origin of magnetism, efforts are also underway to develop new materials with higher magnetic temperatures for spintronics applications. However, so far, efforts toward quantum-dots(QDs)-based DMS materials are plagued with problems of phase separation, leading to nonuniform distribution of dopant ions. In this work, we have developed a strategy to synthesize highly crystalline, single-domain DMS system starting from a small magnetic core and allowing it to diffuse uniformly inside a thick CdS semiconductor matrix and achieve DMS QDs. X-ray absorption fine structure (XAFS) spectroscopy and energy-dispersive X-ray spectroscopy-scanning transmission electron microscopy (STEM-EDX) indicates the homogeneous distribution of magnetic impurities inside the semiconductor QDs leading to superior magnetic property. Further, the versatility of this technique was demonstrated by obtaining ultra large particles (∼60 nm) with uniform doping concentration as well as demonstrating the high quality magnetic response. PMID:27295453

  2. Carbon dot based nanopowders and their application for fingerprint recovery.

    PubMed

    Fernandes, D; Krysmann, M J; Kelarakis, A

    2015-03-21

    The incorporation of a minor amount of carbogenic nanoparticles into powder compositions imparts remarkable colour-tuneability, without compromising the flowability. In a proof-of-concept demonstration we report the use of these hybrid nanopowders for the visual enhancement of latent fingerprints where they effectively resolve issues arising from poor contrast against multi-coloured or patterned backgrounds.

  3. InN Quantum Dot Based Infra-Red Photodetectors.

    PubMed

    Shetty, Arjun; Kumar, Mahesh; Roull, Basanta; Vinoy, K J; Krupanidhj, S B

    2016-01-01

    Self-assembled InN quantum dots (QDs) were grown on Si(111) substrate using plasma assisted molecular beam epitaxy (PA-MBE). Single-crystalline wurtzite structure of InN QDs was confirmed by X-ray diffraction. The dot densities were varied by varying the indium flux. Variation of dot density was confirmed by FESEM images. Interdigitated electrodes were fabricated using standard lithog- raphy steps to form metal-semiconductor-metal (MSM) photodetector devices. The devices show strong infrared response. It was found that the samples with higher density of InN QDs showed lower dark current and higher photo current. An explanation was provided for the observations and the experimental results were validated using Silvaco Atlas device simulator. PMID:27398511

  4. Synthesis and application of quantum dots-based biosensor

    NASA Astrophysics Data System (ADS)

    Hai Nguyen, Ngoc; Giang Duong, Thi; Hoang, Van Nong; Thang Pham, Nam; Cao Dao, Tran; Nga Pham, Thu

    2015-03-01

    Trichlorfon (TF) is one of the organophosphorus pesticides used widely in agriculture. The content of this paper includes the exploitation of dominant optical properties of the quantum dots consisting of a core and multilayer shell CdSe/ZnSe/ZnS (QD). A biosensor was fabricated on the basis of this QD for rapidly detecting the residues of trichlofon pesticide with concentrations of 0.01 ppm to 5 ppm. The measurements were carried out to examine the morphology of the QD structure and fluorescent properties such as transmission electron microscopy, x-ray diffraction, absorption spectroscopy and fluorescence spectroscopy. The linking mechanism among biological agents and the specificity of the acetylcholinesterase enzymes in hydrolysis reaction of acetylthiolcholine was applied to create the changes in surroundings, affecting the fluorescence of the QD. In particular, the mechanism of bioluminescence resonance energy transfer (BRET) is discussed to clearly explain the recombination of electrons and holes in the QD.

  5. Quantum Dot-Based Nanoprobes for In Vivo Targeted Imaging

    PubMed Central

    Zhu, Yian; Hong, Hao; Xu, Zhi Ping; Li, Zhen; Cai, Weibo

    2013-01-01

    Fluorescent semiconductor quantum dots (QDs) have attracted tremendous attention over the last decade. The superior optical properties of QDs over conventional organic dyes make them attractive labels for a wide variety of biomedical applications, whereas their potential toxicity and instability in biological environment has puzzled scientific researchers. Much research effort has been devoted to surface modification and functionalization of QDs to make them versatile probes for biomedical applications, and significant progress has been made over the last several years. This review article aims to describe the current state-of-the-art of the synthesis, modification, bioconjugation, and applications of QDs for in vivo targeted imaging. In addition, QD-based multifunctional nanoprobes are also summarized. PMID:24206136

  6. Quantum Dots Based Rad-Hard Computing and Sensors

    NASA Technical Reports Server (NTRS)

    Fijany, A.; Klimeck, G.; Leon, R.; Qiu, Y.; Toomarian, N.

    2001-01-01

    Quantum Dots (QDs) are solid-state structures made of semiconductors or metals that confine a small number of electrons into a small space. The confinement of electrons is achieved by the placement of some insulating material(s) around a central, well-conducting region. Thus, they can be viewed as artificial atoms. They therefore represent the ultimate limit of the semiconductor device scaling. Additional information is contained in the original extended abstract.

  7. Prospects of quantum-dots-based liquid-crystal displays

    NASA Astrophysics Data System (ADS)

    Luo, Zhenyue; Xu, Su; Chen, Yuan; Liu, Yifan; Wu, Shin-Tson

    2014-02-01

    We report a systematic photometric study of LCD based on quantum dot (QD) backlight, and find the optimal emission spectrum combination in terms of system efficiency and wide color gamut. A QD-based LCD has potential to achieve 120% AdobeRGB color gamut in CIE 1931 and 140% in CIE 1976 color space, while keeping the same energy efficiency as conventional backlights. Moreover, we present a transmissive color display based on voltage-stretchable liquid crystal droplet and quantum dot backlight. This polarizer-free display exhibits highly saturated colors, wide viewing angle and reasonably good contrast ratio. QD backlight allows LCD to display original colors with high fidelity, which makes LCD more competitive to organic LED. The prime time for QD-enhanced LCDs is near.

  8. Probing the kinetics of quantum dot-based proteolytic sensors.

    PubMed

    Díaz, Sebastián A; Malonoski, Anthony P; Susumu, Kimihiro; Hofele, Romina V; Oh, Eunkeu; Medintz, Igor L

    2015-09-01

    As an enzyme superfamily, proteases are rivaled only by kinases in terms of their abundance within the human genome. Two ratiometric quantum dot (QD) Förster resonance energy transfer-based sensors designed to monitor the activity of the proteolytic enzymes collagenase and elastase are investigated here. Given the unique material constraints of these sensing constructs, assays are realized utilizing excess enzyme and fixed substrate in progress curve format to yield enzyme specificity or k cat/K m ratios. The range of k cat/Km values derived is 0.5-1.1 mM(-1) s(-1) for the collagenase sensor and 3.7-4.2 mM(-1) s(-1) for the elastase sensor. Of greater interest is the observation that the elastase sensor can be well represented by the Michaelis-Menten model while the collagenase sensor cannot. The latter demonstrates increased specificity at higher peptide substrate/QD loading values and an apparent QD-caused reversible inhibition as the reaction progresses. Understanding the detailed kinetic mechanisms that underpin these types of sensors will be important especially for their further quantitative utilization.

  9. Quantum-Dots Based Electrochemical Immunoassay of Interleukin-1α

    SciTech Connect

    Wu, Hong; Liu, Guodong; Wang, Jun; Lin, Yuehe

    2007-07-01

    We describe a quantum-dot (QD, CdSe@ZnS)-based electrochemical immunoassay to detect a protein biomarker, interleukin-1α (IL-1α). QD conjugated with anti-IL-1α antibody was used as a label in an immunorecognition event. After a complete sandwich immunoreaction among the primary IL-1α antibody (immobilized on the avidin-modified magnetic beads), IL-1α, and the QD-labeled secondary antibody, QD labels were attached to the magnetic-bead surface through the antibody-antigen immunocomplex. Electrochemical stripping analysis of the captured QDs was used to quantify the concentration of IL-1α after an acid-dissolution step. The streptavidin-modified magnetic beads and the magnetic separation platform were used to integrate a facile antibody immobilization (through a biotin/streptavidin interaction) with immunoreactions and the isolation of immunocomplexes from reaction solutions in the assay. The voltammetric response is highly linear over the range of 0.5 to 50 ng mL-1 IL 1α, and the limit of detection is estimated to be 0.3 ng mL-1 (18 pM). This QD-based electrochemical immunoassay shows great promise for rapid, simple, and cost-effective analysis of protein biomarkers.

  10. Uniform Doping in Quantum-Dots-Based Dilute Magnetic Semiconductor.

    PubMed

    Saha, Avijit; Shetty, Amitha; Pavan, A R; Chattopadhyay, Soma; Shibata, Tomohiro; Viswanatha, Ranjani

    2016-07-01

    Effective manipulation of magnetic spin within a semiconductor leading to a search for ferromagnets with semiconducting properties has evolved into an important field of dilute magnetic semiconductors (DMS). Although a lot of research is focused on understanding the still controversial origin of magnetism, efforts are also underway to develop new materials with higher magnetic temperatures for spintronics applications. However, so far, efforts toward quantum-dots(QDs)-based DMS materials are plagued with problems of phase separation, leading to nonuniform distribution of dopant ions. In this work, we have developed a strategy to synthesize highly crystalline, single-domain DMS system starting from a small magnetic core and allowing it to diffuse uniformly inside a thick CdS semiconductor matrix and achieve DMS QDs. X-ray absorption fine structure (XAFS) spectroscopy and energy-dispersive X-ray spectroscopy-scanning transmission electron microscopy (STEM-EDX) indicates the homogeneous distribution of magnetic impurities inside the semiconductor QDs leading to superior magnetic property. Further, the versatility of this technique was demonstrated by obtaining ultra large particles (∼60 nm) with uniform doping concentration as well as demonstrating the high quality magnetic response.

  11. Comparison of indirect and direct quantification of esters of monochloropropanediol in vegetable oil.

    PubMed

    Dubois, Mathieu; Tarres, Adrienne; Goldmann, Till; Empl, Anna Maria; Donaubauer, Alfred; Seefelder, Walburga

    2012-05-01

    The presence of fatty acid esters of monochloropropanediol (MEs) in food is a recent concern raised due to the carcinogenicity of their hydrolysable moieties 2- and 3-monochloropropanediol (2- and 3-MCPD). Several indirect methods for the quantification of MEs have been developed and are commonly in use until today, however significant discrepancies among analytical results obtained are challenging their reliability. The aim of the present study was therefore to test the trueness of an indirect method by comparing it to a newly developed direct method using palm oil and palm olein as examples. The indirect method was based on ester cleavage under acidic conditions, derivatization of the liberated 2- and 3-MCPD with heptafluorobutyryl imidazole and GC-MS determination. The direct method was comprised of two extraction procedures targeting 2-and 3-MCPD mono esters (co-extracting as well glycidyl esters) by the use of double solid phase extraction (SPE), and 2- and 3-MCPD di-esters by the use of silica gel column, respectively. Detection was carried out by liquid chromatography coupled to time of flight mass spectrometry (LC-ToF-MS). Accurate quantification of the intact compounds was assured by means of matrix matched standard addition on extracts. Analysis of 22 palm oil and 7 palm olein samples (2- plus 3-MCPD contamination ranged from 0.3 to 8.8 μg/g) by both methods revealed no significant bias. Both methods were therefore considered as comparable in terms of results; however the indirect method was shown to require less analytical standards, being less tedious and furthermore applicable to all type of different vegetable oils and hence recommended for routine application.

  12. Reproducibility and observer variability of tissue phase mapping for the quantification of regional myocardial velocities.

    PubMed

    Lin, Kai; Chowdhary, Varun; Benzuly, Keith H; Yancy, Clyde W; Lomasney, Jon W; Rigolin, Vera H; Anderson, Allen S; Wilcox, Jane; Carr, James; Markl, Michael

    2016-08-01

    To systematically investigate the reproducibility of global and segmental left ventricular (LV) velocities derived from tissue phase mapping (TPM). Breath held and ECG synchronized TPM data (spatial/temporal resolution = 2 × 2 mm(2)/20.8 ms) were acquired in 18 healthy volunteers. To analyze scan-rescan variability, TPM was repeated in all subjects during a second visit separated by 16 ± 5 days. Data analysis included LV segmentation, and quantification of global and regional (AHA 16-segment modal) metrics of LV function [velocity-time curves, systolic and diastolic peak and time-to-peak (TTP) velocities] for radial (Vr), long-axis (Vz) and circumferential (VΦ) LV velocities. Mean velocity time curves in basal, mid-ventricular, and apical locations showed highly similar LV motion patterns for all three velocity components (Vr, VΦ, Vz) for scan and rescan. No significant differences for both systolic and diastolic peak and TTP myocardial velocities were observed. Segmental analysis revealed similar regional peak Vr and Vz during both systole and diastole except for three LV segments (p = 0.045, p = 0.033, and p = 0.009). Excellent (p < 0.001) correlations between scans and rescan for peak Vr (R(2) = 0.92), peak Vz (R(2) = 0.90), radial TTP (R(2) = 0.91) and long-axis TTP (R(2) = 0.88) confirmed good agreement. Bland-Altman analysis demonstrated excellent intra-observer and good inter-observer analysis agreement but increased variability for long axis peak velocities. TPM based analysis of global and regional myocardial velocities can be performed with good reproducibility. Robustness of regional quantification of long-axis velocities was limited but spatial velocity distributions across the LV could reliably be replicated. PMID:27116238

  13. The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification

    SciTech Connect

    Tsuchiya, Hikaru; Tanaka, Keiji Saeki, Yasushi

    2013-06-28

    Highlights: •The parallel reaction monitoring method was applied to ubiquitin quantification. •The ubiquitin PRM method is highly sensitive even in biological samples. •Using the method, we revealed that Ufd4 assembles the K29-linked ubiquitin chain. -- Abstract: Ubiquitylation is an essential posttranslational protein modification that is implicated in a diverse array of cellular functions. Although cells contain eight structurally distinct types of polyubiquitin chains, detailed function of several chain types including K29-linked chains has remained largely unclear. Current mass spectrometry (MS)-based quantification methods are highly inefficient for low abundant atypical chains, such as K29- and M1-linked chains, in complex mixtures that typically contain highly abundant proteins. In this study, we applied parallel reaction monitoring (PRM), a quantitative, high-resolution MS method, to quantify ubiquitin chains. The ubiquitin PRM method allows us to quantify 100 attomole amounts of all possible ubiquitin chains in cell extracts. Furthermore, we quantified ubiquitylation levels of ubiquitin-proline-β-galactosidase (Ub-P-βgal), a historically known model substrate of the ubiquitin fusion degradation (UFD) pathway. In wild-type cells, Ub-P-βgal is modified with ubiquitin chains consisting of 21% K29- and 78% K48-linked chains. In contrast, K29-linked chains are not detected in UFD4 knockout cells, suggesting that Ufd4 assembles the K29-linked ubiquitin chain(s) on Ub-P-βgal in vivo. Thus, the ubiquitin PRM is a novel, useful, quantitative method for analyzing the highly complicated ubiquitin system.

  14. RNA-Seq quantification of the human small airway epithelium transcriptome

    PubMed Central

    2012-01-01

    Background The small airway epithelium (SAE), the cell population that covers the human airway surface from the 6th generation of airway branching to the alveoli, is the major site of lung disease caused by smoking. The focus of this study is to provide quantitative assessment of the SAE transcriptome in the resting state and in response to chronic cigarette smoking using massive parallel mRNA sequencing (RNA-Seq). Results The data demonstrate that 48% of SAE expressed genes are ubiquitous, shared with many tissues, with 52% enriched in this cell population. The most highly expressed gene, SCGB1A1, is characteristic of Clara cells, the cell type unique to the human SAE. Among other genes expressed by the SAE are those related to Clara cell differentiation, secretory mucosal defense, and mucociliary differentiation. The high sensitivity of RNA-Seq permitted quantification of gene expression related to infrequent cell populations such as neuroendocrine cells and epithelial stem/progenitor cells. Quantification of the absolute smoking-induced changes in SAE gene expression revealed that, compared to ubiquitous genes, more SAE-enriched genes responded to smoking with up-regulation, and those with the highest basal expression levels showed most dramatic changes. Smoking had no effect on SAE gene splicing, but was associated with a shift in molecular pattern from Clara cell-associated towards the mucus-secreting cell differentiation pathway with multiple features of cancer-associated molecular phenotype. Conclusions These observations provide insights into the unique biology of human SAE by providing quantit-ative assessment of the global transcriptome under physiological conditions and in response to the stress of chronic cigarette smoking. PMID:22375630

  15. Titan Casts Revealing Shadow

    NASA Astrophysics Data System (ADS)

    2004-05-01

    A rare celestial event was captured by NASA's Chandra X-ray Observatory as Titan -- Saturn's largest moon and the only moon in the Solar System with a thick atmosphere -- crossed in front of the X-ray bright Crab Nebula. The X-ray shadow cast by Titan allowed astronomers to make the first X-ray measurement of the extent of its atmosphere. On January 5, 2003, Titan transited the Crab Nebula, the remnant of a supernova explosion that was observed to occur in the year 1054. Although Saturn and Titan pass within a few degrees of the Crab Nebula every 30 years, they rarely pass directly in front of it. "This may have been the first transit of the Crab Nebula by Titan since the birth of the Crab Nebula," said Koji Mori of Pennsylvania State University in University Park, and lead author on an Astrophysical Journal paper describing these results. "The next similar conjunction will take place in the year 2267, so this was truly a once in a lifetime event." Animation of Titan's Shadow on Crab Nebula Animation of Titan's Shadow on Crab Nebula Chandra's observation revealed that the diameter of the X-ray shadow cast by Titan was larger than the diameter of its solid surface. The difference in diameters gives a measurement of about 550 miles (880 kilometers) for the height of the X-ray absorbing region of Titan's atmosphere. The extent of the upper atmosphere is consistent with, or slightly (10-15%) larger, than that implied by Voyager I observations made at radio, infrared, and ultraviolet wavelengths in 1980. "Saturn was about 5% closer to the Sun in 2003, so increased solar heating of Titan may account for some of this atmospheric expansion," said Hiroshi Tsunemi of Osaka University in Japan, one of the coauthors on the paper. The X-ray brightness and extent of the Crab Nebula made it possible to study the tiny X-ray shadow cast by Titan during its transit. By using Chandra to precisely track Titan's position, astronomers were able to measure a shadow one arcsecond in

  16. Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing.

    PubMed

    Miyaoka, Yuichiro; Berman, Jennifer R; Cooper, Samantha B; Mayerl, Steven J; Chan, Amanda H; Zhang, Bin; Karlin-Neumann, George A; Conklin, Bruce R

    2016-01-01

    Precise genome-editing relies on the repair of sequence-specific nuclease-induced DNA nicking or double-strand breaks (DSBs) by homology-directed repair (HDR). However, nonhomologous end-joining (NHEJ), an error-prone repair, acts concurrently, reducing the rate of high-fidelity edits. The identification of genome-editing conditions that favor HDR over NHEJ has been hindered by the lack of a simple method to measure HDR and NHEJ directly and simultaneously at endogenous loci. To overcome this challenge, we developed a novel, rapid, digital PCR-based assay that can simultaneously detect one HDR or NHEJ event out of 1,000 copies of the genome. Using this assay, we systematically monitored genome-editing outcomes of CRISPR-associated protein 9 (Cas9), Cas9 nickases, catalytically dead Cas9 fused to FokI, and transcription activator-like effector nuclease at three disease-associated endogenous gene loci in HEK293T cells, HeLa cells, and human induced pluripotent stem cells. Although it is widely thought that NHEJ generally occurs more often than HDR, we found that more HDR than NHEJ was induced under multiple conditions. Surprisingly, the HDR/NHEJ ratios were highly dependent on gene locus, nuclease platform, and cell type. The new assay system, and our findings based on it, will enable mechanistic studies of genome-editing and help improve genome-editing technology. PMID:27030102

  17. Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca

    PubMed Central

    Zhang, Junxiang; Jiang, Guihua; Miao, Lixiang; Han, Guofen; Liu, Yuexue; Li, He; Zhang, Zhihong

    2015-01-01

    Fragaria vesca (2n = 2x = 14), the woodland strawberry, is a perennial herbaceous plant with a small sequenced genome (240 Mb). It is commonly used as a genetic model plant for the Fragaria genus and the Rosaceae family. Fruit skin color is one of the most important traits for both the commercial and esthetic value of strawberry. Anthocyanins are the most prominent pigments in strawberry that bring red, pink, white, and yellow hues to the fruits in which they accumulate. In this study, we conducted a de novo assembly of the fruit transcriptome of woodland strawberry and compared the gene expression profiles with yellow (Yellow Wonder, YW) and red (Ruegen, RG) fruits. De novo assembly yielded 75,426 unigenes, 21.3% of which were longer than 1,000 bp. Among the high-quality unique sequences, 45,387 (60.2%) had at least one significant match to an existing gene model. A total of 595 genes, representing 0.79% of total unigenes, were differentially expressed in YW and RG. Among them, 224 genes were up-regulated and 371 genes were down-regulated in the fruit of YW. Particularly, some flavonoid biosynthetic pathway genes, including C4H, CHS, CHI, F3H, DFR and ANS, as well as some transcription factors (TFs), including MYB (putative MYB86 and MYB39), WDR and MADS, were down-regulated in YW fruit, concurrent with a reduction in anthocyanin accumulation in the yellow pigment phenotype, whereas a putative transcription repressor MYB1R was up-regulated in YW fruit. The altered expression levels of the genes encoding flavonoid biosynthetic enzymes and TFs were confirmed by quantitative RT-PCR. Our study provides important insights into the molecular mechanisms underlying the yellow pigment phenotype in F. vesca. PMID:26636322

  18. Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca.

    PubMed

    Zhang, Yuchao; Li, Weijia; Dou, Yujuan; Zhang, Junxiang; Jiang, Guihua; Miao, Lixiang; Han, Guofen; Liu, Yuexue; Li, He; Zhang, Zhihong

    2015-01-01

    Fragaria vesca (2n = 2x = 14), the woodland strawberry, is a perennial herbaceous plant with a small sequenced genome (240 Mb). It is commonly used as a genetic model plant for the Fragaria genus and the Rosaceae family. Fruit skin color is one of the most important traits for both the commercial and esthetic value of strawberry. Anthocyanins are the most prominent pigments in strawberry that bring red, pink, white, and yellow hues to the fruits in which they accumulate. In this study, we conducted a de novo assembly of the fruit transcriptome of woodland strawberry and compared the gene expression profiles with yellow (Yellow Wonder, YW) and red (Ruegen, RG) fruits. De novo assembly yielded 75,426 unigenes, 21.3% of which were longer than 1,000 bp. Among the high-quality unique sequences, 45,387 (60.2%) had at least one significant match to an existing gene model. A total of 595 genes, representing 0.79% of total unigenes, were differentially expressed in YW and RG. Among them, 224 genes were up-regulated and 371 genes were down-regulated in the fruit of YW. Particularly, some flavonoid biosynthetic pathway genes, including C4H, CHS, CHI, F3H, DFR and ANS, as well as some transcription factors (TFs), including MYB (putative MYB86 and MYB39), WDR and MADS, were down-regulated in YW fruit, concurrent with a reduction in anthocyanin accumulation in the yellow pigment phenotype, whereas a putative transcription repressor MYB1R was up-regulated in YW fruit. The altered expression levels of the genes encoding flavonoid biosynthetic enzymes and TFs were confirmed by quantitative RT-PCR. Our study provides important insights into the molecular mechanisms underlying the yellow pigment phenotype in F. vesca.

  19. Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca.

    PubMed

    Zhang, Yuchao; Li, Weijia; Dou, Yujuan; Zhang, Junxiang; Jiang, Guihua; Miao, Lixiang; Han, Guofen; Liu, Yuexue; Li, He; Zhang, Zhihong

    2015-01-01

    Fragaria vesca (2n = 2x = 14), the woodland strawberry, is a perennial herbaceous plant with a small sequenced genome (240 Mb). It is commonly used as a genetic model plant for the Fragaria genus and the Rosaceae family. Fruit skin color is one of the most important traits for both the commercial and esthetic value of strawberry. Anthocyanins are the most prominent pigments in strawberry that bring red, pink, white, and yellow hues to the fruits in which they accumulate. In this study, we conducted a de novo assembly of the fruit transcriptome of woodland strawberry and compared the gene expression profiles with yellow (Yellow Wonder, YW) and red (Ruegen, RG) fruits. De novo assembly yielded 75,426 unigenes, 21.3% of which were longer than 1,000 bp. Among the high-quality unique sequences, 45,387 (60.2%) had at least one significant match to an existing gene model. A total of 595 genes, representing 0.79% of total unigenes, were differentially expressed in YW and RG. Among them, 224 genes were up-regulated and 371 genes were down-regulated in the fruit of YW. Particularly, some flavonoid biosynthetic pathway genes, including C4H, CHS, CHI, F3H, DFR and ANS, as well as some transcription factors (TFs), including MYB (putative MYB86 and MYB39), WDR and MADS, were down-regulated in YW fruit, concurrent with a reduction in anthocyanin accumulation in the yellow pigment phenotype, whereas a putative transcription repressor MYB1R was up-regulated in YW fruit. The altered expression levels of the genes encoding flavonoid biosynthetic enzymes and TFs were confirmed by quantitative RT-PCR. Our study provides important insights into the molecular mechanisms underlying the yellow pigment phenotype in F. vesca. PMID:26636322

  20. Systems-level quantification of division timing reveals a common genetic architecture controlling asynchrony and fate asymmetry.

    PubMed

    Ho, Vincy Wing Sze; Wong, Ming-Kin; An, Xiaomeng; Guan, Daogang; Shao, Jiaofang; Ng, Hon Chun Kaoru; Ren, Xiaoliang; He, Kan; Liao, Jinyue; Ang, Yingjin; Chen, Long; Huang, Xiaotai; Yan, Bin; Xia, Yiji; Chan, Leanne Lai Hang; Chow, King Lau; Yan, Hong; Zhao, Zhongying

    2015-06-10

    Coordination of cell division timing is crucial for proper cell fate specification and tissue growth. However, the differential regulation of cell division timing across or within cell types during metazoan development remains poorly understood. To elucidate the systems-level genetic architecture coordinating division timing, we performed a high-content screening for genes whose depletion produced a significant reduction in the asynchrony of division between sister cells (ADS) compared to that of wild-type during Caenorhabditis elegans embryogenesis. We quantified division timing using 3D time-lapse imaging followed by computer-aided lineage analysis. A total of 822 genes were selected for perturbation based on their conservation and known roles in development. Surprisingly, we find that cell fate determinants are not only essential for establishing fate asymmetry, but also are imperative for setting the ADS regardless of cellular context, indicating a common genetic architecture used by both cellular processes. The fate determinants demonstrate either coupled or separate regulation between the two processes. The temporal coordination appears to facilitate cell migration during fate specification or tissue growth. Our quantitative dataset with cellular resolution provides a resource for future analyses of the genetic control of spatial and temporal coordination during metazoan development.

  1. Systematic quantification of HDR and NHEJ reveals effects of locus, nuclease, and cell type on genome-editing

    PubMed Central

    Miyaoka, Yuichiro; Berman, Jennifer R.; Cooper, Samantha B.; Mayerl, Steven J.; Chan, Amanda H.; Zhang, Bin; Karlin-Neumann, George A.; Conklin, Bruce R.

    2016-01-01

    Precise genome-editing relies on the repair of sequence-specific nuclease-induced DNA nicking or double-strand breaks (DSBs) by homology-directed repair (HDR). However, nonhomologous end-joining (NHEJ), an error-prone repair, acts concurrently, reducing the rate of high-fidelity edits. The identification of genome-editing conditions that favor HDR over NHEJ has been hindered by the lack of a simple method to measure HDR and NHEJ directly and simultaneously at endogenous loci. To overcome this challenge, we developed a novel, rapid, digital PCR–based assay that can simultaneously detect one HDR or NHEJ event out of 1,000 copies of the genome. Using this assay, we systematically monitored genome-editing outcomes of CRISPR-associated protein 9 (Cas9), Cas9 nickases, catalytically dead Cas9 fused to FokI, and transcription activator–like effector nuclease at three disease-associated endogenous gene loci in HEK293T cells, HeLa cells, and human induced pluripotent stem cells. Although it is widely thought that NHEJ generally occurs more often than HDR, we found that more HDR than NHEJ was induced under multiple conditions. Surprisingly, the HDR/NHEJ ratios were highly dependent on gene locus, nuclease platform, and cell type. The new assay system, and our findings based on it, will enable mechanistic studies of genome-editing and help improve genome-editing technology. PMID:27030102

  2. Revealing the Beast Within

    NASA Astrophysics Data System (ADS)

    2003-07-01

    Deeply Embedded Massive Stellar Clusters Discovered in Milky Way Powerhouse Summary Peering into a giant molecular cloud in the Milky Way galaxy - known as W49 - astronomers from the European Southern Observatory (ESO) have discovered a whole new population of very massive newborn stars . This research is being presented today at the International Astronomical Union's 25th General Assembly held in Sydney, Australia, by ESO-scientist João Alves. With the help of infrared images obtained during a period of excellent observing conditions with the ESO 3.5-m New Technology Telescope (NTT) at the La Silla Observatory (Chile), the astronomers looked deep into this molecular cloud and discovered four massive stellar clusters, with hot and energetic stars as massive as 120 solar masses. The exceedingly strong radiation from the stars in the largest of these clusters is "powering" a 20 light-year diameter region of mostly ionized hydrogen gas (a "giant HII region"). W49 is one of the most energetic regions of star formation in the Milky Way. With the present discovery, the true sources of the enormous energy have now been revealed for the first time, finally bringing to an end some decades of astronomical speculations and hypotheses. PR Photo 21a/03 : Colour Composite of W49A (NTT+SOFI). PR Photo 21b/03 : Radio and Near-Infrared Composite of W49A Giant molecular clouds Stars form predominantly inside Giant Molecular Clouds which populate our Galaxy, the Milky Way. One of the most prominent of these is W49 , which has a mass of a million solar masses. It is located some 37,000 light-years away and is the most luminous star-forming region known in our home galaxy: its luminosity is several million times the luminosity of our Sun. A smaller region within this cloud is denoted W49A - this is one of the strongest radio-emitting areas known in the Galaxy . Massive stars are excessive in all ways. Compared to their smaller and ligther brethren, they form at an Olympic speed and

  3. Highly Precise Quantification of Protein Molecules per Cell During Stress and Starvation Responses in Bacillus subtilis *

    PubMed Central

    Maaβ, Sandra; Wachlin, Gerhild; Bernhardt, Jörg; Eymann, Christine; Fromion, Vincent; Riedel, Katharina; Becher, Dörte; Hecker, Michael

    2014-01-01

    Systems biology based on high quality absolute quantification data, which are mandatory for the simulation of biological processes, successively becomes important for life sciences. We provide protein concentrations on the level of molecules per cell for more than 700 cytosolic proteins of the Gram-positive model bacterium Bacillus subtilis during adaptation to changing growth conditions. As glucose starvation and heat stress are typical challenges in B. subtilis' natural environment and induce both, specific and general stress and starvation proteins, these conditions were selected as models for starvation and stress responses. Analyzing samples from numerous time points along the bacterial growth curve yielded reliable and physiologically relevant data suitable for modeling of cellular regulation under altered growth conditions. The analysis of the adaptational processes based on protein molecules per cell revealed stress-specific modulation of general adaptive responses in terms of protein amount and proteome composition. Furthermore, analysis of protein repartition during glucose starvation showed that biomass seems to be redistributed from proteins involved in amino acid biosynthesis to enzymes of the central carbon metabolism. In contrast, during heat stress most resources of the cell, namely those from amino acid synthetic pathways, are used to increase the amount of chaperones and proteases. Analysis of dynamical aspects of protein synthesis during heat stress adaptation revealed, that these proteins make up almost 30% of the protein mass accumulated during early phases of this stress. PMID:24878497

  4. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    NASA Astrophysics Data System (ADS)

    Warren, J.; Bilheux, H.; Kang, M.; Voisin, S.; Cheng, C.; Horita, J.; Perfect, E.

    2011-12-01

    In situ quantification of soil-plant water fluxes have not been fully successful due to a lack of non-destructive techniques capable of revealing roots or water fluxes at relevant spatial scales. Neutron imaging is a unique non-invasive tool that can assess sub-millimeter scale material properties and transport in situ, and which has been successfully applied to characterize soil and plant water status. Here, we have applied neutron radiography and tomography to quantify water transport through individual maize roots in response to internal plant demand. Zea mays seedlings were grown for 10 days in Flint silica sand within 2.6 cm diameter Al chambers. Using a reactor-based neutron source at Oak Ridge National Laboratory (HFIR), water fluxes were tracked through the maize soil-root systems by collecting consecutive neutron radiographs over a 12 h period following irrigation with D2O. D has a much lower neutron attenuation than H, thus D2O displacement of existing H2O within the plant vascular system, or influx of D2O into previously dry tissue or soil is readily tracked by changes in image intensity through time. Plant water release and uptake was regulated by periodically cycling on a high-intensity grow light. From each maize replicate, selected regions of interest (ROI) were delineated around individual roots, root free soil, stem and leaf segments. Changes in ROI were tracked through time to reveal patterns of water flux. The hydration of root and stem tissue cycled in response to illumination; root water content often increased during darkness, then decreased with illumination as water was transported from the root into the stem. Relative root-shoot hydration through time illustrates the balance between demand, storage capacity and uptake, which varies depending on root characteristics and its localized soil environment. The dynamic transport of water between soil, individual roots, stems and leaves was readily visualized and quantified illustrating the value

  5. Identification and quantification of caffeoylquinic acids and flavonoids from artichoke (Cynara scolymus L.) heads, juice, and pomace by HPLC-DAD-ESI/MS(n).

    PubMed

    Schütz, Katrin; Kammerer, Dietmar; Carle, Reinhold; Schieber, Andreas

    2004-06-30

    A method for the identification and quantification of phenolic compounds from artichoke (Cynara scolymus L.) heads, juice, and pomace by HPLC with diode array and mass spectrometric detection was developed. Among the 22 major compounds, 11 caffeoylquinic acids and 8 flavonoids were detected. Quantification of individual compounds was carried out by external calibration. Apigenin 7-O-glucuronide was found to be the major flavonoid in all samples investigated. 1,5-Di-O-caffeoylquinic acid represented the major hydroxycinnamic acid, with 3890 mg/kg in artichoke heads and 3269 mg/kg in the pomace, whereas in the juice 1,3-di-O-caffeoylquinic acid (cynarin) was predominant, due to the isomerization during processing. Total phenolic contents of approximately 12 g/kg on a dry matter basis revealed that artichoke pomace is a promising source of phenolic compounds that might be recovered and used as natural antioxidants or functional food ingredients.

  6. The role of PET quantification in cardiovascular imaging

    PubMed Central

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

    2014-01-01

    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 (18FDG) 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 13N-ammonia, 15O-water and 82Rb radiotracers. The agreement between software methods available for such analysis is excellent. Relative quantification of 82Rb PET myocardial perfusion, based on comparisons to normal databases, demonstrates high performance for the detection of obstructive coronary disease. New tracers, such as 18F-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 18FDG and 18F-sodium fluoride tracers in carotids, aorta and coronary arteries has been

  7. A flexible numerical approach for quantification of epistemic uncertainty

    NASA Astrophysics Data System (ADS)

    Chen, Xiaoxiao; Park, Eun-Jae; Xiu, Dongbin

    2013-05-01

    In the field of uncertainty quantification (UQ), epistemic uncertainty often refers to the kind of uncertainty whose complete probabilistic description is not available, largely due to our lack of knowledge about the uncertainty. Quantification of the impacts of epistemic uncertainty is naturally difficult, because most of the existing stochastic tools rely on the specification of the probability distributions and thus do not readily apply to epistemic uncertainty. And there have been few studies and methods to deal with epistemic uncertainty. A recent work can be found in [J. Jakeman, M. Eldred, D. Xiu, Numerical approach for quantification of epistemic uncertainty, J. Comput. Phys. 229 (2010) 4648-4663], where a framework for numerical treatment of epistemic uncertainty was proposed. The method is based on solving an encapsulation problem, without using any probability information, in a hypercube that encapsulates the unknown epistemic probability space. If more probabilistic information about the epistemic variables is known a posteriori, the solution statistics can then be evaluated at post-process steps. In this paper, we present a new method, similar to that of Jakeman et al. but significantly extending its capabilities. Most notably, the new method (1) does not require the encapsulation problem to be in a bounded domain such as a hypercube; (2) does not require the solution of the encapsulation problem to converge point-wise. In the current formulation, the encapsulation problem could reside in an unbounded domain, and more importantly, its numerical approximation could be sought in Lp norm. These features thus make the new approach more flexible and amicable to practical implementation. Both the mathematical framework and numerical analysis are presented to demonstrate the effectiveness of the new approach.

  8. Quantification of brain endocannabinoid levels: methods, interpretations and pitfalls

    PubMed Central

    Buczynski, Matthew W; Parsons, Loren H

    2010-01-01

    Endocannabinoids play an important role in a diverse range of neurophysiological processes including neural development, neuroimmune function, synaptic plasticity, pain, reward and affective state. This breadth of influence and evidence for altered endocannabinoid signalling in a variety of neuropathologies has fuelled interest in the accurate quantification of these lipids in brain tissue. Established methods for endocannabinoid quantification primarily employ solvent-based lipid extraction with further sample purification by solid phase extraction. In recent years in vivo microdialysis methods have also been developed for endocannabinoid sampling from the brain interstitial space. However, considerable variability in estimates of endocannabinoid content has led to debate regarding the physiological range of concentrations present in various brain regions. This paper provides a critical review of factors that influence the quantification of brain endocannabinoid content as determined by lipid extraction from bulk tissue and by in vivo microdialysis. A variety of methodological issues are discussed including analytical approaches, endocannabinoid extraction and purification, post-mortem changes in brain endocannabinoid content, cellular reactions to microdialysis probe implantation and caveats related to lipid sampling from the extracellular space. The application of these methods for estimating brain endocannabinoid content and the effects of endocannabinoid clearance inhibition are discussed. The benefits, limitations and pitfalls associated with each approach are emphasized, with an eye toward the appropriate interpretation of data gathered by each method. This article is part of a themed issue on Cannabinoids. To view the editorial for this themed issue visit http://dx.doi.org/10.1111/j.1476-5381.2010.00831.x PMID:20590555

  9. A flexible numerical approach for quantification of epistemic uncertainty

    SciTech Connect

    Chen, Xiaoxiao; Park, Eun-Jae; Xiu, Dongbin

    2013-05-01

    In the field of uncertainty quantification (UQ), epistemic uncertainty often refers to the kind of uncertainty whose complete probabilistic description is not available, largely due to our lack of knowledge about the uncertainty. Quantification of the impacts of epistemic uncertainty is naturally difficult, because most of the existing stochastic tools rely on the specification of the probability distributions and thus do not readily apply to epistemic uncertainty. And there have been few studies and methods to deal with epistemic uncertainty. A recent work can be found in [J. Jakeman, M. Eldred, D. Xiu, Numerical approach for quantification of epistemic uncertainty, J. Comput. Phys. 229 (2010) 4648–4663], where a framework for numerical treatment of epistemic uncertainty was proposed. The method is based on solving an encapsulation problem, without using any probability information, in a hypercube that encapsulates the unknown epistemic probability space. If more probabilistic information about the epistemic variables is known a posteriori, the solution statistics can then be evaluated at post-process steps. In this paper, we present a new method, similar to that of Jakeman et al. but significantly extending its capabilities. Most notably, the new method (1) does not require the encapsulation problem to be in a bounded domain such as a hypercube; (2) does not require the solution of the encapsulation problem to converge point-wise. In the current formulation, the encapsulation problem could reside in an unbounded domain, and more importantly, its numerical approximation could be sought in L{sup p} norm. These features thus make the new approach more flexible and amicable to practical implementation. Both the mathematical framework and numerical analysis are presented to demonstrate the effectiveness of the new approach.

  10. Quantification in histopathology—Can magnetic particles help?

    NASA Astrophysics Data System (ADS)

    Mitchels, John; Hawkins, Peter; Luxton, Richard; Rhodes, Anthony

    2007-04-01

    Every year, more than 270,000 people are diagnosed with cancer in the UK alone; this means that one in three people worldwide contract cancer within their lifetime. Histopathology is the principle method for confirming cancer and directing treatment. In this paper, a novel application of magnetic particles is proposed to help address the problem of subjectivity in histopathology. Preliminary results indicate that magnetic nanoparticles cannot only be used to assist diagnosis through improving quantification but also potentially increase throughput, hence offering a way of dramatically reducing costs within the routine histopathology laboratory.

  11. Quantification of protein concentration using UV absorbance and Coomassie dyes.

    PubMed

    Noble, James E

    2014-01-01

    The measurement of a solubilized protein concentration in solution is an important assay in biochemistry research and development labs for applications ranging from enzymatic studies to providing data for biopharmaceutical lot release. Spectrophotometric protein quantification assays are methods that use UV and visible spectroscopy to rapidly determine the concentration of protein, relative to a standard, or using an assigned extinction coefficient. Where multiple samples need measurement, and/or the sample volume and concentration is limited, preparations of the Coomassie dye commonly known as the Bradford assay can be used. PMID:24423263

  12. Source-Code Instrumentation and Quantification of Events

    NASA Technical Reports Server (NTRS)

    Filman, Robert E.; Havelund, Klaus; Clancy, Daniel (Technical Monitor)

    2002-01-01

    Aspect Oriented Programming (AOP) is making quantified programmatic assertions over programs that otherwise are not annotated to receive these assertions. Varieties of AOP systems are characterized by which quantified assertions they allow, what they permit in the actions of the assertions (including how the actions interact with the base code), and what mechanisms they use to achieve the overall effect. Here, we argue that all quantification is over dynamic events, and describe our preliminary work in developing a system that maps dynamic events to transformations over source code. We discuss possible applications of this system, particularly with respect to debugging concurrent systems.

  13. Quantification of risks from technology for improved plant reliability

    SciTech Connect

    Rode, D.M.

    1996-12-31

    One of the least understood and therefore appreciated threats to profitability are risks from power plant technologies such as steam generators, turbines, and electrical systems. To effectively manage technological risks, business decisions need to be based on knowledge. The scope of the paper describes a quantification or risk process that combines technical knowledge and judgments with commercial consequences. The three principle alternatives to manage risks as well as risk mitigation techniques for significant equipment within a power plant are reported. The result is to equip the decision maker with a comprehensive picture of the risk exposures enabling cost effective activities to be undertaken to improve a plant`s reliability.

  14. Recurrence plots and recurrence quantification analysis of human motion data

    NASA Astrophysics Data System (ADS)

    Josiński, Henryk; Michalczuk, Agnieszka; Świtoński, Adam; Szczesna, Agnieszka; Wojciechowski, Konrad

    2016-06-01

    The authors present exemplary application of recurrence plots, cross recurrence plots and recurrence quantification analysis for the purpose of exploration of experimental time series describing selected aspects of human motion. Time series were extracted from treadmill gait sequences which were recorded in the Human Motion Laboratory (HML) of the Polish-Japanese Academy of Information Technology in Bytom, Poland by means of the Vicon system. Analysis was focused on the time series representing movements of hip, knee, ankle and wrist joints in the sagittal plane.

  15. Development of magnetic resonance technology for noninvasive boron quantification

    SciTech Connect

    Bradshaw, K.M.

    1990-11-01

    Boron magnetic resonance imaging (MRI) and spectroscopy (MRS) were developed in support of the noninvasive boron quantification task of the Idaho National Engineering Laboratory (INEL) Power Burst Facility/Boron Neutron Capture Therapy (PBF/BNCT) program. The hardware and software described in this report are modifications specific to a GE Signa{trademark} MRI system, release 3.X and are necessary for boron magnetic resonance operation. The technology developed in this task has been applied to obtaining animal pharmacokinetic data of boron compounds (drug time response) and the in-vivo localization of boron in animal tissue noninvasively. 9 refs., 21 figs.

  16. Uncertainty Quantification in Fission Cross Section Measurements at LANSCE

    SciTech Connect

    Tovesson, F.

    2015-01-15

    Neutron-induced fission cross sections have been measured for several isotopes of uranium and plutonium at the Los Alamos Neutron Science Center (LANSCE) over a wide range of incident neutron energies. The total uncertainties in these measurements are in the range 3–5% above 100 keV of incident neutron energy, which results from uncertainties in the target, neutron source, and detector system. The individual sources of uncertainties are assumed to be uncorrelated, however correlation in the cross section across neutron energy bins are considered. The quantification of the uncertainty contributions will be described here.

  17. Preliminary Results on Uncertainty Quantification for Pattern Analytics

    SciTech Connect

    Stracuzzi, David John; Brost, Randolph; Chen, Maximillian Gene; Malinas, Rebecca; Peterson, Matthew Gregor; Phillips, Cynthia A.; Robinson, David G.; Woodbridge, Diane

    2015-09-01

    This report summarizes preliminary research into uncertainty quantification for pattern ana- lytics within the context of the Pattern Analytics to Support High-Performance Exploitation and Reasoning (PANTHER) project. The primary focus of PANTHER was to make large quantities of remote sensing data searchable by analysts. The work described in this re- port adds nuance to both the initial data preparation steps and the search process. Search queries are transformed from does the specified pattern exist in the data? to how certain is the system that the returned results match the query? We show example results for both data processing and search, and discuss a number of possible improvements for each.

  18. Automatic quantification of neurite outgrowth by means of image analysis

    NASA Astrophysics Data System (ADS)

    Van de Wouwer, Gert; Nuydens, Rony; Meert, Theo; Weyn, Barbara

    2004-07-01

    A system for quantification of neurite outgrowth in in-vitro experiments is described. The system is developed for routine use in a high-throughput setting and is therefore needs fast, cheap, and robust. It relies on automated digital microscopical imaging of microtiter plates. Image analysis is applied to extract features for characterisation of neurite outgrowth. The system is tested in a dose-response experiment on PC12 cells + Taxol. The performance of the system and its ability to measure changes on neuronal morphology is studied.

  19. Trace cancer biomarker quantification using polystyrene-functionalized gold nanorods

    PubMed Central

    Wu, Jian; Li, Wei; Hajisalem, Ghazal; Lukach, Ariella; Kumacheva, Eugenia; Hof, Fraser; Gordon, Reuven

    2014-01-01

    We demonstrate the application of polystyrene-functionalized gold nanorods (AuNRs) as a platform for surface enhanced Raman scattering (SERS) quantification of the exogenous cancer biomarker Acetyl Amantadine (AcAm). We utilize the hydrophobicity of the polystyrene attached to the AuNR surface to capture the hydrophobic AcAm from solution, followed by drying and detection using SERS. We achieve a detection limit of 16 ng/mL using this platform. This result shows clinical potential for low-cost early cancer detection. PMID:25574423

  20. Uncertainty quantification in fission cross section measurements at LANSCE

    DOE PAGES

    Tovesson, F.

    2015-01-09

    Neutron-induced fission cross sections have been measured for several isotopes of uranium and plutonium at the Los Alamos Neutron Science Center (LANSCE) over a wide range of incident neutron energies. The total uncertainties in these measurements are in the range 3–5% above 100 keV of incident neutron energy, which results from uncertainties in the target, neutron source, and detector system. The individual sources of uncertainties are assumed to be uncorrelated, however correlation in the cross section across neutron energy bins are considered. The quantification of the uncertainty contributions will be described here.

  1. Stereometric Measurement System For Quantification Of Object Forms

    NASA Astrophysics Data System (ADS)

    Fischer, P.; Mesqui, F.; Kaeser, F.

    1986-07-01

    A three-dimensional camera unit has been developed at the Dental School of the University of Zurich for jaw motion recording. Since the system is designed to detect and reconstruct the spatial position of a light source, it can easily be used to digitize an object surface being scanned by a laser beam. This is performed by an additional device which has been developed in order to enlarge the application field of the camera unit as well as to prove the feasibility and find out the limits of such a simple and low-cost quantification system.

  2. Selected methods for quantification of community exposure to aircraft noise

    NASA Technical Reports Server (NTRS)

    Edge, P. M., Jr.; Cawthorn, J. M.

    1976-01-01

    A review of the state-of-the-art for the quantification of community exposure to aircraft noise is presented. Physical aspects, people response considerations, and practicalities of useful application of scales of measure are included. Historical background up through the current technology is briefly presented. The developments of both single-event and multiple-event scales are covered. Selective choice is made of scales currently in the forefront of interest and recommended methodology is presented for use in computer programing to translate aircraft noise data into predictions of community noise exposure. Brief consideration is given to future programing developments and to supportive research needs.

  3. Nuclear Data Uncertainty Quantification: Past, Present and Future

    SciTech Connect

    Smith, D.L.

    2015-01-15

    An historical overview is provided of the mathematical foundations of uncertainty quantification and the roles played in the more recent past by nuclear data uncertainties in nuclear data evaluations and nuclear applications. Significant advances that have established the mathematical framework for contemporary nuclear data evaluation methods, as well as the use of uncertainty information in nuclear data evaluation and nuclear applications, are described. This is followed by a brief examination of the current status concerning nuclear data evaluation methodology, covariance data generation, and the application of evaluated nuclear data uncertainties in contemporary nuclear technology. A few possible areas for future investigation of this subject are also suggested.

  4. Progressive damage state evolution and quantification in composites

    NASA Astrophysics Data System (ADS)

    Patra, Subir; Banerjee, Sourav

    2016-04-01

    Precursor damage state quantification can be helpful for safety and operation of aircraft and defense equipment's. Damage develops in the composite material in the form of matrix cracking, fiber breakages and deboning, etc. However, detection and quantification of the damage modes at their very early stage is not possible unless modifications of the existing indispensable techniques are conceived, particularly for the quantification of multiscale damages at their early stage. Here, we present a novel nonlocal mechanics based damage detection technique for precursor damage state quantification. Micro-continuum physics is used by modifying the Christoffel equation. American society of testing and materials (ASTM) standard woven carbon fiber (CFRP) specimens were tested under Tension-Tension fatigue loading at the interval of 25,000 cycles until 500,000 cycles. Scanning Acoustic Microcopy (SAM) and Optical Microscopy (OM) were used to examine the damage development at the same interval. Surface Acoustic Wave (SAW) velocity profile on a representative volume element (RVE) of the specimen were calculated at the regular interval of 50,000 cycles. Nonlocal parameters were calculated form the micromorphic wave dispersion curve at a particular frequency of 50 MHz. We used a previously formulated parameter called "Damage entropy" which is a measure of the damage growth in the material calculated with the loading cycle. Damage entropy (DE) was calculated at every pixel on the RVE and the mean of DE was plotted at the loading interval of 25,000 cycle. Growth of DE with fatigue loading cycles was observed. Optical Imaging also performed at the interval of 25,000 cycles to investigate the development of damage inside the materials. We also calculated the mean value of the Surface Acoustic Wave (SAW) velocity and plotted with fatigue cycle which is correlated further with Damage Entropy (DE). Statistical analysis of the Surface Acoustic Wave profile (SAW) obtained at different

  5. Quantification of skin wrinkles using low coherence interferometry

    NASA Astrophysics Data System (ADS)

    Oh, Jung-Taek; Kim, Beop-Min; Son, Sang-Ryoon; Lee, Sang-Won; Kim, Dong-Yoon; Kim, Youn-Soo

    2004-07-01

    We measure the skin wrinkle topology by means of low coherence interferometry (LCI), which forms the basis of the optical coherence tomography (OCT). The skin topology obtained using LCI and corresponding 2-D fast Fourier transform allow quantification of skin wrinkles. It took approximately 2 minutes to obtain 2.1 mm x 2.1 mm topological image with 4 um and 16 um resolutions in axial and transverse directions, respectively. Measurement examples show the particular case of skin contour change after-wrinkle cosmeceutical treatments and atopic dermatitis

  6. Quantification of toxicological effects for dichloromethane. Final report

    SciTech Connect

    Not Available

    1992-01-01

    The document discusses the quantification of non-carcinogenic effects and carcinogenic effects for dichloromethane. The evaluation of non-carcinogenic effects includes a study of short and long term effects in animals and humans, as well as the development of the one-day, ten-day, and long term health advisories. The evaluation of carcinogenic effects includes a categorization of carcinogenic potential and risks estimates. There is a brief discussion on existing guidelines or standards and special considerations such as high risk groups.

  7. Aspect-Oriented Programming is Quantification and Implicit Invocation

    NASA Technical Reports Server (NTRS)

    Filman, Robert E.; Friedman, Daniel P.; Koga, Dennis (Technical Monitor)

    2001-01-01

    We propose that the distinguishing characteristic of Aspect-Oriented Programming (AOP) languages is that they allow programming by making quantified programmatic assertions over programs that lack local notation indicating the invocation of these assertions. This suggests that AOP systems can be analyzed with respect to three critical dimensions: the kinds of quantifications allowed, the nature of the interactions 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 metabolism: they are sufficiently expressive to allow straightforwardly programming an AOP system within them.

  8. Nuclear magnetic resonance-based quantification of organic diphosphates.

    PubMed

    Lenevich, Stepan; Distefano, Mark D

    2011-01-15

    Phosphorylated compounds are ubiquitous in life. Given their central role, many such substrates and analogs have been prepared for subsequent evaluation. Prior to biological experiments, it is typically necessary to determine the concentration of the target molecule in solution. Here we describe a method where concentrations of stock solutions of organic diphosphates and bisphosphonates are quantified using (31)P nuclear magnetic resonance (NMR) spectroscopy with standard instrumentation using a capillary tube with a secondary standard. The method is specific and is applicable down to a concentration of 200 μM. The capillary tube provides the reference peak for quantification and deuterated solvent for locking. PMID:20833124

  9. Quantification of quantum discord in a antiferromagnetic Heisenberg compound

    SciTech Connect

    Singh, H. Chakraborty, T. Mitra, C.

    2014-04-24

    An experimental quantification of concurrence and quantum discord from heat capacity (C{sub p}) measurement performed over a solid state system has been reported. In this work, thermodynamic measurements were performed on copper nitrate (CN, Cu(NO{sub 3}){sub 2}⋅2.5H{sub 2}O) single crystals which is an alternating antiferromagnet Heisenberg spin 1/2 system. CN being a weak dimerized antiferromagnet is an ideal system to investigate correlations between spins. The theoretical expressions were used to obtain concurrence and quantum discord curves as a function of temperature from heat capacity data of a real macroscopic system, CN.

  10. Quantification of octacalcium phosphate, authigenic apatite and detrital apatite in coastal sediments using differential dissolution and standard addition

    NASA Astrophysics Data System (ADS)

    Oxmann, J. F.; Schwendenmann, L.

    2014-01-01

    Knowledge of calcium phosphate (Ca-P) solubility is crucial for understanding temporal and spatial variations of phosphorus (P) concentrations in water bodies and sedimentary reservoirs. In-situ relationships between liquid and solid-phase levels cannot be fully explained by dissolved analytes alone and need to be verified by determination of particular sediment P species. Lack of quantification methods for these species limits the knowledge of the P cycle. To address this issue, we (i) optimized a specifically developed conversion-extraction (CONVEX) method for P species quantification using standard additions; and (ii) simultaneously determined solubilities of Ca-P standards by measuring their pH-dependent contents in the sediment matrix. Ca-P minerals including various carbonate fluorapatite (CFAP) specimens from different localities, fluorapatite (FAP), fish bone apatite, synthetic hydroxylapatite (HAP) and octacalcium phosphate (OCP) were characterized by XRD, Raman, FTIR and elemental analysis. Sediment samples were incubated with and without these reference minerals and then sequentially extracted to quantify Ca-P species by their differential dissolution at pH values between 3 and 8. The quantification of solid-phase phosphates at varying pH revealed solubilities in the following order: OCP > HAP > CFAP (4.5% CO3) > CFAP (3.4% CO3) > CFAP (2.2% CO3) > FAP. Thus, CFAP was less soluble in sediment than HAP, and CFAP solubility increased with carbonate content. Unspiked sediment analyses together with standard addition analyses indicated consistent differential dissolution of natural sediment species vs. added reference species and therefore verified the applicability of the CONVEX method in separately determining the most prevalent Ca-P minerals. We found surprisingly high OCP contents in the analyzed coastal sediments which supports the hypothesis of apatite formation by an OCP precursor.

  11. Quantification of octacalcium phosphate, authigenic apatite and detrital apatite in coastal sediments using differential dissolution and standard addition

    NASA Astrophysics Data System (ADS)

    Oxmann, J. F.; Schwendenmann, L.

    2014-06-01

    Knowledge of calcium phosphate (Ca-P) solubility is crucial for understanding temporal and spatial variations of phosphorus (P) concentrations in water bodies and sedimentary reservoirs. In situ relationships between liquid- and solid-phase levels cannot be fully explained by dissolved analytes alone and need to be verified by determining particular sediment P species. Lack of quantification methods for these species limits the knowledge of the P cycle. To address this issue, we (i) optimized a specifically developed conversion-extraction (CONVEX) method for P species quantification using standard additions, and (ii) simultaneously determined solubilities of Ca-P standards by measuring their pH-dependent contents in the sediment matrix. Ca-P minerals including various carbonate fluorapatite (CFAP) specimens from different localities, fluorapatite (FAP), fish bone apatite, synthetic hydroxylapatite (HAP) and octacalcium phosphate (OCP) were characterized by XRD, Raman, FTIR and elemental analysis. Sediment samples were incubated with and without these reference minerals and then sequentially extracted to quantify Ca-P species by their differential dissolution at pH values between 3 and 8. The quantification of solid-phase phosphates at varying pH revealed solubilities in the following order: OCP > HAP > CFAP (4.5% CO3) > CFAP (3.4% CO3) > CFAP (2.2% CO3) > FAP. Thus, CFAP was less soluble in sediment than HAP, and CFAP solubility increased with carbonate content. Unspiked sediment analyses together with standard addition analyses indicated consistent differential dissolution of natural sediment species vs. added reference species and therefore verified the applicability of the CONVEX method in separately determining the most prevalent Ca-P minerals. We found surprisingly high OCP contents in the coastal sediments analyzed, which supports the hypothesis of apatite formation by an OCP precursor mechanism.

  12. Proteomic Identification and Quantification of S-glutathionylation in Mouse Macrophages Using Resin-Assisted Enrichment and Isobaric Labeling

    SciTech Connect

    Su, Dian; Gaffrey, Matthew J.; Guo, Jia; Hatchell, Kayla E.; Chu, Rosalie K.; Clauss, Therese RW; Aldrich, Joshua T.; Wu, Si; Purvine, Samuel O.; Camp, David G.; Smith, Richard D.; Thrall, Brian D.; Qian, Weijun

    2014-02-11

    Protein S-glutathionylation (SSG) is an important regulatory posttranslational modification of protein cysteine (Cys) thiol redox switches, yet the role of specific cysteine residues as targets of modification is poorly understood. We report a novel quantitative mass spectrometry (MS)-based proteomic method for site-specific identification and quantification of S-glutathionylation across different conditions. Briefly, this approach consists of initial blocking of free thiols by alkylation, selective reduction of glutathionylated thiols and enrichment using thiol affinity resins, followed by on-resin tryptic digestion and isobaric labeling with iTRAQ (isobaric tags for relative and absolute quantitation) for MS-based identification and quantification. The overall approach was validated by application to RAW 264.7 mouse macrophages treated with different doses of diamide to induce glutathionylation. A total of 1071 Cys-sites from 690 proteins were identified in response to diamide treatment, with ~90% of the sites displaying >2-fold increases in SSG-modification compared to controls.. This approach was extended to identify potential SSG modified Cys-sites in response to H2O2, an endogenous oxidant produced by activated macrophages and many pathophysiological stimuli. The results revealed 364 Cys-sites from 265 proteins that were sensitive to S-glutathionylation in response to H2O2 treatment. These proteins covered a range of molecular types and molecular functions with free radical scavenging, and cell death and survival included as the most significantly enriched functional categories. Overall the results demonstrate that our approach is effective for site-specific identification and quantification of S-glutathionylated proteins. The analytical strategy also provides a unique approach to determining the major pathways and cell processes most susceptible to glutathionylation at a proteome-wide scale.

  13. The Metabolite Pathway between Bundle Sheath and Mesophyll: Quantification of Plasmodesmata in Leaves of C3 and C4 Monocots.

    PubMed

    Danila, Florence R; Quick, William Paul; White, Rosemary G; Furbank, Robert T; von Caemmerer, Susanne

    2016-06-01

    C4 photosynthesis is characterized by a CO2-concentrating mechanism between mesophyll (M) and bundle sheath (BS) cells of leaves. This generates high metabolic fluxes between these cells, through interconnecting plasmodesmata (PD). Quantification of these symplastic fluxes for modeling studies requires accurate quantification of PD, which has proven difficult using transmission electron microscopy. Our new quantitative technique combines scanning electron microscopy and 3D immunolocalization in intact leaf tissues to compare PD density on cell interfaces in leaves of C3 (rice [Oryza sativa] and wheat [Triticum aestivum]) and C4 (maize [Zea mays] and Setaria viridis) monocot species. Scanning electron microscopy quantification of PD density revealed that C4 species had approximately twice the number of PD per pitfield area compared with their C3 counterparts. 3D immunolocalization of callose at pitfields using confocal microscopy showed that pitfield area per M-BS interface area was 5 times greater in C4 species. Thus, the two C4 species had up to nine times more PD per M-BS interface area (S. viridis, 9.3 PD µm(-2); maize, 7.5 PD µm(-2); rice 1.0 PD µm(-2); wheat, 2.6 PD µm(-2)). Using these anatomical data and measured photosynthetic rates in these C4 species, we have now calculated symplastic C4 acid flux per PD across the M-BS interface. These quantitative data are essential for modeling studies and gene discovery strategies needed to introduce aspects of C4 photosynthesis to C3 crops. PMID:27288224

  14. Prospective Comparison of Liver Stiffness Measurements between Two Point Shear Wave Elastography Methods: Virtual Touch Quantification and Elastography Point Quantification

    PubMed Central

    Yoo, Hyunsuk; Yoon, Jeong Hee; Lee, Dong Ho; Chang, Won; Han, Joon Koo

    2016-01-01

    Objective 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. Materials and Methods 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 χ2 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). Results 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. Conclusion 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. PMID:27587964

  15. 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.

    PubMed

    Beck, Andrew H; Weng, Ziming; Witten, Daniela M; Zhu, Shirley; Foley, Joseph W; Lacroute, Phil; Smith, Cheryl L; Tibshirani, Robert; van de Rijn, Matt; Sidow, Arend; West, Robert B

    2010-01-01

    Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast majority of archival tumor samples. To address this limitation of gene expression microarrays, we designed a novel procedure (3'-end sequencing for expression quantification (3SEQ)) for gene expression profiling from FFPET using next-generation sequencing. We performed gene expression profiling by 3SEQ and microarray on both frozen tissue and FFPET from two soft tissue tumors (desmoid type fibromatosis (DTF) and solitary fibrous tumor (SFT)) (total n = 23 samples, which were each profiled by at least one of the four platform-tissue preparation combinations). Analysis of 3SEQ data revealed many genes differentially expressed between the tumor types (FDR<0.01) on both the frozen tissue (approximately 9.6K genes) and FFPET (approximately 8.1K genes). Analysis of microarray data from frozen tissue revealed fewer differentially expressed genes (approximately 4.64K), and analysis of microarray data on FFPET revealed very few (69) differentially expressed genes. Functional gene set analysis of 3SEQ data from both frozen tissue and FFPET identified biological pathways known to be important in DTF and SFT pathogenesis and suggested several additional candidate oncogenic pathways in these tumors. These findings demonstrate that 3SEQ is an effective technique for gene expression profiling from archival tumor samples and may facilitate significant advances in translational cancer research.

  16. Investigations of Some Liquid Matrixes for Analyte Quantification by MALDI

    NASA Astrophysics Data System (ADS)

    Moon, Jeong Hee; Park, Kyung Man; Ahn, Sung Hee; Lee, Seong Hoon; Kim, Myung Soo

    2015-06-01

    Sample inhomogeneity is one of the obstacles preventing the generation of reproducible mass spectra by MALDI and to their use for the purpose of analyte quantification. As a potential solution to this problem, we investigated MALDI with some liquid matrixes prepared by nonstoichiometric mixing of acids and bases. Out of 27 combinations of acids and bases, liquid matrixes could be produced from seven. When the overall spectral features were considered, two liquid matrixes using α-cyano-4-hydroxycinnamic acid as the acid and 3-aminoquinoline and N,N-diethylaniline as bases were the best choices. In our previous study of MALDI with solid matrixes, we found that three requirements had to be met for the generation of reproducible spectra and for analyte quantification: (1) controlling the temperature by fixing the total ion count, (2) plotting the analyte-to-matrix ion ratio versus the analyte concentration as the calibration curve, and (3) keeping the matrix suppression below a critical value. We found that the same requirements had to be met in MALDI with liquid matrixes as well. In particular, although the liquid matrixes tested here were homogeneous, they failed to display spot-to-spot spectral reproducibility unless the first requirement above was met. We also found that analyte-derived ions could not be produced efficiently by MALDI with the above liquid matrixes unless the analyte was sufficiently basic. In this sense, MALDI processes with solid and liquid matrixes should be regarded as complementary techniques rather than as competing ones.

  17. Quantification Model for Estimating Temperature Field Distributions of Apple Fruit

    NASA Astrophysics Data System (ADS)

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

    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 distribution in the cooling process. Then there was obvious difference between apple fruit temperature and environment temperature. Compared to the change of environment temperature, a long hysteresis phenomenon happened to the temperature of apple fruit body. That is to say, there was a significant temperature change of apple fruit body in a period of time after environment temperature dropping. And then the change of temerature of apple fruit body in the cooling process became slower and slower. This can explain the time delay phenomenon of biology. After that, the temperature differences of every layer increased from centre to surface of apple fruit gradually. That is to say, the minimum temperature differences closed to centre of apple fruit body and the maximum temperature differences closed to the surface of apple fruit body. Finally, the temperature of every part of apple fruit body will tend to consistent and be near to the environment temperature in the cooling process. It was related to the metabolism heat of plant body at any time.

  18. High-throughput quantification of early stages of phagocytosis.

    PubMed

    Yeo, Jeremy Changyu; Wall, Adam Alexander; Stow, Jennifer Lea; Hamilton, Nicholas Ahti

    2013-09-01

    Phagocytosis--the engulfment of cells and foreign bodies--is an important cellular process in innate immunity, development, and disease. Quantification of various stages of phagocytosis, especially in a rapid screening fashion, is an invaluable tool for elucidating protein function during this process. However, current methods for assessing phagocytosis are largely limited to flow cytometry and manual image-based assays, providing limited information. Here, we present an image-based, semi-automated phagocytosis assay to rapidly quantitate three distinct stages during the early engulfment of opsonized beads. Captured images are analyzed using the image-processing software ImageJ and quantified using a macro. Modifications to this method allowed quantification of phagocytosis only in fluorescently labeled transfected cells. Additionally, the time course of bead internalization could be measured using this approach. The assay could discriminate perturbations to stages of phagocytosis induced by known pharmacological inhibitors of filamentous actin and phosphoinositol-3-kinase. Our methodology offers the ability to automatically categorize large amounts of image data into the three early stages of phagocytosis within minutes, clearly demonstrating its potential value in investigating aberrant phagocytosis when manipulating proteins of interest in drug screens and disease.

  19. Quantification of Methylated Selenium, Sulfur, and Arsenic in the Environment

    PubMed Central

    Vriens, Bas; Ammann, Adrian A.; Hagendorfer, Harald; Lenz, Markus; Berg, Michael; Winkel, Lenny H. E.

    2014-01-01

    Biomethylation and volatilization of trace elements may contribute to their redistribution in the environment. However, quantification of volatile, methylated species in the environment is complicated by a lack of straightforward and field-deployable air sampling methods that preserve element speciation. This paper presents a robust and versatile gas trapping method for the simultaneous preconcentration of volatile selenium (Se), sulfur (S), and arsenic (As) species. Using HPLC-HR-ICP-MS and ESI-MS/MS analyses, we demonstrate that volatile Se and S species efficiently transform into specific non-volatile compounds during trapping, which enables the deduction of the original gaseous speciation. With minor adaptations, the presented HPLC-HR-ICP-MS method also allows for the quantification of 13 non-volatile methylated species and oxyanions of Se, S, and As in natural waters. Application of these methods in a peatland indicated that, at the selected sites, fluxes varied between 190–210 ng Se·m−2·d−1, 90–270 ng As·m−2·d−1, and 4–14 µg S·m−2·d−1, and contained at least 70% methylated Se and S species. In the surface water, methylated species were particularly abundant for As (>50% of total As). Our results indicate that methylation plays a significant role in the biogeochemical cycles of these elements. PMID:25047128

  20. A Spanish model for quantification and management of construction waste

    SciTech Connect

    Solis-Guzman, Jaime Marrero, Madelyn; Montes-Delgado, Maria Victoria; Ramirez-de-Arellano, Antonio

    2009-09-15

    Currently, construction and demolition waste (C and D waste) is a worldwide issue that concerns not only governments but also the building actors involved in construction activity. In Spain, a new national decree has been regulating the production and management of C and D waste since February 2008. The present work describes the waste management model that has inspired this decree: the Alcores model implemented with good results in Los Alcores Community (Seville, Spain). A detailed model is also provided to estimate the volume of waste that is expected to be generated on the building site. The quantification of C and D waste volume, from the project stage, is essential for the building actors to properly plan and control its disposal. This quantification model has been developed by studying 100 dwelling projects, especially their bill of quantities, and defining three coefficients to estimate the demolished volume (CT), the wreckage volume (CR) and the packaging volume (CE). Finally, two case studies are included to illustrate the usefulness of the model to estimate C and D waste volume in both new construction and demolition projects.

  1. Quantification of HEV RNA by Droplet Digital PCR

    PubMed Central

    Nicot, Florence; Cazabat, Michelle; Lhomme, Sébastien; Marion, Olivier; Sauné, Karine; Chiabrando, Julie; Dubois, Martine; Kamar, Nassim; Abravanel, Florence; Izopet, Jacques

    2016-01-01

    The sensitivity of real-time PCR for hepatitis E virus (HEV) RNA quantification differs greatly among techniques. Standardized tools that measure the real quantity of virus are needed. We assessed the performance of a reverse transcription droplet digital PCR (RT-ddPCR) assay that gives absolute quantities of HEV RNA. Analytical and clinical validation was done on HEV genotypes 1, 3 and 4, and was based on open reading frame (ORF)3 amplification. The within-run and between-run reproducibilities were very good, the analytical sensitivity was 80 HEV RNA international units (IU)/mL and linearities of HEV genotype 1, 3 and 4 were very similar. Clinical validation based on 45 samples of genotype 1, 3 or 4 gave results that correlated well with a validated reverse transcription quantitative PCR (RT-qPCR) assay (Spearman rs = 0.89, p < 0.0001). The RT-ddPCR assay is a sensitive method and could be a promising tool for standardizing HEV RNA quantification in various sample types. PMID:27548205

  2. Thallium lung-to-heart quantification: three methods of evaluation

    SciTech Connect

    Harler, M.B.; Mahoney, M.; Bartlett, B.; Patel, K.; Turbiner, E.

    1986-12-01

    Lung-to-heart quantification, when used in conjunction with visual assessment of /sup 201/Tl stress test images, has been found useful in diagnosing cardiac dysfunction. The authors evaluated three methods of quantification in terms of inter- and intraobserver variability and reproducibility. Fifty anterior /sup 201/Tl stress images were quantified by each of the following methods: Method A (sum region), which involved one region of interest (ROI) in the measurement of pulmonary activity relative to that of the myocardium; Method B (count density), which required two ROIs, the lung-to-heart ratio being dependent on count density; and Method C (maximum pixel), which used the gray scale of the computer to determine the most intense pixels in the lung field and myocardium. Statistical evaluation has shown that the three methods assess clinical data equally well. Method C was found to be most reproducible in terms of inter- and intraobserver variability followed by Methods A and B. Although nearly equivalent in terms of statistics, the three methods possess inherent differences and therefore should not be used interchangeably without conversion factors.

  3. Generation, Quantification, and Tracing of Metabolically Labeled Fluorescent Exosomes.

    PubMed

    Coscia, Carolina; Parolini, Isabella; Sanchez, Massimo; Biffoni, Mauro; Boussadia, Zaira; Zanetti, Cristiana; Fiani, Maria Luisa; Sargiacomo, Massimo

    2016-01-01

    Over the last 10 years, the constant progression in exosome (Exo)-related studies highlighted the importance of these cell-derived nano-sized vesicles in cell biology and pathophysiology. Functional studies on Exo uptake and intracellular trafficking require accurate quantification to assess sufficient and/or necessary Exo particles quantum able to elicit measurable effects on target cells. We used commercially available BODIPY(®) fatty acid analogues to label a primary melanoma cell line (Me501) that highly and spontaneously secrete nanovesicles. Upon addition to cell culture, BODIPY fatty acids are rapidly incorporated into major phospholipid classes ultimately producing fluorescent Exo as direct result of biogenesis. Our metabolic labeling protocol produced bright fluorescent Exo that can be examined and quantified with conventional non-customized flow cytometry (FC) instruments by exploiting their fluorescent emission rather than light-scattering detection. Furthermore, our methodology permits the measurement of single Exo-associated fluorescence transfer to cells making quantitative the correlation between Exo uptake and activation of cellular processes. Thus the protocol presented here appears as an appropriate tool to who wants to investigate mechanisms of Exo functions in that it allows for direct and rapid characterization and quantification of fluorescent Exo number, intensity, size, and eventually evaluation of their kinetic of uptake/secretion in target cells. PMID:27317184

  4. Applying uncertainty quantification to multiphase flow computational fluid dynamics

    SciTech Connect

    Gel, A; Garg, R; Tong, C; Shahnam, M; Guenther, C

    2013-07-01

    Multiphase computational fluid dynamics plays a major role in design and optimization of fossil fuel based reactors. There is a growing interest in accounting for the influence of uncertainties associated with physical systems to increase the reliability of computational simulation based engineering analysis. The U.S. Department of Energy's National Energy Technology Laboratory (NETL) has recently undertaken an initiative to characterize uncertainties associated with computer simulation of reacting multiphase flows encountered in energy producing systems such as a coal gasifier. The current work presents the preliminary results in applying non-intrusive parametric uncertainty quantification and propagation techniques with NETL's open-source multiphase computational fluid dynamics software MFIX. For this purpose an open-source uncertainty quantification toolkit, PSUADE developed at the Lawrence Livermore National Laboratory (LLNL) has been interfaced with MFIX software. In this study, the sources of uncertainty associated with numerical approximation and model form have been neglected, and only the model input parametric uncertainty with forward propagation has been investigated by constructing a surrogate model based on data-fitted response surface for a multiphase flow demonstration problem. Monte Carlo simulation was employed for forward propagation of the aleatory type input uncertainties. Several insights gained based on the outcome of these simulations are presented such as how inadequate characterization of uncertainties can affect the reliability of the prediction results. Also a global sensitivity study using Sobol' indices was performed to better understand the contribution of input parameters to the variability observed in response variable.

  5. Simple and inexpensive quantification of ammonia in whole blood.

    PubMed

    Ayyub, Omar B; Behrens, Adam M; Heligman, Brian T; Natoli, Mary E; Ayoub, Joseph J; Cunningham, Gary; Summar, Marshall; Kofinas, Peter

    2015-01-01

    Quantification of ammonia in whole blood has applications in the diagnosis and management of many hepatic diseases, including cirrhosis and rare urea cycle disorders, amounting to more than 5 million patients in the United States. Current techniques for ammonia measurement suffer from limited range, poor resolution, false positives or large, complex sensor set-ups. Here we demonstrate a technique utilizing inexpensive reagents and simple methods for quantifying ammonia in 100 μL of whole blood. The sensor comprises a modified form of the indophenol reaction, which resists sources of destructive interference in blood, in conjunction with a cation-exchange membrane. The presented sensing scheme is selective against other amine containing molecules such as amino acids and has a shelf life of at least 50 days. Additionally, the resulting system has high sensitivity and allows for the accurate reliable quantification of ammonia in whole human blood samples at a minimum range of 25 to 500 μM, which is clinically for rare hyperammonemic disorders and liver disease. Furthermore, concentrations of 50 and 100 μM ammonia could be reliably discerned with p = 0.0001.

  6. Instantaneous Wavenumber Estimation for Damage Quantification in Layered Plate Structures

    NASA Technical Reports Server (NTRS)

    Mesnil, Olivier; Leckey, Cara A. C.; Ruzzene, Massimo

    2014-01-01

    This paper illustrates the application of instantaneous and local wavenumber damage quantification techniques for high frequency guided wave interrogation. The proposed methodologies can be considered as first steps towards a hybrid structural health monitoring/ nondestructive evaluation (SHM/NDE) approach for damage assessment in composites. The challenges and opportunities related to the considered type of interrogation and signal processing are explored through the analysis of numerical data obtained via EFIT simulations of damage in CRFP plates. Realistic damage configurations are modeled from x-ray CT scan data of plates subjected to actual impacts, in order to accurately predict wave-damage interactions in terms of scattering and mode conversions. Simulation data is utilized to enhance the information provided by instantaneous and local wavenumbers and mitigate the complexity related to the multi-modal content of the plate response. Signal processing strategies considered for this purpose include modal decoupling through filtering in the frequency/wavenumber domain, the combination of displacement components, and the exploitation of polarization information for the various modes as evaluated through the dispersion analysis of the considered laminate lay-up sequence. The results presented assess the effectiveness of the proposed wavefield processing techniques as a hybrid SHM/NDE technique for damage detection and quantification in composite, plate-like structures.

  7. Unilateral Condylar Hyperplasia: A 3-Dimensional Quantification of Asymmetry

    PubMed Central

    Maal, Thomas J. J.; Bergé, Stefaan J.; Becking, Alfred G.

    2013-01-01

    Purpose Objective quantifications of facial asymmetry in patients with Unilateral Condylar Hyperplasia (UCH) have not yet been described in literature. The aim of this study was to objectively quantify soft-tissue asymmetry in patients with UCH and to compare the findings with a control group using a new method. Material and Methods Thirty 3D photographs of patients diagnosed with UCH were compared with 30 3D photographs of healthy controls. As UCH presents particularly in the mandible, a new method was used to isolate the lower part of the face to evaluate asymmetry of this part separately. The new method was validated by two observers using 3D photographs of five patients and five controls. Results A significant difference (0.79 mm) between patients and controls whole face asymmetry was found. Intra- and inter-observer differences of 0.011 mm (−0.034–0.011) and 0.017 mm (−0.007–0.042) respectively were found. These differences are irrelevant in clinical practice. Conclusion After objective quantification, a significant difference was identified in soft-tissue asymmetry between patients with UCH and controls. The method used to isolate mandibular asymmetry was found to be valid and a suitable tool to evaluate facial asymmetry. PMID:23544063

  8. Quantification of liver fibrosis in chronic hepatitis B virus infection

    PubMed Central

    Jieanu, CF; Ungureanu, BS; Săndulescu, DL; Gheonea, IA; Tudorașcu, DR; Ciurea, ME; Purcărea, VL

    2015-01-01

    Chronic hepatitis B virus infection (HBV) is considered a global public issue with more than 78.000 people per year dying of its evolution. With liver transplantation as the only viable therapeutic option but only in end-stage disease, hepatitis B progression may generally be influenced by various factors. Assessing fibrosis stage plays an important part in future decisions on the patients’ wealth with available antiviral agents capable of preventing fibrosis passing to an end-stage liver disease. Several methods have been taken into consideration as an alternative for HBV quantification status, such as imaging techniques and serum based biomarkers. Magnetic resonance imaging, ultrasound, and elastography are considered non-invasive imaging techniques frequently used to quantify disease progression as well as patients future prognostic. Consequently, both direct and indirect biomarkers have been studied for differentiating between fibrosis stages. This paper reviews the current standings in HBV non-invasive liver fibrosis quantification, presenting the prognostic factors and available assessment procedures that might eventually replace liver biopsy. PMID:26351528

  9. Functional error modeling for uncertainty quantification in hydrogeology

    NASA Astrophysics Data System (ADS)

    Josset, L.; Ginsbourger, D.; Lunati, I.

    2015-02-01

    Approximate models (proxies) can be employed to reduce the computational costs of estimating uncertainty. The price to pay is that the approximations introduced by the proxy model can lead to a biased estimation. To avoid this problem and ensure a reliable uncertainty quantification, we propose to combine functional data analysis and machine learning to build error models that allow us to obtain an accurate prediction of the exact response without solving the exact model for all realizations. We build the relationship between proxy and exact model on a learning set of geostatistical realizations for which both exact and approximate solvers are run. Functional principal components analysis (FPCA) is used to investigate the variability in the two sets of curves and reduce the dimensionality of the problem while maximizing the retained information. Once obtained, the error model can be used to predict the exact response of any realization on the basis of the sole proxy response. This methodology is purpose-oriented as the error model is constructed directly for the quantity of interest, rather than for the state of the system. Also, the dimensionality reduction performed by FPCA allows a diagnostic of the quality of the error model to assess the informativeness of the learning set and the fidelity of the proxy to the exact model. The possibility of obtaining a prediction of the exact response for any newly generated realization suggests that the methodology can be effectively used beyond the context of uncertainty quantification, in particular for Bayesian inference and optimization.

  10. Ultrasound strain imaging for quantification of tissue function: cardiovascular applications

    NASA Astrophysics Data System (ADS)

    de Korte, Chris L.; Lopata, Richard G. P.; Hansen, Hendrik H. G.

    2013-03-01

    With ultrasound imaging, the motion and deformation of tissue can be measured. Tissue can be deformed by applying a force on it and the resulting deformation is a function of its mechanical properties. Quantification of this resulting tissue deformation to assess the mechanical properties of tissue is called elastography. If the tissue under interrogation is actively deforming, the deformation is directly related to its function and quantification of this deformation is normally referred as `strain imaging'. Elastography can be used for atherosclerotic plaques characterization, while the contractility of the heart or skeletal muscles can be assessed with strain imaging. We developed radio frequency (RF) based ultrasound methods to assess the deformation at higher resolution and with higher accuracy than commercial methods using conventional image data (Tissue Doppler Imaging and 2D speckle tracking methods). However, the improvement in accuracy is mainly achieved when measuring strain along the ultrasound beam direction, so 1D. We further extended this method to multiple directions and further improved precision by using compounding of data acquired at multiple beam steered angles. In arteries, the presence of vulnerable plaques may lead to acute events like stroke and myocardial infarction. Consequently, timely detection of these plaques is of great diagnostic value. Non-invasive ultrasound strain compounding is currently being evaluated as a diagnostic tool to identify the vulnerability of plaques. In the heart, we determined the strain locally and at high resolution resulting in a local assessment in contrary to conventional global functional parameters like cardiac output or shortening fraction.

  11. Quantification of cumulated physical fatigue at the workplace.

    PubMed

    Pichot, Vincent; Bourin, Emmanuelle; Roche, Frédéric; Garet, Martin; Gaspoz, Jean-Michel; Duverney, David; Antoniadis, Anestis; Lacour, Jean-René; Barthélémy, Jean-Claude

    2002-11-01

    Quantification of physical fatigue remains a challenge. We hypothesized that its effects on central autonomic nervous system activity could be explored for such a quantification. To test this relationship, we prospectively measured central autonomic nervous activity through nocturnal heart rate variability (HRV) in six French garbage collectors, aged 32.1+/-4.3 years, twice a week during 3 consecutive weeks of work, and during the following week of rest. Eight healthy sedentary males formed a control group. HRV indices were calculated by applying standard temporal domain and wavelet transform analyses to standard ECG recordings. During the 3 consecutive weeks of work, there was a significantly progressive decrease in HRV indices, particularly pNN50 (-34.2%, P<0.05), as well as the high (-33.3%, P<0.05) and low (-22.2%, P<0.01) frequency components of wavelet transform, while there was an increase, although non-significant, of the ratio of low to high frequencies (9.1%). During the resting period, there was a significant recovery of HRV indices, notably of its high (50.0%, P<0.05) and low (28.6%, P<0.05) frequency components. No such changes occurred in the control group. A central signature of cumulated physical fatigue can thus be detected and quantified through nocturnal autonomic nervous system activity. Its characteristics are those of a progressive parasympathetic withdrawal.

  12. Uncertainty Quantification in State Estimation using the Probabilistic Collocation Method

    SciTech Connect

    Lin, Guang; Zhou, Ning; Ferryman, Thomas A.; Tuffner, Francis K.

    2011-03-23

    In this study, a new efficient uncertainty quantification technique, probabilistic collocation method (PCM) on sparse grid points is employed to enable the evaluation of uncertainty in state estimation. The PCM allows us to use just a small number of ensembles to quantify the uncertainty in estimating the state variables of power systems. By sparse grid points, the PCM approach can handle large number of uncertain parameters in power systems with relatively lower computational cost, when comparing with classic Monte Carlo (MC) simulations. The algorithm and procedure is outlined and we demonstrate the capability and illustrate the application of PCM on sparse grid points approach on uncertainty quantification in state estimation of the IEEE 14 bus model as an example. MC simulations have also been conducted to verify accuracy of the PCM approach. By comparing the results obtained from MC simulations with PCM results for mean and standard deviation of uncertain parameters, it is evident that the PCM approach is computationally more efficient than MC simulations.

  13. An on-bacterium flow cytometric immunoassay for protein quantification.

    PubMed

    Lan, Wen-Jun; Lan, Wei; Wang, Hai-Yan; Yan, Lei; Wang, Zhe-Li

    2013-09-01

    The polystyrene bead-based flow cytometric immunoassay has been widely reported. However, the preparation of functional polystyrene bead is still inconvenient. This study describes a simple and easy on-bacterium flow cytometric immunoassay for protein quantification, in which Staphylococcus aureus (SAC) is used as an antibody-antigen carrier to replace the polystyrene bead. The SAC beads were prepared by carboxyfluorescein diacetate succinimidyl ester (CFSE) labeling, paraformaldehyde fixation and antibody binding. Carcinoembryonic antigen (CEA) and cytokeratin-19 fragment (CYFRA 21-1) proteins were used as models in the test system. Using prepared SAC beads, biotinylated proteins, and streptavidin-phycoerythrin (SA-PE), the on-bacterium flow cytometric immunoassay was validated by quantifying CEA and CYFRA 21-1 in sample. Obtained data demonstrated a concordant result between the logarithm of the protein concentration and the logarithm of the PE mean fluorescence intensity (MFI). The limit of detection (LOD) in this immunoassay was at least 0.25 ng/ml. Precision and accuracy assessments appeared that either the relative standard deviation (R.S.D.) or the relative error (R.E.) was <10%. The comparison between this immunoassay and a polystyrene bead-based flow cytometric immunoassay showed a correlation coefficient of 0.998 for serum CEA or 0.996 for serum CYFRA 21-1. In conclusion, the on-bacterium flow cytometric immunoassay may be of use in the quantification of serum protein. PMID:23739299

  14. A critical view on microplastic quantification in aquatic organisms.

    PubMed

    Vandermeersch, Griet; Van Cauwenberghe, Lisbeth; Janssen, Colin R; Marques, Antonio; Granby, Kit; Fait, Gabriella; Kotterman, Michiel J J; Diogène, Jorge; Bekaert, Karen; Robbens, Johan; Devriese, Lisa

    2015-11-01

    Microplastics, plastic particles and fragments smaller than 5mm, are ubiquitous in the marine environment. Ingestion and accumulation of microplastics have previously been demonstrated for diverse marine species ranging from zooplankton to bivalves and fish, implying the potential for microplastics to accumulate in the marine food web. In this way, microplastics can potentially impact food safety and human health. Although a few methods to quantify microplastics in biota have been described, no comparison and/or intercalibration of these techniques have been performed. Here we conducted a literature review on all available extraction and quantification methods. Two of these methods, involving wet acid destruction, were used to evaluate the presence of microplastics in field-collected mussels (Mytilus galloprovincialis) from three different "hotspot" locations in Europe (Po estuary, Italy; Tagus estuary, Portugal; Ebro estuary, Spain). An average of 0.18±0.14 total microplastics g(-1) w.w. for the Acid mix Method and 0.12±0.04 total microplastics g(-1) w.w. for the Nitric acid Method was established. Additionally, in a pilot study an average load of 0.13±0.14 total microplastics g(-1) w.w. was recorded in commercial mussels (Mytilus edulis and M. galloprovincialis) from five European countries (France, Italy, Denmark, Spain and The Netherlands). A detailed analysis and comparison of methods indicated the need for further research to develop a standardised operating protocol for microplastic quantification and monitoring.

  15. Guided Wave Delamination Detection and Quantification With Wavefield Data Analysis

    NASA Technical Reports Server (NTRS)

    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.

  16. Concurrent quantification of tryptophan and its major metabolites.

    PubMed

    Lesniak, Wojciech G; Jyoti, Amar; Mishra, Manoj K; Louissaint, Nicolette; Romero, Roberto; Chugani, Diane C; Kannan, Sujatha; Kannan, Rangaramanujam M

    2013-12-15

    An imbalance in tryptophan (TRP) metabolites is associated with several neurological and inflammatory disorders. Therefore, analytical methods allowing for simultaneous quantification of TRP and its major metabolites would be highly desirable, and may be valuable as potential biomarkers. We have developed a HPLC method for concurrent quantitative determination of tryptophan, serotonin, 5-hydroxyindoleacetic acid, kynurenine, and kynurenic acid in tissue and fluids. The method utilizes the intrinsic spectroscopic properties of TRP and its metabolites that enable UV absorbance and fluorescence detection by HPLC, without additional labeling. The origin of the peaks related to analytes of interest was confirmed by UV-Vis spectral patterns using a PDA detector and mass spectrometry. The developed methods were validated in rabbit fetal brain and amniotic fluid at gestational day 29. Results are in excellent agreement with those reported in the literature for the same regions. This method allows for rapid quantification of tryptophan and four of its major metabolites concurrently. A change in the relative ratios of these metabolites can provide important insights in predicting the presence and progression of neuroinflammation in disorders such as cerebral palsy, autism, multiple sclerosis, Alzheimer disease, and schizophrenia. PMID:24036037

  17. Quantification of 5-methyl-2'-deoxycytidine in the DNA.

    PubMed

    Giel-Pietraszuk, Małgorzata; Insińska-Rak, Małgorzata; Golczak, Anna; Sikorski, Marek; Barciszewska, Mirosława; Barciszewski, Jan

    2015-01-01

    Methylation at position 5 of cytosine (Cyt) at the CpG sequences leading to formation of 5-methyl-cytosine (m(5)Cyt) is an important element of epigenetic regulation of gene expression. Modification of the normal methylation pattern, unique to each organism, leads to the development of pathological processes and diseases, including cancer. Therefore, quantification of the DNA methylation and analysis of changes in the methylation pattern is very important from a practical point of view and can be used for diagnostic purposes, as well as monitoring of the treatment progress. In this paper we present a new method for quantification of 5-methyl-2'deoxycytidine (m(5)C) in the DNA. The technique is based on conversion of m(5)C into fluorescent 3,N(4)-etheno-5-methyl-2'deoxycytidine (εm(5)C) and its identification by reversed-phase high-performance liquid chromatography (RP-HPLC). The assay was used to evaluate m(5)C concentration in DNA of calf thymus and peripheral blood of cows bred under different conditions. This approach can be applied for measuring of 5-methylcytosine in cellular DNA from different cells and tissues. PMID:26098716

  18. Structural quantification of cartilage changes using statistical parametric mapping

    NASA Astrophysics Data System (ADS)

    Tamez-Peña, José Gerardo; Barbu-McInnis, Monica; Totterman, Saara

    2007-03-01

    The early detection of Osteoarthritis (OA) treatment efficacy requires monitoring of small changes in cartilage morphology. Current approaches rely in carefully monitoring global cartilage parameters. However, they are not very sensitive to the detection of focal morphological changes in cartilage structure. This work presents the use of the statistical parametric mapping (SPM) for the detection and quantification of changes in cartilage morphology. The SPM is computed by first registering the baseline and the follow-up three dimensional (3D) reconstructions of the cartilage tissue. Once the registration is complete, the thickness changes for every cartilage point is computed which is followed by a model based estimation of the variance of thickness error. The cartilage thickness change and the variance estimations are used to compute the z-score map. The map is used to visualize and quantify significant changes in cartilage thickness. The z-map quantification provides the area of significant changes, the associated volume of changes as well as the average thickness of cartilage loss. Furthermore, thickness change distributions functions are normalized to provide the probability distribution functions (PDF). The PDF can be used to understand and quantify the differences among different treatment groups. The performance of the approach on simulated data and real subject data will be presented.

  19. Quantification of HEV RNA by Droplet Digital PCR.

    PubMed

    Nicot, Florence; Cazabat, Michelle; Lhomme, Sébastien; Marion, Olivier; Sauné, Karine; Chiabrando, Julie; Dubois, Martine; Kamar, Nassim; Abravanel, Florence; Izopet, Jacques

    2016-01-01

    The sensitivity of real-time PCR for hepatitis E virus (HEV) RNA quantification differs greatly among techniques. Standardized tools that measure the real quantity of virus are needed. We assessed the performance of a reverse transcription droplet digital PCR (RT-ddPCR) assay that gives absolute quantities of HEV RNA. Analytical and clinical validation was done on HEV genotypes 1, 3 and 4, and was based on open reading frame (ORF)3 amplification. The within-run and between-run reproducibilities were very good, the analytical sensitivity was 80 HEV RNA international units (IU)/mL and linearities of HEV genotype 1, 3 and 4 were very similar. Clinical validation based on 45 samples of genotype 1, 3 or 4 gave results that correlated well with a validated reverse transcription quantitative PCR (RT-qPCR) assay (Spearman rs = 0.89, p < 0.0001). The RT-ddPCR assay is a sensitive method and could be a promising tool for standardizing HEV RNA quantification in various sample types. PMID:27548205

  20. Targeted cofactor quantification in metabolically engineered E. coli using solid phase extraction and hydrophilic interaction liquid chromatography-mass spectrometry.

    PubMed

    Li, Zhucui; Yang, Afang; Li, Yujing; Liu, Pingping; Zhang, Zhidan; Zhang, Xueli; Shui, Wenqing

    2016-03-01

    Quantification of energy and redox cofactors is of great value to synthetic biologists to infer the balance of energy metabolism in engineered microbial strains and assess each strain's potential for further improvement. Most currently used methods for intracellular cofactor measurement suffer from incomplete coverage, low reproducibility, suboptimal sensitivity or specificity. In this study, we described an SPE-HILIC/MS approach for simultaneous determination of six cofactor targets (ATP, ADP, NAD, NADH, NADP, NADPH) in Escherichia coli cells. Sufficient linearity, precision and metabolite recoveries of this new approach justified its reliability in targeted cofactor quantification. Our approach was then compared with conventional enzymatic assays to demonstrate its superior performance. We applied the SPE-HILIC/MS approach to profile shift of cofactor balances in several engineered E. coli strains with varying isobutanol production. Our cofactor analysis clearly revealed that optimal energy fitness was achieved in the highest-yield strain through combined modulation of a transhydrogenase and a NAD(+) kinase. Apart from the targeted cofactors, the SPE enrichment procedure also allowed for confident identification of 39 groups of polar metabolites mainly involved in central carbon metabolism in E. coli cells.

  1. Sensitive and simultaneous quantification of zinc pyrithione and climbazole deposition from anti-dandruff shampoos onto human scalp.

    PubMed

    Chen, Guoqiang; Miao, Miao; Hoptroff, Michael; Fei, Xiaoqing; Collins, Luisa Z; Jones, Andrew; Janssen, Hans-Gerd

    2015-10-15

    A sensitive ultrahigh performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method has been developed and validated for simultaneous quantification of zinc pyrithione (ZPT) and climbazole (CBZ) deposited onto human scalp from anti-dandruff (AD) shampoos. Scrubbing with a buffer solution was used as the sampling method for the extraction of ZPT and CBZ from scalp. Derivatization of ZPT was carried out prior to UHPLC-MS/MS analysis. The identification of ZPT and CBZ was performed by examining ratios of selected multiple reaction monitoring (MRM) transitions in combination with UHPLC retention times. The limit of detection for ZPT and CBZ was established to be 1 and 2ng/mL, respectively. This sensitivity enables the quantification of ZPT and CBZ at deposition levels in the low ng/cm(2) range. The method was successfully applied for the analysis of scalp buffer scrub samples from an in vivo study. The levels of ZPT and CBZ deposited on the scalp at different time points after application of the AD shampoo were measured. The results revealed that dual-active AD shampoo delivered more ZPT onto the scalp in a single wash than single active shampoo did. The amount of ZPT and CBZ retained on the scalp after AD shampoo application declined over 72h.

  2. In-depth evaluation of software tools for data-independent acquisition based label-free quantification.

    PubMed

    Kuharev, Jörg; Navarro, Pedro; Distler, Ute; Jahn, Olaf; Tenzer, Stefan

    2015-09-01

    Label-free quantification (LFQ) based on data-independent acquisition workflows currently experiences increasing popularity. Several software tools have been recently published or are commercially available. The present study focuses on the evaluation of three different software packages (Progenesis, synapter, and ISOQuant) supporting ion mobility enhanced data-independent acquisition data. In order to benchmark the LFQ performance of the different tools, we generated two hybrid proteome samples of defined quantitative composition containing tryptically digested proteomes of three different species (mouse, yeast, Escherichia coli). This model dataset simulates complex biological samples containing large numbers of both unregulated (background) proteins as well as up- and downregulated proteins with exactly known ratios between samples. We determined the number and dynamic range of quantifiable proteins and analyzed the influence of applied algorithms (retention time alignment, clustering, normalization, etc.) on quantification results. Analysis of technical reproducibility revealed median coefficients of variation of reported protein abundances below 5% for MS(E) data for Progenesis and ISOQuant. Regarding accuracy of LFQ, evaluation with synapter and ISOQuant yielded superior results compared to Progenesis. In addition, we discuss reporting formats and user friendliness of the software packages. The data generated in this study have been deposited to the ProteomeXchange Consortium with identifier PXD001240 (http://proteomecentral.proteomexchange.org/dataset/PXD001240).

  3. Target detection and quantification using a hybrid hand-held diffuse optical tomography and photoacoustic tomography system

    NASA Astrophysics Data System (ADS)

    Kumavor, Patrick D.; Xu, Chen; Aguirre, Andres; Gamelin, John; Ardeshirpour, Yasaman; Tavakoli, Behnoosh; Zanganeh, Saeid; Alqasemi, Umar; Yang, Yi; Zhu, Quing

    2011-04-01

    We present a photoacoustic tomography-guided diffuse optical tomography approach using a hand-held probe for detection and characterization of deeply-seated targets embedded in a turbid medium. Diffuse optical tomography guided by coregistered ultrasound, MRI, and x ray has demonstrated a great clinical potential to overcome lesion location uncertainty and to improve light quantification accuracy. However, due to the different contrast mechanisms, some lesions may not be detectable by a nonoptical modality but yet have high optical contrast. Photoacoustic tomography utilizes a short-pulsed laser beam to diffusively penetrate into tissue. Upon absorption of the light by the target, photoacoustic waves are generated and used to reconstruct, at ultrasound resolution, the optical absorption distribution that reveals optical contrast. However, the robustness of optical property quantification of targets by photoacoustic tomography is complicated because of the wide range of ultrasound transducer sensitivity, the orientation and shape of the targets relative to the ultrasound array, and the uniformity of the laser beam. We show in this paper that the relative optical absorption map provided by photoacoustic tomography can potentially guide the diffuse optical tomography to accurately reconstruct target absorption maps.

  4. Evaluating the use of a continuous approximation for model-based quantification of pulsed chemical exchange saturation transfer (CEST)

    NASA Astrophysics Data System (ADS)

    Tee, Y. K.; Khrapitchev, A. A.; Sibson, N. R.; Payne, S. J.; Chappell, M. A.

    2012-09-01

    Many potential clinical applications of chemical exchange saturation transfer (CEST) have been studied in recent years. However, due to various limitations such as specific absorption rate guidelines and scanner hardware constraints, most of the proposed applications have yet to be translated into routine diagnostic tools. Currently, pulsed CEST which uses multiple short pulses to perform the saturation is the only viable irradiation scheme for clinical translation. However, performing quantitative model-based analysis on pulsed CEST is time consuming because it is necessary to account for the time dependent amplitude of the saturation pulses. As a result, pulsed CEST is generally treated as continuous CEST by finding its equivalent average field or power. Nevertheless, theoretical analysis and simulations reveal that the resulting magnetization is different when the different irradiation schemes are applied. In this study, the quantification of important model parameters such as the amine proton exchange rate from a pulsed CEST experiment using quantitative model-based analyses were examined. Two model-based approaches were considered - discretized and continuous approximation to the time dependent RF irradiation pulses. The results showed that the discretized method was able to fit the experimental data substantially better than its continuous counterpart, but the smaller fitted error of the former did not translate to significantly better fit for the important model parameters. For quantification of the endogenous CEST effect, such as in amide proton transfer imaging, a model-based approach using the average power equivalent saturation can thus be used in place of the discretized approximation.

  5. Sensitive and simultaneous quantification of zinc pyrithione and climbazole deposition from anti-dandruff shampoos onto human scalp.

    PubMed

    Chen, Guoqiang; Miao, Miao; Hoptroff, Michael; Fei, Xiaoqing; Collins, Luisa Z; Jones, Andrew; Janssen, Hans-Gerd

    2015-10-15

    A sensitive ultrahigh performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) method has been developed and validated for simultaneous quantification of zinc pyrithione (ZPT) and climbazole (CBZ) deposited onto human scalp from anti-dandruff (AD) shampoos. Scrubbing with a buffer solution was used as the sampling method for the extraction of ZPT and CBZ from scalp. Derivatization of ZPT was carried out prior to UHPLC-MS/MS analysis. The identification of ZPT and CBZ was performed by examining ratios of selected multiple reaction monitoring (MRM) transitions in combination with UHPLC retention times. The limit of detection for ZPT and CBZ was established to be 1 and 2ng/mL, respectively. This sensitivity enables the quantification of ZPT and CBZ at deposition levels in the low ng/cm(2) range. The method was successfully applied for the analysis of scalp buffer scrub samples from an in vivo study. The levels of ZPT and CBZ deposited on the scalp at different time points after application of the AD shampoo were measured. The results revealed that dual-active AD shampoo delivered more ZPT onto the scalp in a single wash than single active shampoo did. The amount of ZPT and CBZ retained on the scalp after AD shampoo application declined over 72h. PMID:26397749

  6. Proteomic Quantification and Site-Mapping of S-Nitrosylated Proteins Using Isobaric iodoTMT Reagents

    PubMed Central

    2015-01-01

    S-Nitrosylation is a redox-based protein post-translational modification in response to nitric oxide signaling and is involved in a wide range of biological processes. Detection and quantification of protein S-nitrosylation have been challenging tasks due to instability and low abundance of the modification. Many studies have used mass spectrometry (MS)-based methods with different thiol-reactive reagents to label and identify proteins with S-nitrosylated cysteine (SNO-Cys). In this study, we developed a novel iodoTMT switch assay (ISA) using an isobaric set of thiol-reactive iodoTMTsixplex reagents to specifically detect and quantify protein S-nitrosylation. Irreversible labeling of SNO-Cys with the iodoTMTsixplex reagents enables immune-affinity detection of S-nitrosylated proteins, enrichment of iodoTMT-labeled peptides by anti-TMT resin, and importantly, unambiguous modification site-mapping and multiplex quantification by liquid chromatography–tandem MS. Additionally, we significantly improved anti-TMT peptide enrichment efficiency by competitive elution. Using ISA, we identified a set of SNO-Cys sites responding to lipopolysaccharide (LPS) stimulation in murine BV-2 microglial cells and revealed effects of S-allyl cysteine from garlic on LPS-induced protein S-nitrosylation in antioxidative signaling and mitochondrial metabolic pathways. ISA proved to be an effective proteomic approach for quantitative analysis of S-nitrosylation in complex samples and will facilitate the elucidation of molecular mechanisms of nitrosative stress in disease. PMID:24926564

  7. Microwave- and ultrasound-assisted extraction of vanillin and its quantification by high-performance liquid chromatography in Vanilla planifolia.

    PubMed

    Sharma, Anuj; Verma, Subash Chandra; Saxena, Nisha; Chadda, Neetu; Singh, Narendra Pratap; Sinha, Arun Kumar

    2006-03-01

    Microwave-assisted extraction (MAE), ultrasound-assisted extraction (UAE) and conventional extraction of vanillin and its quantification by HPLC in pods of Vanilla planifolia is described. A range of nonpolar to polar solvents were used for the extraction of vanillin employing MAE, UAE and conventional methods. Various extraction parameters such as nature of the solvent, solvent volume, time of irradiation, microwave and ultrasound energy inputs were optimized. HPLC was performed on RP ODS column (4.6 mm ID x 250 mm, 5 microm, Waters), a photodiode array detector (Waters 2996) using gradient solvent system of ACN and ortho-phosphoric acid in water (0.001:99.999 v/v) at 25 degrees C. Regression equation revealed a linear relationship (r2 > 0.9998) between the mass of vanillin injected and the peak areas. The detection limit (S/N = 3) and limit of quantification (S/N = 10) were 0.65 and 1.2 microg/g, respectively. Recovery was achieved in the range 98.5-99.6% for vanillin. Maximum yield of vanilla extract (29.81, 29.068 and 14.31% by conventional extraction, MAE and UAE, respectively) was found in a mixture of ethanol/water (40:60 v/v). Dehydrated ethanolic extract showed the highest amount of vanillin (1.8, 1.25 and 0.99% by MAE, conventional extraction and UAE, respectively).

  8. Identification and quantification of triacylglycerols containing n-3 long-chain polyunsaturated fatty acids in bovine milk.

    PubMed

    Liu, Zhiqian; Moate, Peter; Ezerniks, Vilnis; Cocks, Benjamin G; Rochfort, Simone

    2015-12-01

    The n-3 long-chain polyunsaturated fatty acids (LC-PUFA) are low-abundance components in milk fat, but have great potential in promoting human health. A comprehensive survey on triacylglycerol (TAG) molecular species in milk that contain at least one type of n-3 LC-PUFA, namely eicosapentaenoic acid, docosahexaenoic acid, and docosapentaenoic acid, was conducted in this work using HPLC-linear trap quadrupole-Orbitrap and HPLC-triple quadrupole mass spectrometry techniques. A total of 51 TAG species that contain n-3 LC-PUFA have been identified in bovine milk and their structures assigned. The TAG species containing docosahexaenoic acid were found in much smaller number and at much lower abundance compared with the other 2 types of TAG. An HPLC-triple quadrupole mass spectrometry-based method was developed, which provides relative quantification of all these TAG species in a run of 36 min. Application of this method to the quantification of n-3 LC-PUFA-incorporated TAG in 32 individual animal milk samples allowed us to determine variation between animals, identify strong metabolic relationships between TAG species, and reveal negative effect of a grape marc supplement on the accumulation of eicosapentaenoic acid in milk.

  9. Identification and quantification of triacylglycerols containing n-3 long-chain polyunsaturated fatty acids in bovine milk.

    PubMed

    Liu, Zhiqian; Moate, Peter; Ezerniks, Vilnis; Cocks, Benjamin G; Rochfort, Simone

    2015-12-01

    The n-3 long-chain polyunsaturated fatty acids (LC-PUFA) are low-abundance components in milk fat, but have great potential in promoting human health. A comprehensive survey on triacylglycerol (TAG) molecular species in milk that contain at least one type of n-3 LC-PUFA, namely eicosapentaenoic acid, docosahexaenoic acid, and docosapentaenoic acid, was conducted in this work using HPLC-linear trap quadrupole-Orbitrap and HPLC-triple quadrupole mass spectrometry techniques. A total of 51 TAG species that contain n-3 LC-PUFA have been identified in bovine milk and their structures assigned. The TAG species containing docosahexaenoic acid were found in much smaller number and at much lower abundance compared with the other 2 types of TAG. An HPLC-triple quadrupole mass spectrometry-based method was developed, which provides relative quantification of all these TAG species in a run of 36 min. Application of this method to the quantification of n-3 LC-PUFA-incorporated TAG in 32 individual animal milk samples allowed us to determine variation between animals, identify strong metabolic relationships between TAG species, and reveal negative effect of a grape marc supplement on the accumulation of eicosapentaenoic acid in milk. PMID:26476942

  10. 21 CFR 530.24 - Procedure for announcing analytical methods for drug residue quantification.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Procedure for announcing analytical methods for...-Producing Animals § 530.24 Procedure for announcing analytical methods for drug residue quantification. (a) FDA may issue an order announcing a specific analytical method or methods for the quantification...

  11. Towards efficient uncertainty quantification in complex and large-scale biomechanical problems based on a Bayesian multi-fidelity scheme.

    PubMed

    Biehler, Jonas; Gee, Michael W; Wall, Wolfgang A

    2015-06-01

    . Additionally, the employed approach results in a tremendous reduction of computational costs, rendering uncertainty quantification with complex patient-specific nonlinear biomechanical models practical for the first time. Second, we also analyze the impact of the uncertainty in the input parameter on mechanical quantities typically related to abdominal aortic aneurysm rupture potential such as von Mises stress, von Mises strain and strain energy. Thus, providing first estimates on the variability of these mechanical quantities due to an uncertain constitutive parameter, and revealing the potential error made by assuming population averaged mean values in patient-specific simulations of abdominal aortic aneurysms. Moreover, the influence of correlation length of the random field is investigated in a parameter study using MC.

  12. Optical methods for the quantification of the fibrillation degree of bleached MFC materials.

    PubMed

    Chinga-Carrasco, Gary

    2013-05-01

    In this study, the suitability of optical devices for quantification of the fibrillation degree of bleached microfibrillated cellulose (MFC) materials has been assessed. The techniques for optical assessment include optical scanner, UV-vis spectrophotometry, turbidity, quantification of the fiber fraction and a camera system for dynamic measurements. The results show that the assessed optical devices are most adequate for quantification of the light transmittance of bleached MFC materials. Such quantification yields an estimation of the fibrillation degree. Films made of poorly fibrillated materials are opaque, while films made of highly fibrillated materials containing a major fraction of nanofibrils are translucent, with light transmittance larger than 90%. Finally, the concept of using images acquired with a CCD camera system, for estimating the fibrillation degree in dynamic conditions was exemplified. Such systems are most interesting as this will widen the applicability of optical methods for quantification of fibrillation degree online in production lines, which is expected to appear in the years to come.

  13. PCR amplification of repetitive sequences as a possible approach in relative species quantification.

    PubMed

    Ballin, N Z; Vogensen, F K; Karlsson, A H

    2012-02-01

    Both relative and absolute quantifications are possible in species quantification when single copy genomic DNA is used. However, amplification of single copy genomic DNA does not allow a limit of detection as low as one obtained from amplification of repetitive sequences. Amplification of repetitive sequences is therefore frequently used in absolute quantification but problems occur in relative quantification as the number of repetitive sequences is unknown. A promising approach was developed where data from amplification of repetitive sequences were used in relative quantification of species in binary mixtures. PCR LUX primers were designed that amplify repetitive and single copy sequences to establish the species dependent number (constants) (SDC) of amplified repetitive sequences per genome. The SDCs and data from amplification of repetitive sequences were tested for their applicability to relatively quantify the amount of chicken DNA in a binary mixture of chicken DNA and pig DNA. However, the designed PCR primers lack the specificity required for regulatory species control.

  14. Multivariate Quantification of the Solid State Phase Composition of Co-Amorphous Naproxen-Indomethacin.

    PubMed

    Beyer, Andreas; Grohganz, Holger; Löbmann, Korbinian; Rades, Thomas; Leopold, Claudia S

    2015-10-27

    To benefit from the optimized dissolution properties of active pharmaceutical ingredients in their amorphous forms, co-amorphisation as a viable tool to stabilize these amorphous phases is of both academic and industrial interest. Reports dealing with the physical stability and recrystallization behavior of co-amorphous systems are however limited to qualitative evaluations based on the corresponding X-ray powder diffractograms. Therefore, the objective of the study was to develop a quantification model based on X-ray powder diffractometry (XRPD), followed by a multivariate partial least squares regression approach that enables the simultaneous determination of up to four solid state fractions: crystalline naproxen, γ-indomethacin, α-indomethacin as well as co-amorphous naproxen-indomethacin. For this purpose, a calibration set that covers the whole range of possible combinations of the four components was prepared and analyzed by XRPD. In order to test the model performances, leave-one-out cross validation was performed and revealed root mean square errors of validation between 3.11% and 3.45% for the crystalline molar fractions and 5.57% for the co-amorphous molar fraction. In summary, even four solid state phases, involving one co-amorphous phase, can be quantified with this XRPD data-based approach.

  15. Simultaneous quantification of depolymerization and mineralization rates by a novel 15N tracing model

    NASA Astrophysics Data System (ADS)

    Andresen, Louise C.; Björsne, Anna-Karin; Bodé, Samuel; Klemedtsson, Leif; Boeckx, Pascal; Rütting, Tobias

    2016-09-01

    The depolymerization of soil organic matter, such as proteins and (oligo-)peptides, into monomers (e.g. amino acids) is currently considered to be the rate-limiting step for nitrogen (N) availability in terrestrial ecosystems. The mineralization of free amino acids (FAAs), liberated by the depolymerization of peptides, is an important fraction of the total mineralization of organic N. Hence, the accurate assessment of peptide depolymerization and FAA mineralization rates is important in order to gain a better process-based understanding of the soil N cycle. In this paper, we present an extended numerical 15N tracing model Ntrace, which incorporates the FAA pool and related N processes in order to provide a more robust and simultaneous quantification of depolymerization and gross mineralization rates of FAAs and soil organic N. We discuss analytical and numerical approaches for two forest soils, suggest improvements of the experimental work for future studies, and conclude that (i) when about half of all depolymerized peptide N is directly mineralized, FAA mineralization can be as important a rate-limiting step for total gross N mineralization as peptide depolymerization rate; (ii) gross FAA mineralization and FAA immobilization rates can be used to develop FAA use efficiency (NUEFAA), which can reveal microbial N or carbon (C) limitation.

  16. Experimental improvements in combining CARD-FISH and flow cytometry for bacterial cell quantification.

    PubMed

    Manti, Anita; Boi, Paola; Amalfitano, Stefano; Puddu, Alberto; Papa, Stefano

    2011-12-01

    Flow cytometry and Fluorescence In Situ Hybridization are common methods of identifying and quantifying bacterial cells. The combination of cytometric rapidity and multi-parametric accuracy with the phylogenetic specificity of oligonucleotide FISH probes has been regarded as a powerful and emerging tool in aquatic microbiology. In the present work, tests were carried out on E. coli pure culture and marine bacteria using an in-solution hybridization protocol revealing high efficiency hybridization signal for the first one and a lower for the second one. Other experiments were conducted on natural samples following the established CARD-FISH protocol on filter performed in a closed system, with the aim of improving cell detachment and detection. The hybridized cells were then subsequently re-suspended from the membrane filters by means of an optimized detachment procedure. The cytometric enumeration of hybridized marine bacteria reached 85.7%±18.1% of total events. The quality of the cytograms suggests that the procedures described may be applicable to the cytometric quantification of phylogenetic groups within natural microbial communities.

  17. ToF-SIMS Applications in Microelectronics: Quantification of Organic Surface Contamination

    NASA Astrophysics Data System (ADS)

    Trouiller, C.; Signamarcheix, T.; Juhel, M.; Petitdidier, S.; Fontaine, H.; Veillerot, M.; Kwakman, L. F. Tz.; Wyon, C.

    2005-09-01

    An overview of our main Time-Of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS) applications is first given that highlights the strengths but also reveals some development needs for this technique especially where it comes to contaminants quantification. In this work, as a step towards better quantified data, we have elaborated a method to quantify Airborne Molecular Contamination (AMC) on Silicon. For this a protocol using liquid nitrogen sample cooling was set up to reduce the desorption of the most volatile species under the Ultra High Vacuum (UHV) of the ToF-SIMS analysis chamber and thus to enable a more stable, reliable and representative measurement. Using this protocol for the ToF-SIMS analysis and a careful analytical sequence, good correlation between Wafer Thermal Desorption Gas Chromatography Mass Spectroscopy (W-TDGCMS) and ToF-SIMS results on wafers exposed for varying time under the clean-room air flow containing 2,2,4-trimethyl 1,3-pentanediol diisobutyrate (TXIB) and Phthalates — two main organic clean-room contaminants — is obtained. Relative Sensitivity Factors (RSF) are deduced. With the used measurement setups, the ToF-SIMS low detection limits (DL) lie around 1E11 - 1E12 atoms Carbon/cm2 (atC/cm2) depending on species and are comparable to that of W-TDGCMS at 1E11 atC/cm2.

  18. Signal Intensities Derived from Different NMR Probes and Parameters Contribute to Variations in Quantification of Metabolites

    PubMed Central

    Finkel, Michael; Karnovsky, Alla; Woehler, Scott; Lewis, Michael J.; Chang, David; Stringer, Kathleen A.

    2014-01-01

    We discovered that serious issues could arise that may complicate interpretation of metabolomic data when identical samples are analyzed at more than one NMR facility, or using slightly different NMR parameters on the same instrument. This is important because cross-center validation metabolomics studies are essential for the reliable application of metabolomics to clinical biomarker discovery. To test the reproducibility of quantified metabolite data at multiple sites, technical replicates of urine samples were assayed by 1D-1H-NMR at the University of Alberta and the University of Michigan. Urine samples were obtained from healthy controls under a standard operating procedure for collection and processing. Subsequent analysis using standard statistical techniques revealed that quantitative data across sites can be achieved, but also that previously unrecognized NMR parameter differences can dramatically and widely perturb results. We present here a confirmed validation of NMR analysis at two sites, and report the range and magnitude that common NMR parameters involved in solvent suppression can have on quantitated metabolomics data. Specifically, saturation power levels greatly influenced peak height intensities in a frequency-dependent manner for a number of metabolites, which markedly impacted the quantification of metabolites. We also investigated other NMR parameters to determine their effects on further quantitative accuracy and precision. Collectively, these findings highlight the importance of and need for consistent use of NMR parameter settings within and across centers in order to generate reliable, reproducible quantified NMR metabolomics data. PMID:24465670

  19. Quantification of the bed load effects on turbulent open-channel flows

    NASA Astrophysics Data System (ADS)

    Liu, Detian; Liu, Xiaofeng; Fu, Xudong; Wang, Guangqian

    2016-04-01

    With a computational model combining large eddy simulation and a discrete element model, detailed quantification of the bed load effects on turbulent open-channel flows is presented. The objective is the revelation of bed load particle impact on the mean flow properties and coherent structures. Two comparative numerical experiments with mobile and immobile beds are conducted. Mean properties (e.g., velocity and Reynolds stress profiles) show good agreement with experimental data. Comparing the mobile and immobile cases, the effective bed position is nearly the same, whereas the equivalent sand roughness is changed. The flow experiences higher bottom shear stress over immobile bed. To quantify impact on turbulent structures, a revised quadrant analysis is performed to calculate four key parameters of ejection and sweep events (duration, maximum shear stress, transported momentum, and period). Results show that the ejection and sweep events have comparable importance in the outer region. However, sweep becomes dominant in the near-wall region. The motion of particles enhances the sweep dominance by breaking up the ejection structures and decreasing their occurrence ratio. The results also suggest that the ejection events are easier to be influenced by the particle motions because they originate from the near-wall region. The duration, maximum shear stress, and transported momentum decrease close to the bed. The period remains relatively constant in the outer region but decreases near the bed. Visualization of the coherent structure reveals that the instantaneous particle motion has strong correlation with the bursting cycle events.

  20. Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging.

    PubMed

    Wang, Xiaolei; Cui, Yi; Irudayaraj, Joseph

    2015-12-22

    Epigenetic modifications on DNA, especially on cytosine, play a critical role in regulating gene expression and genome stability. It is known that the levels of different cytosine derivatives are highly dynamic and are regulated by a variety of factors that act on the chromatin. Here we report an optical methodology based on hyperspectral dark-field imaging (HSDFI) using plasmonic nanoprobes to quantify the recently identified cytosine modifications on DNA in single cells. Gold (Au) and silver (Ag) nanoparticles (NPs) functionalized with specific antibodies were used as contrast-generating agents due to their strong local surface plasmon resonance (LSPR) properties. With this powerful platform we have revealed the spatial distribution and quantity of 5-carboxylcytosine (5caC) at the different stages in cell cycle and demonstrated that 5caC was a stably inherited epigenetic mark. We have also shown that the regional density of 5caC on a single chromosome can be mapped due to the spectral sensitivity of the nanoprobes in relation to the interparticle distance. Notably, HSDFI enables an efficient removal of the scattering noises from nonspecifically aggregated nanoprobes, to improve accuracy in the quantification of different cytosine modifications in single cells. Further, by separating the LSPR fingerprints of AuNPs and AgNPs, multiplex detection of two cytosine modifications was also performed. Our results demonstrate HSDFI as a versatile platform for spatial and spectroscopic characterization of plasmonic nanoprobe-labeled nuclear targets at the single-cell level for quantitative epigenetic screening. PMID:26505210

  1. Pseudo isobaric peptide termini labelling for relative proteome quantification by SWATH MS acquisition.

    PubMed

    Zhang, Shen; Chen, Lingfan; Shan, Yichu; Sui, Zhigang; Wu, Qi; Zhang, Lihua; Liang, Zhen; Zhang, Yukui

    2016-08-01

    The pseudo isobaric peptide termini labeling (IPTL) method is a remarkable strategy in quantitative proteomics, and has been efficiently applied in biological studies due to its high quantitative accuracy. However, irreproducible precursor ion selection caused by data dependent acquisition and the chromatographic shift caused by isotope effects limit the wide application of this method. Herein, we expand the use of pseudo IPTL to SWATH MS application and develop a novel quantitative strategy, termed SWATH-pseudo-IPTL, by which the relative quantification could be achieved by comparing the "complete" extracted ion chromatogram (XIC) intensity of MS/MS scan instead of a single intensity measurement in DDA-pseudo-IPTL which only reflected the peptide abundances at that given time. The quantitative analysis of various proportions of mixed HeLa samples revealed the strong accuracy and precision of our SWATH-pseudo-IPTL method, both of which were better than that of the DDA-pseudo-IPTL strategy. SWATH-pseudo-IPTL was also applied to the quantitative profiling of the proteome from human hepatocellular carcinoma cell lines with high and low metastatic potential, and most of the differentially expressed proteins were related to tumorigenesis and tumor metastasis, demonstrating the feasibility of this methodology for biological applications.

  2. Molecular identification and quantification of tetracycline and erythromycin resistance genes in Spanish and Italian retail cheeses.

    PubMed

    Belén Flórez, Ana; Alegría, Ángel; Rossi, Franca; Delgado, Susana; Felis, Giovanna E; Torriani, Sandra; Mayo, Baltasar

    2014-01-01

    Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is, tet(K), tet(L), tet(M), tet(O), tet(S), and tet(W), and two with respect to erythromycin, that is, erm(B) and erm(F). The most common resistance genes in the analysed cheeses were tet(S), tet(W), tet(M), and erm(B). The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to 10.18log10/g). DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions for tet(W)-carrying cheeses, though the similarity of the sequences suggests this tet(W) to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants. PMID:25302306

  3. Quantification of Organic Porosity and Water Accessibility in Marcellus Shale Using Neutron Scattering

    DOE PAGES

    Gu, Xin; Mildner, David F. R.; Cole, David R.; Rother, Gernot; Slingerland, Rudy; Brantley, Susan L.

    2016-04-28

    Pores within organic matter (OM) are a significant contributor to the total pore system in gas shales. These pores contribute most of the storage capacity in gas shales. Here we present a novel approach to characterize the OM pore structure (including the porosity, specific surface area, pore size distribution, and water accessibility) in Marcellus shale. By using ultrasmall and small-angle neutron scattering, and by exploiting the contrast matching of the shale matrix with suitable mixtures of deuterated and protonated water, both total and water-accessible porosity were measured on centimeter-sized samples from two boreholes from the nanometer to micrometer scale withmore » good statistical coverage. Samples were also measured after combustion at 450 °C. Analysis of scattering data from these procedures allowed quantification of OM porosity and water accessibility. OM hosts 24–47% of the total porosity for both organic-rich and -poor samples. This porosity occupies as much as 29% of the OM volume. In contrast to the current paradigm in the literature that OM porosity is organophilic and therefore not likely to contain water, our results demonstrate that OM pores with widths >20 nm exhibit the characteristics of water accessibility. In conclusion, our approach reveals the complex structure and wetting behavior of the OM porosity at scales that are hard to interrogate using other techniques.« less

  4. Uncertainty Quantification of Nonlinear Electrokinetic Response in a Microchannel-Membrane Junction

    NASA Astrophysics Data System (ADS)

    Alizadeh, Shima; Iaccarino, Gianluca; Mani, Ali

    2015-11-01

    We have conducted uncertainty quantification (UQ) for electrokinetic transport of ionic species through a hybrid microfluidic system using different probabilistic techniques. The system of interest is an H-configuration consisting of two parallel microchannels that are connected via a nafion junction. This system is commonly used for ion preconcentration and stacking by utilizing a nonlinear response at the channel-nafion junction that leads to deionization shocks. In this work, the nafion medium is modeled as many parallel nano-pores where, the nano-pore diameter, nafion porosity, and surface charge density are independent random variables. We evaluated the resulting uncertainty on the ion concentration fields as well as the deionization shock location. The UQ methods predicted consistent statistics for the outputs and the results revealed that the shock location is weakly sensitive to the nano-pore surface charge and primarily driven by nano-pore diameters. The present study can inform the design of electrokinetic networks with increased robustness to natural manufacturing variability. Applications include water desalination and lab-on-a-chip systems. Shima is a graduate student in the department of Mechanical Engineering at Stanford University. She received her Master's degree from Stanford in 2011. Her research interests include Electrokinetics in porous structures and high performance computing.

  5. Noninvasive bi-graphical analysis for the quantification of slowly reversible radioligand binding

    NASA Astrophysics Data System (ADS)

    Seo, Seongho; Kim, Su Jin; Yoo, Hye Bin; Lee, Jee-Young; Kyeong Kim, Yu; Lee, Dong Soo; Zhou, Yun; Lee, Jae Sung

    2016-09-01

    In this paper, we presented a novel reference-region-based (noninvasive) bi-graphical analysis for the quantification of a reversible radiotracer binding that may be too slow to reach relative equilibrium (RE) state during positron emission tomography (PET) scans. The proposed method indirectly implements the noninvasive Logan plot, through arithmetic combination of the parameters of two other noninvasive methods and the apparent tissue-to-plasma efflux rate constant for the reference region (k2\\prime ). We investigated its validity and statistical properties, by performing a simulation study with various noise levels and k2\\prime values, and also evaluated its feasibility for [18F]FP-CIT PET in human brain. The results revealed that the proposed approach provides distribution volume ratio estimation comparable to the Logan plot at low noise levels while improving underestimation caused by non-RE state differently depending on k2\\prime . Furthermore, the proposed method was able to avoid noise-induced bias of the Logan plot, and the variability of its results was less dependent on k2\\prime than the Logan plot. Therefore, this approach, without issues related to arterial blood sampling given a pre-estimate of k2\\prime (e.g. population-based), could be useful in parametric image generation for slow kinetic tracers staying in a non-RE state within a PET scan.

  6. Quantification of the activity of biomolecules in microarrays obtained by direct laser transfer.

    PubMed

    Dinca, V; Ranella, A; Farsari, M; Kafetzopoulos, D; Dinescu, M; Popescu, A; Fotakis, C

    2008-10-01

    The direct-writing technique laser-induced forward transfer has been employed for the micro-array printing of liquid solutions of the enzyme horseradish peroxidase and the protein Titin on nitrocellulose solid surfaces. The effect of two UV laser pulse lengths, femtosecond and nanosecond has been studied in relation with maintaining the activity of the transferred biomolecules. The quantification of the active biomolecules after transfer has been carried out using Bradford assay, quantitative colorimetric enzymatic assay and fluorescence techniques. Spectrophotometric measurements of the HRP and the Titin activity as well as chromatogenic and fluorescence assay studies have revealed a connection between the properties of the deposited, biologically active biomolecules, the experimental conditions and the target composition. The bioassays have shown that up to 78% of the biomolecules remained active after femtosecond laser transfer, while this value reduced to 54% after nanosecond laser transfer. The addition of glycerol in a percentage up to 70% in the solution to be transferred has contributed to the stabilization of the micro-array patterns and the increase of their resolution.

  7. Molecular Identification and Quantification of Tetracycline and Erythromycin Resistance Genes in Spanish and Italian Retail Cheeses

    PubMed Central

    Flórez, Ana Belén; Alegría, Ángel; Delgado, Susana

    2014-01-01

    Large antibiotic resistance gene pools in the microbiota of foods may ultimately pose a risk for human health. This study reports the identification and quantification of tetracycline- and erythromycin-resistant populations, resistance genes, and gene diversity in traditional Spanish and Italian cheeses, via culturing, conventional PCR, real-time quantitative PCR (qPCR), and denaturing gradient gel electrophoresis (DGGE). The numbers of resistant bacteria varied widely among the antibiotics and the different cheese varieties; in some cheeses, all the bacterial populations seemed to be resistant. Up to eight antibiotic resistance genes were sought by gene-specific PCR, six with respect to tetracycline, that is, tet(K), tet(L), tet(M), tet(O), tet(S), and tet(W), and two with respect to erythromycin, that is, erm(B) and erm(F). The most common resistance genes in the analysed cheeses were tet(S), tet(W), tet(M), and erm(B). The copy numbers of these genes, as quantified by qPCR, ranged widely between cheeses (from 4.94 to 10.18log⁡10/g). DGGE analysis revealed distinct banding profiles and two polymorphic nucleotide positions for tet(W)-carrying cheeses, though the similarity of the sequences suggests this tet(W) to have a monophyletic origin. Traditional cheeses would therefore appear to act as reservoirs for large numbers of many types of antibiotic resistance determinants. PMID:25302306

  8. Development and validation of a sensitive UPLC-ESI-MS/MS method for the simultaneous quantification of 15 endocannabinoids and related compounds in milk and other biofluids.

    PubMed

    Gouveia-Figueira, Sandra; Nording, Malin L

    2014-01-21

    The endocannabinoid (eCB) system has gained an increasing interest over the past decades since the discovery of anandamide and 2-arachidonoyl glycerol (2-AG). These, and structurally related compounds, are associated with a wide variety of physiological processes. For instance, eCB levels in milk have been associated with infants' feeding and sleeping behavior. A method based on ultraperformance liquid chromatography coupled with electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) was developed and validated for the simultaneous quantification of 15 eCBs and related compounds, including both fatty acid amides and glycerols. Linearity (0.9845 < R(2) < 1), limit of detection and quantification (0.52-293 pg on column), inter- and intraday accuracy (>70%) and precision (CV < 15%), stability, and recovery (in milk and plasma) were established in accordance to the U.S. Food and Drug Administration guidelines. The method was successfully applied to bovine and elk milk revealing species-specific eCB profiles, with significant different levels of 2-AG, 2-linoleoyl glycerol, docosahexaenoyl ethanolamide, palmitoyl ethanolamide, and oleoyl ethanolamide. Furthermore, stearoyl ethanolamide and docosatetraenoyl ethanolamide were only detected in elk milk. In summary, our UPLC-ESI-MS/MS method may be used for quantification of eCBs and related compounds in different biofluids and applied to investigations of the role of these emerging compounds in various physiological processes. PMID:24377270

  9. Interplay between misfit strain relief and Stranski-Krastanov growth in fcc (111)/bcc (110) ultrathin film epitaxy. Part 2. Quantification using embedded atom method potentials

    NASA Astrophysics Data System (ADS)

    van der Merwe, J. H.; Tönsing, D. L.

    2000-03-01

    The main objective of this investigation has been to study the influence of misfit strain (MS) relief on the transition from monolayer-by-monolayer (ML-by-ML) Frank-van der Merwe (FM) to Stranski-Krastanov (SK) growth. The investigation involves (a) selection of appropriate materials [Cu, Pd, Pt on Fe(110)] to hopefully meet the appropriate stability criteria for misfit accommodation and bond strength, and of atomic interaction potentials [embedded atom method (EAM)] needed for quantification, and (b) development of appropriate analytical procedures to facilitate the description and quantification of the relevant parameters. The computations revealed that MS relief by misfit dislocations (MDs), for the selected materials, falls outside the SK transition thickness regime. The investigation has thus been limited to MS relief by a misfit vernier. The main objective of assessing the influence of MS relief on the transition to SK growth has been accomplished by showing that the growth mode discriminants, needed to predict quasi-equilibrium growth mode development, change with MS relief. The computation that culminated in the quantification of growth mode discriminants also yielded as by-product several interesting results of wider application in the field of epitaxy — the dependence on substrate proximity and bond strengths of: interlayer and intralayer relaxation, equilibrium misfit, critical misfit and thickness, substrate coverage change, optimum Fourier coefficients of periodic epilayer-substrate interaction potentials and stability of misfit accommodation and growth modes.

  10. Development of analytical strategies using U-HPLC-MS/MS and LC-ToF-MS for the quantification of micropollutants in marine organisms.

    PubMed

    Wille, Klaas; Kiebooms, Julie A L; Claessens, Michiel; Rappé, Karen; Vanden Bussche, Julie; Noppe, Herlinde; Van Praet, Nander; De Wulf, Eric; Van Caeter, Peter; Janssen, Colin R; De Brabander, Hubert F; Vanhaecke, Lynn

    2011-05-01

    Organic micropollutants such as pharmaceuticals, perfluorinated compounds (PFCs), and pesticides, are important environmental contaminants. To obtain more information regarding their presence in marine organisms, an increasing demand exists for reliable analytical methods for quantification of these micropollutants in biotic matrices. Therefore, we developed extraction procedures and new analytical methods for the quantification of 14 pesticides, 10 PFCs, and 11 pharmaceuticals in tissue of marine organisms, namely blue mussels (Mytilus edulis). This paper presents these optimized analytical procedures and their application to M. edulis, deployed at five stations in the Belgian coastal zone. The methods consisted of a pressurized liquid extraction and solid-phase extraction (SPE) followed by ultra high-performance liquid chromatography coupled to triple quadrupole mass spectrometry for pharmaceuticals and pesticides, and of a liquid extraction using acetonitrile and SPE, followed by liquid chromatography coupled to time-of-flight mass spectrometry for PFCs. The limits of quantification of the three newly optimized analytical procedures in M. edulis tissue varied between 0.1 and 10 ng g(-1), and satisfactory linearities (≥0.98) and recoveries (90-106%) were obtained. Application of these methods to M. edulis revealed the presence of five pharmaceuticals, two PFCs, and seven pesticides at levels up to 490, 5, and 60 ng g(-1), respectively. The most prevalent micropollutants were salicylic acid, paracetamol, perfluorooctane sulfonate, chloridazon, and dichlorvos. PMID:21442366

  11. Improved semiquantitative Western blot technique with increased quantification range.

    PubMed

    Heidebrecht, F; Heidebrecht, A; Schulz, I; Behrens, S-E; Bader, A

    2009-06-30

    With the development of new interdisciplinary fields such as systems biology, the quantitative analysis of protein expression in biological samples gains more and more importance. Although the most common method for this is ELISA, Western blot also has advantages: The separation of proteins by size allows the evaluation of only specifically bound protein. This work examines the Western blot signal chain, determines some of the parameters relevant for quantitative analysis and proposes a mathematical model of the reaction kinetics. Using this model, a semiquantitative Western blot method for simultaneous quantification of different proteins using a hyperbolic calibration curve was developed. A program was written for the purpose of hyperbolic regression that allows quick determination of the calibration curve coefficients. This program can be used also for approximation of calibration curves in other applications such as ELISA, BCA or Bradford assays. PMID:19351538

  12. Quantification of chromatin condensation level by image processing.

    PubMed

    Irianto, Jerome; Lee, David A; Knight, Martin M

    2014-03-01

    The level of chromatin condensation is related to the silencing/activation of chromosomal territories and therefore impacts on gene expression. Chromatin condensation changes during cell cycle, progression and differentiation, and is influenced by various physicochemical and epigenetic factors. This study describes a validated experimental technique to quantify chromatin condensation. A novel image processing procedure is developed using Sobel edge detection to quantify the level of chromatin condensation from nuclei images taken by confocal microscopy. The algorithm was developed in MATLAB and used to quantify different levels of chromatin condensation in chondrocyte nuclei achieved through alteration in osmotic pressure. The resulting chromatin condensation parameter (CCP) is in good agreement with independent multi-observer qualitative visual assessment. This image processing technique thereby provides a validated unbiased parameter for rapid and highly reproducible quantification of the level of chromatin condensation.

  13. Quantification of osteolytic bone lesions in a preclinical rat trial

    NASA Astrophysics Data System (ADS)

    Fränzle, Andrea; Bretschi, Maren; Bäuerle, Tobias; Giske, Kristina; Hillengass, Jens; Bendl, Rolf

    2013-10-01

    In breast cancer, most of the patients who died, have developed bone metastasis as disease progression. Bone metastases in case of breast cancer are mainly bone destructive (osteolytic). To understand pathogenesis and to analyse response to different treatments, animal models, in our case rats, are examined. For assessment of treatment response to bone remodelling therapies exact segmentations of osteolytic lesions are needed. Manual segmentations are not only time-consuming but lack in reproducibility. Computerized segmentation tools are essential. In this paper we present an approach for the computerized quantification of osteolytic lesion volumes using a comparison to a healthy reference model. The presented qualitative and quantitative evaluation of the reconstructed bone volumes show, that the automatically segmented lesion volumes complete missing bone in a reasonable way.

  14. Quantification of tidal parameters from Solar System data

    NASA Astrophysics Data System (ADS)

    Lainey, Valéry

    2016-11-01

    Tidal dissipation is the main driver of orbital evolution of natural satellites and a key point to understand the exoplanetary system configurations. Despite its importance, its quantification from observations still remains difficult for most objects of our own Solar System. In this work, we overview the method that has been used to determine, directly from observations, the tidal parameters, with emphasis on the Love number k_2 and the tidal quality factor Q. Up-to-date values of these tidal parameters are summarized. Last, an assessment on the possible determination of the tidal ratio k_2/Q of Uranus and Neptune is done. This may be particularly relevant for coming astrometric campaigns and future space missions focused on these systems.

  15. Quantification of intracerebral steal in patients with arteriovenous malformation

    SciTech Connect

    Homan, R.W.; Devous, M.D. Sr.; Stokely, E.M.; Bonte, F.J.

    1986-08-01

    Eleven patients with angiographically and/or pathologically proved arteriovenous malformations (AVMs) were studied using dynamic, single-photon-emission computed tomography (DSPECT). Quantification of regional cerebral blood flow in structurally normal areas remote from the AVM disclosed areas of decreased flow compared with normal controls in eight of 11 patients examined. Areas of hypoperfusion correlated with altered function as manifested by epileptogenic foci and impaired cognitive function. Dynamic, single-photon-emission computed tomography provides a noninvasive technique to monitor quantitatively hemodynamic changes associated with AVMs. Our findings suggest that such changes are present in the majority of patients with AVMs and that they may be clinically significant. The potential application of regional cerebral blood flow imaging by DSPECT in the management of patients with AVMs is discussed.

  16. UQTools: The Uncertainty Quantification Toolbox - Introduction and Tutorial

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

    UQTools is the short name for the Uncertainty Quantification Toolbox, a software package designed to efficiently quantify the impact of parametric uncertainty on engineering systems. UQTools is a MATLAB-based software package and was designed to be discipline independent, employing very generic representations of the system models and uncertainty. Specifically, UQTools accepts linear and nonlinear system models and permits arbitrary functional dependencies between the system s measures of interest and the probabilistic or non-probabilistic parametric uncertainty. One of the most significant features incorporated into UQTools is the theoretical development centered on homothetic deformations and their application to set bounding and approximating failure probabilities. Beyond the set bounding technique, UQTools provides a wide range of probabilistic and uncertainty-based tools to solve key problems in science and engineering.

  17. Quantification of Diffuse Hydrothermal Flows Using Multibeam Sonar

    NASA Astrophysics Data System (ADS)

    Ivakin, A. N.; Jackson, D. R.; Bemis, K. G.; Xu, G.

    2014-12-01

    The Cabled Observatory Vent Imaging Sonar (COVIS) deployed at the Main Endeavour node of the NEPTUNE Canada observatory has provided acoustic time series extending over 2 years. This includes 3D images of plume scattering strength and Doppler velocity measurements as well as 2D images showing regions of diffuse flow. The diffuse-flow images display the level of decorrelation between sonar echos with transmissions separated by 0.2 s. The present work aims to provide further information on the strength of diffuse flows. Two approaches are used: Measurement of the dependence of decorrelation on lag and measurement of phase shift of sonar echos, with lags in 3-hour increments up to several days. The phase shifts and decorrelation are linked to variations of temperature above the seabed, which allows quantification of those variations, their magnitudes, spatial and temporal scales, and energy spectra. These techniques are illustrated using COVIS data obtained near the Grotto vent complex.

  18. Quantification of airway deposition of intact and fragmented pollens.

    PubMed

    Horváth, Alpár; Balásházy, Imre; Farkas, Arpád; Sárkány, Zoltán; Hofmann, Werner; Czitrovszky, Aladár; Dobos, Erik

    2011-12-01

    Although pollen is one of the most widespread agents that can cause allergy, its airway transport and deposition is far from being fully explored. The objective of this study was to characterize the airway deposition of pollens and to contribute to the debate related to the increasing number of asthma attacks registered after thunderstorms. For the quantification of the deposition of inhaled pollens in the airways computer simulations were performed. Our results demonstrated that smaller and fragmented pollens may penetrate into the thoracic airways and deposit there, supporting the theory that fragmented pollen particles are responsible for the increasing incidence of asthma attacks following thunderstorms. Pollen deposition results also suggest that children are the most exposed to the allergic effects of pollens. Finally, pollens between 0.5 and 20 μm deposit more efficiently in the lung of asthmatics than in the healthy lung, especially in the bronchial region. PMID:21563012

  19. Quantification of Posterior Globe Flattening: Methodology Development and Validation

    NASA Technical Reports Server (NTRS)

    Lumpkins, Sarah B.; Garcia, Kathleen M.; Sargsyan, Ashot E.; Hamilton, Douglas R.; Berggren, Michael D.; Ebert, Douglas

    2012-01-01

    Microgravity exposure affects visual acuity in a subset of astronauts and mechanisms may include structural changes in the posterior globe and orbit. Particularly, posterior globe flattening has been implicated in the eyes of several astronauts. This phenomenon is known to affect some terrestrial patient populations and has been shown to be associated with intracranial hypertension. It is commonly assessed by magnetic resonance imaging (MRI), computed tomography (CT) or B-mode Ultrasound (US), without consistent objective criteria. NASA uses a semiquantitative scale of 0-3 as part of eye/orbit MRI and US analysis for occupational monitoring purposes. The goal of this study was ot initiate development of an objective quantification methodology to monitor small changes in posterior globe flattening.

  20. Quantification of Posterior Globe Flattening: Methodology Development and Validationc

    NASA Technical Reports Server (NTRS)

    Lumpkins, S. B.; Garcia, K. M.; Sargsyan, A. E.; Hamilton, D. R.; Berggren, M. D.; Antonsen, E.; Ebert, D.

    2011-01-01

    Microgravity exposure affects visual acuity in a subset of astronauts, and mechanisms may include structural changes in the posterior globe and orbit. Particularly, posterior globe flattening has been implicated in several astronauts. This phenomenon is known to affect some terrestrial patient populations, and has been shown to be associated with intracranial hypertension. It is commonly assessed by magnetic resonance imaging (MRI), computed tomography (CT), or B-mode ultrasound (US), without consistent objective criteria. NASA uses a semi-quantitative scale of 0-3 as part of eye/orbit MRI and US analysis for occupational monitoring purposes. The goal of this study was to initiate development of an objective quantification methodology for posterior globe flattening.

  1. [Quantification in psychiatry: from psychometrics to quantitative psychiatry].

    PubMed

    Pichot, P

    1994-01-01

    The development of quantitative techniques to analyse psychopathological states is reviewed from the XVIIIth Century till today. As far as back as the XIXth Century, Quetelet, Louis and Galton introduced and advocated the use of quantitative methods in medical and psychological sciences. The advent of psychometry dates back 1905, when Alfred Binet published his Intelligence Scale. The construction of instruments like Wechsler and MMPI scales in the forties starts using psychometry in psychiatry. At end of World War II, historical factors (selection and guidance of military recruits) in conjunction with technical advancements (beginning of psychopharmacology, multivariate statistics development and first computers arrival) favor the growth of quantitative psychopathology that further takes four great different courses: 1. Psychometry proper, 2. Symptom-quantifying assessment scales such as BPRS or Hamilton scales, 3. New nosological models constructed using quantified psychopathological data and mathematical procedures, 4. Diagnostic systems relying on operationalized criteria based on psychopathological quantification, such as DSM III.

  2. A novel definition for quantification of mode shape complexity

    NASA Astrophysics Data System (ADS)

    Koruk, Hasan; Sanliturk, Kenan Y.

    2013-07-01

    Complex mode shapes are quite often encountered in structural dynamics. However, there is no universally accepted parameter for the quantification of mode shape complexity. After reviewing the existing methods, a novel approach is proposed in this paper in order to quantify mode shape complexity for general structures. The new parameter proposed in this paper is based on conservation of energy principle when a structure is vibrating at a specific mode during a period of vibration. The levels of complexity of the individual mode shapes of a sample structure are then quantified using the proposed new parameter and the other parameters available in the literature. The corresponding results are compared, the validity and the generality of the new parameter are demonstrated for various damping scenarios.

  3. Quantification of chicken anaemia virus by competitive polymerase chain reaction.

    PubMed

    Yamaguchi, S; Kaji, N; Munang'andu, H M; Kojima, C; Mase, M; Tsukamoto, K

    2000-08-01

    A quantitative method for chicken anaemia virus (CAV) was developed using competitive polymerase chain reaction (PCR). Competitive template was constructed by deletion of 33 nucleotides from a wildtype DNA clone of CAV. Quantification of CAV DNA molecules by the competitive PCR was rapid and highly reproducible when compared with conventional infectivity titration methods. The ratios of the viral DNA molecules and infectivity titres in MDCC-MSB1 cells varied between 1.3 and 3.55 log(10) among several isolates, suggesting the existence of different infection efficiencies to MDCC-MSB1 cells by isolates. The competitive PCR will be useful for studying CAV infection in vivo and/or in vitro.

  4. Quantification of tidal parameters from Solar System data

    NASA Astrophysics Data System (ADS)

    Lainey, Valéry

    2016-05-01

    Tidal dissipation is the main driver of orbital evolution of natural satellites and a key point to understand the exoplanetary system configurations. Despite its importance, its quantification from observations still remains difficult for most objects of our own Solar System. In this work, we overview the method that has been used to determine, directly from observations, the tidal parameters, with emphasis on the Love number k_2 and the tidal quality factor Q. Up-to-date values of these tidal parameters are summarized. Last, an assessment on the possible determination of the tidal ratio k_2/Q of Uranus and Neptune is done. This may be particularly relevant for coming astrometric campaigns and future space missions focused on these systems.

  5. Raman spectroscopy for DNA quantification in cell nucleus.

    PubMed

    Okotrub, K A; Surovtsev, N V; Semeshin, V F; Omelyanchuk, L V

    2015-01-01

    Here we demonstrate the feasibility of a novel approach to quantify DNA in cell nuclei. This approach is based on spectroscopy analysis of Raman light scattering, and avoids the problem of nonstoichiometric binding of dyes to DNA, as it directly measures the signal from DNA. Quantitative analysis of nuclear DNA contribution to Raman spectrum could be reliably performed using intensity of a phosphate mode at 1096 cm(-1) . When compared to the known DNA standards from cells of different animals, our results matched those values at error of 10%. We therefore suggest that this approach will be useful to expand the list of DNA standards, to properly adjust the duration of hydrolysis in Feulgen staining, to assay the applicability of fuchsines for DNA quantification, as well as to measure DNA content in cells with complex hydrolysis patterns, when Feulgen densitometry is inappropriate.

  6. Sensitive quantification of somatic mutations using molecular inversion probes.

    PubMed

    Hirani, Rena; Connolly, Ashley R; Putral, Lisa; Dobrovic, Alexander; Trau, Matt

    2011-11-01

    Somatic mutations in DNA can serve as cancer specific biomarkers and are increasingly being used to direct treatment. However, they can be difficult to detect in tissue biopsies because there is often only a minimal amount of sample and the mutations are often masked by the presence of wild type alleles from nontumor material in the sample. To facilitate the sensitive and specific analysis of DNA mutations in tissues, a multiplex assay capable of detecting nucleotide changes in less than 150 cells was developed. The assay extends the application of molecular inversion probes to enable sensitive discrimination and quantification of nucleotide mutations that are present in less than 0.1% of a cell population. The assay was characterized by detecting selected mutations in the KRAS gene, which has been implicated in up to 25% of all cancers. These mutations were detected in a single multiplex assay by incorporating the rapid flow cytometric readout of multiplexable DNA biosensors.

  7. Cytofluorometric Quantification of Cell Death Elicited by NLR Proteins.

    PubMed

    Sica, Valentina; Manic, Gwenola; Kroemer, Guido; Vitale, Ilio; Galluzzi, Lorenzo

    2016-01-01

    Nucleotide-binding domain and leucine-rich repeat containing (NLR) proteins, also known as NOD-like receptors, are critical components of the molecular machinery that senses intracellular danger signals to initiate an innate immune response against invading pathogens or endogenous sources of hazard. The best characterized effect of NLR signaling is the secretion of various cytokines with immunostimulatory effects, including interleukin (IL)-1β and IL-18. Moreover, at least under specific circumstances, NLRs can promote regulated variants of cell death. Here, we detail two protocols for the cytofluorometric quantification of cell death-associated parameters that can be conveniently employed to assess the lethal activity of specific NLRs or their ligands.

  8. A surrogate accelerated multicanonical Monte Carlo method for uncertainty quantification

    NASA Astrophysics Data System (ADS)

    Wu, Keyi; Li, Jinglai

    2016-09-01

    In this work we consider a class of uncertainty quantification problems where the system performance or reliability is characterized by a scalar parameter y. The performance parameter y is random due to the presence of various sources of uncertainty in the system, and our goal is to estimate the probability density function (PDF) of y. We propose to use the multicanonical Monte Carlo (MMC) method, a special type of adaptive importance sampling algorithms, to compute the PDF of interest. Moreover, we develop an adaptive algorithm to construct local Gaussian process surrogates to further accelerate the MMC iterations. With numerical examples we demonstrate that the proposed method can achieve several orders of magnitudes of speedup over the standard Monte Carlo methods.

  9. [Demographic and epidemiological quantification in Balearic hygienism, 1850-1930].

    PubMed

    Pujadas-Mora, Joana-Maria

    2012-01-01

    At the end of the 19th century, social medicine promoted the use of quantification as a means to evaluate the health status of populations. In Majorca, hygienists such as the physicians Enric Fajarnés, Bernat Riera, Antoni Mayol and Emili Darder and the civil engineer Eusebi Estada sought a better understanding of health status by considering the population growth, the demographic and epidemiological profile and the influence of weather on mortality. These calculations showed that the Balearic population had a good health status in comparison to the population of mainland Spain, although less so in the international context. These results were explained by the benevolence of the insular climate, a factor that would also guarantee the success of the public health reforms proposed.

  10. Quantification of hydroxyacetone and glycolaldehyde using chemical ionization mass spectrometry

    NASA Astrophysics Data System (ADS)

    Spencer, K. M.; Beaver, M. R.; St. Clair, J. M.; Crounse, J. D.; Paulot, F.; Wennberg, P. O.

    2011-08-01

    Chemical ionization mass spectrometry (CIMS) enables online, fast, in situ detection and quantification of hydroxyacetone and glycolaldehyde. Two different CIMS approaches are demonstrated employing the strengths of single quadrupole mass spectrometry and triple quadrupole (tandem) mass spectrometry. Both methods are capable of the measurement of hydroxyacetone, an analyte with minimal isobaric interferences. Tandem mass spectrometry provides direct separation of the isobaric compounds glycolaldehyde and acetic acid using distinct, collision-induced dissociation daughter ions. Measurement of hydroxyacetone and glycolaldehyde by these methods was demonstrated during the ARCTAS-CARB 2008 campaign and the BEARPEX 2009 campaign. Enhancement ratios of these compounds in ambient biomass burning plumes are reported for the ARCTAS-CARB campaign. BEARPEX observations are compared to simple photochemical box model predictions of biogenic volatile organic compound oxidation at the site.

  11. Thermostability of Biological Systems: Fundamentals, Challenges, and Quantification

    PubMed Central

    He, Xiaoming

    2011-01-01

    This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems. PMID:21769301

  12. Graphene wrinkling induced by monodisperse nanoparticles: facile control and quantification

    PubMed Central

    Vejpravova, Jana; Pacakova, Barbara; Endres, Jan; Mantlikova, Alice; Verhagen, Tim; Vales, Vaclav; Frank, Otakar; Kalbac, Martin

    2015-01-01

    Controlled wrinkling of single-layer graphene (1-LG) at nanometer scale was achieved by introducing monodisperse nanoparticles (NPs), with size comparable to the strain coherence length, underneath the 1-LG. Typical fingerprint of the delaminated fraction is identified as substantial contribution to the principal Raman modes of the 1-LG (G and G’). Correlation analysis of the Raman shift of the G and G’ modes clearly resolved the 1-LG in contact and delaminated from the substrate, respectively. Intensity of Raman features of the delaminated 1-LG increases linearly with the amount of the wrinkles, as determined by advanced processing of atomic force microscopy data. Our study thus offers universal approach for both fine tuning and facile quantification of the graphene topography up to ~60% of wrinkling. PMID:26530787

  13. Expert judgement and uncertainty quantification for climate change

    NASA Astrophysics Data System (ADS)

    Oppenheimer, Michael; Little, Christopher M.; Cooke, Roger M.

    2016-05-01

    Expert judgement is an unavoidable element of the process-based numerical models used for climate change projections, and the statistical approaches used to characterize uncertainty across model ensembles. Here, we highlight the need for formalized approaches to unifying numerical modelling with expert judgement in order to facilitate characterization of uncertainty in a reproducible, consistent and transparent fashion. As an example, we use probabilistic inversion, a well-established technique used in many other applications outside of climate change, to fuse two recent analyses of twenty-first century Antarctic ice loss. Probabilistic inversion is but one of many possible approaches to formalizing the role of expert judgement, and the Antarctic ice sheet is only one possible climate-related application. We recommend indicators or signposts that characterize successful science-based uncertainty quantification.

  14. From Quantification to Visualization: A Taxonomy of Uncertainty Visualization Approaches

    PubMed Central

    Potter, Kristin; Rosen, Paul; Johnson, Chris R.

    2014-01-01

    Quantifying uncertainty is an increasingly important topic across many domains. The uncertainties present in data come with many diverse representations having originated from a wide variety of disciplines. Communicating these uncertainties is a task often left to visualization without clear connection between the quantification and visualization. In this paper, we first identify frequently occurring types of uncertainty. Second, we connect those uncertainty representations to ones commonly used in visualization. We then look at various approaches to visualizing this uncertainty by partitioning the work based on the dimensionality of the data and the dimensionality of the uncertainty. We also discuss noteworthy exceptions to our taxonomy along with future research directions for the uncertainty visualization community. PMID:25663949

  15. Aspect-Oriented Programming is Quantification and Obliviousness

    NASA Technical Reports Server (NTRS)

    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.

  16. [Comparison of methods for quantification of MVOC in indoor environments].

    PubMed

    Fischer, G; Möller, M; Gabrio, T; Palmgren, U; Keller, R; Richter, H; Dott, W; Paul, R

    2005-01-01

    For several years now, MVOC have been regarded as indicators for microbial growth in indoor environments. Until now, a direct correlation between the occurrence of microfungi and MVOC could not be shown in scientific investigations. One reason may be that different analytical methods were applied, and moreover they were not validated sufficiently. The present investigation aimed to test the comparability of both methods (Tenax adsorption/thermal desorption; charcoal adsorption/elution). It turned out that with both methods comparable results can be achieved if the technical handling of the calibration is standardized to a wide extent. Thus, highest demands have to be made on quality assurance. Therefore, it is necessary to formulate technical regulations for the quantification of MVOC.

  17. Quantification of surface emissions: An historical perspective from GEIA

    NASA Astrophysics Data System (ADS)

    Granier, C.; Denier Van Der Gon, H.; Doumbia, E. H. T.; Frost, G. J.; Guenther, A. B.; Hassler, B.; Janssens-Maenhout, G. G. A.; Lasslop, G.; Melamed, M. L.; Middleton, P.; Sindelarova, K.; Tarrason, L.; van Marle, M.; W Kaiser, J.; van der Werf, G.

    2015-12-01

    Assessments of the composition of the atmosphere and its evolution require accurate knowledge of the surface emissions of atmospheric compounds. The first community development of global surface emissions started in 1990, when GEIA was established as a component of the International Global Atmospheric Chemistry (IGAC) project. At that time, GEIA meant "Global Emissions Inventory Activity". Since its inception, GEIA has brought together people to understand emissions from anthropogenic, biomass burning and natural sources. The first goal of GEIA was to establish a "best" inventory for the base year 1985 at 1x1 degree resolution. Since then many inventories have been developed by various groups at the global and regional scale at different temporal and spatial resolutions. GEIA, which now means the "Global Emissions Initiative", has evolved into assessing, harmonizing and distributing emissions datasets. We will review the main achievements of GEIA, and show how the development and evaluation of surface emissions has evolved during the last 25 years. We will discuss the use of surface, in-situ and remote sensing observations to evaluate and improve the quantification of emissions. We will highlight the main uncertainties currently limiting emissions datasets, such as the spatial and temporal evolution of emissions at different resolutions, the quantification of emerging emission sources (such as oil/gas extraction and distribution, biofuels, etc.), the speciation of the emissions of volatile organic compounds and of particulate matter, the capacity building necessary for organizing the development of regional emissions across the world, emissions from shipping, etc. We will present the ECCAD (Emissions of Atmospheric Compounds and Compilation of Ancillary Data) database, developed as part of GEIA to facilitate the access and evaluation of emission inventories.

  18. Rapid quantification method for Legionella pneumophila in surface water.

    PubMed

    Wunderlich, Anika; Torggler, Carmen; Elsässer, Dennis; Lück, Christian; Niessner, Reinhard; Seidel, Michael

    2016-03-01

    World-wide legionellosis outbreaks caused by evaporative cooling systems have shown that there is a need for rapid screening methods for Legionella pneumophila in water. Antibody-based methods for the quantification of L. pneumophila are rapid, non-laborious, and relatively cheap but not sensitive enough for establishment as a screening method for surface and drinking water. Therefore, preconcentration methods have to be applied in advance to reach the needed sensitivity. In a basic test, monolithic adsorption filtration (MAF) was used as primary preconcentration method that adsorbs L. pneumophila with high efficiency. Ten-liter water samples were concentrated in 10 min and further reduced to 1 mL by centrifugal ultrafiltration (CeUF). The quantification of L. pneumophila strains belonging to the monoclonal subtype Bellingham was performed via flow-based chemiluminescence sandwich microarray immunoassays (CL-SMIA) in 36 min. The whole analysis process takes 90 min. A polyclonal antibody (pAb) against L. pneumophila serogroup 1-12 and a monoclonal antibody (mAb) against L. pneumophila SG 1 strain Bellingham were immobilized on a microarray chip. Without preconcentration, the detection limit was 4.0 × 10(3) and 2.8 × 10(3) CFU/mL determined by pAb and mAb 10/6, respectively. For samples processed by MAF-CeUF prior to SMIA detection, the limit of detection (LOD) could be decreased to 8.7 CFU/mL and 0.39 CFU/mL, respectively. A recovery of 99.8 ± 15.9% was achieved for concentrations between 1-1000 CFU/mL. The established combined analytical method is sensitive for rapid screening of surface and drinking water to allow fast hygiene control of L. pneumophila. PMID:26873217

  19. Quantification of the genetic risk of environmental mutagens

    SciTech Connect

    Ehling, U.H.

    1988-03-01

    Screening methods are used for hazard identification. Assays for heritable mutations in mammals are used for the confirmation of short-term test results and for the quantification of the genetic risk. There are two main approaches in making genetic risk estimates. One of these, termed the direct method, expresses risk in terms of the expected frequency of genetic changes induced per unit. The other, referred to as the doubling dose method or the indirect method, expresses risk in relation to the observed incidence of genetic disorders now present in man. The indirect method uses experimental data only for the calculation of the doubling dose. The quality of the risk estimation depends on the assumption of persistence of the induced mutations and the ability to determine the current incidence of genetic diseases. The difficulties of improving the estimates of current incidences of genetic diseases or the persistence of the genes in the population led them to the development of an alternative method, the direct estimation of the genetic risk. The direct estimation uses experimental data for the induced frequency for dominant mutations in mice. For the verification of these quantifications one can use the data of Hiroshima and Nagasaki. According to the estimation with the direct method, one would expect less than 1 radiation-induced dominant cataract in 19,000 children with one or both parents exposed. The expected overall frequency of dominant mutations in the first generation would be 20-25, based on radiation-induced dominant cataract mutations. It is estimated that 10 times more recessive than dominant mutations are induced. The same approaches can be used to determine the impact of chemical mutagens.

  20. Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Datta, Susmita; Payne, Samuel H.; Kang, Jiyun; Bramer, Lisa M.; Nicora, Carrie D.; Shukla, Anil K.; Metz, Thomas O.; Rodland, Karin D.; Smith, Richard D.; Tardiff, Mark F.; McDermott, Jason E.; Pounds, Joel G.; Waters, Katrina M.

    2014-12-01

    As the capability of mass spectrometry-based proteomics has matured, tens of thousands of peptides can be measured simultaneously, which has the benefit of offering a systems view of protein expression. However, a major challenge is that with an increase in throughput, protein quantification estimation from the native measured peptides has become a computational task. A limitation to existing computationally-driven protein quantification methods is that most ignore protein variation, such as alternate splicing of the RNA transcript and post-translational modifications or other possible proteoforms, which will affect a significant fraction of the proteome. The consequence of this assumption is that statistical inference at the protein level, and consequently downstream analyses, such as network and pathway modeling, have only limited power for biomarker discovery. Here, we describe a Bayesian model (BP-Quant) that uses statistically derived peptides signatures to identify peptides that are outside the dominant pattern, or the existence of multiple over-expressed patterns to improve relative protein abundance estimates. It is a research-driven approach that utilizes the objectives of the experiment, defined in the context of a standard statistical hypothesis, to identify a set of peptides exhibiting similar statistical behavior relating to a protein. This approach infers that changes in relative protein abundance can be used as a surrogate for changes in function, without necessarily taking into account the effect of differential post-translational modifications, processing, or splicing in altering protein function. We verify the approach using a dilution study from mouse plasma samples and demonstrate that BP-Quant achieves similar accuracy as the current state-of-the-art methods at proteoform identification with significantly better specificity. BP-Quant is available as a MatLab ® and R packages at https://github.com/PNNL-Comp-Mass-Spec/BP-Quant.

  1. Stochastic methods for uncertainty quantification in radiation transport

    SciTech Connect

    Fichtl, Erin D; Prinja, Anil K; Warsa, James S

    2009-01-01

    The use of generalized polynomial chaos (gPC) expansions is investigated for uncertainty quantification in radiation transport. The gPC represents second-order random processes in terms of an expansion of orthogonal polynomials of random variables and is used to represent the uncertain input(s) and unknown(s). We assume a single uncertain input-the total macroscopic cross section-although this does not represent a limitation of the approaches considered here. Two solution methods are examined: The Stochastic Finite Element Method (SFEM) and the Stochastic Collocation Method (SCM). The SFEM entails taking Galerkin projections onto the orthogonal basis, which, for fixed source problems, yields a linear system of fully -coupled equations for the PC coefficients of the unknown. For k-eigenvalue calculations, the SFEM system is non-linear and a Newton-Krylov method is employed to solve it. The SCM utilizes a suitable quadrature rule to compute the moments or PC coefficients of the unknown(s), thus the SCM solution involves a series of independent deterministic transport solutions. The accuracy and efficiency of the two methods are compared and contrasted. The PC coefficients are used to compute the moments and probability density functions of the unknown(s), which are shown to be accurate by comparing with Monte Carlo results. Our work demonstrates that stochastic spectral expansions are a viable alternative to sampling-based uncertainty quantification techniques since both provide a complete characterization of the distribution of the flux and the k-eigenvalue. Furthermore, it is demonstrated that, unlike perturbation methods, SFEM and SCM can handle large parameter uncertainty.

  2. Neurostereology protocol for unbiased quantification of neuronal injury and neurodegeneration

    PubMed Central

    Golub, Victoria M.; Brewer, Jonathan; Wu, Xin; Kuruba, Ramkumar; Short, Jenessa; Manchi, Maunica; Swonke, Megan; Younus, Iyan; Reddy, Doodipala Samba

    2015-01-01

    Neuronal injury and neurodegeneration are the hallmark pathologies in a variety of neurological conditions such as epilepsy, stroke, traumatic brain injury, Parkinson’s disease and Alzheimer’s disease. Quantification of absolute neuron and interneuron counts in various brain regions is essential to understand the impact of neurological insults or neurodegenerative disease progression in animal models. However, conventional qualitative scoring-based protocols are superficial and less reliable for use in studies of neuroprotection evaluations. Here, we describe an optimized stereology protocol for quantification of neuronal injury and neurodegeneration by unbiased counting of neurons and interneurons. Every 20th section in each series of 20 sections was processed for NeuN(+) total neuron and parvalbumin(+) interneuron immunostaining. The sections that contain the hippocampus were then delineated into five reliably predefined subregions. Each region was separately analyzed with a microscope driven by the stereology software. Regional tissue volume was determined by using the Cavalieri estimator, as well as cell density and cell number were determined by using the optical disector and optical fractionator. This protocol yielded an estimate of 1.5 million total neurons and 0.05 million PV(+) interneurons within the rat hippocampus. The protocol has greater predictive power for absolute counts as it is based on 3D features rather than 2D images. The total neuron counts were consistent with literature values from sophisticated systems, which are more expensive than our stereology system. This unbiased stereology protocol allows for sensitive, medium-throughput counting of total neurons in any brain region, and thus provides a quantitative tool for studies of neuronal injury and neurodegeneration in a variety of acute brain injury and chronic neurological models. PMID:26582988

  3. A General Uncertainty Quantification Methodology for Cloud Microphysical Property Retrievals

    NASA Astrophysics Data System (ADS)

    Tang, Q.; Xie, S.; Chen, X.; Zhao, C.

    2014-12-01

    The US Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program provides long-term (~20 years) ground-based cloud remote sensing observations. However, there are large uncertainties in the retrieval products of cloud microphysical properties based on the active and/or passive remote-sensing measurements. To address this uncertainty issue, a DOE Atmospheric System Research scientific focus study, Quantification of Uncertainties in Cloud Retrievals (QUICR), has been formed. In addition to an overview of recent progress of QUICR, we will demonstrate the capacity of an observation-based general uncertainty quantification (UQ) methodology via the ARM Climate Research Facility baseline cloud microphysical properties (MICROBASE) product. This UQ method utilizes the Karhunen-Loéve expansion (KLE) and Central Limit Theorems (CLT) to quantify the retrieval uncertainties from observations and algorithm parameters. The input perturbations are imposed on major modes to take into account the cross correlations between input data, which greatly reduces the dimension of random variables (up to a factor of 50) and quantifies vertically resolved full probability distribution functions of retrieved quantities. Moreover, this KLE/CLT approach has the capability of attributing the uncertainties in the retrieval output to individual uncertainty source and thus sheds light on improving the retrieval algorithm and observations. We will present the results of a case study for the ice water content at the Southern Great Plains during an intensive observing period on March 9, 2000. This work is performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  4. Quantification of Carbohydrates in Grape Tissues Using Capillary Zone Electrophoresis

    PubMed Central

    Zhao, Lu; Chanon, Ann M.; Chattopadhyay, Nabanita; Dami, Imed E.; Blakeslee, Joshua J.

    2016-01-01

    Soluble sugars play an important role in freezing tolerance in both herbaceous and woody plants, functioning in both the reduction of freezing-induced dehydration and the cryoprotection of cellular constituents. The quantification of soluble sugars in plant tissues is, therefore, essential in understanding freezing tolerance. While a number of analytical techniques and methods have been used to quantify sugars, most of these are expensive and time-consuming due to complex sample preparation procedures which require the derivatization of the carbohydrates being analyzed. Analysis of soluble sugars using capillary zone electrophoresis (CZE) under alkaline conditions with direct UV detection has previously been used to quantify simple sugars in fruit juices. However, it was unclear whether CZE-based methods could be successfully used to quantify the broader range of sugars present in complex plant extracts. Here, we present the development of an optimized CZE method capable of separating and quantifying mono-, di-, and tri-saccharides isolated from plant tissues. This optimized CZE method employs a column electrolyte buffer containing 130 mM NaOH, pH 13.0, creating a current of 185 μA when a separation voltage of 10 kV is employed. The optimized CZE method provides limits-of-detection (an average of 1.5 ng/μL) for individual carbohydrates comparable or superior to those obtained using gas chromatography–mass spectrometry, and allows resolution of non-structural sugars and cell wall components (structural sugars). The optimized CZE method was successfully used to quantify sugars from grape leaves and buds, and is a robust tool for the quantification of plant sugars found in vegetative and woody tissues. The increased analytical efficiency of this CZE method makes it ideal for use in high-throughput metabolomics studies designed to quantify plant sugars. PMID:27379118

  5. Quantification of Carbohydrates in Grape Tissues Using Capillary Zone Electrophoresis.

    PubMed

    Zhao, Lu; Chanon, Ann M; Chattopadhyay, Nabanita; Dami, Imed E; Blakeslee, Joshua J

    2016-01-01

    Soluble sugars play an important role in freezing tolerance in both herbaceous and woody plants, functioning in both the reduction of freezing-induced dehydration and the cryoprotection of cellular constituents. The quantification of soluble sugars in plant tissues is, therefore, essential in understanding freezing tolerance. While a number of analytical techniques and methods have been used to quantify sugars, most of these are expensive and time-consuming due to complex sample preparation procedures which require the derivatization of the carbohydrates being analyzed. Analysis of soluble sugars using capillary zone electrophoresis (CZE) under alkaline conditions with direct UV detection has previously been used to quantify simple sugars in fruit juices. However, it was unclear whether CZE-based methods could be successfully used to quantify the broader range of sugars present in complex plant extracts. Here, we present the development of an optimized CZE method capable of separating and quantifying mono-, di-, and tri-saccharides isolated from plant tissues. This optimized CZE method employs a column electrolyte buffer containing 130 mM NaOH, pH 13.0, creating a current of 185 μA when a separation voltage of 10 kV is employed. The optimized CZE method provides limits-of-detection (an average of 1.5 ng/μL) for individual carbohydrates comparable or superior to those obtained using gas chromatography-mass spectrometry, and allows resolution of non-structural sugars and cell wall components (structural sugars). The optimized CZE method was successfully used to quantify sugars from grape leaves and buds, and is a robust tool for the quantification of plant sugars found in vegetative and woody tissues. The increased analytical efficiency of this CZE method makes it ideal for use in high-throughput metabolomics studies designed to quantify plant sugars.

  6. Quantification and Localization of Mast Cells in Periapical Lesions

    PubMed Central

    Mahita, VN; Manjunatha, BS; Shah, R; Astekar, M; Purohit, S; Kovvuru, S

    2015-01-01

    Background: Periapical lesions occur in response to chronic irritation in periapical tissue, generally resulting from an infected root canal. Specific etiological agents of induction, participating cell population and growth factors associated with maintenance and resolution of periapical lesions are incompletely understood. Among the cells found in periapical lesions, mast cells have been implicated in the inflammatory mechanism. Aim: Quantifications and the possible role played by mast cells in the periapical granuloma and radicular cyst. Hence, this study is to emphasize the presence (localization) and quantification of mast cells in periapical granuloma and radicular cyst. Materials and Methods: A total of 30 cases and out of which 15 of periapical granuloma and 15 radicular cyst, each along with the case details from the previously diagnosed cases in the department of oral pathology were selected for the study. The gender distribution showed male 8 (53.3%) and females 7 (46.7%) in periapical granuloma cases and male 10 (66.7%) and females 5 (33.3%) in radicular cyst cases. The statistical analysis used was unpaired t-test. Results: Mean mast cell count in periapical granuloma subepithelial and deeper connective tissue, was 12.40 (0.99%) and 7.13 (0.83%), respectively. The mean mast cell counts in subepithelial and deeper connective tissue of radicular cyst were 17.64 (1.59%) and 12.06 (1.33%) respectively, which was statistically significant. No statistical significant difference was noted among males and females. Conclusion: Mast cells were more in number in radicular cyst. Based on the concept that mast cells play a critical role in the induction of inflammation, it is logical to use therapeutic agents to alter mast cell function and secretion, to thwart inflammation at its earliest phases. These findings may suggest the possible role of mast cells in the pathogenesis of periapical lesions. PMID:25861530

  7. Quantification of regional fat volume in rat MRI

    NASA Astrophysics Data System (ADS)

    Sacha, Jaroslaw P.; Cockman, Michael D.; Dufresne, Thomas E.; Trokhan, Darren

    2003-05-01

    Multiple initiatives in the pharmaceutical and beauty care industries are directed at identifying therapies for weight management. Body composition measurements are critical for such initiatives. Imaging technologies that can be used to measure body composition noninvasively include DXA (dual energy x-ray absorptiometry) and MRI (magnetic resonance imaging). Unlike other approaches, MRI provides the ability to perform localized measurements of fat distribution. Several factors complicate the automatic delineation of fat regions and quantification of fat volumes. These include motion artifacts, field non-uniformity, brightness and contrast variations, chemical shift misregistration, and ambiguity in delineating anatomical structures. We have developed an approach to deal practically with those challenges. The approach is implemented in a package, the Fat Volume Tool, for automatic detection of fat tissue in MR images of the rat abdomen, including automatic discrimination between abdominal and subcutaneous regions. We suppress motion artifacts using masking based on detection of implicit landmarks in the images. Adaptive object extraction is used to compensate for intensity variations. This approach enables us to perform fat tissue detection and quantification in a fully automated manner. The package can also operate in manual mode, which can be used for verification of the automatic analysis or for performing supervised segmentation. In supervised segmentation, the operator has the ability to interact with the automatic segmentation procedures to touch-up or completely overwrite intermediate segmentation steps. The operator's interventions steer the automatic segmentation steps that follow. This improves the efficiency and quality of the final segmentation. Semi-automatic segmentation tools (interactive region growing, live-wire, etc.) improve both the accuracy and throughput of the operator when working in manual mode. The quality of automatic segmentation has been

  8. Respiratory Mucosal Proteome Quantification in Human Influenza Infections

    PubMed Central

    Marion, Tony; Elbahesh, Husni; Thomas, Paul G.; DeVincenzo, John P.; Webby, Richard; Schughart, Klaus

    2016-01-01

    Respiratory influenza virus infections represent a serious threat to human health. Underlying medical conditions and genetic make-up predispose some influenza patients to more severe forms of disease. To date, only a few studies have been performed in patients to correlate a selected group of cytokines and chemokines with influenza infection. Therefore, we evaluated the potential of a novel multiplex micro-proteomics technology, SOMAscan, to quantify proteins in the respiratory mucosa of influenza A and B infected individuals. The analysis included but was not limited to quantification of cytokines and chemokines detected in previous studies. SOMAscan quantified more than 1,000 secreted proteins in small nasal wash volumes from infected and healthy individuals. Our results illustrate the utility of micro-proteomic technology for analysis of proteins in small volumes of respiratory mucosal samples. Furthermore, when we compared nasal wash samples from influenza-infected patients with viral load ≥ 28 and increased IL-6 and CXCL10 to healthy controls, we identified 162 differentially-expressed proteins between the two groups. This number greatly exceeds the number of DEPs identified in previous studies in human influenza patients. Most of the identified proteins were associated with the host immune response to infection, and changes in protein levels of 151 of the DEPs were significantly correlated with viral load. Most important, SOMAscan identified differentially expressed proteins heretofore not associated with respiratory influenza infection in humans. Our study is the first report for the use of SOMAscan to screen nasal secretions. It establishes a precedent for micro-proteomic quantification of proteins that reflect ongoing response to respiratory infection. PMID:27088501

  9. Respiratory Mucosal Proteome Quantification in Human Influenza Infections.

    PubMed

    Marion, Tony; Elbahesh, Husni; Thomas, Paul G; DeVincenzo, John P; Webby, Richard; Schughart, Klaus

    2016-01-01

    Respiratory influenza virus infections represent a serious threat to human health. Underlying medical conditions and genetic make-up predispose some influenza patients to more severe forms of disease. To date, only a few studies have been performed in patients to correlate a selected group of cytokines and chemokines with influenza infection. Therefore, we evaluated the potential of a novel multiplex micro-proteomics technology, SOMAscan, to quantify proteins in the respiratory mucosa of influenza A and B infected individuals. The analysis included but was not limited to quantification of cytokines and chemokines detected in previous studies. SOMAscan quantified more than 1,000 secreted proteins in small nasal wash volumes from infected and healthy individuals. Our results illustrate the utility of micro-proteomic technology for analysis of proteins in small volumes of respiratory mucosal samples. Furthermore, when we compared nasal wash samples from influenza-infected patients with viral load ≥ 2(8) and increased IL-6 and CXCL10 to healthy controls, we identified 162 differentially-expressed proteins between the two groups. This number greatly exceeds the number of DEPs identified in previous studies in human influenza patients. Most of the identified proteins were associated with the host immune response to infection, and changes in protein levels of 151 of the DEPs were significantly correlated with viral load. Most important, SOMAscan identified differentially expressed proteins heretofore not associated with respiratory influenza infection in humans. Our study is the first report for the use of SOMAscan to screen nasal secretions. It establishes a precedent for micro-proteomic quantification of proteins that reflect ongoing response to respiratory infection.

  10. Quantification of blood flow and topology in developing vascular networks.

    PubMed

    Kloosterman, Astrid; Hierck, Beerend; Westerweel, Jerry; Poelma, Christian

    2014-01-01

    Since fluid dynamics plays a critical role in vascular remodeling, quantification of the hemodynamics is crucial to gain more insight into this complex process. Better understanding of vascular development can improve prediction of the process, and may eventually even be used to influence the vascular structure. In this study, a methodology to quantify hemodynamics and network structure of developing vascular networks is described. The hemodynamic parameters and topology are derived from detailed local blood flow velocities, obtained by in vivo micro-PIV measurements. The use of such detailed flow measurements is shown to be essential, as blood vessels with a similar diameter can have a large variation in flow rate. Measurements are performed in the yolk sacs of seven chicken embryos at two developmental stages between HH 13+ and 17+. A large range of flow velocities (1 µm/s to 1 mm/s) is measured in blood vessels with diameters in the range of 25-500 µm. The quality of the data sets is investigated by verifying the flow balances in the branching points. This shows that the quality of the data sets of the seven embryos is comparable for all stages observed, and the data is suitable for further analysis with known accuracy. When comparing two subsequently characterized networks of the same embryo, vascular remodeling is observed in all seven networks. However, the character of remodeling in the seven embryos differs and can be non-intuitive, which confirms the necessity of quantification. To illustrate the potential of the data, we present a preliminary quantitative study of key network topology parameters and we compare these with theoretical design rules.

  11. Rapid quantification method for Legionella pneumophila in surface water.

    PubMed

    Wunderlich, Anika; Torggler, Carmen; Elsässer, Dennis; Lück, Christian; Niessner, Reinhard; Seidel, Michael

    2016-03-01

    World-wide legionellosis outbreaks caused by evaporative cooling systems have shown that there is a need for rapid screening methods for Legionella pneumophila in water. Antibody-based methods for the quantification of L. pneumophila are rapid, non-laborious, and relatively cheap but not sensitive enough for establishment as a screening method for surface and drinking water. Therefore, preconcentration methods have to be applied in advance to reach the needed sensitivity. In a basic test, monolithic adsorption filtration (MAF) was used as primary preconcentration method that adsorbs L. pneumophila with high efficiency. Ten-liter water samples were concentrated in 10 min and further reduced to 1 mL by centrifugal ultrafiltration (CeUF). The quantification of L. pneumophila strains belonging to the monoclonal subtype Bellingham was performed via flow-based chemiluminescence sandwich microarray immunoassays (CL-SMIA) in 36 min. The whole analysis process takes 90 min. A polyclonal antibody (pAb) against L. pneumophila serogroup 1-12 and a monoclonal antibody (mAb) against L. pneumophila SG 1 strain Bellingham were immobilized on a microarray chip. Without preconcentration, the detection limit was 4.0 × 10(3) and 2.8 × 10(3) CFU/mL determined by pAb and mAb 10/6, respectively. For samples processed by MAF-CeUF prior to SMIA detection, the limit of detection (LOD) could be decreased to 8.7 CFU/mL and 0.39 CFU/mL, respectively. A recovery of 99.8 ± 15.9% was achieved for concentrations between 1-1000 CFU/mL. The established combined analytical method is sensitive for rapid screening of surface and drinking water to allow fast hygiene control of L. pneumophila.

  12. Spatiotemporal quantification of subcellular ATP levels in a single HeLa cell during changes in morphology.

    PubMed

    Suzuki, Rika; Hotta, Kohji; Oka, Kotaro

    2015-11-17

    The quantitative relationship between change in cell shape and ATP consumption is an unsolved problem in cell biology. In this study, a simultaneous imaging and image processing analysis allowed us to observe and quantify these relationships under physiological conditions, for the first time. We focused on two marginal regions of cells: the microtubule-rich 'lamella' and the actin-rich 'peripheral structure'. Simultaneous imaging and correlation analysis revealed that microtubule dynamics cause lamellar shape change accompanying an increase in ATP level. Also, image processing and spatiotemporal quantification enabled to visualize a chronological change of the relationships between the protrusion length and ATP levels, and it suggested they are influencing each other. Furthermore, inhibition of microtubule dynamics diminished motility in the peripheral structure and the range of fluctuation of ATP level in the lamella. This work clearly demonstrates that cellular motility and morphology are regulated by ATP-related cooperative function between microtubule and actin dynamics.

  13. Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

    PubMed Central

    2013-01-01

    The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay (‘QFI-PCR’) that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing. PMID:24001039

  14. Detection and quantification of soy allergens in food: study of two commercial enzyme-linked immunosorbent assays.

    PubMed

    L'Hocine, Lamia; Boye, Joyce Irene; Munyana, Christella

    2007-04-01

    The objective of this study was to evaluate the efficacy of 2 commercially available soy enzyme-linked immunosorbent assays (ELISA) and use them in detecting soy proteins in selected food commodities. Both ELISA kits exhibited high sensitivity. The determined limits of detection (LOD) (approximately 2 and <1 microg/mL for Tepnel Biosystems and Elisa Systems kits, respectively) were lower than those claimed by the manufacturer. Quantification range for both kits was, however, narrower and in a lower concentration range than defined by the kit providers. Our examination revealed a positive cross-reactivity with chickpea proteins and matrix interferences for both kits. The immunoreactivity of soy proteins, when tested by the Tepnel Biosystems kit, was partially reduced by papain and bromelain hydrolysis; it was significantly decreased by protein glycation (>47%). Nondenatured and nonheated soy protein isolate (SPI) samples were also significantly less antigenic than the treated ones.

  15. Quantification of phnAc and nahAc in contaminated New Zealand soils by competitive PCR

    SciTech Connect

    Laurie, A.D.; Lloyd-Jones, G.

    2000-05-01

    Unculturable polycyclic aromatic hydrocarbon (PAH)-degrading bacteria are a significant reservoir of the microbial potential to catabolize low-molecular-weight PAHs. The population of these bacteria is larger than the population of nah-like bacteria that are the dominant organisms in culture-based studies. The authors used the recently described phn genes of Burkholderia sp. strain RP007, which feature only rarely in culture-based studies, as an alternative genotype for naphthalene and phenanthrene degradation and compared this genotype with the genotypically distinct but ubiquitous nah-like class in different soils. Competitive PCR quantification of phnAc and nahAc, which encode the iron sulfur protein large ({alpha}) subunits of PAH dioxygenases in nah-like and phn catabolic operons, revealed that the phn genotype can have a greater ecological significance than the nah-like genotype.

  16. Proteomics Reveals Novel Drosophila Seminal Fluid Proteins Transferred at Mating

    PubMed Central

    Findlay, Geoffrey D; Yi, Xianhua; MacCoss, Michael J; Swanson, Willie J

    2008-01-01

    Across diverse taxa, seminal fluid proteins (Sfps) transferred at mating affect the reproductive success of both sexes. Such reproductive proteins often evolve under positive selection between species; because of this rapid divergence, Sfps are hypothesized to play a role in speciation by contributing to reproductive isolation between populations. In Drosophila, individual Sfps have been characterized and are known to alter male sperm competitive ability and female post-mating behavior, but a proteomic-scale view of the transferred Sfps has been missing. Here we describe a novel proteomic method that uses whole-organism isotopic labeling to detect transferred Sfps in mated female D. melanogaster. We identified 63 proteins, which were previously unknown to function in reproduction, and confirmed the transfer of dozens of predicted Sfps. Relative quantification of protein abundance revealed that several of these novel Sfps are abundant in seminal fluid. Positive selection and tandem gene duplication are the prevailing forces of Sfp evolution, and comparative proteomics with additional species revealed lineage-specific changes in seminal fluid content. We also report a proteomic-based gene discovery method that uncovered 19 previously unannotated genes in D. melanogaster. Our results demonstrate an experimental method to identify transferred proteins in any system that is amenable to isotopic labeling, and they underscore the power of combining proteomic and evolutionary analyses to shed light on the complex process of Drosophila reproduction. PMID:18666829

  17. Quantification of target analytes in various biofluids using a postcolumn infused-internal standard method combined with matrix normalization factors in liquid chromatography-electrospray ionization mass spectrometry.

    PubMed

    Liao, Hsiao-Wei; Tsai, I-Lin; Chen, Guan-Yuan; Lu, Yen-Shen; Lin, Ching-Hung; Kuo, Ching-Hua

    2014-09-01

    Liquid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS) has become one of the most widely used methods in pharmaceutical laboratories. Although LC-ESI-MS provides high sensitivity and high specificity for quantifying target analytes in complicated biofluids, the associated severe matrix effects (MEs) generally result in large quantification errors. Here, we propose a novel strategy for correcting MEs in various biofluids using a postcolumn infused-internal standard (PCI-IS) method in combination with matrix normalization factors (MNFs). We used the MNFs to normalize the encountered MEs in various biofluids to the MEs encountered in standard solutions. The use of a postcolumn infused-internal standard also corrects the MEs for individual samples. When using the PCI-IS method in combination with MNFs, the calibration curve generated from standard solutions can be applied to quantify the target analytes in various biofluids. We applied this new approach to quantify etoposide and etoposide catechol in plasma and CSF. The accuracy of the test results showed that over 93% of the data have quantification errors less than 20% and that 99% of the data have quantification errors less than 30%. The successful application of this method to evaluate real clinical samples revealed that our proposed MNFs in combination with the PCI-IS method largely simplifies the entire method development and validation processes, saves a great deal of time and cost without sacrificing quantification accuracy, and provides a simple means of quantifying target analytes in various biofluids. This method will be particularly useful in fields in which the same target analytes need to be quantified in various types of matrices, including bioanalysis, forensic toxicology, environmental studies, and food safety control. PMID:25022483

  18. Direct Quantification of Cell-Free, Circulating DNA from Unpurified Plasma

    PubMed Central

    Breitbach, Sarah; Tug, Suzan; Helmig, Susanne; Zahn, Daniela; Kubiak, Thomas; Michal, Matthias; Gori, Tommaso; Ehlert, Tobias; Beiter, Thomas; Simon, Perikles

    2014-01-01

    Cell-free DNA (cfDNA) in body tissues or fluids is extensively investigated in clinical medicine and other research fields. In this article we provide a direct quantitative real-time PCR (qPCR) as a sensitive tool for the measurement of cfDNA from plasma without previous DNA extraction, which is known to be accompanied by a reduction of DNA yield. The primer sets were designed to amplify a 90 and 222 bp multi-locus L1PA2 sequence. In the first module, cfDNA concentrations in unpurified plasma were compared to cfDNA concentrations in the eluate and the flow-through of the QIAamp DNA Blood Mini Kit and in the eluate of a phenol-chloroform isoamyl (PCI) based DNA extraction, to elucidate the DNA losses during extraction. The analyses revealed 2.79-fold higher cfDNA concentrations in unpurified plasma compared to the eluate of the QIAamp DNA Blood Mini Kit, while 36.7% of the total cfDNA were found in the flow-through. The PCI procedure only performed well on samples with high cfDNA concentrations, showing 87.4% of the concentrations measured in plasma. The DNA integrity strongly depended on the sample treatment. Further qualitative analyses indicated differing fractions of cfDNA fragment lengths in the eluate of both extraction methods. In the second module, cfDNA concentrations in the plasma of 74 coronary heart disease patients were compared to cfDNA concentrations of 74 healthy controls, using the direct L1PA2 qPCR for cfDNA quantification. The patient collective showed significantly higher cfDNA levels (mean (SD) 20.1 (23.8) ng/ml; range 5.1–183.0 ng/ml) compared to the healthy controls (9.7 (4.2) ng/ml; range 1.6–23.7 ng/ml). With our direct qPCR, we recommend a simple, economic and sensitive procedure for the quantification of cfDNA concentrations from plasma that might find broad applicability, if cfDNA became an established marker in the assessment of pathophysiological conditions. PMID:24595313

  19. Effective chromatic texture coding for robust skin disease minimal descriptor quantification

    NASA Astrophysics Data System (ADS)

    Fiorini, Rodolfo A.; Crivellini, M.; Codagnone, G.; Dacquino, Gianfranco F.; Libertini, M.; Morresi, A.

    1997-04-01

    Among the various skin diseases skin tumors are the most serious ones and skin melanoma is particularly dangerous. Its malignant evolution lasts about 5 or 6 years and ends with the death of the patient. Early diagnosis is a powerful means of preventing this evolution allowing sudden intervention which increases probability of recover and survival. Purpose of this paper is to present an active support system (ASS) able to reveal and quantify the stage of disease evolution. The work focuses the problem encountered in chromatic information encoding the morphological aspects quantification. A new method is proposed which permits robust and reliable quantification of image data obtained via a digital epiluminescence dermatoscopy apparatus (DELM) designed and built with interesting new features. The image information extraction is based on minimal descriptor set of parameters in order to classify chromatic texture and morphological features. The active support systems is based on DELM technique, taking advantage of polarized light guided by optical fibers. In the purpose to discriminate between malignant and benign melanocytic lesions, several dermatoscopical features have been proposed by different research groups. Nevertheless many are the attempts to reach a reliable and objective classification procedure. We adopt, as reference, the approach used by Stanganelli and Kenet. Through a bioengineering analysis we can organize reference grids that offer the possibility to extract the maximum information content from dermatological data. The classification takes into account the Spread and Intrinsic Descriptors and correspond to the best operative description. Therefore these grids are the more suitable tools for application which require ASS for diagnosis. In fact it is possible to obtain quantitative evaluations too. We propose a method based on geometrical synthetical descriptors. All that permits a reliable early diagnosis of melanotic disease and to follow its

  20. Dual-beam optical coherence tomography system for quantification of flow velocity in capillary phantoms

    NASA Astrophysics Data System (ADS)

    Daly, S. M.; Silien, C.; Leahy, M. J.

    2012-03-01

    The quantification of (blood) flow velocity within the vasculature has potent diagnostic and prognostic potential. Assessment of flow irregularities in the form of increased permeability (micro haemorrhaging), the presence of avascular areas, or conversely the presence of vessels with enlarged or increased tortuosity in the acral regions of the body may provide a means of non-invasive in vivo assessment. If assessment of dermal flow dynamics were performed in a routine manner, the existence and prevalence of ailments such as diabetes mellitus, psoriatic arthritis and Raynaud's condition may be confirmed prior to clinical suspicion. This may prove advantageous in cases wherein the efficacy of a prescribed treatment is dictated by a prompt diagnosis and to alleviate patient discomfort through early detection. Optical Coherence Tomography (OCT) is an imaging modality which utilises the principle of optical interferometry to distinguish between spatial changes in refractive index within the vasculature and thus formulate a multi-dimensional representation of the structure of the epi- and dermal skin layers. The use of the Doppler functionality has been the predominant force for the quantification of moving particles within media, elucidated via estimation of the phase shift in OCT A-scans. However, the theoretical formulation for the assessment of these phase shifts dictates that the angle between the incident light source and the vessel under question be known a priori; this may be achieved via excisional biopsy of the tissue segment in question, but is counter to the non-invasive premise of the OCT technique. To address the issue of angular dependence, an alternate means of estimating absolute flow velocity is presented. The design and development of a dual-beam (db) system incorporating an optical switch mechanism for signal discrimination of two spatially disparate points enabling quasi-simultaneous multiple specimen scanning is described. A crosscorrelation (c

  1. Quantification of human infection risk caused by rotavirus in surface waters from Córdoba, Argentina.

    PubMed

    Prez, V E; Gil, P I; Temprana, C F; Cuadrado, P R; Martínez, L C; Giordano, M O; Masachessi, G; Isa, M B; Ré, V E; Paván, J V; Nates, S V; Barril, P A

    2015-12-15

    Fecal contamination of water is a worrying problem because it is associated with the transmission of enteric pathogenic microorganisms that can cause many infectious diseases. In this study, an environmental survey was conducted to assess the level of viral contamination by viable enterovirus and rotavirus genome in two recreational rivers (Suquía and Xanaes) of Córdoba, Argentina. Quantitative microbial risk assessment (QMRA) was calculated to estimate the risk of rotavirus infection. Water sampling was carried out during a one-year period, the presence of total and fecal coliforms was determined and water samples were then concentrated for viral determination. Cell culture and indirect immunofluorescence were applied for enterovirus detection and RT-qPCR for rotavirus quantification. Coliform bacteria levels found in Suquía River often far exceeded the guideline limits for recreational waters. The Xanaes exhibited a lower level of bacterial contamination, frequently within the guideline limits. Enterovirus and rotavirus were frequently detected in the monitoring rivers (percentage of positive samples in Suquía: 78.6% enterovirus, 100% rotavirus; in Xanaes: 87.5% enterovirus, 18.7% rotavirus). Rotavirus was detected at a media concentration of 5.7×10(5) genome copies/L (gc/L) in the Suquía and 8.5×10(0)gc/L in the Xanaes. QMRA revealed high risk of rotavirus infection in the Suquía, at sampling points with acceptable and non-acceptable bacteria numbers. The Xanaes showed significantly lower health risk of rotavirus infection but it proved to be a public health hazard. The viral occurrence was not readily explained by the levels of bacteria indicators, thus viral monitoring should be included to determine microbiological water quality. These findings provide the first data of QMRA for recreational waters in Argentina and reveal the need for public awareness of the health implications of the use of the river waters.

  2. Quantification of human infection risk caused by rotavirus in surface waters from Córdoba, Argentina.

    PubMed

    Prez, V E; Gil, P I; Temprana, C F; Cuadrado, P R; Martínez, L C; Giordano, M O; Masachessi, G; Isa, M B; Ré, V E; Paván, J V; Nates, S V; Barril, P A

    2015-12-15

    Fecal contamination of water is a worrying problem because it is associated with the transmission of enteric pathogenic microorganisms that can cause many infectious diseases. In this study, an environmental survey was conducted to assess the level of viral contamination by viable enterovirus and rotavirus genome in two recreational rivers (Suquía and Xanaes) of Córdoba, Argentina. Quantitative microbial risk assessment (QMRA) was calculated to estimate the risk of rotavirus infection. Water sampling was carried out during a one-year period, the presence of total and fecal coliforms was determined and water samples were then concentrated for viral determination. Cell culture and indirect immunofluorescence were applied for enterovirus detection and RT-qPCR for rotavirus quantification. Coliform bacteria levels found in Suquía River often far exceeded the guideline limits for recreational waters. The Xanaes exhibited a lower level of bacterial contamination, frequently within the guideline limits. Enterovirus and rotavirus were frequently detected in the monitoring rivers (percentage of positive samples in Suquía: 78.6% enterovirus, 100% rotavirus; in Xanaes: 87.5% enterovirus, 18.7% rotavirus). Rotavirus was detected at a media concentration of 5.7×10(5) genome copies/L (gc/L) in the Suquía and 8.5×10(0)gc/L in the Xanaes. QMRA revealed high risk of rotavirus infection in the Suquía, at sampling points with acceptable and non-acceptable bacteria numbers. The Xanaes showed significantly lower health risk of rotavirus infection but it proved to be a public health hazard. The viral occurrence was not readily explained by the levels of bacteria indicators, thus viral monitoring should be included to determine microbiological water quality. These findings provide the first data of QMRA for recreational waters in Argentina and reveal the need for public awareness of the health implications of the use of the river waters. PMID:26311578

  3. Absolute protein quantification of the yeast chaperome under conditions of heat shock

    PubMed Central

    Mackenzie, Rebecca J.; Lawless, Craig; Holman, Stephen W.; Lanthaler, Karin; Beynon, Robert J.; Grant, Chris M.; Hubbard, Simon J.

    2016-01-01

    Chaperones are fundamental to regulating the heat shock response, mediating protein recovery from thermal‐induced misfolding and aggregation. Using the QconCAT strategy and selected reaction monitoring (SRM) for absolute protein quantification, we have determined copy per cell values for 49 key chaperones in Saccharomyces cerevisiae under conditions of normal growth and heat shock. This work extends a previous chemostat quantification study by including up to five Q‐peptides per protein to improve confidence in protein quantification. In contrast to the global proteome profile of S. cerevisiae in response to heat shock, which remains largely unchanged as determined by label‐free quantification, many of the chaperones are upregulated with an average two‐fold increase in protein abundance. Interestingly, eight of the significantly upregulated chaperones are direct gene targets of heat shock transcription factor‐1. By performing absolute quantification of chaperones under heat stress for the first time, we were able to evaluate the individual protein‐level response. Furthermore, this SRM data was used to calibrate label‐free quantification values for the proteome in absolute terms, thus improving relative quantification between the two conditions. This study significantly enhances the largely transcriptomic data available in the field and illustrates a more nuanced response at the protein level. PMID:27252046

  4. Multicentric performance analysis of HCV quantification assays and its potential relevance for HCV treatment.

    PubMed

    Wiesmann, F; Naeth, G; Berger, A; Hirsch, H H; Regenass, S; Ross, R S; Sarrazin, C; Wedemeyer, H; Knechten, H; Braun, P

    2016-06-01

    An accurate quantification of low viremic HCV RNA plasma samples has gained importance since the approval of direct acting antivirals and since only one single measurement predicts the necessity of a prolonged or shortened therapy. As reported previously, HCV quantification assays such as Abbott RealTime HCV and Roche COBAS AmpliPrep/COBAS TaqMan HCV version 2 (CTM v2) may vary in sensitivity and precision particularly in low-level viremia. Importantly, substantial variations were previously demonstrated between some of these assays compared to the Roche High Pure System/COBAS TaqMan assay (HPS) reference assay, which was used to establish the clinical decision points in clinical studies. In this study, the reproducibility of assay performances across several laboratories was assessed by analysing quantification results generated by six independent laboratories (3× RealTime, 3× CTM v2) in comparison with one HPS reference laboratory. The 4th WHO Standard was diluted to 100, 25 and 10 IU/ml, and aliquots were tested in triplicates in 5 independent runs by each assay in the different laboratories to assess assay precision and detection rates. In a second approach, 2 clinical samples (GT 1a & GT 1b) were diluted to 100 and 25 IU/ml and tested as described above. While the result range for WHO 100 IU/ml replicates across all laboratories was similar in this analysis, the CVs of each laboratory ranged from 19.3 to 25.6 % for RealTime laboratories and were lower than CVs of CTM v2 laboratories with a range of 26.1-47.3 %, respectively, and also in comparison with the CV of the HPS reference laboratory (34.9 %). At WHO standard dilution of 25 IU/ml, 24 replicates were quantified by RealTime compared to 8 replicates with CTM v2. Results of clinical samples again revealed a higher variation of CTM v2 results as compared to RealTime values. (CVs at 100 IU/ml: RealTime: 13.1-21.0 % and CTM v2: 15.0-32.3 %; CVs at 25 IU/ml: RealTime 17.6-34.9 % and CTM v2 28

  5. A new objective method for acquisition and quantification of reflex receptive fields.

    PubMed

    Jensen, Michael Brun; Manresa, José Biurrun; Andersen, Ole Kæseler

    2015-03-01

    The nociceptive withdrawal reflex (NWR) is a polysynaptic spinal reflex correlated with pain perception. Assessment of this objective physiological measure constitutes the core of existing methods for quantification of reflex receptive fields (RRFs), which however still suffer from a certain degree of subjective involvement. This article proposes a strictly objective methodology for RRF quantification based on automated identification of NWR thresholds (NWR-Ts). Nociceptive withdrawal reflex thresholds were determined for 10 individual stimulation sites using an interleaved up-down staircase method. Reflexes were detected from electromyography by evaluation of interval peak z scores and application of conduction velocity analysis. Reflex receptive field areas were quantified from interpolated mappings of NWR-Ts and compared with existing RRF quantifications. A total of 3 repeated measures were performed in 2 different sessions to evaluate the test-retest reliability of the various quantifications, using coefficients of repeatability (CRs) and hypothetical sample sizes. The novel quantifications based on identification of NWR-Ts showed a similar level of reliability within and between sessions, whereas existing quantifications all demonstrated worse between-session than within-session reliability. The NWR-T-based quantifications required a smaller sample size than any of the existing RRF measures to detect a clinically relevant effect in a crossover study design involving more than 1 session. Of all measures, quantification from mapping of inversed NWR-Ts demonstrated superior reliability both within (CR, 0.25) and between sessions (CR, 0.28). The study presents a more reliable and robust quantification of the RRF to be used as biomarker of pain hypersensitivity in clinical and experimental research.

  6. [Remarks on application of acupuncture instruments in acupuncture quantification and normalization studies].

    PubMed

    Liu, Jian; Fan, Xiao-Nong; Wang, Shu; Shi, Xue-Min

    2009-01-01

    Acupuncture manipulation quantification is an important link of acupuncture normalization study. Because traditional acupuncture manipulation are complicated with difficulty of quantification, acupuncture instruments provide a new way for acupuncture manipulation quantification and acupuncture normalization. It is necessary to increase the understanding of the importance of developing acupuncture instruments, strengthen the study of related theory and development of acupuncture measurement instruments and acupuncture imitation instruments, enlarge serviceable range, verify efficacy, develop the theory of acupuncture manipulation, richen the study methods of acupuncture normalization, so as to promote internationalization of acupuncture.

  7. UV-Vis as quantification tool for solubilized lignin following a single-shot steam process.

    PubMed

    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.

  8. Two Unique Glioma Subtypes Revealed.

    PubMed

    Poh, Alissa

    2016-04-01

    A comprehensive analysis of 1,122 diffuse glioma samples from The Cancer Genome Atlas has revealed two new subtypes of this common brain cancer, with molecular and clinical features that diverge from the norm. The study findings also support the use of DNA methylation profiles to improve glioma classification and treatment.

  9. Electrocardiograph abnormalities revealed during laparoscopy.

    PubMed

    Nijjer, Sukhjinder; Dubrey, Simon William

    2010-01-01

    This brief case presents a well patient in whom an electrocardiograph abnormality consistent with an accessory pathway was found during a routine procedure. We present the electrocardiographs, explain the underlying condition, and consider why the abnormality was revealed in this manner.

  10. Coral Pigments: Quantification Using HPLC and Detection by Remote Sensing

    NASA Technical Reports Server (NTRS)

    Cottone, Mary C.

    1995-01-01

    Widespread coral bleaching (loss of pigments of symbiotic dinoflagellates), and the corresponding decline in coral reef health worldwide, mandates the monitoring of coral pigmentation. Samples of the corals Porites compressa and P. lobata were collected from a healthy reef at Puako, Hawaii, and chlorophyll (chl) a, peridinin, and Beta-carotene (Beta-car) were quantified using reverse-phase high performance liquid chromatography (HPLC). Detailed procedures are presented for the extraction of the coral pigments in 90% acetone, and the separation, identification, and quantification of the major zooxanthellar pigments using spectrophotometry and a modification of the HPLC system described by Mantoura and Llewellyn (1983). Beta-apo-8-carotenal was found to be inadequate as in internal standard, due to coelution with chl b and/or chl a allomer in the sample extracts. Improvements are suggested, which may result in better resolution of the major pigments and greater accuracy in quantification. Average concentrations of peridinin, chl a, and Beta-car in corals on the reef were 5.01, 8.59, and 0.29, micro-grams/cm(exp 2), respectively. Average concentrations of peridinin and Beta-car did not differ significantly between the two coral species sampled; however, the mean chl a concentration in P. compressa specimens (7.81 ,micro-grams/cm(exp 2) was significantly lower than that in P. lobata specimens (9.96 11g/cm2). Chl a concentrations determined spectrophotometrically were significantly higher than those generated through HPLC, suggesting that spectrophotometry overestimates chl a concentrations. The average ratio of chl a-to-peridinin concentrations was 1.90, with a large (53%) coefficient of variation and a significant difference between the two species sampled. Additional data are needed before conclusions can be drawn regarding average pigment concentrations in healthy corals and the consistency of the chl a/peridinin ratio. The HPLC pigment concentration values

  11. Collaborative framework for PIV uncertainty quantification: the experimental database

    NASA Astrophysics Data System (ADS)

    Neal, Douglas R.; Sciacchitano, Andrea; Smith, Barton L.; Scarano, Fulvio

    2015-07-01

    The uncertainty quantification of particle image velocimetry (PIV) measurements has recently become a topic of great interest as shown by the recent appearance of several different methods within the past few years. These approaches have different working principles, merits and limitations, which have been speculated upon in subsequent studies. This paper reports a unique experiment that has been performed specifically to test the efficacy of PIV uncertainty methods. The case of a rectangular jet, as previously studied by Timmins et al (2012) and Wilson and Smith (2013b), is used. The novel aspect of the experiment is simultaneous velocity measurements using two different time-resolved PIV systems and a hot-wire anemometry (HWA) system. The first PIV system, called the PIV measurement system (‘PIV-MS’), is intended for nominal measurements of which the uncertainty is to be evaluated. It is based on a single camera and features a dynamic velocity range (DVR) representative of typical PIV experiments. The second PIV system, called the ‘PIV-HDR’ (high dynamic range) system, features a significantly higher DVR obtained with a higher digital imaging resolution. The hot-wire is placed in close proximity to the PIV measurement domain. The three measurement systems were carefully set to simultaneously measure the flow velocity at the same time and location. The comparison between the PIV-HDR system and the HWA provides an estimate of the measurement precision of the reference velocity for evaluation of the instantaneous error in the measurement system. The discrepancy between the PIV-MS and the reference data provides the measurement error, which is later used to assess the different uncertainty quantification methods proposed in the literature. A detailed comparison of the uncertainty estimation methods based on the present datasets is presented in a second paper from Sciacchitano et al (2015). Furthermore, this database offers the potential to be used for

  12. Multimodality medical image fusion: probabilistic quantification, segmentation, and registration

    NASA Astrophysics Data System (ADS)

    Wang, Yue J.; Freedman, Matthew T.; Xuan, Jian Hua; Zheng, Qinfen; Mun, Seong K.

    1998-06-01

    Multimodality medical image fusion is becoming increasingly important in clinical applications, which involves information processing, registration and visualization of interventional and/or diagnostic images obtained from different modalities. This work is to develop a multimodality medical image fusion technique through probabilistic quantification, segmentation, and registration, based on statistical data mapping, multiple feature correlation, and probabilistic mean ergodic theorems. The goal of image fusion is to geometrically align two or more image areas/volumes so that pixels/voxels representing the same underlying anatomical structure can be superimposed meaningfully. Three steps are involved. To accurately extract the regions of interest, we developed the model supported Bayesian relaxation labeling, and edge detection and region growing integrated algorithms to segment the images into objects. After identifying the shift-invariant features (i.e., edge and region information), we provided an accurate and robust registration technique which is based on matching multiple binary feature images through a site model based image re-projection. The image was initially segmented into specified number of regions. A rough contour can be obtained by delineating and merging some of the segmented regions. We applied region growing and morphological filtering to extract the contour and get rid of some disconnected residual pixels after segmentation. The matching algorithm is implemented as follows: (1) the centroids of PET/CT and MR images are computed and then translated to the center of both images. (2) preliminary registration is performed first to determine an initial range of scaling factors and rotations, and the MR image is then resampled according to the specified parameters. (3) the total binary difference of the corresponding binary maps in both images is calculated for the selected registration parameters, and the final registration is achieved when the

  13. Development of hydrate risk quantification in oil and gas production

    NASA Astrophysics Data System (ADS)

    Chaudhari, Piyush N.

    order to reduce the parametric study that may require a long duration of time using The Colorado School of Mines Hydrate Kinetic Model (CSMHyK). The evolution of the hydrate plugging risk along flowline-riser systems is modeled for steady state and transient operations considering the effect of several critical parameters such as oil-hydrate slip, duration of shut-in, and water droplet size on a subsea tieback system. This research presents a novel platform for quantification of the hydrate plugging risk, which in-turn will play an important role in improving and optimizing current hydrate management strategies. The predictive strength of the hydrate risk quantification and hydrate prediction models will have a significant impact on flow assurance engineering and design with respect to building safe and efficient hydrate management techniques for future deep-water developments.

  14. Optimization of an automatic counting system for the quantification of Staphylococcus epidermidis cells in biofilms.

    PubMed

    Freitas, Ana Isabel; Vasconcelos, Carlos; Vilanova, Manuel; Cerca, Nuno

    2014-07-01

    Biofilm formation is recognized as the main virulence factor in a variety of chronic infections. In vitro evaluation of biofilm formation is often achieved by quantification of viable or total cells. However, these methods depend on biofilm disruption, which is often achieved by vortexing or sonication. In this study, we investigated the effects of sonication on the elimination of Staphylococcus epidermidis cell clusters from biofilms grown over time, and quantification was performed by three distinct analytical techniques. Even when a higher number of sonication cycles was used, some stable cell clusters remained in the samples obtained from 48- and 72-h-old biofilms, interfering with the quantification of sessile bacteria by plate counting. On the other hand, the fluorescence microscopy automatic counting system allowed proper quantification of biofilm samples that had undergone any of the described sonication cycles, suggesting that this is a more accurate method for assessing the cell concentration in S. epidermidis biofilms, especially in mature biofilms.

  15. Best practices for metabolite quantification in drug development: updated recommendation from the European Bioanalysis Forum.

    PubMed

    Timmerman, Philip; Blech, Stefan; White, Stephen; Green, Martha; Delatour, Claude; McDougall, Stuart; Mannens, Geert; Smeraglia, John; Williams, Stephen; Young, Graeme

    2016-06-01

    Metabolite quantification and profiling continues to grow in importance in today's drug development. The guidance provided by the 2008 FDA Metabolites in Safety Testing Guidance and the subsequent ICH M3(R2) Guidance (2009) has led to a more streamlined process to assess metabolite exposures in preclinical and clinical studies in industry. In addition, the European Bioanalysis Forum (EBF) identified an opportunity to refine the strategies on metabolite quantification considering the experience to date with their recommendation paper on the subject dating from 2010 and integrating the recent discussions on the tiered approach to bioanalytical method validation with focus on metabolite quantification. The current manuscript summarizes the discussion and recommendations from a recent EBF Focus Workshop into an updated recommendation for metabolite quantification in drug development.

  16. Quantification of hesperidin in citrus-based foods using a fungal diglycosidase.

    PubMed

    Mazzaferro, Laura S; Breccia, Javier D

    2012-10-15

    A simple enzymatic-spectrophotometric method for hesperidin quantification was developed by means of a specific fungal enzyme. The method utilises the diglycosidase α-rhamnosyl-β-glucosidase (EC 3.2.1.168) to quantitatively hydrolyse hesperidin to hesperetin, and the last is measured by its intrinsic absorbance in the UV range at 323 nm. The application of this method to quantify hesperidin in orange (Citrus sinensis) juices was shown to be reliable in comparison with the standard method for flavonoid quantification (high performance liquid chromatography, HPLC). The enzymatic method was found to have a limit of quantification of 1.8 μM (1.1 mg/L) hesperidin, similar to the limit usually achieved by HPLC. Moreover, it was feasible to be applied to raw juice, without sample extraction. This feature eliminated the sample pre-treatment, which is mandatory for HPLC, with the consequent reduction of the time required for the quantification.

  17. Monte Carlo Simulation for Quantification of Light Transport Features in Apples

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Light interaction with turbid biological materials involves absorption and scattering. Quantitative understanding of light propagation features in the fruit is critical to designing better optical systems for inspection of food quality. This article reports on the quantification of light propagation...

  18. Detection and quantification of delamination in laminated plates from the phase of appropriate guided wave modes

    NASA Astrophysics Data System (ADS)

    Amjad, Umar; Yadav, Susheel Kumar; Kundu, Tribikram

    2016-01-01

    Applicability of specific Lamb wave modes for delamination detection and quantification in a laminated aluminum plate is investigated. The Lamb modes were generated in the plate using a broadband piezoelectric transducer structured with a rigid electrode. Appropriate excitation frequencies and modes for inspection were selected from theoretical dispersion curves. Sensitivity of antisymmetric and symmetric modes for delamination detection and quantification has been investigated using the Hilbert-Huang transform. The mode conversion phenomenon of Lamb waves during progressive delamination is observed. The antisymmetric mode is found to be more reliable for delamination detection and quantification. In this investigation, the changes in the phase of guided Lamb wave modes are related to the degree of delamination, unlike other studies, where mostly the attenuation of the propagating waves has been related to the extent of the internal damage, such as cracks and corrosions. Appropriate features for delamination detection and quantification are extracted from the experimental data.

  19. The Effect of AOP on Software Engineering, with Particular Attention to OIF and Event Quantification

    NASA Technical Reports Server (NTRS)

    Havelund, Klaus; Filman, Robert; Korsmeyer, David (Technical Monitor)

    2003-01-01

    We consider the impact of Aspect-Oriented Programming on Software Engineering, and, in particular, analyze two AOP systems, one of which does component wrapping and the other, quantification over events, for their software engineering effects.

  20. Relative quantification of biomarkers using mixed-isotope labeling coupled with MS

    PubMed Central

    Chapman, Heidi M; Schutt, Katherine L; Dieter, Emily M; Lamos, Shane M

    2013-01-01

    The identification and quantification of important biomarkers is a critical first step in the elucidation of biological systems. Biomarkers take many forms as cellular responses to stimuli and can be manifested during transcription, translation, and/or metabolic processing. Increasingly, researchers have relied upon mixed-isotope labeling (MIL) coupled with MS to perform relative quantification of biomarkers between two or more biological samples. MIL effectively tags biomarkers of interest for ease of identification and quantification within the mass spectrometer by using isotopic labels that introduce a heavy and light form of the tag. In addition to MIL coupled with MS, a number of other approaches have been used to quantify biomarkers including protein gel staining, enzymatic labeling, metabolic labeling, and several label-free approaches that generate quantitative data from the MS signal response. This review focuses on MIL techniques coupled with MS for the quantification of protein and small-molecule biomarkers. PMID:23157360

  1. In vivo cell tracking and quantification method in adult zebrafish

    NASA Astrophysics Data System (ADS)

    Zhang, Li; Alt, Clemens; Li, Pulin; White, Richard M.; Zon, Leonard I.; Wei, Xunbin; Lin, Charles P.

    2012-03-01

    Zebrafish have become a powerful vertebrate model organism for drug discovery, cancer and stem cell research. A recently developed transparent adult zebrafish using double pigmentation mutant, called casper, provide unparalleled imaging power in in vivo longitudinal analysis of biological processes at an anatomic resolution not readily achievable in murine or other systems. In this paper we introduce an optical method for simultaneous visualization and cell quantification, which combines the laser scanning confocal microscopy (LSCM) and the in vivo flow cytometry (IVFC). The system is designed specifically for non-invasive tracking of both stationary and circulating cells in adult zebrafish casper, under physiological conditions in the same fish over time. The confocal imaging part in this system serves the dual purposes of imaging fish tissue microstructure and a 3D navigation tool to locate a suitable vessel for circulating cell counting. The multi-color, multi-channel instrument allows the detection of multiple cell populations or different tissues or organs simultaneously. We demonstrate initial testing of this novel instrument by imaging vasculature and tracking circulating cells in CD41: GFP/Gata1: DsRed transgenic casper fish whose thrombocytes/erythrocytes express the green and red fluorescent proteins. Circulating fluorescent cell incidents were recorded and counted repeatedly over time and in different types of vessels. Great application opportunities in cancer and stem cell researches are discussed.

  2. Immobilized Particle Imaging for Quantification of Nano- and Microparticles.

    PubMed

    Cui, Jiwei; Hibbs, Benjamin; Gunawan, Sylvia T; Braunger, Julia A; Chen, Xi; Richardson, Joseph J; Hanssen, Eric; Caruso, Frank

    2016-04-12

    The quantification of nano- and microparticles is critical for diverse applications relying on the exact knowledge of the particle concentration. Although many techniques are available for counting particles, there are some limitations in regards to counting with low-scattering materials and facile counting in harsh organic solvents. Herein, we introduce an easy and rapid particle counting technique, termed "immobilized particle imaging" (IPI), to quantify fluorescent particles with different compositions (i.e., inorganic or organic), structures (i.e., solid, porous, or hollow), and sizes (50-1000 nm) dispersed in either aqueous or organic solutions. IPI is achieved by immobilizing particles of interest in a cell matrix-like scaffold (e.g., agarose) and imaging using standard microscopy techniques. Imaging a defined volume of the immobilized particles allows for the particle concentration to be calculated from the count numbers in a fixed volume. IPI provides a general and facile approach to quantify advanced nano- and microparticles, which may be helpful to researchers to obtain new insights for different applications (e.g., nanomedicine).

  3. Dynamic control and quantification of bacterial population dynamics in droplets

    PubMed Central

    Huang, Shuqiang; Srimani, Jaydeep K.; Lee, Anna J.; Zhang, Ying; Lopatkin, Allison J.; Leong, Kam W.; You, Lingchong

    2015-01-01

    Culturing and measuring bacterial population dynamics are critical to develop insights into gene regulation or bacterial physiology. Traditional methods, based on bulk culture to obtain such quantification, have the limitations of higher cost/volume of reagents, non-amendable to small size of population and more laborious manipulation. To this end, droplet-based microfluidics represents a promising alternative that is cost-effective and high-throughput. However, difficulties in manipulating the droplet environment and monitoring encapsulated bacterial population for long-term experiments limit its utilization. To overcome these limitations, we used an electrode-free injection technology to modulate the chemical environment in droplets. This ability is critical for precise control of bacterial dynamics in droplets. Moreover, we developed a trapping device for long-term monitoring of population dynamics in individual droplets for at least 240 h. We demonstrated the utility of this new microfluidic system by quantifying population dynamics of natural and engineered bacteria. Our approach can further improve the analysis for systems and synthetic biology in terms of manipulability and high temporal resolution. PMID:26005763

  4. Uncertainty quantification in the catalytic partial oxidation of methane

    NASA Astrophysics Data System (ADS)

    Navalho, Jorge E. P.; Pereira, José M. C.; Ervilha, Ana R.; Pereira, José C. F.

    2013-12-01

    This work focuses on uncertainty quantification of eight random parameters required as input for 1D modelling of methane catalytic partial oxidation within a highly dense foam reactor. Parameters related to geometrical properties, reactor thermophysics and catalyst loading are taken as uncertain. A widely applied 1D heterogeneous mathematical model that accounts for proper transport and surface chemistry steps is considered for the evaluation of deterministic samples. The non-intrusive spectral projection approach based on polynomial chaos expansion is applied to determine the stochastic temperature and species profiles along the reactor axial direction as well as their ensemble mean and error bars with a confidence interval of 95%. Probability density functions of relevant variables in specific reactor sections are also analysed. A different contribution is noticed from each random input to the total uncertainty range. Porosity, specific surface area and catalyst loading appear as the major sources of uncertainty to bulk gas and surface temperature and species molar profiles. Porosity and the mean pore diameter have an important impact on the pressure drop along the whole reactor as expected. It is also concluded that any trace of uncertainty in the eight input random variables can be almost dissipated near the catalyst outlet section for a long-enough catalyst, mainly due to the approximation to thermodynamic equilibrium.

  5. Integrated Assessment Modeling for Carbon Storage Risk and Uncertainty Quantification

    NASA Astrophysics Data System (ADS)

    Bromhal, G. S.; Dilmore, R.; Pawar, R.; Stauffer, P. H.; Gastelum, J.; Oldenburg, C. M.; Zhang, Y.; Chu, S.

    2013-12-01

    The National Risk Assessment Partnership (NRAP) has developed tools to perform quantitative risk assessment at site-specific locations for long-term carbon storage. The approach that is being used is to divide the storage and containment system into components (e.g., reservoirs, seals, wells, groundwater aquifers), to develop detailed models for each component, to generate reduced order models (ROMs) based on the detailed models, and to reconnect the reduced order models within an integrated assessment model (IAM). CO2-PENS, developed at Los Alamos National Lab, is being used as the IAM for the simulations in this study. The benefit of this approach is that simulations of the complete system can be generated on a relatively rapid time scale so that Monte Carlo simulation can be performed. In this study, hundreds of thousands of runs of the IAMs have been generated to estimate likelihoods of the quantity of CO2 released to the atmosphere, size of aquifer impacted by pH, size of aquifer impacted by TDS, and size of aquifer with different metals concentrations. Correlations of the output variables with different reservoir, seal, wellbore, and aquifer parameters have been generated. Importance measures have been identified, and inputs have been ranked in the order of their impact on the output quantities. Presentation will describe the approach used, representative results, and implications for how the Monte Carlo analysis is implemented on uncertainty quantification.

  6. Uncertainty quantification in nanomechanical measurements using the atomic force microscope.

    PubMed

    Wagner, Ryan; Moon, Robert; Pratt, Jon; Shaw, Gordon; Raman, Arvind

    2011-11-11

    Quantifying uncertainty in measured properties of nanomaterials is a prerequisite for the manufacture of reliable nanoengineered materials and products. Yet, rigorous uncertainty quantification (UQ) is rarely applied for material property measurements with the atomic force microscope (AFM), a widely used instrument that can measure properties at nanometer scale resolution of both inorganic and biological surfaces and nanomaterials. We present a framework to ascribe uncertainty to local nanomechanical properties of any nanoparticle or surface measured with the AFM by taking into account the main uncertainty sources inherent in such measurements. We demonstrate the framework by quantifying uncertainty in AFM-based measurements of the transverse elastic modulus of cellulose nanocrystals (CNCs), an abundant, plant-derived nanomaterial whose mechanical properties are comparable to Kevlar fibers. For a single, isolated CNC the transverse elastic modulus was found to have a mean of 8.1 GPa and a 95% confidence interval of 2.7-20 GPa. A key result is that multiple replicates of force-distance curves do not sample the important sources of uncertainty, which are systematic in nature. The dominant source of uncertainty is the nondimensional photodiode sensitivity calibration rather than the cantilever stiffness or Z-piezo calibrations. The results underscore the great need for, and open a path towards, quantifying and minimizing uncertainty in AFM-based material property measurements of nanoparticles, nanostructured surfaces, thin films, polymers and biomaterials. PMID:21992899

  7. Quantification of osmotic water transport in vivo using fluorescent albumin.

    PubMed

    Morelle, Johann; Sow, Amadou; Vertommen, Didier; Jamar, François; Rippe, Bengt; Devuyst, Olivier

    2014-10-15

    Osmotic water transport across the peritoneal membrane is applied during peritoneal dialysis to remove the excess water accumulated in patients with end-stage renal disease. The discovery of aquaporin water channels and the generation of transgenic animals have stressed the need for novel and accurate methods to unravel molecular mechanisms of water permeability in vivo. Here, we describe the use of fluorescently labeled albumin as a reliable indicator of osmotic water transport across the peritoneal membrane in a well-established mouse model of peritoneal dialysis. After detailed evaluation of intraperitoneal tracer mass kinetics, the technique was validated against direct volumetry, considered as the gold standard. The pH-insensitive dye Alexa Fluor 555-albumin was applied to quantify osmotic water transport across the mouse peritoneal membrane resulting from modulating dialysate osmolality and genetic silencing of the water channel aquaporin-1 (AQP1). Quantification of osmotic water transport using Alexa Fluor 555-albumin closely correlated with direct volumetry and with estimations based on radioiodinated ((125)I) serum albumin (RISA). The low intraperitoneal pressure probably accounts for the negligible disappearance of the tracer from the peritoneal cavity in this model. Taken together, these data demonstrate the appropriateness of pH-insensitive Alexa Fluor 555-albumin as a practical and reliable intraperitoneal volume tracer to quantify osmotic water transport in vivo.

  8. Quantification of Covariance in Tropical Cyclone Activity across Teleconnected Basins

    NASA Astrophysics Data System (ADS)

    Tolwinski-Ward, S. E.; Wang, D.

    2015-12-01

    Rigorous statistical quantification of natural hazard covariance across regions has important implications for risk management, and is also of fundamental scientific interest. We present a multivariate Bayesian Poisson regression model for inferring the covariance in tropical cyclone (TC) counts across multiple ocean basins and across Saffir-Simpson intensity categories. Such covariability results from the influence of large-scale modes of climate variability on local environments that can alternately suppress or enhance TC genesis and intensification, and our model also simultaneously quantifies the covariance of TC counts with various climatic modes in order to deduce the source of inter-basin TC covariability. The model explicitly treats the time-dependent uncertainty in observed maximum sustained wind data, and hence the nominal intensity category of each TC. Differences in annual TC counts as measured by different agencies are also formally addressed. The probabilistic output of the model can be probed for probabilistic answers to such questions as: - Does the relationship between different categories of TCs differ statistically by basin? - Which climatic predictors have significant relationships with TC activity in each basin? - Are the relationships between counts in different basins conditionally independent given the climatic predictors, or are there other factors at play affecting inter-basin covariability? - How can a portfolio of insured property be optimized across space to minimize risk? Although we present results of our model applied to TCs, the framework is generalizable to covariance estimation between multivariate counts of natural hazards across regions and/or across peril types.

  9. Relative Quantification of Several Plasma Proteins during Liver Transplantation Surgery

    PubMed Central

    Parviainen, Ville; Joenväärä, Sakari; Tukiainen, Eija; Ilmakunnas, Minna; Isoniemi, Helena; Renkonen, Risto

    2011-01-01

    Plasma proteome is widely used in studying changes occurring in human body during disease or other disturbances. Immunological methods are commonly used in such studies. In recent years, mass spectrometry has gained popularity in high-throughput analysis of plasma proteins. In this study, we tested whether mass spectrometry and iTRAQ-based protein quantification might be used in proteomic analysis of human plasma during liver transplantation surgery to characterize changes in protein abundances occurring during early graft reperfusion. We sampled blood from systemic circulation as well as blood entering and exiting the liver. After immunodepletion of six high-abundant plasma proteins, trypsin digestion, iTRAQ labeling, and cation-exchange fractionation, the peptides were analyzed by reverse phase nano-LC-MS/MS. In total, 72 proteins were identified of which 31 could be quantified in all patient specimens collected. Of these 31 proteins, ten, mostly medium-to-high abundance plasma proteins with a concentration range of 50–2000 mg/L, displayed relative abundance change of more than 10%. The changes in protein abundance observed in this study allow further research on the role of several proteins in ischemia-reperfusion injury during liver transplantation and possibly in other surgery. PMID:22187521

  10. Relative quantification of several plasma proteins during liver transplantation surgery.

    PubMed

    Parviainen, Ville; Joenväärä, Sakari; Tukiainen, Eija; Ilmakunnas, Minna; Isoniemi, Helena; Renkonen, Risto

    2011-01-01

    Plasma proteome is widely used in studying changes occurring in human body during disease or other disturbances. Immunological methods are commonly used in such studies. In recent years, mass spectrometry has gained popularity in high-throughput analysis of plasma proteins. In this study, we tested whether mass spectrometry and iTRAQ-based protein quantification might be used in proteomic analysis of human plasma during liver transplantation surgery to characterize changes in protein abundances occurring during early graft reperfusion. We sampled blood from systemic circulation as well as blood entering and exiting the liver. After immunodepletion of six high-abundant plasma proteins, trypsin digestion, iTRAQ labeling, and cation-exchange fractionation, the peptides were analyzed by reverse phase nano-LC-MS/MS. In total, 72 proteins were identified of which 31 could be quantified in all patient specimens collected. Of these 31 proteins, ten, mostly medium-to-high abundance plasma proteins with a concentration range of 50-2000 mg/L, displayed relative abundance change of more than 10%. The changes in protein abundance observed in this study allow further research on the role of several proteins in ischemia-reperfusion injury during liver transplantation and possibly in other surgery.

  11. Uranium quantification in semen by inductively coupled plasma mass spectrometry.

    PubMed

    Todorov, Todor I; Ejnik, John W; Guandalini, Gustavo; Xu, Hanna; Hoover, Dennis; Anderson, Larry; Squibb, Katherine; McDiarmid, Melissa A; Centeno, Jose A

    2013-01-01

    In this study we report uranium analysis for human semen samples. Uranium quantification was performed by inductively coupled plasma mass spectrometry. No additives, such as chymotrypsin or bovine serum albumin, were used for semen liquefaction, as they showed significant uranium content. For method validation we spiked 2g aliquots of pooled control semen at three different levels of uranium: low at 5 pg/g, medium at 50 pg/g, and high at 1000 pg/g. The detection limit was determined to be 0.8 pg/g uranium in human semen. The data reproduced within 1.4-7% RSD and spike recoveries were 97-100%. The uranium level of the unspiked, pooled control semen was 2.9 pg/g of semen (n=10). In addition six semen samples from a cohort of Veterans exposed to depleted uranium (DU) in the 1991 Gulf War were analyzed with no knowledge of their exposure history. Uranium levels in the Veterans' semen samples ranged from undetectable (<0.8 pg/g) to 3350 pg/g. This wide concentration range for uranium in semen is consistent with known differences in current DU body burdens in these individuals, some of whom have retained embedded DU fragments.

  12. Uncertainty Quantification for Polynomial Systems via Bernstein Expansions

    NASA Technical Reports Server (NTRS)

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

    2012-01-01

    This paper presents a unifying framework to uncertainty quantification for systems having polynomial response metrics that depend on both aleatory and epistemic uncertainties. The approach proposed, which is based on the Bernstein expansions of polynomials, enables bounding the range of moments and failure probabilities of response metrics as well as finding supersets of the extreme epistemic realizations where the limits of such ranges occur. These bounds and supersets, whose analytical structure renders them free of approximation error, can be made arbitrarily tight with additional computational effort. Furthermore, this framework enables determining the importance of particular uncertain parameters according to the extent to which they affect the first two moments of response metrics and failure probabilities. This analysis enables determining the parameters that should be considered uncertain as well as those that can be assumed to be constants without incurring significant error. The analytical nature of the approach eliminates the numerical error that characterizes the sampling-based techniques commonly used to propagate aleatory uncertainties as well as the possibility of under predicting the range of the statistic of interest that may result from searching for the best- and worstcase epistemic values via nonlinear optimization or sampling.

  13. Quantification of intracellular payload release from polymersome nanoparticles

    PubMed Central

    Scarpa, Edoardo; Bailey, Joanne L.; Janeczek, Agnieszka A.; Stumpf, Patrick S.; Johnston, Alexander H.; Oreffo, Richard O. C.; Woo, Yin L.; Cheong, Ying C.; Evans, Nicholas D.; Newman, Tracey A.

    2016-01-01

    Polymersome nanoparticles (PMs) are attractive candidates for spatio-temporal controlled delivery of therapeutic agents. Although many studies have addressed cellular uptake of solid nanoparticles, there is very little data available on intracellular release of molecules encapsulated in membranous carriers, such as polymersomes. Here, we addressed this by developing a quantitative assay based on the hydrophilic dye, fluorescein. Fluorescein was encapsulated stably in PMs of mean diameter 85 nm, with minimal leakage after sustained dialysis. No fluorescence was detectable from fluorescein PMs, indicating quenching. Following incubation of L929 cells with fluorescein PMs, there was a gradual increase in intracellular fluorescence, indicating PM disruption and cytosolic release of fluorescein. By combining absorbance measurements with flow cytometry, we quantified the real-time intracellular release of a fluorescein at a single-cell resolution. We found that 173 ± 38 polymersomes released their payload per cell, with significant heterogeneity in uptake, despite controlled synchronisation of cell cycle. This novel method for quantification of the release of compounds from nanoparticles provides fundamental information on cellular uptake of nanoparticle-encapsulated compounds. It also illustrates the stochastic nature of population distribution in homogeneous cell populations, a factor that must be taken into account in clinical use of this technology. PMID:27404770

  14. Spectroscopic detection and quantification of heme and heme degradation products.

    PubMed

    Neugebauer, U; März, A; Henkel, T; Schmitt, M; Popp, J

    2012-12-01

    Heme and heme degradation products play critical roles in numerous biological phenomena which until now have only been partially understood. One reason for this is the very low concentrations at which free heme, its complexes and the partly unstable degradation products occur in living cells. Therefore, powerful and specific detection methods are needed. In this contribution, the potential of nondestructive Raman spectroscopy for the detection, quantification and discrimination of heme and heme degradation products is investigated. Resonance Raman spectroscopy using different excitation wavelengths (413, 476, 532, and 752 nm) is employed to estimate the limit of detection for hemin, myoglobin, biliverdin, and bilirubin. Concentrations in the low micromolar range (down to 3 μmol/L) could be reliably detected when utilizing the resonance enhancement effect. Furthermore, a systematic study on the surface-enhanced Raman spectroscopy (SERS) detection of hemin in the presence of other cellular components, such as the highly similar cytochrome c, DNA, and the important antioxidant glutathione, is presented. A microfluidic device was used to reproducibly create a segmented flow of aqueous droplets and oil compartments. Those aqueous droplets acted as model chambers where the analytes have to compete for the colloid. With the help of statistical analysis, it was possible to detect and differentiate the pure substances as well as the binary mixtures and gain insights into their interaction.

  15. Quantification of HBsAg: basic virology for clinical practice.

    PubMed

    Lee, Jung Min; Ahn, Sang Hoon

    2011-01-21

    Hepatitis B surface antigen (HBsAg) is produced and secreted through a complex mechanism that is still not fully understood. In clinical fields, HBsAg has long served as a qualitative diagnostic marker for hepatitis B virus infection. Notably, advances have been made in the development of quantitative HBsAg assays, which have allowed viral replication monitoring, and there is an opportunity to make maximal use of quantitative HBsAg to elucidate its role in clinical fields. Yet, it needs to be underscored that a further understanding of HBsAg, not only from clinical point of view but also from a virologic point of view, would enable us to deepen our insights, so that we could more widely expand and apply its utility. It is also important to be familiar with HBsAg variants and their clinical consequences in terms of immune escape mutants, issues resulting from overlap with corresponding mutation in the P gene, and detection problems for the HBsAg variants. In this article, we review current concepts and issues on the quantification of HBsAg titers with respect to their biologic nature, method principles, and clinically relevant topics.

  16. Automated quantification of one-dimensional nanostructure alignment on surfaces

    NASA Astrophysics Data System (ADS)

    Dong, Jianjin; Goldthorpe, Irene A.; Mohieddin Abukhdeir, Nasser

    2016-06-01

    A method for automated quantification of the alignment of one-dimensional (1D) nanostructures from microscopy imaging is presented. Nanostructure alignment metrics are formulated and shown to be able to rigorously quantify the orientational order of nanostructures within a two-dimensional domain (surface). A complementary image processing method is also presented which enables robust processing of microscopy images where overlapping nanostructures might be present. Scanning electron microscopy (SEM) images of nanowire-covered surfaces are analyzed using the presented methods and it is shown that past single parameter alignment metrics are insufficient for highly aligned domains. Through the use of multiple parameter alignment metrics, automated quantitative analysis of SEM images is shown to be possible and the alignment characteristics of different samples are able to be quantitatively compared using a similarity metric. The results of this work provide researchers in nanoscience and nanotechnology with a rigorous method for the determination of structure/property relationships, where alignment of 1D nanostructures is significant.

  17. A novel automated image analysis method for accurate adipocyte quantification

    PubMed Central

    Osman, Osman S; Selway, Joanne L; Kępczyńska, Małgorzata A; Stocker, Claire J; O’Dowd, Jacqueline F; Cawthorne, Michael A; Arch, Jonathan RS; Jassim, Sabah; Langlands, Kenneth

    2013-01-01

    Increased adipocyte size and number are associated with many of the adverse effects observed in metabolic disease states. While methods to quantify such changes in the adipocyte are of scientific and clinical interest, manual methods to determine adipocyte size are both laborious and intractable to large scale investigations. Moreover, existing computational methods are not fully automated. We, therefore, developed a novel automatic method to provide accurate measurements of the cross-sectional area of adipocytes in histological sections, allowing rapid high-throughput quantification of fat cell size and number. Photomicrographs of H&E-stained paraffin sections of murine gonadal adipose were transformed using standard image processing/analysis algorithms to reduce background and enhance edge-detection. This allowed the isolation of individual adipocytes from which their area could be calculated. Performance was compared with manual measurements made from the same images, in which adipocyte area was calculated from estimates of the major and minor axes of individual adipocytes. Both methods identified an increase in mean adipocyte size in a murine model of obesity, with good concordance, although the calculation used to identify cell area from manual measurements was found to consistently over-estimate cell size. Here we report an accurate method to determine adipocyte area in histological sections that provides a considerable time saving over manual methods. PMID:23991362

  18. Interactive image quantification tools in nuclear material forensics

    SciTech Connect

    Porter, Reid B; Ruggiero, Christy; Hush, Don; Harvey, Neal; Kelly, Pat; Scoggins, Wayne; Tandon, Lav

    2011-01-03

    Morphological and microstructural features visible in microscopy images of nuclear materials can give information about the processing history of a nuclear material. Extraction of these attributes currently requires a subject matter expert in both microscopy and nuclear material production processes, and is a time consuming, and at least partially manual task, often involving multiple software applications. One of the primary goals of computer vision is to find ways to extract and encode domain knowledge associated with imagery so that parts of this process can be automated. In this paper we describe a user-in-the-loop approach to the problem which attempts to both improve the efficiency of domain experts during image quantification as well as capture their domain knowledge over time. This is accomplished through a sophisticated user-monitoring system that accumulates user-computer interactions as users exploit their imagery. We provide a detailed discussion of the interactive feature extraction and segmentation tools we have developed and describe our initial results in exploiting the recorded user-computer interactions to improve user productivity over time.

  19. Mesh refinement for uncertainty quantification through model reduction

    SciTech Connect

    Li, Jing Stinis, Panos

    2015-01-01

    We present a novel way of deciding when and where to refine a mesh in probability space in order to facilitate uncertainty quantification in the presence of discontinuities in random space. A discontinuity in random space makes the application of generalized polynomial chaos expansion techniques prohibitively expensive. The reason is that for discontinuous problems, the expansion converges very slowly. An alternative to using higher terms in the expansion is to divide the random space in smaller elements where a lower degree polynomial is adequate to describe the randomness. In general, the partition of the random space is a dynamic process since some areas of the random space, particularly around the discontinuity, need more refinement than others as time evolves. In the current work we propose a way to decide when and where to refine the random space mesh based on the use of a reduced model. The idea is that a good reduced model can monitor accurately, within a random space element, the cascade of activity to higher degree terms in the chaos expansion. In turn, this facilitates the efficient allocation of computational sources to the areas of random space where they are more needed. For the Kraichnan–Orszag system, the prototypical system to study discontinuities in random space, we present theoretical results which show why the proposed method is sound and numerical results which corroborate the theory.

  20. Experimental model for civilian ballistic brain injury biomechanics quantification.

    PubMed

    Zhang, Jiangyue; Yoganandan, Narayan; Pintar, Frank A; Guan, Yabo; Gennarelli, Thomas A

    2007-01-01

    Biomechanical quantification of projectile penetration using experimental head models can enhance the understanding of civilian ballistic brain injury and advance treatment. Two of the most commonly used handgun projectiles (25-cal, 275 m/s and 9 mm, 395 m/s) were discharged to spherical head models with gelatin and Sylgard simulants. Four ballistic pressure transducers recorded temporal pressure distributions at 308kHz, and temporal cavity dynamics were captured at 20,000 frames/second (fps) using high-speed digital video images. Pressures ranged from 644.6 to -92.8 kPa. Entry pressures in gelatin models were higher than exit pressures, whereas in Sylgard models entry pressures were lower or equivalent to exit pressures. Gelatin responded with brittle-type failure, while Sylgard demonstrated a ductile pattern through formation of micro-bubbles along projectile path. Temporary cavities in Sylgard models were 1.5-2x larger than gelatin models. Pressures in Sylgard models were more sensitive to projectile velocity and diameter increase, indicating Sylgard was more rate sensitive than gelatin. Based on failure patterns and brain tissue rate-sensitive characteristics, Sylgard was found to be an appropriate simulant. Compared with spherical projectile data, full-metal jacket (FMJ) projectiles produced different temporary cavity and pressures, demonstrating shape effects. Models using Sylgard gel and FMJ projectiles are appropriate to enhance understanding and mechanisms of ballistic brain injury. PMID:17166502

  1. Subspace-based Inverse Uncertainty Quantification for Nuclear Data Assessment

    SciTech Connect

    Khuwaileh, B.A. Abdel-Khalik, H.S.

    2015-01-15

    Safety analysis and design optimization depend on the accurate prediction of various reactor attributes. Predictions can be enhanced by reducing the uncertainty associated with the attributes of interest. An inverse problem can be defined and solved to assess the sources of uncertainty, and experimental effort can be subsequently directed to further improve the uncertainty associated with these sources. In this work a subspace-based algorithm for inverse sensitivity/uncertainty quantification (IS/UQ) has been developed to enable analysts account for all sources of nuclear data uncertainties in support of target accuracy assessment-type analysis. An approximate analytical solution of the optimization problem is used to guide the search for the dominant uncertainty subspace. By limiting the search to a subspace, the degrees of freedom available for the optimization search are significantly reduced. A quarter PWR fuel assembly is modeled and the accuracy of the multiplication factor and the fission reaction rate are used as reactor attributes whose uncertainties are to be reduced. Numerical experiments are used to demonstrate the computational efficiency of the proposed algorithm. Our ongoing work is focusing on extending the proposed algorithm to account for various forms of feedback, e.g., thermal-hydraulics and depletion effects.

  2. Quantification of infectious duck hepatitis B virus by radioimmunofocus assay.

    PubMed

    Anderson, D A; Grgacic, E V; Luscombe, C A; Gu, X; Dixon, R

    1997-08-01

    A simple method is described for the precise quantification of infectious duck hepatitis B virus (DHBV) in cell culture, using a radioimmunofocus assay (RIFA). Primary duck hepatocyte cell cultures were infected with serial dilutions of viral samples as for a plaque assay, but then maintained with liquid overlay medium. After incubation for up to 14 days, cell monolayers were fixed with acetone, then stained with a monoclonal antibody to DHBV L protein followed by secondary antibody labelled with 125I. Foci of infection (representing individual infectious particles in the inoculum) were detected by autoradiography. The number of foci recovered was increased by addition of dimethyl sulphoxide to culture medium, but was not appreciably altered by the use of semi-solid medium. The titre of virus suspensions determined by RIFA correlated well with titration in ducklings. The RIFA is a useful method for titration of DHBV, as it has a wide dynamic range and is well suited to parallel titration of large numbers of samples. This assay will have wide use for the analysis of DHBV growth kinetics, antiviral efficacy, and virus inactivation procedures.

  3. Towards drug quantification in human skin with confocal Raman microscopy.

    PubMed

    Franzen, Lutz; Selzer, Dominik; Fluhr, Joachim W; Schaefer, Ulrich F; Windbergs, Maike

    2013-06-01

    Understanding the penetration behaviour of drugs into human skin is a prerequisite for the rational development and evaluation of effective dermal drug delivery. The general procedure for the acquisition of quantitative drug penetration profiles in human skin is performed by sequential segmentation and extraction. Unfortunately, this technique is destructive, laborious and lacks spatial resolution. Confocal Raman microscopy bares the potential of a chemically selective, label free and nondestructive analysis. However, the acquisition of quantitative drug depth profiles within skin by Raman microscopy is impeded by imponderable signal attenuation inside the tissue. In this study, we present a chemical semi-solid matrix system simulating the optical properties of human skin. This system serves as a skin surrogate for investigation of Raman signal attenuation under controlled conditions. Caffeine was homogeneously incorporated within the skin surrogate, and Raman intensity depth profiles were acquired. A mathematical algorithm describing the Raman signal attenuation within the surrogate was derived from these profiles. Human skin samples were incubated with caffeine, and Raman intensity depth profiles were similarly acquired. The surrogate algorithm was successfully applied to correct the drug profiles in human skin for signal attenuation. For the first time, a mathematical algorithm was established, which allows correction of Raman signal attenuation in human skin, thus facilitating reliable drug quantification in human skin by confocal Raman spectroscopy.

  4. Quantification of oxidative metabolism in masseter muscle of denture wearers.

    PubMed

    Fujii, A; Shinogaya, T; Toda, S; Hayakawa, I

    2005-09-01

    This study aimed to quantify oxidative metabolism in masseter muscle using near-infrared spectroscopy, in particular for denture wearers. Fourteen normal dentate subjects without malocclusion (ND group, 25-50 years) participated in the quantification of oxidative metabolism. Eleven partially edentulous patients without occlusal stops (PD group, 64-80 years) and ten edentulous patients (CD group, 57-84 years) also participated after prosthodontic treatment. Oxidative metabolism was recorded during gum chewing, maximum clenching and regulated clenching at 5 kgf. The oxygenated hemoglobin at 5 kgf clenching level was normalized to the oxygenated hemoglobin at the lowest blood flow and expressed as oxygen consumption rate (OCR). The relationship of the OCR to the maximum clenching force was analyzed using Pearson's correlation coefficient, and differences between the PD and CD groups were tested by unpaired Student's t-test. The OCR showed a significant negative correlation with maximum clenching force in the ND group. The OCR of the PD group was significantly greater than that of the CD group, although the difference in maximum clenching force was not significant between both groups. These results suggest that the aerobic ability of masseter muscle in complete denture wearers is relatively greater than in partial denture wearers with same age level.

  5. Uncertainty quantification in nanomechanical measurements using the atomic force microscope.

    PubMed

    Wagner, Ryan; Moon, Robert; Pratt, Jon; Shaw, Gordon; Raman, Arvind

    2011-11-11

    Quantifying uncertainty in measured properties of nanomaterials is a prerequisite for the manufacture of reliable nanoengineered materials and products. Yet, rigorous uncertainty quantification (UQ) is rarely applied for material property measurements with the atomic force microscope (AFM), a widely used instrument that can measure properties at nanometer scale resolution of both inorganic and biological surfaces and nanomaterials. We present a framework to ascribe uncertainty to local nanomechanical properties of any nanoparticle or surface measured with the AFM by taking into account the main uncertainty sources inherent in such measurements. We demonstrate the framework by quantifying uncertainty in AFM-based measurements of the transverse elastic modulus of cellulose nanocrystals (CNCs), an abundant, plant-derived nanomaterial whose mechanical properties are comparable to Kevlar fibers. For a single, isolated CNC the transverse elastic modulus was found to have a mean of 8.1 GPa and a 95% confidence interval of 2.7-20 GPa. A key result is that multiple replicates of force-distance curves do not sample the important sources of uncertainty, which are systematic in nature. The dominant source of uncertainty is the nondimensional photodiode sensitivity calibration rather than the cantilever stiffness or Z-piezo calibrations. The results underscore the great need for, and open a path towards, quantifying and minimizing uncertainty in AFM-based material property measurements of nanoparticles, nanostructured surfaces, thin films, polymers and biomaterials.

  6. Uncertainty Quantification for Monitoring of Civil Structures from Vibration Measurements

    NASA Astrophysics Data System (ADS)

    Döhler, Michael; Mevel, Laurent

    2014-05-01

    Health Monitoring of civil structures can be performed by detecting changes in the modal parameters of a structure, or more directly in the measured vibration signals. For a continuous monitoring the excitation of a structure is usually ambient, thus unknown and assumed to be noise. Hence, all estimates from the vibration measurements are realizations of random variables with inherent uncertainty due to (unknown) process and measurement noise and finite data length. In this talk, a strategy for quantifying the uncertainties of modal parameter estimates from a subspace-based system identification approach is presented and the importance of uncertainty quantification in monitoring approaches is shown. Furthermore, a damage detection method is presented, which is based on the direct comparison of the measured vibration signals without estimating modal parameters, while taking the statistical uncertainty in the signals correctly into account. The usefulness of both strategies is illustrated on data from a progressive damage action on a prestressed concrete bridge. References E. Carden and P. Fanning. Vibration based condition monitoring: a review. Structural Health Monitoring, 3(4):355-377, 2004. M. Döhler and L. Mevel. Efficient multi-order uncertainty computation for stochastic subspace identification. Mechanical Systems and Signal Processing, 38(2):346-366, 2013. M. Döhler, L. Mevel, and F. Hille. Subspace-based damage detection under changes in the ambient excitation statistics. Mechanical Systems and Signal Processing, 45(1):207-224, 2014.

  7. Uncertainty quantification for large-scale ocean circulation predictions.

    SciTech Connect

    Safta, Cosmin; Debusschere, Bert J.; Najm, Habib N.; Sargsyan, Khachik

    2010-09-01

    Uncertainty quantificatio in climate models is challenged by the sparsity of the available climate data due to the high computational cost of the model runs. Another feature that prevents classical uncertainty analyses from being easily applicable is the bifurcative behavior in the climate data with respect to certain parameters. A typical example is the Meridional Overturning Circulation in the Atlantic Ocean. The maximum overturning stream function exhibits discontinuity across a curve in the space of two uncertain parameters, namely climate sensitivity and CO{sub 2} forcing. We develop a methodology that performs uncertainty quantificatio in the presence of limited data that have discontinuous character. Our approach is two-fold. First we detect the discontinuity location with a Bayesian inference, thus obtaining a probabilistic representation of the discontinuity curve location in presence of arbitrarily distributed input parameter values. Furthermore, we developed a spectral approach that relies on Polynomial Chaos (PC) expansions on each sides of the discontinuity curve leading to an averaged-PC representation of the forward model that allows efficient uncertainty quantification and propagation. The methodology is tested on synthetic examples of discontinuous data with adjustable sharpness and structure.

  8. Quantification of Nociceptive Escape Response in C.elegans

    NASA Astrophysics Data System (ADS)

    Leung, Kawai; Mohammadi, Aylia; Ryu, William; Nemenman, Ilya

    2013-03-01

    Animals cannot rank and communicate their pain consciously. Thus in pain studies on animal models, one must infer the pain level from high precision experimental characterization of behavior. This is not trivial since behaviors are very complex and multidimensional. Here we explore the feasibility of C.elegans as a model for pain transduction. The nematode has a robust neurally mediated noxious escape response, which we show to be partially decoupled from other sensory behaviors. We develop a nociceptive behavioral response assay that allows us to apply controlled levels of pain by locally heating worms with an IR laser. The worms' motions are captured by machine vision programming with high spatiotemporal resolution. The resulting behavioral quantification allows us to build a statistical model for inference of the experienced pain level from the behavioral response. Based on the measured nociceptive escape of over 400 worms, we conclude that none of the simple characteristics of the response are reliable indicators of the laser pulse strength. Nonetheless, a more reliable statistical inference of the pain stimulus level from the measured behavior is possible based on a complexity-controlled regression model that takes into account the entire worm behavioral output. This work was partially supported by NSF grant No. IOS/1208126 and HFSP grant No. RGY0084/2011.

  9. Bioluminescence regenerative cycle (BRC) system for nucleic acid quantification assays

    NASA Astrophysics Data System (ADS)

    Hassibi, Arjang; Lee, Thomas H.; Davis, Ronald W.; Pourmand, Nader

    2003-07-01

    A new label-free methodology for nucleic acid quantification has been developed where the number of pyrophosphate molecules (PPi) released during polymerization of the target nucleic acid is counted and correlated to DNA copy number. The technique uses the enzymatic complex of ATP-sulfurylase and firefly luciferase to generate photons from PPi. An enzymatic unity gain positive feedback is also implemented to regenerate the photon generation process and compensate any decay in light intensity by self regulation. Due to this positive feedback, the total number of photons generated by the bioluminescence regenerative cycle (BRC) can potentially be orders of magnitude higher than typical chemiluminescent processes. A system level kinetic model that incorporates the effects of contaminations and detector noise was used to show that the photon generation process is in fact steady and also proportional to the nucleic acid quantity. Here we show that BRC is capable of detecting quantities of DNA as low as 1 amol (10-18 mole) in 40μlit aqueous solutions, and this enzymatic assay has a controllable dynamic range of 5 orders of magnitude. The sensitivity of this technology, due to the excess number of photons generated by the regenerative cycle, is not constrained by detector performance, but rather by possible PPi or ATP (adenosine triphosphate) contamination, or background bioluminescence of the enzymatic complex.

  10. A posteriori uncertainty quantification of PIV-based pressure data

    NASA Astrophysics Data System (ADS)

    Azijli, Iliass; Sciacchitano, Andrea; Ragni, Daniele; Palha, Artur; Dwight, Richard P.

    2016-05-01

    A methodology for a posteriori uncertainty quantification of pressure data retrieved from particle image velocimetry (PIV) is proposed. It relies upon the Bayesian framework, where the posterior distribution (probability distribution of the true velocity, given the PIV measurements) is obtained from the prior distribution (prior knowledge of properties of the velocity field, e.g., divergence-free) and the statistical model of PIV measurement uncertainty. Once the posterior covariance matrix of the velocity is known, it is propagated through the discretized Poisson equation for pressure. Numerical assessment of the proposed method on a steady Lamb-Oseen vortex shows excellent agreement with Monte Carlo simulations, while linear uncertainty propagation underestimates the uncertainty in the pressure by up to 30 %. The method is finally applied to an experimental test case of a turbulent boundary layer in air, obtained using time-resolved tomographic PIV. Simultaneously with the PIV measurements, microphone measurements were carried out at the wall. The pressure reconstructed from the tomographic PIV data is compared to the microphone measurements. Realizing that the uncertainty of the latter is significantly smaller than the PIV-based pressure, this allows us to obtain an estimate for the true error of the former. The comparison between true error and estimated uncertainty demonstrates the accuracy of the uncertainty estimates on the pressure. In addition, enforcing the divergence-free constraint is found to result in a significantly more accurate reconstructed pressure field. The estimated uncertainty confirms this result.

  11. Micelle Mediated Trace Level Sulfide Quantification through Cloud Point Extraction

    PubMed Central

    Devaramani, Samrat; Malingappa, Pandurangappa

    2012-01-01

    A simple cloud point extraction protocol has been proposed for the quantification of sulfide at trace level. The method is based on the reduction of iron (III) to iron (II) by the sulfide and the subsequent complexation of metal ion with nitroso-R salt in alkaline medium. The resulting green-colored complex was extracted through cloud point formation using cationic surfactant, that is, cetylpyridinium chloride, and the obtained surfactant phase was homogenized by ethanol before its absorbance measurement at 710 nm. The reaction variables like metal ion, ligand, surfactant concentration, and medium pH on the cloud point extraction of the metal-ligand complex have been optimized. The interference effect of the common anions and cations was studied. The proposed method has been successfully applied to quantify the trace level sulfide in the leachate samples of the landfill and water samples from bore wells and ponds. The validity of the proposed method has been studied by spiking the samples with known quantities of sulfide as well as comparing with the results obtained by the standard method. PMID:22619597

  12. Direct field method for root biomass quantification in agroecosystems.

    PubMed

    Frasier, Ileana; Noellemeyer, Elke; Fernández, Romina; Quiroga, Alberto

    2016-01-01

    The present article describes a field auger sampling method for row-crop root measurements. In agroecosystems where crops are planted in a specific design (row crops), sampling procedures for root biomass quantification need to consider the spatial variability of the root system. This article explains in detail how to sample and calculate root biomass considering the sampling position in the field and the differential weight of the root biomass in the inter-row compared to the crop row when expressing data per area unit. This method is highly reproducible in the field and requires no expensive equipment and/or special skills. It proposes to use a narrow auger thus reducing field labor with less destructive sampling, and decreases laboratory time because samples are smaller. The small sample size also facilitates the washing and root separation with tweezers. This method is suitable for either winter- or summer crop roots. •Description of a direct field method for row-crop root measurements.•Description of data calculation for total root-biomass estimation per unit area.•The proposed method is simple, less labor- and less time consuming. PMID:27630821

  13. Current analytical methods for plant auxin quantification--A review.

    PubMed

    Porfírio, Sara; Gomes da Silva, Marco D R; Peixe, Augusto; Cabrita, Maria J; Azadi, Parastoo

    2016-01-01

    Plant hormones, and especially auxins, are low molecular weight compounds highly involved in the control of plant growth and development. Auxins are also broadly used in horticulture, as part of vegetative plant propagation protocols, allowing the cloning of genotypes of interest. Over the years, large efforts have been put in the development of more sensitive and precise methods of analysis and quantification of plant hormone levels in plant tissues. Although analytical techniques have evolved, and new methods have been implemented, sample preparation is still the limiting step of auxin analysis. In this review, the current methods of auxin analysis are discussed. Sample preparation procedures, including extraction, purification and derivatization, are reviewed and compared. The different analytical techniques, ranging from chromatographic and mass spectrometry methods to immunoassays and electrokinetic methods, as well as other types of detection are also discussed. Considering that auxin analysis mirrors the evolution in analytical chemistry, the number of publications describing new and/or improved methods is always increasing and we considered appropriate to update the available information. For that reason, this article aims to review the current advances in auxin analysis, and thus only reports from the past 15 years will be covered.

  14. Quantification of collagen contraction in three-dimensional cell culture.

    PubMed

    Kopanska, Katarzyna S; Bussonnier, Matthias; Geraldo, Sara; Simon, Anthony; Vignjevic, Danijela; Betz, Timo

    2015-01-01

    Many different cell types including fibroblasts, smooth muscle cells, endothelial cells, and cancer cells exert traction forces on the fibrous components of the extracellular matrix. This can be observed as matrix contraction both macro- and microscopically in three-dimensional (3D) tissues models such as collagen type I gels. The quantification of local contraction at the micron scale, including its directionality and speed, in correlation with other parameters such as cell invasion, local protein or gene expression, can provide useful information to study wound healing, organism development, and cancer metastasis. In this article, we present a set of tools to quantify the flow dynamics of collagen contraction, induced by cells migrating out of a multicellular cancer spheroid into a three-dimensional (3D) collagen matrix. We adapted a pseudo-speckle technique that can be applied to bright-field and fluorescent microscopy time series. The image analysis presented here is based on an in-house written software developed in the Matlab (Mathworks) programming environment. The analysis program is freely available from GitHub following the link: http://dx.doi.org/10.5281/zenodo.10116. This tool provides an automatized technique to measure collagen contraction that can be utilized in different 3D cellular systems.

  15. Quantification of sugars in breakfast cereals using capillary electrophoresis.

    PubMed

    Toutounji, Michelle R; Van Leeuwen, Matthew P; Oliver, James D; Shrestha, Ashok K; Castignolles, Patrice; Gaborieau, Marianne

    2015-05-18

    About 80% of the Australian population consumes breakfast cereal (BC) at least five days a week. With high prevalence rates of obesity and other diet-related diseases, improved methods for monitoring sugar levels in breakfast cereals would be useful in nutrition research. The heterogeneity of the complex matrix of BCs can make carbohydrate analysis challenging or necessitate tedious sample preparation leading to potential sugar loss or starch degradation into sugars. A recently established, simple and robust free solution capillary electrophoresis (CE) method was used in a new application to 13 BCs (in Australia) and compared with several established methods for quantification of carbohydrates. Carbohydrates identified in BCs by CE included sucrose, maltose, glucose and fructose. The CE method is simple requiring no sample preparation or derivatization and carbohydrates are detected by direct UV detection. CE was shown to be a more robust and accurate method for measuring carbohydrates than Fehling method, DNS (3,5-dinitrosalicylic acid) assay and HPLC (high performance liquid chromatography).

  16. An experimental database for evaluating PIV uncertainty quantification methods

    NASA Astrophysics Data System (ADS)

    Warner, Scott; Neal, Douglas; Sciacchitano, Andrea

    2014-11-01

    Uncertainty quantification for particle image velocimetry (PIV) data has recently become a topic of great interest as shown by the publishing of several different methods within the past few years. A unique experiment has been designed to test the efficacy of PIV uncertainty methods, using a rectangular jet as the flow field. The novel aspect of the experimental setup consists of simultaneous measurements by means of two different time-resolved PIV systems and a hot-wire anemometer (HWA). The first PIV system, called the ``PIV-Measurement'' system, collects the data for which uncertainty is to be evaluated. It is based on a single camera and features a dynamic velocity range (DVR) representative of many PIV experiments. The second PIV system, called the ``PIV-HDR'' (high dynamic range) system, has a significantly higher DVR obtained with a higher digital imaging resolution. The hot-wire was placed in close proximity to the PIV measurement domain. All three of the measurement systems were carefully set to simultaneously collect time-resolved data on a point-by-point basis. The HWA validates the PIV-HDR system as the reference velocity so that it can be used to evaluate the instantaneous error in the PIV-measurement system.

  17. Quantification of hydroxyacetone and glycolaldehyde using chemical ionization mass spectrometry

    NASA Astrophysics Data System (ADS)

    St. Clair, J. M.; Spencer, K. M.; Beaver, M. R.; Crounse, J. D.; Paulot, F.; Wennberg, P. O.

    2014-04-01

    Chemical ionization mass spectrometry (CIMS) enables online, rapid, in situ detection and quantification of hydroxyacetone and glycolaldehyde. Two different CIMS approaches are demonstrated employing the strengths of single quadrupole mass spectrometry and triple quadrupole (tandem) mass spectrometry. Both methods are generally capable of the measurement of hydroxyacetone, an analyte with known but minimal isobaric interferences. Tandem mass spectrometry provides direct separation of the isobaric compounds glycolaldehyde and acetic acid using distinct, collision-induced dissociation daughter ions. The single quadrupole CIMS measurement of glycolaldehyde was demonstrated during the ARCTAS-CARB (Arctic Research of the Composition of the Troposphere from Aircraft and Satellites - California Air Resources Board) 2008 campaign, while triple quadrupole CIMS measurements of glycolaldehyde and hydroxyacetone were demonstrated during the BEARPEX (Biosphere Effects on Aerosols and Photochemistry Experiment) 2009 campaign. Enhancement ratios of glycolaldehyde in ambient biomass-burning plumes are reported for the ARCTAS-CARB campaign. BEARPEX observations are compared to simple photochemical box model predictions of biogenic volatile organic compound oxidation at the site.

  18. Quantification of brodifacoum in plasma and liver tissue by HPLC.

    PubMed

    O'Bryan, S M; Constable, D J

    1991-01-01

    A simple high-performance liquid chromatographic method has been developed for detection and quantification of brodifacoum in plasma and liver tissue. After adding difenacoum as the internal standard, brodifacoum and difenacoum are extracted from 2 mL of plasma with two sequential 10-mL volumes of acetonitrile-ethyl ether (9:1) and from 2 g of liver tissue by grinding the tissue with 10 mL acetonitrile. The extracts are evaporated to dryness under nitrogen, 2 mL of acetonitrile is added to reconstitute the residues, and the resulting solution is analyzed using reversed-phase chromatography and fluorescence detection. The limits of detection for plasma and tissue are 2 micrograms/L and 5 ng/g, respectively. Using internal standardization, the mean intra-assay recovery from plasma is 92% and the mean inter-assay recoveries is 109%. The mean intra-assay and inter-assay recoveries from tissue are 96%. No interferences were observed with any of the following related compounds: brodifacoum, bromadiolone, coumarin, difenacoum, diphacinone, warfarin, and vitamin K1. PMID:1943058

  19. VESGEN Software for Mapping and Quantification of Vascular Regulators

    NASA Technical Reports Server (NTRS)

    Parsons-Wingerter, Patricia A.; Vickerman, Mary B.; Keith, Patricia A.

    2012-01-01

    VESsel GENeration (VESGEN) Analysis is an automated software that maps and quantifies effects of vascular regulators on vascular morphology by analyzing important vessel parameters. Quantification parameters include vessel diameter, length, branch points, density, and fractal dimension. For vascular trees, measurements are reported as dependent functions of vessel branching generation. VESGEN maps and quantifies vascular morphological events according to fractal-based vascular branching generation. It also relies on careful imaging of branching and networked vascular form. It was developed as a plug-in for ImageJ (National Institutes of Health, USA). VESGEN uses image-processing concepts of 8-neighbor pixel connectivity, skeleton, and distance map to analyze 2D, black-and-white (binary) images of vascular trees, networks, and tree-network composites. VESGEN maps typically 5 to 12 (or more) generations of vascular branching, starting from a single parent vessel. These generations are tracked and measured for critical vascular parameters that include vessel diameter, length, density and number, and tortuosity per branching generation. The effects of vascular therapeutics and regulators on vascular morphology and branching tested in human clinical or laboratory animal experimental studies are quantified by comparing vascular parameters with control groups. VESGEN provides a user interface to both guide and allow control over the users vascular analysis process. An option is provided to select a morphological tissue type of vascular trees, network or tree-network composites, which determines the general collections of algorithms, intermediate images, and output images and measurements that will be produced.

  20. Effect of heat processing on DNA quantification of meat species.

    PubMed

    Şakalar, Ergün; Abasiyanik, M Fatih; Bektik, Emre; Tayyrov, Annageldi

    2012-09-01

    In this study, real-time polymerase chain reaction (PCR) was used for identifying the effects of different temperatures and times of heat treatment on the DNA of meat products. For this purpose, beef, pork, and chicken were baked at 200 °C for 10, 20, 30, 40, 50 min, and for 30 min at 30, 60, 90, 120, 150, 180, 210 °C and also cooked by boiling at 99 °C for 10, 30, 60, 90, 120, 150, 180, 210, and 240 min. The DNA was then extracted from all samples after the heat treatment. Further, a region of 374, 290, and 183-bp of mitochondrial DNA of beef, pork, and chicken, respectively, was amplified by real-time PCR. It was found that baking and boiling of the beef, pork, and chicken resulted in decreases in the detectable copy numbers of specific genes, which varied with the heating time and degree. The results indicated that species determination and quantification using real-time PCR are affected by the temperature, duration of the heat treatment, and size of the DNA fragment to be amplified.