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Sample records for dot-based quantification revealed

  1. Highly sensitive polymerase chain reaction-free quantum dot-based quantification of forensic genomic DNA.

    PubMed

    Tak, Yu Kyung; Kim, Won Young; Kim, Min Jung; Han, Eunyoung; Han, Myun Soo; Kim, Jong Jin; Kim, Wook; Lee, Jong Eun; Song, Joon Myong

    2012-04-06

    Forensic DNA samples can degrade easily due to exposure to light and moisture at the crime scene. In addition, the amount of DNA acquired at a criminal site is inherently limited. This limited amount of human DNA has to be quantified accurately after the process of DNA extraction. The accurately quantified extracted genomic DNA is then used as a DNA template in polymerase chain reaction (PCR) amplification for short tandem repeat (STR) human identification. Accordingly, highly sensitive and human-specific quantification of forensic DNA samples is an essential issue in forensic study. In this work, a quantum dot (Qdot)-labeled Alu sequence was developed as a probe to simultaneously satisfy both the high sensitivity and human genome selectivity for quantification of forensic DNA samples. This probe provided PCR-free determination of human genomic DNA and had a 2.5-femtogram detection limit due to the strong emission and photostability of the Qdot. The Qdot-labeled Alu sequence has been used successfully to assess 18 different forensic DNA samples for STR human identification.

  2. Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals.

    PubMed

    Crooks, Kevin R; Burdett, Christopher L; Theobald, David M; King, Sarah R B; Di Marco, Moreno; Rondinini, Carlo; Boitani, Luigi

    2017-07-18

    Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world's terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, and most high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world's terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation.

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

    PubMed

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

    2014-09-01

    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.

  4. 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

  5. Quantification of Left Ventricular Function with Premature Ventricular Complexes Reveals Variable Hemodynamics

    PubMed Central

    Contijoch, Francisco; Rogers, Kelly; Rears, Hannah; Shahid, Mohammed; Kellman, Peter; Gorman, Joseph; Gorman, Robert C.; Yushkevich, Paul; Zado, Erica S.; Supple, Gregory E.; Marchlinski, Francis E.; Witschey, Walter R.T.; Han, Yuchi

    2016-01-01

    Background Premature ventricular complexes (PVC) are prevalent in the general population and are sometimes associated with reduced ventricular function. Current echocardiographic and cardiovascular magnetic resonance imaging (CMR) techniques do not adequately address the effect of PVCs on left ventricular function. Methods and Results Fifteen subjects with a history of frequent PVCs undergoing CMR had real-time slice volume quantification performed using a 2D real-time CMR imaging technique. Synchronization of 2D real-time imaging with patient ECG allowed for different beats to be categorized by the loading beat RR-duration and beat RR-duration. For each beat type, global volumes were quantified via summation over all slices covering the entire ventricle. Different patterns of ectopy including isolated PVCs, bigeminy, trigeminy, and interpolated PVCs were observed. Global functional measurement of the different beat types based on timing demonstrated differences in preload, stroke volume, and ejection fraction. An average of hemodynamic function was quantified for each subject depending on the frequency of each observed beat type. Conclusions Application of real-time CMR imaging in patients with PVCs revealed differential contribution of PVCs to hemodynamics. PMID:27009416

  6. Quantification of ploidy in proteobacteria revealed the existence of monoploid, (mero-)oligoploid and polyploid species.

    PubMed

    Pecoraro, Vito; Zerulla, Karolin; Lange, Christian; Soppa, Jörg

    2011-01-31

    Bacteria are generally assumed to be monoploid (haploid). This assumption is mainly based on generalization of the results obtained with the most intensely studied model bacterium, Escherichia coli (a gamma-proteobacterium), which is monoploid during very slow growth. However, several species of proteobacteria are oligo- or polyploid, respectively. To get a better overview of the distribution of ploidy levels, genome copy numbers were quantified in four species of three different groups of proteobacteria. A recently developed Real Time PCR approach, which had been used to determine the ploidy levels of halophilic archaea, was optimized for the quantification of genome copy numbers of bacteria. Slow-growing (doubling time 103 minutes) and fast-growing (doubling time 25 minutes) E. coli cultures were used as a positive control. The copy numbers of the origin and terminus region of the chromosome were determined and the results were in excellent agreement with published data. The approach was also used to determine the ploidy levels of Caulobacter crescentus (an alpha-proteobacterium) and Wolinella succinogenes (an epsilon-proteobacterium), both of which are monoploid. In contrast, Pseudomonas putida (a gamma-proteobacterium) contains 20 genome copies and is thus polyploid. A survey of the proteobacteria with experimentally-determined genome copy numbers revealed that only three to four of 11 species are monoploid and thus monoploidy is not typical for proteobacteria. The ploidy level is not conserved within the groups of proteobacteria, and there are no obvious correlations between the ploidy levels with other parameters like genome size, optimal growth temperature or mode of life.

  7. Quantification of Ploidy in Proteobacteria Revealed the Existence of Monoploid, (Mero-)Oligoploid and Polyploid Species

    PubMed Central

    Pecoraro, Vito; Zerulla, Karolin; Lange, Christian; Soppa, Jörg

    2011-01-01

    Bacteria are generally assumed to be monoploid (haploid). This assumption is mainly based on generalization of the results obtained with the most intensely studied model bacterium, Escherichia coli (a gamma-proteobacterium), which is monoploid during very slow growth. However, several species of proteobacteria are oligo- or polyploid, respectively. To get a better overview of the distribution of ploidy levels, genome copy numbers were quantified in four species of three different groups of proteobacteria. A recently developed Real Time PCR approach, which had been used to determine the ploidy levels of halophilic archaea, was optimized for the quantification of genome copy numbers of bacteria. Slow-growing (doubling time 103 minutes) and fast-growing (doubling time 25 minutes) E. coli cultures were used as a positive control. The copy numbers of the origin and terminus region of the chromosome were determined and the results were in excellent agreement with published data. The approach was also used to determine the ploidy levels of Caulobacter crescentus (an alpha-proteobacterium) and Wolinella succinogenes (an epsilon-proteobacterium), both of which are monoploid. In contrast, Pseudomonas putida (a gamma-proteobacterium) contains 20 genome copies and is thus polyploid. A survey of the proteobacteria with experimentally-determined genome copy numbers revealed that only three to four of 11 species are monoploid and thus monoploidy is not typical for proteobacteria. The ploidy level is not conserved within the groups of proteobacteria, and there are no obvious correlations between the ploidy levels with other parameters like genome size, optimal growth temperature or mode of life. PMID:21305010

  8. 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.

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

    PubMed Central

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

    2016-01-01

    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

  10. Variation of phlorotannins among three populations of Fucus vesiculosus as revealed by HPLC and colorimetric quantification.

    PubMed

    Koivikko, R; Eränen, J K; Loponen, J; Jormalainen, V

    2008-01-01

    In ecological studies, phlorotannins have conventionally been quantified as a group with similar functionality. Since this group consists of oligo- and polymers, the quantification of their pooled contents alone may not sufficiently describe the variation of these metabolites. Genetic variation, plastic responses to environment, and the ecological functions of separate phlorotannin oligo- and polymers may differ. Two analyses, i.e., the colorimetric Folin-Ciocalteu assay and a normal-phase high-performance liquid chromatographic (HPLC) method were used to study genetic and environmental variation in phlorotannins of the brown alga Fucus vesiculosus (L.). The colorimetric method provides the total phlorotannin content, the latter a profile of 14 separate traces from the phenolic extract that represent an individual or groups of phlorotannins. We reared the algae that originated from three separate populations in a common garden for 3 months under ambient and enriched-nutrient availability and found that they differed in both their total phlorotannin content and in phlorotannin profiles. Some individual traces of the profiles separated the populations more clearly than the colorimetric assay. Although nutrient enrichment decreased total phlorotannin content, it did not show a significant influence on the phlorotannin profile. This implies that plastic responses of compounds other than phlorotannins may interfere with the determination of total phlorotannins. However, the phlorotannin profile and the total content showed genetic variation among local populations of F. vesiculosus; therefore, phlorotannins may respond to natural selection and evolve both quantitatively and qualitatively.

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

    PubMed Central

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

    2014-01-01

    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

  12. In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

    PubMed Central

    Hicks, Kiley A.; Howe, Dana K.; Leung, Aubrey; Denver, Dee R.; Estes, Suzanne

    2012-01-01

    We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives. PMID:22952781

  13. Quantification of Calcified Particles in Human Valve Tissue Reveals Asymmetry of Calcific Aortic Valve Disease Development.

    PubMed

    Yabusaki, Katsumi; Hutcheson, Joshua D; Vyas, Payal; Bertazzo, Sergio; Body, Simon C; Aikawa, Masanori; Aikawa, Elena

    2016-01-01

    Recent studies indicated that small calcified particles observable by scanning electron microscopy (SEM) may initiate calcification in cardiovascular tissues. We hypothesized that if the calcified particles precede gross calcification observed in calcific aortic valve disease (CAVD), they would exhibit a regional asymmetric distribution associated with CAVD development, which always initiates at the base of aortic valve leaflets adjacent to the aortic outflow in a region known as the fibrosa. Testing this hypothesis required counting the calcified particles in histological sections of aortic valve leaflets. SEM images, however, do not provide high contrast between components within images, making the identification and quantification of particles buried within tissue extracellular matrix difficult. We designed a new unique pattern-matching based technique to allow for flexibility in recognizing particles by creating a gap zone in the detection criteria that decreased the influence of non-particle image clutter in determining whether a particle was identified. We developed this flexible pattern particle-labeling (FpPL) technique using synthetic test images and human carotid artery tissue sections. A conventional image particle counting method (preinstalled in ImageJ) did not properly recognize small calcified particles located in noisy images that include complex extracellular matrix structures and other commonly used pattern-matching methods failed to detect the wide variation in size, shape, and brightness exhibited by the particles. Comparative experiments with the ImageJ particle counting method demonstrated that our method detected significantly more (p < 2 × 10(-7)) particles than the conventional method with significantly fewer (p < 0.0003) false positives and false negatives (p < 0.0003). We then applied the FpPL technique to CAVD leaflets and showed a significant increase in detected particles in the fibrosa at the base of the leaflets (p

  14. Quantification of Calcified Particles in Human Valve Tissue Reveals Asymmetry of Calcific Aortic Valve Disease Development

    PubMed Central

    Yabusaki, Katsumi; Hutcheson, Joshua D.; Vyas, Payal; Bertazzo, Sergio; Body, Simon C.; Aikawa, Masanori; Aikawa, Elena

    2016-01-01

    Recent studies indicated that small calcified particles observable by scanning electron microscopy (SEM) may initiate calcification in cardiovascular tissues. We hypothesized that if the calcified particles precede gross calcification observed in calcific aortic valve disease (CAVD), they would exhibit a regional asymmetric distribution associated with CAVD development, which always initiates at the base of aortic valve leaflets adjacent to the aortic outflow in a region known as the fibrosa. Testing this hypothesis required counting the calcified particles in histological sections of aortic valve leaflets. SEM images, however, do not provide high contrast between components within images, making the identification and quantification of particles buried within tissue extracellular matrix difficult. We designed a new unique pattern-matching based technique to allow for flexibility in recognizing particles by creating a gap zone in the detection criteria that decreased the influence of non-particle image clutter in determining whether a particle was identified. We developed this flexible pattern particle-labeling (FpPL) technique using synthetic test images and human carotid artery tissue sections. A conventional image particle counting method (preinstalled in ImageJ) did not properly recognize small calcified particles located in noisy images that include complex extracellular matrix structures and other commonly used pattern-matching methods failed to detect the wide variation in size, shape, and brightness exhibited by the particles. Comparative experiments with the ImageJ particle counting method demonstrated that our method detected significantly more (p < 2 × 10−7) particles than the conventional method with significantly fewer (p < 0.0003) false positives and false negatives (p < 0.0003). We then applied the FpPL technique to CAVD leaflets and showed a significant increase in detected particles in the fibrosa at the base of the leaflets (p

  15. Quantification of Cell Edge Velocities and Traction Forces Reveals Distinct Motility Modules during Cell Spreading

    PubMed Central

    Cai, Yunfei; Xenias, Harry; Spielman, Ingrid; Shneidman, Anna V.; David, Lawrence A.; Döbereiner, Hans-Günther; Wiggins, Chris H.; Sheetz, Michael P.

    2008-01-01

    Actin-based cell motility and force generation are central to immune response, tissue development, and cancer metastasis, and understanding actin cytoskeleton regulation is a major goal of cell biologists. Cell spreading is a commonly used model system for motility experiments – spreading fibroblasts exhibit stereotypic, spatially-isotropic edge dynamics during a reproducible sequence of functional phases: 1) During early spreading, cells form initial contacts with the surface. 2) The middle spreading phase exhibits rapidly increasing attachment area. 3) Late spreading is characterized by periodic contractions and stable adhesions formation. While differences in cytoskeletal regulation between phases are known, a global analysis of the spatial and temporal coordination of motility and force generation is missing. Implementing improved algorithms for analyzing edge dynamics over the entire cell periphery, we observed that a single domain of homogeneous cytoskeletal dynamics dominated each of the three phases of spreading. These domains exhibited a unique combination of biophysical and biochemical parameters – a motility module. Biophysical characterization of the motility modules revealed that the early phase was dominated by periodic, rapid membrane blebbing; the middle phase exhibited continuous protrusion with very low traction force generation; and the late phase was characterized by global periodic contractions and high force generation. Biochemically, each motility module exhibited a different distribution of the actin-related protein VASP, while inhibition of actin polymerization revealed different dependencies on barbed-end polymerization. In addition, our whole-cell analysis revealed that many cells exhibited heterogeneous combinations of motility modules in neighboring regions of the cell edge. Together, these observations support a model of motility in which regions of the cell edge exhibit one of a limited number of motility modules that, together

  16. Quantification of the rat spinal microglial response to peripheral nerve injury as revealed by immunohistochemical image analysis and flow cytometry

    PubMed Central

    Blackbeard, J.; O’Dea, K.P.; Wallace, V.C.J.; Segerdahl, A.; Pheby, T.; Takata, M.; Field, M.J.; Rice, A.S.C.

    2007-01-01

    Microgliosis is implicated in the pathophysiology of several neurological disorders, including neuropathic pain. Consequently, perturbation of microgliosis is a mechanistic and drug development target in neuropathic pain, which highlights the requirement for specific, sensitive and reproducible methods of microgliosis measurement. In this study, we used the spinal microgliosis associated with L5 spinal nerve transection and minocycline-induced attenuation thereof to: (1) evaluate novel software based semi-quantitative image analysis paradigms for the assessment of immunohistochemical images. Microgliosis was revealed by immunoreactivity to OX42. Several image analysis paradigms were assessed and compared to a previously validated subjective categorical rating scale. This comparison revealed that grey scale measurement of the proportion of a defined area of spinal cord occupied by OX42 immunoreactive cells is a robust image analysis paradigm. (2) Develop and validate a flow cytometric approach for quantification of spinal microgliosis. The flow cytometric technique reliably quantified microgliosis in spinal cord cell suspensions, using OX42 and ED9 immunoreactivity to identify microglia. The results suggest that image analysis of immunohistochemical revelation of microgliosis reliably detects the spinal microgliosis in response to peripheral nerve injury and pharmacological attenuation thereof. In addition, flow cytometry provides an alternative approach for quantitative analysis of spinal microgliosis elicited by nerve injury. PMID:17553569

  17. Quantification of the rat spinal microglial response to peripheral nerve injury as revealed by immunohistochemical image analysis and flow cytometry.

    PubMed

    Blackbeard, J; O'Dea, K P; Wallace, V C J; Segerdahl, A; Pheby, T; Takata, M; Field, M J; Rice, A S C

    2007-08-30

    Microgliosis is implicated in the pathophysiology of several neurological disorders, including neuropathic pain. Consequently, perturbation of microgliosis is a mechanistic and drug development target in neuropathic pain, which highlights the requirement for specific, sensitive and reproducible methods of microgliosis measurement. In this study, we used the spinal microgliosis associated with L5 spinal nerve transection and minocycline-induced attenuation thereof to: (1) evaluate novel software based semi-quantitative image analysis paradigms for the assessment of immunohistochemical images. Microgliosis was revealed by immunoreactivity to OX42. Several image analysis paradigms were assessed and compared to a previously validated subjective categorical rating scale. This comparison revealed that grey scale measurement of the proportion of a defined area of spinal cord occupied by OX42 immunoreactive cells is a robust image analysis paradigm. (2) Develop and validate a flow cytometric approach for quantification of spinal microgliosis. The flow cytometric technique reliably quantified microgliosis in spinal cord cell suspensions, using OX42 and ED9 immunoreactivity to identify microglia. The results suggest that image analysis of immunohistochemical revelation of microgliosis reliably detects the spinal microgliosis in response to peripheral nerve injury and pharmacological attenuation thereof. In addition, flow cytometry provides an alternative approach for quantitative analysis of spinal microgliosis elicited by nerve injury.

  18. Quantification of Maize Fine Streak Virus Genomic and Positive-sense RNAs in Infected Maize Reveals High Level Accumulation of ORF 3 and 4 MFSV Transcripts

    USDA-ARS?s Scientific Manuscript database

    Quantification of Maize fine streak virus genomic and positive-sense RNAs in infected maize reveals high level accumulation of ORF 3 and 4 MFSV transcripts. We improved methods to analyze RNA produced by Maize fine streak virus (MVSF) within infected maize tissue using real-time RT-qPCR. We designe...

  19. 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.

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

    DOE PAGES

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; ...

    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

  1. Quantification of Leukocyte Genomic 5-Methylcytosine Levels Reveals Epigenetic Plasticity in Healthy Adult Cloned Cattle

    PubMed Central

    de Montera, Béatrice; El Zeihery, Dalia; Müller, Sigrid; Jammes, Hélène; Brem, Gottfried; Reichenbach, Horst-Dieter; Scheipl, Fabian; Chavatte-Palmer, Pascale; Zakhartchenko, Valeri; Schmitz, Oliver J.; Wolf, Eckhard; Renard, Jean-Paul

    2010-01-01

    Abstract Successful somatic cell nuclear transfer (SCNT) requires epigenetic reprogramming of a differentiated donor cell nucleus. Incorrect reprogramming of epigenetic markings such as DNA methylation is associated with compromised prenatal development and postnatal abnormalities. Clones that survive into adulthood, in contrast, are assumed to possess a normalized epigenome corresponding to their normal phenotype. To address this point, we used capillary electrophoresis to measure 5-methylcytosine (5mC) levels in leukocyte DNA of 38 healthy female bovine clones that represented five genotypes from the Simmental breed and four genotypes from the Holstein breed. The estimated variance in 5mC level within clone genotypes of both breeds [0.104, 95% confidence interval (CI): 0.070–0.168] was higher than between clone genotypes (0, CI: 0–0.047). We quantified the contribution of SCNT to this unexpected variability by comparing the 19 Simmental clones with 12 female Simmental monozygotic twin pairs of similar age. In Simmental clones, the estimated variability within genotype (0.0636, CI: 0.0358–0.127) was clearly higher than in twin pairs (0.0091, CI: 0.0047–0.0229). In clones, variability within genotype (0.0636) was again higher than between genotypes (0, CI: 0–0.077). Twins, in contrast, showed lower variability within genotypes (0.0091) than between genotypes (0.0136, CI: 0.00250–0.0428). Importantly, the absolute deviations of 5mC values of individual SCNT clones from their genotype means were fivefold increased in comparison to twins. Further comparisons with noncloned controls revealed DNA hypermethylation in most of the clones. The clone-specific variability in DNA methylation and DNA hypermethylation clearly show that healthy adult SCNT clones must be considered as epigenome variants. PMID:20677931

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

    PubMed Central

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

    2014-01-01

    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

  3. 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.

  4. Regional specificity of MRI contrast parameter changes in normal ageing revealed by voxel-based quantification (VBQ).

    PubMed

    Draganski, B; Ashburner, J; Hutton, C; Kherif, F; Frackowiak, R S J; Helms, G; Weiskopf, N

    2011-04-15

    Normal ageing is associated with characteristic changes in brain microstructure. Although in vivo neuroimaging captures spatial and temporal patterns of age-related changes of anatomy at the macroscopic scale, our knowledge of the underlying (patho)physiological processes at cellular and molecular levels is still limited. The aim of this study is to explore brain tissue properties in normal ageing using quantitative magnetic resonance imaging (MRI) alongside conventional morphological assessment. Using a whole-brain approach in a cohort of 26 adults, aged 18-85years, we performed voxel-based morphometric (VBM) analysis and voxel-based quantification (VBQ) of diffusion tensor, magnetization transfer (MT), R1, and R2* relaxation parameters. We found age-related reductions in cortical and subcortical grey matter volume paralleled by changes in fractional anisotropy (FA), mean diffusivity (MD), MT and R2*. The latter were regionally specific depending on their differential sensitivity to microscopic tissue properties. VBQ of white matter revealed distinct anatomical patterns of age-related change in microstructure. Widespread and profound reduction in MT contrasted with local FA decreases paralleled by MD increases. R1 reductions and R2* increases were observed to a smaller extent in overlapping occipito-parietal white matter regions. We interpret our findings, based on current biophysical models, as a fingerprint of age-dependent brain atrophy and underlying microstructural changes in myelin, iron deposits and water. The VBQ approach we present allows for systematic unbiased exploration of the interaction between imaging parameters and extends current methods for detection of neurodegenerative processes in the brain. The demonstrated parameter-specific distribution patterns offer insights into age-related brain structure changes in vivo and provide essential baseline data for studying disease against a background of healthy ageing.

  5. Comprehensive proteome quantification reveals NgBR as a new regulator for epithelial-mesenchymal transition of breast tumor cells.

    PubMed

    Zhao, Baofeng; Xu, Bo; Hu, Wenquan; Song, Chunxia; Wang, Fangjun; Liu, Zhong; Ye, Mingliang; Zou, Hanfa; Miao, Qing R

    2015-01-01

    Nogo-B receptor (NgBR) is a type I receptor and specifically binds to ligand Nogo-B. Our previous work has shown that NgBR is highly expressed in human breast invasive ductal carcinoma. Here, comprehensive proteome quantification was performed to examine the alteration of protein expression profile in MDA-MB-231 breast tumor cells after knocking down NgBR using lentivirus-mediated shRNA approach. Among a total of 1771 proteins feasibly quantified, 994 proteins were quantified in two biological replicates with RSD <50%. There are 122 proteins significantly down-regulated in NgBR knockdown MDA-MB-231 breast tumor cells, such as vimentin and S100A4, well-known markers for mesenchymal cells, and CD44, a stemness indicator. The decrease of vimentin, S100A4 and CD44 protein expression levels was further confirmed by Western blot analysis. MDA-MB-231 cells are typical breast invasive ductal carcinoma cells showing mesenchymal phenotype. Cell morphology analysis demonstrates NgBR knockdown in MDA-MB-231 cells results in reversibility of epithelial-mesenchymal transition (EMT), which is one of the major mechanisms involved in breast cancer metastasis. Furthermore, we demonstrated that NgBR knockdown in MCF-7 cells significantly prevented the TGF-β-induced EMT process as determined by the morphology change, and staining of E-cadherin intercellular junction as well as the decreased expression of vimentin. Our previous publication showed that NgBR is highly expressed in human breast invasive ductal carcinoma. However, the roles of NgBR and NgBR-mediated signaling pathway in breast tumor cells are still unclear. Here, we not only demonstrated that the quantitative proteomics analysis is a powerful tool to investigate the global biological function of NgBR, but also revealed that NgBR is involved in the transition of breast epithelial cells to mesenchymal stem cells, which is one of the major mechanisms involved in breast cancer metastasis. These findings provide new insights

  6. 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.

  7. Quantum dot-based image sensors for cutting-edge commercial multispectral cameras

    NASA Astrophysics Data System (ADS)

    Mandelli, Emanuele; Beiley, Zach M.; Kolli, Naveen; Pattantyus-Abraham, Andras G.

    2016-09-01

    This work presents the development of a quantum dot-based photosensitive film engineered to be integrated on standard CMOS process wafers. It enables the design of exceptionally high performance, reliable image sensors. Quantum dot solids absorb light much more rapidly than typical silicon-based photodiodes do, and with the ability to tune the effective material bandgap, quantum dot-based imagers enable higher quantum efficiency over extended spectral bands, both in the Visible and IR regions of the spectrum. Moreover, a quantum dot-based image sensor enables desirable functions such as ultra-small pixels with low crosstalk, high full well capacity, global shutter and wide dynamic range at a relatively low manufacturing cost. At InVisage, we have optimized the manufacturing process flow and are now able to produce high-end image sensors for both visible and NIR in quantity.

  8. 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.

  9. 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.

  10. Serum apolipoprotein A-1 quantification by LC–MS with a SILAC internal standard reveals reduced levels in smokers

    PubMed Central

    Wang, Qingqing; Zhang, Suhong; Guo, Lili; Busch, Christine M; Jian, Wenying; Weng, Naidong; Snyder, Nathaniel W; Rangiah, Kannan; Mesaros, Clementina; Blair, Ian A

    2015-01-01

    Background: Absolute quantification of protein biomarkers such as serum apolipoprotein A1 by both immunoassays and LC–MS can provide misleading results. Results: Recombinant ApoA-1 internal standard was prepared using stable isotope labeling by amino acids in cell culture with [13C615N2]-lysine and [13C915N1]-tyrosine in human cells. A stable isotope dilution LC–MS method for serum ApoA-1 was validated and levels analyzed for 50 nonsmokers and 50 smokers. Conclusion: The concentration of ApoA-1 in nonsmokers was 169.4 mg/dl with an 18.4% reduction to 138.2 mg/dl in smokers. The validated assay will have clinical utility for assessing effects of smoking cessation and therapeutic or dietary interventions in high-risk populations. PMID:26394123

  11. Sugar nucleotide quantification by liquid chromatography tandem mass spectrometry reveals a distinct profile in Plasmodium falciparum sexual stage parasites

    PubMed Central

    López-Gutiérrez, Borja; Dinglasan, Rhoel R.

    2017-01-01

    The obligate intracellular lifestyle of Plasmodium falciparum and the difficulties in obtaining sufficient amounts of biological material have hampered the study of specific metabolic pathways in the malaria parasite. Thus, for example, the pools of sugar nucleotides required to fuel glycosylation reactions have never been studied in-depth in well-synchronized asexual parasites or in other stages of its life cycle. These metabolites are of critical importance, especially considering the renewed interest in the presence of N-, O-, and other glycans in key parasite proteins. In this work, we adapted a liquid chromatography tandem mass spectrometry (LC-MS/MS) method based on the use of porous graphitic carbon (PGC) columns and MS-friendly solvents to quantify sugar nucleotides in the malaria parasite. We report the thorough quantification of the pools of these metabolites throughout the intraerythrocytic cycle of P. falciparum. The sensitivity of the method enabled, for the first time, the targeted analysis of these glycosylation precursors in gametocytes, the parasite sexual stages that are transmissible to the mosquito vector. PMID:28104756

  12. Sugar nucleotide quantification by liquid chromatography tandem mass spectrometry reveals a distinct profile in Plasmodium falciparum sexual stage parasites.

    PubMed

    López-Gutiérrez, Borja; Dinglasan, Rhoel R; Izquierdo, Luis

    2017-03-07

    The obligate intracellular lifestyle of Plasmodium falciparum and the difficulties in obtaining sufficient amounts of biological material have hampered the study of specific metabolic pathways in the malaria parasite. Thus, for example, the pools of sugar nucleotides required to fuel glycosylation reactions have never been studied in-depth in well-synchronized asexual parasites or in other stages of its life cycle. These metabolites are of critical importance, especially considering the renewed interest in the presence of N-, O-, and other glycans in key parasite proteins. In this work, we adapted a liquid chromatography tandem mass spectrometry (LC-MS/MS) method based on the use of porous graphitic carbon (PGC) columns and MS-friendly solvents to quantify sugar nucleotides in the malaria parasite. We report the thorough quantification of the pools of these metabolites throughout the intraerythrocytic cycle of P. falciparum The sensitivity of the method enabled, for the first time, the targeted analysis of these glycosylation precursors in gametocytes, the parasite sexual stages that are transmissible to the mosquito vector.

  13. Highly abundant defense proteins in human sweat as revealed by targeted proteomics and label free quantification mass spectrometry

    PubMed Central

    Csősz, Éva; Emri, Gabriella; Kalló, Gergő; Tsaprailis, George; Tőzsér, József

    2015-01-01

    BACKGROUND The healthy human skin with its effective antimicrobial defense system forms an efficient barrier against invading pathogens. There is evidence suggesting that the composition of this chemical barrier varies between diseases, making the easily-collected sweat an ideal candidate for biomarker discoveries. OBJECTIVE Our aim was to provide information about the normal composition of the sweat, and to study the chemical barrier found at the surface of skin. METHODS Sweat samples from healthy individuals were collected during sauna bathing, and the global protein panel was analyzed by label-free mass spectrometry. SRM-based targeted proteomic methods were designed and stable isotope labeled reference peptides were used for method validation. RESULTS 95 sweat proteins were identified, 20 of them were novel proteins. It was shown that dermcidin is the most abundant sweat protein, and along with apolipoprotein D, clusterin, prolactin inducible protein and serum albumin, they make up 91% of secreted sweat proteins. The roles of these highly abundant proteins were reviewed; all of which have protective functions, highlighting the importance of sweat glands in composing the first line of innate immune defense system, and maintaining the epidermal barrier integrity. CONCLUSION Our findings in regards to the proteins forming the chemical barrier of the skin as determined by label free quantification and targeted proteomics methods are in accordance with previous studies, and can be further used as a starting point for non-invasive sweat biomarker research. PMID:26307449

  14. A new efficient method for synaptic vesicle quantification reveals differences between medial prefrontal cortex perforated and nonperforated synapses.

    PubMed

    Nava, Nicoletta; Chen, Fenghua; Wegener, Gregers; Popoli, Maurizio; Nyengaard, Jens Randel

    2014-02-01

    Communication between neurons is mediated by the release of neurotransmitter-containing vesicles from presynaptic terminals. Quantitative characterization of synaptic vesicles can be highly valuable for understanding mechanisms underlying synaptic function and plasticity. We performed a quantitative ultrastructural analysis of cortical excitatory synapses by mean of a new, efficient method, as an alternative to three-dimensional (3D) reconstruction. Based on a hierarchical sampling strategy and unequivocal identification of the region of interest, serial sections from excitatory synapses of medial prefrontal cortex (mPFC) of six Sprague-Dawley rats were acquired with a transmission electron microscope. Unbiased estimates of total 3D volume of synaptic terminals were obtained through the Cavalieri estimator, and adequate correction factors for vesicle profile number estimation were applied for final vesicle quantification. Our analysis was based on 79 excitatory synapses, nonperforated (NPSs) and perforated (PSs) subtypes. We found that total number of docked and reserve-pool vesicles in PSs significantly exceeded that in NPSs (by, respectively, 77% and 78%). These differences were found to be related to changes in size between the two subtypes (active zone area by 86%; bouton volume by 105%) rather than to postsynaptic density shape. Positive significant correlations were found between number of docked and reserve-pool vesicles, active zone area and docked vesicles, and bouton volume and reserve pool vesicles. Our method confirmed the large size of mPFC PSs and a linear correlation between presynaptic features of typical hippocampal synapses. Moreover, a greater number of docked vesicles in PSs may promote a high synaptic strength of these synapses.

  15. 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.

  16. 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.

  17. Quantum-Dot-Based Telecommunication-Wavelength Quantum Relay

    NASA Astrophysics Data System (ADS)

    Huwer, J.; Stevenson, R. M.; Skiba-Szymanska, J.; Ward, M. B.; Shields, A. J.; Felle, M.; Farrer, I.; Ritchie, D. A.; Penty, R. V.

    2017-08-01

    The development of quantum relays for long-haul and attack-proof quantum communication networks operating with weak coherent laser pulses requires entangled photon sources at telecommunication wavelengths with intrinsic single-photon emission for most practical implementations. Using a semiconductor quantum dot emitting entangled photon pairs in the telecommunication O band, we demonstrate a quantum relay fulfilling both of these conditions. The system achieves a maximum fidelity of 94.5% for implementation of a standard four-state protocol with input states generated by a laser. We further investigate robustness against frequency detuning of the narrow-band input and perform process tomography of the teleporter, revealing operation for arbitrary pure input states, with an average gate fidelity of 83.6%. The results highlight the potential of semiconductor light sources for compact and robust quantum-relay technology that is compatible with existing communication infrastructures.

  18. Quantum dot-based energy transfer: perspectives and potential for applications in photodynamic therapy.

    PubMed

    Samia, Anna C S; Dayal, Smita; Burda, Clemens

    2006-01-01

    Quantum dots have emerged as an important class of material that offers great promise to a diverse range of applications ranging from energy conversion to biomedicine. Here, we review the potential of using quantum dots and quantum dot conjugates as sensitizers for photodynamic therapy (PDT). The photophysics of singlet oxygen generation in relation to quantum dot-based energy transfer is discussed and the possibility of using quantum dots as photosensitizer in PDT is assessed, including their current limitations to applications in biological systems. The biggest advantage of quantum dots over molecular photosensitizers that comes into perspective is their tunable optical properties and surface chemistries. Recent developments in the preparation and photophysical characterization of quantum dot energy transfer processes are also presented in this review, to provide insights on the future direction of quantum dot-based photosensitization studies from the viewpoint of our ongoing research.

  19. The ecological roles of bacterial populations in the surface sediments of coastal lagoon environments in Japan as revealed by quantification and qualification of 16S rDNA.

    PubMed

    Tsuboi, Shun; Amemiya, Takashi; Seto, Koji; Itoh, Kiminori; Rajendran, Narasimmalu

    2013-05-01

    Based on quantification and qualification of bacterial 16S rDNA, we verified the bacterial ecological characteristics of surface sediments of Lakes Shinji and Nakaumi, which are representative of coastal lagoons in Japan. Quantification and qualification of the 16S rDNA sequences was carried out using real time polymerase chain reaction and polymerase chain reaction denaturing gradient gel electrophoresis and non-metric multidimensional scaling, respectively. The results revealed that the copy number per gram of sediment ranged from 8.33 × 10(8) (Lake Nakaumi) to 1.69 × 10(11) (Honjo area), suggesting that bacterial carbon contributed only 0.05-9.64 % of the total carbon content in the samples. Compared with other aquatic environments, these results indicate that sedimentary bacteria are not likely to be important transporters of nutrients to higher trophic levels, or to act as carbon sinks in the lagoons. The bacterial compositions of Lake Shinji and Lake Nakaumi and the Honjo area were primarily influenced by sediment grain sizes and salinity, respectively. Statistical comparisons of the environmental properties suggested that the areas that were oxygen-abundant (Lake Shinji) and at a higher temperature (Honjo area) presented efficient organic matter degradation. The 16S rDNA copy number per gram of carbon and nitrogen showed the same tendency. Consequently, the primary roles of bacteria were degradation and preservation of organic materials, and this was affected by oxygen and temperature. These roles were supported by the bacterial diversity rather than the differences in the community compositions of the sedimentary bacteria in these coastal lagoons.

  20. Label-free quantification proteomics reveals novel calcium binding proteins in matrix vesicles isolated from mineralizing Saos-2 cells.

    PubMed

    Zhou, Xiaoying; Cui, Yazhou; Luan, Jing; Zhou, Xiaoyan; Zhang, Genglin; Zhang, Xiumei; Han, Jinxiang

    2013-06-01

    Matrix vesicles (MVs) involved in the initiation of mineralization by deposition of hydroxyapatite (HA) in their lumen are released by the budding of mineralization-competent cells during skeletogenesis and bone development. To identify additional mineralization-related proteins, MVs were isolated from non-stimulated and stimulated Saos-2 cells in culture via an Exoquick™ approach and the corresponding proteomes were identified and quantified with label-free quantitative proteome technology. The isolated MVs were confirmed by electron microscopy, alkaline phosphatase activity (ALP), biomarkers, and mineral formation analyses. Label-free quantitative proteome analysis revealed that 19 calcium binding proteins (CaBPs), including Grp94, calnexin, calreticulin, calmodulin, and S100A4/A10, were up-regulated in MVs of Saos-2 cells upon stimulation of mineralization. This result provides new clues to study the mechanism of the initiation of MV-mediated mineralization.

  1. 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.

  2. Unexpected patterns of Epstein-Barr virus transcription revealed by a high throughput PCR array for absolute quantification of viral mRNA.

    PubMed

    Tierney, Rosemary J; Shannon-Lowe, Claire D; Fitzsimmons, Leah; Bell, Andrew I; Rowe, Martin

    2015-01-01

    We have validated a flexible, high-throughput and relatively inexpensive RT-QPCR array platform for absolute quantification of Epstein-Barr virus transcripts in different latent and lytic infection states. Several novel observations are reported. First, during infection of normal B cells, Wp-initiated latent gene transcripts remain far more abundant following activation of the Cp promoter than was hitherto suspected. Second, EBNA1 transcript levels are remarkably low in all forms of latency, typically ranging from 1 to 10 transcripts per cell. EBNA3A, -3B and -3C transcripts are likewise very low in Latency III, typically at levels similar to or less than EBNA1 transcripts. Thirdly, a subset of lytic gene transcripts is detectable in Burkitt lymphoma lines at low levels, including: BILF1, which has oncogenic properties, and the poorly characterized LF1, LF2 and LF3 genes. Analysis of seven African BL biopsies confirmed this transcription profile but additionally revealed significant expression of LMP2 transcripts.

  3. Structures of polymeric pigments in red wine and their derived quantification markers revealed by high-resolution quadrupole time-of-flight mass spectrometry.

    PubMed

    Zeng, Liming; Teissèdre, Pierre-Louis; Jourdes, Michaël

    2016-01-15

    The quantification of polymeric pigment families in red wine through their derived quantification markers released during phloroglucinolysis will allow the understanding of their formation kinetics and evolutions during aging which has not been achieved until now and is in urgent need. The identification of these quantification markers was achieved by high-resolution mass spectrometry (HRMS) in this study. HRMS was used to clarify the fragmentation patterns in positive mode of polymeric pigments and identify their derived quantification markers released during phloroglucinolysis. With HRMS, identification of (epi)catechin-malvidin-3-O-glucoside adducts was simplified to MS/MS, and the fragmentation pattern of malvidin-3-O-glucoside-(epi)catechin adducts was clearly demonstrated. The attribution of four detected ions at m/z 1071.2765 in red wine to the trimeric structure of (epi)catechin-[malvidin-3-O-glucoside-A type linkage-(epi)catechin] and [malvidin-3-O-glucoside-A type linkage-(epi)catechin]-(epi)catechin was achieved for the first time by MS/MS and evidence given by phloroglucinolysis. Moreover, four kinds of derived quantification markers released from polymeric pigments during phloroglucinolysis were also identified. The fragmentation pathways of polymeric pigments in red wine and their derived quantification markers released during acidic chemical depolymerisation were clarified which will allow their quantification in red wine. Copyright © 2015 John Wiley & Sons, Ltd.

  4. 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.

  5. 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.

  6. 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.

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

    PubMed Central

    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.

    2015-01-01

    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. PMID:26022924

  8. NMR-based metabolomics and LC-MS/MS quantification reveal metal-specific tolerance and redox homeostasis in Chlorella vulgaris.

    PubMed

    Zhang, Wenlin; Tan, Nicole G J; Li, Sam F Y

    2014-01-01

    Live green algae are promising candidates for phytoremediation, but a suitable algal species which bio-accumulates high concentrations of heavy metals, and survives well in industrial water is yet to be identified. Potential metabolic engineering may be applied to improve algal phytoremediation performance, but the metal tolerance and bioaccumulation mechanisms in green algae have to be first fully understood. In this study, NMR-based metabolomics was used to study the effect of different metal species (copper, cadmium and lead) and metal concentrations in green microalgae, Chlorella vulgaris. High Cu concentrations influenced substantial decrease in organic osmolytes (betaine and glycerophosphocholine), which indicated Cu-induced redox imbalance. Accompanying redox imbalance, growth inhibition and photosynthesis impairments in Cu-spiked C. vulgaris revealed a clear relationship between Cu toxicity and redox homeostasis. As these metabolic changes were less prominent in Cd and Pb-spiked cultures, we inferred metal-specific toxicity in C. vulgaris, where redox active Cu(2+) is more potent than non-redox active Cd(2+) and Pb(2+) in causing redox imbalance. Subsequently, ICP-MS and LC-MS/MS quantification shed light on the metal-specific bioaccumulation and detoxification mechanisms. The metal bioconcentration factor (BCF) correlated well with the phytochelatin (PC) content in Cu and Cd-spiked C. vulgaris biomass. High BCF and PC levels with increasing Cu and Cd exposure concentrations indicated that PCs played a significant role in Cu and Cd bioaccumulation and detoxification. In contrast, the undetectable PC levels in Pb-spiked cultures despite high Pb BCF suggest an alternative detoxification mechanism for Pb: either by passive absorption to the algal cell wall or interaction with glutathione (GSH).

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

    PubMed Central

    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

  10. Quantum dot based detections of propagating plasmonic modes excited by bowtie antennas

    NASA Astrophysics Data System (ADS)

    Wen, Jing; Wang, Kang; Feng, Hui; Lv, Yating; Chen, Jiannong; Zhang, Dawei

    2017-03-01

    Propagating plasmonic modes excited by bowtie apertures based on emissions from a layer of CdSe/ZnS quantum dots are experimentally detected. The mode distributions with a cladding of 20 nm thick Al2O3 film in between the silver and the quantum dot layers are more homogenous compared to the uncoated structure. The variation discipline of the effective indexes and the decay lengths of the plasmonic modes are discussed for various refractive indexes and thicknesses of the cladding. The three dimensional field distributions of the structure are simulated and the plasmonic fields are only excited in and around the cladding layer on top of the silver film. Such quantum dots based detection methods are promising tools for simultaneous imaging of near field optical distributions in integrated plasmonic nano-circuits.

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

    PubMed

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

    2016-01-07

    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.

  12. Quantum-Dot-Based Immunochromatographic Assay for Total IgE in Human Serum

    PubMed Central

    Berlina, Anna N.; Taranova, Nadezhda A.; Zherdev, Anatoly V.; Sankov, Mikhail N.; Andreev, Igor V.; Martynov, Alexandr I.; Dzantiev, Boris B.

    2013-01-01

    To rapidly quantify total immunoglobulin E levels in human serum, we developed a novel quantum-dot-based immunochromatographic assay that employs digital recording of fluorescence. It can detect IgE levels of 5–1000 kU/L, with a coefficient of variation ranging from 2.0 to 9.5%. The assay can be processed in 10 min. The developed assay was tested on 95 serum samples. The correlation coefficient between the IgE values obtained by the proposed assay and those obtained by a commercial ELISA kit was 0.9884. Our assay thus shows promise as a new diagnostic tool for IgE detection. PMID:24204841

  13. 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

  14. Harnessing Sun's Energy with Quantum Dots Based Next Generation Solar Cell.

    PubMed

    Halim, Mohammad A

    2012-12-27

    Our energy consumption relies heavily on the three components of fossil fuels (oil, natural gas and coal) and nearly 83% of our current energy is consumed from those sources. The use of fossil fuels, however, has been viewed as a major environmental threat because of their substantial contribution to greenhouse gases which are responsible for increasing the global average temperature. Last four decades, scientists have been searching for alternative sources of energy which need to be environmentally clean, efficient, cost-effective, renewable, and sustainable. One of the promising sustainable sources of energy can be achieved by harnessing sun energy through silicon wafer, organic polymer, inorganic dye, and quantum dots based solar cells. Among them, quantum dots have an exceptional property in that they can excite multiple electrons using only one photon. These dots can easily be synthesized, processed in solution, and incorporated into solar cell application. Interestingly, the quantum dots solar cells can exceed the Shockley-Queisser limit; however, it is a great challenge for other solar cell materials to exceed the limit. Theoretically, the quantum dots solar cell can boost the power conversion efficiency up to 66% and even higher to 80%. Moreover, in changing the size of the quantum dots one can utilize the Sun's broad spectrum of visible and infrared ranges. This review briefly overviews the present performance of different materials-based solar cells including silicon wafer, dye-sensitized, and organic solar cells. In addition, recent advances of the quantum dots based solar cells which utilize cadmium sulfide/selenide, lead sulfide/selenide, and new carbon dots as light harvesting materials has been reviewed. A future outlook is sketched as to how one could improve the efficiency up to 10% from the current highest efficiency of 6.6%.

  15. Harnessing Sun’s Energy with Quantum Dots Based Next Generation Solar Cell

    PubMed Central

    Halim, Mohammad A.

    2012-01-01

    Our energy consumption relies heavily on the three components of fossil fuels (oil, natural gas and coal) and nearly 83% of our current energy is consumed from those sources. The use of fossil fuels, however, has been viewed as a major environmental threat because of their substantial contribution to greenhouse gases which are responsible for increasing the global average temperature. Last four decades, scientists have been searching for alternative sources of energy which need to be environmentally clean, efficient, cost-effective, renewable, and sustainable. One of the promising sustainable sources of energy can be achieved by harnessing sun energy through silicon wafer, organic polymer, inorganic dye, and quantum dots based solar cells. Among them, quantum dots have an exceptional property in that they can excite multiple electrons using only one photon. These dots can easily be synthesized, processed in solution, and incorporated into solar cell application. Interestingly, the quantum dots solar cells can exceed the Shockley-Queisser limit; however, it is a great challenge for other solar cell materials to exceed the limit. Theoretically, the quantum dots solar cell can boost the power conversion efficiency up to 66% and even higher to 80%. Moreover, in changing the size of the quantum dots one can utilize the Sun’s broad spectrum of visible and infrared ranges. This review briefly overviews the present performance of different materials-based solar cells including silicon wafer, dye-sensitized, and organic solar cells. In addition, recent advances of the quantum dots based solar cells which utilize cadmium sulfide/selenide, lead sulfide/selenide, and new carbon dots as light harvesting materials has been reviewed. A future outlook is sketched as to how one could improve the efficiency up to 10% from the current highest efficiency of 6.6%. PMID:28348320

  16. 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

  17. Accurate quantification of site-specific acetylation stoichiometry reveals the impact of sirtuin deacetylase CobB on the E. coli acetylome.

    PubMed

    Weinert, Brian Tate; Satpathy, Shankha; Hansen, Bogi Karbech; Lyon, David; Jensen, Lars Juhl; Choudhary, Chunaram

    2017-03-02

    Lysine acetylation is a protein posttranslational modification (PTM) that occurs on thousands of lysine residues in diverse organisms from bacteria to humans. Accurate measurement of acetylation stoichiometry on a proteome-wide scale remains challenging. Most methods employ a comparison of chemically acetylated peptides to native acetylated peptides, however, the potentially large differences in abundance between these peptides presents a challenge for accurate quantification. Stable isotope labeling by amino acids in cell culture (SILAC)-based mass spectrometry (MS) is one of the most widely used quantitative proteomic methods. Here we show that serial dilution of SILAC-labeled peptides (SD-SILAC) can be used to identify accurately quantified peptides and to estimate the quantification error rate. We applied SD-SILAC to determine absolute acetylation stoichiometry in exponentially-growing and stationary-phase wild type and Sirtuin deacetylase CobB-deficient cells. To further analyze CobB-regulated sites under conditions of globally increased or decreased acetylation, we measured stoichiometry in phophotransacetylase (ptaΔ) and acetate kinase (ackAΔ) mutant strains in the presence and absence of the Sirtuin inhibitor nicotinamide. We measured acetylation stoichiometry at 3,669 unique sites and found that the vast majority of acetylation occurred at a low stoichiometry. Manipulations that cause increased nonenzymatic acetylation by acetyl-phosphate (AcP), such as stationary-phase arrest and deletion of ackA, resulted in globally increased acetylation stoichiometry. Comparison to relative quantification under the same conditions validated our stoichiometry estimates at hundreds of sites, demonstrating the accuracy of our method. Similar to Sirtuin deacetylase 3 (SIRT3) in mitochondria, CobB suppressed acetylation to lower than median stoichiometry in WT, ptaΔ, and ackAΔ cells. Together, our results provide a detailed view of acetylation stoichiometry in E. coli

  18. Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding.

    PubMed

    Samanta, Sudipta; Mukherjee, Sanchita

    2017-09-04

    The p53 protein activation protects the organism from propagation of cells with damaged DNA having oncogenic mutations. In normal cells, activity of p53 is controlled by interaction with MDM2. The well understood p53-MDM2 interaction facilitates design of ligands that could potentially disrupt or prevent the complexation owing to its emergence as an important objective for cancer therapy. However, thermodynamic quantification of the p53-peptide induced structural changes of the MDM2-protein remains an area to be explored. This study attempts to understand the conformational free energy and entropy costs due to this complex formation from the histograms of dihedral angles generated from molecular dynamics simulations. Residue-specific quantification illustrates that, hydrophobic residues of the protein contribute maximum to the conformational thermodynamic changes. Thermodynamic quantification of structural changes of the protein unfold the fact that, p53 binding provides a source of inter-element cooperativity among the protein secondary structural elements, where the highest affected structural elements (α2 and α4) found at the binding site of the protein affects faraway structural elements (β1 and Loop1) of the protein. The communication perhaps involves water mediated hydrogen bonded network formation. Further, we infer that in inhibitory F19A mutation of P53, though Phe19 is important in the recognition process, it has less prominent contribution in the stability of the complex. Collectively, this study provides vivid microscopic understanding of the interaction within the protein complex along with exploring mutation sites, which will contribute further to engineer the protein function and binding affinity.

  19. Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding

    NASA Astrophysics Data System (ADS)

    Samanta, Sudipta; Mukherjee, Sanchita

    2017-09-01

    The p53 protein activation protects the organism from propagation of cells with damaged DNA having oncogenic mutations. In normal cells, activity of p53 is controlled by interaction with MDM2. The well understood p53-MDM2 interaction facilitates design of ligands that could potentially disrupt or prevent the complexation owing to its emergence as an important objective for cancer therapy. However, thermodynamic quantification of the p53-peptide induced structural changes of the MDM2-protein remains an area to be explored. This study attempts to understand the conformational free energy and entropy costs due to this complex formation from the histograms of dihedral angles generated from molecular dynamics simulations. Residue-specific quantification illustrates that, hydrophobic residues of the protein contribute maximum to the conformational thermodynamic changes. Thermodynamic quantification of structural changes of the protein unfold the fact that, p53 binding provides a source of inter-element cooperativity among the protein secondary structural elements, where the highest affected structural elements (α2 and α4) found at the binding site of the protein affects faraway structural elements (β1 and Loop1) of the protein. The communication perhaps involves water mediated hydrogen bonded network formation. Further, we infer that in inhibitory F19A mutation of P53, though Phe19 is important in the recognition process, it has less prominent contribution in the stability of the complex. Collectively, this study provides vivid microscopic understanding of the interaction within the protein complex along with exploring mutation sites, which will contribute further to engineer the protein function and binding affinity.

  20. Current cross-correlations in double quantum dot based Cooper pair splitters with ferromagnetic leads

    NASA Astrophysics Data System (ADS)

    Wrześniewski, Kacper; Trocha, Piotr; Weymann, Ireneusz

    2017-05-01

    We investigate the current cross-correlations in a double quantum dot based Cooper pair splitter coupled to one superconducting and two ferromagnetic electrodes. The analysis is performed by assuming a weak coupling between the double dot and ferromagnetic leads, while the coupling to the superconductor is arbitrary. Employing the perturbative real-time diagrammatic technique, we study the Andreev transport properties of the device, focusing on the Andreev current cross-correlations, for various parameters of the model, both in the linear and nonlinear response regimes. Depending on parameters and transport regime, we find both positive and negative current cross-correlations. Enhancement of the former type of cross-correlations indicates transport regimes, in which the device works with high Cooper pair splitting efficiency, contrary to the latter type of correlations, which imply negative influence on the splitting. The processes and mechanisms leading to both types of current cross-correlations are thoroughly examined and discussed, giving a detailed insight into the Andreev transport properties of the considered device.

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

    PubMed

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

    2015-11-07

    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.

  2. Current cross-correlations in double quantum dot based Cooper pair splitters with ferromagnetic leads.

    PubMed

    Wrześniewski, Kacper; Trocha, Piotr; Weymann, Ireneusz

    2017-05-17

    We investigate the current cross-correlations in a double quantum dot based Cooper pair splitter coupled to one superconducting and two ferromagnetic electrodes. The analysis is performed by assuming a weak coupling between the double dot and ferromagnetic leads, while the coupling to the superconductor is arbitrary. Employing the perturbative real-time diagrammatic technique, we study the Andreev transport properties of the device, focusing on the Andreev current cross-correlations, for various parameters of the model, both in the linear and nonlinear response regimes. Depending on parameters and transport regime, we find both positive and negative current cross-correlations. Enhancement of the former type of cross-correlations indicates transport regimes, in which the device works with high Cooper pair splitting efficiency, contrary to the latter type of correlations, which imply negative influence on the splitting. The processes and mechanisms leading to both types of current cross-correlations are thoroughly examined and discussed, giving a detailed insight into the Andreev transport properties of the considered device.

  3. A fluorescent carbon-dots-based mitochondria-targetable nanoprobe for peroxynitrite sensing in living cells.

    PubMed

    Wu, Xiaoxue; Sun, Shan; Wang, Yuhui; Zhu, Jiali; Jiang, Kai; Leng, Yumin; Shu, Qinghai; Lin, Hengwei

    2017-04-15

    Mitochondria, the power generators in cell, are a primary organelle of oxygen consumption and a main source of reactive oxygen/nitrogen species (ROS/RNS). Peroxynitrite (ONOO(-)), known as a kind of RNS, has been considered to be a significant factor in many cell-related biological processes, and there is great desire to develop fluorescent probes that can sensitively and selectively detect peroxynitrite in living cells. Herein, we developed a fluorescent carbon-dots (C-dots) based mitochondria-targetable nanoprobe with high sensitivity and selectivity for peroxynitrite sensing in living cells. The C-dots with its surface rich in amino groups was synthesized using o-phenylenediamine as carbon precursor, and it could be covalently conjugated with a mitochondria-targeting moiety, i.e. triphenylphosphonium (TPP). In the presence of peroxynitrite, the fluorescence of the constructed nanoprobe (C-dots-TPP) was efficiently quenched via a mechanism of photoinduced electron transfer (PET). The nanoprobe exhibited relatively high sensitivity (limit of detection: 13.5nM) and selectivity towards peroxynitrite in aqueous buffer. The performance of the nanoprobe for fluorescence imaging of peroxynitrite in mitochondria was investigated. The results demonstrated that the nanoprobe showed fine mitochondria-targeting ability and imaging contrast towards peroxynitrite in living cells. We anticipate that the proposed nanoprobe will provide a facile tool to explore the role played by peroxynitrite in cytobiology. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Highly sensitive and accurate detection of C-reactive protein by CdSe/ZnS quantum dot-based fluorescence-linked immunosorbent assay.

    PubMed

    Lv, Yanbing; Wu, Ruili; Feng, Kunrui; Li, Jinjie; Mao, Qing; Yuan, Hang; Shen, Huaibin; Chai, Xiangdong; Li, Lin Song

    2017-05-02

    The conventional and widely used enzyme-linked immunosorbent assays (ELISA), due to specificity and high-sensitivity, were suitable in vitro diagnosis. But enzymes are vulnerable to the external conditions, and the complex operation steps limit its application. Semiconductor quantum dots have been successfully used in biological and medical research due to the high photoluminescence and high resistance to photobleaching. In this study, we have developed a novel quantum dot-labeled immunosorbent assay for rapid disease detection of C-reactive protein (CRP). The assay for the detection of CRP can provide a wide analytical range of 1.56-400 ng/mL with the limit of detection (LOD) = 0.46 ng/mL and the limit of quantification = 1.53 ng/mL. The precision of the assay has been confirmed for low coefficient of variation, less than 10% (intra-assay) and less than 15% (inter-assay). The accuracy of assay meets the requirements with the recoveries of 95.4-105.7%. Furthermore, clinical samples have been collected and used for correlation analysis between this FLISA and gold standard Roche immunoturbidimetry. It shows excellent accurate concordance and the correlation coefficient value (R) is as high as 0.989 (n = 34). This in vitro quantum dot-based detection method offers a lower LOD and a wide liner detection range than ELISA. The total reaction time is only 50 min, which is much shorter than the commercialization ELISA (about 120 min). All of the results show that a convenient, sensitive, and accurate fluorescence-linked immunosorbent assay method has been well established for the detection of CRP samples. Therefore, this method has immense potential for the development of rapid and cost-effective in vitro diagnostic kits.

  5. 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

  6. Multi-color colloidal quantum dot based light emitting diodes micropatterned on silicon hole transporting layers

    NASA Astrophysics Data System (ADS)

    Gopal, Ashwini; Hoshino, Kazunori; Kim, Sunmin; Zhang, Xiaojing

    2009-06-01

    We present a colloidal quantum dot based light emitting diode (QD-LED) which utilizes the p-type silicon substrate as the hole transporting layer. A microcontact printing technique was introduced to pattern self-assembled CdSe/ZnS QD films, which allowed creation of an LED with well-defined geometry suitable for monolithic integration on silicon substrates. Our QD-LED consists of multi-layers of inorganic materials: a combination of Au (thickness: 5 nm) and Ag (12 nm) as the cathode, a ZnO:SnO2 mixture (ratio 3:1, 40 nm) as the electron transporting layer, CdSe/ZnS QDs as the light emission layer, 1 nm SiO2 as an energy barrier layer, and p-type silicon as the hole transporting layer. These printed QD-LEDs are capable of multi-color emission peaked at wavelengths of 576 nm, 598 nm, and 622 nm, corresponding to sizes of the embedded QDs with the diameters of 8.4 nm, 9.0 nm, and 9.8 nm respectively. The optimal thickness of the quantum dot layers needed for light emission is characterized using atomic force microscopy: for 8.4 nm QDs, the value is 33 nm (± 5 nm) or ~4 ML (monolayers). Larger turn on voltages were measured (2, 4 and 5 V) for the smaller average particle diameters (9.8 nm, 9.0 nm and 8.4 nm, respectively). The mixture ratio of Zn and Sn was optimized (40% Zn and 25% Sn) to maintain proper hole-electron recombination at the QD layer and avoid the yellowish-white emission from ZnO/SnO2.

  7. 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.

  8. 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.

  9. A fully validated GC-TOF-MS method for the quantification of fatty acids revealed alterations in the metabolic profile of fatty acids after smoking cessation.

    PubMed

    Goettel, Michael; Niessner, Reinhard; Pluym, Nikola; Scherer, Gerhard; Scherer, Max

    2017-01-15

    We developed and validated an efficient and robust method for the simultaneous quantification of 44 fatty acid species in human plasma via GC-TOF-MS. The method is characterized by its robustness, accuracy and precision covering a wide range of fatty acid species with various saturation degrees including short chain fatty acids (beginning with FA 4:0) and long chain fatty acids (up to FA 32:0). The fatty acids were methylated prior to analyses and subsequently detected as fatty acid methyl esters by means of GC-TOF-MS. A highly substituted polar column allowed the separation of geometrical and positional isomers of fatty acid species. The method was applied to plasma samples of a strictly diet controlled clinical smoking cessation study including 39 smokers followed over the course of three months after having quit. Statistical significant alterations within the fatty acid profile were observed when comparing the baseline (subjects still smoking) with one week, one month and three months of smoking cessation. After 3 months of smoking cessation, a partial recovery of alterations in the fatty acid profile evoked by smoking was observed. In conclusion, the developed fatty acid profiling method using GC-TOF-MS has proven as a reliable tool for the quantitative determination of 44 individual fatty acid species within clinical studies.

  10. Quantum dot-based quantitative immunofluorescence detection and spectrum analysis of epidermal growth factor receptor in breast cancer tissue arrays

    PubMed Central

    Yang, Xue-Qin; Chen, Chuang; Peng, Chun-Wei; Hou, Jin-Xuan; Liu, Shao-Ping; Qi, Chu-Bo; Gong, Yi-Ping; Zhu, Xiao-Bo; Pang, Dai-Wen; Li, Yan

    2011-01-01

    Background The epidermal growth factor receptor (EGFR) is a promising therapeutic target in cancer, but its clinical value in breast cancer remains controversial. Our previous studies have found that quantitative analysis of biomarkers with quantum dot-based nanotechnology had better detection performance than conventional immunohistochemistry. The present study was undertaken to investigate the prognostic value of EGFR in breast cancer using quantum dot-based quantitative spectral analysis. Methods EGFR expression in 65 breast cancer specimens was detected by immunohistochemistry and quantum dot-immunohistochemistry, and comparisons were made between the two methods. EGFR expression in tissue microarrays of 240 breast cancer patients was then detected by quantum dot-immunohistochemistry and spectral analysis. The prognostic value of EGFR immunofluorescence area (EGFR area) for five-year recurrence-free survival was investigated. Results The same antigen localization, high correlation of staining rates (r = 0.914), and high agreement of measurement (κ = 0.848) of EGFR expression in breast cancer were found by quantum dot-immunohistochemistry and immunohistochemistry. The EGFR area showed significant differences by tumor grade, lymph node status, HER2 status, and hormone receptor status (all P < 0.05). Patients in the large EGFR area (≥30.51) group had a significantly higher five-year recurrence rate (47.2% versus 27.4%, P = 0.002) and worse five-year recurrence-free survival (log-rank test, P = 0.0015) than those in the small EGFR area (<30.51) group. In the subgroups, EGFR area was an independent prognosticator in the HER2-positive and lymph node-positive subgroups. Conclusion Quantum dot-based quantitative detection demonstrates the prognostic value of EGFR area in the HER2-positive and lymph node-positive subgroups of invasive breast cancer. PMID:22072864

  11. 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

  12. Dystrophin quantification

    PubMed Central

    Anthony, Karen; Arechavala-Gomeza, Virginia; Taylor, Laura E.; Vulin, Adeline; Kaminoh, Yuuki; Torelli, Silvia; Feng, Lucy; Janghra, Narinder; Bonne, Gisèle; Beuvin, Maud; Barresi, Rita; Henderson, Matt; Laval, Steven; Lourbakos, Afrodite; Campion, Giles; Straub, Volker; Voit, Thomas; Sewry, Caroline A.; Morgan, Jennifer E.; Flanigan, Kevin M.

    2014-01-01

    Objective: We formed a multi-institution collaboration in order to compare dystrophin quantification methods, reach a consensus on the most reliable method, and report its biological significance in the context of clinical trials. Methods: Five laboratories with expertise in dystrophin quantification performed a data-driven comparative analysis of a single reference set of normal and dystrophinopathy muscle biopsies using quantitative immunohistochemistry and Western blotting. We developed standardized protocols and assessed inter- and intralaboratory variability over a wide range of dystrophin expression levels. Results: Results from the different laboratories were highly concordant with minimal inter- and intralaboratory variability, particularly with quantitative immunohistochemistry. There was a good level of agreement between data generated by immunohistochemistry and Western blotting, although immunohistochemistry was more sensitive. Furthermore, mean dystrophin levels determined by alternative quantitative immunohistochemistry methods were highly comparable. Conclusions: Considering the biological function of dystrophin at the sarcolemma, our data indicate that the combined use of quantitative immunohistochemistry and Western blotting are reliable biochemical outcome measures for Duchenne muscular dystrophy clinical trials, and that standardized protocols can be comparable between competent laboratories. The methodology validated in our study will facilitate the development of experimental therapies focused on dystrophin production and their regulatory approval. PMID:25355828

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

    PubMed

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

    2016-12-01

    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 ( PSS) hole injection layer (HIL). By varying the concentration and dimension of Au nanoparticle (NP) dopants in 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. 80 % enhancement of efficency of quantum dot-based light-emitting diodes with gold nanoparticle doped hole-injection-layer.

  14. Nano-LC-MS/MS for Quantification of Lyso-Gb3 and Its Analogues Reveals a Useful Biomarker for Fabry Disease.

    PubMed

    Sueoka, Hideaki; Ichihara, Junji; Tsukimura, Takahiro; Togawa, Tadayasu; Sakuraba, Hitoshi

    2015-01-01

    Biomarkers useful for diagnosis and evaluation of treatment for patients with Fabry disease are urgently needed. Recently, plasma globotriaosylsphingosine (lyso-Gb3) and lyso-Gb3-related analogues have attracted attention as promising biomarkers of Fabry disease. However, the plasma concentrations of lyso-Gb3 and its analogues are extremely low or below the detection limits in some Fabry patients as well as in healthy subjects. In this paper, we introduce the novel application of a nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) system to the measurement of lyso-Gb3 and its analogues in plasma. Nano-LC-MS/MS requires smaller amounts of samples and is more sensitive than conventional techniques. Using this method, we measured the plasma concentrations of lyso-Gb3 and its analogues in 40 healthy subjects, 5 functional variants (males with E66Q), and various Fabry patients (9 classic Fabry males/9 mutations; 7 later-onset Fabry males/5 mutations; and 10 Fabry females/9 mutations). The results revealed that the mean lyso-Gb3 and lyso-Gb3(-2) concentrations in all the Fabry patient subgroups were statistically higher, especially in the classic Fabry males, than those in the functional variants and healthy subjects. The plasma concentrations of lyso-Gb3 and its analogues in healthy subjects, functional variants, and some Fabry patients with specific mutations (R112H and M296I) that cannot be established by conventional techniques were successfully determined by means of nano-LC-MS/MS. The lyso-Gb3 and lyso-Gb3(-2) concentrations in male patients with these mutations were lower than those in most Fabry patients having other mutations, but higher than those in the functional variants and healthy subjects. This new method is expected to be useful for sensitive determination of the plasma concentrations of lyso-Gb3 and its analogues. This study also revealed that not only lyso-Gb3 but also lyso-Gb3(-2) in plasma is a useful biomarker for the diagnosis of

  15. Nano-LC-MS/MS for Quantification of Lyso-Gb3 and Its Analogues Reveals a Useful Biomarker for Fabry Disease

    PubMed Central

    Sueoka, Hideaki; Ichihara, Junji; Tsukimura, Takahiro; Togawa, Tadayasu; Sakuraba, Hitoshi

    2015-01-01

    Biomarkers useful for diagnosis and evaluation of treatment for patients with Fabry disease are urgently needed. Recently, plasma globotriaosylsphingosine (lyso-Gb3) and lyso-Gb3-related analogues have attracted attention as promising biomarkers of Fabry disease. However, the plasma concentrations of lyso-Gb3 and its analogues are extremely low or below the detection limits in some Fabry patients as well as in healthy subjects. In this paper, we introduce the novel application of a nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) system to the measurement of lyso-Gb3 and its analogues in plasma. Nano-LC-MS/MS requires smaller amounts of samples and is more sensitive than conventional techniques. Using this method, we measured the plasma concentrations of lyso-Gb3 and its analogues in 40 healthy subjects, 5 functional variants (males with E66Q), and various Fabry patients (9 classic Fabry males/9 mutations; 7 later-onset Fabry males/5 mutations; and 10 Fabry females/9 mutations). The results revealed that the mean lyso-Gb3 and lyso-Gb3(-2) concentrations in all the Fabry patient subgroups were statistically higher, especially in the classic Fabry males, than those in the functional variants and healthy subjects. The plasma concentrations of lyso-Gb3 and its analogues in healthy subjects, functional variants, and some Fabry patients with specific mutations (R112H and M296I) that cannot be established by conventional techniques were successfully determined by means of nano-LC-MS/MS. The lyso-Gb3 and lyso-Gb3(-2) concentrations in male patients with these mutations were lower than those in most Fabry patients having other mutations, but higher than those in the functional variants and healthy subjects. This new method is expected to be useful for sensitive determination of the plasma concentrations of lyso-Gb3 and its analogues. This study also revealed that not only lyso-Gb3 but also lyso-Gb3(-2) in plasma is a useful biomarker for the diagnosis of

  16. 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.

  17. Excitability in optically injected semiconductor lasers: Contrasting quantum- well- and quantum-dot-based devices

    NASA Astrophysics Data System (ADS)

    Kelleher, B.; Bonatto, C.; Huyet, G.; Hegarty, S. P.

    2011-02-01

    Excitability is a generic prediction for an optically injected semiconductor laser. However, the details of the phenomenon differ depending on the type of device in question. For quantum-well lasers very complicated multipulse trajectories can be found, while for quantum-dot lasers the situation is much simpler. Experimental observations show the marked differences in the pulse shapes while theoretical considerations reveal the underlying mechanism responsible for the contrast, identifying the increased stability of quantum-dot lasers to perturbations as the root.

  18. Excitability in optically injected semiconductor lasers: contrasting quantum-well- and quantum-dot-based devices.

    PubMed

    Kelleher, B; Bonatto, C; Huyet, G; Hegarty, S P

    2011-02-01

    Excitability is a generic prediction for an optically injected semiconductor laser. However, the details of the phenomenon differ depending on the type of device in question. For quantum-well lasers very complicated multipulse trajectories can be found, while for quantum-dot lasers the situation is much simpler. Experimental observations show the marked differences in the pulse shapes while theoretical considerations reveal the underlying mechanism responsible for the contrast, identifying the increased stability of quantum-dot lasers to perturbations as the root.

  19. 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.

  20. 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.

  1. A graphene quantum dot-based FRET system for nuclear-targeted and real-time monitoring of drug delivery.

    PubMed

    Chen, Hui; Wang, Zhuyuan; Zong, Shenfei; Chen, Peng; Zhu, Dan; Wu, Lei; Cui, Yiping

    2015-10-07

    A graphene quantum dot-based FRET system is demonstrated for nuclear-targeted drug delivery, which allows for real-time monitoring of the drug release process through FRET signals. In such a system, graphene quantum dots (GQDs) simultaneously serve as the carriers of drugs and donors of FRET pairs. Additionally, a peptide TAT as the nuclear localization signal is conjugated to GQDs, which facilitates the transportation of the delivery system to the nucleus. We have demonstrated that: (a) both the conjugated TAT and small size of GQDs contribute to targeting the nucleus, which results in a significantly enhanced intranuclear accumulation of drugs; (b) FRET signals being extremely sensitive to the distance between donors and acceptors are capable of real-time monitoring of the separation process of drugs and GQDs, which is more versatile in tracking the drug release dynamics. Our strategy for the assembly of a FRET-based drug delivery system may be unique and universal for monitoring the dynamic release process. This study may give more exciting new opportunities for improving the therapeutic efficacy and tracking precision.

  2. Multiplexed detection of influenza A virus subtype H5 and H9 via quantum dot-based immunoassay.

    PubMed

    Wu, Feng; Yuan, Hang; Zhou, Changhua; Mao, Mao; Liu, Qian; Shen, Huaibin; Cen, Yu; Qin, Zhifeng; Ma, Lan; Song Li, Ling

    2016-03-15

    A quantum dot-based lateral flow immunoassay system (QD-LFIAS) was developed to simultaneously detect both influenza A virus subtypes H5 and H9. Water-soluble carboxyl-functionalized quantum dots (QDs) were used as fluorescent tags. The QDs were conjugated to specific influenza A virus subtype H5 and H9 antibodies via an amide bond. When influenza A virus subtype H5 or H9 was added to the QD-LFIAS, the QD-labeled antibodies specifically bound to the H5 or H9 subtype viruses and were then captured by the coating antibodies at test line 1 or 2 to form a sandwich complex. This complex produced a bright fluorescent band in response to 365 nm ultraviolet excitation. The intensity of fluorescence can be detected using an inexpensive, low-maintenance instrument, and the virus concentration directly correlates with the fluorescence intensity. The detection limit of the QD-LFIAS for influenza A virus subtype H5 was 0.016 HAU, and the detection limit of the QD-LFIAS for influenza A virus subtype H9 was 0.25 HAU. The specificity and reproducibility were good. The simple analysis step and objective results that can be obtained within 15 min indicate that this QD-LFIAS is a highly efficient test that can be used to monitor and prevent both Influenza A virus subtypes H5 and H9.

  3. Silicon Quantum Dot-Based Fluorescence Turn-On Metal Ion Sensors in Live Cells.

    PubMed

    Dhenadhayalan, Namasivayam; Lee, Hsin-Lung; Yadav, Kanchan; Lin, King-Chuen; Lin, Yih-Tyng; Chang, A H H

    2016-09-14

    Multiple sensor systems are designed by varying aza-crown ether moiety in silicon quantum dots (SiQDs) for detecting individual Mg(2+), Ca(2+), and Mn(2+) metal ions with significant selectivity and sensitivity. The detection limit of Mg(2+), Ca(2+), and Mn(2+) can reach 1.81, 3.15, and 0.47 μM, respectively. Upon excitation of the SiQDs which are coordinated with aza-crown ethers, the photoinduced electron transfer (PET) takes place from aza-crown ether moiety to the valence band of SiQDs core such that the reduced probability of electron-hole recombination may diminish the subsequent fluorescence. The fluorescence suppression caused by such PET effect will be relieved after selective metal ion is added. The charge-electron binding force between the metal ion and aza-crown ether hinders the PET and thereby restores the fluorescence of SiQDs. The design of sensor system is based on the fluorescence "turn-on" of SiQDs while in search of the appropriate metal ion. For practical application, the sensing capabilities of metal ions in the live cells are performed and the confocal image results reveal their promising applicability as an effective and nontoxic metal ion sensor.

  4. 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.

  5. Statistical image quantification toward optimal scan fusion and change quantification

    NASA Astrophysics Data System (ADS)

    Potesil, Vaclav; Zhou, Xiang Sean

    2007-03-01

    Recent advance of imaging technology has brought new challenges and opportunities for automatic and quantitative analysis of medical images. With broader accessibility of more imaging modalities for more patients, fusion of modalities/scans from one time point and longitudinal analysis of changes across time points have become the two most critical differentiators to support more informed, more reliable and more reproducible diagnosis and therapy decisions. Unfortunately, scan fusion and longitudinal analysis are both inherently plagued with increased levels of statistical errors. A lack of comprehensive analysis by imaging scientists and a lack of full awareness by physicians pose potential risks in clinical practice. In this paper, we discuss several key error factors affecting imaging quantification, studying their interactions, and introducing a simulation strategy to establish general error bounds for change quantification across time. We quantitatively show that image resolution, voxel anisotropy, lesion size, eccentricity, and orientation are all contributing factors to quantification error; and there is an intricate relationship between voxel anisotropy and lesion shape in affecting quantification error. Specifically, when two or more scans are to be fused at feature level, optimal linear fusion analysis reveals that scans with voxel anisotropy aligned with lesion elongation should receive a higher weight than other scans. As a result of such optimal linear fusion, we will achieve a lower variance than naïve averaging. Simulated experiments are used to validate theoretical predictions. Future work based on the proposed simulation methods may lead to general guidelines and error lower bounds for quantitative image analysis and change detection.

  6. Quantification of endogenous retinoids.

    PubMed

    Kane, Maureen A; Napoli, Joseph L

    2010-01-01

    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.

  7. In vivo MRS metabolite quantification using genetic optimization

    NASA Astrophysics Data System (ADS)

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

    2011-11-01

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

  8. Trap-Assisted Transport and Non-Uniform Charge Distribution in Sulfur-Rich PbS Colloidal Quantum Dot-based Solar Cells with Selective Contacts.

    PubMed

    Malgras, Victor; Zhang, Guanran; Nattestad, Andrew; Clarke, Tracey M; Mozer, Attila J; Yamauchi, Yusuke; Kim, Jung Ho

    2015-12-09

    This study reports evidence of dispersive transport in planar PbS colloidal quantum dot heterojunction-based devices as well as the effect of incorporating a MoO3 hole selective layer on the charge extraction behavior. Steady state and transient characterization techniques are employed to determine the complex recombination processes involved in such devices. The addition of a selective contact drastically improves the device efficiency up to 3.15% (especially due to increased photocurrent and decreased series resistance) and extends the overall charge lifetime by suppressing the main first-order recombination pathway observed in device without MoO3. The lifetime and mobility calculated for our sulfur-rich PbS-based devices are similar to previously reported values in lead-rich quantum dots-based solar cells. Nevertheless, strong Shockley-Read-Hall mechanisms appear to keep restricting charge transport, as the equilibrium voltage takes more than 1 ms to be established.

  9. A non-invasive specimen collection method and a novel simian foamy virus (SFV) DNA quantification assay in New World primates reveal aspects of tissue tropism and improved SFV detection.

    PubMed

    Muniz, Cláudia P; Zheng, HaoQiang; Jia, Hongwei; Cavalcante, Liliane T F; Augusto, Anderson M; Fedullo, Luiz P; Pissinatti, Alcides; Soares, Marcelo A; Switzer, William M; Santos, André F

    2017-01-01

    Simian foamy viruses (SFVs) co-evolved with a wide range of Old World and New World primates (OWPs and NWPs, respectively) and occasionally transmit to humans. Previous studies of OWPs showed that the predominant site of SFV replication is the oral mucosa. However, very little is known about SFV viral loads (VLs) in the oral mucosa or blood of NWPs. NWPs have smaller body sizes, limiting collection of sufficient whole blood volumes to molecularly detect and quantify SFV. Our study evaluated the use of noninvasively collected buccal swabs to detect NWP SFV compared with detection in blood using a new NWP SFV quantitative PCR (qPCR) assay. Buccal and blood samples were collected from 107 captive NWPs in Brazil comprising eleven distinct genera at the Primate Center of Rio de Janeiro (n = 58) and at Fundação Jardim Zoológico da Cidade do Rio Janeiro (n = 49). NWP SFV western blot (WB) testing was performed on a subset of animals for comparison with PCR results. The qPCR assay was validated using distinct SFV polymerase sequences from seven NWP genera (Callithrix, Sapajus, Saimiri, Ateles, Alouatta, Cacajao and Pithecia). Assay sensitivity was 20 copies/106 cells, detectable in 90% of replicates. SFV DNA VLs were higher in buccal swabs (5 log copies/106 cells) compared to peripheral blood mononuclear cells (PBMCs) (3 log copies/106 cells). The qPCR assay was also more sensitive than nested PCR for detection of NWP SFV infection and identified an additional 27 SFV-infected monkeys of which 18 (90%) were WB-positive and three that were WB-negative. We show the utility of using both blood and buccal swabs and our new qPCR assay for detection and quantification of diverse NWP SFV, which will assist a better understanding of the epidemiology of SFV in NWPs and any potential zoonotic infection risk for humans exposed to NWPs.

  10. Quantification of micro stickies

    Treesearch

    Mahendra. Doshi; Jeffrey. Dyer; Salman. Aziz; Kristine. Jackson; Said M. Abubakr

    1997-01-01

    The objective of this project was to compare the different methods for the quantification of micro stickies. The hydrophobic materials investigated in this project for the collection of micro stickies were Microfoam* (polypropylene packing material), low density polyethylene film (LDPE), high density polyethylene (HDPE; a flat piece from a square plastic bottle), paper...

  11. 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.

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

    PubMed

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

    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). 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. 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). QD-IIQAS was an easy and accurate method for detecting and assessing TOP2A. The TOP2A expression was an independent prognostic indicator of 5-DFS in TNBC. Our study provides a good

  13. 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

  14. Quantification and imaging of HER2 protein using nanocrystals conjugated with single-domain antibodies

    NASA Astrophysics Data System (ADS)

    Glukhov, S.; Berestovoy, M.; Chames, P.; Baty, D.; Nabiev, I.; Sukhanova, A.

    2017-01-01

    This study dealt with quantification and imaging of human epidermal growth factor receptor 2 (HER2), an important prognostic marker for cancer diagnosis and treatment, using specific quantum-dot-based conjugates. Fluorescent inorganic nanocrystals or quantum dots (QDs) are extremely highly resistant to photobleaching and have a high emission quantum yield and a continuous range of emission spectra, from the ultraviolet to the infrared regions. Ultrasmall nanoprobes consisting of highly affine anti-HER2 single-domain antibodies (sdAbs or "nanobodies") conjugated with QDs in a strictly oriented manner have been designed. QDs with a fluorescence peak maxima at wavelengths of 562 nm, 569 nm, 570 nm or in the near-infrared region were used. Here, we present our results of ISA quantification of HER2 protein, in situ imaging of HER2 protein on the surface of HER2-positive SK-BR-3 cells in immunohistochemical experiments, and counting of stained with anti-HER2 conjugates HER2-positive SK-BR-3 cells in their mixture with unstained cells of the same culture in flow cytometry experiments. The data demonstrate that the anti-HER2 QD-sdAb conjugates obtained are highly specific and sensitive and could be used in numerous applications for advanced integrated diagnosis.

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

    DOE PAGES

    Liu, Wenyan; Zhang, Yu; Ruan, Cheng; ...

    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

  16. Carrier transport and emission efficiency in InGaN quantum-dot based light-emitting diodes.

    PubMed

    Barettin, Daniele; Auf der Maur, Matthias; di Carlo, Aldo; Pecchia, Alessandro; Tsatsulnikov, Andrei F; Lundin, Wsevolod V; Sakharov, Alexei V; Nikolaev, Andrei E; Korytov, Maxim; Cherkashin, Nikolay; Hÿtch, Martin J; Karpov, Sergey Yu

    2017-07-07

    We present a study of blue III-nitride light-emitting diodes (LEDs) with multiple quantum well (MQW) and quantum dot (QD) active regions (ARs), comparing experimental and theoretical results. The LED samples were grown by metalorganic vapor phase epitaxy, utilizing growth interruption in the hydrogen/nitrogen atmosphere and variable reactor pressure to control the AR microstructure. Realistic configuration of the QD AR implied in simulations was directly extracted from HRTEM characterization of the grown QD-based structures. Multi-scale 2D simulations of the carrier transport inside the multiple QD AR have revealed a non-trivial pathway for carrier injection into the dots. Electrons and holes are found to penetrate deep into the multi-layer AR through the gaps between individual QDs and get into the dots via their side edges rather than via top and bottom interfaces. This enables a more homogeneous carrier distribution among the dots situated in different layers than among the laterally uniform quantum well (QWs) in the MQW AR. As a result, a lower turn-on voltage is predicted for QD-based LEDs, as compared to MQW ones. Simulations did not show any remarkable difference in the efficiencies of the MQW and QD-based LEDs, if the same recombination coefficients are utilized, i.e. a similar crystal quality of both types of LED structures is assumed. Measurements of the current-voltage characteristics of LEDs with both kinds of the AR have shown their close similarity, in contrast to theoretical predictions. This implies the conventional assumption of laterally uniform QWs not to be likely an adequate approximation for the carrier transport in MQW LED structures. Optical characterization of MQW and QD-based LEDs has demonstrated that the later ones exhibit a higher efficiency, which could be attributed to better crystal quality of the grown QD-based structures. The difference in the crystal quality explains the recently observed correlation between the growth pressure of

  17. Carrier transport and emission efficiency in InGaN quantum-dot based light-emitting diodes

    NASA Astrophysics Data System (ADS)

    Barettin, Daniele; Auf der Maur, Matthias; di Carlo, Aldo; Pecchia, Alessandro; Tsatsulnikov, Andrei F.; Lundin, Wsevolod V.; Sakharov, Alexei V.; Nikolaev, Andrei E.; Korytov, Maxim; Cherkashin, Nikolay; Hÿtch, Martin J.; Karpov, Sergey Yu

    2017-07-01

    We present a study of blue III-nitride light-emitting diodes (LEDs) with multiple quantum well (MQW) and quantum dot (QD) active regions (ARs), comparing experimental and theoretical results. The LED samples were grown by metalorganic vapor phase epitaxy, utilizing growth interruption in the hydrogen/nitrogen atmosphere and variable reactor pressure to control the AR microstructure. Realistic configuration of the QD AR implied in simulations was directly extracted from HRTEM characterization of the grown QD-based structures. Multi-scale 2D simulations of the carrier transport inside the multiple QD AR have revealed a non-trivial pathway for carrier injection into the dots. Electrons and holes are found to penetrate deep into the multi-layer AR through the gaps between individual QDs and get into the dots via their side edges rather than via top and bottom interfaces. This enables a more homogeneous carrier distribution among the dots situated in different layers than among the laterally uniform quantum well (QWs) in the MQW AR. As a result, a lower turn-on voltage is predicted for QD-based LEDs, as compared to MQW ones. Simulations did not show any remarkable difference in the efficiencies of the MQW and QD-based LEDs, if the same recombination coefficients are utilized, i.e. a similar crystal quality of both types of LED structures is assumed. Measurements of the current-voltage characteristics of LEDs with both kinds of the AR have shown their close similarity, in contrast to theoretical predictions. This implies the conventional assumption of laterally uniform QWs not to be likely an adequate approximation for the carrier transport in MQW LED structures. Optical characterization of MQW and QD-based LEDs has demonstrated that the later ones exhibit a higher efficiency, which could be attributed to better crystal quality of the grown QD-based structures. The difference in the crystal quality explains the recently observed correlation between the growth pressure of

  18. Detection of prostate stem cell antigen expression in human prostate cancer using quantum-dot-based technology.

    PubMed

    Ruan, Yuan; Yu, Weimin; Cheng, Fan; Zhang, Xiaobin; Larré, Stéphane

    2012-01-01

    Quantum dots (QDs) are a new class of fluorescent labeling for biological and biomedical applications. In this study, we detected prostate stem cell antigen (PSCA) expression correlated with tumor grade and stage in human prostate cancer by QDs-based immunolabeling and conventional immunohistochemistry (IHC), and evaluated the sensitivity and stability of QDs-based immunolabeling in comparison with IHC. Our data revealed that increasing levels of PSCA expression accompanied advanced tumor grade (QDs labeling, r = 0.732, p < 0.001; IHC, r = 0.683, p < 0.001) and stage (QDs labeling, r = 0.514, p = 0.001; IHC, r = 0.432, p = 0.005), and the similar tendency was detected by the two methods. In addition, by comparison between the two methods, QDs labeling was consistent with IHC in detecting the expression of PSCA in human prostate tissue correlated with different pathological types (K = 0.845, p < 0.001). During the observation time, QDs exhibited superior stability. The intensity of QDs fluorescence remained stable for two weeks (p = 0.083) after conjugation to the PSCA protein, and nearly 93% of positive expression with their fluorescence still could be seen after four weeks.

  19. Advances in forensic DNA quantification: a review.

    PubMed

    Lee, Steven B; McCord, Bruce; Buel, Eric

    2014-11-01

    This review focuses upon a critical step in forensic biology: detection and quantification of human DNA from biological samples. Determination of the quantity and quality of human DNA extracted from biological evidence is important for several reasons. Firstly, depending on the source and extraction method, the quality (purity and length), and quantity of the resultant DNA extract can vary greatly. This affects the downstream method as the quantity of input DNA and its relative length can determine which genotyping procedure to use-standard short-tandem repeat (STR) typing, mini-STR typing or mitochondrial DNA sequencing. Secondly, because it is important in forensic analysis to preserve as much of the evidence as possible for retesting, it is important to determine the total DNA amount available prior to utilizing any destructive analytical method. Lastly, results from initial quantitative and qualitative evaluations permit a more informed interpretation of downstream analytical results. Newer quantitative techniques involving real-time PCR can reveal the presence of degraded DNA and PCR inhibitors, that provide potential reasons for poor genotyping results and may indicate methods to use for downstream typing success. In general, the more information available, the easier it is to interpret and process the sample resulting in a higher likelihood of successful DNA typing. The history of the development of quantitative methods has involved two main goals-improving precision of the analysis and increasing the information content of the result. This review covers advances in forensic DNA quantification methods and recent developments in RNA quantification.

  20. Semiautomatic quantification of angiogenesis.

    PubMed

    Boettcher, Markus; Gloe, Torsten; de Wit, Cor

    2010-07-01

    Angiogenesis is of major interest in developmental biology and cancer research. Different experimental approaches are available to study angiogenesis that have in common the need for microscopy, image acquisition, and analysis. Problems that are encountered hereby are the size of the structures, which requires generation of composite images and difficulties in quantifying angiogenic activity reliably and rapidly. Most graphic software packages lack some of the required functions for easy, semiautomatic quantification of angiogenesis and, consequently, multiple software packages or expensive programs have to be used to cover all necessary functions. A software package (AQuaL) to analyze angiogenic activity was developed using Java, which can be used platform-independently. It includes image acquisition relying on the Java Media Framework and an easy to use image alignment tool. Multiple overlapping images can be aligned and saved without limitations and loss of resolution into a composite image, which requires only the selection of a single point representing a characteristic structure in adjacent images. Angiogenic activity can be quantified in composite images semiautomatically by the assessment of the area overgrown by cells after filtering and image binarization. In addition, tagging of capillary-like structures allows quantification of their length and branching pattern. Both developed methods deliver reliable and correlating data as exemplified in the aortic ring angiogenesis assay. The developed software provides modular functions specifically targeted to quantify angiogenesis. Whereas the area measurement is time saving, length measurement provides additional information about the branching patterns, which is required for a qualitative differentiation of capillary growth. (c) 2010 Elsevier Inc. All rights reserved.

  1. 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.

  2. Quantum dot-based theranostics

    NASA Astrophysics Data System (ADS)

    Ho, Yi-Ping; Leong, Kam W.

    2010-01-01

    Luminescent semiconductor nanocrystals, also known as quantum dots (QDs), have advanced the fields of molecular diagnostics and nanotherapeutics. Much of the initial progress for QDs in biology and medicine has focused on developing new biosensing formats to push the limit of detection sensitivity. Nevertheless, QDs can be more than passive bio-probes or labels for biological imaging and cellular studies. The high surface-to-volume ratio of QDs enables the construction of a ``smart'' multifunctional nanoplatform, where the QDs serve not only as an imaging agent but also a nanoscaffold catering for therapeutic and diagnostic (theranostic) modalities. This mini review highlights the emerging applications of functionalized QDs as fluorescence contrast agents for imaging or as nanoscale vehicles for delivery of therapeutics, with special attention paid to the promise and challenges towards QD-based theranostics.

  3. 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.

  4. Wrappers, Aspects, Quantification and Events

    NASA Technical Reports Server (NTRS)

    Filman, Robert E.

    2005-01-01

    Talk overview: Object infrastructure framework (OIF). A system development to simplify building distributed applications by allowing independent implementation of multiple concern. Essence and state of AOP. Trinity. Quantification over events. Current work on a generalized AOP technology.

  5. Uncertainty Quantification in Aeroelasticity

    NASA Astrophysics Data System (ADS)

    Beran, Philip; Stanford, Bret; Schrock, Christopher

    2017-01-01

    Physical interactions between a fluid and structure, potentially manifested as self-sustained or divergent oscillations, can be sensitive to many parameters whose values are uncertain. Of interest here are aircraft aeroelastic interactions, which must be accounted for in aircraft certification and design. Deterministic prediction of these aeroelastic behaviors can be difficult owing to physical and computational complexity. New challenges are introduced when physical parameters and elements of the modeling process are uncertain. By viewing aeroelasticity through a nondeterministic prism, where key quantities are assumed stochastic, one may gain insights into how to reduce system uncertainty, increase system robustness, and maintain aeroelastic safety. This article reviews uncertainty quantification in aeroelasticity using traditional analytical techniques not reliant on computational fluid dynamics; compares and contrasts this work with emerging methods based on computational fluid dynamics, which target richer physics; and reviews the state of the art in aeroelastic optimization under uncertainty. Barriers to continued progress, for example, the so-called curse of dimensionality, are discussed.

  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. Micro-RNA quantification using DNA polymerase and pyrophosphate quantification.

    PubMed

    Yu, Hsiang-Ping; Hsiao, Yi-Ling; Pan, Hung-Yin; Huang, Chih-Hung; Hou, Shao-Yi

    2011-12-15

    A rapid quantification method for micro-RNA based on DNA polymerase activity and pyrophosphate quantification has been developed. The tested micro-RNA serves as the primer, unlike the DNA primer in all DNA sequencing methods, and the DNA probe serves as the template for DNA replication. After the DNA synthesis, the pyrophosphate detection and quantification indicate the existence and quantity of the tested miRNA. Five femtomoles of the synthetic RNA could be detected. In 20-100 μg RNA samples purified from SiHa cells, the measurement was done using the proposed assay in which hsa-miR-16 and hsa-miR-21 are 0.34 fmol/μg RNA and 0.71 fmol/μg RNA, respectively. This simple and inexpensive assay takes less than 5 min after total RNA purification and preparation. The quantification is not affected by the pre-miRNA which cannot serve as the primer for the DNA synthesis in this assay. This assay is general for the detection of the target RNA or DNA with a known matched DNA template probe, which could be widely used for detection of small RNA, messenger RNA, RNA viruses, and DNA. Therefore, the method could be widely used in RNA and DNA assays.

  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. Absolute quantification of myocardial blood flow.

    PubMed

    Yoshinaga, Keiichiro; Manabe, Osamu; Tamaki, Nagara

    2016-07-21

    With the increasing availability of positron emission tomography (PET) myocardial perfusion imaging, the absolute quantification of myocardial blood flow (MBF) has become popular in clinical settings. Quantitative MBF provides an important additional diagnostic or prognostic information over conventional visual assessment. The success of MBF quantification using PET/computed tomography (CT) has increased the demand for this quantitative diagnostic approach to be more accessible. In this regard, MBF quantification approaches have been developed using several other diagnostic imaging modalities including single-photon emission computed tomography, CT, and cardiac magnetic resonance. This review will address the clinical aspects of PET MBF quantification and the new approaches to MBF quantification.

  11. MODEL VALIDATION AND UNCERTAINTY QUANTIFICATION.

    SciTech Connect

    Hemez, F.M.; Doebling, S.W.

    2000-10-01

    This session offers an open forum to discuss issues and directions of research in the areas of model updating, predictive quality of computer simulations, model validation and uncertainty quantification. Technical presentations review the state-of-the-art in nonlinear dynamics and model validation for structural dynamics. A panel discussion introduces the discussion on technology needs, future trends and challenges ahead with an emphasis placed on soliciting participation of the audience, One of the goals is to show, through invited contributions, how other scientific communities are approaching and solving difficulties similar to those encountered in structural dynamics. The session also serves the purpose of presenting the on-going organization of technical meetings sponsored by the U.S. Department of Energy and dedicated to health monitoring, damage prognosis, model validation and uncertainty quantification in engineering applications. The session is part of the SD-2000 Forum, a forum to identify research trends, funding opportunities and to discuss the future of structural dynamics.

  12. Uncertainty Quantification for Airfoil Icing

    NASA Astrophysics Data System (ADS)

    DeGennaro, Anthony Matteo

    Ensuring the safety of airplane flight in icing conditions is an important and active arena of research in the aerospace community. Notwithstanding the research, development, and legislation aimed at certifying airplanes for safe operation, an analysis of the effects of icing uncertainties on certification quantities of interest is generally lacking. The central objective of this thesis is to examine and analyze problems in airfoil ice accretion from the standpoint of uncertainty quantification. We focus on three distinct areas: user-informed, data-driven, and computational uncertainty quantification. In the user-informed approach to uncertainty quantification, we discuss important canonical icing classifications and show how these categories can be modeled using a few shape parameters. We then investigate the statistical effects of these parameters. In the data-driven approach, we build statistical models of airfoil ice shapes from databases of actual ice shapes, and quantify the effects of these parameters. Finally, in the computational approach, we investigate the effects of uncertainty in the physics of the ice accretion process, by perturbing the input to an in-house numerical ice accretion code that we develop in this thesis.

  13. 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.

  14. 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.

  15. Quantification of ethnic differences in facial profile.

    PubMed

    Sheridan, C S; Thomas, C D; Clement, J G

    1997-03-01

    The concept of facial aesthetics is becoming increasingly important and with the expanding application of orthodontic, orthognathic, plastic and reconstructive techniques to patients from continually diversifying ethnic backgrounds, it is timely that more elaborate methods for the evaluation of facial form are adopted. The aim of the present study was to further investigate the use of Fourier shape analysis in the quantification of facial profile and to investigate differences between racial groups. One hundred and twenty-two undergraduate dental students were photographed and surveyed for information pertaining to ethnic origin. Student's t-tests revealed significant differences (p < 0.05) in higher-order (fourth- and above) Fourier harmonics between male and female profiles, as well as between intervention and non-intervention groups. A comparison of multiple means test revealed significant differences (p < 0.05) in the third-order Fourier harmonic (vertex projection) between the Asian group and three other groups--Anglo-Celtic, Eastern European and Western European. Differences correlated with convexity in the lower third of the face, which was demonstrated by Fourier reconstruction.

  16. Experimental validation of 2D uncertainty quantification for DIC.

    SciTech Connect

    Reu, Phillip L.

    2010-06-01

    Because digital image correlation (DIC) has become such an important and standard tool in the toolbox of experimental mechanicists, a complete uncertainty quantification of the method is needed. It should be remembered that each DIC setup and series of images will have a unique uncertainty based on the calibration quality and the image and speckle quality of the analyzed images. Any pretest work done with a calibrated DIC stereo-rig to quantify the errors using known shapes and translations, while useful, do not necessarily reveal the uncertainty of a later test. This is particularly true with high-speed applications where actual test images are often less than ideal. Work has previously been completed on the mathematical underpinnings of DIC uncertainty quantification and is already published, this paper will present corresponding experimental work used to check the validity of the uncertainty equations.

  17. Hemispheric specialization in quantification processes.

    PubMed

    Pasini, M; Tessari, A

    2001-01-01

    Three experiments were carried out to study hemispheric specialization for subitizing (the rapid enumeration of small patterns) and counting (the serial quantification process based on some formal principles). The experiments consist of numerosity identification of dot patterns presented in one visual field, with a tachistoscopic technique, or eye movements monitored through glasses, and comparison between centrally presented dot patterns and lateralized tachistoscopically presented digits. Our experiments show left visual field advantage in the identification and comparison tasks in the subitizing range, whereas right visual field advantage has been found in the comparison task for the counting range.

  18. Damage quantification in confined ceramics

    SciTech Connect

    Xu Yueping; Espinosa, Horacio D.

    1998-07-10

    Impact recovery experiments on confined ceramic rods and multi-layer ceramic targets are performed for failure identification and damage quantification. In-material stress measurements with manganin gauges and velocity histories are recorded with interferometric techniques. Observations on recovered samples are made through Optical Microscopy. Microscopy results show that microcracking is the dominant failure mode in ceramic rods and multi-layer ceramic targets. Macrocrack surface per unit area is estimated on various sections along several orientations. Correlation between dynamic loading and crack density is established. Moreover, multiple penetrator defeat is observed in ceramic targets recovered from penetration experiments.

  19. Quantum dots-based quantitative and in situ multiple imaging on ki67 and cytokeratin to improve ki67 assessment in breast cancer.

    PubMed

    Yuan, Jing Ping; Wang, Lin Wei; Qu, Ai Ping; Chen, Jia Mei; Xiang, Qing Ming; Chen, Chuang; Sun, Sheng-Rong; Pang, Dai-Wen; Liu, Juan; Li, Yan

    2015-01-01

    As a marker for tumor cell proliferation, Ki67 has important impacts on breast cancer (BC) prognosis. Although immunohistochemical staining is the current standard method, variations in analytical practice make it difficult for pathologists to manually measure Ki67 index. This study was to develop a fluorescent spectrum-based quantitative analysis of Ki67 expression by quantum-dots (QDs) multiple imaging technique. A QDs-based in situ multiple fluorescent imaging method was developed, which stained nuclear Ki67 as red signal and cytoplasmic cytokeratin (CK) as green signal. Both Ki67 and CK signals were automatically separated and quantified by professional spectrum analysis software. This technique was applied to tissue microarrays from 240 BC patients. Both Ki67 and CK values, and Ki67/CK ratio were obtained for each patient, and their prognostic value on 5-year disease free survival was assessed. This method simultaneously stains nuclear Ki67 and cytoplasmic CK with clear signal contrast, making it easy for signal separation and quantification. The total fluorescent signal intensities of both Ki67 sum and CK sum were obtained, and Ki67/CK ratio calculated. Ki67 sum and Ki67/CK ratio were each attributed into two grades by X-tile software based on the best P value principle. Multivariate analysis showed Ki67 grade (P = 0.047) and Ki67/CK grade (P = 0.004) were independent prognostic factors. Furthermore, area under curve (AUC) of ROC analysis for Ki67/CK grade (AUC: 0.683, 95%CI: 0.613-0.752) was higher than Ki67 grade (AUC: 0.665, 95%CI: 0.596-0.734) and HER-2 gene (AUC: 0.586, 95%CI: 0.510-0.661), but lower than N stage (AUC: 0.760, 95%CI: 0.696-0.823) and histological grade (AUC: 0.756, 95%CI: 0.692-0.820) on predicting the risk for recurrence. A QDs-based quantitative and in situ multiple imaging on Ki67 and CK was developed to improve Ki67 assessment in BC, and Ki67/CK grade had better performance than Ki67 grade in predicting prognosis.

  20. Fuller Revealed

    NASA Image and Video Library

    2015-03-16

    MESSENGER's low-altitude campaign has enabled imaging of Fuller crater (named after American architect Buckminster Fuller) in greater detail than previously possible. The top left panel shows an image of Fuller, with the crater rim outlined in pink and the edge of a low-altitude broadband MDIS image in green. The large panel applies a different stretch to the same MDIS broadband image in the first panel, revealing details of the shadowed surface inside Fuller! In particular, as highlighted with yellow arrows in the bottom left panel, the image reveals a region inside Fuller that is lower in reflectance. The edge of the low-reflectance region has a sharp and well-defined boundary, even when imaged at 46 m/pixel, suggesting that the low-reflectance material is sufficiently young to have preserved a sharp boundary against lateral mixing by impact cratering. Models for surface and near-surface temperature within Fuller crater predict a region that is sufficiently cold to host long-lived water ice beneath the surface but too hot to support water ice at the surface. The low-reflectance region revealed in the images matches the thermal characteristics expected for a lag deposit of volatile, organic-rich material that overlies the water ice. http://photojournal.jpl.nasa.gov/catalog/PIA19244

  1. Quantification of wastewater sludge dewatering.

    PubMed

    Skinner, Samuel J; Studer, Lindsay J; Dixon, David R; Hillis, Peter; Rees, Catherine A; Wall, Rachael C; Cavalida, Raul G; Usher, Shane P; Stickland, Anthony D; Scales, Peter J

    2015-10-01

    Quantification and comparison of the dewatering characteristics of fifteen sewage sludges from a range of digestion scenarios are described. The method proposed uses laboratory dewatering measurements and integrity analysis of the extracted material properties. These properties were used as inputs into a model of filtration, the output of which provides the dewatering comparison. This method is shown to be necessary for quantification and comparison of dewaterability as the permeability and compressibility of the sludges varies by up to ten orders of magnitude in the range of solids concentration of interest to industry. This causes a high sensitivity of the dewaterability comparison to the starting concentration of laboratory tests, thus simple dewaterability comparison based on parameters such as the specific resistance to filtration is difficult. The new approach is demonstrated to be robust relative to traditional methods such as specific resistance to filtration analysis and has an in-built integrity check. Comparison of the quantified dewaterability of the fifteen sludges to the relative volatile solids content showed a very strong correlation in the volatile solids range from 40 to 80%. The data indicate that the volatile solids parameter is a strong indicator of the dewatering behaviour of sewage sludges. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. 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

  3. Assessment of cardiac fibrosis: a morphometric method comparison for collagen quantification.

    PubMed

    Schipke, Julia; Brandenberger, Christina; Rajces, Alexandra; Manninger, Martin; Alogna, Alessio; Post, Heiner; Mühlfeld, Christian

    2017-04-01

    Fibrotic remodeling of the heart is a frequent condition linked to various diseases and cardiac dysfunction. Collagen quantification is an important objective in cardiac fibrosis research; however, a variety of different histological methods are currently used that may differ in accuracy. Here, frequently applied collagen quantification techniques were compared. A porcine model of early stage heart failure with preserved ejection fraction was used as an example. Semiautomated threshold analyses were imprecise, mainly due to inclusion of noncollagen structures or failure to detect certain collagen deposits. In contrast, collagen assessment by automated image analysis and light microscopy (LM)-stereology was more sensitive. Depending on the quantification method, the amount of estimated collagen varied and influenced intergroup comparisons. PicroSirius Red, Masson's trichrome, and Azan staining protocols yielded similar results, whereas the measured collagen area increased with increasing section thickness. Whereas none of the LM-based methods showed significant differences between the groups, electron microscopy (EM)-stereology revealed a significant collagen increase between cardiomyocytes in the experimental group, but not at other localizations. In conclusion, in contrast to the staining protocol, section thickness and the quantification method being used directly influence the estimated collagen content and thus, possibly, intergroup comparisons. EM in combination with stereology is a precise and sensitive method for collagen quantification if certain prerequisites are considered. For subtle fibrotic alterations, consideration of collagen localization may be necessary. Among LM methods, LM-stereology and automated image analysis are appropriate to quantify fibrotic changes, the latter depending on careful control of algorithm and comparable section staining.NEW & NOTEWORTHY Direct comparison of frequently applied histological fibrosis assessment techniques

  4. 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

  5. Consistency of flow quantifications in tridirectional phase-contrast MRI

    NASA Astrophysics Data System (ADS)

    Unterhinninghofen, R.; Ley, S.; Dillmann, R.

    2009-02-01

    Tridirectionally encoded phase-contrast MRI is a technique to non-invasively acquire time-resolved velocity vector fields of blood flow. These may not only be used to analyze pathological flow patterns, but also to quantify flow at arbitrary positions within the acquired volume. In this paper we examine the validity of this approach by analyzing the consistency of related quantifications instead of comparing it with an external reference measurement. Datasets of the thoracic aorta were acquired from 6 pigs, 1 healthy volunteer and 3 patients with artificial aortic valves. Using in-house software an elliptical flow quantification plane was placed manually at 6 positions along the descending aorta where it was rotated to 5 different angles. For each configuration flow was computed based on the original data and data that had been corrected for phase offsets. Results reveal that quantifications are more dependent on changes in position than on changes in angle. Phase offset correction considerably reduces this dependency. Overall consistency is good with a maximum variation coefficient of 9.9% and a mean variation coefficient of 7.2%.

  6. Nuclear and mitochondrial DNA quantification of various forensic materials.

    PubMed

    Andréasson, H; Nilsson, M; Budowle, B; Lundberg, H; Allen, M

    2006-12-01

    Due to the different types and quality of forensic evidence materials, their DNA content can vary substantially, and particularly low quantities can impact the results in an identification analysis. In this study, the quantity of mitochondrial and nuclear DNA was determined in a variety of materials using a previously described real-time PCR method. DNA quantification in the roots and distal sections of plucked and shed head hairs revealed large variations in DNA content particularly between the root and the shaft of plucked hairs. Also large intra- and inter-individual variations were found among hairs. In addition, DNA content was estimated in samples collected from fingerprints and accessories. The quantification of DNA on various items also displayed large variations, with some materials containing large amounts of nuclear DNA while no detectable nuclear DNA and only limited amounts of mitochondrial DNA were seen in others. Using this sensitive real-time PCR quantification assay, a better understanding was obtained regarding DNA content and variation in commonly analysed forensic evidence materials and this may guide the forensic scientist as to the best molecular biology approach for analysing various forensic evidence materials.

  7. 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

  8. Classification and quantification of leaf curvature.

    PubMed

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

    2010-06-01

    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.

  9. 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

  10. Quantum-dot-based technology for sensitive and stable detection of prostate stem cell antigen expression in human transitional cell carcinoma.

    PubMed

    Cheng, Fan; Yu, Weimin; Zhang, Xiaobin; Ruan, Yuan

    2009-01-01

    Quantum dots (QDs) as a biological labeling material for medical applications need to be evaluated for the sensitivity and stability of their fluorescence. Comparison of QD-based immunolabeling and commonly used immunohistochemical staining in detecting the expression of prostate stem cell antigen (PSCA) in bladder tumor tissues revealed that the two methods had similar sensitivity in the differential display of PSCA expression correlated with tumor stage and grade (kappa=0.92, p<0.001). In addition, the intensity of QD fluorescence remained stable for at least 10 days after conjugation to the PSCA protein and nearly 96% of the positive expression in samples lasted for one month.

  11. 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

  12. 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

  13. Revealing Rembrandt

    PubMed Central

    Parker, Andrew J.

    2014-01-01

    The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI). Our results emphasized the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt's portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings. PMID:24795552

  14. Error models for uncertainty quantification

    NASA Astrophysics Data System (ADS)

    Josset, L.; Scheidt, C.; Lunati, I.

    2012-12-01

    In groundwater modeling, uncertainty on the permeability field leads to a stochastic description of the aquifer system, in which the quantities of interests (e.g., groundwater fluxes or contaminant concentrations) are considered as stochastic variables and described by their probability density functions (PDF) or by a finite number of quantiles. Uncertainty quantification is often evaluated using Monte-Carlo simulations, which employ a large number of realizations. As this leads to prohibitive computational costs, techniques have to be developed to keep the problem computationally tractable. The Distance-based Kernel Method (DKM) [1] limits the computational cost of the uncertainty quantification by reducing the stochastic space: first, the realizations are clustered based on the response of a proxy; then, the full model is solved only for a subset of realizations defined by the clustering and the quantiles are estimated from this limited number of realizations. Here, we present a slightly different strategy that employs an approximate model rather than a proxy: we use the Multiscale Finite Volume method (MsFV) [2,3] to compute an approximate solution for each realization, and to obtain a first assessment of the PDF. In this context, DKM is then used to identify a subset of realizations for which the exact model is solved and compared with the solution of the approximate model. This allows highlighting and correcting possible errors introduced by the approximate model, while keeping full statistical information on the ensemble of realizations. Here, we test several strategies to compute the model error, correct the approximate model and achieve an optimal PDF estimation. We present a case study in which we predict the breakthrough curve of an ideal tracer for an ensemble of realizations generated via Multiple Point Direct Sampling [4] with a training image obtained from a 2D section of the Herten permeability field [5]. [1] C. Scheidt and J. Caers, "Representing

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

    SciTech Connect

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

    2016-07-15

    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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Accessible quantification of multiparticle entanglement

    NASA Astrophysics Data System (ADS)

    Cianciaruso, Marco; Bromley, Thomas R.; Adesso, Gerardo

    2016-10-01

    Entanglement is a key ingredient for quantum technologies and a fundamental signature of quantumness in a broad range of phenomena encompassing many-body physics, thermodynamics, cosmology and life sciences. For arbitrary multiparticle systems, entanglement quantification typically involves nontrivial optimisation problems, and it may require demanding tomographical techniques. Here, we develop an experimentally feasible approach to the evaluation of geometric measures of multiparticle entanglement. Our framework provides analytical results for particular classes of mixed states of N qubits, and computable lower bounds to global, partial, or genuine multiparticle entanglement of any general state. For global and partial entanglement, useful bounds are obtained with minimum effort, requiring local measurements in just three settings for any N. For genuine entanglement, a number of measurements scaling linearly with N are required. We demonstrate the power of our approach to estimate and quantify different types of multiparticle entanglement in a variety of N-qubit states useful for quantum information processing and recently engineered in laboratories with quantum optics and trapped ion setups.

  1. 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.

  2. Precise quantification of nanoparticle internalization.

    PubMed

    Gottstein, Claudia; Wu, Guohui; Wong, Benjamin J; Zasadzinski, Joseph Anthony

    2013-06-25

    Nanoparticles have opened new exciting avenues for both diagnostic and therapeutic applications in human disease, and targeted nanoparticles are increasingly used as specific drug delivery vehicles. The precise quantification of nanoparticle internalization is of importance to measure the impact of physical and chemical properties on the uptake of nanoparticles into target cells or into cells responsible for rapid clearance. Internalization of nanoparticles has been measured by various techniques, but comparability of data between different laboratories is impeded by lack of a generally accepted standardized assay. Furthermore, the distinction between associated and internalized particles has been a challenge for many years, although this distinction is critical for most research questions. Previously used methods to verify intracellular location are typically not quantitative and do not lend themselves to high-throughput analysis. Here, we developed a mathematical model which integrates the data from high-throughput flow cytometry measurements with data from quantitative confocal microscopy. The generic method described here will be a useful tool in biomedical nanotechnology studies. The method was then applied to measure the impact of surface coatings of vesosomes on their internalization by cells of the reticuloendothelial system (RES). RES cells are responsible for rapid clearance of nanoparticles, and the resulting fast blood clearance is one of the major challenges in biomedical applications of nanoparticles. Coating of vesosomes with long chain polyethylene glycol showed a trend for lower internalization by RES cells.

  3. Absolute quantification by droplet digital PCR versus analog real-time PCR

    PubMed Central

    Hindson, Christopher M; Chevillet, John R; Briggs, Hilary A; Gallichotte, Emily N; Ruf, Ingrid K; Hindson, Benjamin J; Vessella, Robert L; Tewari, Muneesh

    2014-01-01

    Nanoliter-sized droplet technology paired with digital PCR (ddPCR) holds promise for highly precise, absolute nucleic acid quantification. Our comparison of microRNA quantification by ddPCR and real-time PCR revealed greater precision (coefficients of variation decreased by 37–86%) and improved day-to-day reproducibility (by a factor of seven) of ddPCR but with comparable sensitivity. When we applied ddPCR to serum microRNA biomarker analysis, this translated to superior diagnostic performance for identifying individuals with cancer. PMID:23995387

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

    PubMed

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

    2011-07-01

    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 and pixel-level (rather than cell-based) quantification methods. 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, estrogen 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. 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 their 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. © 2011 Blackwell Publishing Limited.

  5. 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

  6. Uncertainty Quantification in Climate Modeling

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

    We address challenges that sensitivity analysis and uncertainty quantification methods face when dealing with complex computational models. In particular, climate models are computationally expensive and typically depend on a large number of input parameters. We consider the Community Land Model (CLM), which consists of a nested computational grid hierarchy designed to represent the spatial heterogeneity of the land surface. Each computational cell can be composed of multiple land types, and each land type can incorporate one or more sub-models describing the spatial and depth variability. Even for simulations at a regional scale, the computational cost of a single run is quite high and the number of parameters that control the model behavior is very large. Therefore, the parameter sensitivity analysis and uncertainty propagation face significant difficulties for climate models. This work employs several algorithmic avenues to address some of the challenges encountered by classical uncertainty quantification methodologies when dealing with expensive computational models, specifically focusing on the CLM as a primary application. First of all, since the available climate model predictions are extremely sparse due to the high computational cost of model runs, we adopt a Bayesian framework that effectively incorporates this lack-of-knowledge as a source of uncertainty, and produces robust predictions with quantified uncertainty even if the model runs are extremely sparse. In particular, we infer Polynomial Chaos spectral expansions that effectively encode the uncertain input-output relationship and allow efficient propagation of all sources of input uncertainties to outputs of interest. Secondly, the predictability analysis of climate models strongly suffers from the curse of dimensionality, i.e. the large number of input parameters. While single-parameter perturbation studies can be efficiently performed in a parallel fashion, the multivariate uncertainty analysis

  7. Uncertainty quantification for environmental models

    USGS Publications Warehouse

    Hill, Mary C.; Lu, Dan; Kavetski, Dmitri; Clark, Martyn P.; Ye, Ming

    2012-01-01

    Environmental models are used to evaluate the fate of fertilizers in agricultural settings (including soil denitrification), the degradation of hydrocarbons at spill sites, and water supply for people and ecosystems in small to large basins and cities—to mention but a few applications of these models. They also play a role in understanding and diagnosing potential environmental impacts of global climate change. The models are typically mildly to extremely nonlinear. The persistent demand for enhanced dynamics and resolution to improve model realism [17] means that lengthy individual model execution times will remain common, notwithstanding continued enhancements in computer power. In addition, high-dimensional parameter spaces are often defined, which increases the number of model runs required to quantify uncertainty [2]. Some environmental modeling projects have access to extensive funding and computational resources; many do not. The many recent studies of uncertainty quantification in environmental model predictions have focused on uncertainties related to data error and sparsity of data, expert judgment expressed mathematically through prior information, poorly known parameter values, and model structure (see, for example, [1,7,9,10,13,18]). Approaches for quantifying uncertainty include frequentist (potentially with prior information [7,9]), Bayesian [13,18,19], and likelihood-based. A few of the numerous methods, including some sensitivity and inverse methods with consequences for understanding and quantifying uncertainty, are as follows: Bayesian hierarchical modeling and Bayesian model averaging; single-objective optimization with error-based weighting [7] and multi-objective optimization [3]; methods based on local derivatives [2,7,10]; screening methods like OAT (one at a time) and the method of Morris [14]; FAST (Fourier amplitude sensitivity testing) [14]; the Sobol' method [14]; randomized maximum likelihood [10]; Markov chain Monte Carlo (MCMC) [10

  8. Uncertainty quantification in molecular dynamics

    NASA Astrophysics Data System (ADS)

    Rizzi, Francesco

    This dissertation focuses on uncertainty quantification (UQ) in molecular dynamics (MD) simulations. The application of UQ to molecular dynamics is motivated by the broad uncertainty characterizing MD potential functions and by the complexity of the MD setting, where even small uncertainties can be amplified to yield large uncertainties in the model predictions. Two fundamental, distinct sources of uncertainty are investigated in this work, namely parametric uncertainty and intrinsic noise. Intrinsic noise is inherently present in the MD setting, due to fluctuations originating from thermal effects. Averaging methods can be exploited to reduce the fluctuations, but due to finite sampling, this effect cannot be completely filtered, thus yielding a residual uncertainty in the MD predictions. Parametric uncertainty, on the contrary, is introduced in the form of uncertain potential parameters, geometry, and/or boundary conditions. We address the UQ problem in both its main components, namely the forward propagation, which aims at characterizing how uncertainty in model parameters affects selected observables, and the inverse problem, which involves the estimation of target model parameters based on a set of observations. The dissertation highlights the challenges arising when parametric uncertainty and intrinsic noise combine to yield non-deterministic, noisy MD predictions of target macroscale observables. Two key probabilistic UQ methods, namely Polynomial Chaos (PC) expansions and Bayesian inference, are exploited to develop a framework that enables one to isolate the impact of parametric uncertainty on the MD predictions and, at the same time, properly quantify the effect of the intrinsic noise. Systematic applications to a suite of problems of increasing complexity lead to the observation that an uncertain PC representation built via Bayesian regression is the most suitable model for the representation of uncertain MD predictions of target observables in the

  9. 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.

  10. Advanced sample preparation for the molecular quantification of Staphylococcus aureus in artificially and naturally contaminated milk.

    PubMed

    Aprodu, Iuliana; Walcher, Georg; Schelin, Jenny; Hein, Ingeborg; Norling, Börje; Rådström, Peter; Nicolau, Anca; Wagner, Martin

    2011-03-01

    Sample treatment is an essential element when using real-time PCR for quantification of pathogens directly on food samples. This study comparatively evaluated three different principles of sample treatment, i.e. immunomagnetic separation based on phage-derived cell wall binding molecules, matrix solubilization and flotation, in order to establish their suitability for quantifying low numbers of Staphylococcus aureus in milk. All three procedures succeeded to remove S. aureus from the milk matrix, either raw or pasteurized, and, as a result of the concentration of the target cells, minimized the effect of milk associated PCR inhibitors. Sample preparation based on immunomagnetic separation albeit of being user friendly, specific and rapid, failed to allow quantification of low and medium numbers (<10(4)CFU) of S. aureus. In a mastitic milk model cell wall binding domain (CBD)-based target cell extraction revealed results most closely matching those derived from culture-based quantification. Both matrix lysis and flotation allowed quantification of S. aureus at a level of 1-10 cells per ml. Both methods resulted in higher numbers of bacterial cell equivalents (bce) than plating could reveal. Since both methods harvest cells that have been subjected to either mechanical and chemical stresses before quantification, we concluded that the higher bce numbers resulted from a disaggregation of S. aureus clusters initially present in the inoculum. Conclusively, since likely each S. aureus cell of a toxigenic strain contributes to enterotoxin production, molecular quantification could provide an even more realistic impact assessment in outbreak investigations than plating does.

  11. 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.

  12. 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).

  13. 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

  14. Tumor Quantification in Clinical Positron Emission Tomography

    PubMed Central

    Bai, Bing; Bading, James; Conti, Peter S

    2013-01-01

    Positron emission tomography (PET) is used extensively in clinical oncology for tumor detection, staging and therapy response assessment. Quantitative measurements of tumor uptake, usually in the form of standardized uptake values (SUVs), have enhanced or replaced qualitative interpretation. In this paper we review the current status of tumor quantification methods and their applications to clinical oncology. Factors that impede quantitative assessment and limit its accuracy and reproducibility are summarized, with special emphasis on SUV analysis. We describe current efforts to improve the accuracy of tumor uptake measurements, characterize overall metabolic tumor burden and heterogeneity of tumor uptake, and account for the effects of image noise. We also summarize recent developments in PET instrumentation and image reconstruction and their impact on tumor quantification. Finally, we offer our assessment of the current development needs in PET tumor quantification, including practical techniques for fully quantitative, pharmacokinetic measurements. PMID:24312151

  15. Limitations and challenges of genetic barcode quantification

    PubMed Central

    Thielecke, Lars; Aranyossy, Tim; Dahl, Andreas; Tiwari, Rajiv; Roeder, Ingo; Geiger, Hartmut; Fehse, Boris; Glauche, Ingmar; Cornils, Kerstin

    2017-01-01

    Genetic barcodes are increasingly used to track individual cells and to quantitatively assess their clonal contributions over time. Although barcode quantification relies entirely on counting sequencing reads, detailed studies about the method’s accuracy are still limited. We report on a systematic investigation of the relation between barcode abundance and resulting read counts after amplification and sequencing using cell-mixtures that contain barcodes with known frequencies (“miniBulks”). We evaluated the influence of protocol modifications to identify potential sources of error and elucidate possible limitations of the quantification approach. Based on these findings we designed an advanced barcode construct (BC32) to improved barcode calling and quantification, and to ensure a sensitive detection of even highly diluted barcodes. Our results emphasize the importance of using curated barcode libraries to obtain interpretable quantitative data and underline the need for rigorous analyses of any utilized barcode library in terms of reliability and reproducibility. PMID:28256524

  16. Quantum dot based 3D photonic devices

    NASA Astrophysics Data System (ADS)

    Sakellari, Ioanna; Kabouraki, Elmina; Gray, David; Vamvakaki, Maria; Farsari, Maria

    2017-02-01

    In this work, we present our most recent results on the fabrication of 3D high-resolution woodpile photonic crystals containing an organic-inorganic silicon-zirconium (Si-Zr) composite and cadmium sulfide (CdS) quantum dots (QDs). The structures are fabricated by combining 3D Direct Laser Writing by two-photon absorption and in-situ synthesis of CdS nanoparticles inside the 3D photonic matrix. The CdS-Zr-Si composite material exhibits a high nonlinear refractive index value measured by means of Z-scan method. 3D woodpile photonic structures with varying inlayer periodicity from 600nm to 500nm show clear photonic stop bands in the wavelength region between 1000nm to 450nm.

  17. Quantum-dot-based cell motility assay.

    PubMed

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

    2005-06-28

    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.

  18. Single-quantum-dot-based DNA nanosensor

    NASA Astrophysics Data System (ADS)

    Zhang, Chun-Yang; Yeh, Hsin-Chih; Kuroki, Marcos T.; Wang, Tza-Huei

    2005-11-01

    Rapid and highly sensitive detection of DNA is critical in diagnosing genetic diseases. Conventional approaches often rely on cumbersome, semi-quantitative amplification of target DNA to improve detection sensitivity. In addition, most DNA detection systems (microarrays, for example), regardless of their need for target amplification, require separation of unhybridized DNA strands from hybridized stands immobilized on a solid substrate, and are thereby complicated by solution-surface binding kinetics. Here, we report an ultrasensitive nanosensor based on fluorescence resonance energy transfer (FRET) capable of detecting low concentrations of DNA in a separation-free format. This system uses quantum dots (QDs) linked to DNA probes to capture DNA targets. The target strand binds to a dye-labelled reporter strand thus forming a FRET donor-acceptor ensemble. The QD also functions as a concentrator that amplifies the target signal by confining several targets in a nanoscale domain. Unbound nanosensors produce near-zero background fluorescence, but on binding to even a small amount of target DNA (~50 copies or less) they generate a very distinct FRET signal. A nanosensor-based oligonucleotide ligation assay has been demonstrated to successfully detect a point mutation typical of some ovarian tumours in clinical samples.

  19. Automatic Segmentation and Quantification of Filamentous Structures in Electron Tomography

    PubMed Central

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

    2016-01-01

    Electron tomography is a promising technology for imaging ultrastructures at nanoscale resolutions. However, image and quantitative analyses are often hindered by high levels of noise, staining heterogeneity, and material damage either as a result of the electron beam or sample preparation. We have developed and built a framework that allows for automatic segmentation and quantification of filamentous objects in 3D electron tomography. Our approach consists of three steps: (i) local enhancement of filaments by Hessian filtering; (ii) detection and completion (e.g., gap filling) of filamentous structures through tensor voting; and (iii) delineation of the filamentous networks. Our approach allows for quantification of filamentous networks in terms of their compositional and morphological features. We first validate our approach using a set of specifically designed synthetic data. We then apply our segmentation framework to tomograms of plant cell walls that have undergone different chemical treatments for polysaccharide extraction. The subsequent compositional and morphological analyses of the plant cell walls reveal their organizational characteristics and the effects of the different chemical protocols on specific polysaccharides. PMID:28090597

  20. Predicting Human Age with Bloodstains by sjTREC Quantification

    PubMed Central

    Wang, Huan; Wang, Hong-sheng; Lu, Hui-ling; Sun, Hong-yu

    2012-01-01

    The age-related decline of signal joint T-cell receptor rearrangement excision circles (sjTRECs) in human peripheral blood has been demonstrated in our previous study and other reports. Until now, only a few studies on sjTREC detection in bloodstain samples were reported, which were based on a small sample of subjects of a limited age range, although bloodstains are much more frequently encountered in forensic practice. In this present study, we adopted the sensitive Taqman real-time quantitative polymerase chain reaction (qPCR) method to perform sjTREC quantification in bloodstains from individuals ranging from 0–86 years old (n = 264). The results revealed that sjTREC contents in human bloodstains were declined in an age-dependent manner (r = −0.8712). The formula of age estimation was Age  = −7.1815Y−42.458±9.42 (Y dCtTBP-sjTREC; 9.42 standard error). Furthermore, we tested for the influence of short- or long- storage time by analyzing fresh and stored bloodstains from the same individuals. Remarkably, no statistically significant difference in sjTREC contents was found between the fresh and old DNA samples over a 4-week of storage time. However, significant loss (0.16–1.93 dCt) in sjTREC contents was detected after 1.5 years of storage in 31 samples. Moreover, preliminary sjTREC quantification from up to 20-year-old bloodstains showed that though the sjTREC contents were detectable in all samples and highly correlated with donor age, a time-dependent decrease in the correlation coefficient r was found, suggesting the predicting accuracy of this described assay would be deteriorated in aged samples. Our findings show that sjTREC quantification might be also suitable for age prediction in bloodstains, and future researches into the time-dependent or other potential impacts on sjTREC quantification might allow further improvement of the predicting accuracy. PMID:22879970

  1. 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

    2010-10-06

    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.

  2. 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.

  3. 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.

  4. Quantification of fluorescent reporters in plant cells.

    PubMed

    Pound, Michael; French, Andrew P; Wells, Darren M

    2015-01-01

    Fluorescent reporters are powerful tools for plant research. Many studies require accurate determination of fluorescence intensity and localization. Here, we describe protocols for the quantification of fluorescence intensity in plant cells from confocal laser scanning microscope images using semiautomated software and image analysis techniques.

  5. Cues, quantification, and agreement in language comprehension.

    PubMed

    Tanner, Darren; Bulkes, Nyssa Z

    2015-12-01

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

  6. DOSCATs: Double standards for protein quantification

    PubMed Central

    Bennett, Richard J.; Simpson, Deborah M.; Holman, Stephen W.; Ryan, Sheila; Brownridge, Philip; Eyers, Claire E.; Colyer, John; Beynon, Robert J.

    2017-01-01

    The two most common techniques for absolute protein quantification are based on either mass spectrometry (MS) or on immunochemical techniques, such as western blotting (WB). Western blotting is most often used for protein identification or relative quantification, but can also be deployed for absolute quantification if appropriate calibration standards are used. MS based techniques offer superior data quality and reproducibility, but WB offers greater sensitivity and accessibility to most researchers. It would be advantageous to apply both techniques for orthogonal quantification, but workflows rarely overlap. We describe DOSCATs (DOuble Standard conCATamers), novel calibration standards based on QconCAT technology, to unite these platforms. DOSCATs combine a series of epitope sequences concatenated with tryptic peptides in a single artificial protein to create internal tryptic peptide standards for MS as well as an intact protein bearing multiple linear epitopes. A DOSCAT protein was designed and constructed to quantify five proteins of the NF-κB pathway. For three target proteins, protein fold change and absolute copy per cell values measured by MS and WB were in excellent agreement. This demonstrates that DOSCATs can be used as multiplexed, dual purpose standards, readily deployed in a single workflow, supporting seamless quantitative transition from MS to WB. PMID:28368040

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Quantification of sterol lipids in plants by quadrupole time-of-flight mass spectrometry

    PubMed Central

    Wewer, Vera; Dombrink, Isabel; vom Dorp, Katharina; Dörmann, Peter

    2011-01-01

    Glycerolipids, sphingolipids, and sterol lipids constitute the major lipid classes in plants. Sterol lipids are composed of free and conjugated sterols, i.e., sterol esters, sterol glycosides, and acylated sterol glycosides. Sterol lipids play crucial roles during adaption to abiotic stresses and plant-pathogen interactions. Presently, no comprehensive method for sterol lipid quantification in plants is available. We used nanospray ionization quadrupole-time-of-flight mass spectrometry (Q-TOF MS) to resolve and identify the molecular species of all four sterol lipid classes from Arabidopsis thaliana. Free sterols were derivatized with chlorobetainyl chloride. Sterol esters, sterol glycosides, and acylated sterol glycosides were ionized as ammonium adducts. Quantification of molecular species was achieved in the positive mode after fragmentation in the presence of internal standards. The amounts of sterol lipids quantified by Q-TOF MS/MS were validated by comparison with results obtained with TLC/GC. Quantification of sterol lipids from leaves and roots of phosphate-deprived A. thaliana plants revealed changes in the amounts and molecular species composition. The Q-TOF method is far more sensitive than GC or HPLC. Therefore, Q-TOF MS/MS provides a comprehensive strategy for sterol lipid quantification that can be adapted to other tandem mass spectrometers. PMID:21382968

  13. Quantification of sterol lipids in plants by quadrupole time-of-flight mass spectrometry.

    PubMed

    Wewer, Vera; Dombrink, Isabel; vom Dorp, Katharina; Dörmann, Peter

    2011-05-01

    Glycerolipids, sphingolipids, and sterol lipids constitute the major lipid classes in plants. Sterol lipids are composed of free and conjugated sterols, i.e., sterol esters, sterol glycosides, and acylated sterol glycosides. Sterol lipids play crucial roles during adaption to abiotic stresses and plant-pathogen interactions. Presently, no comprehensive method for sterol lipid quantification in plants is available. We used nanospray ionization quadrupole-time-of-flight mass spectrometry (Q-TOF MS) to resolve and identify the molecular species of all four sterol lipid classes from Arabidopsis thaliana. Free sterols were derivatized with chlorobetainyl chloride. Sterol esters, sterol glycosides, and acylated sterol glycosides were ionized as ammonium adducts. Quantification of molecular species was achieved in the positive mode after fragmentation in the presence of internal standards. The amounts of sterol lipids quantified by Q-TOF MS/MS were validated by comparison with results obtained with TLC/GC. Quantification of sterol lipids from leaves and roots of phosphate-deprived A. thaliana plants revealed changes in the amounts and molecular species composition. The Q-TOF method is far more sensitive than GC or HPLC. Therefore, Q-TOF MS/MS provides a comprehensive strategy for sterol lipid quantification that can be adapted to other tandem mass spectrometers.

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

    PubMed

    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

    2016-11-01

    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.

  15. Uncertainty quantification for porous media flows

    SciTech Connect

    Christie, Mike . E-mail: mike.christie@pet.hw.ac.uk; Demyanov, Vasily; Erbas, Demet

    2006-09-01

    Uncertainty quantification is an increasingly important aspect of many areas of computational science, where the challenge is to make reliable predictions about the performance of complex physical systems in the absence of complete or reliable data. Predicting flows of oil and water through oil reservoirs is an example of a complex system where accuracy in prediction is needed primarily for financial reasons. Simulation of fluid flow in oil reservoirs is usually carried out using large commercially written finite difference simulators solving conservation equations describing the multi-phase flow through the porous reservoir rocks. This paper examines a Bayesian Framework for uncertainty quantification in porous media flows that uses a stochastic sampling algorithm to generate models that match observed data. Machine learning algorithms are used to speed up the identification of regions in parameter space where good matches to observed data can be found.

  16. 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.

  17. Quantification of Amyloid Precursor Protein Isoforms Using Quantification Concatamer Internal Standard

    PubMed Central

    Chen, Junjun; Wang, Meiyao; Turko, Illarion V.

    2014-01-01

    It is likely that expression and/or post-translational generation of various protein isoforms can be indicative of initial pathological changes or pathology development. However, selective quantification of individual protein isoforms remains a challenge, because they simultaneously possess common and unique amino acid sequences. Quantification concatamer (QconCAT) internal standards were originally designed for a large-scale proteome quantification and are artificial proteins that are concatamers of tryptic peptides for several proteins. We developed a QconCAT for quantification of various isoforms of amyloid precursor protein (APP). APP-QconCAT includes tryptic peptides that are common for all isoforms of APP concatenated with those tryptic peptides that are unique for specific APP isoforms. Isotope-labeled APP-QconCAT was expressed, purified, characterized, and further used for quantification of total APP, APP695, and amyloid-β (Aβ) in the human frontal cortex from control and severe Alzheimer’s disease donors. Potential biological implications of our quantitative measurements are discussed. It is also expected that using APP-QconCAT(s) will advance our understanding of biological mechanism by which various APP isoforms involved in the pathogenesis of Alzheimer’s disease. PMID:23186391

  18. Quantification of amyloid precursor protein isoforms using quantification concatamer internal standard.

    PubMed

    Chen, Junjun; Wang, Meiyao; Turko, Illarion V

    2013-01-02

    It is likely that expression and/or post-translational generation of various protein isoforms can be indicative of initial pathological changes or pathology development. However, selective quantification of individual protein isoforms remains a challenge, because they simultaneously possess common and unique amino acid sequences. Quantification concatamer (QconCAT) internal standards were originally designed for a large-scale proteome quantification and are artificial proteins that are concatamers of tryptic peptides for several proteins. We developed a QconCAT for quantification of various isoforms of amyloid precursor protein (APP). APP-QconCAT includes tryptic peptides that are common for all isoforms of APP concatenated with those tryptic peptides that are unique for specific APP isoforms. Isotope-labeled APP-QconCAT was expressed, purified, characterized, and further used for quantification of total APP, APP695, and amyloid-β (Aβ) in the human frontal cortex from control and severe Alzheimer's disease donors. Potential biological implications of our quantitative measurements are discussed. It is also expected that using APP-QconCAT(s) will advance our understanding of biological mechanism by which various APP isoforms involved in the pathogenesis of Alzheimer's disease.

  19. Phylogenetic Quantification of Intra-tumour Heterogeneity

    PubMed Central

    Schwarz, Roland F.; Trinh, Anne; Sipos, Botond; Brenton, James D.; Goldman, Nick; Markowetz, Florian

    2014-01-01

    Intra-tumour genetic heterogeneity is the result of ongoing evolutionary change within each cancer. The expansion of genetically distinct sub-clonal populations may explain the emergence of drug resistance, and if so, would have prognostic and predictive utility. However, methods for objectively quantifying tumour heterogeneity have been missing and are particularly difficult to establish in cancers where predominant copy number variation prevents accurate phylogenetic reconstruction owing to horizontal dependencies caused by long and cascading genomic rearrangements. To address these challenges, we present MEDICC, a method for phylogenetic reconstruction and heterogeneity quantification based on a Minimum Event Distance for Intra-tumour Copy-number Comparisons. Using a transducer-based pairwise comparison function, we determine optimal phasing of major and minor alleles, as well as evolutionary distances between samples, and are able to reconstruct ancestral genomes. Rigorous simulations and an extensive clinical study show the power of our method, which outperforms state-of-the-art competitors in reconstruction accuracy, and additionally allows unbiased numerical quantification of tumour heterogeneity. Accurate quantification and evolutionary inference are essential to understand the functional consequences of tumour heterogeneity. The MEDICC algorithms are independent of the experimental techniques used and are applicable to both next-generation sequencing and array CGH data. PMID:24743184

  20. Protein quantification using a cleavable reporter peptide.

    PubMed

    Duriez, Elodie; Trevisiol, Stephane; Domon, Bruno

    2015-02-06

    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.

  1. In situ flavonoid analysis by FT-Raman spectroscopy: identification, distribution, and quantification of aspalathin in green rooibos (Aspalathus linearis).

    PubMed

    Baranska, Malgorzata; Schulz, Hartwig; Joubert, Elizabeth; Manley, Marena

    2006-11-15

    FT-Raman spectroscopy was used for the first time for in situ identification of aspalathin and quantification of the dihyrochalcones in dried, green rooibos (Aspalathus linearis). With the support of two-dimensional correlation spectroscopy, characteristic key bands of aspalathin, the main flavonoid and antioxidant occurring in rooibos, were localized and identified in the spectra obtained from various plant samples. Application of Raman mapping revealed the spatial distribution of this valuable dihydrochalcone within the intact dried leaves. Based on the spectral data and reference HPLC values, reliable multivariate calibration models were developed for quantification of aspalathin, nothofagin, and the combined dihydrochalcone contents of dried, green rooibos.

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

    PubMed

    Walterová, Zuzana; Horský, Jiří

    2011-05-05

    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

  3. Uncertainty Quantification for GPM-era Precipitation Measurements

    NASA Astrophysics Data System (ADS)

    Tian, Yudong

    2014-05-01

    Uncertainty quantification will remain a challenge for GPM-era precipitation measurements. Our studies with TRMM-era products can provide useful guidance and improved procedures. For satellite-borne precipitation measurements, uncertainty originates from many error sources, including sampling errors, systematic errors and random errors. This presentation summarizes our efforts to quantify these errors in six different TRMM-era precipitation products (3B42, 3B42RT, CMORPH, PERSIANN, NRL and GSMaP), and proposes improved error modeling and validation procedures for GPM-era products. For systematic errors, we devised an error decomposition scheme to separate errors in precipitation estimates into three independent components, hit biases, missed precipitation and false precipitation (Tian et al., 2009). This decomposition scheme reveals more error features and provides a better link to the error sources than conventional analysis, because in the latter these error components tend to cancel one another when aggregated or averaged in space or time. To evaluate the random errors, we calculated the measurement spread from the ensemble of these six quasi-independent products, and produced a global map of measurement uncertainties (Tian and Peters-Lidard, 2010). The map yields a global view of the error characteristics and their regional and seasonal variations. More recently, we have established the fitness of a multiplicative error model to predict the uncertainties when ground validation data are not available (Tian et al., 2013), and have shown that this model is superior to the commonly-used additive error model in describing and predicting the uncertainty in precipitation measurements. Thus we propose an improved procedure based on error decomposition and the multiplicative error model for GPM-era uncertainty quantification.

  4. Real-time quantification of TEL-AML1 fusion transcripts for MRD detection in relapsed childhood acute lymphoblastic leukaemia. Comparison with antigen receptor-based MRD quantification methods.

    PubMed

    Taube, Tillmann; Eckert, Cornelia; Körner, Gabriele; Henze, Günter; Seeger, Karlheinz

    2004-07-01

    Response to therapy of ALL assessed by molecular methods has been proved to be a predictor of outcome. Alternatively to established but very labour-intensive DNA-based PCR-techniques the TEL-AML1 fusion transcript can serve as a marker for MRD monitoring. MRD quantification using TEL-AML1 is of particular interest if the results are directly comparable to data obtained by established DNA-based assays. Investigation of the potential of MRD monitoring using LightCycler technology for TEL-AML1 real-time quantification and comparison to results from established DNA-based MRD assays revealed corresponding results. Accordingly, TEL-AML1 MRD quantification is a sensitive, specific and rapid method that can supplement clone-specific MRD detection.

  5. Precise protein quantification based on peptide quantification using iTRAQ™

    PubMed Central

    Boehm, Andreas M; Pütz, Stephanie; Altenhöfer, Daniela; Sickmann, Albert; Falk, Michael

    2007-01-01

    Background Mass spectrometry based quantification of peptides can be performed using the iTRAQ™ reagent in conjunction with mass spectrometry. This technology yields information about the relative abundance of single peptides. A method for the calculation of reliable quantification information is required in order to obtain biologically relevant data at the protein expression level. Results A method comprising sound error estimation and statistical methods is presented that allows precise abundance analysis plus error calculation at the peptide as well as at the protein level. This yields the relevant information that is required for quantitative proteomics. Comparing the performance of our method named Quant with existing approaches the error estimation is reliable and offers information for precise bioinformatic models. Quant is shown to generate results that are consistent with those produced by ProQuant™, thus validating both systems. Moreover, the results are consistent with that of Mascot™ 2.2. The MATLAB® scripts of Quant are freely available via and , each under the GNU Lesser General Public License. Conclusion The software Quant demonstrates improvements in protein quantification using iTRAQ™. Precise quantification data can be obtained at the protein level when using error propagation and adequate visualization. Quant integrates both and additionally provides the possibility to obtain more reliable results by calculation of wise quality measures. Peak area integration has been replaced by sum of intensities, yielding more reliable quantification results. Additionally, Quant allows the combination of quantitative information obtained by iTRAQ™ with peptide and protein identifications from popular tandem MS identification tools. Hence Quant is a useful tool for the proteomics community and may help improving analysis of proteomic experimental data. In addition, we have shown that a lognormal distribution fits the data of mass spectrometry based

  6. 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. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. The pitfalls of protein quantification in wastewater treatment studies.

    PubMed

    Avella, A C; Görner, T; de Donato, Ph

    2010-09-15

    Proteins, as one of the principal components of organic matter in wastewater, require adequate quantification to determine their concentration in the different stages of wastewater treatment process. Recent studies have used the corrected Lowry Method for protein quantification arguing that this method can differentiate proteins from interfering humic substances. In this study, the classic Lowry Method, the corrected Lowry Method and a commercial assay kit were assessed for the protein quantification in the presence of humic acid.

  8. Comparison of targeted peptide quantification assays for reductive dehalogenases by selective reaction monitoring (SRM) and precursor reaction monitoring (PRM).

    PubMed

    Schiffmann, Christian; Hansen, Rasmus; Baumann, Sven; Kublik, Anja; Nielsen, Per Halkjær; Adrian, Lorenz; von Bergen, Martin; Jehmlich, Nico; Seifert, Jana

    2014-01-01

    Targeted absolute protein quantification yields valuable information about physiological adaptation of organisms and is thereby of high interest. Especially for this purpose, two proteomic mass spectrometry-based techniques namely selective reaction monitoring (SRM) and precursor reaction monitoring (PRM) are commonly applied. The objective of this study was to establish an optimal quantification assay for proteins with the focus on those involved in housekeeping functions and putative reductive dehalogenase proteins from the strictly anaerobic bacterium Dehalococcoides mccartyi strain CBDB1. This microbe is small and slow-growing; hence, it provides little biomass for comprehensive proteomic analysis. We therefore compared SRM and PRM techniques. Eleven peptides were successfully quantified by both methods. In addition, six peptides were solely quantified by SRM and four by PRM, respectively. Peptides were spiked into a background of Escherichia coli lysate and the majority of peptides were quantifiable down to 500 amol absolute on column by both methods. Peptide quantification in CBDB1 lysate resulted in the detection of 15 peptides using SRM and 14 peptides with the PRM assay. Resulting quantification of five dehalogenases revealed copy numbers of <10 to 115 protein molecules per cell indicating clear differences in abundance of RdhA proteins during growth on hexachlorobenzene. Our results indicated that both methods show comparable sensitivity and that the combination of the mass spectrometry assays resulted in higher peptide coverage and thus more reliable protein quantification.

  9. Experimental validation of 2D uncertainty quantification for digital image correlation.

    SciTech Connect

    Reu, Phillip L.

    2010-03-01

    Because digital image correlation (DIC) has become such an important and standard tool in the toolbox of experimental mechanicists, a complete uncertainty quantification of the method is needed. It should be remembered that each DIC setup and series of images will have a unique uncertainty based on the calibration quality and the image and speckle quality of the analyzed images. Any pretest work done with a calibrated DIC stereo-rig to quantify the errors using known shapes and translations, while useful, do not necessarily reveal the uncertainty of a later test. This is particularly true with high-speed applications where actual test images are often less than ideal. Work has previously been completed on the mathematical underpinnings of DIC uncertainty quantification and is already published, this paper will present corresponding experimental work used to check the validity of the uncertainty equations.

  10. Investigation of complexity dynamics in a DC glow discharge magnetized plasma using recurrence quantification analysis

    SciTech Connect

    Mitra, Vramori; Sarma, Bornali; Sarma, Arun; Janaki, M. S.; Sekar Iyengar, A. N.; Kurths, Jürgen

    2016-06-15

    Recurrence is an ubiquitous feature which provides deep insights into the dynamics of real dynamical systems. A suitable tool for investigating recurrences is recurrence quantification analysis (RQA). It allows, e.g., the detection of regime transitions with respect to varying control parameters. We investigate the complexity of different coexisting nonlinear dynamical regimes of the plasma floating potential fluctuations at different magnetic fields and discharge voltages by using recurrence quantification variables, in particular, DET, L{sub max}, and Entropy. The recurrence analysis reveals that the predictability of the system strongly depends on discharge voltage. Furthermore, the persistent behaviour of the plasma time series is characterized by the Detrended fluctuation analysis technique to explore the complexity in terms of long range correlation. The enhancement of the discharge voltage at constant magnetic field increases the nonlinear correlations; hence, the complexity of the system decreases, which corroborates the RQA analysis.

  11. 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.

  12. Quantification of annual sediment deposits for sustainable sand management in Aghanashini river estuary.

    PubMed

    Ramachandra, T V; Vinay, S; Subash Chandran, M D

    2017-08-11

    Sedimentation involving the process of silt transport also carries nutrients from upstream to downstream of a river/stream. Sand being one of the important fraction of these sediments is extracted in order to cater infrastructural/housing needs in the region. This communication is based on field research in the Aghanshini river basin, west coast of India. Silt yield in the river basin and the sedimentation rate assessed using empirical techniques supplemented with field quantifications using soundings (SONAR), show the sediment yield of 1105-1367 kilo cum per year and deposition of sediment of 61 (2016) to 71 (2015) cm. Quantifications of extractions at five locations, reveal of over exploitation of sand to an extent of 30% with damages to the breeding ground of fishes, reduced productivity of bivalves, etc., which has affected dependent people's livelihood. This study provides vital insights towards sustainable sand harvesting through stringent management practices. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Interference microscopes for tribology and corrosion quantification

    NASA Astrophysics Data System (ADS)

    Novak, Erik; Blewett, Nelson; Stout, Tom

    2007-06-01

    Interference microscopes remain one of the most accurate, repeatable, and versatile metrology systems for precision surface measurements. Such systems successfully measure material in both research labs and production lines in micro-optics, MEMS, data storage, medical device, and precision machining industries to sub-nanometer vertical resolution. Increasingly, however, these systems are finding uses outside of traditional surface-measurement applications, including film thickness determination, environmental responses of material, and determination of behavior under actuation. Most recently, these systems are enabling users to examine behavior of materials over varying time-scales as they are used in cutting or grinding operations or where the material is merely in continual contact with another such as in medical implants. In particular, quantification of wear of surfaces with varying coatings and under different conditions is of increasing value as tolerances decrease and consistency in final products is more valuable. Also, response of materials in corrosive environments allows users to quantify the gains of varying surface treatments against the cost of those treatments. Such quantification requires novel hardware and software for the system to ensure results are fast, accurate, and relevant. In this paper we explore three typical applications in tribology and corrosion. Deterioration of the cutting surfaces on a multi-blade razor is explored, with quantification of key surface features. Next, wear of several differently coated drill bits under similar use conditions is examined. Thirdly, in situ measurement of corrosion of several metal surfaces in harsh environmental conditions is performed. These case studies highlight how standard interference microscopes are evolving to serve novel industrial applications.

  14. Stereo-particle image velocimetry uncertainty quantification

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  15. Simultaneous quantification of multiple magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Rauwerdink, Adam M.; Giustini, Andrew J.; Weaver, John B.

    2010-11-01

    Distinct magnetic nanoparticle designs can have unique spectral responses to an AC magnetic field in a technique called the magnetic spectroscopy of Brownian motion (MSB). The spectra of the particles have been measured using desktop spectrometers and in vivo measurements. If multiple particle types are present in a region of interest, the unique spectral signatures allow for the simultaneous quantification of the various particles. We demonstrate such a potential experimentally with up to three particle types. This ability to concurrently detect multiple particles will enable new biomedical applications.

  16. Quantification and analysis of intramolecular interactions.

    PubMed

    Gonthier, Jérôme F; Corminboeuf, Clémence

    2014-01-01

    Non-covalent interactions play a prominent role in chemistry and biology. While a myriad of theoretical methods have been devised to quantify and analyze intermolecular interactions, the theoretical toolbox for the intramolecular analogues is much scarcer. Yet interactions within molecules govern fundamental phenomena as illustrated by the energetic differences between structural isomers. Their accurate quantification is of utmost importance. This paper gives an overview of the most common approaches able to probe intramolecular interactions and stresses both their characteristics and limitations. We finally introduce our recent theoretical approach, which represents the first step towards the development of an intramolecular version of Symmetry-Adapted Perturbation Theory (SAPT).

  17. Adjoint-Based Uncertainty Quantification with MCNP

    NASA Astrophysics Data System (ADS)

    Seifried, Jeffrey Edwin

    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.

  18. NMR-based quantification of organic diphosphates

    PubMed Central

    Lenevich, Stepan

    2010-01-01

    Phosphorylated compounds are ubiquitous in life. Given their central role, many such substrates and analogues 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 31P 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

  19. 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.

  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. 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.

  3. Digital Quantification of Gene Expression in Sequential Breast Cancer Biopsies Reveals Activation of an Immune Response

    PubMed Central

    Jeselsohn, Rinath M.; Werner, Lillian; Regan, Meredith M.; Fatima, Aquila; Gilmore, Lauren; Collins, Laura C.; Beck, Andrew H.; Bailey, Shannon T.; He, Housheng Hansen; Buchwalter, Gilles; Brown, Myles; Iglehart, J. Dirk; Richardson, Andrea; Come, Steven E.

    2013-01-01

    Advancements in molecular biology have unveiled multiple breast cancer promoting pathways and potential therapeutic targets. Large randomized clinical trials remain the ultimate means of validating therapeutic efficacy, but they require large cohorts of patients and are lengthy and costly. A useful approach is to conduct a window of opportunity study in which patients are exposed to a drug pre-surgically during the interval between the core needle biopsy and the definitive surgery. These are non-therapeutic studies and the end point is not clinical or pathological response but rather evaluation of molecular changes in the tumor specimens that can predict response. However, since the end points of the non-therapeutic studies are biologic, it is critical to first define the biologic changes that occur in the absence of treatment. In this study, we compared the molecular profiles of breast cancer tumors at the time of the diagnostic biopsy versus the definitive surgery in the absence of any intervention using the Nanostring nCounter platform. We found that while the majority of the transcripts did not vary between the two biopsies, there was evidence of activation of immune related genes in response to the first biopsy and further investigations of the immune changes after a biopsy in early breast cancer seem warranted. PMID:23741308

  4. 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.

  5. 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.

  6. Lineage tracing quantification reveals symmetric stem cell division in Drosophila male germline stem cells.

    PubMed

    Salzmann, Viktoria; Inaba, Mayu; Cheng, Jun; Yamashita, Yukiko M

    2013-12-01

    In the homeostatic state, adult stem cells divide either symmetrically to increase the stem cell number to compensate stem cell loss, or asymmetrically to maintain the population while producing differentiated cells. We have investigated the mode of stem cell division in the testes of Drosophila melanogaster by lineage tracing and confirm the presence of symmetric stem cell division in this system. We found that the rate of symmetric division is limited to 1-2% of total germline stem cell (GSC) divisions, but it increases with expression of a cell adhesion molecule, E-cadherin, or a regulator of the actin cytoskeleton, Moesin, which may modulate adhesiveness of germ cells to the stem cell niche. Our results indicate that the decision regarding asymmetric vs. symmetric division is a dynamically regulated process that contributes to tissue homeostasis, responding to the needs of the tissue.

  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 Detergents Complexed with Membrane Proteins

    PubMed Central

    Chaptal, Vincent; Delolme, Frédéric; Kilburg, Arnaud; Magnard, Sandrine; Montigny, Cédric; Picard, Martin; Prier, Charlène; Monticelli, Luca; Bornert, Olivier; Agez, Morgane; Ravaud, Stéphanie; Orelle, Cédric; Wagner, Renaud; Jawhari, Anass; Broutin, Isabelle; Pebay-Peyroula, Eva; Jault, Jean-Michel; Kaback, H. Ronald; le Maire, Marc; Falson, Pierre

    2017-01-01

    Most membrane proteins studies require the use of detergents, but because of the lack of a general, accurate and rapid method to quantify them, many uncertainties remain that hamper proper functional and structural data analyses. To solve this problem, we propose a method based on matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS) that allows quantification of pure or mixed detergents in complex with membrane proteins. We validated the method with a wide variety of detergents and membrane proteins. We automated the process, thereby allowing routine quantification for a broad spectrum of usage. As a first illustration, we show how to obtain information of the amount of detergent in complex with a membrane protein, essential for liposome or nanodiscs reconstitutions. Thanks to the method, we also show how to reliably and easily estimate the detergent corona diameter and select the smallest size, critical for favoring protein-protein contacts and triggering/promoting membrane protein crystallization, and to visualize the detergent belt for Cryo-EM studies. PMID:28176812

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Quantification noise in single cell experiments

    PubMed Central

    Reiter, M.; Kirchner, B.; Müller, H.; Holzhauer, C.; Mann, W.; Pfaffl, M. W.

    2011-01-01

    In quantitative single-cell studies, the critical part is the low amount of nucleic acids present and the resulting experimental variations. In addition biological data obtained from heterogeneous tissue are not reflecting the expression behaviour of every single-cell. These variations can be derived from natural biological variance or can be introduced externally. Both have negative effects on the quantification result. The aim of this study is to make quantitative single-cell studies more transparent and reliable in order to fulfil the MIQE guidelines at the single-cell level. The technical variability introduced by RT, pre-amplification, evaporation, biological material and qPCR itself was evaluated by using RNA or DNA standards. Secondly, the biological expression variances of GAPDH, TNFα, IL-1β, TLR4 were measured by mRNA profiling experiment in single lymphocytes. The used quantification setup was sensitive enough to detect single standard copies and transcripts out of one solitary cell. Most variability was introduced by RT, followed by evaporation, and pre-amplification. The qPCR analysis and the biological matrix introduced only minor variability. Both conducted studies impressively demonstrate the heterogeneity of expression patterns in individual cells and showed clearly today's limitation in quantitative single-cell expression analysis. PMID:21745823

  15. Detection and quantification of levoglucosan in atmospheric aerosols: a review.

    PubMed

    Schkolnik, Gal; Rudich, Yinon

    2006-05-01

    Levoglucosan is a tracer for biomass burning sources in atmospheric aerosol particles. Therefore, much effort has been recently put into developing methods for its quantification. This review describes and compares both established and emerging analytical methods for levoglucosan quantification in ambient aerosol samples, with the special needs of the environmental analytical chemist in mind.

  16. 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

  17. Fluorometric Quantification of Polyphosphate in Environmental Plankton Samples: Extraction Protocols, Matrix Effects, and Nucleic Acid Interference

    PubMed Central

    Martin, Patrick

    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. PMID:23104409

  18. Localization and in situ absolute quantification of chlordecone in the mouse liver by MALDI imaging.

    PubMed

    Lagarrigue, Mélanie; Lavigne, Régis; Tabet, Elise; Genet, Valentine; Thomé, Jean-Pierre; Rondel, Karine; Guével, Blandine; Multigner, Luc; Samson, Michel; Pineau, Charles

    2014-06-17

    Chlordecone is an organochlorine pesticide that was extensively used in the French West Indies to fight weevils in banana plantations from 1973 to 1993. This has led to a persistent pollution of the environment and to the contamination of the local population for several decades with effects demonstrated on human health. Chlordecone accumulates mainly in the liver where it is known to potentiate the action of hepatotoxic agents. However, there is currently no information on its in situ localization in the liver. We have thus evaluated a matrix-assisted laser desorption ionization (MALDI) imaging quantification method based on labeled normalization for the in situ localization and quantification of chlordecone. After validating the linearity and the reproducibility of this method, quantitative MALDI imaging was used to study the accumulation of chlordecone in the mouse liver. Our results revealed that normalized intensities measured by MALDI imaging could be first converted in quantitative units. These quantities appeared to be different from absolute quantities of chlordecone determined by gas chromatography (GC), but they were perfectly correlated (R(2) = 0.995). The equation of the corresponding correlation curve was thus efficiently used to convert quantities measured by MALDI imaging into absolute quantities. Our method combining labeled normalization and calibration with an orthogonal technique allowed the in situ absolute quantification of chlordecone by MALDI imaging. Finally, our results obtained on the pathological mouse liver illustrate the advantages of quantitative MALDI imaging which preserves information on in situ localization without radioactive labeling and with a simple sample preparation.

  19. Is biofilm removal properly assessed? Comparison of different quantification methods in a 96-well plate system.

    PubMed

    Stiefel, Philipp; Rosenberg, Urs; Schneider, Jana; Mauerhofer, Stefan; Maniura-Weber, Katharina; Ren, Qun

    2016-05-01

    Various methods have been reported to quantify total biofilm or different components of biofilm; however, these methods are often confusedly used, leading to discrepancies and misleading results. In this study, different methods for quantification of biofilm, including those for total biomass, total amount of bacterial cells, viable cell number, and amount of extracellular polymeric substances, were systematically compared in microtiter plates. To evaluate which method is suitable for assessment of biofilm removal and for bacterial killing, biofilm samples were treated with various cleaners possessing removing and/or killing capacities. It was found that most of the methods tested in this study in general exhibited high reproducibility and repeatability. Crystal Violet staining was a simple but reliable method for total biomass quantification. Total bacteria cell numbers could be reliably quantified by the fluorescent DNA-binding dye Acridine Orange. Viable cells could be quantified by either an ATP-based assay or a proliferation assay. Both of these viability methods showed a broad detection range and led to precise measurement. For quantification of proteins in the biofilm, staining with fluorescein isothiocyanate was most suitable. Furthermore, it was revealed that a combination of different methods is required to determine if a cleaner kills or removes biofilm.

  20. A sandwich enzyme-linked immunosorbent assay for the quantification of insoluble membrane and scaffold proteins.

    PubMed

    Geumann, Constanze; Grønborg, Mads; Hellwig, Michaela; Martens, Henrik; Jahn, Reinhard

    2010-07-15

    Enzyme-linked immunosorbent assays (ELISAs) are applied for the quantification of a vast diversity of small molecules. However, ELISAs require that the antigen is present in a soluble form in the sample. Accordingly, the few ELISAs described so far targeting insoluble proteins such as integral membrane and scaffold proteins have been restricted by limited extraction efficiencies and the need to establish an individual solubilization protocol for each protein. Here we describe a sandwich ELISA that allows the quantification of a diverse array of synaptic membrane and scaffold proteins such as munc13-1, gephyrin, NMDA R1 (N-methyl-d-aspartate receptor subunit 1), synaptic vesicle membrane proteins, and SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors). The assay is based on initial solubilization by the denaturing detergent sodium dodecyl sulfate (SDS), followed by partial SDS removal using the detergent Triton X-100, which restores antigenicity while keeping the proteins in solution. Using recombinant standard proteins, we determined assay sensitivities of 78ng/ml to 77pg/ml (or 74-0.1fmol). Calibration of the assay using both immunoblotting and mass spectroscopy revealed that in some cases correction factors need to be included for absolute quantification. The assay is versatile, allows parallel processing and automation, and should be applicable to a wide range of hitherto inaccessible proteins.

  1. Characterisation and quantification of regional diurnal SST cycles from SEVIRI

    NASA Astrophysics Data System (ADS)

    Karagali, I.; Høyer, J. L.

    2014-09-01

    Hourly SST (sea surface temperature) fields from the geostationary Spinning Enhanced Visible and Infrared Imager (SEVIRI) offer a unique opportunity for the characterisation and quantification of the diurnal cycle of SST in the Atlantic Ocean, the Mediterranean Sea and the northern European shelf seas. Six years of SST fields from SEVIRI are validated against the Advanced Along-Track Scanning Radiometer (AATSR) Reprocessed for Climate (ARC) data set. The overall SEVIRI-AATSR bias is -0.07 K, and the standard deviation is 0.51 K, based on more than 53 × 106 match-ups. Identification of the diurnal signal requires an SST foundation temperature field representative of well-mixed conditions which typically occur at night-time or under moderate and strong winds. Such fields are generated from the SEVIRI archive and are validated against pre-dawn SEVIRI SSTs and night-time SSTs from drifting buoys. The different methodologies tested for the foundation temperature fields reveal variability introduced by averaging night-time SSTs over many days compared to single-day, pre-dawn values. Diurnal warming is most pronounced in the Mediterranean and Baltic seas while weaker diurnal signals are found in the tropics. Longer diurnal warming duration is identified in the high latitudes compared to the tropics. The maximum monthly mean diurnal signal can be up to 0.5 K in specific regions.

  2. Characterisation and quantification of regional diurnal SST cycles from SEVIRI

    NASA Astrophysics Data System (ADS)

    Karagali, I.; Høyer, J. L.

    2014-04-01

    Hourly SST fields from the geostationary Spinning Enhanced Visible and Infrared Imager (SEVIRI) offer a unique opportunity for the characterisation and quantification of the diurnal cycle of SST in the Atlantic Ocean, the Mediterranean Sea and the Northern European Shelf seas. Six years of SST fields from the SEVIRI dataset are validated against the polar orbiting Advanced Along Track Scanning Radiometer (AATSR) archive to identify biases in the SEVIRI data. Identification of the diurnal signal requires a night-time SST field representative of foundation temperatures, i.e. well-mixed conditions and free of any diurnal signal. Such fields are generated from the SEVIRI archive and are validated against pre-dawn SEVIRI SSTs and night-time SSTs from drifting buoys. The overall SEVIRI-AATSR bias is -0.07 K, and the standard deviation is 0.51 K, based on more than 53 × 106 match-ups. The different methodologies tested for the foundation temperature fields reveal variability introduced by averaging night-time SSTs over many days compared to single-day, pre-dawn values. Diurnal warming is most pronounced in the Mediterranean and Baltic Seas while smallest diurnal signals are found in the Tropics. Longer diurnal warming duration is identified in the high latitudes compared to the Tropics. The mean diurnal signal of monthly mean SST can be up to 0.5° in specific regions.

  3. 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.

  4. Low order models for uncertainty quantification in acoustic propagation problems

    NASA Astrophysics Data System (ADS)

    Millet, Christophe

    2016-11-01

    Long-range sound propagation problems are characterized by both a large number of length scales and a large number of normal modes. In the atmosphere, these modes are confined within waveguides causing the sound to propagate through multiple paths to the receiver. For uncertain atmospheres, the modes are described as random variables. Concise mathematical models and analysis reveal fundamental limitations in classical projection techniques due to different manifestations of the fact that modes that carry small variance can have important effects on the large variance modes. In the present study, we propose a systematic strategy for obtaining statistically accurate low order models. The normal modes are sorted in decreasing Sobol indices using asymptotic expansions, and the relevant modes are extracted using a modified iterative Krylov-based method. The statistics of acoustic signals are computed by decomposing the original pulse into a truncated sum of modal pulses that can be described by a stationary phase method. As the low-order acoustic model preserves the overall structure of waveforms under perturbations of the atmosphere, it can be applied to uncertainty quantification. The result of this study is a new algorithm which applies on the entire phase space of acoustic fields.

  5. 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.

    2016-05-10

    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 as well 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.

  6. 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

  7. Recurrence quantification analysis of two solar cycle indices

    NASA Astrophysics Data System (ADS)

    Stangalini, Marco; Ermolli, Ilaria; Consolini, Giuseppe; Giorgi, Fabrizio

    2017-02-01

    Solar activity affects the whole heliosphere and near-Earth space environment. It has been reported in the literature that the mechanism responsible for the solar activity modulation behaves like a low-dimensional chaotic system. Studying these kind of physical systems and, in particular, their temporal evolution requires non-linear analysis methods. To this regard, in this work we apply the recurrence quantification analysis (RQA) to the study of two of the most commonly used solar cycle indicators; i.e. the series of the sunspot number (SSN), and the radio flux 10.7 cm, with the aim of identifying possible dynamical transitions in the system; a task which is particularly suited to the RQA. The outcome of this analysis reveals the presence of large fluctuations of two RQA measures: namely the determinism and the laminarity. In addition, large differences are also seen between the evolution of the RQA measures of the SSN and the radio flux. That suggests the presence of transitions in the dynamics underlying the solar activity. Besides it also shows and quantifies the different nature of these two solar indices. Furthermore, in order to check whether our results are affected by dataartefacts, we have also applied the RQA to both the recently recalibrated SSN series and the previous one, unveiling the main differences between the two data sets. The results are discussed in light of the recent literature on the subject.

  8. Cloning and quantification of ferret serum amyloid A.

    PubMed

    Aratani, Hitoshi; Segawa, Takao; Itou, Takuya; Sakai, Takeo

    2013-01-31

    Serum amyloid A (SAA) is used as a biomarker for infections and inflammation in humans and veterinary medicine. We cloned ferret cDNA encoding SAA from the liver of a ferret via reverse transcription PCR (RT-PCR). The sequence of the cDNA clone revealed that ferret SAA has an open reading frame of 387 bp that encodes 129 amino acids. The deduced amino acid sequence of ferret SAA has 96.1, 89.9, 86.0, 83.8, 83.0, 73.8 and 65.3% similarity to the mink, dog, cat, cattle, horse, human and mouse SAA genes, respectively. Compared to human SAA, the deduced ferret SAA amino acid sequence had an insertion of an 8-amino acid fragment between amino acids 88 and 95. Recombinant ferret SAA (rfrSAA) was expressed using an Escherichia coli (E. coli) strain, BL21 Star. Using Western blot analysis, anti-SAA mAb provided with the multispecies SAA ELISA kit reacted with purified rfrSAA. A significant dose-response relationship was observed between the rfrSAA protein and a commercial multispecies SAA ELISA kit. In contrast, rfrSAA was not recognized with the antibodies included in a commercial human SAA ELISA kit. These results suggest that the structure of ferret SAA is antigenically similar to other domestic animal SAAs, and the multispecies ELISA kit allows for the detection and quantification of ferret SAA in vivo.

  9. NMR method for accurate quantification of polysorbate 80 copolymer composition.

    PubMed

    Zhang, Qi; Wang, Aifa; Meng, Yang; Ning, Tingting; Yang, Huaxin; Ding, Lixia; Xiao, Xinyue; Li, Xiaodong

    2015-10-06

    (13)C NMR spectroscopic integration employing short relaxation delays and a 30° pulse width was evaluated as a quantitative tool for analyzing the components of polysorbate 80. (13)C NMR analysis revealed that commercial polysorbate 80 formulations are a complex oligomeric mixture of sorbitan polyethoxylate esters and other intermediates, such as isosorbide polyethoxylate esters and poly(ethylene glycol) (PEG) esters. This novel approach facilitates the quantification of the component ratios. In this study, the ratios of the three major oligomers in polysorbate 80 were measured and the PEG series was found to be the major component of commercial polysorbate 80. The degree of polymerization of -CH2CH2O- groups and the ratio of free to bonded -CH2CH2O- end groups, which correlate with the hydrophilic/hydrophobic nature of the polymer, were analyzed, and were suggested to be key factors for assessing the likelihood of adverse biological reactions to polysorbate 80. The (13)C NMR data suggest that the feed ratio of raw materials and reaction conditions in the production of polysorbate 80 are not well controlled. Our results demonstrate that (13)C NMR is a universal, powerful tool for polysorbate analysis. Such analysis is crucial for the synthesis of a high-quality product, and is difficult to obtain by other methods.

  10. 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

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

    DOE PAGES

    Karp, Eric M.; Nimlos, Claire T.; Deutch, Steve; ...

    2016-05-10

    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 alkalinemore » 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 as well 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.« less

  12. Multiscale quantification of tissue behavior during amniote embryo axis elongation.

    PubMed

    Bénazéraf, Bertrand; Beaupeux, Mathias; Tchernookov, Martin; Wallingford, Allison; Salisbury, Tasha; Shirtz, Amelia; Shirtz, Andrew; Huss, David; Pourquié, Olivier; François, Paul; Lansford, Rusty

    2017-08-23

    Embryonic axis elongation is a complex multi-tissue morphogenetic process responsible for the formation of the posterior part of the amniote body. How movements and growth are coordinated between the different posterior tissues (e.g. neural tube, axial and paraxial mesoderm, lateral plate, ectoderm, endoderm) to drive axis morphogenesis remain largely unknown. Here, we use quail embryos to quantify cell behavior and tissue movements during elongation. We quantify the tissue-specific contribution to axis elongation by using 3D volumetric techniques, then quantify tissue-specific parameters such as cell density and proliferation. To study cell behavior at a multi-tissue scale, we used high-resolution 4D imaging of transgenic quail embryos expressing fluorescent proteins. We developed specific tracking and image analysis techniques to analyze cell motion and compute tissue deformations in 4D. This analysis reveals extensive sliding between tissues during axis extension. Further quantification of tissue tectonics showed patterns of rotations, contractions and expansions, which are coherent with the multi-tissue behavior observed previously. Our approach defines a quantitative and multiscale method to analyze the coordination between tissue behaviors during early vertebrate embryo morphogenetic events. © 2017. Published by The Company of Biologists Ltd.

  13. Comparison of two methods, UHPLC-UV and UHPLC-MS/MS, for the quantification of polyphenols in cider apple juices.

    PubMed

    Verdu, Cindy F; Gatto, Julia; Freuze, Ingrid; Richomme, Pascal; Laurens, François; Guilet, David

    2013-08-22

    The aim of this study was to develop faster and more efficient phenotyping methods for in-depth genetic studies on cider apple progeny. The UHPLC chromatographic system was chosen to separate polyphenolic compounds, and quantifications were then simultaneously performed with a UV-PDA detector and an ESI-triple quadrupole mass analyzer (SRM mode). Both quantification methods were validated for 15 major compounds using two apple juice samples, on the basis of linearity, limits of detection and quantification, recovery and precision tests. The comparison between UV and SRM quantifications in 120 different samples of a cider apple progeny showed an excellent correlation for major compounds quantified with both methods. However, an overestimation was revealed for five compounds with the UV detector and the mass analyzer. Co-elution and matrix effects are discussed to explain this phenomenon. SRM methods should therefore be considered with restrictions in some cases for quantification measurements when several phenolic compounds are simultaneously quantified in complex matrices such as apple juices. For both methods, analyses were carried out over short periods of time while maintaining a high quality for the simultaneous quantification of phenolic compounds in apple juice. Each method is relevant for more in-depth genetic studies of the polyphenol content of apple juice.

  14. 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.

  15. Quantification of Osteon Morphology Using Geometric Histomorphometrics.

    PubMed

    Dillon, Scott; Cunningham, Craig; Felts, Paul

    2016-03-01

    Many histological methods in forensic anthropology utilize combinations of traditional histomorphometric parameters which may not accurately describe the morphology of microstructural features. Here, we report the novel application of a geometric morphometric method suitable when considering structures without anatomically homologous landmarks for the quantification of complete secondary osteon size and morphology. The method is tested for its suitability in the measurement of intact secondary osteons using osteons digitized from transverse femoral diaphyseal sections prepared from two human individuals. The results of methodological testing demonstrate the efficacy of the technique when applied to intact secondary osteons. In providing accurate characterization of micromorphology within the robust mathematical framework of geometric morphometrics, this method may surpass traditional histomorphometric variables currently employed in forensic research and practice. A preliminary study of the intersectional histomorphometric variation within the femoral diaphysis is made using this geometric histomorphometric method to demonstrate its potential. © 2015 American Academy of Forensic Sciences.

  16. Uncertainty quantification of acoustic emission filtering techniques

    NASA Astrophysics Data System (ADS)

    Zárate, Boris A.; Caicedo, Juan M.; Ziehl, Paul

    2012-04-01

    This paper compares six different filtering protocols used in Acoustic Emission (AE) monitoring of fatigue crack growth. The filtering protocols are combination of three different filtering techniques which are based on Swansong-like filters and load filters. The filters are compared deterministically and probabilistically. The deterministic comparison is based on the coefficient of determination of the resulting AE data, while the probabilistic comparison is based on the quantification of the uncertainty of the different filtering protocols. The uncertainty of the filtering protocols is quantified by calculating the entropy of the probability distribution of some AE and fracture mechanics parameters for the given filtering protocol. The methodology is useful in cases where several filtering protocols are available and there is no reason to choose one over the others. Acoustic Emission data from a compact tension specimen tested under cyclic load is used for the comparison.

  17. 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. Copyright © 2016 American Federation for Medical Research.

  18. 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.

  19. Usage of human reliability quantification methods.

    PubMed

    Grozdanovic, Miroljub

    2005-01-01

    Human reliability quantification (HRQ) methods are becoming increasingly important in risk and accident assessment in systems these terms are usually related to (hi-tech industrial systems, including nuclear and chemical plants). These methods began to intensively develop after numerous accidents caused by human error or inadequate activity of people who controlled and managed complex technological processes. For already existing systems, but also for new ones, it is important to assess the possibility of an accident. Determination of possible preventive activities, which include the influence of human error on the safety of a system, is also required. These are the main goals of the HRQ method. Using Absolute Probability Judgment (APJ) and Success Likelihood Index Methods (SLIM) HRQ techniques in control and management centers in electro-power systems in Belgrade and railway traffic in Nis (both in Serbia and Montenegro) are shown in this paper.

  20. Human cytomegalovirus: propagation, quantification, and storage.

    PubMed

    Britt, William J

    2010-08-01

    Human cytomegalovirus (HCMV) is the largest and perhaps the most structurally complex member of the family of human herpesviruses. It is the prototypic virus of the beta-herpesvirus subfamily. As with other cytomegaloviruses, HCMV is exquisitely species specific and undergoes lytic replication only in cells of human origin. In addition, its replication is limited almost entirely to primary cells and a limited number of transformed cell lines. Together with its prolonged replicative cycle of approximately 48 hr, the propagation and quantification of HCMV can present technical challenges. In this brief set of protocols, the propagation of laboratory strains of HCMV and their quantitation is described. In a third series of protocols, the concentration and gradient purification of HCMV for more specialized downstream applications is described.

  1. 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.

  2. Quantification of variability in trichome patterns

    PubMed Central

    Greese, Bettina; Hülskamp, Martin; Fleck, Christian

    2014-01-01

    While pattern formation is studied in various areas of biology, little is known about the noise leading to variations between individual realizations of the pattern. One prominent example for de novo pattern formation in plants is the patterning of trichomes on Arabidopsis leaves, which involves genetic regulation and cell-to-cell communication. These processes are potentially variable due to, e.g., the abundance of cell components or environmental conditions. To elevate the understanding of regulatory processes underlying the pattern formation it is crucial to quantitatively analyze the variability in naturally occurring patterns. Here, we review recent approaches toward characterization of noise on trichome initiation. We present methods for the quantification of spatial patterns, which are the basis for data-driven mathematical modeling and enable the analysis of noise from different sources. Besides the insight gained on trichome formation, the examination of observed trichome patterns also shows that highly regulated biological processes can be substantially affected by variability. PMID:25431575

  3. Quantification of variability in trichome patterns.

    PubMed

    Greese, Bettina; Hülskamp, Martin; Fleck, Christian

    2014-01-01

    While pattern formation is studied in various areas of biology, little is known about the noise leading to variations between individual realizations of the pattern. One prominent example for de novo pattern formation in plants is the patterning of trichomes on Arabidopsis leaves, which involves genetic regulation and cell-to-cell communication. These processes are potentially variable due to, e.g., the abundance of cell components or environmental conditions. To elevate the understanding of regulatory processes underlying the pattern formation it is crucial to quantitatively analyze the variability in naturally occurring patterns. Here, we review recent approaches toward characterization of noise on trichome initiation. We present methods for the quantification of spatial patterns, which are the basis for data-driven mathematical modeling and enable the analysis of noise from different sources. Besides the insight gained on trichome formation, the examination of observed trichome patterns also shows that highly regulated biological processes can be substantially affected by variability.

  4. 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

  5. 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)

  6. Automated Quantification and Integrative Analysis of 2D and 3D Mitochondrial Shape and Network Properties

    PubMed Central

    Nikolaisen, Julie; Nilsson, Linn I. H.; Pettersen, Ina K. N.; Willems, Peter H. G. M.; Lorens, James B.; Koopman, Werner J. H.; Tronstad, Karl J.

    2014-01-01

    Mitochondrial morphology and function are coupled in healthy cells, during pathological conditions and (adaptation to) endogenous and exogenous stress. In this sense mitochondrial shape can range from small globular compartments to complex filamentous networks, even within the same cell. Understanding how mitochondrial morphological changes (i.e. “mitochondrial dynamics”) are linked to cellular (patho) physiology is currently the subject of intense study and requires detailed quantitative information. During the last decade, various computational approaches have been developed for automated 2-dimensional (2D) analysis of mitochondrial morphology and number in microscopy images. Although these strategies are well suited for analysis of adhering cells with a flat morphology they are not applicable for thicker cells, which require a three-dimensional (3D) image acquisition and analysis procedure. Here we developed and validated an automated image analysis algorithm allowing simultaneous 3D quantification of mitochondrial morphology and network properties in human endothelial cells (HUVECs). Cells expressing a mitochondria-targeted green fluorescence protein (mitoGFP) were visualized by 3D confocal microscopy and mitochondrial morphology was quantified using both the established 2D method and the new 3D strategy. We demonstrate that both analyses can be used to characterize and discriminate between various mitochondrial morphologies and network properties. However, the results from 2D and 3D analysis were not equivalent when filamentous mitochondria in normal HUVECs were compared with circular/spherical mitochondria in metabolically stressed HUVECs treated with rotenone (ROT). 2D quantification suggested that metabolic stress induced mitochondrial fragmentation and loss of biomass. In contrast, 3D analysis revealed that the mitochondrial network structure was dissolved without affecting the amount and size of the organelles. Thus, our results demonstrate that 3D

  7. A spectral graph theoretic approach to quantification and calibration of collective morphological differences in cell images

    PubMed Central

    Lin, Yu-Shi; Lin, Chung-Chih; Tsai, Yuh-Show; Ku, Tien-Chuan; Huang, Yi-Hung; Hsu, Chun-Nan

    2010-01-01

    Motivation: High-throughput image-based assay technologies can rapidly produce a large number of cell images for drug screening, but data analysis is still a major bottleneck that limits their utility. Quantifying a wide variety of morphological differences observed in cell images under different drug influences is still a challenging task because the result can be highly sensitive to sampling and noise. Results: We propose a graph-based approach to cell image analysis. We define graph transition energy to quantify morphological differences between image sets. A spectral graph theoretic regularization is applied to transform the feature space based on training examples of extremely different images to calibrate the quantification. Calibration is essential for a practical quantification method because we need to measure the confidence of the quantification. We applied our method to quantify the degree of partial fragmentation of mitochondria in collections of fluorescent cell images. We show that with transformation, the quantification can be more accurate and sensitive than that without transformation. We also show that our method outperforms competing methods, including neighbourhood component analysis and the multi-variate drug profiling method by Loo et al. We illustrate its utility with a study of Annonaceous acetogenins, a family of compounds with drug potential. Our result reveals that squamocin induces more fragmented mitochondria than muricin A. Availability: Mitochondrial cell images, their corresponding feature sets (SSLF and WSLF) and the source code of our proposed method are available at http://aiia.iis.sinica.edu.tw/. Contact: chunnan@iis.sinica.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20529919

  8. Computer Model Inversion and Uncertainty Quantification in the Geosciences

    NASA Astrophysics Data System (ADS)

    White, Jeremy T.

    The subject of this dissertation is use of computer models as data analysis tools in several different geoscience settings, including integrated surface water/groundwater modeling, tephra fallout modeling, geophysical inversion, and hydrothermal groundwater modeling. The dissertation is organized into three chapters, which correspond to three individual publication manuscripts. In the first chapter, a linear framework is developed to identify and estimate the potential predictive consequences of using a simple computer model as a data analysis tool. The framework is applied to a complex integrated surface-water/groundwater numerical model with thousands of parameters. Several types of predictions are evaluated, including particle travel time and surface-water/groundwater exchange volume. The analysis suggests that model simplifications have the potential to corrupt many types of predictions. The implementation of the inversion, including how the objective function is formulated, what minimum of the objective function value is acceptable, and how expert knowledge is enforced on parameters, can greatly influence the manifestation of model simplification. Depending on the prediction, failure to specifically address each of these important issues during inversion is shown to degrade the reliability of some predictions. In some instances, inversion is shown to increase, rather than decrease, the uncertainty of a prediction, which defeats the purpose of using a model as a data analysis tool. In the second chapter, an efficient inversion and uncertainty quantification approach is applied to a computer model of volcanic tephra transport and deposition. The computer model simulates many physical processes related to tephra transport and fallout. The utility of the approach is demonstrated for two eruption events. In both cases, the importance of uncertainty quantification is highlighted by exposing the variability in the conditioning provided by the observations used for

  9. 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.

  10. Quantification of low levels of fluorine content in thin films

    NASA Astrophysics Data System (ADS)

    Ferrer, F. J.; Gil-Rostra, J.; Terriza, A.; Rey, G.; Jiménez, C.; García-López, J.; Yubero, F.

    2012-03-01

    Fluorine quantification in thin film samples containing different amounts of fluorine atoms was accomplished by combining proton-Rutherford Backscattering Spectrometry (p-RBS) and proton induced gamma-ray emission (PIGE) using proton beams of 1550 and 2330 keV for p-RBS and PIGE measurements, respectively. The capabilities of the proposed quantification method are illustrated with examples of the analysis of a series of samples of fluorine-doped tin oxides, fluorinated silica, and fluorinated diamond-like carbon films. It is shown that this procedure allows the quantification of F contents as low as 1 at.% in thin films with thicknesses in the 100-400 nm range.

  11. 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

  12. Wireless accelerometer reflex quantification system characterizing response and latency.

    PubMed

    LeMoyne, Robert; Coroian, Cristian; Mastroianni, Timothy

    2009-01-01

    The evaluation of the deep tendon reflex is a standard aspect of a neurological evaluation, which is frequently evoked through the patellar tendon reflex. Important features of the reflex are response and latency, providing insight to status for peripheral neuropathy and upper motor neuron syndrome. A wireless accelerometer reflex quantification system has been developed, tested, and evaluated. The reflex input is derived from a potential energy setting. Wireless accelerometers characterize the reflex hammer strike and reflex response acceleration waveforms, enabling the quantification of reflex response and latency. Spectral analysis of the reflex response acceleration waveform elucidates the frequency domain, opening the potential for new reflex classification metrics. The wireless accelerometer reflex quantification system yields accurate and consistent quantification of reflex response and latency.

  13. Recent application of quantification II in Japanese medical research.

    PubMed Central

    Suzuki, T; Kudo, A

    1979-01-01

    Hayashi's Quantification II is a method of multivariate discrimination analysis to manipulate attribute data as predictor variables. It is very useful in the medical research field for estimation, diagnosis, prognosis, evaluation of epidemiological factors, and other problems based on multiplicity of attribute data. In Japan, this method is so well known that most of the computer program packages include the Hayashi Quantification, but it seems to be yet unfamiliar with the method for researchers outside Japan. In view of this situation, we introduced 19 selected articles of recent applications of the Quantification II in Japanese medical research. In reviewing these papers, special mention is made to clarify how the researchers were satisfied with findings provided by the method. At the same time, some recommendations are made about terminology and program packages. Also a brief discussion of the background of the quantification methods is given with special reference to the Behaviormetric Society of Japan. PMID:540587

  14. Multiphysics modeling and uncertainty quantification for an active composite reflector

    NASA Astrophysics Data System (ADS)

    Peterson, Lee D.; Bradford, S. C.; Schiermeier, John E.; Agnes, Gregory S.; Basinger, Scott A.

    2013-09-01

    A multiphysics, high resolution simulation of an actively controlled, composite reflector panel is developed to extrapolate from ground test results to flight performance. The subject test article has previously demonstrated sub-micron corrected shape in a controlled laboratory thermal load. This paper develops a model of the on-orbit performance of the panel under realistic thermal loads, with an active heater control system, and performs an uncertainty quantification of the predicted response. The primary contribution of this paper is the first reported application of the Sandia developed Sierra mechanics simulation tools to a spacecraft multiphysics simulation of a closed-loop system, including uncertainty quantification. The simulation was developed so as to have sufficient resolution to capture the residual panel shape error that remains after the thermal and mechanical control loops are closed. An uncertainty quantification analysis was performed to assess the predicted tolerance in the closed-loop wavefront error. Key tools used for the uncertainty quantification are also described.

  15. A quantification model for the structure of clay materials.

    PubMed

    Tang, Liansheng; Sang, Haitao; Chen, Haokun; Sun, Yinlei; Zhang, Longjian

    2016-07-04

    In this paper, the quantification for clay structure is explicitly explained, and the approach and goals of quantification are also discussed. The authors consider that the purpose of the quantification for clay structure is to determine some parameters that can be used to quantitatively characterize the impact of clay structure on the macro-mechanical behaviour. According to the system theory and the law of energy conservation, a quantification model for the structure characteristics of clay materials is established and three quantitative parameters (i.e., deformation structure potential, strength structure potential and comprehensive structure potential) are proposed. And the corresponding tests are conducted. The experimental results show that these quantitative parameters can accurately reflect the influence of clay structure on the deformation behaviour, strength behaviour and the relative magnitude of structural influence on the above two quantitative parameters, respectively. These quantitative parameters have explicit mechanical meanings, and can be used to characterize the structural influences of clay on its mechanical behaviour.

  16. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    PubMed Central

    Karakosta, Theano D.; Soosaipillai, Antoninus; Batruch, Ihor

    2016-01-01

    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

  18. Sentinel Lymph Node Biopsy: Quantification of Lymphedema Risk Reduction

    DTIC Science & Technology

    2006-10-01

    Quantification of Lymphedema Risk Reduction PRINCIPAL INVESTIGATOR: Andrea L. Cheville, M.D. CONTRACTING ORGANIZATION: University of...Biopsy: Quantification of Lymphedema Risk Reduction 5b. GRANT NUMBER DAMD17-00-1-0649 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Andrea L. Cheville...Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Lymphedema is a common complication of primary breast cancer therapy. It

  19. A regularized method for peptide quantification.

    PubMed

    Yang, Chao; Yang, Can; Yu, Weichuan

    2010-05-07

    Peptide abundance estimation is generally the first step in protein quantification. In peptide abundance estimation, peptide overlapping and peak intensity variation are two challenges. The main objective of this paper is to estimate peptide abundance by taking advantage of peptide isotopic distribution and smoothness of peptide elution profile. Our method proposes to solve the peptide overlapping problem and provides a way to control the variance of estimation. We compare our method with a commonly used method on simulated data sets and two real data sets of standard protein mixtures. The results show that our method achieves more accurate estimation of peptide abundance on different samples. In our method, there is a variance-related parameter. Considering the well-known trade-off between the variance and the bias of estimation, we should not only focus on reducing the variance in real applications. A suggestion about parameter selection is given based on the discussion of variance and bias. Matlab source codes and detailed experimental results are available at http://bioinformatics.ust.hk/PeptideQuant/peptidequant.htm.

  20. 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.

  1. Quantification of periodic breathing in premature infants

    PubMed Central

    Mohr, Mary A.; Fairchild, Karen D.; Patel, Manisha; Sinkin, Robert A.; Clark, Matthew T.; Moorman, J. Randall; Lake, Douglas E.; Kattwinkel, John; Delos, John B.

    2015-01-01

    Background Periodic breathing (PB), regular cycles of short apneic pauses and breaths, is common in newborn infants. To characterize normal and potentially pathologic PB, we used our automated apnea detection system and developed a novel method for quantifying PB. We identified a preterm infant who died of SIDS and who, on review of her breathing pattern while in the NICU, had exaggerated PB. Methods We analyzed the chest impedance signal for short apneic pauses and developed a wavelet transform method to identify repetitive 10–40 second cycles of apnea/breathing. Clinical validation was performed to distinguish PB from apnea clusters and determine the wavelet coefficient cutoff having optimum diagnostic utility. We applied this method to analyze the chest impedance signals throughout the entire NICU stays of all 70 infants born at 32 weeks’ gestation admitted over a two-and-a-half year period. This group includes an infant who died of SIDS and her twin. Results For infants of 32 weeks’ gestation, the fraction of time spent in PB peaks 7–14 days after birth at 6.5%. During that time the infant that died of SIDS spent 40% of each day in PB and her twin spent 15% of each day in PB. Conclusions This wavelet transform method allows quantification of normal and potentially pathologic PB in NICU patients. PMID:26012526

  2. Quantification of biological aging in young adults.

    PubMed

    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

    2015-07-28

    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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Broadband acoustic quantification of stratified turbulence.

    PubMed

    Lavery, Andone C; Geyer, W Rockwell; Scully, Malcolm E

    2013-07-01

    High-frequency broadband acoustic scattering techniques have enabled the remote, high-resolution imaging and quantification of highly salt-stratified turbulence in an estuary. Turbulent salinity spectra in the stratified shear layer have been measured acoustically and by in situ turbulence sensors. The acoustic frequencies used span 120-600 kHz, which, for the highly stratified and dynamic estuarine environment, correspond to wavenumbers in the viscous-convective subrange (500-2500 m(-1)). The acoustically measured spectral levels are in close agreement with spectral levels measured with closely co-located micro-conductivity probes. The acoustically measured spectral shapes allow discrimination between scattering dominated by turbulent salinity microstructure and suspended sediments or swim-bladdered fish, the two primary sources of scattering observed in the estuary in addition to turbulent salinity microstructure. The direct comparison of salinity spectra inferred acoustically and by the in situ turbulence sensors provides a test of both the acoustic scattering model and the quantitative skill of acoustical remote sensing of turbulence dissipation in a strongly sheared and salt-stratified estuary.

  8. 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.

  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. Mouse Polyomavirus: Propagation, Purification, Quantification, and Storage.

    PubMed

    Horníková, Lenka; Žíla, Vojtěch; Španielová, Hana; Forstová, Jitka

    2015-08-03

    Mouse polyomavirus (MPyV) is a member of the Polyomaviridae family, which comprises non-enveloped tumorigenic viruses infecting various vertebrates including humans and causing different pathogenic responses in the infected organisms. Despite the variations in host tropism and pathogenicity, the structure of the virions of these viruses is similar. The capsid, with icosahedral symmetry (ø, 45 nm, T = 7d), is composed of a shell of 72 capsomeres of structural proteins, arranged around the nucleocore containing approximately 5-kbp-long circular dsDNA in complex with cellular histones. MPyV has been one of the most studied polyomaviruses and serves as a model virus for studies of the mechanisms of cell transformation and virus trafficking, and for use in nanotechnology. It can be propagated in primary mouse cells (e.g., in whole mouse embryo cells) or in mouse epithelial or fibroblast cell lines. In this unit, propagation, purification, quantification, and storage of MPyV virions are presented.

  11. 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

  12. Characterization and quantification of biochar alkalinity.

    PubMed

    Fidel, Rivka B; Laird, David A; Thompson, Michael L; Lawrinenko, Michael

    2017-01-01

    Lack of knowledge regarding the nature of biochar alkalis has hindered understanding of pH-sensitive biochar-soil interactions. Here we investigate the nature of biochar alkalinity and present a cohesive suite of methods for its quantification. Biochars produced from cellulose, corn stover and wood feedstocks had significant low-pKa organic structural (0.03-0.34 meq g(-1)), other organic (0-0.92 meq g(-1)), carbonate (0.02-1.5 meq g(-1)), and other inorganic (0-0.26 meq g(-1)) alkalinities. All four categories of biochar alkalinity contributed to total biochar alkalinity and are therefore relevant to pH-sensitive soil processes. Total biochar alkalinity was strongly correlated with base cation concentration, but biochar alkalinity was not a simple function of elemental composition, soluble ash, fixed carbon, or volatile matter content. More research is needed to characterize soluble biochar alkalis other than carbonates and to establish predictive relationships among biochar production parameters and the composition of biochar alkalis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. 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.

  14. 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.

  15. Uncertainty Quantification in High Throughput Screening ...

    EPA Pesticide Factsheets

    Using uncertainty quantification, we aim to improve the quality of modeling data from high throughput screening assays for use in risk assessment. ToxCast is a large-scale screening program that analyzes thousands of chemicals using over 800 assays representing hundreds of biochemical and cellular processes, including endocrine disruption, cytotoxicity, and zebrafish development. Over 2.6 million concentration response curves are fit to models to extract parameters related to potency and efficacy. Models built on ToxCast results are being used to rank and prioritize the toxicological risk of tested chemicals and to predict the toxicity of tens of thousands of chemicals not yet tested in vivo. However, the data size also presents challenges. When fitting the data, the choice of models, model selection strategy, and hit call criteria must reflect the need for computational efficiency and robustness, requiring hard and somewhat arbitrary cutoffs. When coupled with unavoidable noise in the experimental concentration response data, these hard cutoffs cause uncertainty in model parameters and the hit call itself. The uncertainty will then propagate through all of the models built on the data. Left unquantified, this uncertainty makes it difficult to fully interpret the data for risk assessment. We used bootstrap resampling methods to quantify the uncertainty in fitting models to the concentration response data. Bootstrap resampling determines confidence intervals for

  16. 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.

  17. Raman spectroscopic quantification of milk powder constituents.

    PubMed

    McGoverin, C M; Clark, A S S; Holroyd, S E; Gordon, K C

    2010-07-12

    Raman spectroscopy has significant potential for the quantification of food products. Milk powder is an important foodstuff and ingredient that is produced on large scale (over 20 million tonnes per annum). Raman spectroscopy, unlike near- and mid-infrared spectroscopies, has not been used extensively to quantify milk powder constituents. The effect of sample presentation on spectroscopic calibrations of protein and fat for 136 New Zealand milk powders was assessed using Raman spectroscopy. Prediction models were produced to quantify a protein concentration range of 32.19-37.65% w/w for skim milk powder, and a protein concentration range of 23.34-25.02% w/w and a fat concentration range of 26.26-29.68% w/w for whole milk powder (where ratios of prediction to deviation exceeded 2.6 with one exception). The resultant calibrations were not influenced by sample orientation; the sample temperature during data collection did affect the calibrations. Calcium fortification in the form of calcium carbonate was identified within a sub-set of samples, reinforcing the efficacy of Raman spectroscopy for identifying both crystalline and non-crystalline constituents within milk powder.

  18. Quantification of bromophenols in Islay whiskies.

    PubMed

    Bendig, Paul; Lehnert, Katja; Vetter, Walter

    2014-04-02

    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.

  19. Quantification of furandiones in ambient aerosol

    NASA Astrophysics Data System (ADS)

    Al-Naiema, Ibrahim M.; Roppo, Hannah M.; Stone, Elizabeth A.

    2017-03-01

    Furandiones are products of the photooxidation of anthropogenic volatile organic compounds (VOC), like toluene, and contribute to secondary organic aerosol (SOA). Because few molecular tracers of anthropogenic SOA are used to assess this source in ambient aerosol, developing a quantification method for furandiones holds a great importance. In this study, we developed a direct and highly sensitive gas chromatography-mass spectrometry method for the quantitative analysis of furandiones in fine particulate matter that is mainly free from interference by structurally-related dicarboxylic acids. Our application of this method in Iowa City, IA provides the first ambient measurements of four furandiones: 2,5-furandione, 3-methyl-2,5-furandione, dihydro-2,5-furandione, and dihydro-3-methyl-2,5-furandione. Furandiones were detected in all collected samples with a daily average concentration of 9.1 ± 3.8 ng m-3. The developed method allows for the accurate measurement of the furandiones concentrations in ambient aerosol, which will support future evaluation of these compounds as tracers for anthropogenic SOA and assessment of their potential health impacts.

  20. Uncertainty quantification in flood risk assessment

    NASA Astrophysics Data System (ADS)

    Blöschl, Günter; Hall, Julia; Kiss, Andrea; Parajka, Juraj; Perdigão, Rui A. P.; Rogger, Magdalena; Salinas, José Luis; Viglione, Alberto

    2017-04-01

    Uncertainty is inherent to flood risk assessments because of the complexity of the human-water system, which is characterised by nonlinearities and interdependencies, because of limited knowledge about system properties and because of cognitive biases in human perception and decision-making. On top of the uncertainty associated with the assessment of the existing risk to extreme events, additional uncertainty arises because of temporal changes in the system due to climate change, modifications of the environment, population growth and the associated increase in assets. Novel risk assessment concepts are needed that take into account all these sources of uncertainty. They should be based on the understanding of how flood extremes are generated and how they change over time. They should also account for the dynamics of risk perception of decision makers and population in the floodplains. In this talk we discuss these novel risk assessment concepts through examples from Flood Frequency Hydrology, Socio-Hydrology and Predictions Under Change. We believe that uncertainty quantification in flood risk assessment should lead to a robust approach of integrated flood risk management aiming at enhancing resilience rather than searching for optimal defense strategies.

  1. 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.

  2. Uncertainty quantification in volumetric Particle Image Velocimetry

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Sayantan; Charonko, John; Vlachos, Pavlos

    2016-11-01

    Particle Image Velocimetry (PIV) uncertainty quantification is challenging due to coupled sources of elemental uncertainty and complex data reduction procedures in the measurement chain. Recent developments in this field have led to uncertainty estimation methods for planar PIV. However, no framework exists for three-dimensional volumetric PIV. In volumetric PIV the measurement uncertainty is a function of reconstructed three-dimensional particle location that in turn is very sensitive to the accuracy of the calibration mapping function. Furthermore, the iterative correction to the camera mapping function using triangulated particle locations in space (volumetric self-calibration) has its own associated uncertainty due to image noise and ghost particle reconstructions. Here we first quantify the uncertainty in the triangulated particle position which is a function of particle detection and mapping function uncertainty. The location uncertainty is then combined with the three-dimensional cross-correlation uncertainty that is estimated as an extension of the 2D PIV uncertainty framework. Finally the overall measurement uncertainty is quantified using an uncertainty propagation equation. The framework is tested with both simulated and experimental cases. For the simulated cases the variation of estimated uncertainty with the elemental volumetric PIV error sources are also evaluated. The results show reasonable prediction of standard uncertainty with good coverage.

  3. Quantification of cocontraction in spastic cerebral palsy.

    PubMed

    Ikeda, A J; Abel, M F; Granata, K P; Damiano, D L

    1998-12-01

    Antagonist cocontraction was hypothesized to limit net moment production in children with spastic diplegic cerebral palsy (CP). A second hypothesis was that concontraction would vary with joint angle. To test these hypotheses, surface EMG activity and moment data from the quadriceps and hamstrings muscle groups were obtained from children with CP and compared with normally developing children during isometric flexion and extension exertions. A biomechanical model was developed to predict individual moments produced by the agonist and antagonist muscle groups. Concontraction was defined as the percentage of the net moment that was negated by the antagonist moment. The model performed well in predicting the measured moment as illustrated by high R2 correlation coefficients and low prediction errors. The mean maximum moment produced was greater in normally developing children than children with CP in both flexion and extension. Antagonist cocontraction during extension was greater in children with CP (12.2 +/- 14.4%) than in normally developing children (4.9 +/- 3.8%), implying that antagonist cocontraction is one explanation for the observed extension weakness in children with CP. However, during flexion, cocontraction was not significantly different between the two groups. Cocontraction differed significantly with joint angle in both groups during flexion and in the normally developing children during extension. Although quantifying coactivation based on EMG activity alone produced similar results, it underestimated the effect of the antagonist. The quantification of cocontraction has potential applications for characterizing spastic muscle dysfunction and thereby improving clinical outcomes in children with CP.

  4. 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

  5. In vivo quantification of human lung dose response relationship

    NASA Astrophysics Data System (ADS)

    O'Dell, Walter; Wang, Peng; Liu, Haisong; Fuller, David; Schell, Michael C.; Okunieff, Paul

    2007-03-01

    Purpose: To implement a new non-invasive in-vivo assay to compute the dose-response relationship following radiation-induced injury to normal lung tissue, using computed tomography (CT) scans of the chest. Methods and Materials: Follow-up volumetric CT scans were acquired in patients with metastatic tumors to the lung treated using stereotactic radiation therapy. The images reveal a focal region of fibrosis corresponding to the high-dose region and no observable long-term damage in distant sites. For each pixel in the follow-up image the treatment dose and the change in apparent tissue density was compiled. For each of 12 pre-selected dose levels the average pixel tissue density change was computed and fit to a two-parameter dose-response model. The sensitivity of the resulting fits to registration error was also quantified. Results: Complete in vivo dose-response relationships in human normal lung tissue were computed. Increasing radiation sensitivity was found with larger treatment volume. Radiation sensitivity increased also over time up to 12 months, but decreased at later time points. The time-course of dose response correlated with the time-course of levels of circulating IL-1α, TGFβ and MCP-1. The method was found to be robust to registration errors up to 3 mm. Conclusions: This approach for the first time enables the quantification of the full range dose response relationship in human subjects. The method may be used to assess quantitatively the efficacy of various agents thought to illicit radiation protection to the lung.

  6. Identification, distribution, and quantification of biominerals in a deciduous forest.

    PubMed

    Krieger, C; Calvaruso, C; Morlot, C; Uroz, S; Salsi, L; Turpault, M-P

    2017-03-01

    Biomineralization is a common process in most vascular plants, but poorly investigated for trees. Although the presence of calcium oxalate and silica accumulation has been reported for some tree species, the chemical composition, abundance, and quantification of biominerals remain poorly documented. However, biominerals may play important physiological and structural roles in trees, especially in forest ecosystems, which are characterized by nutrient-poor soils. In this context, our study aimed at investigating the morphology, distribution, and relative abundance of biominerals in the different vegetative compartments (foliage, branch, trunk, and root) of Fagus sylvatica L. and Acer pseudoplatanus L. using a combination of scanning electron microscopy and tomography analyses. Biomineral crystallochemistry was assessed by X-ray diffraction and energy-dispersive X-ray analyses, while calcium, silicon, and oxalic acid were quantified in the compartments and at the forest scale. Our analyses revealed that biominerals occurred as crystals or coating layers mostly in bark and leaves and were identified as opal, whewellite, and complex biominerals. In both tree species, opal was mostly found in the external tissues of trunk, branch, and leaves, but also in the roots of beech. In the stand, opal represents around 170 kg/ha. Whewellite was found to suit to conductive tissues (i.e., axial phloem parenchyma, vascular bundles, vessel element) in all investigated compartments of the two tree species. The shape of whewellite was prismatic and druses in beech, and almost all described shapes were seen in sycamore maple. Notably, the amount of whewellite was strongly correlated with the total calcium in all investigated compartments whatever the tree species is, suggesting a biologic control of whewellite precipitation. The amount of whewellite in the aboveground biomass of Montiers forest was more important than that of opal and was around 1170 kg/ha. Therefore, biominerals

  7. Real Time Free Cortisol Quantification Among Critically Ill Children

    PubMed Central

    Zimmerman, Jerry J.; Donaldson, Amy; Barker, Ruth M.; Meert, Kathleen L.; Harrison, Rick; Carcillo, Joseph A.; Anand, Kanwaljeet J. S.; Newth, Christopher J. L.; Berger, John; Willson, Douglas F.; Jack, Rhona; Nicholson, Carol; Dean, J. Michael

    2013-01-01

    Objectives Ascertainment of adrenal function assessing free (FC) rather that total (TC) cortisol may be beneficial for the diagnosis of critical illness related cortisol insufficiency (CIRCI). We hypothesized that centrifugal ultrafiltration (CUF) would provide timely FC data that highly correlated with the gold standard, but logistically cumbersome, equilibrium dialysis (EQD) technique when the FC fractions were identically quantified by chemiluminescence immunoassay. We also hypothesized that FC would correlate with illness severity in a large cohort of critically ill children. Design Prospective, multi-institutional, observational cohort investigation. Setting Seven pediatric intensive care units (PICUs) within the Eunice Kennedy Shriver National Institute of Child Health and Human Development Collaborative Pediatric Critical Care Research Network. Patients 165 critically ill children across the spectrum of illness severity. Interventions Blood sampling. Measurements and main results Time to derive plasma FC concentrations following CUF or EQD fractionation with chemiluminescence immunoassay was ~2 versus ~24 hours, respectively. Utilizing CUF, mean plasma FC was 4.1 ± 6.7 ug/dL (median 1.6, range 0.2-43.6), representing an average of 15.2 ± 9.4% of total cortisol. Nearly 60% of subjects exhibited FC < 2 and 30% < 0.8 ug/dL, previously suggested threshold concentrations for defining CIRCI. Plasma FC concentrations comparing CUF versus EQD fractionation demonstrated a strong correlation (R2 = 0.97). For FC < 2 ug/dL Bland-Altman analysis revealed minimal negative bias for the CUF technique. Illness severity assessed by PRISM III correlated moderately with FC and percent TC as FC. Conclusions Determination of CUF fractionated FC was fast and results correlated highly with EQD fractionated FC. Many children exhibited FC < 2 and < 0.8 ug/dL, but did not demonstrate clinical evidence of CIRCI. This study ascertains that real time FC quantification is feasible to

  8. Heterochromatic Flicker Photometry for Objective Lens Density Quantification.

    PubMed

    Najjar, Raymond P; Teikari, Petteri; Cornut, Pierre-Loïc; Knoblauch, Kenneth; Cooper, Howard M; Gronfier, Claude

    2016-03-01

    Although several methods have been proposed to evaluate lens transmittance, to date there is no consensual in vivo approach in clinical practice. The aim of this study was to compare ocular lens density and transmittance measurements obtained by an improved psychophysical scotopic heterochromatic flicker photometry (sHFP) technique to the results obtained by three other measures: a psychophysical threshold technique, a Scheimpflug imaging technique, and a clinical assessment using a validated subjective scale. Forty-three subjects (18 young, 9 middle aged, and 16 older) were included in the study. Individual lens densities were measured and transmittance curves were derived from sHFP indexes. Ocular lens densities were compared across methods by using linear regression analysis. The four approaches showed a quadratic increase in lens opacification with age. The sHFP technique revealed that transmittance decreased with age over the entire visual spectrum. This decrease was particularly pronounced between young and older participants in the short (53.03% decrease in the 400-500 nm range) wavelength regions of the light spectrum. Lens density derived from sHFP highly correlated with the values obtained with the other approaches. Compared to other objective measures, sHFP also showed the lowest variability and the best fit with a quadratic trend (r2 = 0.71) of lens density increase as a function of age. The sHFP technique offers a practical, reliable, and accurate method to measure lens density in vivo and predict lens transmittance over the visible spectrum. An accurate quantification of lens transmittance should be obtained in clinical practice, but also in research in visual and nonvisual photoreception.

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

    PubMed

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

    2016-07-15

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

  10. 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

  11. Quantification of water in hydrous ringwoodite

    SciTech Connect

    Thomas, Sylvia -Monique; Jacobsen, Steven D.; Bina, Craig R.; Reichart, Patrick; Moser, Marcus; Hauri, Erik H.; Koch-Muller, Monika; Smyth, Joseph R.; Dollinger, Gunther

    2015-01-28

    Here, ringwoodite, γ-(Mg,Fe)2SiO4, in the lower 150 km of Earth’s mantle transition zone (410-660 km depth) can incorporate up to 1.5-2 wt% H2O as hydroxyl defects. We present a mineral-specific IR calibration for the absolute water content in hydrous ringwoodite by combining results from Raman spectroscopy, secondary ion mass spectrometery (SIMS) and proton-proton (pp)-scattering on a suite of synthetic Mg- and Fe-bearing hydrous ringwoodites. H2O concentrations in the crystals studied here range from 0.46 to 1.7 wt% H2O (absolute methods), with the maximum H2O in the same sample giving 2.5 wt% by SIMS calibration. Anchoring our spectroscopic results to absolute H-atom concentrations from pp-scattering measurements, we report frequency-dependent integrated IR-absorption coefficients for water in ringwoodite ranging from 78180 to 158880 L mol-1cm-2, depending upon frequency of the OH absorption. We further report a linear wavenumber IR calibration for H2O quantification in hydrous ringwoodite across the Mg2SiO4-Fe2SiO4 solid solution, which will lead to more accurate estimations of the water content in both laboratory-grown and naturally occurring ringwoodites. Re-evaluation of the IR spectrum for a natural hydrous ringwoodite inclusion in diamond from the study of the crystal contains 1.43 ± 0.27 wt% H2O, thus confirming near-maximum amounts of H2O for this sample from the transition zone.

  12. GPU-accelerated voxelwise hepatic perfusion quantification

    NASA Astrophysics Data System (ADS)

    Wang, H.; Cao, Y.

    2012-09-01

    Voxelwise quantification of hepatic perfusion parameters from dynamic contrast enhanced (DCE) imaging greatly contributes to assessment of liver function in response to radiation therapy. However, the efficiency of the estimation of hepatic perfusion parameters voxel-by-voxel in the whole liver using a dual-input single-compartment model requires substantial improvement for routine clinical applications. In this paper, we utilize the parallel computation power of a graphics processing unit (GPU) to accelerate the computation, while maintaining the same accuracy as the conventional method. Using compute unified device architecture-GPU, the hepatic perfusion computations over multiple voxels are run across the GPU blocks concurrently but independently. At each voxel, nonlinear least-squares fitting the time series of the liver DCE data to the compartmental model is distributed to multiple threads in a block, and the computations of different time points are performed simultaneously and synchronically. An efficient fast Fourier transform in a block is also developed for the convolution computation in the model. The GPU computations of the voxel-by-voxel hepatic perfusion images are compared with ones by the CPU using the simulated DCE data and the experimental DCE MR images from patients. The computation speed is improved by 30 times using a NVIDIA Tesla C2050 GPU compared to a 2.67 GHz Intel Xeon CPU processor. To obtain liver perfusion maps with 626 400 voxels in a patient's liver, it takes 0.9 min with the GPU-accelerated voxelwise computation, compared to 110 min with the CPU, while both methods result in perfusion parameters differences less than 10-6. The method will be useful for generating liver perfusion images in clinical settings.

  13. Quantification of asphaltene precipitation by scaling equation

    NASA Astrophysics Data System (ADS)

    Janier, Josefina Barnachea; Jalil, Mohamad Afzal B. Abd.; Samin, Mohamad Izhar B. Mohd; Karim, Samsul Ariffin B. A.

    2015-02-01

    Asphaltene precipitation from crude oil is one of the issues for the oil industry. The deposition of asphaltene occurs during production, transportation and separating process. The injection of carbon dioxide (CO2) during enhance oil recovery (EOR) is believed to contribute much to the precipitation of asphaltene. Precipitation can be affected by the changes in temperature and pressure on the crude oil however, reduction in pressure contribute much to the instability of asphaltene as compared to temperature. This paper discussed the quantification of precipitated asphaltene in crude oil at different high pressures and at constant temperature. The derived scaling equation was based on the reservoir condition with variation in the amount of carbon dioxide (CO2) mixed with Dulang a light crude oil sample used in the experiment towards the stability of asphaltene. A FluidEval PVT cell with Solid Detection System (SDS) was the instrument used to gain experimental knowledge on the behavior of fluid at reservoir conditions. Two conditions were followed in the conduct of the experiment. Firstly, a 45cc light crude oil was mixed with 18cc (40%) of CO2 and secondly, the same amount of crude oil sample was mixed with 27cc (60%) of CO2. Results showed that for a 45cc crude oil sample combined with 18cc (40%) of CO2 gas indicated a saturation pressure of 1498.37psi and asphaltene onset point was 1620psi. Then for the same amount of crude oil combined with 27cc (60%) of CO2, the saturation pressure was 2046.502psi and asphaltene onset point was 2230psi. The derivation of the scaling equation considered reservoir temperature, pressure, bubble point pressure, mole percent of the precipitant the injected gas CO2, and the gas molecular weight. The scaled equation resulted to a third order polynomial that can be used to quantify the amount of asphaltene in crude oil.

  14. Quantification of water in hydrous ringwoodite

    DOE PAGES

    Thomas, Sylvia -Monique; Jacobsen, Steven D.; Bina, Craig R.; ...

    2015-01-28

    Here, ringwoodite, γ-(Mg,Fe)2SiO4, in the lower 150 km of Earth’s mantle transition zone (410-660 km depth) can incorporate up to 1.5-2 wt% H2O as hydroxyl defects. We present a mineral-specific IR calibration for the absolute water content in hydrous ringwoodite by combining results from Raman spectroscopy, secondary ion mass spectrometery (SIMS) and proton-proton (pp)-scattering on a suite of synthetic Mg- and Fe-bearing hydrous ringwoodites. H2O concentrations in the crystals studied here range from 0.46 to 1.7 wt% H2O (absolute methods), with the maximum H2O in the same sample giving 2.5 wt% by SIMS calibration. Anchoring our spectroscopic results to absolutemore » H-atom concentrations from pp-scattering measurements, we report frequency-dependent integrated IR-absorption coefficients for water in ringwoodite ranging from 78180 to 158880 L mol-1cm-2, depending upon frequency of the OH absorption. We further report a linear wavenumber IR calibration for H2O quantification in hydrous ringwoodite across the Mg2SiO4-Fe2SiO4 solid solution, which will lead to more accurate estimations of the water content in both laboratory-grown and naturally occurring ringwoodites. Re-evaluation of the IR spectrum for a natural hydrous ringwoodite inclusion in diamond from the study of the crystal contains 1.43 ± 0.27 wt% H2O, thus confirming near-maximum amounts of H2O for this sample from the transition zone.« less

  15. Quantification of wound oedema after dermatological surgery.

    PubMed

    McGrath, E J; Kersey, P

    2009-12-01

    Postoperative wound oedema causing increased suture tension is thought to be a possible cause of scars known as suture marks. Quantification of such oedema has not previously been reported in the literature. Measures to accommodate wound oedema may include the adoption of alternative suture techniques and the use of more elastic suture materials. To quantify wound expansion after skin surgery and to identify any contributory factors, and to determine the ability of eight commonly used skin suture materials to stretch under increasing tension. Forty consecutive adult patients attending a dermatology department for routine skin surgery in December 2002 were recruited. Details including body site, nature of the lesion excised and dimensions of the open wound were recorded. The distance between entry and exit points of an untied suture at the time of skin surgery was measured and then repeated 24 h postoperatively. The ability of eight different suture materials to stretch when an increasing force was applied was measured by hanging standard weights from the sutures and measuring the suture length for each force applied. Thirty-nine patients completed the study. All wounds expanded postoperatively, with a mean lateral expansion of 1.0 mm. There was a strong association between the width of the unsutured wound after excision and the subsequent wound expansion. Commonly used sutures in skin surgery were found to be relatively inelastic at forces under 0.2 kg. The monofilament Novofil (Davis & Geck, Danbury, CT, U.S.A.) exhibited the greatest degree of stretch of those tested. There is considerable oedema in the first 24 h after skin surgery, particularly with wider excisions. This needs to be considered when choosing suturing materials and techniques to avoid excessive suture tension.

  16. Extended quantification of the generalized recurrence plot

    NASA Astrophysics Data System (ADS)

    Riedl, Maik; Marwan, Norbert; Kurths, Jürgen

    2016-04-01

    The generalized recurrence plot is a modern tool for quantification of complex spatial patterns. Its application spans the analysis of trabecular bone structures, Turing structures, turbulent spatial plankton patterns, and fractals. But, it is also successfully applied to the description of spatio-temporal dynamics and the detection of regime shifts, such as in the complex Ginzburg-Landau- equation. The recurrence plot based determinism is a central measure in this framework quantifying the level of regularities in temporal and spatial structures. We extend this measure for the generalized recurrence plot considering additional operations of symmetry than the simple translation. It is tested not only on two-dimensional regular patterns and noise but also on complex spatial patterns reconstructing the parameter space of the complex Ginzburg-Landau-equation. The extended version of the determinism resulted in values which are consistent to the original recurrence plot approach. Furthermore, the proposed method allows a split of the determinism into parts which based on laminar and non-laminar regions of the two-dimensional pattern of the complex Ginzburg-Landau-equation. A comparison of these parts with a standard method of image classification, the co-occurrence matrix approach, shows differences especially in the description of patterns associated with turbulence. In that case, it seems that the extended version of the determinism allows a distinction of phase turbulence and defect turbulence by means of their spatial patterns. This ability of the proposed method promise new insights in other systems with turbulent dynamics coming from climatology, biology, ecology, and social sciences, for example.

  17. 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.

  18. GPU-accelerated voxelwise hepatic perfusion quantification.

    PubMed

    Wang, H; Cao, Y

    2012-09-07

    Voxelwise quantification of hepatic perfusion parameters from dynamic contrast enhanced (DCE) imaging greatly contributes to assessment of liver function in response to radiation therapy. However, the efficiency of the estimation of hepatic perfusion parameters voxel-by-voxel in the whole liver using a dual-input single-compartment model requires substantial improvement for routine clinical applications. In this paper, we utilize the parallel computation power of a graphics processing unit (GPU) to accelerate the computation, while maintaining the same accuracy as the conventional method. Using compute unified device architecture-GPU, the hepatic perfusion computations over multiple voxels are run across the GPU blocks concurrently but independently. At each voxel, nonlinear least-squares fitting the time series of the liver DCE data to the compartmental model is distributed to multiple threads in a block, and the computations of different time points are performed simultaneously and synchronically. An efficient fast Fourier transform in a block is also developed for the convolution computation in the model. The GPU computations of the voxel-by-voxel hepatic perfusion images are compared with ones by the CPU using the simulated DCE data and the experimental DCE MR images from patients. The computation speed is improved by 30 times using a NVIDIA Tesla C2050 GPU compared to a 2.67 GHz Intel Xeon CPU processor. To obtain liver perfusion maps with 626 400 voxels in a patient's liver, it takes 0.9 min with the GPU-accelerated voxelwise computation, compared to 110 min with the CPU, while both methods result in perfusion parameters differences less than 10(-6). The method will be useful for generating liver perfusion images in clinical settings.

  19. Quantification and Reconstruction in Photoacoustic Tomography

    NASA Astrophysics Data System (ADS)

    Guo, Zijian

    Optical absorption is closely associated with many physiological important parameters, such as the concentration and oxygen saturation of hemoglobin. Conventionally, accurate quantification in PAT requires knowledge of the optical fluence attenuation, acoustic pressure attenuation, and detection bandwidth. We circumvent this requirement by quantifying the optical absorption coefficients from the acoustic spectra of PA signals acquired at multiple optical wavelengths. We demonstrate the method using the optical-resolution photoacoustic microscopy (OR-PAM) and the acoustical-resolution photoacoustic microscopy (AR-PAM) in the optical ballistic regime and in the optical diffusive regime, respectively. The data acquisition speed in photoacoustic computed tomography (PACT) is limited by the laser repetition rate and the number of parallel ultrasound detecting channels. Reconstructing an image with fewer measurements can effectively accelerate the data acquisition and reduce the system cost. We adapted Compressed Sensing (CS) for the reconstruction in PACT. CS-based PACT was implemented as a non-linear conjugate gradient descent algorithm and tested with both phantom and in vivo experiments. Speckles have been considered ubiquitous in all scattering-based coherent imaging technologies. As a coherent imaging modality based on optical absorption, photoacoustic (PA) tomography (PAT) is generally devoid of speckles. PAT suppresses speckles by building up prominent boundary signals, via a mechanism similar to that of specular reflection. When imaging smooth boundary absorbing targets, the speckle visibility in PAT, which is defined as the ratio of the square root of the average power of speckles to that of boundaries, is inversely proportional to the square root of the absorber density. If the surfaces of the absorbing targets have uncorrelated height fluctuations, however, the boundary features may become fully developed speckles. The findings were validated by simulations

  20. Bistatic Sonar and Quantification of Seafloor Processes

    NASA Astrophysics Data System (ADS)

    McCloghrie, P.; BLONDEL, P.; Pace, N. G.; Heald, G. J.; Brothers, R.

    2001-12-01

    Sonar has proved the best tool for investigation of seafloor processes. Calibrated sonars provide a wealth of quantitative information unattainable through other means, but are limited to backscattering geometries, where the acoustic source and receiver are on the same platform. Recent developments in acoustic theory and design have shown the advantage of bistatic instruments, where the source and receiver(s) are physically decoupled and can be anywhere in the water column. Although there are many theoretical studies of bistatic scattering, their applicability is limited by the very low number of actual experiments. Using the large tank facilities at the University of Bath, we are currently investigating the bistatic scattering from several realistic types of seabeds and different morphologies, at high frequency (250 kHz). These studies are used in conjunction with state-of-the-art acoustic models (Blondel et al., 2001), and compared with data from complementary sea trials (Pace et al., in prep.). The results show the huge potential of bistatic systems for accurate and detailed mapping of seafloor structures and their topography. We also demonstrate how the relative contributions of surface and volume processes to acoustic scattering change with the imaging geometry, and how this can be used to maximise the information gained during mapping. Versatile and efficient, bistatic systems can be deployed from surface vessels, ROVs or AUVs. These new tools can be used for Rapid Environmental Assessment, to study sediment transport and deposition, and to access the detailed morphology of the seabed and the near sub-surface. They can in particular be used for the investigation of the small-scale structure of sand ridges and ripples, the distribution of tidal or glacial deposits on the seabed, and the quantification of multi-scale surface roughness in sedimentary and non-sedimentary terrains alike. Crown Copyright 2001 DERA. Published with the permission of the Defence

  1. GPU-Accelerated Voxelwise Hepatic Perfusion Quantification

    PubMed Central

    Wang, H; Cao, Y

    2012-01-01

    Voxelwise quantification of hepatic perfusion parameters from dynamic contrast enhanced (DCE) imaging greatly contributes to assessment of liver function in response to radiation therapy. However, the efficiency of the estimation of hepatic perfusion parameters voxel-by-voxel in the whole liver using a dual-input single-compartment model requires substantial improvement for routine clinical applications. In this paper, we utilize the parallel computation power of a graphics processing unit (GPU) to accelerate the computation, while maintaining the same accuracy as the conventional method. Using CUDA-GPU, the hepatic perfusion computations over multiple voxels are run across the GPU blocks concurrently but independently. At each voxel, non-linear least squares fitting the time series of the liver DCE data to the compartmental model is distributed to multiple threads in a block, and the computations of different time points are performed simultaneously and synchronically. An efficient fast Fourier transform in a block is also developed for the convolution computation in the model. The GPU computations of the voxel-by-voxel hepatic perfusion images are compared with ones by the CPU using the simulated DCE data and the experimental DCE MR images from patients. The computation speed is improved by 30 times using a NVIDIA Tesla C2050 GPU compared to a 2.67 GHz Intel Xeon CPU processor. To obtain liver perfusion maps with 626400 voxels in a patient’s liver, it takes 0.9 min with the GPU-accelerated voxelwise computation, compared to 110 min with the CPU, while both methods result in perfusion parameters differences less than 10−6. The method will be useful for generating liver perfusion images in clinical settings. PMID:22892645

  2. Uncertainty quantification for optical model parameters

    DOE PAGES

    Lovell, A. E.; Nunes, F. M.; Sarich, J.; ...

    2017-02-21

    Although uncertainty quantification has been making its way into nuclear theory, these methods have yet to be explored in the context of reaction theory. For example, it is well known that different parameterizations of the optical potential can result in different cross sections, but these differences have not been systematically studied and quantified. The purpose of our work is to investigate the uncertainties in nuclear reactions that result from fitting a given model to elastic-scattering data, as well as to study how these uncertainties propagate to the inelastic and transfer channels. We use statistical methods to determine a best fitmore » and create corresponding 95% confidence bands. A simple model of the process is fit to elastic-scattering data and used to predict either inelastic or transfer cross sections. In this initial work, we assume that our model is correct, and the only uncertainties come from the variation of the fit parameters. Here, we study a number of reactions involving neutron and deuteron projectiles with energies in the range of 5–25 MeV/u, on targets with mass A=12–208. We investigate the correlations between the parameters in the fit. The case of deuterons on 12C is discussed in detail: the elastic-scattering fit and the prediction of 12C(d,p)13C transfer angular distributions, using both uncorrelated and correlated χ2 minimization functions. The general features for all cases are compiled in a systematic manner to identify trends. This work shows that, in many cases, the correlated χ2 functions (in comparison to the uncorrelated χ2 functions) provide a more natural parameterization of the process. These correlated functions do, however, produce broader confidence bands. Further optimization may require improvement in the models themselves and/or more information included in the fit.« less

  3. Automated and nonbiased regional quantification of functional neuroimaging data.

    PubMed

    Parker, Jason G; Speidel, Benjamin; Sherwood, Matthew S

    2015-02-01

    In the quantification of functional neuroimaging data, region-of-interest (ROI) analysis can be used to assess a variety of properties of the activation signal, but taken alone these properties are susceptible to noise and may fail to accurately describe overall regional involvement. Here, the authors present and evaluate an automated method for quantification and localization of functional neuroimaging data that combines multiple properties of the activation signal to generate rank-order lists of regional activation results. The proposed automated quantification method, referred to as neuroimaging results decomposition (NIRD), begins by decomposing an activation map into a hierarchical list of ROIs using a digital atlas. In an intermediate step, the ROIs are rank-ordered according to extent, mean intensity, and total intensity. A final rank-order list (NIRD average rank) is created by sorting the ROIs according to the average of their ranks from the intermediate step. The authors hypothesized that NIRD average rank would have improved regional quantification accuracy compared to all other quantitative metrics, including methods based on properties of statistical clusters. To test their hypothesis, NIRD rankings were directly compared to three common cluster-based methods using simulated fMRI data both with and without realistic head motion. For both the no-motion and motion datasets, an analysis of variance found that significant differences between the quantification methods existed (F = 64.8, p < 0.0001 for no motion; F = 55.2, p < 0.0001 for motion), and a post-hoc test found that NIRD average rank was the most accurate quantification method tested (p < 0.05 for both datasets). Furthermore, all variants of the NIRD method were found to be significantly more accurate than the cluster-based methods in all cases. These results confirm their hypothesis and demonstrate that the proposed NIRD methodology provides improved regional quantification accuracy compared to

  4. US weapons secrets revealed

    SciTech Connect

    Norris, R.S.; Arkin, W.M.

    1993-03-01

    Extraordinary details have only recently been revealed about the struggle over the control of early U.S. nuclear weapons and their initial deployments abroad. The information comes from a newly declassified top secret report, part of a larger study, The History of the Strategic Arms Competition, 1945-1972, commissioned by Defense Secretary James R. Schlisinger in summer 1974.

  5. Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations.

    PubMed

    Higgs, Richard E; Butler, Jon P; Han, Bomie; Knierman, Michael D

    2013-01-01

    Recent improvements in the mass accuracy and resolution of mass spectrometers have led to renewed interest in label-free quantification using data from the primary mass spectrum (MS1) acquired from data-dependent proteomics experiments. The capacity for higher specificity quantification of peptides from samples enriched for proteins of biological interest offers distinct advantages for hypothesis generating experiments relative to immunoassay detection methods or prespecified peptide ions measured by multiple reaction monitoring (MRM) approaches. Here we describe an evaluation of different methods to post-process peptide level quantification information to support protein level inference. We characterize the methods by examining their ability to recover a known dilution of a standard protein in background matrices of varying complexity. Additionally, the MS1 quantification results are compared to a standard, targeted, MRM approach on the same samples under equivalent instrument conditions. We show the existence of multiple peptides with MS1 quantification sensitivity similar to the best MRM peptides for each of the background matrices studied. Based on these results we provide recommendations on preferred approaches to leveraging quantitative measurements of multiple peptides to improve protein level inference.

  6. Cytomegalovirus quantification: where to next in optimising patient management?

    PubMed

    Atkinson, Claire; Emery, Vincent C

    2011-08-01

    Over the years quantification of cytomegalovirus (HCMV) load in blood has become a mainstay of clinical management helping direct deployment of antiviral therapy, assess response to therapy and highlight cases of drug resistance. The review focuses on a brief historical perspective of HCMV quantification and the ways in which viral load is being used to improve patient management. A review of the published literature and also personal experience at the Royal Free Hospital. Quantification of HCMV is essential for efficient patient management. The ability to use real time quantitative PCR to drive pre-emptive therapy has improved patient management after transplantation although the threshold viral loads for deployment differ between laboratories. The field would benefit from access to a universal standard for quantification. We see that HCMV quantification will continue to be central to delivering individualised patient management and facilitating multicentre trials of new antiviral agents and vaccines in a variety of clinical settings. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. 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.

  8. Absolute and relative quantification of RNA modifications via biosynthetic isotopomers

    PubMed Central

    Kellner, Stefanie; Ochel, Antonia; Thüring, Kathrin; Spenkuch, Felix; Neumann, Jennifer; Sharma, Sunny; Entian, Karl-Dieter; Schneider, Dirk; Helm, Mark

    2014-01-01

    In the resurging field of RNA modifications, quantification is a bottleneck blocking many exciting avenues. With currently over 150 known nucleoside alterations, detection and quantification methods must encompass multiple modifications for a comprehensive profile. LC–MS/MS approaches offer a perspective for comprehensive parallel quantification of all the various modifications found in total RNA of a given organism. By feeding 13C-glucose as sole carbon source, we have generated a stable isotope-labeled internal standard (SIL-IS) for bacterial RNA, which facilitates relative comparison of all modifications. While conventional SIL-IS approaches require the chemical synthesis of single modifications in weighable quantities, this SIL-IS consists of a nucleoside mixture covering all detectable RNA modifications of Escherichia coli, yet in small and initially unknown quantities. For absolute in addition to relative quantification, those quantities were determined by a combination of external calibration and sample spiking of the biosynthetic SIL-IS. For each nucleoside, we thus obtained a very robust relative response factor, which permits direct conversion of the MS signal to absolute amounts of substance. The application of the validated SIL-IS allowed highly precise quantification with standard deviations <2% during a 12-week period, and a linear dynamic range that was extended by two orders of magnitude. PMID:25129236

  9. Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations

    PubMed Central

    Higgs, Richard E.; Butler, Jon P.; Han, Bomie; Knierman, Michael D.

    2013-01-01

    Recent improvements in the mass accuracy and resolution of mass spectrometers have led to renewed interest in label-free quantification using data from the primary mass spectrum (MS1) acquired from data-dependent proteomics experiments. The capacity for higher specificity quantification of peptides from samples enriched for proteins of biological interest offers distinct advantages for hypothesis generating experiments relative to immunoassay detection methods or prespecified peptide ions measured by multiple reaction monitoring (MRM) approaches. Here we describe an evaluation of different methods to post-process peptide level quantification information to support protein level inference. We characterize the methods by examining their ability to recover a known dilution of a standard protein in background matrices of varying complexity. Additionally, the MS1 quantification results are compared to a standard, targeted, MRM approach on the same samples under equivalent instrument conditions. We show the existence of multiple peptides with MS1 quantification sensitivity similar to the best MRM peptides for each of the background matrices studied. Based on these results we provide recommendations on preferred approaches to leveraging quantitative measurements of multiple peptides to improve protein level inference. PMID:23710359

  10. Stochastic methods for uncertainty quantification in radiation transport

    NASA Astrophysics Data System (ADS)

    Fichtl, Erin D.

    -Krylov method is employed to solve it. The SCM utilizes a suitable quadrature rule to compute the moments or PC coefficients of the flux and k-eigenvalue, and thus involves the solution of a system of independent deterministic transport equations. The accuracy and efficiency of the two methods are compared and contrasted. Both are shown to accurately compute the PC coefficients of the unknown, and numerical proof is provided that the two methods are in fact equivalent in certain cases. The PC coefficients are used to compute the moments and probability density functions of the unknowns, which are shown to be accurate by comparing with Monte Carlo results. An analytic diffusion analysis, corroborated by numerical results, reveals that the random transport equation is well approximated by a deterministic diffusion equation when the medium is diffusive with respect to the average cross section but without constraint on the amplitude of the random fluctuations. Our work shows that stochastic spectral expansions are a viable alternative to random 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.

  11. Quantification of carbonate by gas chromatography-mass spectrometry.

    PubMed

    Tsikas, Dimitrios; Chobanyan-Jürgens, Kristine

    2010-10-01

    Carbon dioxide and carbonates are widely distributed in nature, are constituents of inorganic and organic matter, and are essential in vegetable and animal organisms. CO(2) is the principal greenhouse gas in the atmosphere. In human blood, CO(2)/HCO(3)(-) is an important buffering system. Quantification of bicarbonate and carbonate in inorganic and organic matter and in biological fluids such as blood or blood plasma by means of the GC-MS technology has been impossible so far, presumably because of the lack of suitable derivatization reactions to produce volatile and thermally stable derivatives. Here, a novel derivatization reaction is described for carbonate that allows for its quantification in aqueous alkaline solutions and alkalinized plasma and urine. Carbonate in acetonic solutions of these matrices (1:4 v/v) and added (13)C-labeled carbonate for use as the internal standard were heated in the presence of the derivatization agent pentafluorobenzyl (PFB) bromide for 60 min and 50 °C. Investigations with (12)CO(3)(2-), (13)CO(3)(2-), (CH(3))(2)CO, and (CD(3))(2)CO in alkaline solutions and GC-MS and GC-MS/MS analyses under negative-ion chemical ionization (NICI) or electron ionization (EI) conditions of toluene extracts of the reactants revealed formation of two minor [i.e., PFB-OCOOH and O=CO(2)-(PFB)(2)] and two major [i.e., CH(3)COCH(2)-C(OH)(OPFB)(2) and CH(3)COCH=C(OPFB)(2)] carbonate derivatives. The latter have different retention times (7.9 and 7.5 min, respectively) but virtually identical EI and NICI mass spectra. It is assumed that CH(3)COCH(2)-C(OH)(OPFB)(2) is formed from the reaction of the carbonate dianion with two molecules of PFB bromide to form the diPFB ester of carbonic acid, which further reacts with one molecule of acetone. Subsequent loss of water finally generates the major derivative CH(3)COCH=C(OPFB)(2). This derivatization reaction was utilized to quantify total CO(2)/HCO(3)(-)/CO(3)(2-) (tCO(2)) in human plasma and urine by GC

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

    PubMed

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

    2017-01-01

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

  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. Uncertainty quantification for holographic interferographic images

    NASA Astrophysics Data System (ADS)

    Centauri, Laurie Ann

    Current comparison methods for experimental and simulated holographic interferometric images are qualitative in nature. Previous comparisons of holographic interferometric images with computational fluid dynamics (CFD) simulations for validation have been performed qualitatively through visual comparison by a data analyst. By validating the experiments and CFD simulations in a quantifiable manner using a consistency analysis, the validation becomes a repeatable process that gives a consistency measure and a range of inputs over which the experiments and CFD simulations give consistent results. The quantification of uncertainty in four holographic interferometric experiments was performed for use in a data collaboration with CFD simulations for the purpose of validation. The model uncertainty from image-processing, the measurement uncertainty from experimental data variation, and the scenario uncertainty from the bias and parameter uncertainty was quantified. The scenario uncertainty was determined through comparison with an analytical solution at the helium inlet (height, x = 0), including the uncertainty in the experimental parameters from historical weather data. The model uncertainty was calculated through a Box-Behnkin sensitivity analysis on three image-processing code parameters. Measurement uncertainty was determined through a statistical analysis to determine the time-average and standard deviation in the interference fringe positions. An experimental design matrix of CFD simulations was performed by Weston Eldredge using a Box-Behnkin design with helium velocity, temperature, and air co-flow velocity as parameters in conjunction to provide simulated measurements for the data collaboration Data set. Over 3,200 holographic interferometric images were processed through the course of this study. When each permutation of these images is taken into account through all the image-processing steps, the total number of images processed is over 13,000. Probability

  15. Methane bubbling: from speculation to quantification

    NASA Astrophysics Data System (ADS)

    Grinham, A. R.; Dunbabin, M.; Yuan, Z.

    2013-12-01

    magnitude from 500 to 100 000 mg m-2 d-1 depending on time of day and water depth. Average storage bubble flux rates between reservoirs varied by two orders of magnitude from 1 200 to 15 000 mg m-2 d-1, with the primary driver likely to be catchment forest cover. The relative contribution of bubbling to total fluxes varied from 10% to more than 90% depending on the reservoir and time of sampling. This method was consistently shown to greatly improve the spatial mapping and quantification of methane bubbling rates from reservoir surfaces and reduces the uncertainty associated with the determining the relative contribution of bubbling to total flux.

  16. Extended Forward Sensitivity Analysis for Uncertainty Quantification

    SciTech Connect

    Haihua Zhao; Vincent A. Mousseau

    2011-09-01

    Verification and validation (V&V) are playing more important roles to quantify uncertainties and realize high fidelity simulations in engineering system analyses, such as transients happened in a complex nuclear reactor system. Traditional V&V in the reactor system analysis focused more on the validation part or did not differentiate verification and validation. The traditional approach to uncertainty quantification is based on a 'black box' approach. The simulation tool is treated as an unknown signal generator, a distribution of inputs according to assumed probability density functions is sent in and the distribution of the outputs is measured and correlated back to the original input distribution. The 'black box' method mixes numerical errors with all other uncertainties. It is also not efficient to perform sensitivity analysis. Contrary to the 'black box' method, a more efficient sensitivity approach can take advantage of intimate knowledge of the simulation code. In these types of approaches equations for the propagation of uncertainty are constructed and the sensitivities are directly solved for as variables in the simulation. This paper presents the forward sensitivity analysis as a method to help uncertainty qualification. By including time step and potentially spatial step as special sensitivity parameters, the forward sensitivity method is extended as one method to quantify numerical errors. Note that by integrating local truncation errors over the whole system through the forward sensitivity analysis process, the generated time step and spatial step sensitivity information reflect global numerical errors. The discretization errors can be systematically compared against uncertainties due to other physical parameters. This extension makes the forward sensitivity method a much more powerful tool to help uncertainty qualification. By knowing the relative sensitivity of time and space steps with other interested physical parameters, the simulation is allowed

  17. Uncertainty Quantification in Climate Modeling and Projection

    SciTech Connect

    Qian, Yun; Jackson, Charles; Giorgi, Filippo; Booth, Ben; Duan, Qingyun; Forest, Chris; Higdon, Dave; Hou, Z. Jason; Huerta, Gabriel

    2016-05-01

    The projection of future climate is one of the most complex problems undertaken by the scientific community. Although scientists have been striving to better understand the physical basis of the climate system and to improve climate models, the overall uncertainty in projections of future climate has not been significantly reduced (e.g., from the IPCC AR4 to AR5). With the rapid increase of complexity in Earth system models, reducing uncertainties in climate projections becomes extremely challenging. Since uncertainties always exist in climate models, interpreting the strengths and limitations of future climate projections is key to evaluating risks, and climate change information for use in Vulnerability, Impact, and Adaptation (VIA) studies should be provided with both well-characterized and well-quantified uncertainty. The workshop aimed at providing participants, many of them from developing countries, information on strategies to quantify the uncertainty in climate model projections and assess the reliability of climate change information for decision-making. The program included a mixture of lectures on fundamental concepts in Bayesian inference and sampling, applications, and hands-on computer laboratory exercises employing software packages for Bayesian inference, Markov Chain Monte Carlo methods, and global sensitivity analyses. The lectures covered a range of scientific issues underlying the evaluation of uncertainties in climate projections, such as the effects of uncertain initial and boundary conditions, uncertain physics, and limitations of observational records. Progress in quantitatively estimating uncertainties in hydrologic, land surface, and atmospheric models at both regional and global scales was also reviewed. The application of Uncertainty Quantification (UQ) concepts to coupled climate system models is still in its infancy. The Coupled Model Intercomparison Project (CMIP) multi-model ensemble currently represents the primary data for

  18. 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

  19. SERS Quantification and Characterization of Proteins and Other Biomolecules.

    PubMed

    Feliu, Neus; Hassan, Moustapha; Garcia Rico, Eduardo; Cui, Daxiang; Parak, Wolfgang; Alvarez-Puebla, Ramon

    2017-09-26

    Changes in protein expression levels and protein structure may indicate genomic mutations and may be related to some diseases. Therefore, the precise quantification and characterization of proteins can be used for disease diagnosis. Compared with several other alternative methods, surface-enhanced Raman scattering (SERS) spectroscopy is regarded as an excellent choice for the quantification and structural characterization of proteins. Herein, we review the main advance of using plasmonic nanostructures as SERS sensing platform for this purpose. Three design approaches, including direct SERS, indirect SERS, and SERS-encoded nanoparticles, are discussed in the direction of developing new precise approaches of quantification and characterization of proteins. While this Review is focused on proteins, in order to highlight concepts of SERS-based sensors also detection of other biomolecules will be discussed.

  20. Next generation of food allergen quantification using mass spectrometric systems.

    PubMed

    Koeberl, Martina; Clarke, Dean; Lopata, Andreas L

    2014-08-01

    Food allergies are increasing worldwide and becoming a public health concern. Food legislation requires detailed declarations of potential allergens in food products and therefore an increased capability to analyze for the presence of food allergens. Currently, antibody-based methods are mainly utilized to quantify allergens; however, these methods have several disadvantages. Recently, mass spectrometry (MS) techniques have been developed and applied to food allergen analysis. At present, 46 allergens from 11 different food sources have been characterized using different MS approaches and some specific signature peptides have been published. However, quantification of allergens using MS is not routinely employed. This review compares the different aspects of food allergen quantification using advanced MS techniques including multiple reaction monitoring. The latter provides low limits of quantification for multiple allergens in simple or complex food matrices, while being robust and reproducible. This review provides an overview of current approaches to analyze food allergens, with specific focus on MS systems and applications.

  1. Isobaric Labeling-Based Relative Quantification in Shotgun Proteomics

    PubMed Central

    2015-01-01

    Mass spectrometry plays a key role in relative quantitative comparisons of proteins in order to understand their functional role in biological systems upon perturbation. In this review, we review studies that examine different aspects of isobaric labeling-based relative quantification for shotgun proteomic analysis. In particular, we focus on different types of isobaric reagents and their reaction chemistry (e.g., amine-, carbonyl-, and sulfhydryl-reactive). Various factors, such as ratio compression, reporter ion dynamic range, and others, cause an underestimation of changes in relative abundance of proteins across samples, undermining the ability of the isobaric labeling approach to be truly quantitative. These factors that affect quantification and the suggested combinations of experimental design and optimal data acquisition methods to increase the precision and accuracy of the measurements will be discussed. Finally, the extended application of isobaric labeling-based approach in hyperplexing strategy, targeted quantification, and phosphopeptide analysis are also examined. PMID:25337643

  2. Quantification of neural functional connectivity during an active avoidance task.

    PubMed

    Silva, Catia S; Hazrati, Mehrnaz K; Keil, Andreas; Principe, Jose C; Silva, Catia S; Hazrati, Mehrnaz K; Keil, Andreas; Principe, Jose C; Keil, Andreas; Principe, Jose C; Hazrati, Mehrnaz K; Silva, Catia S

    2016-08-01

    Many behavioral and cognitive processes are associated with spatiotemporal dynamic communication between brain areas. Thus, the quantification of functional connectivity with high temporal resolution is highly desirable for capturing in vivo brain function. However, brain functional network quantification from EEG recordings has been commonly used in a qualitative manner. In this paper, we consider pairwise dependence measures as random variables and estimate the pdf for each electrode of the arrangement. A metric imposed by the quadratic Cauchy-Schwartz Mutual Information quantifies these pdfs. We present the results by brain regions simplifying the analysis and visualization drastically. The proposed metric of functional connectivity quantification is addressed for temporal dependencies of the brain network that can be related to the task.

  3. Development of a Protein Standard Absolute Quantification (PSAQ™) assay for the quantification of Staphylococcus aureus enterotoxin A in serum.

    PubMed

    Adrait, Annie; Lebert, Dorothée; Trauchessec, Mathieu; Dupuis, Alain; Louwagie, Mathilde; Masselon, Christophe; Jaquinod, Michel; Chevalier, Benoît; Vandenesch, François; Garin, Jérôme; Bruley, Christophe; Brun, Virginie

    2012-06-06

    Enterotoxin A (SEA) is a staphylococcal virulence factor which is suspected to worsen septic shock prognosis. However, the presence of SEA in the blood of sepsis patients has never been demonstrated. We have developed a mass spectrometry-based assay for the targeted and absolute quantification of SEA in serum. To enhance sensitivity and specificity, we combined an immunoaffinity-based sample preparation with mass spectrometry analysis in the selected reaction monitoring (SRM) mode. Absolute quantification of SEA was performed using the PSAQ™ method (Protein Standard Absolute Quantification), which uses a full-length isotope-labeled SEA as internal standard. The lower limit of detection (LLOD) and lower limit of quantification (LLOQ) were estimated at 352pg/mL and 1057pg/mL, respectively. SEA recovery after immunocapture was determined to be 7.8±1.4%. Therefore, we assumed that less than 1femtomole of each SEA proteotypic peptide was injected on the liquid chromatography column before SRM analysis. From a 6-point titration experiment, quantification accuracy was determined to be 77% and precision at LLOQ was lower than 5%. With this sensitive PSAQ-SRM assay, we expect to contribute to decipher the pathophysiological role of SEA in severe sepsis. This article is part of a Special Issue entitled: Proteomics: The clinical link. Copyright © 2011 Elsevier B.V. All rights reserved.

  4. Graphene oxide interfaces in serum based autoantibody quantification.

    PubMed

    Xu, Qiao; Cheng, Ho; Lehr, Joshua; Patil, Amol V; Davis, Jason J

    2015-01-06

    A reliable quantification of protein markers will undoubtedly underpin profound developments in disease surveillance, diagnostics, and improved therapy. Although there potentially exist numerous means of achieving this, electrochemical impedimetric techniques offer scale of sensitivity, cost, convenience, and a flexibility with which few alternatives can compete. Though there have been marked developments in electroanalytical protein detection, the demands associated with accessing the inherent assay sensitivity in complex biological media largely remains. We report herein the use of cysteamine-graphene oxide modified gold microelectrode arrays in underpinning the ultrasensitive and entirely label free non-faradaic quantification of Parkinson's-relevant autoantibodies in human serum.

  5. 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)

  6. 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.

  7. A highly sensitive quantification of phytosterols through an inexpensive derivatization.

    PubMed

    Liu, Songbai; Ruan, Huina

    2013-01-01

    A highly sensitive method for quantification of phytosterols based on HPLC has been developed by derivatization with the benzoyl chromophore. Introduction of the chromophore, benzoyl group, to phytosterols via simple and inexpensive derivatization greatly improved the UV response at 254 nm. Quantification of phytosterols was effectively performed by HPLC analysis with methyl benzoate as the internal standard after derivatization. This new method demonstrated outstanding yield of recovery (> 95%) and excellent sensitivity (ng level) and was applicable for sterols from either plant or animal sources. This method is generally useful in phytosterol studies.

  8. Uncertainty Quantification for Safety Verification Applications in Nuclear Power Plants

    NASA Astrophysics Data System (ADS)

    Boafo, Emmanuel

    There is an increasing interest in computational reactor safety analysis to systematically replace the conservative calculations by best estimate calculations augmented by quantitative uncertainty analysis methods. This has been necessitated by recent regulatory requirements that have permitted the use of such methods in reactor safety analysis. Stochastic uncertainty quantification methods have shown great promise, as they are better suited to capture the complexities in real engineering problems. This study proposes a framework for performing uncertainty quantification based on the stochastic approach, which can be applied to enhance safety analysis. (Abstract shortened by ProQuest.).

  9. 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.

  10. Implications for Metabolite Quantification by Mass Spectrometry in the Absence of Authentic Standards.

    PubMed

    Hatsis, Panos; Waters, Nigel J; Argikar, Upendra A

    2017-03-02

    Quantification of metabolites by mass spectrometry in the absence of authentic reference standards or without a radiolabel is often called 'semi-quantitative', which acknowledges that mass spectrometric responses are not truly quantitative. For many researchers, it is tempting to pursue this practice of semi-quantification in early drug discovery and even preclinical development, when radiolabeled ADME studies are being deferred to later stages of drug development. The caveats of quantifying metabolites based on parent drug response are explored in this investigation. A set of 71 clinically relevant drugs/metabolites encompassing common biotransformation pathways, was subjected to flow injection analysis coupled with electrospray ionization mass spectrometry (ESI-MS). The results revealed a large variation in ESI response even for structurally similar parent drug/metabolite pairs. The ESI response of each metabolite was normalized to that of the parent drug, to generate an ESI relative response factor. Overall, relative response factors ranged from 0.014 (> 70-fold lower response than parent) to 8.6 (8.6-fold higher response than parent). Various 2D molecular descriptors were calculated that describe physicochemical, topological and structural properties for each drug/metabolite. The molecular descriptors, along with the ESI response factors were used in univariate analyses as well as a principal components analysis to ascertain which molecular descriptors best account for the observed discrepancies in drug/metabolite ESI response. This investigation has shown that the practice of using parent drug response to quantify metabolites should be used with caution.

  11. 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.

  12. The detection and quantification of adulteration in olive oil by near-infrared spectroscopy and chemometrics.

    PubMed

    Christy, Alfred A; Kasemsumran, Sumaporn; Du, Yiping; Ozaki, Yukihiro

    2004-06-01

    A new procedure has been developed for the classification and quantification of the adulteration of pure olive oil by soya oil, sun flower oil, corn oil, walnut oil and hazelnut oil. The study was based on a chemometric analysis of the near-infrared (NIR) spectra of olive-oil mixtures containing different adulterants. The adulteration of olive oil was carefully carried out gravimetrically in a 4 mm quartz cuvette, starting with pure olive oil in the cuvette first. NIR spectra of the 525 adulterated mixtures were measured in the region of 12,000-4000 cm(-1). The spectra were subjected batch wise to multiplicative signal correction (MSC) before calculating the principal component (PCA) models. The MSC-corrected data were subjected to Savitzky-Golay smoothing and a mean normalization procedure before developing partial least-squares calibration (PLS) models. The results revealed that the models predicted the adulterants, corn oil, sun flower oil, soya oil, walnut oil and hazelnut oil involved in olive oil with error limits +/-0.57, +/-1.32, +/-0.96, +/-0.56 and +/-0.57% weight/weight, respectively. Furthermore, the PCA developed models were able to classify unknown adulterated olive oil mixtures with almost 100% certainty. Quantification of the adulterants was carried out using their respective PLS models within the same error limits as mentioned above.

  13. Quantification of exocytosis kinetics by DIC image analysis of cortical lawns.

    PubMed

    Mooney, James; Thakur, Saumitra; Kahng, Peter; Trapani, Josef G; Poccia, Dominic

    2014-04-01

    Cortical lawns prepared from sea urchin eggs have offered a robust in vitro system for study of regulated exocytosis and membrane fusion events since their introduction by Vacquier almost 40 years ago (Vacquier in Dev Biol 43:62-74, 1975). Lawns have been imaged by phase contrast, darkfield, differential interference contrast, and electron microscopy. Quantification of exocytosis kinetics has been achieved primarily by light scattering assays. We present simple differential interference contrast image analysis procedures for quantifying the kinetics and extent of exocytosis in cortical lawns using an open vessel that allows rapid solvent equilibration and modification. These preparations maintain the architecture of the original cortices, allow for cytological and immunocytochemical analyses, and permit quantification of variation within and between lawns. When combined, these methods can shed light on factors controlling the rate of secretion in a spatially relevant cellular context. We additionally provide a subroutine for IGOR Pro® that converts raw data from line scans of cortical lawns into kinetic profiles of exocytosis. Rapid image acquisition reveals spatial variations in time of initiation of individual granule fusion events with the plasma membrane not previously reported.

  14. Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry

    PubMed Central

    Krautkramer, Kimberly A.; Reiter, Lukas; Denu, John M.; Dowell, James A.

    2015-01-01

    Histone post-translational modifications (PTMs) are important regulators of chromatin structure and gene expression. Quantitative analysis of histone PTMs by mass spectrometry remains extremely challenging due to the complex and combinatorial nature of histone PTMs. The most commonly used mass spectrometry-based method for high-throughput histone PTM analysis is data-dependent acquisition (DDA). However, stochastic precursor selection and dependence on MS1 ions for quantification impede comprehensive interrogation of histone PTM states using DDA methods. To overcome these limitations, we utilized a data-independent acquisition (DIA) workflow that provides superior run-to-run consistency and post-acquisition flexibility in comparison to DDA methods. In addition, we developed a novel DIA-based methodology to quantify isobaric, co-eluting histone peptides that lack unique MS2 transitions. Our method enabled deconvolution and quantification of histone PTMs that are otherwise refractory to quantitation, including the heavily acetylated tail of histone H4. Using this workflow, we investigated the effects of the histone deacetylase inhibitor SAHA (suberoylanilide hydroxamic acid) on the global histone PTM state of human breast cancer MCF7 cells. A total of 62 unique histone PTMs were quantified, revealing novel SAHA-induced changes in acetylation and methylation of histones H3 and H4. PMID:26120868

  15. Quantification of hypoglycin A in serum using aTRAQ(®) assay.

    PubMed

    Boemer, François; Deberg, Michelle; Schoos, Roland; Baise, Etienne; Amory, Hélène; Gault, Gilbert; Carlier, Jeremy; Gaillard, Yvan; Marcillaud-Pitel, Christel; Votion, Dominique

    2015-08-01

    Hypoglycin A has been recently identified has the causal agent of atypical myopathy (AM) in horses. Its identification and quantification in equine's biological fluids is thus a major concern to confirm maple poisoning and to provide insight into the poorly understood mechanism of hypoglycin A intoxication. Quantification of hypoglycin A has been achieved with the aTRAQ kit for amino acid analysis of physiological fluids (AB Sciex). Acquisition method on mass spectrometer has been updated to record the hypoglycin A specific MRM transition. Outlined accuracy profiles demonstrated very reliable data. A good linearity was observed from 0.09 to 50μmol/L and precision was very good with coefficient of variation below 8%. Fifty-five samples collected from 25 confirmed AM horses revealed significant hypoglycin A concentrations, while toxin was not found in serum of 8 control animals. The described aTRAQ variant method has been analytically and clinically validated. The reliability of our approach is thus demonstrated into the workup of atypical myopathy. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Classification of mild cognitive impairment EEG using combined recurrence and cross recurrence quantification analysis.

    PubMed

    Timothy, Leena T; Krishna, Bindu M; Nair, Usha

    2017-10-01

    The present study is aimed at the classification of mild cognitive impairment (MCI) EEG by combining complexity and synchronization features based on quantifiers from the common platform of recurrence based analysis. Recurrence rate (RR) of recurrence quantification analysis (RQA) is used for complexity analysis and RR of cross recurrence quantification analysis (CRQA) is used for synchronization analysis. The investigations are carried out on EEG from two states (i) resting eyes closed (EC) and (ii) short term memory task (STM).The results of our analysis show lower levels of complexity and higher levels of inter and intra hemispheric synchronisation in the MCI EEG compared to that of normal controls (NC) as indicated by the statistically significant higher value of RQA RR and CRQA RR. The results also evidence the effectiveness of memory activation task by bringing out the characteristic features of MCI EEG in task specific regions of temporal, parietal and frontal lobes under the STM condition.A new approach of combining complexity and synchronization features for EEG classification of MCI subjects is proposed, based on the geometrical signal separation in a feature space formed by RQA and CRQA RR values. The results of linear classification analysis of MCI and NC EEG also reveals the effectiveness of task state analysis by the enhanced classification efficiency under the cognitive load of STM condition compared to that of EC condition. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Absolute Quantification of Bionanoparticles by Electrospray Differential Mobility Analysis: An Application to Lipoprotein Particle Concentration Measurements.

    PubMed

    Clouet-Foraison, Noémie; Gaie-Levrel, Francois; Coquelin, Loic; Ebrard, Géraldine; Gillery, Philippe; Delatour, Vincent

    2017-02-21

    This study presents an upgraded electrospray differential mobility analysis (ES-DMA) setup for the absolute quantification of bionanoparticle concentrations in biological samples, with a special focus on non-high-density-lipoprotein particle concentrations (non-HDL-P). Metrological characterization of the system's analytical performances for concentration measurements shows that the mean intermediate precision relative standard deviation is 14% for biological samples, 6% for silica nanoparticles, and less than 1% for diameter measurements. This study also demonstrates that the most accurate method for non-HDL-P quantification in native serum samples implies daily calculation of the electrospray transmission efficiency (E) of the system with the WHO SP3-08 reference material. The establishment of the uncertainty budget reveals that the main contribution to particle concentration measurement uncertainties is the electrospray transmission efficiency. This data additionally shows that E is not only low (approximately 15-20%) but also highly variable over time and strongly affected by sample composition. This work suggests that absolute enumeration of bionanoparticles is achievable with ES-DMA but provided that a special care is taken to quantifying E with a calibrator of nature and matrix highly similar to the samples ones.

  18. 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.

  19. 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

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

    PubMed

    Morschett, Holger; Wiechert, Wolfgang; Oldiges, Marco

    2016-02-09

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

  1. 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

  2. A rapid, reproducible, on-the-fly orthogonal array optimization method for targeted protein quantification by LC/MS and its application for accurate and sensitive quantification of carbonyl reductases in human liver.

    PubMed

    Cao, Jin; Gonzalez-Covarrubias, Vanessa; Covarrubias, Vanessa M; Straubinger, Robert M; Wang, Hao; Duan, Xiaotao; Yu, Haoying; Qu, Jun; Blanco, Javier G

    2010-04-01

    Liquid chromatography (LC)/mass spectrometry (MS) in selected-reactions-monitoring (SRM) mode provides a powerful tool for targeted protein quantification. However, efficient, high-throughput strategies for proper selection of signature peptides (SP) for protein quantification and accurate optimization of their SRM conditions remain elusive. Here we describe an on-the-fly, orthogonal array optimization (OAO) approach that enables rapid, comprehensive, and reproducible SRM optimization of a large number of candidate peptides in a single nanoflow-LC/MS run. With the optimized conditions, many peptide candidates can be evaluated in biological matrixes for selection of the final SP. The OAO strategy employs a systematic experimental design that strategically varies product ions, declustering energy, and collision energy in a cycle of 25 consecutive SRM trials, which accurately reveals the effects of these factors on the signal-to-noise ratio of a candidate peptide and optimizes each. As proof of concept, we developed a highly sensitive, accurate, and reproducible method for the quantification of carbonyl reductases CBR1 and CBR3 in human liver. Candidate peptides were identified by nano-LC/LTQ/Orbitrap, filtered using a stringent set of criteria, and subjected to OAO. After evaluating both sensitivity and stability of the candidates, two SP were selected for quantification of each protein. As a result of the accurate OAO of assay conditions, sensitivities of 80 and 110 amol were achieved for CBR1 and CBR3, respectively. The method was validated and used to quantify the CBRs in 33 human liver samples. The mean level of CBR1 was 93.4 +/- 49.7 (range: 26.2-241) ppm of total protein, and of CBR3 was 7.69 +/- 4.38 (range: 1.26-17.9) ppm. Key observations of this study: (i) evaluation of peptide stability in the target matrix is essential for final selection of the SP; (ii) utilization of two unique SP contributes to high reliability of target protein quantification; (iii

  3. A rapid, reproducible, on-the-fly orthogonal array optimization method for targeted protein quantification by LC/MS and its application for accurate and sensitive quantification of carbonyl reductases in human liver

    PubMed Central

    Cao, Jin; Gonzalez-Covarrubias, Vanessa; Straubinger, Robert M.; Wang, Hao; Duan, Xiaotao; Yu, Haoying; Qu, Jun; Blanco, Javier G.

    2010-01-01

    Liquid chromatography (LC)/mass spectrometry (MS) in selected-reactions-monitoring (SRM) mode provides a powerful tool for targeted protein quantification. However, efficient, high-throughput strategies for proper selection of signature peptides (SP) for protein quantification and accurate optimization of their SRM conditions remain elusive. Here we describe an on-the-fly, orthogonal array optimization (OAO) approach that enables rapid, comprehensive, and reproducible SRM optimization of a large number of candidate peptides in a single nanoflow-LC/MS run. With the optimized conditions, many peptide candidates can be evaluated in biological matrices for selection of the final SP. The OAO strategy employs a systematic experimental design that strategically varies product ions, de-clustering energy and collision energy in a cycle of 25 consecutive SRM trials, which accurately reveals the effects of these factors on the single-to-noise ratio of a candidate peptide, and optimizes each. As proof of concept, we developed a highly sensitive, accurate, and reproducible method for the quantification of carbonyl reductases CBR1 and CBR3 in human liver. Candidate peptides were identified by nano-LC/LTQ/Orbitrap, filtered using a stringent set of criteria, and subjected to OAO. After evaluating both sensitivity and stability of the candidates, two SP were selected for quantification of each protein. As a result of the accurate OAO of assay conditions, sensitivities of 80 and 110 amol were achieved for CBR1 and CBR3, respectively. The method was validated and used to quantify the CBRs in 33 human liver samples. The mean level of CBR1 was 93.4±49.7 (range: 26.2–241) ppm of total protein, and for CBR3 was 7.69±4.38 (range: 1.26–17.9) ppm. Key observations of this study are that: i) evaluation of peptide stability in the target matrix is essential for final selection of the SP; ii) utilization of two unique SP contributes to high reliability of target protein quantification

  4. 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.

  5. 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...

  6. Quantification of facial and smile esthetics.

    PubMed

    Koidou, Vasiliki P; Chatzopoulos, Georgios S; Rosenstiel, Stephen F

    2017-05-26

    Whether deviations in alignment discrepancy, width-to-length ratio, application of the golden proportion, or number of teeth revealed in smile affect attractiveness is yet unknown. The purpose of this analytical study was to quantify dental and facial esthetics to determine whether individuals identified as having superior smiles display differences in alignment discrepancies (angulation between interpupillary and commissure line); width-to-length ratios of maxillary anterior teeth; application of the golden proportion (approximately 1.618:1); and number of teeth revealed in an animated smile when compared with an average population. An Internet search for "best smile" and "celebrity" identified 108 celebrities. Photographs showing smiles within 10 degrees of a frontal view were collected, while photographs of dental students were used for the control group. Alignment discrepancies, widths and lengths of the anterior teeth, and number of teeth revealed in an animated smile were measured with photo-editing software, and ratios were calculated. The groups were compared with repeated-measures ANOVA, the Mann-Whitney U test, and the Wilcoxon signed-rank test (α=.05). Usable photographs were obtained for 90 celebrities (58 women, 32 men) and compared with photographs of 97 dental students (54 women, 43 men). Statistically significant differences were found for alignment discrepancies (celebrities 0.97, students 1.25, P=.034) and for the number of teeth displayed (P=.049); 22.2% of the celebrities revealed 12 teeth, versus 6.2% of the students. In both groups, significant differences from the golden ratio (1.618:1) for the width of the central incisor/lateral incisor right and left and for the width of the lateral incisor/canine right and left were observed through 95% confidence intervals. Sex and left-right were nonsignificant factors. Celebrities identified as having a best smile had smaller mean alignment discrepancies and revealed a greater number of teeth in an

  7. Revealing power in truth

    PubMed Central

    Lee, Kelley

    2015-01-01

    Jeremy Shiffman’s editorial appropriately calls on making all forms of power more apparent and accountable, notably productive power derived from expertise and claims to moral authority. This commentary argues that relationships based on productive power can be especially difficult to reveal in global health policy because of embedded notions about the nature of power and politics. Yet, it is essential to recognize that global health is shot through with power relationships, that they can take many forms, and that their explicit acknowledgement should be part of, rather than factored out of, any reform of global health governance. PMID:25844390

  8. Longitudinal quantification of radical bursts during pulmonary ischaemia and reperfusion.

    PubMed

    Gielis, Jan F; Boulet, Gaëlle A; Briedé, Jacob J; Horemans, Tessa; Debergh, Tom; Kussé, Max; Cos, Paul; Van Schil, Paul E Y

    2015-10-01

    Pulmonary ischaemia-reperfusion injury (IRI) is associated with several life-threatening pulmonary disorders, and may severely compromise the outcome of lung transplantation. Highly reactive molecules such as superoxide, nitric oxide (NO) and peroxynitrite (ONOO(-)) are presumed to contribute to IRI pathogenesis, but this assumption is based on indirect measurements. We use electron spin resonance (ESR) to directly quantify free radical formation after pulmonary ischaemia and reperfusion. Five groups of 10 Swiss mice were subjected to left pulmonary hilum clamping for 1 h of ischaemia followed by 0, 1, 4 and 24 h of reperfusion or to sham thoracotomy alone as control procedure. In five mice per group, ESR was used to measure iron-diethyldithio-carbamate trihydrate-trapped NO in the lung. In the other group of 5, reactive oxygen species generation in the lung and in blood was quantified with ESR by detection of ascorbyl radical and CMH spin probe, respectively. Pulmonary ONOO(-) was monitored with nitrotyrosine Western blotting. After 1 h of reperfusion, a pulmonary NO peak (14.69 ± 0.91 × 10(4) Arbitrary Units (A.U.). vs 1.84 ± 0.75 × 10(4) A.U. in sham; P < 0.001) coincided with a significant increase in nitrosated proteins (0.105 ± 0.015 A.U.) compared with sham (0.047 ± 0.006 A.U.); P < 0.005). Peripheral blood showed a significant free radical burst after 1 h of ischaemia (11 774 ± 728 A.U. vs 6660 ± 833 A.U. in sham; P < 0.001). Longitudinal quantification of free radicals during IRI reveals the occurrence of two major radical bursts. The radical peak in peripheral blood after ischaemia may be related to systemic hypoxia. After 1 h of reperfusion, the lung tissue shows a significant increase of superoxide, NO and their reaction products, which are probably involved in IRI pathogenesis. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

  9. Objectified quantification of uncertainties in Bayesian atmospheric inversions

    NASA Astrophysics Data System (ADS)

    Berchet, A.; Pison, I.; Chevallier, F.; Bousquet, P.; Bonne, J.-L.; Paris, J.-D.

    2014-07-01

    with different transport patterns, flux distributions and total prior amounts of emitted gas. The method proves to consistently reproduce the known "truth" in most cases, with satisfactory tolerance intervals. Additionnaly, the method explicitly provides influence scores and posterior correlation matrices. An in-depth interpretation of the inversion results is then possible. The more objective quantification of the influence of the observations on the fluxes proposed here allows us to evaluate the impact of the observation network on the characterization of the surface fluxes. The explicit correlations between emission regions reveal the mis-separated regions, hence the typical temporal and spatial scales the inversion can analyze. These scales proved to be consistent with the chosen aggregation patterns.

  10. Objectified quantification of uncertainties in Bayesian atmospheric inversions

    NASA Astrophysics Data System (ADS)

    Berchet, A.; Pison, I.; Chevallier, F.; Bousquet, P.; Bonne, J.-L.; Paris, J.-D.

    2015-05-01

    simulation experiments are carried out with different transport patterns, flux distributions and total prior amounts of emitted methane. The method proves to consistently reproduce the known "truth" in most cases, with satisfactory tolerance intervals. Additionally, the method explicitly provides influence scores and posterior correlation matrices. An in-depth interpretation of the inversion results is then possible. The more objective quantification of the influence of the observations on the fluxes proposed here allows us to evaluate the impact of the observation network on the characterization of the surface fluxes. The explicit correlations between emission aggregates reveal the mis-separated regions, hence the typical temporal and spatial scales the inversion can analyse. These scales are consistent with the chosen aggregation patterns.

  11. Desert Stone Mantles: Quantification and Significance of Self-Organisation

    NASA Astrophysics Data System (ADS)

    Higgitt, David; Rosser, Nick

    2010-05-01

    Desert stone mantles exhibit sorting patterns which are evidence of self-organisation. Previous investigations of stone mantles developed on Late Tertiary and Quaternary basalts in arid northeastern Jordan, revealed distinct variations in the nature of stone cover both downslope and between lithologies of different age. However, manual field measurements of clast size and shape did not preserve information about the spatial configuration of the stone surface. Improved digital image capture and analysis techniques, including using a kite-based platform for vertical photography of the surface, has permitted the nature of stone mantles to be examined and modelled in greater detail. Image analysis has been assisted by the strong contrast in colour between the basalt clasts and the underlying surface enabling a binary classification of images, from which data on size, shape and position of clasts can be readily acquired. Quantification of self-organisation through a box-counting technique for measuring fractal dimension and a procedure using Thiessen polygons to determine ‘locking structures' indicates a general increase in organisation of the stone mantle downslope. Recognition of emergent behaviour requires an explanation in terms of positive feedback between controlling process and the influence of surface form. A series of rainfall simulation and infiltration experiments have been undertaken on plots to assess the variation in surface hydrology as a response to variations in ground surface and slope profile form. The relative contribution of runoff events of varying size and the degree to which the ground surface configuration accelerates or restricts modification of the surface influences the overall evolution of slope profiles via the erosion, transfer and deposition of both surface clasts and the underlying fine grained sediments. Critical to this modification is the interplay between the surface configuration, rainfall and runoff. The experiments presented

  12. 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.

  13. Mysterious Blob Galaxies Revealed

    NASA Image and Video Library

    2005-01-11

    This image composite shows a giant galactic blob (red) and the three merging galaxies NASA's Spitzer Space Telescope discovered within it (yellow). Blobs are intensely glowing clouds of hot hydrogen gas that envelop faraway galaxies. They are about 10 times as large as the galaxies they surround. Visible-light images reveal the vast extent of blobs, but don't provide much information about their host galaxies. Using its heat-seeking infrared eyes, Spitzer was able to see the dusty galaxies tucked inside one well-known blob located 11 billion light-years away. The findings reveal three monstrously bright galaxies, trillions of times brighter than the Sun, in the process of merging together. Spitzer also observed three other blobs located in the same cosmic neighborhood, all of which were found to be glaringly bright. One of these blobs is also known to be a galactic merger, only between two galaxies instead of three. It remains to be seen whether the final two blobs studied also contain mergers. The Spitzer data were acquired by its multiband imaging photometer. The visible-light image was taken by the Blanco Telescope at the Cerro Tololo Inter-American Observatory, Chile. http://photojournal.jpl.nasa.gov/catalog/PIA07220

  14. Localization and quantification of drugs in animal tissues by use of desorption electrospray ionization mass spectrometry imaging.

    PubMed

    Vismeh, Ramin; Waldon, Daniel J; Teffera, Yohannes; Zhao, Zhiyang

    2012-06-19

    Mass spectrometric imaging (MSI) has emerged as a powerful technique to obtain spatial arrangement of individual molecular ions in animal tissues. Ambient desorption electrospray ionization (DESI) technique is uniquely suited for such imaging experiments, as it can be performed on animal tissues in their native environment without prior treatments. Although MSI has become a rapid growing technique for localization of proteins, lipids, drugs, and endogenous compounds in different tissues, quantification of imaged targets has not been explored extensively. Here we present a novel MSI approach for localization and quantification of drugs in animal thin tissue sections. DESI-MSI using an Orbitrap mass analyzer in full scan mode was performed on 6 μm coronal brain sections from rats that were administered 2.5 mg/kg clozapine. Clozapine was localized and quantified in individual brain sections 45 min postdose. External calibration curves were prepared by micropipetting standards with internal standard (IS) on top of the tissues, and average response factors were calculated for the scans in which both clozapine and IS were detected. All response factors were normalized to area units. Quantifications from DESI-MSI revealed 0.2-1.2 ng of clozapine in individual brain sections, results that were further confirmed by extraction and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis.

  15. 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).

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

    PubMed

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

    2016-01-01

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

  17. Rapid Quantification of Energy Absorption and Dissipation Metrics for PPE Padding Materials

    DTIC Science & Technology

    2010-01-22

    Oct 2009 4. TITLE AND SUBTITLE 5. FUNDING NUMBERS Rapid Quantification of Energy Absorption & Dissipation Metrics for PPE 55332EGII Padding ...Engineering Seminar Series, Spring 2009 [2] Rapid Quantification of Energy Absorption & Dissipation Metrics for PPE Padding Materials: Final...55332EGII – Part2.pdf, and Part 3, respectively. [1] Rapid Quantification of Energy Absorption & Dissipation Metrics for PPE Padding Materials: Final

  18. Enlisting Ecosystem Benefits: Quantification and Valuation of Ecosystem Services to Inform Installation Management

    DTIC Science & Technology

    2015-05-27

    RC-201113) April 2015 Enlisting Ecosystem Services: Quantification and Valuation of Ecosystem Services to Inform...19  6.1.2  Quantification, Valuation, and Mapping of Ecosystem Services and their Tradeoffs (PO 1-6 & 8-9...Quantification, Valuation, and Mapping of Ecosystem Services and their Tradeoffs (PO 1-6 & 8-9

  19. 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…

  20. 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.

  1. Adenovirus particle quantification in cell lysates using light scattering.

    PubMed

    Hohl, Adrian; Ramms, Anne Sophie; Dohmen, Christian; Mantwill, Klaus; Bielmeier, Andrea; Kolk, Andreas; Ruppert, Andreas; Nawroth, Roman; Holm, Per Sonne

    2017-08-15

    Adenoviral vector production for therapeutic applications is a well-established routine process. However, current methods for measurement of adenovirus particle titers as a quality characteristic require highly purified virus preparations. While purified virus is typically obtained in the last step of downstream purification, rapid and reliable methods for adenovirus particle quantification in intermediate products and crude lysates to allow for optimization and validation of cell cultures and intermediate downstream processing steps are currently not at hand. Light scattering is an established process to measure virus particles' size. Though, due to cell impurities adequate quantification of adenovirus particles in cell lysates by light scattering has been impossible until today. This report describes a new method using light scattering to measure virus concentration in non-purified cell lysates. Here we report application of light scattering, a routine method to measure virus particle size, to virus quantification in enzymatically conditioned crude lysates. Samples are incubated with phospholipase A2 and benzonase and filtered through 0.22 µm filter cartridge prior to quantification by light scattering. Our results show that this treatment provides a precise method for fast and easy determination of total adenovirus particle numbers in cell lysates and is useful to monitor virus recovery throughout all downstream processing.

  2. Uncertainty quantification in nanomechanical measurements using the atomic force microscope

    Treesearch

    Ryan Wagner; Robert Moon; Jon Pratt; Gordon Shaw; Arvind Raman

    2011-01-01

    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...

  3. Quantification of confocal images of biofilms grown on irregular surfaces

    PubMed Central

    Ross, Stacy Sommerfeld; Tu, Mai Han; Falsetta, Megan L.; Ketterer, Margaret R.; Kiedrowski, Megan R.; Horswill, Alexander R.; Apicella, Michael A.; Reinhardt, Joseph M.; Fiegel, Jennifer

    2014-01-01

    Bacterial biofilms grow on many types of surfaces, including flat surfaces such as glass and metal and irregular surfaces such as rocks, biological tissues and polymers. While laser scanning confocal microscopy can provide high-resolution images of biofilms grown on any surface, quantification of biofilm-associated bacteria is currently limited to bacteria grown on flat surfaces. This can limit researchers studying irregular surfaces to qualitative analysis or quantification of only the total bacteria in an image. In this work, we introduce a new algorithm called modified connected volume filtration (MCVF) to quantify bacteria grown on top of an irregular surface that is fluorescently labeled or reflective. Using the MCVF algorithm, two new quantification parameters are introduced. The modified substratum coverage parameter enables quantification of the connected-biofilm bacteria on top of the surface and on the imaging substratum. The utility of MCVF and the modified substratum coverage parameter were shown with Pseudomonas aeruginosa and Staphylococcus aureus biofilms grown on human airway epithelial cells. A second parameter, the percent association, provides quantified data on the colocalization of the bacteria with a labeled component, including bacteria within a labeled tissue. The utility of quantifying the bacteria associated with the cell cytoplasm was demonstrated with Neisseria gonorrhoeae biofilms grown on cervical epithelial cells. This algorithm provides more flexibility and quantitative ability to researchers studying biofilms grown on a variety of irregular substrata. PMID:24632515

  4. Single cell genomic quantification by non-fluorescence nonlinear microscopy

    NASA Astrophysics Data System (ADS)

    Kota, Divya; Liu, Jing

    2017-02-01

    Human epidermal growth receptor 2 (Her2) is a gene which plays a major role in breast cancer development. The quantification of Her2 expression in single cells is limited by several drawbacks in existing fluorescence-based single molecule techniques, such as low signal-to-noise ratio (SNR), strong autofluorescence and background signals from biological components. For rigorous genomic quantification, a robust method of orthogonal detection is highly desirable and we demonstrated it by two non-fluorescent imaging techniques -transient absorption microscopy (TAM) and second harmonic generation (SHG). In TAM, gold nanoparticles (AuNPs) are chosen as an orthogonal probes for detection of single molecules which gives background-free quantifications of single mRNA transcript. In SHG, emission from barium titanium oxide (BTO) nanoprobes was demonstrated which allows stable signal beyond the autofluorescence window. Her2 mRNA was specifically labeled with nanoprobes which are conjugated with antibodies or oligonucleotides and quantified at single copy sensitivity in the cancer cells and tissues. Furthermore, a non-fluorescent super-resolution concept, named as second harmonic super-resolution microscopy (SHaSM), was proposed to quantify individual Her2 transcripts in cancer cells beyond the diffraction limit. These non-fluorescent imaging modalities will provide new dimensions in biomarker quantification at single molecule sensitivity in turbid biological samples, offering a strong cross-platform strategy for clinical monitoring at single cell resolution.

  5. Two-pass alignment improves novel splice junction quantification.

    PubMed

    Veeneman, Brendan A; Shukla, Sudhanshu; Dhanasekaran, Saravana M; Chinnaiyan, Arul M; Nesvizhskii, Alexey I

    2016-01-01

    Discovery of novel splicing from RNA sequence data remains a critical and exciting focus of transcriptomics, but reduced alignment power impedes expression quantification of novel splice junctions. Here, we profile performance characteristics of two-pass alignment, which separates splice junction discovery from quantification. Per sample, across a variety of transcriptome sequencing datasets, two-pass alignment improved quantification of at least 94% of simulated novel splice junctions, and provided as much as 1.7-fold deeper median read depth over those splice junctions. We further demonstrate that two-pass alignment works by increasing alignment of reads to splice junctions by short lengths, and that potential alignment errors are readily identifiable by simple classification. Taken together, two-pass alignment promises to advance quantification and discovery of novel splicing events. arul@med.umich.edu, nesvi@med.umich.edu Two-pass alignment was implemented here as sequential alignment, genome indexing, and re-alignment steps with STAR. Full parameters are provided in Supplementary Table 2. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  6. Two-pass alignment improves novel splice junction quantification

    PubMed Central

    Veeneman, Brendan A.; Shukla, Sudhanshu; Dhanasekaran, Saravana M.; Chinnaiyan, Arul M.; Nesvizhskii, Alexey I.

    2016-01-01

    Motivation: Discovery of novel splicing from RNA sequence data remains a critical and exciting focus of transcriptomics, but reduced alignment power impedes expression quantification of novel splice junctions. Results: Here, we profile performance characteristics of two-pass alignment, which separates splice junction discovery from quantification. Per sample, across a variety of transcriptome sequencing datasets, two-pass alignment improved quantification of at least 94% of simulated novel splice junctions, and provided as much as 1.7-fold deeper median read depth over those splice junctions. We further demonstrate that two-pass alignment works by increasing alignment of reads to splice junctions by short lengths, and that potential alignment errors are readily identifiable by simple classification. Taken together, two-pass alignment promises to advance quantification and discovery of novel splicing events. Contact: arul@med.umich.edu, nesvi@med.umich.edu Availability and implementation: Two-pass alignment was implemented here as sequential alignment, genome indexing, and re-alignment steps with STAR. Full parameters are provided in Supplementary Table 2. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26519505

  7. Quantified PIRT and Uncertainty Quantification for Computer Code Validation

    NASA Astrophysics Data System (ADS)

    Luo, Hu

    This study is intended to investigate and propose a systematic method for uncertainty quantification for the computer code validation application. Uncertainty quantification has gained more and more attentions in recent years. U.S. Nuclear Regulatory Commission (NRC) requires the use of realistic best estimate (BE) computer code to follow the rigorous Code Scaling, Application and Uncertainty (CSAU) methodology. In CSAU, the Phenomena Identification and Ranking Table (PIRT) was developed to identify important code uncertainty contributors. To support and examine the traditional PIRT with quantified judgments, this study proposes a novel approach, the Quantified PIRT (QPIRT), to identify important code models and parameters for uncertainty quantification. Dimensionless analysis to code field equations to generate dimensionless groups (pi groups) using code simulation results serves as the foundation for QPIRT. Uncertainty quantification using DAKOTA code is proposed in this study based on the sampling approach. Nonparametric statistical theory identifies the fixed number of code run to assure the 95 percent probability and 95 percent confidence in the code uncertainty intervals.

  8. Normal Databases for the Relative Quantification of Myocardial Perfusion

    PubMed Central

    Rubeaux, Mathieu; Xu, Yuan; Germano, Guido; Berman, Daniel S.; Slomka, Piotr J.

    2016-01-01

    Purpose of review Myocardial perfusion imaging (MPI) with SPECT is performed clinically worldwide to detect and monitor coronary artery disease (CAD). MPI allows an objective quantification of myocardial perfusion at stress and rest. This established technique relies on normal databases to compare patient scans against reference normal limits. In this review, we aim to introduce the process of MPI quantification with normal databases and describe the associated perfusion quantitative measures that are used. Recent findings New equipment and new software reconstruction algorithms have been introduced which require the development of new normal limits. The appearance and regional count variations of normal MPI scan may differ between these new scanners and standard Anger cameras. Therefore, these new systems may require the determination of new normal limits to achieve optimal accuracy in relative myocardial perfusion quantification. Accurate diagnostic and prognostic results rivaling those obtained by expert readers can be obtained by this widely used technique. Summary Throughout this review, we emphasize the importance of the different normal databases and the need for specific databases relative to distinct imaging procedures. use of appropriate normal limits allows optimal quantification of MPI by taking into account subtle image differences due to the hardware and software used, and the population studied. PMID:28138354

  9. Normal Databases for the Relative Quantification of Myocardial Perfusion.

    PubMed

    Rubeaux, Mathieu; Xu, Yuan; Germano, Guido; Berman, Daniel S; Slomka, Piotr J

    2016-08-01

    Myocardial perfusion imaging (MPI) with SPECT is performed clinically worldwide to detect and monitor coronary artery disease (CAD). MPI allows an objective quantification of myocardial perfusion at stress and rest. This established technique relies on normal databases to compare patient scans against reference normal limits. In this review, we aim to introduce the process of MPI quantification with normal databases and describe the associated perfusion quantitative measures that are used. New equipment and new software reconstruction algorithms have been introduced which require the development of new normal limits. The appearance and regional count variations of normal MPI scan may differ between these new scanners and standard Anger cameras. Therefore, these new systems may require the determination of new normal limits to achieve optimal accuracy in relative myocardial perfusion quantification. Accurate diagnostic and prognostic results rivaling those obtained by expert readers can be obtained by this widely used technique. Throughout this review, we emphasize the importance of the different normal databases and the need for specific databases relative to distinct imaging procedures. use of appropriate normal limits allows optimal quantification of MPI by taking into account subtle image differences due to the hardware and software used, and the population studied.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  11. Quantification and Single-Spore Detection of Phakopsora pachyrhizi

    USDA-ARS?s Scientific Manuscript database

    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

    USDA-ARS?s Scientific Manuscript database

    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. The Role of Uncertainty Quantification for Reactor Physics

    SciTech Connect

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

  14. Macroscopic inspection of ape feces: what's in a quantification method?

    PubMed

    Phillips, Caroline A; McGrew, William C

    2014-06-01

    Macroscopic inspection of feces has been used to investigate primate diet. The limitations of this method to identify food-items to species level have long been recognized, but ascertaining aspects of diet (e.g., folivory) are achievable by quantifying food-items in feces. Quantification methods applied include rating food-items using a scale of abundance, estimating their percentage volume, and weighing food-items. However, verification as to whether or not composition data differ, depending on which quantification method is used during macroscopic inspection, has not been done. We analyzed feces collected from ten adult chimpanzees (Pan troglodytes schweinfurthii) of the Kanyawara community in Kibale National Park, Uganda. We compare dietary composition totals obtained from using different quantification methods and ascertain if sieve mesh size influences totals calculated. Finally, this study validates findings from direct observation of feeding by the same individuals from whom the fecal samples had been collected. Contrasting diet composition totals obtained by using different quantification methods and sieve mesh sizes can influence folivory and frugivory estimates. However, our findings were based on the assumption that fibrous matter contained pith and leaf fragments only, which remains to be verified. We advocate macroscopic inspection of feces can be a valuable tool to provide a generalized overview of dietary composition for primate populations. As most populations remain unhabituated, scrutinizing and validating indirect measures are important if they are to be applied to further understand inter- and intra-species dietary variation.

  15. 15 CFR 990.52 - Injury assessment-quantification.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 3 2011-01-01 2011-01-01 false Injury assessment-quantification. 990.52 Section 990.52 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE OIL POLLUTION...

  16. 15 CFR 990.52 - Injury assessment-quantification.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 15 Commerce and Foreign Trade 3 2014-01-01 2014-01-01 false Injury assessment-quantification. 990.52 Section 990.52 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE OIL POLLUTION...

  17. 15 CFR 990.52 - Injury assessment-quantification.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Injury assessment-quantification. 990.52 Section 990.52 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE OIL POLLUTION...

  18. 15 CFR 990.52 - Injury assessment-quantification.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 15 Commerce and Foreign Trade 3 2012-01-01 2012-01-01 false Injury assessment-quantification. 990.52 Section 990.52 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE OIL POLLUTION...

  19. 15 CFR 990.52 - Injury assessment-quantification.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 15 Commerce and Foreign Trade 3 2013-01-01 2013-01-01 false Injury assessment-quantification. 990.52 Section 990.52 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE OIL POLLUTION...

  20. Current Issues in the Quantification of Federal Reserved Water Rights

    NASA Astrophysics Data System (ADS)

    Brookshire, David S.; Watts, Gary L.; Merrill, James L.

    1985-11-01

    This paper examines the quantification of federal reserved water rights from legal, institutional, and economic perspectives. Special attention is directed toward Indian reserved water rights and the concept of practicably irrigable acreage. We conclude by examining current trends and exploring alternative approaches to the dilemma of quantifying Indian reserved water rights.

  1. Improved Quantification of Cerebral Vein Oxygenation Using Partial Volume Correction.

    PubMed

    Ward, Phillip G D; Fan, Audrey P; Raniga, Parnesh; Barnes, David G; Dowe, David L; Ng, Amanda C L; Egan, Gary F

    2017-01-01

    Purpose: Quantitative susceptibility mapping (QSM) enables cerebral venous characterization and physiological measurements, such as oxygen extraction fraction (OEF). The exquisite sensitivity of QSM to deoxygenated blood makes it possible to image small veins; however partial volume effects must be addressed for accurate quantification. We present a new method, Iterative Cylindrical Fitting (ICF), to estimate voxel-based partial volume effects for susceptibility maps and use it to improve OEF quantification of small veins with diameters between 1.5 and 4 voxels. Materials and Methods: Simulated QSM maps were generated to assess the performance of the ICF method over a range of vein geometries with varying echo times and noise levels. The ICF method was also applied to in vivo human brain data to assess the feasibility and behavior of OEF measurements compared to the maximum intensity voxel (MIV) method. Results: Improved quantification of OEF measurements was achieved for vessels with contrast to noise greater than 3.0 and vein radii greater than 0.75 voxels. The ICF method produced improved quantitative accuracy of OEF measurement compared to the MIV approach (mean OEF error 7.7 vs. 12.4%). The ICF method provided estimates of vein radius (mean error <27%) and partial volume maps (root mean-squared error <13%). In vivo results demonstrated consistent estimates of OEF along vein segments. Conclusion: OEF quantification in small veins (1.5-4 voxels in diameter) had lower error when using partial volume estimates from the ICF method.

  2. Improved Quantification of Cerebral Vein Oxygenation Using Partial Volume Correction

    PubMed Central

    Ward, Phillip G. D.; Fan, Audrey P.; Raniga, Parnesh; Barnes, David G.; Dowe, David L.; Ng, Amanda C. L.; Egan, Gary F.

    2017-01-01

    Purpose: Quantitative susceptibility mapping (QSM) enables cerebral venous characterization and physiological measurements, such as oxygen extraction fraction (OEF). The exquisite sensitivity of QSM to deoxygenated blood makes it possible to image small veins; however partial volume effects must be addressed for accurate quantification. We present a new method, Iterative Cylindrical Fitting (ICF), to estimate voxel-based partial volume effects for susceptibility maps and use it to improve OEF quantification of small veins with diameters between 1.5 and 4 voxels. Materials and Methods: Simulated QSM maps were generated to assess the performance of the ICF method over a range of vein geometries with varying echo times and noise levels. The ICF method was also applied to in vivo human brain data to assess the feasibility and behavior of OEF measurements compared to the maximum intensity voxel (MIV) method. Results: Improved quantification of OEF measurements was achieved for vessels with contrast to noise greater than 3.0 and vein radii greater than 0.75 voxels. The ICF method produced improved quantitative accuracy of OEF measurement compared to the MIV approach (mean OEF error 7.7 vs. 12.4%). The ICF method provided estimates of vein radius (mean error <27%) and partial volume maps (root mean-squared error <13%). In vivo results demonstrated consistent estimates of OEF along vein segments. Conclusion: OEF quantification in small veins (1.5–4 voxels in diameter) had lower error when using partial volume estimates from the ICF method. PMID:28289372

  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. 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

  6. 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

  7. A Subspace Approach to Spectral Quantification for MR Spectroscopic Imaging.

    PubMed

    Li, Yudu; Lam, Fan; Clifford, Bryan; Liang, Zhi-Pei

    2017-08-18

    To provide a new approach for incorporating both spatial and spectral priors into the solution of the spectral quantification problem for magnetic resonance spectroscopic imaging (MRSI). A novel signal model is proposed, which represents the spectral distributions of each molecule as a subspace and the entire spectrum as a union-of-subspaces. Based on this model, the spectral quantification can be solved in two steps: a) subspace estimation based on the empirical distributions of the spectral parameters estimated using spectral priors, and b) parameter estimation for the union-of-subspaces model incorporating spatial priors. The proposed method has been evaluated using both simulated and experimental data, producing impressive results. The proposed union-of-subspaces representation of spatiospectral functions provides an effective computational framework for solving the MRSI spectral quantification problem with spatiospectral constraints. The proposed approach transforms how the MRSI spectral quantification problem is solved and enables efficient and effective use of spatiospectral priors to improve parameter estimation. The resulting algorithm is expected to be useful for a wide range of quantitative metabolic imaging studies using MRSI.

  8. 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.

  9. Droplet digital PCR for absolute quantification of pathogens.

    PubMed

    Gutiérrez-Aguirre, Ion; Rački, Nejc; Dreo, Tanja; Ravnikar, Maja

    2015-01-01

    The recent advent of different digital PCR (dPCR) platforms is enabling the expansion of this technology for research and diagnostic applications worldwide. The main principle of dPCR, as in other PCR-based methods including quantitative PCR (qPCR), is the specific amplification of a nucleic acid target. The distinctive feature of dPCR is the separation of the reaction mixture into thousands to millions of partitions which is followed by a real time or end point detection of the amplification. The distribution of target sequences into partitions is described by the Poisson distribution, thus allowing accurate and absolute quantification of the target from the ratio of positive against all partitions at the end of the reaction. This omits the need to use reference materials with known target concentrations and increases the accuracy of quantification at low target concentrations compared to qPCR. dPCR has also shown higher resilience to inhibitors in a number of different types of samples. In this chapter we describe the droplet digital PCR (ddPCR) workflow for the detection and quantification of pathogens using the droplet digital Bio-Rad platform QX100. We present as an example the quantification of the quarantine plant pathogenic bacterium, Erwinia amylovora.

  10. 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…

  11. 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.

  12. Ancient River revealed

    NASA Astrophysics Data System (ADS)

    Recent flights of the Spaceborne Imaging Radar-C/X-band Synthetic Aperture Radar (SIR-C/X-SAR) mission aboard the space shuttle Endeavour discovered a previously unknown branch of an ancient river. The images, released at AGU's Spring Meeting, show the river channel buried under thousands of years worth of windblown sand in a region of North Africa's Sahara Desert near the Kufra Oasis in southeast Libya, centered at 23.3°N latitude, 22.9°E longitude. The image from the flight last October reveals a system of old, now inactive stream valleys, called “paleodrainage systems,” which carried running water northward across the Sahara during periods of wetter climate.

  13. 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.

  14. 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.

  15. Quantification of Microstructure-Properties-Behavior Relations in Magnesium Alloys Using a Hybrid Approach

    NASA Astrophysics Data System (ADS)

    Hazeli, K.; Cuadra, J.; Vanniamparambil, P. A.; Carmi, R.; Kontsos, A.

    This study presents a hybrid experimental mechanics approach combining multi-scale mechanical testing, in situ nondestructive evaluation and targeted microscopic quantification to identify and quantify critical micro structural parameters that affect properties and overall plasticity of Mg alloys. Room temperature monotonic and cyclic experiments monitored by Digital Image Correlation (DIC) coupled with Acoustic Emission (AE) of Mg Alloys of the AZ series were used for this investigation. Data obtained using the optico-acoustic nondestructive system revealed for the first time the direct connection between surface strain localization effects similar to Luder's bands and pronounced twin activity. Electron Back Scatter Diffraction (EBSD) measurements showed the profuse and spatially inhomogeneous nature of twinning at early stages of plasticity which is related with the onset of yielding and the macroscopic plateau region in the stress-strain curve. Furthermore, twinning/detwinning activity was identified in several grains of tested specimens and during characteristic points of fatigue cycles.

  16. 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.

  17. 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

  18. Use of heterologous immunoassays for quantification of serum proteins: The case of canine C-reactive protein

    PubMed Central

    Muñoz-Prieto, Alberto; Tvarijonaviciute, Asta; Escribano, Damián; Martínez-Subiela, Silvia; Cerón, José J.

    2017-01-01

    The use of heterologous immunoassays containing antibodies raised against a different biological species for quantification of serum proteins is studied and discussed, taking as example the case of the use of a commercially available heterologous assay containing antibodies against human C-reactive protein (hCRP) for quantification of CRP in serum of dogs. This assay was adapted and validated for measurements of canine CRP (cCRP) and compared with three different homologous assays containing species-specific canine antibodies, which are currently commercially available for cCRP determination. Serum samples from healthy and diseased dogs (n = 44) were used. Analytical evaluation included precision, accuracy, limit of detection and lower limit of quantification for all assays. In the case of the heterologous assay also cross-reactivity of the antibody of the heterologous assay with cCRP was evaluated by a Western-Blot analysis giving a positive result. The heterologous assay showed similar results than the homologous assays in all the tests of the analytical evaluation that indicated that the assay was precise and accurate. Method comparison showed a high correlation between all assays (r≥0.9). The Bland-Altman test revealed that the heterologous assay showed a proportional error when compared with the homologous automated assays and a random error when compared with the point-of-care assay. All four CRP assays were able to detect higher CRP values in dogs with inflammatory conditions compared with healthy dogs. It is concluded that heterologous immunoassays could be used for quantification of serum proteins in different species, provided that the antibody has cross-reactivity with the protein to be measured and the assay give satisfactory results in the analytical validation tests. In addition, use of species-specific calibrators and an appropriate batch validation are recommended in these cases. PMID:28222144

  19. SU-D-218-05: Material Quantification in Spectral X-Ray Imaging: Optimization and Validation.

    PubMed

    Nik, S J; Thing, R S; Watts, R; Meyer, J

    2012-06-01

    To develop and validate a multivariate statistical method to optimize scanning parameters for material quantification in spectral x-rayimaging. An optimization metric was constructed by extensively sampling the thickness space for the expected number of counts for m (two or three) materials. This resulted in an m-dimensional confidence region ofmaterial quantities, e.g. thicknesses. Minimization of the ellipsoidal confidence region leads to the optimization of energy bins. For the given spectrum, the minimum counts required for effective material separation can be determined by predicting the signal-to-noise ratio (SNR) of the quantification. A Monte Carlo (MC) simulation framework using BEAM was developed to validate the metric. Projection data of the m-materials was generated and material decomposition was performed for combinations of iodine, calcium and water by minimizing the z-score between the expected spectrum and binned measurements. The mean square error (MSE) and variance were calculated to measure the accuracy and precision of this approach, respectively. The minimum MSE corresponds to the optimal energy bins in the BEAM simulations. In the optimization metric, this is equivalent to the smallest confidence region. The SNR of the simulated images was also compared to the predictions from the metric. TheMSE was dominated by the variance for the given material combinations,which demonstrates accurate material quantifications. The BEAMsimulations revealed that the optimization of energy bins was accurate to within 1keV. The SNRs predicted by the optimization metric yielded satisfactory agreement but were expectedly higher for the BEAM simulations due to the inclusion of scattered radiation. The validation showed that the multivariate statistical method provides accurate material quantification, correct location of optimal energy bins and adequateprediction of image SNR. The BEAM code system is suitable for generating spectral x- ray imaging simulations.

  20. The impact of carbon-13 and deuterium on relative quantification of proteins using stable isotope diethyl labeling.

    PubMed

    Koehler, Christian J; Arntzen, Magnus Ø; Thiede, Bernd

    2015-05-15

    Stable isotopic labeling techniques are useful for quantitative proteomics. A cost-effective and convenient method for diethylation by reductive amination was established. The impact using either carbon-13 or deuterium on quantification accuracy and precision was investigated using diethylation. We established an effective approach for stable isotope labeling by diethylation of amino groups of peptides. The approach was validated using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and nanospray liquid chromatography/electrospray ionization (nanoLC/ESI)-ion trap/orbitrap for mass spectrometric analysis as well as MaxQuant for quantitative data analysis. Reaction conditions with low reagent costs, high yields and minor side reactions were established for diethylation. Furthermore, we showed that diethylation can be applied to up to sixplex labeling. For duplex experiments, we compared diethylation in the analysis of the proteome of HeLa cells using acetaldehyde-(13) C(2)/(12) C(2) and acetaldehyde-(2) H(4)/(1) H(4). Equal numbers of proteins could be identified and quantified; however, (13) C(4)/(12) C(4) -diethylation revealed a lower variance of quantitative peptide ratios within proteins resulting in a higher precision of quantified proteins and less falsely regulated proteins. The results were compared with dimethylation showing minor effects because of the lower number of deuteriums. The described approach for diethylation of primary amines is a cost-effective and accurate method for up to sixplex relative quantification of proteomes. (13) C(4)/(12) C(4) -diethylation enables duplex quantification based on chemical labeling without using deuterium which reduces identification of false-negatives and increases the quality of the quantification results. Copyright © 2015 John Wiley & Sons, Ltd.

  1. Use of heterologous immunoassays for quantification of serum proteins: The case of canine C-reactive protein.

    PubMed

    Muñoz-Prieto, Alberto; Tvarijonaviciute, Asta; Escribano, Damián; Martínez-Subiela, Silvia; Cerón, José J

    2017-01-01

    The use of heterologous immunoassays containing antibodies raised against a different biological species for quantification of serum proteins is studied and discussed, taking as example the case of the use of a commercially available heterologous assay containing antibodies against human C-reactive protein (hCRP) for quantification of CRP in serum of dogs. This assay was adapted and validated for measurements of canine CRP (cCRP) and compared with three different homologous assays containing species-specific canine antibodies, which are currently commercially available for cCRP determination. Serum samples from healthy and diseased dogs (n = 44) were used. Analytical evaluation included precision, accuracy, limit of detection and lower limit of quantification for all assays. In the case of the heterologous assay also cross-reactivity of the antibody of the heterologous assay with cCRP was evaluated by a Western-Blot analysis giving a positive result. The heterologous assay showed similar results than the homologous assays in all the tests of the analytical evaluation that indicated that the assay was precise and accurate. Method comparison showed a high correlation between all assays (r≥0.9). The Bland-Altman test revealed that the heterologous assay showed a proportional error when compared with the homologous automated assays and a random error when compared with the point-of-care assay. All four CRP assays were able to detect higher CRP values in dogs with inflammatory conditions compared with healthy dogs. It is concluded that heterologous immunoassays could be used for quantification of serum proteins in different species, provided that the antibody has cross-reactivity with the protein to be measured and the assay give satisfactory results in the analytical validation tests. In addition, use of species-specific calibrators and an appropriate batch validation are recommended in these cases.

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

    PubMed

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

    2017-03-01

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

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

    PubMed Central

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

    2017-01-01

    There has been increasing interest in standardized and quantitative Epstein-Barr virus (EBV) DNA testing for the management of EBV disease. We evaluated the performance of the Real-Q EBV Quantification Kit (BioSewoom, Korea) in whole blood (WB). Nucleic acid extraction and real-time PCR were performed by using the MagNA Pure 96 (Roche Diagnostics, Germany) and 7500 Fast real-time PCR system (Applied Biosystems, USA), respectively. Assay sensitivity, linearity, and conversion factor were determined by using the World Health Organization international standard diluted in EBV-negative WB. We used 81 WB clinical specimens to compare performance of the Real-Q EBV Quantification Kit and artus EBV RG PCR Kit (Qiagen, Germany). The limit of detection (LOD) and limit of quantification (LOQ) for the Real-Q kit were 453 and 750 IU/mL, respectively. The conversion factor from EBV genomic copies to IU was 0.62. The linear range of the assay was from 750 to 106 IU/mL. Viral load values measured with the Real-Q assay were on average 0.54 log10 copies/mL higher than those measured with the artus assay. The Real-Q assay offered good analytical performance for EBV DNA quantification in WB. PMID:28029001

  4. 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

  5. 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.

  6. Colloidal quantum dot based solar cells: from materials to devices.

    PubMed

    Song, Jung Hoon; Jeong, Sohee

    2017-01-01

    Colloidal quantum dots (CQDs) have attracted attention as a next-generation of photovoltaics (PVs) capable of a tunable band gap and low-cost solution process. Understanding and controlling the surface of CQDs lead to the significant development in the performance of CQD PVs. Here we review recent progress in the realization of low-cost, efficient lead chalcogenide CQD PVs based on the surface investigation of CQDs. We focus on improving the electrical properties and air stability of the CQD achieved by material approaches and growing the power conversion efficiency (PCE) of the CQD PV obtained by structural approaches. Finally, we summarize the manners to improve the PCE of CQD PVs through optical design. The various issues mentioned in this review may provide insight into the commercialization of CQD PVs in the near future.

  7. Thermoelectric properties of an interacting quantum dot based heat engine

    NASA Astrophysics Data System (ADS)

    Erdman, Paolo Andrea; Mazza, Francesco; Bosisio, Riccardo; Benenti, Giuliano; Fazio, Rosario; Taddei, Fabio

    2017-06-01

    We study the thermoelectric properties and heat-to-work conversion performance of an interacting, multilevel quantum dot (QD) weakly coupled to electronic reservoirs. We focus on the sequential tunneling regime. The dynamics of the charge in the QD is studied by means of master equations for the probabilities of occupation. From here we compute the charge and heat currents in the linear response regime. Assuming a generic multiterminal setup, and for low temperatures (quantum limit), we obtain analytical expressions for the transport coefficients which account for the interplay between interactions (charging energy) and level quantization. In the case of systems with two and three terminals we derive formulas for the power factor Q and the figure of merit Z T for a QD-based heat engine, identifying optimal working conditions which maximize output power and efficiency of heat-to-work conversion. Beyond the linear response we concentrate on the two-terminal setup. We first study the thermoelectric nonlinear coefficients assessing the consequences of large temperature and voltage biases, focusing on the breakdown of the Onsager reciprocal relation between thermopower and Peltier coefficient. We then investigate the conditions which optimize the performance of a heat engine, finding that in the quantum limit output power and efficiency at maximum power can almost be simultaneously maximized by choosing appropriate values of electrochemical potential and bias voltage. At last we study how energy level degeneracy can increase the output power.

  8. Single Quantum-dot-based Aptameric Nanosensor for Cocaine

    PubMed Central

    Zhang, Chun-yang; Johnson, Lawrence W

    2009-01-01

    Recent advances in single-molecule detection, nanotechnology and aptameric sensors hold exciting promise for many potential applications. By functionalizing the surface of a quantum dot (QD) with aptamers which can recognize cocaine, and taking advantage of single-molecule detection and fluorescence resonance energy transfer (FRET) between 605QD and Cy5 and Iowa Black RQ, we develop a single-QD-based aptameric sensor that is capable of sensing the presence of cocaine through both signal-off and signal-on modes. In comparison with the established aptameric sensors, this single-QD-based aptameric sensor has the significant advantages of simple sample preparation, high sensitivity and extremely low sample consumption. With the advance in the development of varieties of aptamers for small molecules, nucleic acids, metal ions and proteins, this single-QD-based aptameric sensor might find wide application in forensic analysis, environmental monitoring and clinic diagnostics. PMID:19298058

  9. PbSe quantum dot based luminescent solar concentrators

    NASA Astrophysics Data System (ADS)

    Waldron, Dennis L.; Preske, Amanda; Zawodny, Joseph M.; Krauss, Todd D.; Gupta, Mool C.

    2017-03-01

    The results are presented for luminescent solar concentrators (LSCs) fabricated with poly(lauryl methacrylate-co-ethylene glycol dimethacrylate) (P(LMA-co-EGDMA)) and Angstrom Bond, Inc. AB9093 acrylic epoxy matrix, high quantum yield (> 70%) PbSe quantum dots (QDs) and silicon photovoltaic (Si PV) cells. LSCs were tested under a lamp with broadband illumination, photon flux-matched to a standard solar spectrum and verified under a calibrated solar lamp source. The P(LMA-co-EGDMA) sample demonstrated the highest power conversion efficiency of any known LSC fabricated with either QDs or Si PV cells, 4.74%. Additionally, increased temperature was shown to reduce efficiency.

  10. 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.

  11. PbSe quantum dot based luminescent solar concentrators.

    PubMed

    Waldron, Dennis L; Preske, Amanda; Zawodny, Joseph M; Krauss, Todd D; Gupta, Mool C

    2017-03-03

    The results are presented for luminescent solar concentrators (LSCs) fabricated with poly(lauryl methacrylate-co-ethylene glycol dimethacrylate) (P(LMA-co-EGDMA)) and Angstrom Bond, Inc. AB9093 acrylic epoxy matrix, high quantum yield (> 70%) PbSe quantum dots (QDs) and silicon photovoltaic (Si PV) cells. LSCs were tested under a lamp with broadband illumination, photon flux-matched to a standard solar spectrum and verified under a calibrated solar lamp source. The P(LMA-co-EGDMA) sample demonstrated the highest power conversion efficiency of any known LSC fabricated with either QDs or Si PV cells, 4.74%. Additionally, increased temperature was shown to reduce efficiency.

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

    PubMed

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

    2016-07-07

    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.

  13. Colloidal quantum dot based solar cells: from materials to devices

    NASA Astrophysics Data System (ADS)

    Song, Jung Hoon; Jeong, Sohee

    2017-08-01

    Colloidal quantum dots (CQDs) have attracted attention as a next-generation of photovoltaics (PVs) capable of a tunable band gap and low-cost solution process. Understanding and controlling the surface of CQDs lead to the significant development in the performance of CQD PVs. Here we review recent progress in the realization of low-cost, efficient lead chalcogenide CQD PVs based on the surface investigation of CQDs. We focus on improving the electrical properties and air stability of the CQD achieved by material approaches and growing the power conversion efficiency (PCE) of the CQD PV obtained by structural approaches. Finally, we summarize the manners to improve the PCE of CQD PVs through optical design. The various issues mentioned in this review may provide insight into the commercialization of CQD PVs in the near future.

  14. Carbon dots based FRET for the detection of DNA damage.

    PubMed

    Kudr, Jiri; Richtera, Lukas; Xhaxhiu, Kledi; Hynek, David; Heger, Zbynek; Zitka, Ondrej; Adam, Vojtech

    2017-02-09

    Here, we aimed our attention at the synthesis of carbon dots (C-dots) with the ability to interact with DNA to suggest an approach for the detection of DNA damage. Primarily, C-dots modified with amine moieties were synthesized using the one-step microwave pyrolysis of citric acid in the presence of diethylenetriamine. The C-dots showed strong photoluminescence with a quantum yield of 4%. In addition, the C-dots (2.8±0.8nm) possessed a good colloidal stability and exhibited a positive surface charge (ζ=36mV) at a neutral pH. An interaction study of the C-dots and the DNA fragment of λ bacteriophage was performed, and the DNA binding resulted in changes to the photoluminescent and absorption properties of the C-dots. A binding of the C-dots to DNA was also observed as a change to DNA electrophoretic mobility and a decreased ability to intercalate ethidium bromide (EtBr). Moreover, the Förster (or fluorescence) resonance energy transfer (FRET) between the C-dots and EtBr was studied, in which the C-dots serve as an excitation energy donor and the EtBr serves as an acceptor. When DNA was damaged using ultraviolet (UV) radiation (λ=254nm) and hydroxyl radicals, the intensity of the emitted photoluminescence at 612nm significantly decreased. The concept was proved on analysis of the genomic DNA from PC-3 cells and DNA isolated from melanoma tissues.

  15. Quantum-dots-based photoelectrochemical bioanalysis highlighted with recent examples.

    PubMed

    Zhang, Nan; Zhang, Ling; Ruan, Yi-Fan; Zhao, Wei-Wei; Xu, Jing-Juan; Chen, Hong-Yuan

    2017-03-07

    Photoelectrochemical (PEC) bioanalysis is a newly developed methodology that provides an exquisite route for innovative biomolecular detection. Quantum dots (QDs) are semiconductor nanocrystals with unique photophysical properties that have attracted tremendous attentions among the analytical community. QDs-based PEC bioanalysis comprises an important research hotspot in the field of PEC bioanalysis due to its combined advantages and potentials. Currently, it has ignited increasing interests as demonstrated by increased research papers. This review aims to cover the most recent advances in this field. With the discussion of recent examples of QDs-PEC bioanalysis from the literatures, special emphasis will be placed on work reporting on fundamental advances in the signaling strategies of QDs-based PEC bioanalysis from 2013 to now. Future prospects in this field are also discussed.

  16. 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

  17. Development of a Quantum Dot Based Luminescent Solar Concentrator

    NASA Astrophysics Data System (ADS)

    Suter, John David

    Luminescent solar concentrators (LSCs) have been proposed as a lower cost and more aesthetically pleasing alternative to traditional photovoltaic devices. The LSC presented in this thesis will use II-VI semiconducting quantum dots (QDs) as luminescent material. CdSe/ZnSe core/shell QDs; CdSe/ZnS core/shell QDs; and CdxZn1-xSe QDs can be synthesized with high quality (quantum yield >50%) using simple, reproducible methods. Furthermore, two methods of incorporating the QDs into an LSC will be discussed. In the first method, single QD thick monolayers or multilayered QD thin films can be deposited onto an optically clear medium using Langmuir-Blodgett (LB) deposition. However, these QD films have poor optical qualities making them unfit for use in a LSC. Alternatively, QDs can be incorporated into a polymer slide. These highly fluorescent QD-polymer slides act as waveguides directing the photons emitted by the QDs towards the edges of the slide.

  18. Preparation of carbon quantum dots based high photostability luminescent membranes.

    PubMed

    Zhao, Jinxing; Liu, Cui; Li, Yunchuan; Liang, Jiyuan; Liu, Jiyan; Qian, Tonghui; Ding, Jianjun; Cao, Yuan-Cheng

    2017-06-01

    Urethane acrylate (UA) was used to prepare carbon quantum dots (C-dots) luminescent membranes and the resultants were examined with FT-IR, mechanical strength, scanning electron microscope (SEM) and quantum yields (QYs). FT-IR results showed the polyurethane acrylate (PUA) prepolymer -C = C-vibration at 1101 cm(-1) disappeared but there was strong vibration at1687cm(-1) which was contributed from the-C = O groups in cross-linking PUA. Mechanical strength results showed that the different quantity of C-dots loadings and UV-curing time affect the strength. SEM observations on the cross-sections of the membranes are uniform and have no structural defects, which prove that the C-dots are compatible with the water-soluble PUA resin. The C-dot loading was increased from 0 to 1 g, the maximum tensile stress was nearly 2.67 MPa, but the tensile strain was decreased from 23.4% to 15.1% and 7.2% respectively. QYs results showed that the C-dots in the membrane were stable after 120 h continuous irradiation. Therefore, the C-dots photoluminescent film is the promising material for the flexible devices in the future applications. Copyright © 2016 John Wiley & Sons, Ltd.

  19. 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.

  20. 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.

  1. 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.

  2. Quantum dot based rapid tests for zearalenone detection.

    PubMed

    Beloglazova, N V; Speranskaya, E S; De Saeger, S; Hens, Z; Abé, S; Goryacheva, I Yu

    2012-07-01

    Three different kinds of immunosorbent assays with luminescence detection were developed for the determination of zearalenone (ZEN), a secondary toxic metabolite of Fusarium fungi. CdSe/ZnS core/shell quantum dots (QDs) were used as a label in quantitative micro-well plate immunoassays (fluorescent-labeled immunosorbent assay, FLISA) and in qualitative column test methods. As carriers for QD-based column tests, sepharose gel (for covalent binding of antibody) and polyethylene frits (for physical absorption of antibody) were used and compared. The application of QDs as a label resulted in a fourfold decrease in the IC(50) value with FLISA (0.1 ng mL(-1)) with a detection limit of 0.03 ng mL(-1) when compared with the traditional immunosorbent assay which makes use of horseradish peroxidase as the enzyme label. The cutoff levels for both qualitative column test methods were selected based on the maximum level for ZEN in unprocessed cereals established by the European Commission (100 μg kg(-1)) as 5 ng mL(-1) taking into account extraction and dilution. The different developed immumoassays were tested for ZEN determination in raw wheat samples. As a confirmatory method, liquid chromatography coupled to tandem mass spectrometry was used. The obtained results allow using FLISA and both qualitative column test methods for the analysis of analytes with very low established maximum limits, even in very complicated food matrices, owing to the high dilution of the sample extract.

  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.

  4. Statistical challenges in the quantification of gunshot residue evidence.

    PubMed

    Gauriot, Romain; Gunaratnam, Lawrence; Moroni, Rossana; Reinikainen, Tapani; Corander, Jukka

    2013-09-01

    The discharging of a gun results in the formation of extremely small particles known as gunshot residues (GSR). These may be deposited on the skin and clothing of the shooter, on other persons present, and on nearby items or surfaces. Several factors and their complex interactions affect the number of detectable GSR particles, which can deeply influence the conclusions drawn from likelihood ratios or posterior probabilities for prosecution hypotheses of interest. We present Bayesian network models for casework examples and demonstrate that probabilistic quantification of GSR evidence can be very sensitive to the assumptions concerning the model structure, prior probabilities, and the likelihood components. This finding has considerable implications for the use of statistical quantification of GSR evidence in the legal process.

  5. 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.

  6. 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

  7. 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.

  8. Multiscale recurrence quantification analysis of order recurrence plots

    NASA Astrophysics Data System (ADS)

    Xu, Mengjia; Shang, Pengjian; Lin, Aijing

    2017-03-01

    In this paper, we propose a new method of multiscale recurrence quantification analysis (MSRQA) to analyze the structure of order recurrence plots. The MSRQA is based on order patterns over a range of time scales. Compared with conventional recurrence quantification analysis (RQA), the MSRQA can show richer and more recognizable information on the local characteristics of diverse systems which successfully describes their recurrence properties. Both synthetic series and stock market indexes exhibit their properties of recurrence at large time scales that quite differ from those at a single time scale. Some systems present more accurate recurrence patterns under large time scales. It demonstrates that the new approach is effective for distinguishing three similar stock market systems and showing some inherent differences.

  9. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Uncertainty Quantification for Large-Scale Ice Sheet Modeling

    SciTech Connect

    Ghattas, Omar

    2016-02-05

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

  11. Standardless Quantification of Heavy Elements by Electron Probe Microanalysis.

    PubMed

    Moy, Aurélien; Merlet, Claude; Dugne, Olivier

    2015-08-04

    Absolute Mα and Mβ X-ray intensities were measured for the elements Pt, Au, Pb, U, and Th by electron impact for energies ranging from 6 to 38 keV. Experimental data were obtained by measuring the X-ray intensity emitted from bulk samples with an electron microprobe using high-resolution wavelength-dispersive spectrometers. Recorded X-ray intensities were converted into absolute X-ray yields by evaluation of the detector efficiency and then compared with X-ray intensities calculated by means of Monte Carlo simulations. Simulated Mα and Mβ X-ray intensities were found to be in good agreement with the measurements, allowing their use in standardless quantification methods. A procedure and a software program were developed to accurately obtain virtual standard values. Standardless quantifications of Pb and U were tested on standards of PbS, PbTe, PbCl2, vanadinite, and UO2.

  12. Uncertainty Quantification and Validation for RANS Turbulence Models

    NASA Astrophysics Data System (ADS)

    Oliver, Todd; Moser, Robert

    2011-11-01

    Uncertainty quantification and validation procedures for RANS turbulence models are developed and applied. The procedures used here rely on a Bayesian view of probability. In particular, the uncertainty quantification methodology requires stochastic model development, model calibration, and model comparison, all of which are pursued using tools from Bayesian statistics. Model validation is also pursued in a probabilistic framework. The ideas and processes are demonstrated on a channel flow example. Specifically, a set of RANS models--including Baldwin-Lomax, Spalart-Allmaras, k- ɛ, k- ω, and v2- f--and uncertainty representations are analyzed using DNS data for fully-developed channel flow. Predictions of various quantities of interest and the validity (or invalidity) of the various models for making those predictions will be examined. This work is supported by the Department of Energy [National Nuclear Security Administration] under Award Number [DE-FC52-08NA28615].

  13. Collaborative framework for PIV uncertainty quantification: comparative assessment of methods

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  14. Bquant - Novel script for batch quantification of LCMS data.

    PubMed

    Rožman, Marko; Petrović, Mira

    2016-01-01

    Quantitative target analysis by liquid chromatography coupled to mass spectrometry (LCMS) is ubiquitous in environmental, metabolomic and toxicological studies. Targeted LCMS methods are capable of the simultaneous determination of literally hundreds of analytes. Although acquiring of instrumental data is very fast, data post-processing i.e. quantification can be time consuming step (and)or dependent to various commercial software packages. In attempt to facilitate this drawback Wolfram Mathematica script for batch quantification of LCMS data was created. Script works with direct outputs of integration algorithms created by different instrument control software's or custom created outputs. Key benefits of Bquant script are: •simple and automated routine for batch mode quantification•vast improvement in processing time (especially compared to manual interpretation)•data can be quickly re-analysed using different inputs Script was validated on various datasets and some of these were provided as working examples.

  15. Metering error quantification under voltage and current waveform distortion

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Wang, Jia; Xie, Zhi; Zhang, Ran

    2017-09-01

    With integration of more and more renewable energies and distortion loads into power grid, the voltage and current waveform distortion results in metering error in the smart meters. Because of the negative effects on the metering accuracy and fairness, it is an important subject to study energy metering combined error. In this paper, after the comparing between metering theoretical value and real recorded value under different meter modes for linear and nonlinear loads, a quantification method of metering mode error is proposed under waveform distortion. Based on the metering and time-division multiplier principles, a quantification method of metering accuracy error is proposed also. Analyzing the mode error and accuracy error, a comprehensive error analysis method is presented which is suitable for new energy and nonlinear loads. The proposed method has been proved by simulation.

  16. Analytical Methods for the Quantification of Histamine and Histamine Metabolites.

    PubMed

    Bähre, Heike; Kaever, Volkhard

    2017-03-21

    The endogenous metabolite histamine (HA) is synthesized in various mammalian cells but can also be ingested from exogenous sources. It is involved in a plethora of physiological and pathophysiological processes. So far, four different HA receptors (H1R-H4R) have been described and numerous HAR antagonists have been developed. Contemporary investigations regarding the various roles of HA and its main metabolites have been hampered by the lack of highly specific and sensitive analytic methods for all of these analytes. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) is the method of choice for identification and sensitive quantification of many low-molecular weight endogenous metabolites. In this chapter, different methodological aspects of HA quantification as well as recommendations for LC-MS/MS methods suitable for analysis of HA and its main metabolites are summarized.

  17. Feature quantification and abnormal detection on cervical squamous epithelial cells.

    PubMed

    Zhao, Mingzhu; Chen, Lei; Bian, Linjie; Zhang, Jianhua; Yao, Chunyan; Zhang, Jianwei

    2015-01-01

    Feature analysis and classification detection of abnormal cells from images for pathological analysis are an important issue for the realization of computer assisted disease diagnosis. This paper studies a method for cervical squamous epithelial cells. Based on cervical cytological classification standard and expert diagnostic experience, expressive descriptors are extracted according to morphology, color, and texture features of cervical scales epithelial cells. Further, quantificational descriptors related to cytopathology are derived as well, including morphological difference degree, cell hyperkeratosis, and deeply stained degree. The relationship between quantified value and pathological feature can be established by these descriptors. Finally, an effective method is proposed for detecting abnormal cells based on feature quantification. Integrated with clinical experience, the method can realize fast abnormal cell detection and preliminary cell classification.

  18. Quantification of Trace Chemicals Using Vehicle Cabin Atmosphere Monitor

    NASA Technical Reports Server (NTRS)

    Lee, Seungwon; Mandrake, Lukas; Bornstein, Benjamin; Bue, Brian

    2009-01-01

    A system to monitor the concentrations of trace chemicals in cabin atmosphere is one of the most critical components in long-duration human flight missions. The Vehicle Cabin Atmosphere Monitor (VCAM) is a miniature gas chromatograph mass spectrometer system to be used to detect and quantify trace chemicals in the International Space Station. We developed an autonomous computational process to quantify trace chemicals for use in VCAM. The process involves the design of a measured signal quantification scheme, the construction of concentration curves (i.e. the relationship between concentration and ion count measured by VCAM), the decision rule of applying high- or low-gain concentration curves, and the detection of saturation, low-signals, and outliers. When the developed quantification process is applied, the average errors of concentration for most of trace chemicals are found to be between 14% and 66%.

  19. Targeted Quantification of the Glycated Peptides of Human Serum Albumin.

    PubMed

    Vannuruswamy, Garikapati; Korwar, Arvind M; Jagadeeshaprasad, Mashanipalya G; Kulkarni, Mahesh J

    2017-01-01

    Glycated human serum albumin (HSA) serves as an important marker for monitoring the glycemic status. Developing methods for unambiguous identification and quantification of glycated peptides of HSA using high-throughput technologies such as mass spectrometry has a great clinical significance. The following protocol describes the construction of reference spectral libraries for Amadori-modified lysine (AML), N(ε)-(carboxymethyl) lysine (CML)-, and N(ε)-(carboxyethyl)lysine (CEL)-modified peptides of synthetically modified HSA using high-resolution mass spectrometers. The protocol also describes work flows, for unambiguous identification and quantification of glycated modified peptides of HSA in clinical plasma using standard spectral libraries by various mass spectrometry approaches such as parallel reaction monitoring (PRM), sequential window acquisition of all theoretical fragment ion spectra (SWATH), and MS(E).

  20. High-throughput quantification of hydroxyproline for determination of collagen.

    PubMed

    Hofman, Kathleen; Hall, Bronwyn; Cleaver, Helen; Marshall, Susan

    2011-10-15

    An accurate and high-throughput assay for collagen is essential for collagen research and development of collagen products. Hydroxyproline is routinely assayed to provide a measurement for collagen quantification. The time required for sample preparation using acid hydrolysis and neutralization prior to assay is what limits the current method for determining hydroxyproline. This work describes the conditions of alkali hydrolysis that, when combined with the colorimetric assay defined by Woessner, provide a high-throughput, accurate method for the measurement of hydroxyproline.

  1. 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.

  2. 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.

  3. Improved Quantification of Plasma Catecholamines by the Radioenzymic Kit Method.

    DTIC Science & Technology

    1982-11-01

    RECIPIENT’S CATALOG NUMBER SAM-TR-8 2-40 n &Ie 4. TITLE (and Subtitle) S. TYPE OF REPORT G PERIOD COVERED IMPROVED QUANTIFICATION OF PLASMA CATECHOLAMINES...side i 1nocesCary and Identily by block nmuber) Human/swine plasma catecholamine assays Plasma catecholamines by kit method Enzymic catecholamine...for plasma catecholamine analyses is reported. The departure features use of "mean net standards" instead of individual internal standards

  4. Quantification of intraocular surgery motions with an electromagnetic tracking system.

    PubMed

    Son, Ji; Bourges, Jean-Louis; Culjat, Martin O; Nistor, Vasile; Dutson, Erik P; Carman, Gregory P; Hubschman, Jean Pierre

    2009-01-01

    Motion tracking was performed during a combined phacoemulsification (PKE) and pars plana vitrectomy (PPV) procedure on a pig eyeball. The UCLA Laparoscopic Training System (UCLA-LTS), which consists of electromagnetic sensors attached to the surgical tools to measure three-dimensional spatial vectors, was modified to enable quantification of intraocular surgery motions. The range of motion and time taken to complete the given task were successfully recorded.

  5. Quantification of Thermal Lensing Using an Artificial Eye

    DTIC Science & Technology

    2013-01-01

    CONTRACT NUMBER FA8650-08-6930 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 0603231F 6. AUTHOR(S) Erica L. Towle , John M. Rickman, Andrew K...ANSI Std. 239.18 i IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS 1 Quantification of Thermal Lensing Using an Artificial Eye Erica L. Towle ...2013; accepted April 22, 2013. E. L. Towle is with the Air Force Research Laboratory, Fort Sam Houston, TX 78234 USA and also with the Biomedical

  6. Semantics and Quantification in Natural Language Question Answering

    DTIC Science & Technology

    1977-11-01

    not universally so (for example, when a function is applied to a quantified noun phrase - see Functional Nesting below). In situations where the...query languages, question-answering, semantic interpretation, semantic rules, syntax - semantics interaction. 20. ABSTRACT (Confinua on ravaraa...Language 17 4.1 Designators 18 4.2 Propositions 18 4.3 Commands 19 4.4 Quantification 19 4.5 Specification of the MRL Syntax 21 4.6 Procedural

  7. 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.

  8. Color correction for automatic fibrosis quantification in liver biopsy specimens

    PubMed Central

    Murakami, Yuri; Abe, Tokiya; Hashiguchi, Akinori; Yamaguchi, Masahiro; Saito, Akira; Sakamoto, Michiie

    2013-01-01

    Context: For a precise and objective quantification of liver fibrosis, quantitative evaluations through image analysis have been utilized. However, manual operations are required in most cases for extracting fiber areas because of color variation included in digital pathology images. Aims: The purpose of this research is to propose a color correction method for whole slide images (WSIs) of Elastica van Gieson (EVG) stained liver biopsy tissue specimens and to realize automated operation of image analysis for fibrosis quantification. Materials and Methods: Our experimental dataset consisted of 38 WSIs of liver biopsy specimens collected from 38 chronic viral hepatitis patients from multiple medical facilities, stained with EVG and scanned at ×20 using a Nano Zoomer 2.0 HT (Hamamatsu Photonics K.K., Hamamatsu, Japan). Color correction was performed by modifying the color distribution of a target WSI so as to fit to the reference, where the color distribution was modeled by a set of two triangle pyramids. Using color corrected WSIs; fibrosis quantification was performed based on tissue classification analysis. Statistical Analysis Used: Spearman's rank correlation coefficients were calculated between liver stiffness measured by transient elastography and median area ratio of collagen fibers calculated based on tissue classification results. Results: Statistical analysis results showed a significant correlation r = 0.61-0.68 even when tissue classifiers were trained by using a subset of WSIs, while the correlation coefficients were reduced to r = 0.40-0.50 without color correction. Conclusions: Fibrosis quantification accompanied with the proposed color correction method could provide an objective evaluation tool for liver fibrosis, which complements semi-quantitative histologic evaluation systems. PMID:24524002

  9. 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.

  10. A refined methodology for modeling volume quantification performance in CT

    NASA Astrophysics Data System (ADS)

    Chen, Baiyu; Wilson, Joshua; Samei, Ehsan

    2014-03-01

    The utility of CT lung nodule volume quantification technique depends on the precision of the quantification. To enable the evaluation of quantification precision, we previously developed a mathematical model that related precision to image resolution and noise properties in uniform backgrounds in terms of an estimability index (e'). The e' was shown to predict empirical precision across 54 imaging and reconstruction protocols, but with different correlation qualities for FBP and iterative reconstruction (IR) due to the non-linearity of IR impacted by anatomical structure. To better account for the non-linearity of IR, this study aimed to refine the noise characterization of the model in the presence of textured backgrounds. Repeated scans of an anthropomorphic lung phantom were acquired. Subtracted images were used to measure the image quantum noise, which was then used to adjust the noise component of the e' calculation measured from a uniform region. In addition to the model refinement, the validation of the model was further extended to 2 nodule sizes (5 and 10 mm) and 2 segmentation algorithms. Results showed that the magnitude of IR's quantum noise was significantly higher in structured backgrounds than in uniform backgrounds (ASiR, 30-50%; MBIR, 100-200%). With the refined model, the correlation between e' values and empirical precision no longer depended on reconstruction algorithm. In conclusion, the model with refined noise characterization relfected the nonlinearity of iterative reconstruction in structured background, and further showed successful prediction of quantification precision across a variety of nodule sizes, dose levels, slice thickness, reconstruction algorithms, and segmentation software.

  11. 3-Nitrotyrosine quantification methods: Current concepts and future challenges.

    PubMed

    Teixeira, Dulce; Fernandes, Rúben; Prudêncio, Cristina; Vieira, Mónica

    2016-06-01

    Measurement of 3-nitrotyrosine (3-NT) in biological samples can be used as a biomarker of nitrosative stress, since it is very stable and suitable for analysis. Increased 3-NT levels in biological samples have been associated with several physiological and pathological conditions. Different methods have been described for the detection and quantification of this molecule, such as (i) immunological methods; (ii) liquid chromatography, namely high-pressure liquid chromatography (HPLC)-based methods that use ultraviolet-visible (UV/VIS) absorption, electrochemical (ECD) and diode array (DAD) detection, liquid chromatography-mass spectrometry (LC-MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS); (iii) gas chromatography, such as gas chromatography-mass spectrometry (GC-MS) and gas chromatography-tandem mass spectrometry (GC-MS/MS). A literature review on nitrosative stress, protein nitration, as well as 3-NT quantification methods was carried out. This review covers the different methods for analysis of 3-NT that have been developed during the last years as well as the latest advances in this field. Overall, all methods present positive and negative aspects, although it is clear that chromatography-based methods present good sensitivity and specificity. Regarding this, GC-based methods exhibit the highest sensibility in the quantification of 3-NT, although it requires a prior time consuming derivatization step. Conversely, HPLC does not require such derivatization step, despite being not as accurate as GC. It becomes clear that all the methods described during this literature review, although accurate for 3-NT quantification, need to be improved regarding both sensitivity and specificity. Moreover, optimization of the protocols that have been described is clearly needed. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  12. Incorporating Functional Gene Quantification into Traditional Decomposition Models

    NASA Astrophysics Data System (ADS)

    Todd-Brown, K. E.; Zhou, J.; Yin, H.; Wu, L.; Tiedje, J. M.; Schuur, E. A. G.; Konstantinidis, K.; Luo, Y.

    2014-12-01

    Incorporating new genetic quantification measurements into traditional substrate pool models represents a substantial challenge. These decomposition models are built around the idea that substrate availablity, with environmental drivers, limit carbon dioxide respiration rates. In this paradigm, microbial communities optimally adapt to a given substrate and environment on much shorter time scales then the carbon flux of interest. By characterizing the relative shift in biomass of these microbial communities, we informed previously poorly constrained parameters in traditional decomposition models. In this study we coupled a 9 month laboratory incubation study with quantitative gene measurements with traditional CO2 flux measurements plus initial soil organic carbon quantification. GeoChip 5.0 was used to quantify the functional genes associated with carbon cycling at 2 weeks, 3 months and 9 months. We then combined the genes which 'collapsed' over the experiment and assumed that this tracked the relative change in the biomass associated with the 'fast' pool. We further assumed that this biomass was proportional to the 'fast' SOC pool and thus were able to constrain the relative change in the fast SOC pool in our 3-pool decomposition model. We found that biomass quantification described above, combined with traditional CO2 flux and SOC measurements, improve the transfer coefficient estimation in traditional decomposition models. Transfer coefficients are very difficult to characterized using traditional CO2 flux measurements, thus DNA quantification provides new and significant information about the system. Over a 100 year simulation, these new biologically informed parameters resulted in an additional 10% of SOC loss over the traditionally informed parameters.

  13. 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.

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

    PubMed Central

    Su, Dian; Gaffrey, Matthew J.; Guo, Jia; Hatchell, Kayla E.; Chu, Rosalie K.; Clauss, Therese R. W.; Aldrich, Joshua T.; Wu, Si; Purvine, Sam; Camp, David G.; Smith, Richard D.; Thrall, Brian D.; Qian, Wei-Jun

    2014-01-01

    S-glutathionylation (SSG) is an important regulatory posttranslational modification on protein cysteine (Cys) thiols, 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 covalent capture of reduced thiols 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 initially 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, thus providing a database of proteins and Cys-sites susceptible to this modification under oxidative stress. Functional analysis revealed that the most significantly enriched molecular function categories for proteins sensitive to SSG modifications were free radical scavenging and cell death/survival. Overall the results demonstrate that our approach is effective for site-specific identification and quantification of SSG-modified proteins. The analytical strategy also provides a unique approach to determining the major pathways and cellular processes most susceptible

  15. Spectral quantification of Southern Baltic seabed roughness

    NASA Astrophysics Data System (ADS)

    Szefler, K.; Tegowski, J.; Nowak, J.

    2012-12-01

    autocorrelation, elevation slope, statistical and wavelet transformation parameters were estimated. The set of parameters was the input to the Principal Component Analysis and next to the unsupervised neural network algorithm which produced maps containing morphologically classified seabed areas. The obtained results revealed that acoustical technique provides very useful capabilities for the seafloor characterisation.

  16. Quantification of rock slope terrain properties

    NASA Astrophysics Data System (ADS)

    Volkwein, Axel; Gerber, Werner

    2017-04-01

    Rockfall trajectory simulation codes need information on the terrain properties to formulate appropriate rebound models. Usually, the manuals of rockfall simulation codes give sketches or photographs of terrain samples [1,2]. Based on these the user can select suitable terrains for the simulation area. We now would like to start a discussion whether it is possible to numerically quantify the terrain properties which would make the ground assignment more objective. Different ground properties play a role for the interaction between a falling rock and the ground: • Elastic deformation • plastic deformation • Energy absorption • friction • hardness • roughness • surface vs. underground • etc. The question is now whether it is possible to quantify above parameters and to finally provide tables that contain appropriate simulation parameters. In a first attempt we suggest different methods or parameters that might be evaluated in situ: • Small scale drop tests • Light weight deflectometer (LWD) • Particle sizes • Sliding angle • Particle distribution • Soil cover • Water content Of course, above measurements will never perfectly fit to different mountain slopes. However, if a number of measurements has been made their spreading will give an idea on the natural variability of the ground properties. As an example, the following table gives an idea on how the ME and Evd values vary for different soils. Table 1: LWD measurements on different soil types [3] Ground type Soil layer Soil humidityEvd (median)σ (median)Evd (average) Humus-carb. < 10cm dry 17.4 6.8 15.6 Regosol 10 - 30cm dry 8.6 3.9 9.4 Brownish 30 - 50cm dry 12.1 3.2 11.7 Calcaric 30 - 50cm dry 7.5 3.3 7.0 Acid brownish70 - 100cmdry 7.8 2.1 7.7 Fahlgley 10 - 30cm dry 9.2 4.0 7.7 References [1] Bartelt P et al (2016) RAMMS::rockfall user manual v1.6. SLF, Davos. [2] Dorren L.K.A., 2015. Rockyfor3D (v5.2) revealed - Transparent description of the complete 3D rockfall model. ecoris

  17. Quantification of jasmonic and salicylic acids in rice seedling leaves.

    PubMed

    Cho, Kyoungwon; Han, Oksoo; Tamogami, Shigeru; Shibato, Junko; Kubo, Akihiro; Agrawal, Ganesh Kumar; Rakwal, Randeep

    2013-01-01

    Jasmonic acid (JA) and salicylic acid (SA) are critical signaling components involved in various aspects of plant growth, development, and defense. Their constitutive levels vary from plant to plant and also from tissue to tissue within the same plant. Moreover, their quantitative levels change when plant is exposed to biotic and abiotic stresses. To better understand the JA- and SA-mediated signaling and metabolic pathways, it is important to precisely quantify their levels in plants/tissues/organs. However, their extraction and quantification are not trivial and still technically challenging. An effort has been made in various laboratories to develop a simple and standard procedure that can be utilized for quantification of JA and SA. Here, we present the experimental procedure and our decade of experience on extracting and quantifying them in an absolute manner in leaves of rice seedlings. We must mention that this method has been applied to both monocotyledonous and dicotyledonous plants for absolute quantification of JA and SA. As collaboration is the key towards rapid progress in science and technology, we are always open to sharing our experience in this field with any active research group with an aim to improve the procedure further and eventually to connect the importance of their (JA and SA) quantitative levels with networks of signaling and metabolic pathways in plants.

  18. Qualification and quantification of fish protein in prepared surimi crabstick.

    PubMed

    Reed, Z H; Park, J W

    2008-06-01

    Species identification and protein quantification in surimi crabstick were achieved using sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE). When the Lowry and Kjeldahl protein determination methods were compared, the former showed more consistent results. Densitometric scanning of the gels was used for quantification of total fish protein as well as total egg white protein. The lower molecular weight proteins, 30 kDa and lower, proved to be the most useful in fish species identification as well as egg white protein addition. Using a combination of the myosin heavy chain band and the species-specific myosin light chain (Alaska pollock: 22.5 kDa; Pacific whiting: 24.4 kDa) proved the most accurate in calculating fish protein content of the crabstick sample, while for those samples that contained egg white, quantification was accomplished from the densitometric analysis of the overlapping bands of actin (45 kDa) from fish and ovalbumin from egg white. Lysozyme (14.3 kDa) proved to be a unique protein band in determining the presence of egg white when the content of dried egg white was equal to or exceeded 0.5% of the total weight of the final crabstick.

  19. 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

  20. Analytical strategies for the global quantification of intact proteins.

    PubMed

    Collier, Timothy S; Muddiman, David Charles

    2012-09-01

    The quantification of intact proteins is a relatively recent development in proteomics. In eukaryotic organisms, proteins are present as multiple isoforms as the result of variations in genetic code, alternative splicing, post-translational modification and other processing events. Understanding the identities and biological functions of these isoforms and how their concentrations vary across different states is the central goal of proteomics. To date, the bulk of proteomics research utilizes a "bottom-up" approach, digesting proteins into their more manageable constitutive peptides, but sacrificing information about the specific isoform and combinations of post-translational modifications present on the protein. Very specific strategies for protein quantification such as the enzyme-linked immunosorbent assay and Western blot are commonplace in laboratories and clinics, but impractical for the study of global biological changes. Herein, we describe strategies for the quantification of intact proteins, their distinct advantages, and challenges to their employment. Techniques contained in this review include the more traditional and widely employed methodology of differential gel electrophoresis and more recently developed mass spectrometry-based techniques including metabolic labeling, chemical labeling, and label-free methodologies.

  1. 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.

  2. Leveraging transcript quantification for fast computation of alternative splicing profiles

    PubMed Central

    Alamancos, Gael P.; Pagès, Amadís; Trincado, Juan L.; Bellora, Nicolás; Eyras, Eduardo

    2015-01-01

    Alternative splicing plays an essential role in many cellular processes and bears major relevance in the understanding of multiple diseases, including cancer. High-throughput RNA sequencing allows genome-wide analyses of splicing across multiple conditions. However, the increasing number of available data sets represents a major challenge in terms of computation time and storage requirements. We describe SUPPA, a computational tool to calculate relative inclusion values of alternative splicing events, exploiting fast transcript quantification. SUPPA accuracy is comparable and sometimes superior to standard methods using simulated as well as real RNA-sequencing data compared with experimentally validated events. We assess the variability in terms of the choice of annotation and provide evidence that using complete transcripts rather than more transcripts per gene provides better estimates. Moreover, SUPPA coupled with de novo transcript reconstruction methods does not achieve accuracies as high as using quantification of known transcripts, but remains comparable to existing methods. Finally, we show that SUPPA is more than 1000 times faster than standard methods. Coupled with fast transcript quantification, SUPPA provides inclusion values at a much higher speed than existing methods without compromising accuracy, thereby facilitating the systematic splicing analysis of large data sets with limited computational resources. The software is implemented in Python 2.7 and is available under the MIT license at https://bitbucket.org/regulatorygenomicsupf/suppa. PMID:26179515

  3. Outcome quantification using SPHARM-PDM toolbox in orthognathic surgery

    PubMed Central

    Cevidanes, Lucia; Zhu, HongTu; Styner, Martin

    2011-01-01

    Purpose Quantification of surgical outcomes in longitudinal studies has led to significant progress in the treatment of dentofacial deformity, both by offering options to patients who might not otherwise have been recommended for treatment and by clarifying the selection of appropriate treatment methods. Most existing surgical treatments have not been assessed in a systematic way. This paper presents the quantification of surgical outcomes in orthognathic surgery via our localized shape analysis framework. Methods In our setting, planning and surgical simulation is performed using the surgery planning software CMFapp. We then employ the SPHARM-PDM to measure the difference between pre-surgery and virtually simulated post-surgery models. This SPHARM-PDM shape framework is validated for use with craniofacial structures via simulating known 3D surgical changes within CMFapp. Results Our results show that SPHARM-PDM analysis accurately measures surgical displacements, compared with known displacement values. Visualization of color maps of virtually simulated surgical displacements describe corresponding surface distances that precisely describe location of changes, and difference vectors indicate directionality and magnitude of changes. Conclusions SPHARM-PDM-based quantification of surgical outcome is feasible. When compared to prior solutions, our method has the potential to make the surgical planning process more flexible, increase the level of detail and accuracy of the plan, yield higher operative precision and control and enhance the follow-up and documentation of clinical cases. PMID:21161693

  4. Efficient inversion and uncertainty quantification of a tephra fallout model

    NASA Astrophysics Data System (ADS)

    White, J. T.; Connor, C. B.; Connor, L.; Hasenaka, T.

    2017-01-01

    An efficient and effective inversion and uncertainty quantification approach is proposed for estimating eruption parameters given a data set collected from a tephra deposit. The approach is model independent and here is applied using Tephra2, a code that simulates advective and dispersive tephra transport and deposition. The Levenburg-Marquardt algorithm is combined with formal Tikhonov and subspace regularization to invert eruption parameters; a linear equation for conditional uncertainty propagation is used to estimate posterior parameter uncertainty. Both the inversion and uncertainty analysis support simultaneous analysis of the full eruption and wind field parameterization. The combined inversion/uncertainty quantification approach is applied to the 1992 eruption of Cerro Negro and the 2011 Kirishima-Shinmoedake eruption. While eruption mass uncertainty is reduced by inversion against tephra isomass data, considerable uncertainty remains for many eruption and wind field parameters, such as plume height. Supplementing the inversion data set with tephra granulometry data is shown to further reduce the uncertainty of most eruption and wind field parameters. The eruption mass of the 2011 Kirishima-Shinmoedake eruption is 0.82 × 1010 kg to 2.6 × 1010 kg, with 95% confidence; total eruption mass for the 1992 Cerro Negro eruption is 4.2 × 1010 kg to 7.3 × 1010 kg, with 95% confidence. These results indicate that eruption classification and characterization of eruption parameters can be significantly improved through this uncertainty quantification approach.

  5. Theoretical limitations of quantification for noncompetitive sandwich immunoassays.

    PubMed

    Woolley, Christine F; Hayes, Mark A; Mahanti, Prasun; Douglass Gilman, S; Taylor, Tom

    2015-11-01

    Immunoassays exploit the highly selective interaction between antibodies and antigens to provide a vital method for biomolecule detection at low concentrations. Developers and practitioners of immunoassays have long known that non-specific binding often restricts immunoassay limits of quantification (LOQs). Aside from non-specific binding, most efforts by analytical chemists to reduce the LOQ for these techniques have focused on improving the signal amplification methods and minimizing the limitations of the detection system. However, with detection technology now capable of sensing single-fluorescence molecules, this approach is unlikely to lead to dramatic improvements in the future. Here, fundamental interactions based on the law of mass action are analytically connected to signal generation, replacing the four- and five-parameter fittings commercially used to approximate sigmoidal immunoassay curves and allowing quantitative consideration of non-specific binding and statistical limitations in order to understand the ultimate detection capabilities of immunoassays. The restrictions imposed on limits of quantification by instrumental noise, non-specific binding, and counting statistics are discussed based on equilibrium relations for a sandwich immunoassay. Understanding the maximal capabilities of immunoassays for each of these regimes can greatly assist in the development and evaluation of immunoassay platforms. While many studies suggest that single molecule detection is possible through immunoassay techniques, here, it is demonstrated that the fundamental limit of quantification (precision of 10 % or better) for an immunoassay is approximately 131 molecules and this limit is based on fundamental and unavoidable statistical limitations.

  6. 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.

  7. HPLC Quantification of astaxanthin and canthaxanthin in Salmonidae eggs.

    PubMed

    Tzanova, Milena; Argirova, Mariana; Atanasov, Vasil

    2017-04-01

    Astaxanthin and canthaxanthin are naturally occurring antioxidants referred to as xanthophylls. They are used as food additives in fish farms to improve the organoleptic qualities of salmonid products and to prevent reproductive diseases. This study reports the development and single-laboratory validation of a rapid method for quantification of astaxanthin and canthaxanthin in eggs of rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis М.). An advantage of the proposed method is the perfect combination of selective extraction of the xanthophylls and analysis of the extract by high-performance liquid chromatography and photodiode array detection. The method validation was carried out in terms of linearity, accuracy, precision, recovery and limits of detection and quantification. The method was applied for simultaneous quantification of the two xanthophylls in eggs of rainbow trout and brook trout after their selective extraction. The results show that astaxanthin accumulations in salmonid fish eggs are larger than those of canthaxanthin. As the levels of these two xanthophylls affect fish fertility, this method can be used to improve the nutritional quality and to minimize the occurrence of the M74 syndrome in fish populations. Copyright © 2016 John Wiley & Sons, Ltd.

  8. 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.

  9. Quantification of Lung PET Images: Challenges and Opportunities.

    PubMed

    Chen, Delphine L; Cheriyan, Joseph; Chilvers, Edwin R; Choudhury, Gourab; Coello, Christopher; Connell, Martin; Fisk, Marie; Groves, Ashley M; Gunn, Roger N; Holman, Beverley F; Hutton, Brian F; Lee, Sarah; MacNee, William; Mohan, Divya; Parr, David; Subramanian, Deepak; Tal-Singer, Ruth; Thielemans, Kris; van Beek, Edwin J R; Vass, Laurence; Wellen, Jeremy W; Wilkinson, Ian; Wilson, Frederick J

    2017-02-01

    Millions of people are affected by respiratory diseases, leading to a significant health burden globally. Because of the current insufficient knowledge of the underlying mechanisms that lead to the development and progression of respiratory diseases, treatment options remain limited. To overcome this limitation and understand the associated molecular changes, noninvasive imaging techniques such as PET and SPECT have been explored for biomarker development, with (18)F-FDG PET imaging being the most studied. The quantification of pulmonary molecular imaging data remains challenging because of variations in tissue, air, blood, and water fractions within the lungs. The proportions of these components further differ depending on the lung disease. Therefore, different quantification approaches have been proposed to address these variabilities. However, no standardized approach has been developed to date. This article reviews the data evaluating (18)F-FDG PET quantification approaches in lung diseases, focusing on methods to account for variations in lung components and the interpretation of the derived parameters. The diseases reviewed include acute respiratory distress syndrome, chronic obstructive pulmonary disease, and interstitial lung diseases such as idiopathic pulmonary fibrosis. Based on review of prior literature, ongoing research, and discussions among the authors, suggested considerations are presented to assist with the interpretation of the derived parameters from these approaches and the design of future studies.

  10. Improving quantification of intravascular fluorescence imaging using structural information

    NASA Astrophysics Data System (ADS)

    Mallas, Georgios; Brooks, Dana H.; Rosenthal, Amir; Nika Nudelman, R.; Mauskapf, Adam; Jaffer, Farouc A.; Ntziachristos, Vasilis

    2012-10-01

    Intravascular near-infrared fluorescence (iNIRF) imaging can enable the in vivo visualization of biomarkers of vascular pathology, including high-risk plaques. The technique resolves the bio-distribution of systemically administered fluorescent probes with molecular specificity in the vessel wall. However, the geometrical variations that may occur in the distance between fibre-tip and vessel wall can lead to signal intensity variations and challenge quantification. Herein we examined whether the use of anatomical information of the cross-section vessel morphology, obtained from co-registered intravascular ultrasound (IVUS), can lead to quantification improvements when fibre-tip and vessel wall distance variations are present. The algorithm developed employs a photon propagation model derived from phantom experiments that is used to calculate the relative attenuation of fluorescence signals as they are collected over 360° along the vessel wall, and utilizes it to restore accurate fluorescence readings. The findings herein point to quantification improvements when employing hybrid iNIRF, with possible implications to the clinical detection of high-risk plaques or blood vessel theranostics.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. Quantification of fibronectin as a method to assess ex vivo extracellular matrix remodeling.

    PubMed

    Bager, C L; Gudmann, N; Willumsen, N; Leeming, D J; Karsdal, M A; Bay-Jensen, A C; Høgdall, E; Balslev, I; He, Y

    2016-09-16

    Altered architecture, composition and quality of the extracellular matrix (ECM) are pathological hallmarks of several inflammatory and fibro-proliferative pathological processes such as osteoarthritis (OA), rheumatoid arthritis (RA), fibrosis and cancer. One of the most important components of the ECM is fibronectin. Fibronectin serves as an adhesion molecule anchoring cells to the underlying basement membrane through direct interaction with integrin receptors. Fibronectin hereby modulates the properties of the ECM and affects cellular processes. Quantification of fibronectin remodeling could therefore be used to assess the changes in the ECM that occur during progression of fibro-proliferative pathologies. Ex vivo models are becoming state-of-the-art tools to study ECM remodeling as the cellular composition and the organization of the ECM are preserved. Ex vivo models may therefore be a valuable tool to study the ECM remodeling that occurs during progression of fibro-proliferative pathologies. The aim of this study was to quantify fibronectin remodeling in ex vivo models of cartilage and cancer. A competitive The enzyme-linked immunosorbent assay (ELISA) against the C-terminus of fibronectin was developed (FBN-C). The assay was evaluated in relation to specificity, technical performance and as a marker for quantification of fibronectin in cartilage and cancer ex vivo models. The ELISA was specific and technically stable. Cleavage of tumor tissue with MMP-2 released significantly higher levels of FBN-C compared to tissue with buffer only and western blot analysis revealed that FBN-C recognizes both full length and degraded fibronectin. When ex vivo cartilage cultures were stimulated with the anabolic factor TGFβ and catabolic factors TNF-α and OSM, significantly higher levels of FBN-C were found in the conditioned media. Lastly, FBN-C was released from a cancer ex vivo model. In conclusion, we were able to quantify fibronectin remodeling in ex vivo models

  16. Performance of high-throughput DNA quantification methods

    PubMed Central

    Haque, Kashif A; Pfeiffer, Ruth M; Beerman, Michael B; Struewing, Jeff P; Chanock, Stephen J; Bergen, Andrew W

    2003-01-01

    Background The accuracy and precision of estimates of DNA concentration are critical factors for efficient use of DNA samples in high-throughput genotype and sequence analyses. We evaluated the performance of spectrophotometric (OD) DNA quantification, and compared it to two fluorometric quantification methods, the PicoGreen® assay (PG), and a novel real-time quantitative genomic PCR assay (QG) specific to a region at the human BRCA1 locus. Twenty-Two lymphoblastoid cell line DNA samples with an initial concentration of ~350 ng/uL were diluted to 20 ng/uL. DNA concentration was estimated by OD and further diluted to 5 ng/uL. The concentrations of multiple aliquots of the final dilution were measured by the OD, QG and PG methods. The effects of manual and robotic laboratory sample handling procedures on the estimates of DNA concentration were assessed using variance components analyses. Results The OD method was the DNA quantification method most concordant with the reference sample among the three methods evaluated. A large fraction of the total variance for all three methods (36.0–95.7%) was explained by sample-to-sample variation, whereas the amount of variance attributable to sample handling was small (0.8–17.5%). Residual error (3.2–59.4%), corresponding to un-modelled factors, contributed a greater extent to the total variation than the sample handling procedures. Conclusion The application of a specific DNA quantification method to a particular molecular genetic laboratory protocol must take into account the accuracy and precision of the specific method, as well as the requirements of the experimental workflow with respect to sample volumes and throughput. While OD was the most concordant and precise DNA quantification method in this study, the information provided by the quantitative PCR assay regarding the suitability of DNA samples for PCR may be an essential factor for some protocols, despite the decreased concordance and precision of this method

  17. Systematic development of a group quantification method using evaporative light scattering detector for relative quantification of ginsenosides in ginseng products.

    PubMed

    Lee, Gwang Jin; Shin, Byong-Kyu; Yu, Yun-Hyun; Ahn, Jongsung; Kwon, Sung Won; Park, Jeong Hill

    2016-09-05

    The determination for the contents of multi-components in ginseng products has come to the fore by demands of in-depth information, but the associated industries confront the high cost of securing pure standards for the continuous quality evaluation of the products. This study aimed to develop a prospective high-performance liquid chromatography-evaporative light scattering detector (HPLC-ELSD) method for relative quantification of ginsenosides in ginseng products without a considerable change from the conventional gradient analysis. We investigated the effects of mobile phase composition and elution bandwidth, which are potential variables affecting the ELSD response in the gradient analysis. Similar ELSD response curves of nine major ginsenosides were obtained under the identical flow injection conditions, and the response increased as the percentage of organic solvent increased. The nine ginsenosides were divided into three groups to confirm the effect of elution bandwidth. The ELSD response significantly decreased in case of the late eluted ginsenoside in the individual groups under the isocratic conditions. With the consideration of the two important effects, stepwise changes of the gradient condition were carried out to reach a group quantification method. The inconsistent responses of the nine ginsenosides were reconstituted to three normalized responses by the stepwise changes of the gradient condition, and this result actualized relative quantification in the individual groups. The availability was confirmed by comparing the ginsenoside contents in a base material of ginseng products determined by the direct and group quantification method. The largest difference in the determination results from the two methods was 8.26%, and the difference of total contents was only 0.91%.

  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. Subtle Morphological Changes in the Mandible of Tabby Mice Revealed by Micro-CT Imaging and Elliptical Fourier Quantification

    PubMed Central

    Bornert, Fabien; Choquet, Philippe; Gros, Catherine I.; Aubertin, Gaelle; Perrin-Schmitt, Fabienne; Clauss, François; Lesot, Hervé; Constantinesco, André; Schmittbuhl, Matthieu

    2011-01-01

    X-linked hypohidrotic ectodermal dysplasia (XLHED) is a genetic disorder due to a mutation of the EDA gene and is mainly characterized by an impaired formation of hair, teeth and sweat glands, and craniofacial dysmorphologies. Although tooth abnormalities in Tabby (Ta) mutant mice – the murine model of XLHED – have been extensively studied, characterization of the craniofacial complex, and more specifically the mandibular morphology has received less attention. From 3D micro-CT reconstructions of the left mandible, the mandibular outline observed in lateral view, was quantified using 2D elliptical Fourier analysis. Comparisons between Ta specimens and their wild-type controls were carried out showing significant shape differences between mouse strains enabling a clear distinction between hemizygous Ta specimens and the other mouse groups (WT and heterozygous EdaTa/+ specimens). Morphological differences associated with HED correspond not only to global mandibular features (restrained development of that bone along dorsoventral axis), but also to subtle aspects such as the marked backward projection of the coronoid process or the narrowing of the mandibular condylar neck. These modifications provide for the first time, evidence of a predominant effect of the Ta mutation on the mandibular morphology. These findings parallel the well described abnormalities of jugal tooth row and skeletal defects in Ta mice, and underline the role played by EDA-A in the reciprocal epithelial–mesenchymal interactions that are of critical importance in normal dental and craniofacial development. PMID:21541253

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

    PubMed Central

    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

    2015-01-01

    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. PMID:26063786

  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. 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

    2016-03-31

    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.

  3. Development of a TT Virus DNA Quantification System Using Real-Time Detection PCR

    PubMed Central

    Kato, Takanobu; Mizokami, Masashi; Mukaide, Motokazu; Orito, Etsuro; Ohno, Tomoyoshi; Nakano, Tatsunori; Tanaka, Yasuhito; Kato, Hideaki; Sugauchi, Fuminaka; Ueda, Ryuzo; Hirashima, Noboru; Shimamatsu, Kazuhide; Kage, Masayoshi; Kojiro, Masamichi

    2000-01-01

    Although TT virus (TTV) was isolated from a cryptogenic posttransfusion hepatitis patient, its pathogenic role remains unclear. It has been reported that the majority of the healthy population is infected with TTV. To elucidate the differences between TTV infection in patients with liver diseases and TTV infection in the healthy population, a quantification system was developed. TTV DNA was quantified by a real-time detection PCR (RTD-PCR) assay on an ABI Prism 7700 sequence detector. With this system, TTV DNA was quantified in 78 hepatitis C virus (HCV)-infected patients (63 with elevated serum alanine aminotransferase [ALT] levels and 15 with normal ALT levels) and in 70 voluntary blood donors (BDs). The quantification range was 2.08 to 7.35 log copies/ml. The intra-assay and interassay coefficients of variation were 0.37 to 6.33% and 0.60 to 7.07%, respectively. The mean serum TTV DNA levels in the HCV-infected patients with both elevated and normal ALT levels and BDs were 3.69 ± 0.89, 3.45 ± 0.76, and 3.45 ± 0.67 log copies/ml, respectively. Comparison of the serum TTV DNA levels among the HCV-infected patients revealed that they were not related to the serum ALT and HCV core protein levels or to the histopathological score on liver biopsy. This study showed that (i) the RTD-PCR assay for the detection of TTV was accurate and had a high degree of sensitivity, (ii) the mean serum TTV DNA level was similar among HCV-infected patients, irrespective of their ALT level, and also among BDs, and (iii) a high serum TTV DNA level does not affect the serum ALT and HCV levels or liver damage in HCV-infected patients. PMID:10618070

  4. COMPARISON OF TOTAL LEUKOCYTE QUANTIFICATION METHODS IN FREE-LIVING GALAPAGOS TORTOISES (CHELONOIDIS SPP.).

    PubMed

    Sheldon, Julie D; Stacy, Nicole I; Blake, Stephen; Cabrera, Fredy; Deem, Sharon L

    2016-03-01

    Reptile hematologic data provide important health information for conservation efforts of vulnerable wildlife species such as the Galapagos tortoise (Chelonoidis spp.). Given the reported discrepancies between manual leukocyte counts for nonmammalian species, two manual leukocyte quantification methods, the Natt and Herrick's (NH) and the Eopette (EO), were compared to white blood cell (WBC) estimates from blood films of 42 free-living, clinically healthy, adult female Galapagos tortoises. To investigate the effects of delay in sample processing, estimated WBC counts and leukocyte differentials were compared for blood films prepared at time of collection under field conditions (T0) to blood films prepared from samples that were stored for 18-23 hr at 4°C in the laboratory (T1). Passing-Bablok regression analysis revealed no constant or proportional error between the NH and WBC estimates (T0 and T1) with slopes of 1.1 and 0.9, respectively. However both constant and proportional errors were present between EO and WBC estimates (T0 and T1) with slopes of 3.1 and 2.7, respectively. Bland Altman plots also showed agreement between the NH and WBC estimates where the points fell within the confidence-interval limit lines and were evenly distributed about the mean. In contrast, the EO and WBC estimate comparisons showed numerous points above the upper limit line, especially at higher concentrations. WBC estimates obtained from T0 and T1 films were in agreement, whereas heterophil and monocyte percentages based on differentials were not. Cell morphology and preservation were superior in T0 blood films because thrombocytes exhibited swelling after storage, becoming difficult to differentiate from lymphocytes. In this study, the highest quality and most reliable hematologic data in Galapagos tortoises were obtained by combining immediate blood film preparation with the NH leukocyte quantification method and a confirmatory WBC estimate from the blood film.

  5. Isolation and quantification of oligomeric and polymeric procyanidins in leaves and flowers of Hawthorn (Crataegus spp.).

    PubMed

    Hellenbrand, N; Sendker, J; Lechtenberg, M; Petereit, F; Hensel, A

    2015-07-01

    Proanthocyanidins (PAs) constitute a class of polyphenols with flavan-3-ols as monomeric building blocks. These polyphenols are mostly quantified by colorimetric methods or by chromatographic determination of monomeric flavan-3-ols or low molecular oligomers as lead compounds. No reliable analytical methods are available for unambiguous identification of the homologues series of oligo- and polymeric PAs. For Hawthorn leaf and flower (Crataegi folium cum flore) from Crataegus spp. (Rosaceae) a protocol for preparative isolation of oligomeric and polymeric PAs from an acetone-water extract was developed, yielding procyanidin reference clusters with defined degree of polymerization (DP) from 2 to 10 besides a procyanidin-polymer. Identity and purity of these clusters were proven by HPLC, MS and in part NMR studies. For identification and quantification from Hawthorn an ICH-Q2 validated UHPLC method with fluorimetric detection and less than 10min runtime was developed. The method enabled quantification of procyanidin clusters with DP from 2 to 10 besides the polymer fraction. Batch analysis revealed procyanidin contents of about 20 to 45mg/g from a homologues series of oligomeric PAs and about 50% of polymer fraction. Monitoring of procyanidin distribution during seasonal growth of fresh plants of Crataegus monogyna showed more or less constant contents between 20 and 55mg/g dry weight of oligomeric procyanidins during the growing season in the different plant organs with strong accumulation in the flowers and fruits (55mg/g dry weight). From these data it can be speculated that procyanidins serve as part of the plants defense system in the reproductive organs of the plant. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Assessment of real-time PCR for quantification of Legionella spp. in spa water.

    PubMed

    Guillemet, T A; Lévesque, B; Gauvin, D; Brousseau, N; Giroux, J-P; Cantin, P

    2010-12-01

    Legionella bacteria ubiquitously colonize natural freshwater and are responsible for legionellosis in humans. Several cases of legionellosis have been associated in particular with the use of whirlpool spas. The objective of this study was to verify whether real-time PCR is applicable for the quantification of Legionella spp. in spa water. The study compared concentrations obtained by real-time PCR vs that obtained by conventional culture for 101 spa water samples. For the culture method, Legionella spp. were detected and quantified in 14 of 101 samples with measured concentrations ranging from 250 to 3.5 × 10(5) CFU l(-1). With the real-time PCR method, Legionella spp. were detected and quantified in 42 of 101 samples with concentrations ranging from 1000 to 6.1 × 10(7) GU l(-1). Results revealed a significant but weak correlation (r(2) = 0.1867) between the two methods. The positive predictive value (35%) of the PCR method compared to conventional culture herein was low. In contrast, the negative predictive value was excellent, reaching 93%. Real-time PCR could be used as a screening tool to rapidly ascertain the absence of Legionella spp. in spa water. However, a positive result involves the need to resort to conventional culture. Data of this study highlighted the pros and cons of quantification of Legionella spp. in spa water with real-time PCR using a commercial quantitative PCR kit in a routine laboratory, when compared to conventional culture. © 2010 The Authors. Letters in Applied Microbiology 51, 639-644 © 2010 The Society for Applied Microbiology.

  7. 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

    2012-05-04

    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.

  8. Assessment of siRNA pharmacokinetics using ELISA-based quantification.