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Sample records for resolution melting application

  1. High Resolution Melting Applications for Clinical Laboratory Medicine

    PubMed Central

    Erali, Maria; Voelkerding, Karl V.; Wittwer, Carl T.

    2008-01-01

    Separation of the two strands of DNA with heat (melting) is a fundamental property of DNA that is conveniently monitored with fluorescence. Conventional melting is performed after PCR on any real-time instrument to monitor product purity (dsDNA dyes) and sequence (hybridization probes). Recent advances include high-resolution instruments and saturating DNA dyes that distinguish many different species. For example, mutation scanning (identifying heterozygotes) by melting is closed-tube and has similar or superior sensitivity and specificity compared to methods that require physical separation. With high resolution melting, SNPs can be genotyped without probes and more complex regions can be typed with unlabeled hybridization probes. Highly polymorphic HLA loci can be melted to establish sequence identity for transplantation matching. Simultaneous genotyping with one or more unlabeled probes and mutation scanning of the entire amplicon can be performed at the same time in the same tube, vastly decreasing or eliminating the need for re-sequencing in genetic analysis. High-resolution PCR product melting is homogeneous, closed-tube, rapid (1–5 min), non-destructive and does not require covalently-labeled fluorescent probes. In the clinical laboratory, it is an ideal format for in-house testing, with minimal cost and time requirements for new assay development. PMID:18502416

  2. Application of high-resolution melting analysis for differentiation of spoilage yeasts.

    PubMed

    Erdem, Mine; Kesmen, Zülal; Özbekar, Esra; Çetin, Bülent; Yetim, Hasan

    2016-09-01

    A new method based on high resolution melting (HRM) analysis was developed for the differentiation and classification of the yeast species that cause food spoilage. A total 134 strains belonging to 21 different yeast species were examined to evaluate the discriminative power of HRM analysis. Two different highly variable DNA regions on the 26 rRNA gene were targeted to produce the HRM profiles of each strain. HRM-based grouping was compared and confirmed by (GTG)5 rep-PCR fingerprinting analysis. All of the yeast species belonging to the genera Pichia, Candida, Kazachstania, Kluyveromyces, Debaryomyces, Dekkera, Saccharomyces, Torulaspora, Ustilago, and Yarrowia, which were produced as species-specific HRM profiles, allowed discrimination at species and/or strain level. The HRM analysis of both target regions provided successful discrimination that correlated with rep-PCR fingerprinting analysis. Consequently, the HRM analysis has the potential for use in the rapid and accurate classification and typing of yeast species isolated from different foods to determine their sources and routes as well as to prevent contamination. PMID:27572511

  3. High Resolution Melting (HRM) applied to wine authenticity.

    PubMed

    Pereira, Leonor; Gomes, Sónia; Castro, Cláudia; Eiras-Dias, José Eduardo; Brazão, João; Graça, António; Fernandes, José R; Martins-Lopes, Paula

    2017-02-01

    Wine authenticity methods are in increasing demand mainly in Denomination of Origin designations. The DNA-based methodologies are a reliable means of tracking food/wine varietal composition. The main aim of this work was the study of High Resolution Melting (HRM) application as a screening method for must and wine authenticity. Three sample types (leaf, must and wine) were used to validate the three developed HRM assays (Vv1-705bp; Vv2-375bp; and Vv3-119bp). The Vv1 HRM assay was only successful when applied to leaf and must samples. The Vv2 HRM assay successfully amplified all sample types, allowing genotype discrimination based on melting temperature values. The smallest amplicon, Vv3, produced a coincident melting curve shape in all sample types (leaf and wine) with corresponding genotypes. This study presents sensitive, rapid and efficient HRM assays applied for the first time to wine samples suitable for wine authenticity purposes. PMID:27596395

  4. High-Resolution DNA Melting Analysis in Plant Research.

    PubMed

    Simko, Ivan

    2016-06-01

    Genetic and genomic studies provide valuable insight into the inheritance, structure, organization, and function of genes. The knowledge gained from the analysis of plant genes is beneficial to all aspects of plant research, including crop improvement. New methods and tools are continually being developed to facilitate rapid and accurate mapping, sequencing, and analyzing of genes. Here, I review the recent progress in the application of high-resolution melting (HRM) analysis of DNA, a method that allows detecting polymorphism in double-stranded DNA by comparing profiles of melting curves. Use of HRM has expanded considerably in the past few years as the method was successfully applied for high-throughput genotyping, mapping genes, testing food products and seeds, and other areas of plant research. PMID:26827247

  5. Ribo HRM--detection of inter- and intra-species polymorphisms within ribosomal DNA by high resolution melting analysis supported by application of artificial allelic standards.

    PubMed

    Masny, Aleksander; Jagiełło, Agata; Płucienniczak, Grażyna; Golab, Elzbieta

    2012-09-01

    Ribo HRM, a single-tube PCR and high resolution melting (HRM) assay for detection of polymorphisms in the large subunit ribosomal DNA expansion segment V, was developed on a Trichinella model. Four Trichinella species: T. spiralis (isolates ISS3 and ISS160), T. nativa (isolates ISS10 and ISS70), T. britovi (isolates ISS2 and ISS392) and T. pseudospiralis (isolates ISS13 and ISS1348) were genotyped. Cloned allelic variants of the expansion segment V were used as standards to prepare reference HRM curves characteristic for single sequences and mixtures of several cloned sequences imitating allelic composition detected in Trichinella isolates. Using the primer pair Tsr1 and Trich1bi, it was possible to amplify a fragment of the ESV and detect PCR products obtained from the genomic DNA of pools of larvae belonging to the four investigated species: T. pseudospiralis, T. spiralis, T. britovi and T. nativa, in a single tube Real-Time PCR reaction. Differences in the shape of the HRM curves of Trichinella isolates suggested the presence of differences between examined isolates of T. nativa, T. britovi and T. pseudospiralis species. No differences were observed between T. spiralis isolates. The presence of polymorphisms within the amplified ESV sequence fragment of T. nativa T. britovi and T. pseudospiralis was confirmed by sequencing of the cloned PCR products. Novel sequences were discovered and deposited in GenBank (GenBank IDs: JN971020-JN971027, JN120902.1, JN120903.1, JN120904.1, JN120906.1, JN120905.1). Screening the ESV region of Trichinella for polymorphism is possible using the genotyping assay Ribo HRM at the current state of its development. The Ribo HRM assay could be useful in phylogenetic studies of the Trichinella genus. PMID:22766326

  6. High resolution melting analysis for the differentiation of Mycobacterium species.

    PubMed

    Issa, Rahizan; Abdul, Hatijah; Hashim, Siti Hasmah; Seradja, Valentinus H; Shaili, Nurul 'Aishah; Hassan, Nurul Akma Mohd

    2014-10-01

    A quantitative real-time PCR (qPCR) followed by high resolution melting (HRM) analysis was developed for the differentiation of Mycobacterium species. Rapid differentiation of Mycobacterium species is necessary for the effective diagnosis and management of tuberculosis. In this study, the 16S rRNA gene was tested as the target since this has been identified as a suitable target for the identification of mycobacteria species. During the temperature gradient and primer optimization process, the melting peak (Tm) analysis was determined at a concentration of 50 ng DNA template and 0.3, 0.4 and 0.5 µM primer. The qPCR assay for the detection of other mycobacterial species was done at the Tm and primer concentration of 62 °C and 0.4 µM, respectively. The HRM analysis generated cluster patterns that were specific and sensitive to distinguished small sequence differences of the Mycobacterium species. This study suggests that the 16S rRNA-based real-time PCR followed by HRM analysis produced unique cluster patterns for species of Mycobacterium and could differentiate the closely related mycobacteria species. PMID:25038139

  7. Mutation Scanning and Genotyping in Plants by High Resolution DNA Melting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High-resolution melting analysis after PCR allows closed-tube mutation scanning and genotyping without processing, labeled probes, real-time monitoring or allele-specific amplification. PCR is performed in the presence of the saturating dye, LCGreen® Plus, with subsequent high-resolution melting ana...

  8. Consequences and Resolution of Lunar Lower Mantle Partial Melt

    NASA Astrophysics Data System (ADS)

    Fuqua, H.; Bremner, P. M.; Diamond, M. R.; Garapic, G.; Lock, S. J.; Mallik, A.; Nishikawa, Y.; Panovska, S.; Shahar, A.; Lognonne, P. H.; Panero, W. R.; Faul, U.; Panning, M. P.; Jimenez-Perez, H.; Schmerr, N. C.; Williams, Q. C.

    2014-12-01

    Existence of a partially molten layer at depth has been proposed to explain the lack of observed farside deep moonquakes, the observation of reflected phases from deep moonquakes, and the dissipation of tidal energy within the lunar interior. However, subsequent models explore the possibility that dissipation due to elevated temperatures alone can explain the observed dissipation factor (Q) and tidal love numbers. We have explored the hypothesis that high titanium melt compositions associated with lunar mantle overturn may sink to the base of the mantle, locally or regionally. We have performed forward calculations varying composition and thickness of layers to evaluate if a partially molten layer at the base of the mantle is well constrained by the observational data. Self-consistent physical parameters are calculated for each compositional model that are then compared against the observed data to determine a subset of permissible models. The data constraints considered by this study include bulk density, moment of inertia, real and imaginary parts of the Love numbers, seismic travel times, and electrical conductivity. Dynamic calculations using ASPECT have also been considered to determine the implications of early lunar mantle convection for the survivability of the partially molten layer. Finally, and as a perspective for a future NASA New Frontiers Geophysical Network, we present 1D synthetic seismograms calculated for each proposed structure of the Moon to investigate the future seismological resolution of these deep lunar structure features. This work was initiated at the CIDER 2014 program.

  9. Y-STR genetic screening by high-resolution melting analysis.

    PubMed

    Deng, J Q; Liu, B Q; Wang, Y; Liu, W; Cai, J F; Long, R; Li, W H

    2016-01-01

    Currently, the widely used automated capillary electrophoresis-based short tandem repeat (STR) genotyping method for genetic screening in forensic practice is laborious, time-consuming, expensive, and technically challenging in some cases. Thus, new molecular-based strategies for conclusively identifying forensically relevant biological evidence are required. Here, we used high-resolution melting analysis (HRM) for Y-chromosome STR genotyping for forensic genetic screening. The reproducibility of the melting profile over dilution, sensitivity, discrimination power, and other factors was preliminarily studied in 10 Y-STR loci. The results showed that HRM-based approaches revealed more genotypes (compared to capillary electrophoresis), showed higher uniformity in replicate tests and diluted samples, and enabled successful detection of DNA at concentrations as low as 0.25 ng. For mixed samples, the melting curve profiles discriminated between mixed samples based on reference samples with high efficiency. The triplex Y-chromosome STR HRM assay was performed and provided a foundation for further studies such as a multiplex HRM assay. The HRM approach is a one-step application and the entire procedure can be completed within 2 h at a low cost. In conclusion, our findings demonstrate that the HRM-based Y-STR assay is a useful screening tool that can be used in forensic practice. PMID:26909950

  10. Kinetics of Melting and Applications to Chondrules

    NASA Astrophysics Data System (ADS)

    Greenwood, James Paul

    1997-12-01

    The congruent melting kinetics of Amelia albite were experimentally determined at 1125o C,/ 1150o C,/ 1175o C, and 1200o C. It was determined that congruent melting is a heterogeneous process. Melting is initiated at external surfaces and cleavage planes. Melting kinetics of albite are best described using a normal growth model. Congruent melting of albite was found to be interface controlled, and rates of melting are directly proportional to the amount of superheat, and inversely proportional to viscosity. Comparison of the results obtained here with previous studies of melting kinetics on other materials (oxides and silicates) finds that the normal growth model can be used to predict melting rates within an order of magnitude. The normal growth model was used to predict congruent melting rates of forsterite and enstatite as well as other minerals which may have been present in the chondrule forming region of the solar nebula. Constraints on the peak temperatures of chondrule formation are thus obtained. Specifically, chondrules containing relict grains of forsteritic olivine and enstatitic pyroxene could not have been heated above 1901o C and 1577o C, respectively, for more than a few seconds. Reanalyses of Na-Al-rich chondrule glasses by EPMA have found that previous EPMA work resulted in loss of Na from the activated volume due to migration in an electrical potential gradient. The Na-Al-rich chondrules have Na/Al ratios of unity, suggesting that they did not lose alkalis during flash heating. Experiments reproduced the chondrule glasses and determined the formational constraints of these chondrules. Specifically, the chondrules needed to have been cooled at low rates (<6o C/hr) at the lower temperature end of chondrule formation.

  11. High resolution melting analysis as a new approach to discriminate gluten-containing cereals.

    PubMed

    Martín-Fernández, Begoña; Costa, Joana; de-Los-Santos-Álvarez, Noemí; López-Ruiz, Beatriz; Oliveira, M Beatriz P P; Mafra, Isabel

    2016-11-15

    With this work, it is intended to propose a novel approach based on high resolution melting (HRM) analysis to detect wheat and discriminate it from other gluten-containing cereals. The method consisted of a real-time PCR assay targeting the gene encoding for the germ agglutinin isolectin A protein (Tri a 18 allergen), using the fluorescent Evagreen dye combined with HRM analysis. The results enabled wheat differentiation from other phylogenetically related cereals, namely barley, rye and oat with high level of confidence. Additionally, a quantitative real-time PCR approach was proposed, allowing detecting and quantifying wheat down to 20mg/kg in rice flour and 20pg of wheat DNA (∼1.1 DNA copies). Its application was successfully achieved in the analysis of processed foods to verify labelling compliance, being considered as a cost-effective tool for the specific detection of cereals in gluten-free foods. PMID:27283646

  12. Silicon purification melting for photovoltaic applications

    SciTech Connect

    VAN DEN AVYLE,JAMES A.; HO,PAULINE; GEE,JAMES M.

    2000-04-01

    The availability of polysilicon feedstock has become a major issue for the photovoltaic (PV) industry in recent years. Most of the current polysilicon feedstock is derived from rejected material from the semiconductor industry. However, the reject material can become scarce and more expensive during periods of expansion in the integrated-circuit industry. Continued rapid expansion of the PV crystalline-silicon industry will eventually require a dedicated supply of polysilicon feedstock to produce solar cells at lower costs. The photovoltaic industry can accept a lower purity polysilicon feedstock (solar-grade) compared to the semiconductor industry. The purity requirements and potential production techniques for solar-grade polysilicon have been reviewed. One interesting process from previous research involves reactive gas blowing of the molten silicon charge. As an example, Dosaj et all reported a reduction of metal and boron impurities from silicon melts using reactive gas blowing with 0{sub 2} and Cl{sub 2}. The same authors later reassessed their data and the literature, and concluded that Cl{sub 2}and 0{sub 2}/Cl{sub 2} gas blowing are only effective for removing Al, Ca, and Mg from the silicon melt. Researchers from Kawasaki Steel Corp. reported removal of B and C from silicon melts using reactive gas blowing with an 0{sub 2}/Ar plasma torch. Processes that purify the silicon melt are believed to be potentially much lower cost compared to present production methods that purify gas species.

  13. Simple models for disequilibrium fractional melting and batch melting with application to REE fractionation in abyssal peridotites

    NASA Astrophysics Data System (ADS)

    Liang, Yan; Liu, Boda

    2016-01-01

    Disequilibrium melting arises when the kinetics of chemical exchange between a residual mineral and partial melt is sluggish compare to the rate of melting. To better understand the role of a finite crystal-melt exchange rate on trace element fractionation during mantle melting, we have developed a disequilibrium melting model for partial melting in an upwelling steady-state column. We use linear kinetics to approximate crystal-melt mass exchange rate and obtain simple analytical solutions for cases of perfect fractional melting and batch melting. A key parameter determining the extent of chemical disequilibrium during partial melting is an element specific dimensionless ratio (ε) defined as the melting rate relative to the solid-melt chemical exchange rate for the trace element of interest. In the case of diffusion in mineral limited chemical exchange, ε is inversely proportional to diffusivity of the element of interest. Disequilibrium melting is important for the trace element when ε is comparable to or greater than the bulk solid-melt partition coefficient for the trace element (k). The disequilibrium fractional melting model is reduced to the equilibrium perfect fractional melting model when ε is much smaller than k. Hence highly incompatible trace elements with smaller mobilities in minerals are more susceptible to disequilibrium melting than moderately incompatible and compatible trace elements. Effect of chemical disequilibrium is to hinder the extent of fractionation between residual solid and partial melt, making the residual solid less depleted and the accumulated melt more depleted in incompatible trace element abundances relative the case of equilibrium melting. Application of the disequilibrium fractional melting model to REE and Y abundances in clinopyroxene in abyssal peridotites from the Central Indian Ridge and the Vema Lithospheric Section, Mid-Atlantic Ridge revealed a positive correlation between the disequilibrium parameter ε and the

  14. Differentiating between monozygotic twins through DNA methylation-specific high-resolution melt curve analysis.

    PubMed

    Stewart, Leander; Evans, Neil; Bexon, Kimberley J; van der Meer, Dieudonne J; Williams, Graham A

    2015-05-01

    Although short tandem repeat profiling is extremely powerful in identifying individuals from crime scene stains, it is unable to differentiate between monozygotic (MZ) twins. Efforts to address this include mutation analysis through whole genome sequencing and through DNA methylation studies. Methylation of DNA is affected by environmental factors; thus, as MZ twins age, their DNA methylation patterns change. This can be characterized by bisulfite treatment followed by pyrosequencing. However, this can be time-consuming and expensive; thus, it is unlikely to be widely used by investigators. If the sequences are different, then in theory the melting temperature should be different. Thus, the aim of this study was to assess whether high-resolution melt curve analysis can be used to differentiate between MZ twins. Five sets of MZ twins provided buccal swabs that underwent extraction, quantification, bisulfite treatment, polymerase chain reaction amplification and high-resolution melting curve analysis targeting two markers, Alu-E2F3 and Alu-SP. Significant differences were observed between all MZ twins targeting Alu-E2F3 and in four of five MZ twins targeting Alu-SP (P<0.05). Thus, it has been demonstrated that bisulfite treatment followed by high-resolution melting curve analysis could be used to differentiate between MZ twins. PMID:25677265

  15. High resolution melting (HRM) analysis of DNA--its role and potential in food analysis.

    PubMed

    Druml, Barbara; Cichna-Markl, Margit

    2014-09-01

    DNA based methods play an increasing role in food safety control and food adulteration detection. Recent papers show that high resolution melting (HRM) analysis is an interesting approach. It involves amplification of the target of interest in the presence of a saturation dye by the polymerase chain reaction (PCR) and subsequent melting of the amplicons by gradually increasing the temperature. Since the melting profile depends on the GC content, length, sequence and strand complementarity of the product, HRM analysis is highly suitable for the detection of single-base variants and small insertions or deletions. The review gives an introduction into HRM analysis, covers important aspects in the development of an HRM analysis method and describes how HRM data are analysed and interpreted. Then we discuss the potential of HRM analysis based methods in food analysis, i.e. for the identification of closely related species and cultivars and the identification of pathogenic microorganisms. PMID:24731338

  16. Submarine Melting of Icebergs from Repeat High-Resolution Digital Elevation Models

    NASA Astrophysics Data System (ADS)

    Enderlin, E. M.; Hamilton, G. S.; Straneo, F.; Cenedese, C.

    2014-12-01

    Icebergs calved from tidewater glaciers act as distributed freshwater sources as they transit through fjords to the surrounding ocean basins. Glacier discharge estimates provide a crude approximation of the total iceberg discharge on inter-annual timescales, but the liquid freshwater flux from icebergs in glacial fjords is largely unknown. Here we use repeat high-resolution digital elevation models (DEMs) to derive meltwater fluxes for 18 icebergs in Sermilik Fjord, East Greenland, during the 2011-2013 boreal summers, and for 33 comparably-sized icebergs in Ilulissat Fjord, West Greenland, during March-April 2011 and July 2012. We find that iceberg melt rates for Sermilik Fjord are in good agreement with simulated melt rates along the vertical terminus of Helheim Glacier in winter, i.e. when melting at the glacier front is not enhanced by subglacial discharge, providing an independent validation of our technique. Variations in meltwater fluxes from icebergs are primarily related to differences in the submerged area of individual icebergs, which is consistent with theory. The stratification of water masses in fjords has a noticeable effect on summertime-derived melt estimates, with lower melt rates (and meltwater fluxes) observed in the relatively cold and fresh Polar Water layer and higher melt rates in the underlying warmer and more saline Atlantic Water layer. The meltwater flux dependence on submerged area, particularly within the deeper Atlantic Water layer, suggests that changes in the characteristics of icebergs (size/shape/keel-depth) calved from a tidewater glacier will alter the magnitude and distribution of meltwater fluxes within the fjord, which may in turn influence fjord circulation and the heat content delivered to the glacier terminus.

  17. Single-melt beta C for spring and fastener applications

    NASA Astrophysics Data System (ADS)

    Yu, K. O.; Crist, E. M.; Pesa, R.; Cecchini, N.; Bugle, C. M.

    2005-12-01

    Beta C is a high-strength metastable titanium alloy widely used for spring and fastener applications. Input stock of these springs and fasteners is currently made by rolling billets forged from conventional double-melt VAR (2×VAR) ingots. Recent advances in plasma arc melting (PAM) single-melt technology offer the potential to reduce the input stock cost by directly rolling as-cast near-net shape PAM ingots instead of the conventional forged billets. A 127 mm (5 in.) diameter as-cast Beta C PAM ingot was rolled into 15 mm (0.6 in.) bars for springs and fasteners. Microstructures and mechanical properties of the bar product are evaluated in this paper.

  18. High-Resolution Melting Analysis of MED12 Mutations in Uterine Leiomyomas in Chinese Patients

    PubMed Central

    Wang, Hua; Qian, Hua; Zhou, Ruifang; Jiang, Jun; Ye, Lihua

    2015-01-01

    Objectives: Somatic mutations in mediator complex subunit 12 (MED12) have emerged as a critical genetic change in the development of uterine leiomyomas. Studies, however, have focused largely on cohorts consisting of Caucasian patients. In this study, uterine leiomyomas from Chinese patients were examined for MED12 mutations. In addition, polymerase chain reaction (PCR)-based high-resolution melting analysis (HRMA) was compared with direct sequencing as a potentially more sensitive method for the detection of MED12 mutations. Methods: Tissue samples with the pathologies of uterine leiomyoma (n=181) and other endometrial diseases (n=157) were collected from Chinese patients at the Taizhou People's Hospital and Taizhou Polytechnic College (Taizhou City, China). Genomic DNA was prepared from all samples. Both PCR-based HRMA and PCR-based direct sequencing were used to detect MED12 mutations. Results: PCR-based HRMA and direct sequencing revealed MED12 mutations in 95/181 (52.5%) and 93/181 (51.4%) uterine leiomyomas, respectively. Nearly half of these mutations (46/93) were found in a single codon, codon 131. The coincidence rate between the two methods was 98.9% (179/181) so that no statistically significant difference was evident in the application of the methodologies (χ2=0.011, p=0.916). In addition, MED12 mutations were identified in 1/157 (4.17%) case of other endometrial pathologies by both methods. Conclusions: MED12 mutations were closely associated with the development of uterine leiomyomas, as opposed to other uterine pathologies in Chinese patients, and PCR-based HRMA was found to be a reliable method for the detection of MED12 mutations. PMID:25615570

  19. Evaluation of High Resolution Melting for MTHFR C677T Genotyping in Congenital Heart Disease

    PubMed Central

    Yue, Shuying; Zhang, Kun; Wang, Hui; Dong, Rui; Yang, Xiaomeng; Liu, Yi; Ma, Yanhui

    2016-01-01

    Background High resolution melting (HRM) is a simple, flexible and low-cost mutation screening technique. The methylenetetrahydrofolate reductase (MTHFR) gene encoding a critical enzyme, potentially affects susceptibility to some congenital defects like congenital heart disease (CHD). We evaluate the performance of HRM for genotyping of the MTHFR gene C677T locus in CHD cases and healthy controls of Chinese Han population. Methods A total of 315 blood samples from 147 CHD patients (male72, female 75) and 168 healthy controls (male 92, female 76) were enrolled in the study. HRM was utilized to genotype MTHFR C677T locus of all the samples. The results were compared to that of PCR-RFLP and Sanger sequencing. The association of the MTHFR C677T genotypes and the risk of CHD was analyzed using odds ratio with their 95% confidence interval (CIs) from unconditional logistic regression. Results All the samples were successfully genotyped by HRM within 1 hour and 30 minutes while at least 6 hours were needed for PCR-RFLP and sequencing. The genotypes of MTHFR C677T CC, CT, and TT were 9.52%, 49.66%, and 40.82% in CHD group but 29.17%, 50% and 20.83% in control group, which were identical using both methods of HRM and PCR-RFLP, demonstrating the sensitivity and specificity of HRM were all 100%. Conclusion MTHFR C677T is a potential risk factor for CHD in our local residents of Shandong province in China. HRM is a fast, sensitive, specific and reliable method for clinical application of genotyping. PMID:26990189

  20. Automated Classification and Cluster Visualization of Genotypes Derived from High Resolution Melt Curves

    PubMed Central

    Kanderian, Sami; Jiang, Lingxia; Knight, Ivor

    2015-01-01

    Introduction High Resolution Melting (HRM) following PCR has been used to identify DNA genotypes. Fluorescent dyes bounded to double strand DNA lose their fluorescence with increasing temperature, yielding different signatures for different genotypes. Recent software tools have been made available to aid in the distinction of different genotypes, but they are not fully automated, used only for research purposes, or require some level of interaction or confirmation from an analyst. Materials and Methods We describe a fully automated machine learning software algorithm that classifies unknown genotypes. Dynamic melt curves are transformed to multidimensional clusters of points whereby a training set is used to establish the distribution of genotype clusters. Subsequently, probabilistic and statistical methods were used to classify the genotypes of unknown DNA samples on 4 different assays (40 VKORC1, CYP2C9*2, CYP2C9*3 samples in triplicate, and 49 MTHFR c.665C>T samples in triplicate) run on the Roche LC480. Melt curves of each of the triplicates were genotyped separately. Results Automated genotyping called 100% of VKORC1, CYP2C9*3 and MTHFR c.665C>T samples correctly. 97.5% of CYP2C9*2 melt curves were genotyped correctly with the remaining 2.5% given a no call due to the inability to decipher 3 melt curves in close proximity as either homozygous mutant or wild-type with greater than 99.5% posterior probability. Conclusions We demonstrate the ability to fully automate DNA genotyping from HRM curves systematically and accurately without requiring any user interpretation or interaction with the data. Visualization of genotype clusters and quantification of the expected misclassification rate is also available to provide feedback to assay scientists and engineers as changes are made to the assay or instrument. PMID:26605797

  1. Probing the atomic structure of basaltic melts generated by partial melting of upper mantle peridotite (KLB-1): Insights from high-resolution solid-state NMR study

    NASA Astrophysics Data System (ADS)

    Park, S. Y.; Lee, S. K.

    2015-12-01

    Probing the structural disorder in multi-component silicate glasses and melts with varying composition is essential to reveal the change of macroscopic properties in natural silicate melts. While a number of NMR studies for the structure of multi-component silicate glasses and melts including basaltic and andesitic glasses have been reported (e.g., Park and Lee, Geochim. Cosmochim. Acta, 2012, 80, 125; Park and Lee, Geochim. Cosmochim. Acta, 2014, 26, 42), many challenges still remain. The composition of multi-component basaltic melts vary with temperature, pressure, and melt fraction (Kushiro, Annu. Rev. Earth Planet. Sci., 2001, 71, 107). Especially, the eutectic point (the composition of first melt) of nepheline-forsterite-quartz (the simplest model of basaltic melts) moves with pressure from silica-saturated to highly undersaturated and alkaline melts. The composition of basaltic melts generated by partial melting of upper mantle peridotite (KLB-1, the xenolith from Kilbourne Hole) also vary with pressure. In this study we report experimental results for the effects of composition on the atomic structure of Na2O-MgO-Al2O3-SiO2 (NMAS) glasses in nepheline (NaAlSiO4)-forsterite (Mg2SiO4)-quartz (SiO2) eutectic composition and basaltic glasses generated by partial melting of upper mantle peridotite (KLB-1) using high-resolution multi-nuclear solid-state NMR. The Al-27 3QMAS (triple quantum magic angle spinning) NMR spectra of NMAS glasses in nepheline-forsterite-quartz eutectic composition show only [4]Al. The Al-27 3QMAS NMR spectra of KLB-1 basaltic glasses show mostly [4]Al and a non-negligible fraction of [5]Al. The fraction of [5]Al, the degree of configurational disorder, increases from 0 at XMgO [MgO/(MgO+Al2O3)]=0.55 to ~3% at XMgO=0.79 in KLB-1 basaltic glasses while only [4]Al are observed in nepheline-forsterite-quartz eutectic composition. The current experimental results provide that the fraction of [5]Al abruptly increases by the effect of

  2. Rapid and inexpensive species differentiation using a multiplex real-time polymerase chain reaction high-resolution melt assay.

    PubMed

    Elkins, Kelly M; Perez, Anjelica C U; Sweetin, Katherine C

    2016-05-01

    We demonstrate a method for developing real-time polymerase chain reaction (PCR) high-resolution melt (HRM) assays to identify multiple species present in a mixture simultaneously using LCGreen Plus and melt temperatures. Highly specific PCR primers are designed to yield amplicons with different melt temperatures for simple routine species identification compared with differentiating melt curve kinetics traces or difference plots. This method is robust and automatable, and it leads to savings in time and reagent costs, is easily modified to probe any species of interest, eliminates the need for post-PCR gel or capillary electrophoresis in routine assays, and requires no expensive dye-labeled primers. PMID:26836486

  3. Identification case of evidence in timber tracing of Pinus radiate, using high-resolution melting (HRM) analysis.

    PubMed

    Solano, Jaime; Anabalón, Leonardo; Encina, Francisco

    2016-03-01

    Fast, accurate detection of plant species and their hybrids using molecular tools will facilitate assessment and monitoring of timber tracing evidence. In this study the origin of unknown pine samples is determined for a case of timber theft in the region of Araucania southern Chile. We evaluate the utility of the trnL marker region for species identification applied to pine wood based on High Resolution Melting. This efficient tracing methods can be incorporated into forestry applications such as certification of origin. The object of this work was genotype identification using high-resolution melting (HRM) and trnL approaches for Pinus radiata (Don) in timber tracing evidence. Our results indicate that trnL is a very sensitive marker for delimiting species and HRM analysis was used successfully for genotyping Pinus samples for timber tracing purposes. Genotyping samples by HRM analysis with the trnL1 approach allowed us to differentiate two wood samples from the Pinaceae family: Pinus radiata (Don) and Pseudotsuga menziesii (Mirb.) Franco. The same approach with Pinus trnL wood was not able to discriminate between samples of Pinus radiata, indicating that the samples were genetically indistinguishable, possibly because they have the same genotype at this locus. Timber tracing with HRM analysis is expected to contribute to future forest certification schemes, control of illegal trading, and molecular traceability of Pinus spp. PMID:26626827

  4. Improved protocol for rapid identification of certain spa types using high resolution melting curve analysis.

    PubMed

    Mayerhofer, Benjamin; Stöger, Anna; Pietzka, Ariane T; Fernandez, Haizpea Lasa; Prewein, Bernhard; Sorschag, Sieglinde; Kunert, Renate; Allerberger, Franz; Ruppitsch, Werner

    2015-01-01

    Methicillin-resistant Staphylococcus aureus is one of the most significant pathogens associated with health care. For efficient surveillance, control and outbreak investigation, S. aureus typing is essential. A high resolution melting curve analysis was developed and evaluated for rapid identification of the most frequent spa types found in an Austrian hospital consortium covering 2,435 beds. Among 557 methicillin-resistant Staphylococcus aureus isolates 38 different spa types were identified by sequence analysis of the hypervariable region X of the protein A gene (spa). Identification of spa types through their characteristic high resolution melting curve profiles was considerably improved by double spiking with genomic DNA from spa type t030 and spa type t003 and allowed unambiguous and fast identification of the ten most frequent spa types t001 (58%), t003 (12%), t190 (9%), t041 (5%), t022 (2%), t032 (2%), t008 (2%), t002 (1%), t5712 (1%) and t2203 (1%), representing 93% of all isolates within this hospital consortium. The performance of the assay was evaluated by testing samples with unknown spa types from the daily routine and by testing three different high resolution melting curve analysis real-time PCR instruments. The ten most frequent spa types were identified from all samples and on all instruments with 100% specificity and 100% sensitivity. Compared to classical spa typing by sequence analysis, this gene scanning assay is faster, cheaper and can be performed in a single closed tube assay format. Therefore it is an optimal screening tool to detect the most frequent endemic spa types and to exclude non-endemic spa types within a hospital. PMID:25768007

  5. Improved Protocol for Rapid Identification of Certain Spa Types Using High Resolution Melting Curve Analysis

    PubMed Central

    Mayerhofer, Benjamin; Stöger, Anna; Pietzka, Ariane T.; Fernandez, Haizpea Lasa; Prewein, Bernhard; Sorschag, Sieglinde; Kunert, Renate; Allerberger, Franz; Ruppitsch, Werner

    2015-01-01

    Methicillin-resistant Staphylococcus aureus is one of the most significant pathogens associated with health care. For efficient surveillance, control and outbreak investigation, S. aureus typing is essential. A high resolution melting curve analysis was developed and evaluated for rapid identification of the most frequent spa types found in an Austrian hospital consortium covering 2,435 beds. Among 557 methicillin-resistant Staphylococcus aureus isolates 38 different spa types were identified by sequence analysis of the hypervariable region X of the protein A gene (spa). Identification of spa types through their characteristic high resolution melting curve profiles was considerably improved by double spiking with genomic DNA from spa type t030 and spa type t003 and allowed unambiguous and fast identification of the ten most frequent spa types t001 (58%), t003 (12%), t190 (9%), t041 (5%), t022 (2%), t032 (2%), t008 (2%), t002 (1%), t5712 (1%) and t2203 (1%), representing 93% of all isolates within this hospital consortium. The performance of the assay was evaluated by testing samples with unknown spa types from the daily routine and by testing three different high resolution melting curve analysis real-time PCR instruments. The ten most frequent spa types were identified from all samples and on all instruments with 100% specificity and 100% sensitivity. Compared to classical spa typing by sequence analysis, this gene scanning assay is faster, cheaper and can be performed in a single closed tube assay format. Therefore it is an optimal screening tool to detect the most frequent endemic spa types and to exclude non-endemic spa types within a hospital. PMID:25768007

  6. Detection of Indel Mutations in Drosophila by High-Resolution Melt Analysis (HRMA).

    PubMed

    Housden, Benjamin E; Perrimon, Norbert

    2016-01-01

    Although CRISPR technology allows specific genome alterations to be created with relative ease, detection of these events can be problematic. For example, CRISPR-induced double-strand breaks are often repaired imprecisely to generate unpredictable short indel mutations. Detection of these events requires the use of molecular screening techniques such as endonuclease assays, restriction profiling, or high-resolution melt analysis (HRMA). Here, we provide detailed protocols for HRMA-based mutation screening in Drosophila and analysis of the resulting data using the online tool HRMAnalyzer. PMID:27587781

  7. Rapid Identification of Medically Important Candida Isolates Using High Resolution Melting Analysis

    PubMed Central

    Nemcova, Eva; Cernochova, Michaela; Ruzicka, Filip; Malisova, Barbora

    2015-01-01

    An increasing trend in non albicans infections and various susceptibility patterns to antifungal agents implies a requirement for the quick and reliable identification of a number of medically important Candida species. Real-time PCR followed by high resolution melting analysis (HRMA) was developed, tested on 25 reference Candida collection strains and validated on an additional 143 clinical isolates in this study. All reference strains and clinical isolates inconclusive when using phenotypic methods and/or HRMA were analysed using ITS2 sequencing. Considering reference and clinical strains together, 23 out of 27 Candida species could be clearly distinguished by HRMA, while the remaining 4 species were grouped in 2 pairs, when applying the mean Tm ± 3 SD values, the shape of the derivative melting curve (dMelt curve) and, in some cases, the normalized and temperature—shifted difference plot against C. krusei. HRMA as a simple, rapid and inexpensive tool was shown to be useful in identifying a wide spectrum of clinically important Candida species. It may complement the current clinical diagnostic approach based on commercially available biochemical kits. PMID:25689781

  8. First screening for Brachyspira hampsonii in Swiss pigs applying a new high resolution melting assay.

    PubMed

    Scherrer, Simone; Borgström, Anna; Frei, Daniel; Wittenbrink, Max M

    2016-09-25

    A new High Resolution Melting (HRM) assay was developed for the rapid detection of Brachyspira (B.) hampsonii. B. hampsonii occurs in different European countries, however, until today it has not been encountered in Switzerland. Four B. hampsonii reference strains were used to develop the HRM assay: B. hampsonii clade I ATCC BAA2463 and clade II ATCC BAA2464 strain, as well as two isolated strains P280/1 from the UK and the German isolate 5369-1x/12. A conserved region of the nox gene was used to design B. hampsonii-specific primers. The HRM melting curves for the four reference strains showed reproducible difference graphs with distinct differences between the four strains based on a slight variation between the four amplicon sequences. In addition, DNA from 22 B. hampsonii strains representing four genetic B. hampsonii groups was used to validate the method. Melting temperatures in the interval between 73.1 and 74°C were obtained for all B. hampsonii strains and allow differentiating B. hampsonii from other Brachyspira species. In total 897 Swiss porcine fecal Brachyspira isolates, cultured between 2009 and 2015, were analysed by the HRM protocol. B. hampsonii was not detected among these Swiss Brachyspira isolates. In conclusion, the rapid and low-cost HRM approach allows a sensitive and specific identification of B. hampsonii. PMID:27599925

  9. One-step species-specific high resolution melting analysis for nosocomial bacteria detection.

    PubMed

    Wong, Yeng Pooi; Chua, Kek Heng; Thong, Kwai Lin

    2014-12-01

    Nosocomial infections are a major public health concern worldwide. Early and accurate identification of nosocomial pathogens which are often multidrug resistant is crucial for prompt treatment. Hence, an alternative real-time polymerase chain reaction coupled with high resolution melting-curve analysis (HRMA) was developed for identification of five nosocomial bacteria. This assay targets species-specific regions of each nosocomial bacteria and produced five distinct melt curves with each representing a particular bacterial species. The melting curves were characterized by peaks of 78.8 ± 0.2 °C for Acinetobacter baumannii, 82.7 ± 0.2 °C for Escherichia coli, 86.3 ± 0.3 °C for Klebsiella pneumoniae, 88.8 ± 0.2 °C for Pseudomonas aeruginosa and 74.6 ± 02 °C for methicillin-resistant Staphylococcus aureus. The assay was able to specifically detect the five bacterial species with an overall detection limit of 2 × 10(-2) ng/μL. In conclusion, the HRM assay developed is a simple and rapid method for identification of the selected nosocomial pathogens. PMID:25307691

  10. Genotyping of classical swine fever virus using high-resolution melt analysis.

    PubMed

    Titov, Ilya; Tsybanov, Sodnom; Malogolovkin, Alexander

    2015-11-01

    Discrimination between different field and vaccine strains of classical swine fever virus (CSFV) is crucial for meaningful disease diagnosis and epidemiological investigation. In this study, a rapid method for differentiating vaccine strains and outbreak CSFV isolates by combined RT-PCR and high-resolution melt (HRM) analysis has been developed. The assay is based on PCR amplification of short fragments from the most variable region of CSFVgene E2, followed by HRM analysis of amplicons. Real-Time PCR/HRM for CSFV detection and differentiation analysis has sensitivity comparable to RT-qPCR and genotyping resolution comparable to E2 nucleotide sequencing. This assay in one step enables rapid and sensitive identification and genotype discrimination of CSFV in field samples, and thus will be valuable for CSF outbreak response and disease control. PMID:26300371

  11. Automated Microfluidic Platform for Serial Polymerase Chain Reaction and High-Resolution Melting Analysis.

    PubMed

    Cao, Weidong; Bean, Brian; Corey, Scott; Coursey, Johnathan S; Hasson, Kenton C; Inoue, Hiroshi; Isano, Taisuke; Kanderian, Sami; Lane, Ben; Liang, Hongye; Murphy, Brian; Owen, Greg; Shinoda, Nobuhiko; Zeng, Shulin; Knight, Ivor T

    2016-06-01

    We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing. PMID:25827436

  12. Use of a New High Resolution Melting Method for Genotyping Pathogenic Leptospira spp.

    PubMed Central

    Naze, Florence; Desvars, Amélie; Picardeau, Mathieu; Bourhy, Pascale; Michault, Alain

    2015-01-01

    Background Leptospirosis is a worldwide zoonosis that is endemic in tropical areas, such as Reunion Island. The species Leptospira interrogans is the primary agent in human infections, but other pathogenic species, such as L. kirschner and L. borgpetersenii, are also associated with human leptospirosis. Methods and Findings In this study, a melting curve analysis of the products that were amplified with the primer pairs lfb1 F/R and G1/G2 facilitated an accurate species classification of Leptospira reference strains. Next, we combined an unsupervised high resolution melting (HRM) method with a new statistical approach using primers to amplify a two variable-number tandem-repeat (VNTR) for typing at the subspecies level. The HRM analysis, which was performed with ScreenClust Software, enabled the identification of genotypes at the serovar level with high resolution power (Hunter-Gaston index 0.984). This method was also applied to Leptospira DNA from blood samples that were obtained from Reunion Island after 1998. We were able to identify a unique genotype that is identical to that of the L. interrogans serovars Copenhageni and Icterohaemorrhagiae, suggesting that this genotype is the major cause of leptospirosis on Reunion Island. Conclusions Our simple, rapid, and robust genotyping method enables the identification of Leptospira strains at the species and subspecies levels and supports the direct genotyping of Leptospira in biological samples without requiring cultures. PMID:26154161

  13. High resolution laser micro sintering / melting using q-switched and high brilliant laser radiation

    NASA Astrophysics Data System (ADS)

    Exner, H.; Streek, A.

    2015-03-01

    Since the discovery of selective laser sintering/melting, numerous modifications have been made to upgrade or customize this technology for industrial purposes. Laser micro sintering (LMS) is one of those modifications: Powders with particles in the range of a few micrometers are used to obtain products with highly resolved structures. Pulses of a q-switched laser had been considered necessary in order to generate sinter layers from the micrometer scaled metal powders. LMS has been applied with powders from metals as well as from ceramic and cermet feedstock's to generate micro parts. Recent technological progress and the application of high brilliant continuous laser radiation have now allowed an efficient laser sintering/melting of micrometer scaled metal powders. Thereby it is remarkable that thin sinter layers are generated using high continuous laser power. The principles of the process, the state of the art in LMS concerning its advantages and limitations and furthermore the latest results of the recent development of this technology will be presented. Laser Micro Sintering / Laser Micro Melting (LMM) offer a vision for a new dimension of additive fabrication of miniature and precise parts also with application potential in all engineering fields.

  14. DNA-based identification of Peucedanum ostruthium specimens and detection of common adulterants by high-resolution melting curve analysis.

    PubMed

    Schmiderer, Corinna; Ruzicka, Joana; Novak, Johannes

    2015-12-01

    Masterwort (Peucedanum ostruthium, syn. Imperatoria ostruthium, Apiaceae) is an old economic plant in Alpine countries cultivated as ornamental plant and used for spirits and in folk medicine. P. ostruthium is a species that has often been confused with related Apiaceae species or morphologically similar roots or tubers resulting in products of minor quality. Masterwort can be distinguished from other Apiaceae species by nrDNA (ITS1 and ITS2). The analysed chloroplast markers (trnK 5' intron, trnT-trnL, and psbA-trnH), however, showed no species-specific mutations. With the application of two primer pairs amplifying parts of ITS and developed for high-resolution melting curve analysis (HRM) the target species was distinguishable from the other Peucedanum and Apiaceae species of our reference set. A multiplex PCR/HRM was developed to detect adulterations with Gentiana spp., Aconitum napellus and Veratrum album. PMID:26493217

  15. Review of selective laser melting: Materials and applications

    SciTech Connect

    Yap, C. Y.; Chua, C. K. Liu, Z. H. Zhang, D. Q. Loh, L. E. Sing, S. L.; Dong, Z. L.

    2015-12-15

    Selective Laser Melting (SLM) is a particular rapid prototyping, 3D printing, or Additive Manufacturing (AM) technique designed to use high power-density laser to melt and fuse metallic powders. A component is built by selectively melting and fusing powders within and between layers. The SLM technique is also commonly known as direct selective laser sintering, LaserCusing, and direct metal laser sintering, and this technique has been proven to produce near net-shape parts up to 99.9% relative density. This enables the process to build near full density functional parts and has viable economic benefits. Recent developments of fibre optics and high-power laser have also enabled SLM to process different metallic materials, such as copper, aluminium, and tungsten. Similarly, this has also opened up research opportunities in SLM of ceramic and composite materials. The review presents the SLM process and some of the common physical phenomena associated with this AM technology. It then focuses on the following areas: (a) applications of SLM materials and (b) mechanical properties of SLM parts achieved in research publications. The review is not meant to put a ceiling on the capabilities of the SLM process but to enable readers to have an overview on the material properties achieved by the SLM process so far. Trends in research of SLM are also elaborated in the last section.

  16. Review of selective laser melting: Materials and applications

    NASA Astrophysics Data System (ADS)

    Yap, C. Y.; Chua, C. K.; Dong, Z. L.; Liu, Z. H.; Zhang, D. Q.; Loh, L. E.; Sing, S. L.

    2015-12-01

    Selective Laser Melting (SLM) is a particular rapid prototyping, 3D printing, or Additive Manufacturing (AM) technique designed to use high power-density laser to melt and fuse metallic powders. A component is built by selectively melting and fusing powders within and between layers. The SLM technique is also commonly known as direct selective laser sintering, LaserCusing, and direct metal laser sintering, and this technique has been proven to produce near net-shape parts up to 99.9% relative density. This enables the process to build near full density functional parts and has viable economic benefits. Recent developments of fibre optics and high-power laser have also enabled SLM to process different metallic materials, such as copper, aluminium, and tungsten. Similarly, this has also opened up research opportunities in SLM of ceramic and composite materials. The review presents the SLM process and some of the common physical phenomena associated with this AM technology. It then focuses on the following areas: (a) applications of SLM materials and (b) mechanical properties of SLM parts achieved in research publications. The review is not meant to put a ceiling on the capabilities of the SLM process but to enable readers to have an overview on the material properties achieved by the SLM process so far. Trends in research of SLM are also elaborated in the last section.

  17. Rapid detection of fungal pathogens in bronchoalveolar lavage samples using panfungal PCR combined with high resolution melting analysis.

    PubMed

    Bezdicek, Matej; Lengerova, Martina; Ricna, Dita; Weinbergerova, Barbora; Kocmanova, Iva; Volfova, Pavlina; Drgona, Lubos; Poczova, Miroslava; Mayer, Jiri; Racil, Zdenek

    2016-10-01

    Despite advances in the treatment of invasive fungal diseases (IFD), mortality rates remain high. Moreover, due to the expanding spectrum of causative agents, fast and accurate pathogen identification is necessary. We designed a panfungal polymerase chain reaction (PCR), which targets the highly variable ITS2 region of rDNA genes and uses high resolution melting analysis (HRM) for subsequent species identification. The sensitivity and specificity of this method was tested on a broad spectrum of the most clinically important fungal pathogens including Aspergillus spp., Candida spp. and mucormycetes. Despite the fact that fluid from bronchoalveolar lavage (BAL) is one of the most frequently tested materials there is a lack of literature sources aimed at panfungal PCR as an IFD diagnostic tool from BAL samples. The applicability of this method in routine practice was evaluated on 104 BAL samples from immunocompromised patients. Due to high ITS region variability, we obtained divergent melting peaks for different fungal species. Thirteen out of 18 patients with proven or probable IFD were positive. Therefore, the sensitivity, specificity, positive predictive value and negative predictive value of our method were 67%, 100%, 100%, and 94%, respectively. In our assay, fungal pathogens identification is based on HRM, therefore omitting the expensive and time consuming sequencing step. With the high specificity, positive and negative predictive values, short time needed to obtain a result, and low price, the presented assay is intended to be used as a quick screening method for patients at risk of IFD. PMID:27161789

  18. Cancer mutation screening: Comparison of high-resolution melt analysis between two platforms.

    PubMed

    Ebili, Henry O; Ilyas, Mohammad

    2015-01-01

    High-resolution melt analysis (HRMA) is a cheap and reliable post-polymerase chain reaction (PCR) cancer mutation screening technique, which is fast gaining clinical relevance. The HRMA capabilities of the LightScanner (Idaho Technology) have been severally studied. However, the ABI 7500 HRM has not been tested against the purpose-built HRM instrument such as the LightScanner. DNA from formalin-fixed, paraffin-embedded gastric cancer, colorectal cancer, and normal tissue as well as from colorectal cancer cell lines were amplified at exons 2, 3, and 4 of KRAS, and at exons 11 and 15 of BRAF in the ABI 7500 fast real-time PCR machine and subjected to melting both on the ABI and on the LightScanner. HRMA data were analysed with the ABI HRM software v2.0.1 and the LightScanner Call-IT 2.5. We tested the ABI 7500 HRM for internal precision, accuracy, sensitivity, and specificity at mutation screening relative to the LightScanner, using crude percentage concordance, kappa statistics, and the area under the receiver operator characteristics (AUROC) curve on SPSS version 19. The results show that the ABI 7500 HRMA has a high internal precision, and excellent concordance, sensitivity, and specificity at mutation screening compared with the LightScanner. However, in contrast to the LightScanner HRM software analysis, the ABI HRM software v.2.0.1, cannot distinguish real from certain pseudovariations in PCR amplicons that are sometimes brought about by the artefacts of the melting process. In conclusion, the ABI HRM has a comparable performance level with the LightScanner, although in certain respects mentioned previously, the LightScanner has an edge over the ABI. PMID:25932046

  19. Exploring crystallization kinetics in natural rhyolitic melts using high resolution CT imagery of spherulites

    NASA Astrophysics Data System (ADS)

    Clow, T. W.; Befus, K. S.; Gardner, J. E.

    2014-12-01

    Little of our understanding of crystallization kinetics has been directly derived from studies of natural samples. We examine crystallization of rhyolitic melts by quantifying spherulite sizes and number densities in obsidian collected from Yellowstone caldera using high-resolution x-ray computed tomography (CT) imagery. Spherulites are spherical to ellipsoidal masses of intergrown alkali feldspar and quartz in a radiating, fibrous structure. They are thought to form in response to relatively rapid crystallization of melt in response to large amounts of undercooling. Recent research using compositional gradients that form outside of spherulites has suggested that they nucleate at 700 to 500 ˚C and their growth slows exponentially until it eventually ceases at ~400 ˚C. By quantifying spherulite textures, and using those temperature constraints, we derive new kinetic information regarding crystallization in natural rhyolitic systems. We find that spherulites range from 0.2 to 12.3 mm in diameter, and are 0.004 to 49.5 mm3 in volume. Such values generate number densities of 70 to 185 spherulites cm-3. Histograms of size display positively skewed distributions indicating small spherulites are far more abundant than larger ones. Those distributions imply nucleation rates change as a function of temperature. At higher temperatures where the melt is undercooled by 400-500 ˚C, nucleation is rare and growth is favored. With decreasing temperature, nucleation rates increase rapidly until cold enough temperatures are reached that diffusion limits crystallization and causes it to cease (undercoolings of ~650 ˚C). Assuming a cooling rate for the host obsidian of 10-5 ˚C s-1, then overall spherulite nucleation rates are 0.01 to 0.03 spherulites cm-3 hour-1.

  20. Reliable Discrimination of 10 Ungulate Species Using High Resolution Melting Analysis of Faecal DNA

    PubMed Central

    Ramón-Laca, Ana; Gleeson, Dianne; Yockney, Ivor; Perry, Michael; Nugent, Graham; Forsyth, David M.

    2014-01-01

    Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla) have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat) from swabs of faecal pellets. A high resolution melting (HRM) assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA. PMID:24637802

  1. Sex Determination in Highly Fragmented Human DNA by High-Resolution Melting (HRM) Analysis

    PubMed Central

    Álvarez-Sandoval, Brenda A.; Manzanilla, Linda R.; Montiel, Rafael

    2014-01-01

    Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design. PMID:25098828

  2. Sex determination in highly fragmented human DNA by high-resolution melting (HRM) analysis.

    PubMed

    Álvarez-Sandoval, Brenda A; Manzanilla, Linda R; Montiel, Rafael

    2014-01-01

    Sex identification in ancient human remains is a common problem especially if the skeletons are sub-adult, incomplete or damaged. In this paper we propose a new method to identify sex, based on real-time PCR amplification of small fragments (61 and 64 bp) of the third exon within the amelogenin gene covering a 3-bp deletion on the AMELX-allele, followed by a High Resolution Melting analysis (HRM). HRM is based on the melting curves of amplified fragments. The amelogenin gene is located on both chromosomes X and Y, showing dimorphism in length. This molecular tool is rapid, sensitive and reduces the risk of contamination from exogenous genetic material when used for ancient DNA studies. The accuracy of the new method described here has been corroborated by using control samples of known sex and by contrasting our results with those obtained with other methods. Our method has proven to be useful even in heavily degraded samples, where other previously published methods failed. Stochastic problems such as the random allele drop-out phenomenon are expected to occur in a less severe form, due to the smaller fragment size to be amplified. Thus, their negative effect could be easier to overcome by a proper experimental design. PMID:25098828

  3. High-Resolution Melting Curve Analysis for Identification of Pasteurellaceae Species in Experimental Animal Facilities.

    PubMed

    Miller, Manuel; Zorn, Julia; Brielmeier, Markus

    2015-01-01

    Pasteurellaceae are among the most prevalent bacterial pathogens isolated from mice housed in experimental animal facilities. Reliable detection and differentiation of Pasteurellaceae are essential for high-quality health monitoring. In this study, we combined a real-time PCR assay amplifying a variable region in the 16S rRNA sequence with high-resolution melting curve analysis (HRM) to identify and differentiate among the commonly isolated species Pasteurella pneumotropica biotypes "Jawetz" and "Heyl", Actinobacillus muris, and Haemophilus influenzaemurium. We used a set of six reference strains for assay development, with the melting profiles of these strains clearly distinguishable due to DNA sequence variations in the amplicon. For evaluation, we used real-time PCR/HRM to test 25 unknown Pasteurellaceae isolates obtained from an external diagnostic laboratory and found the results to be consistent with those of partial 16S rRNA sequencing. The real-time PCR/HRM method provides a sensitive, rapid, and closed-tube approach for Pasteurellaceae species identification for health monitoring of laboratory mice. PMID:26556281

  4. Rapid genotyping of beak and feather disease virus using high-resolution DNA melt curve analysis.

    PubMed

    Sarker, Subir; Ghorashi, Seyed A; Forwood, Jade K; Raidal, Shane R

    2014-11-01

    Beak and feather disease virus (BFDV) is a significant pathogen both for wild and captive psittacine birds globally. Genotypic differentiation of BFDV isolates is crucial to establish effective control strategies for the conservation of endangered species and epidemiological investigations of disease outbreaks. The technique developed in this study is a simple, rapid and inexpensive genotyping method for BFDV using PCR and subsequent high-resolution melt (HRM) curve analysis. This was achieved using PCR amplification of the conserved Rep gene in the presence of a fluorescent DNA intercalating dye (SYTO9). HRM curve analysis of the resultant amplicon could readily differentiate between reference strain (92-SR14) and 18 other BFDV isolates used in this study. Analysis of the nucleotide sequences of the amplicon from each isolate revealed that each melt curve profile was related to a unique DNA sequence. The potential of the PCR-HRM curve analysis to differentiate inter-host genetic variation among critically endangered orange-bellied parrots, lorikeets and cockatoos was also evaluated. Phylogenetic tree topology based on partial Rep gene sequences used in this study showed that BFDV Rep gene sequence patterns were correlated with the results of HRM curve analysis. The results presented in this study indicate that this technique could be used in both clinical research and differentiation of BFDV isolates in a fraction of time without further nucleotide sequencing and provides a novel approach for the genetic screening of BFDV in clinical virology laboratories. PMID:25102431

  5. Reliable discrimination of 10 ungulate species using high resolution melting analysis of faecal DNA.

    PubMed

    Ramón-Laca, Ana; Gleeson, Dianne; Yockney, Ivor; Perry, Michael; Nugent, Graham; Forsyth, David M

    2014-01-01

    Identifying species occupying an area is essential for many ecological and conservation studies. Faecal DNA is a potentially powerful method for identifying cryptic mammalian species. In New Zealand, 10 species of ungulate (Order: Artiodactyla) have established wild populations and are managed as pests because of their impacts on native ecosystems. However, identifying the ungulate species present within a management area based on pellet morphology is unreliable. We present a method that enables reliable identification of 10 ungulate species (red deer, sika deer, rusa deer, fallow deer, sambar deer, white-tailed deer, Himalayan tahr, Alpine chamois, feral sheep, and feral goat) from swabs of faecal pellets. A high resolution melting (HRM) assay, targeting a fragment of the 12S rRNA gene, was developed. Species-specific primers were designed and combined in a multiplex PCR resulting in fragments of different length and therefore different melting behaviour for each species. The method was developed using tissue from each of the 10 species, and was validated in blind trials. Our protocol enabled species to be determined for 94% of faecal pellet swabs collected during routine monitoring by the New Zealand Department of Conservation. Our HRM method enables high-throughput and cost-effective species identification from low DNA template samples, and could readily be adapted to discriminate other mammalian species from faecal DNA. PMID:24637802

  6. High-Resolution Melting Curve Analysis for Identification of Pasteurellaceae Species in Experimental Animal Facilities

    PubMed Central

    Miller, Manuel; Zorn, Julia; Brielmeier, Markus

    2015-01-01

    Pasteurellaceae are among the most prevalent bacterial pathogens isolated from mice housed in experimental animal facilities. Reliable detection and differentiation of Pasteurellaceae are essential for high-quality health monitoring. In this study, we combined a real-time PCR assay amplifying a variable region in the 16S rRNA sequence with high-resolution melting curve analysis (HRM) to identify and differentiate among the commonly isolated species Pasteurella pneumotropica biotypes “Jawetz” and “Heyl”, Actinobacillus muris, and Haemophilus influenzaemurium. We used a set of six reference strains for assay development, with the melting profiles of these strains clearly distinguishable due to DNA sequence variations in the amplicon. For evaluation, we used real-time PCR/HRM to test 25 unknown Pasteurellaceae isolates obtained from an external diagnostic laboratory and found the results to be consistent with those of partial 16S rRNA sequencing. The real-time PCR/HRM method provides a sensitive, rapid, and closed-tube approach for Pasteurellaceae species identification for health monitoring of laboratory mice. PMID:26556281

  7. Glacier surface melt characterization and trend analysis (1992-2011) in the Russian High Arctic from combined resolution-enhanced scatterometer and passive microwave data

    NASA Astrophysics Data System (ADS)

    Zhao, M.; Ramage, J. M.; Semmens, K. A.

    2012-12-01

    Global warming has been pronounced in the remote glacierized archipelagoes (Severnaya Zemlya, Novaya Zemlya and Franz Josef Land) of the Russian High Arctic (RHA) and its effect on the low altitude, high latitude small ice caps needs examination. The timing and spatial variability of snow melt onset, duration and intensity are key factors influencing mass balance and the ice marginal hydrological system as well as important indicators of glacial response to anthropogenic and natural forcings. Characterization and trend analysis of RHA glacier melt behaviors provide insight about assessing the mass loss rate under recent Arctic climate change. However, due to the harsh environment, long term records of glaciological data for RHA are limited, necessitating the application of remotely sensed data to accomplish the research. The high sensitivity to liquid water and the ability to penetrate non-precipitating clouds enables microwave remote sensing to detect glacier surface melt. The appearance of melt water in snow dramatically decreases the returned scatterometer radar signal from active microwave sensors and sharply augments passive microwave emission. Based on this feature, we combined resolution-enhanced ERS-1/2 C-band (1992-2000), QuickSCAT Ku-band (2000-2009), ASCAT C-band (2009-2011) scatterometer data and SSMI 37 GHz (1995-2007) vertically polarized passive microwave products from Brigham Young University and analyzed glacier surface melt trends from 1992 to 2011 with a spatial resolution downscaled to 4.45km. We concatenated scatterometer derived melt behaviors by overlapping years and refined the results based on passive microwave data. Cross-validation shows that melt timing to be consistent between the active and passive sensors. Trend analysis (α < 0.005) reveals that the average glacier surface melt onset date occurs earlier by approximately 0.85 days/year in Severnaya Zemlya which outpaced the mean advancing rate in the pan-Arctic. Surrounded by ocean

  8. Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria.

    PubMed

    Daniels, Rachel; Hamilton, Elizabeth J; Durfee, Katelyn; Ndiaye, Daouda; Wirth, Dyann F; Hartl, Daniel L; Volkman, Sarah K

    2015-01-01

    Despite decades of eradication efforts, malaria remains a global burden. Recent renewed interest in regional elimination and global eradication has been accompanied by increased genomic information about Plasmodium parasite species responsible for malaria, including characteristics of geographical populations as well as variations associated with reduced susceptibility to anti-malarial drugs. One common genetic variation, single-nucleotide polymorphisms (SNPs), offers attractive targets for parasite genotyping. These markers are useful not only for tracking drug resistance markers but also for tracking parasite populations using markers not under drug or other selective pressures. SNP genotyping methods offer the ability to track drug resistance as well as to fingerprint individual parasites for population surveillance, particularly in response to malaria control efforts in regions nearing elimination status. While informative SNPs have been identified that are agnostic to specific genotyping technologies, high-resolution melting (HRM) analysis is particularly suited to field-based studies. Compared to standard fluorescent-probe based methods that require individual SNPs in a single labeled probe and offer at best 10% sensitivity to detect SNPs in samples that contain multiple genomes (polygenomic), HRM offers 2-5% sensitivity. Modifications to HRM, such as blocked probes and asymmetric primer concentrations as well as optimization of amplification annealing temperatures to bias PCR towards amplification of the minor allele, further increase the sensitivity of HRM. While the sensitivity improvement depends on the specific assay, we have increased detection sensitivities to less than 1% of the minor allele. In regions approaching malaria eradication, early detection of emerging or imported drug resistance is essential for prompt response. Similarly, the ability to detect polygenomic infections and differentiate imported parasite types from cryptic local reservoirs

  9. Methods to Increase the Sensitivity of High Resolution Melting Single Nucleotide Polymorphism Genotyping in Malaria

    PubMed Central

    Daniels, Rachel; Hamilton, Elizabeth J.; Durfee, Katelyn; Ndiaye, Daouda; Wirth, Dyann F.; Hartl, Daniel L.; Volkman, Sarah K.

    2015-01-01

    Despite decades of eradication efforts, malaria remains a global burden. Recent renewed interest in regional elimination and global eradication has been accompanied by increased genomic information about Plasmodium parasite species responsible for malaria, including characteristics of geographical populations as well as variations associated with reduced susceptibility to anti-malarial drugs. One common genetic variation, single-nucleotide polymorphisms (SNPs), offers attractive targets for parasite genotyping. These markers are useful not only for tracking drug resistance markers but also for tracking parasite populations using markers not under drug or other selective pressures. SNP genotyping methods offer the ability to track drug resistance as well as to fingerprint individual parasites for population surveillance, particularly in response to malaria control efforts in regions nearing elimination status. While informative SNPs have been identified that are agnostic to specific genotyping technologies, high-resolution melting (HRM) analysis is particularly suited to field-based studies. Compared to standard fluorescent-probe based methods that require individual SNPs in a single labeled probe and offer at best 10% sensitivity to detect SNPs in samples that contain multiple genomes (polygenomic), HRM offers 2-5% sensitivity. Modifications to HRM, such as blocked probes and asymmetric primer concentrations as well as optimization of amplification annealing temperatures to bias PCR towards amplification of the minor allele, further increase the sensitivity of HRM. While the sensitivity improvement depends on the specific assay, we have increased detection sensitivities to less than 1% of the minor allele. In regions approaching malaria eradication, early detection of emerging or imported drug resistance is essential for prompt response. Similarly, the ability to detect polygenomic infections and differentiate imported parasite types from cryptic local reservoirs

  10. Performance and applications of quench melt-growth bulk magnets

    NASA Astrophysics Data System (ADS)

    Nariki, S.; Teshima, H.; Morita, M.

    2016-03-01

    This paper describes the progress in quench melt-growth (QMG) bulk magnets, developed by the Nippon Steel & Sumitomo Metal Corporation, which consist of single crystalline RE123 phase and finely dispersed RE211 particles. QMG bulks can trap high magnetic fields. The field-trapping ability of QMG bulks is largely increased with an improvement in its J c and size, promising the realization of various applications such as flywheel energy-storage systems, ship motors, NMR/MRI spectrometers, wind-power generators and so on. Intensive research has revealed that the optimal RE element is different depending on application requirements. Gd-QMG bulk is the most promising material for several high-field engineering applications. The trapped magnetic field of Gd-QMG bulk 60 mm in diameter at 77 K is twice as large as that of Y-QMG bulk with a similar size due to its excellent J c properties. The large Gd-based QMG bulks up to 150 mm in diameter are fabricated by incorporating the RE compositional gradient method. Compact NMR/MRI spectrometers are one of the promising applications of bulk superconductors. Eu-QMG bulks are suitable for NMR magnets. NMR applications require extremely homogeneous magnetic fields. In the Eu-system, the small paramagnetic moment of a Eu ion compared to a Gd ion improves the field homogeneity in the bulk. For the application of current leads, Dy-based QMG is available by utilizing a low thermal conductivity.

  11. A Rapid Multiplex Real-Time PCR High-Resolution Melt Curve Assay for the Simultaneous Detection of Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus in Food.

    PubMed

    Forghani, Fereidoun; Wei, Shuai; Oh, Deog-Hwan

    2016-05-01

    Three important foodborne pathogens, Bacillus cereus, Listeria monocytogenes, and Staphylococcus aureus, are of great concern for food safety. They may also coexist in food matrices and, in the case of B. cereus and S. aureus, the resulting illnesses can resemble each other owing to similar symptoms. Therefore, their simultaneous detection may have advantages in terms of cost savings and rapidity. Given this context, a rapid multiplex real-time PCR high-resolution melt curve assay for the simultaneous detection of these three pathogens in food was developed. The assay successfully detected B. cereus (gyrB), L. monocytogenes (hly), and S. aureus (nuc) in a single reaction, and the average melting temperatures were 76.23, 80.19, and 74.01°C, respectively. The application of SYTO9 dye and a slow melt curve analysis ramp rate (0.1°C/s) enabled the production of sharp, high-resolution melt curve peaks that were easily distinguishable from each other. The detection limit in food (milk, rice, and lettuce) was 3.7 × 10(3) CFU/g without an enrichment step and 3.7 × 10(1) CFU/g following the 10-h enrichment. Hence, the assay developed here is specific and sensitive, providing an efficient tool for implementation in food for the simultaneous detection of B. cereus, L. monocytogenes, and S. aureus . PMID:27296430

  12. Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species

    PubMed Central

    Osathanunkul, Maslin; Suwannapoom, Chatmongkon; Ounjai, Sarawut; Rora, Jantarika A.; Madesis, Panagiotis; de Boer, Hugo

    2015-01-01

    DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Croton (Euphorbiaceae), one of the largest genera of plants with over 1,200 species. Seven primer pairs were evaluated (matK, rbcL1, rbcL2, rbcL3, rpoC, trnL and ITS1) from four plastid regions, matK, rbcL, rpoC, and trnL, and the nuclear ribosomal marker ITS1. The primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL1 primer pair gave the lowest resolution. It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Our Bar-HRM results here also provide further support for the hypothesis that both sequence and base composition affect DNA duplex stability. PMID:26406615

  13. Rapid Detection and Identification of Human Hookworm Infections through High Resolution Melting (HRM) Analysis

    PubMed Central

    Ngui, Romano; Lim, Yvonne A. L.; Chua, Kek Heng

    2012-01-01

    Background Hookworm infections are still endemic in low and middle income tropical countries with greater impact on the socioeconomic and public health of the bottom billion of the world's poorest people. In this study, a real-time polymerase chain reaction (PCR) coupled with high resolution melting-curve (HRM) analysis was evaluated for an accurate, rapid and sensitive tool for species identification focusing on the five human hookworm species. Methods Real-time PCR coupled with HRM analysis targeting the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA as the genetic marker was used to identify and distinguish hookworm species in human samples. Unique and distinct characteristics of HRM patterns were produced for each of the five hookworm species. The melting curves were characterized by peaks of 79.24±0.05°C and 83.00±0.04°C for Necator americanus, 79.12±0.10°C for Ancylostoma duodenale, 79.40±0.10°C for Ancylostoma ceylanicum, 79.63±0.05°C for Ancylostoma caninum and 79.70±0.14°C for Ancylostoma braziliense. An evaluation of the method's sensitivity and specificity revealed that this assay was able to detect as low as 0.01 ng/µl hookworm DNA and amplification was only recorded for hookworm positive samples. Conclusion The HRM assay developed in this study is a rapid and straightforward method for the diagnosis, identification and discrimination of five human hookworms. This assay is simple compared to other probe-based genotyping methods as it does not require multiplexing, DNA sequencing or post-PCR processing. Therefore, this method offers a new alternative for rapid detection of human hookworm species. PMID:22844538

  14. Rapid Diagnosis of Old World Leishmaniasis by High-Resolution Melting Analysis of the 7SL RNA Gene▿ †

    PubMed Central

    Nasereddin, Abedelmajeed; Jaffe, Charles L.

    2010-01-01

    High-resolution melt analysis PCR (HRM PCR) for diagnosis of Old World Leishmania was developed using the 7SL RNA gene. Cutaneous leishmaniasis samples were analyzed. Sensitivity and specificity of HRM PCR were significantly better (P < 0.001) than those of internal transcribed spacer 1 PCR and similar to those of kinetoplast DNA PCR. PMID:20392923

  15. A PCR–High-Resolution Melt Assay for Rapid Differentiation of Nontypeable Haemophilus influenzae and Haemophilus haemolyticus

    PubMed Central

    Binks, Michael J.; Beissbarth, Jemima; Hare, Kim M.; Kirkham, Lea-Ann S.; Smith-Vaughan, Heidi

    2014-01-01

    We have developed a PCR–high-resolution melt (PCR-HRM) assay to discriminate nontypeable Haemophilus influenzae (NTHi) colonies from Haemophilus haemolyticus. This method is rapid and robust, with 96% sensitivity and 92% specificity compared to the hpd#3 assay. PCR-HRM is ideal for high-throughput screening for NTHi surveillance and clinical trials. PMID:24478508

  16. Silicate-melt inclusions in magmatic rocks: applications to petrology

    NASA Astrophysics Data System (ADS)

    Frezzotti, Maria-Luce

    2001-01-01

    Silicate-melt inclusions in igneous rocks provide important information on the composition and evolution of magmatic systems. Such inclusions represent accidentally trapped silicate melt (±immiscible H 2O and/or CO 2 fluids) that allow one to follow the evolution of magmas through snapshots, corresponding to specific evolution steps. This information is available on condition that they remained isolated from the enclosing magma after their entrapment. The following steps of investigation are discussed: (a) detailed petrographic studies to characterise silicate-melt inclusion primary characters and posttrapping evolution, including melt crystallisation; (b) high temperature studies to rehomogenise the inclusion content and select chemically representative inclusions: chemical compositions should be compared to relevant phase diagrams. Silicate-melt inclusion studies allow us to concentrate on specific topics; inclusion studies in early crystallising phases allow the characterisation of primary magmas, while in more differentiated rocks, they unravel the subsequent chemical evolution. The distribution of volatile species (i.e., H 2O, CO 2, S, Cl) in inclusion glass can provide information on the degassing processes and on recycling of subducted material. In intrusive rocks, silicate melt inclusions may preserve direct evidence of magmatic stage evolution (e.g., immiscibility phenomena). Melt inclusions in mantle xenoliths indicate that high-silica melts can coexist with mantle peridotites and give information on the presence of carbonate melt within the upper mantle. Thus, combining silicate-melt inclusion data with conventional petrological and geochemical information and experimental petrology can increase our ability to model magmatic processes.

  17. Applications of nonequilibrium melting concept to damage-accumulation processes

    SciTech Connect

    Lam, N.Q.; Okamoto, P.R.

    1998-01-01

    The authors recent study of crystalline-to-amorphous transformation led to the successful development of a unified thermodynamic description of disorder-induced amorphization and heat-induced melting, based on a generalized version of the Lindemann melting criterion. The generalized criterion requires that the melting temperature of a defective crystal decreases with increasing static atomic disorder. Hence, any crystal can melt at temperatures below the melting point of its perfect crystalline state when driven far from equilibrium by introducing critical amounts of misfitting solute atoms and lattice imperfections, radiation damage, and/or tensile stresses. This conceptual approach to nonequilibrium melting provides new insight into long-standing materials problems such as brittle fracture, embrittlement, and environmentally-induced cracking, for example irradiation-assisted stress corrosion cracking.

  18. [Molecular identification of hairy antler by analysis of high resolution melting].

    PubMed

    Chen, Kang; Jiang, Chao; Yuan, Yuan; Huang, Lu-qi; Jin, Yan

    2015-02-01

    High resolution melting (HRM) , an important technology for genotyping and mutation scanning, has broad prospects in the authenticity of traditional Chinese medicine. This paper selected universal CO I primers and used HRM to establish a new method for authenticity of Hairy Antler. PCR was conducted at the annealing temperature of 60 °C and 45 cycles. The range of the DNA template concentration, the primer concentration and the Mg2+ ion concentration were further optimized. The results showed that the Tm values of Cervus nippon were (81.96 ± 0.07), (84.51 ± 0.03) °C and Cervus elaphus was(82.58 ± 0.13), (85.95 ± 0.05) °C with 10-100 mg · L(-1) DNA template, 0.2 µLmol · L(-1) primer, 2.0 mmol · L(-1) Mg2+. This method can authenticate of hairy antler and is simple, fast, high-throughput, visualization. PMID:26137679

  19. Identification of Uvaria sp by barcoding coupled with high-resolution melting analysis (Bar-HRM).

    PubMed

    Osathanunkul, M; Madesis, P; Ounjai, S; Pumiputavon, K; Somboonchai, R; Lithanatudom, P; Chaowasku, T; Wipasa, J; Suwannapoom, C

    2016-01-01

    DNA barcoding, which was developed about a decade ago, relies on short, standardized regions of the genome to identify plant and animal species. This method can be used to not only identify known species but also to discover novel ones. Numerous sequences are stored in online databases worldwide. One of the ways to save cost and time (by omitting the sequencing step) in species identification is to use available barcode data to design optimized primers for further analysis, such as high-resolution melting analysis (HRM). This study aimed to determine the effectiveness of the hybrid method Bar-HRM (DNA barcoding combined with HRM) to identify species that share similar external morphological features, rather than conduct traditional taxonomic identification that require major parts (leaf, flower, fruit) of the specimens. The specimens used for testing were those, which could not be identified at the species level and could either be Uvaria longipes or Uvaria wrayias, indicated by morphological identification. Primer pairs derived from chloroplast regions (matK, psbA-trnH, rbcL, and trnL) were used in the Bar-HRM. The results obtained from psbA-trnH primers were good enough to help in identifying the specimen while the rest were not. Bar-HRM analysis was proven to be a fast and cost-effective method for plant species identification. PMID:26909907

  20. Development of High Resolution Melting Analysis for the Diagnosis of Human Malaria

    PubMed Central

    Chua, Kek Heng; Lim, Siew Chee; Ng, Ching Ching; Lee, Ping Chin; Lim, Yvonne Ai Lian; Lau, Tze Pheng; Chai, Hwa Chia

    2015-01-01

    Molecular detection has overcome limitations of microscopic examination by providing greater sensitivity and specificity in Plasmodium species detection. The objective of the present study was to develop a quantitative real-time polymerase chain reaction coupled with high-resolution melting (qRT-PCR-HRM) assay for rapid, accurate and simultaneous detection of all five human Plasmodium spp. A pair of primers targeted the 18S SSU rRNA gene of the Plasmodium spp. was designed for qRT-PCR-HRM assay development. Analytical sensitivity and specificity of the assay were evaluated. Samples collected from 229 malaria suspected patients recruited from Sabah, Malaysia were screened using the assay and results were compared with data obtained using PlasmoNexTM, a hexaplex PCR system. The qRT-PCR-HRM assay was able to detect and discriminate the five Plasmodium spp. with lowest detection limits of 1–100 copy numbers without nonspecific amplifications. The detection of Plasmodium spp. in clinical samples using this assay also achieved 100% concordance with that obtained using PlasmoNexTM. This indicated that the diagnostic sensitivity and specificity of this assay in Plasmodium spp. detection is comparable with those of PlasmoNexTM. The qRT-PCR-HRM assay is simple, produces results in two hours and enables high-throughput screening. Thus, it is an alternative method for rapid and accurate malaria diagnosis. PMID:26507008

  1. High resolution melting: improvements in the genetic diagnosis of hypertrophic cardiomyopathy in a Portuguese cohort

    PubMed Central

    2012-01-01

    Background Hypertrophic Cardiomyopathy (HCM) is a complex myocardial disorder with a recognized genetic heterogeneity. The elevated number of genes and mutations involved in HCM limits a gene-based diagnosis that should be considered of most importance for basic research and clinical medicine. Methodology In this report, we evaluated High Resolution Melting (HRM) robustness, regarding HCM genetic testing, by means of analyzing 28 HCM-associated genes, including the most frequent 4 HCM-associated sarcomere genes, as well as 24 genes with lower reported HCM-phenotype association. We analyzed 80 Portuguese individuals with clinical phenotype of HCM allowing simultaneously a better characterization of this disease in the Portuguese population. Results HRM technology allowed us to identify 60 mutated alleles in 72 HCM patients: 49 missense mutations, 3 nonsense mutations, one 1-bp deletion, one 5-bp deletion, one in frame 3-bp deletion, one insertion/deletion, 3 splice mutations, one 5'UTR mutation in MYH7, MYBPC3, TNNT2, TNNI3, CSRP3, MYH6 and MYL2 genes. Significantly 22 are novel gene mutations. Conclusions HRM was proven to be a technique with high sensitivity and a low false positive ratio allowing a rapid, innovative and low cost genotyping of HCM. In a short return, HRM as a gene scanning technique could be a cost-effective gene-based diagnosis for an accurate HCM genetic diagnosis and hopefully providing new insights into genotype/phenotype correlations. PMID:22429680

  2. High Resolution Melting Analysis for JAK2 Exon 14 and Exon 12 Mutations

    PubMed Central

    Rapado, Inmaculada; Grande, Silvia; Albizua, Enriqueta; Ayala, Rosa; Hernández, José-Angel; Gallardo, Miguel; Gilsanz, Florinda; Martinez-Lopez, Joaquin

    2009-01-01

    JAK2 mutations are important criteria for the diagnosis of Philadelphia chromosome-negative myeloproliferative neoplasms. We aimed to assess JAK2 exon 14 and exon 12 mutations by high-resolution melting (HRM) analysis, which allows variation screening. The exon 14 analysis included 163 patients with polycythemia vera, secondary erythrocytoses, essential thrombocythemia, or secondary thrombocytoses, and 126 healthy subjects. The study of exon 12 included 40 JAK2 V617F-negative patients (nine of which had polycythemia vera, and 31 with splanchnic vein thrombosis) and 30 healthy subjects. HRM analyses of JAK2 exons 14 and 12 gave analytical sensitivities near 1% and both intra- and interday coefficients of variation of less than 1%. For HRM analysis of JAK2 exon 14 in polycythemia vera and essential thrombocythemia, clinical sensitivities were 93.5% and 67.9%, clinical specificities were 98.8% and 97.0%, positive predictive values were 93.5% and 79.2%, and negative predictive values were 98.8% and 94.6, respectively. Correlations were observed between the results from HRM and three commonly used analytical methods. The JAK2 exon 12 HRM results agreed completely with those from sequencing analysis, and the three mutations in exon 12 were detected by both methods. Hence, HRM analysis of exons 14 and 12 in JAK2 shows better diagnostic values than three other routinely used methods against which it was compared. In addition, HRM analysis has the advantage of detecting unknown mutations. PMID:19225136

  3. High-resolution melting system to perform multilocus sequence typing of Campylobacter jejuni.

    PubMed

    Lévesque, Simon; Michaud, Sophie; Arbeit, Robert D; Frost, Eric H

    2011-01-01

    Multi-locus sequence typing (MLST) has emerged as the state-of-the-art method for resolving bacterial population genetics but it is expensive and time consuming. We evaluated the potential of high resolution melting (HRM) to identify known MLST alleles of Campylobacter jejuni at reduced cost and time. Each MLST locus was amplified in two or three sub fragments, which were analyzed by HRM. The approach was investigated using 47 C. jejuni isolates, previously characterized by classical MLST, representing isolates from diverse environmental, animal and clinical sources and including the six most prevalent sequence types (ST) and the most frequent alleles. HRM was then applied to a validation set of 84 additional C. jejuni isolates from chickens; 92% of the alleles were resolved in 35 hours of laboratory time and the cost of reagents per isolate was $20 compared with $100 for sequence-based typing. HRM has the potential to complement sequence-based methods for resolving SNPs and to facilitate a wide range of genotyping studies. PMID:21297862

  4. Development of High Resolution Melting Analysis for the Diagnosis of Human Malaria.

    PubMed

    Chua, Kek Heng; Lim, Siew Chee; Ng, Ching Ching; Lee, Ping Chin; Lim, Yvonne Ai Lian; Lau, Tze Pheng; Chai, Hwa Chia

    2015-01-01

    Molecular detection has overcome limitations of microscopic examination by providing greater sensitivity and specificity in Plasmodium species detection. The objective of the present study was to develop a quantitative real-time polymerase chain reaction coupled with high-resolution melting (qRT-PCR-HRM) assay for rapid, accurate and simultaneous detection of all five human Plasmodium spp. A pair of primers targeted the 18S SSU rRNA gene of the Plasmodium spp. was designed for qRT-PCR-HRM assay development. Analytical sensitivity and specificity of the assay were evaluated. Samples collected from 229 malaria suspected patients recruited from Sabah, Malaysia were screened using the assay and results were compared with data obtained using PlasmoNex(TM), a hexaplex PCR system. The qRT-PCR-HRM assay was able to detect and discriminate the five Plasmodium spp. with lowest detection limits of 1-100 copy numbers without nonspecific amplifications. The detection of Plasmodium spp. in clinical samples using this assay also achieved 100% concordance with that obtained using PlasmoNex(TM). This indicated that the diagnostic sensitivity and specificity of this assay in Plasmodium spp. detection is comparable with those of PlasmoNex(TM). The qRT-PCR-HRM assay is simple, produces results in two hours and enables high-throughput screening. Thus, it is an alternative method for rapid and accurate malaria diagnosis. PMID:26507008

  5. Hot-melt extrusion technology and pharmaceutical application.

    PubMed

    Wilson, Matthew; Williams, Marcia A; Jones, David S; Andrews, Gavin P

    2012-06-01

    The use of hot-melt extrusion (HME) within the pharmaceutical industry is steadily increasing, due to its proven ability to efficiently manufacture novel products. The process has been utilized readily in the plastics industry for over a century and has been used to manufacture medical devices for several decades. The development of novel drugs with poor solubility and bioavailability brought the application of HME into the realm of drug-delivery systems. This has specifically been shown in the development of drug-delivery systems of both solid dosage forms and transdermal patches. HME involves the application of heat, pressure and agitation through an extrusion channel to mix materials together, and subsequently forcing them out through a die. Twin-screw extruders are most popular in solid dosage form development as it imparts both dispersive and distributive mixing. It blends materials while also imparting high shear to break-up particles and disperse them. HME extrusion has been shown to molecularly disperse poorly soluble drugs in a polymer carrier, increasing dissolution rates and bioavailability. The most common difficulty encountered in producing such dispersions is stabilization of amorphous drugs, which prevents them from recrystallization during storage. Pharmaceutical industrial suppliers, of both materials and equipment, have increased their development of equipment and chemicals for specific use with HME. Clearly, HME has been identified as an important and significant process to further enhance drug solubility and solid-dispersion production. PMID:22838073

  6. Development of a fast, simple profiling method for sample screening using high resolution melting (HRM) of STRs.

    PubMed

    Nicklas, Janice A; Noreault-Conti, Trisha; Buel, Eric

    2012-03-01

    A screening assay has been developed to provide preliminary individualization of crime scene samples thus eliminating expensive, time-consuming short tandem repeat (STR) profiling of nonprobative samples. High resolution melting performed in a real-time PCR instrument is used to detect the slight melting differences between the length and sequence variations of 22 forensic STRs. Three STRs (vWA, D18S51, THO1) were chosen to develop an assay which was optimized for Mg++ concentration, annealing/extension time/temperature, assay volume, and bovine serum albumin addition. The assay was tested for reproducibility, uniformity for genotype, melting profile consistency, effects of inhibitors, and mixture effects. The assay could be used to determine DNA concentration when a standard curve is run simultaneously. Calculations of costs show that the assay can save significant time and money for a crime with many samples or suspects. PMID:22150300

  7. Rapid detection of HLA-B*51 by real-time polymerase chain reaction and high-resolution melting analysis.

    PubMed

    Imperiali, C; Alía-Ramos, P; Padró-Miquel, A

    2015-08-01

    HLA-B*51, a class I human leukocyte antigen (HLA) molecule, is the strongest known genetic risk factor for Behçet disease. However, there are only few articles reporting methods to determine the presence or absence of HLA-B51. For this reason, we designed and developed an easy, fast, and inexpensive real-time high-resolution melting (HRM) assay to detect HLA-B*51. We genotyped 61 samples by our HRM assay and by conventional polymerase chain reaction, and no discrepancies were found between results. Besides, a subgroup of 25 samples was also genotyped in a different laboratory, and another subgroup of 16 samples was obtained from the International Histocompatibility Working Group DNA Bank, and a full concordance of results was observed with those obtained by HRM. Regarding the identifying system evaluated, we obtained 100% of specificity, sensibility, and repeatability, and 0% of false positive and false negative rates. Therefore, this HRM analysis is easily applicable to the rapid detection of HLA-B*51, exhibits a high speed, and requires a very low budget. PMID:26176813

  8. A novel method for the rapid and prospective identification of Beijing Mycobacterium tuberculosis strains by high-resolution melting analysis.

    PubMed

    Alonso, M; Navarro, Y; Barletta, F; Martínez Lirola, M; Gotuzzo, E; Bouza, E; García de Viedma, D

    2011-03-01

    Genotypic analysis of Mycobacterium tuberculosis (MTB) has enabled the definition of several lineages. The Beijing family, which is considered highly virulent and transmissible, has been associated with resistance in certain settings and involved in severe outbreaks, making it one of the most closely-monitored lineages. Therefore, rapid prospective identification of Beijing MTB strains could be relevant. In the present study, we evaluate a real-time PCR followed by high-resolution melting (HRM) based on the identification of a single nucleotide polymorphism (SNP) in the Rv2629 gene which defines Beijing lineage (A191C for Beijing genotype and A191A for non-Beijing genotype). This combined methodology efficiently differentiated Beijing and non-Beijing strains in 100% of the isolates from a collection of reference strains without requiring specific DNA probes. Additionally, HRM was able to assign a Beijing/non-Beijing genotype in 90.9% of the respiratory specimens assayed. Its applicability was tested on a Peruvian sample of circulating MTB strains, in which it identified 10.7% as belonging to the Beijing genotype; this proportion reached 20% in the North Lima area. HRM analysis of the A191C SNP is a rapid, reliable, and sensitive method for the efficient prospective survey of high-risk Beijing MTB strains, even in developing settings where MTB culture is often not available. PMID:20384709

  9. Quantitative high-resolution melting PCR analysis for monitoring of fermentation microbiota in sourdough.

    PubMed

    Lin, Xiaoxi B; Gänzle, Michael G

    2014-09-01

    Current methods of monitoring the microbial ecology of food fermentation system are generally labor intensive and/or time consuming. This study developed two methods based on high-resolution melting curves (HRM) to monitor sourdough microbiota during fermentation and to investigate the effect of cereal substrate on microbial ecology. A strain cocktail of Lactobacillus fermentum FUA3165, Lactobacillus plantarum FUA3309, Lactobacillus paracasei FUA3166 and Lactobacillus reuteri FUA3168 was used to ferment red (Town and PAN8609) and white (commercial and Segaolane) sorghum sourdough, and wheat sourdough. The microbial composition of sourdoughs was determined by plate count and HRM-qPCR to differentiate at the species level. The resistance of each species to sorghum phenolic extract was measured. There was no difference in microbial composition among the four sorghum sourdoughs, with L. fermentum FUA3165 in all sourdoughs. The competiveness of the strains in sorghum sourdoughs corresponded to their resistance to sorghum phenolic extract. In a second experiment, five L. reuteri strains, the human-lineage strains FUA3400 and 3401 isolated from wheat sourdough, the rodent-lineage strain FUA5448 isolated from rye sourdough and the sorghum isolates FUA3168 and 3324, were used to ferment wheat, rye and sorghum sourdoughs. The microbial composition of sourdoughs was determined by plate counts and HRM-qPCR to different L. reuteri strains representing different host-adapted lineages. No difference among different substrates was observed; indicating cereal type had no selective effect on sourdough microbial ecology. In conclusion, HRM-qPCR assays were established as rapid and highly specific tool for monitoring of sourdough microbiota. The ability to distinguish highly similar microbes in samples containing only few genotypes makes HRM-qPCR suitable for quality control in other food fermentation systems. The presence of phenolic compounds in sorghum sourdough favored organisms

  10. Detection of a G>C single nucleotide polymorphism within a repetitive DNA sequence by high-resolution DNA melting.

    PubMed

    Schmidt, Ulrike; Hulkkonen, Johannes; Naue, Jana

    2016-09-01

    In standard forensic DNA analysis, single base mutations within short tandem repeats (STR) mostly escape detection. In this study, high-resolution DNA melting (HRM) is compared to minisequencing and Sanger sequencing as to determine the most suitable method for detection of a G to C mutation within a repetitive DNA sequence, the STR system DXS10161. It shows an ATG/ATC polymorphism surrounded by a variable number of (TATC) and (ATCT) motifs. Neutral base changes like G:C to C:G result in very low differences in the melting temperature (T m) of the PCR amplicons. By enhanced resolution of fluorescence vs. temperature in HRM, the technique showed to be suitable for detecting a G to C transversion in this repetitive DNA sequence context. Compared to minisequencing, HRM is more time- and cost-effective. Results were confirmed by Sanger sequencing. PMID:26972692

  11. A Melting Layer Model for Passive/Active Microwave Remote Sensing Applications. Part 1; Model Formulation and Comparison with Observations

    NASA Technical Reports Server (NTRS)

    Olson, William S.; Bauer, Peter; Viltard, Nicolas F.; Johnson, Daniel E.; Tao, Wei-Kuo

    2000-01-01

    In this study, a 1-D steady-state microphysical model which describes the vertical distribution of melting precipitation particles is developed. The model is driven by the ice-phase precipitation distributions just above the freezing level at applicable gridpoints of "parent" 3-D cloud-resolving model (CRM) simulations. It extends these simulations by providing the number density and meltwater fraction of each particle in finely separated size categories through the melting layer. The depth of the modeled melting layer is primarily determined by the initial material density of the ice-phase precipitation. The radiative properties of melting precipitation at microwave frequencies are calculated based upon different methods for describing the dielectric properties of mixed phase particles. Particle absorption and scattering efficiencies at the Tropical Rainfall Measuring Mission Microwave Imager frequencies (10.65 to 85.5 GHz) are enhanced greatly for relatively small (approx. 0.1) meltwater fractions. The relatively large number of partially-melted particles just below the freezing level in stratiform regions leads to significant microwave absorption, well-exceeding the absorption by rain at the base of the melting layer. Calculated precipitation backscatter efficiencies at the Precipitation Radar frequency (13.8 GHz) increase in proportion to the particle meltwater fraction, leading to a "bright-band" of enhanced radar reflectivities in agreement with previous studies. The radiative properties of the melting layer are determined by the choice of dielectric models and the initial water contents and material densities of the "seeding" ice-phase precipitation particles. Simulated melting layer profiles based upon snow described by the Fabry-Szyrmer core-shell dielectric model and graupel described by the Maxwell-Garnett water matrix dielectric model lead to reasonable agreement with radar-derived melting layer optical depth distributions. Moreover, control profiles

  12. A Melting Layer Model for Passive/Active Microwave Remote Sensing Applications. Part 2; Simulation of TRMM Observations

    NASA Technical Reports Server (NTRS)

    Olson, William S.; Bauer, Peter; Kummerow, Christian D.; Tao, Wei-Kuo

    2000-01-01

    The one-dimensional, steady-state melting layer model developed in Part I of this study is used to calculate both the microphysical and radiative properties of melting precipitation, based upon the computed concentrations of snow and graupel just above the freezing level at applicable horizontal gridpoints of 3-dimensional cloud resolving model simulations. The modified 3-dimensional distributions of precipitation properties serve as input to radiative transfer calculations of upwelling radiances and radar extinction/reflectivities at the TRMM Microwave Imager (TMI) and Precipitation Radar (PR) frequencies, respectively. At the resolution of the cloud resolving model grids (approx. 1 km), upwelling radiances generally increase if mixed-phase precipitation is included in the model atmosphere. The magnitude of the increase depends upon the optical thickness of the cloud and precipitation, as well as the scattering characteristics of ice-phase precipitation aloft. Over the set of cloud resolving model simulations utilized in this study, maximum radiance increases of 43, 28, 18, and 10 K are simulated at 10.65, 19.35 GHz, 37.0, and 85.5 GHz, respectively. The impact of melting on TMI-measured radiances is determined not only by the physics of the melting particles but also by the horizontal extent of the melting precipitation, since the lower-frequency channels have footprints that extend over 10''s of kilometers. At TMI resolution, the maximum radiance increases are 16, 15, 12, and 9 K at the same frequencies. Simulated PR extinction and reflectivities in the melting layer can increase dramatically if mixed-phase precipitation is included, a result consistent with previous studies. Maximum increases of 0.46 (-2 dB) in extinction optical depth and 5 dBZ in reflectivity are simulated based upon the set of cloud resolving model simulations.

  13. Co-evolution of tidewater glacier calving front morphology and submarine melt rates in a high resolution ocean model

    NASA Astrophysics Data System (ADS)

    Slater, D. A.; Nienow, P. W.; Goldberg, D. N.; Cowton, T. R.; Sole, A. J.

    2015-12-01

    Rapid dynamic changes at the margins of the Greenland Ice Sheet, synchronous with ocean warming, have raised concern that tidewater glaciers can respond rapidly and sensitively to ocean forcing. One way in which ocean forcing would manifest is through the melting of the submerged parts of tidewater glacier calving fronts, with the spatial distribution of submarine melt a control on their morphology. Calving front morphology has thus far received little attention and yet has the potential to significantly impact calving rates and therefore tidewater glacier dynamics. Here we present a model which allows us to study the evolution of calving front morphology in two dimensions. We outline a new routine for calculating submarine melt rates from ocean models at calving fronts of arbitrary geometry, and for adjusting this geometry according to the calculated melt rates. This routine is applied to a high resolution (~1m) non-hydrostatic ocean model (MITgcm) with a glacier boundary (calving front) which evolves in time according to the simulated submarine melt rates. The model shows, consistent with recent observations, that submarine melting leads to undercutting of tidewater glacier calving fronts. We examine how undercut magnitude, undercut depth and potential steady states respond to variation in subglacial discharge, ice velocity, and fjord depth, temperature and stratification. In addition to this analysis we use a diagnostic full-Stokes flow-line ice model to examine how these geometries affect ice internal stress and potential for calving. In undertaking this work we aim to elucidate a process which - supposing tidewater glaciers are sensitive to ocean forcing - must provide a fundamental link between the ocean and the ice.

  14. Development of a high-resolution melting method for the screening of TNFAIP3 gene mutations.

    PubMed

    Chang, Yuli Christine; Chang, Ya-Sian; Chang, Chun-Chi; Liu, Ta-Chih; Ko, Ying-Chin; Lee, Chien-Chin; Chang, Shun-Jen; Chang, Jan-Gowth

    2016-05-01

    Tumor necrosis factor, α-induced protein 3 (TNFAIP3) which encodes a ubiquitin-modifying enzyme (A20), acts as a negative regulator of the NF-κB pathway, and in lymphoma and autoimmune diseases it is frequently inactivated by mutations and/or deletions. We investigated the prevalence of the inactivation of TNFAIP3 in oral squamous cell carcinoma (OSCC). DNA was extracted from 81 cases of OSCC and 50 peripheral blood samples from normal controls. A high-resolution melting (HRM) analysis was used to characterize TNFAIP3 mutations, and the results were confirmed by direct DNA sequencing. Three mutations and three single-nucleotide polymorphisms (SNPs) were found to be associated with OSCC; the TNFAIP3 mutation occurred in 3.7% (3/81) of the OSCC cases examined. All mutations were in exon 7 [c.1081G>A (p.E361K), c.1398C>G (p.S466R) (rs200878487) and c.1760C>T (p.P587L) (rs150056192)], and p.E361K was identified as a novel mutation. We further used SIFT and PolyPhen-2 software to assess potentially functional mutations. Two SNPs, c.296‑20_296-18delCTC (rs71670547) and c.380T>G (p.F127C) (rs2230926), were located in exon 3, and c.2140C>T (p.P714S) was located in exon 9. A novel SNP, p.P714S differed from the one reported previously (p.P714A) (rs369155845) at that site. We also identified five SNPs in 50 normal Taiwanese individuals, and two of them [c.296‑15C>T (rs377482653) and c.305A>G (p.N102S) (rs146534657)] were not found in our OSCC tissue. HRM facilitated the screening of genetic changes. In addition, our results indicate that the prevalence of the TNFAIP3 mutation is low in OSCC. PMID:26986245

  15. Refining lunar impact chronology through high spatial resolution (40)Ar/(39)Ar dating of impact melts.

    PubMed

    Mercer, Cameron M; Young, Kelsey E; Weirich, John R; Hodges, Kip V; Jolliff, Bradley L; Wartho, Jo-Anne; van Soest, Matthijs C

    2015-02-01

    Quantitative constraints on the ages of melt-forming impact events on the Moon are based primarily on isotope geochronology of returned samples. However, interpreting the results of such studies can often be difficult because the provenance region of any sample returned from the lunar surface may have experienced multiple impact events over the course of billions of years of bombardment. We illustrate this problem with new laser microprobe (40)Ar/(39)Ar data for two Apollo 17 impact melt breccias. Whereas one sample yields a straightforward result, indicating a single melt-forming event at ca. 3.83 Ga, data from the other sample document multiple impact melt-forming events between ca. 3.81 Ga and at least as young as ca. 3.27 Ga. Notably, published zircon U/Pb data indicate the existence of even older melt products in the same sample. The revelation of multiple impact events through (40)Ar/(39)Ar geochronology is likely not to have been possible using standard incremental heating methods alone, demonstrating the complementarity of the laser microprobe technique. Evidence for 3.83 Ga to 3.81 Ga melt components in these samples reinforces emerging interpretations that Apollo 17 impact breccia samples include a significant component of ejecta from the Imbrium basin impact. Collectively, our results underscore the need to quantitatively resolve the ages of different melt generations from multiple samples to improve our current understanding of the lunar impact record, and to establish the absolute ages of important impact structures encountered during future exploration missions in the inner Solar System. PMID:26601128

  16. High-Resolution Melting Analysis as a Powerful Tool to Discriminate and Genotype Pseudomonas savastanoi Pathovars and Strains

    PubMed Central

    Gori, Andrea; Cerboneschi, Matteo; Tegli, Stefania

    2012-01-01

    Pseudomonas savastanoi is a serious pathogen of Olive, Oleander, Ash, and several other Oleaceae. Its epiphytic or endophytic presence in asymptomatic plants is crucial for the spread of Olive and Oleander knot disease, as already ascertained for P. savastanoi pv. savastanoi (Psv) on Olive and for pv. nerii (Psn) on Oleander, while no information is available for pv. fraxini (Psf) on Ash. Nothing is known yet about the distribution on the different host plants and the real host range of these pathovars in nature, although cross-infections were observed following artificial inoculations. A multiplex Real-Time PCR assay was recently developed to simultaneously and quantitatively discriminate in vitro and in planta these P. savastanoi pathovars, for routine culture confirmation and for epidemiological and diagnostical studies. Here an innovative High-Resolution Melting Analysis (HRMA)-based assay was set up to unequivocally discriminate Psv, Psn and Psf, according to several single nucleotide polymorphisms found in their Type Three Secretion System clusters. The genetic distances among 56 P. savastanoi strains belonging to these pathovars were also evaluated, confirming and refining data previously obtained by fAFLP. To our knowledge, this is the first time that HRMA is applied to a bacterial plant pathogen, and one of the few multiplex HRMA-based assays developed so far. This protocol provides a rapid, sensitive, specific tool to differentiate and detect Psv, Psn and Psf strains, also in vivo and against other related bacteria, with lower costs than conventional multiplex Real-Time PCR. Its application is particularly suitable for sanitary certification programs for P. savastanoi, aimed at avoiding the spreading of this phytopathogen through asymptomatic plants. PMID:22295075

  17. Refining lunar impact chronology through high spatial resolution 40Ar/39Ar dating of impact melts

    PubMed Central

    Mercer, Cameron M.; Young, Kelsey E.; Weirich, John R.; Hodges, Kip V.; Jolliff, Bradley L.; Wartho, Jo-Anne; van Soest, Matthijs C.

    2015-01-01

    Quantitative constraints on the ages of melt-forming impact events on the Moon are based primarily on isotope geochronology of returned samples. However, interpreting the results of such studies can often be difficult because the provenance region of any sample returned from the lunar surface may have experienced multiple impact events over the course of billions of years of bombardment. We illustrate this problem with new laser microprobe 40Ar/39Ar data for two Apollo 17 impact melt breccias. Whereas one sample yields a straightforward result, indicating a single melt-forming event at ca. 3.83 Ga, data from the other sample document multiple impact melt–forming events between ca. 3.81 Ga and at least as young as ca. 3.27 Ga. Notably, published zircon U/Pb data indicate the existence of even older melt products in the same sample. The revelation of multiple impact events through 40Ar/39Ar geochronology is likely not to have been possible using standard incremental heating methods alone, demonstrating the complementarity of the laser microprobe technique. Evidence for 3.83 Ga to 3.81 Ga melt components in these samples reinforces emerging interpretations that Apollo 17 impact breccia samples include a significant component of ejecta from the Imbrium basin impact. Collectively, our results underscore the need to quantitatively resolve the ages of different melt generations from multiple samples to improve our current understanding of the lunar impact record, and to establish the absolute ages of important impact structures encountered during future exploration missions in the inner Solar System. PMID:26601128

  18. Antimicrobial thermoplastic materials for biomedical applications prepared by melt processing

    NASA Astrophysics Data System (ADS)

    Botta, L.; Scaffaro, R.; Ceraulo, M.; Gallo, G.

    2014-05-01

    In this work thermoplastic polymers with antimicrobial properties were prepared by incorporating an antibiotic, i.e., ciprofloxacin (CFX), by melt processing. Two different polymers were used as matrices, i.e., polypropylene (PP) and poly(lactid acid) (PLA) and different concentrations of CFX have been incorporated. The antimicrobial properties, the release kinetic and the mechanical performances of the prepared materials were evaluated.

  19. Rapid real-time PCR and high resolution melt analysis in a self-filling thermoplastic chip.

    PubMed

    Sposito, A; Hoang, V; DeVoe, D L

    2016-09-21

    A microfluidic platform designed for point-of-care PCR-based nucleic acid diagnostics is described. Compared to established microfluidic PCR technologies, the system is unique in its ability to achieve exceptionally rapid PCR amplification in a low cost thermoplastic format, together with high temperature accuracy enabling effective validation of reaction product by high resolution melt analysis performed in the same chamber as PCR. In addition, the system employs capillary pumping for automated loading of sample into the reaction chamber, combined with an integrated hydrophilic valve for precise self-metering of sample volumes into the device. Using the microfluidic system to target a mutation in the G6PC gene, efficient PCR from human genomic DNA template is achieved with cycle times as low as 14 s, full amplification in 8.5 min, and final melt analysis accurately identifying the desired amplicon. PMID:27460504

  20. Rapid Discrimination between Anopheles gambiae s.s. and Anopheles arabiensis by High-Resolution Melt (HRM) Analysis

    PubMed Central

    Zianni, Michael R.; Nikbakhtzadeh, Mahmood R.; Jackson, Bryan T.; Panescu, Jenny; Foster, Woodbridge A.

    2013-01-01

    There is a need for more cost-effective options to more accurately discriminate among members of the Anopheles gambiae complex, particularly An. gambiae and Anopheles arabiensis. These species are morphologically indistinguishable in the adult stage, have overlapping distributions, but are behaviorally and ecologically different, yet both are efficient vectors of malaria in equatorial Africa. The method described here, High-Resolution Melt (HRM) analysis, takes advantage of minute differences in DNA melting characteristics, depending on the number of incongruent single nucleotide polymorphisms in an intragenic spacer region of the X-chromosome-based ribosomal DNA. The two species in question differ by an average of 13 single-nucleotide polymorphisms giving widely divergent melting curves. A real-time PCR system, Bio-Rad CFX96, was used in combination with a dsDNA-specific dye, EvaGreen, to detect and measure the melting properties of the amplicon generated from leg-extracted DNA of selected mosquitoes. Results with seven individuals from pure colonies of known species, as well as 10 field-captured individuals unambiguously identified by DNA sequencing, demonstrated that the method provided a high level of accuracy. The method was used to identify 86 field mosquitoes through the assignment of each to the two common clusters with a high degree of certainty. Each cluster was defined by individuals from pure colonies. HRM analysis is simpler to use than most other methods and provides comparable or more accurate discrimination between the two sibling species but requires a specialized melt-analysis instrument and software. PMID:23543777

  1. Rapid and efficient differentiation of Yersinia species using high-resolution melting analysis.

    PubMed

    Souza, Roberto A; Frazão, Miliane R; Almeida, Alzira M P; Falcão, Juliana P

    2015-08-01

    The primary goal of clinical microbiology is the accurate identification of the causative agent of the disease. Here, we describe a method for differentiation between Yersinia species using PCR-HRMA. The results revealed species-specific melting profiles. The herein developed assay can be used as an effective method to differentiate Yersinia species. PMID:25980404

  2. Identification of Brucella spp. isolated from human brucellosis in Malaysia using high-resolution melt (HRM) analysis.

    PubMed

    Mohamed Zahidi, Jama'ayah; Bee Yong, Tay; Hashim, Rohaidah; Mohd Noor, Azura; Hamzah, Siti Hawa; Ahmad, Norazah

    2015-04-01

    Molecular approaches have been investigated to overcome difficulties in identification and differentiation of Brucella spp. using conventional phenotypic methods. In this study, high-resolution melt (HRM) analysis was used for rapid identification and differentiation of members of Brucella genus. A total of 41 Brucella spp. isolates from human brucellosis were subjected to HRM analysis using 4 sets of primers, which identified 40 isolates as Brucella melitensis and 1 as Brucella canis. The technique utilized low DNA concentration and was highly reproducible. The assay is shown to be a useful diagnostic tool, which can rapidly differentiate Brucella up to species level. PMID:25641125

  3. Differentiation of infectious bursal disease virus strains using real-time RT-PCR and high resolution melt curve analysis.

    PubMed

    Ghorashi, Seyed A; O'Rourke, Denise; Ignjatovic, Jagoda; Noormohammadi, Amir H

    2011-01-01

    Differentiation of infectious bursal disease virus (IBDV) strains is crucial for effective vaccination programs and epidemiological investigations. In this study, a combination of real-time RT-PCR and high resolution melt (HRM) curve analysis was developed for simultaneous detection and differentiation of IBDV strains/isolates. The hypervariable region of VP2 gene was amplified from several IBDV strains and subjected to HRM curve analysis. The method could readily differentiate between classical vaccines/isolates and variants. Analysis of the nucleotide sequence of the amplicons from each strain revealed that each melt curve profile was related to a unique DNA sequence. The real-time RT-PCR HRM curve analysis was also able to differentiate IBDV strains/isolates directly in bursal tissues from field submissions and from vaccinated commercial flocks. The differences between melting peaks generated from IBDV strains were significantly different (P<0.0001) demonstrating the high discriminatory power of this technique. The results presented in this study indicated that real-time RT-PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping IBDV isolates/strains and can contribute to effective control of IBDV outbreaks. PMID:21111004

  4. Precise Detection of IDH1/2 and BRAF Hotspot Mutations in Clinical Glioma Tissues by a Differential Calculus Analysis of High-Resolution Melting Data

    PubMed Central

    Hatae, Ryusuke; Yoshimoto, Koji; Kuga, Daisuke; Akagi, Yojiro; Murata, Hideki; Suzuki, Satoshi O.; Mizoguchi, Masahiro; Iihara, Koji

    2016-01-01

    High resolution melting (HRM) is a simple and rapid method for screening mutations. It offers various advantages for clinical diagnostic applications. Conventional HRM analysis often yields equivocal results, especially for surgically obtained tissues. We attempted to improve HRM analyses for more effective applications to clinical diagnostics. HRM analyses were performed for IDH1R132 and IDH2R172 mutations in 192 clinical glioma samples in duplicate and these results were compared with sequencing results. BRAFV600E mutations were analyzed in 52 additional brain tumor samples. The melting profiles were used for differential calculus analyses. Negative second derivative plots revealed additional peaks derived from heteroduplexes in PCR products that contained mutations; this enabled unequivocal visual discrimination of the mutations. We further developed a numerical expression, the HRM-mutation index (MI), to quantify the heteroduplex-derived peak of the mutational curves. Using this expression, all IDH1 mutation statuses matched those ascertained by sequencing, with the exception of three samples. These discordant results were all derived from the misinterpretation of sequencing data. The effectiveness of our approach was further validated by analyses of IDH2R172 and BRAFV600E mutations. The present analytical method enabled an unequivocal and objective HRM analysis and is suitable for reliable mutation scanning in surgically obtained glioma tissues. This approach could facilitate molecular diagnostics in clinical environments. PMID:27529619

  5. Precise Detection of IDH1/2 and BRAF Hotspot Mutations in Clinical Glioma Tissues by a Differential Calculus Analysis of High-Resolution Melting Data.

    PubMed

    Hatae, Ryusuke; Hata, Nobuhiro; Yoshimoto, Koji; Kuga, Daisuke; Akagi, Yojiro; Murata, Hideki; Suzuki, Satoshi O; Mizoguchi, Masahiro; Iihara, Koji

    2016-01-01

    High resolution melting (HRM) is a simple and rapid method for screening mutations. It offers various advantages for clinical diagnostic applications. Conventional HRM analysis often yields equivocal results, especially for surgically obtained tissues. We attempted to improve HRM analyses for more effective applications to clinical diagnostics. HRM analyses were performed for IDH1R132 and IDH2R172 mutations in 192 clinical glioma samples in duplicate and these results were compared with sequencing results. BRAFV600E mutations were analyzed in 52 additional brain tumor samples. The melting profiles were used for differential calculus analyses. Negative second derivative plots revealed additional peaks derived from heteroduplexes in PCR products that contained mutations; this enabled unequivocal visual discrimination of the mutations. We further developed a numerical expression, the HRM-mutation index (MI), to quantify the heteroduplex-derived peak of the mutational curves. Using this expression, all IDH1 mutation statuses matched those ascertained by sequencing, with the exception of three samples. These discordant results were all derived from the misinterpretation of sequencing data. The effectiveness of our approach was further validated by analyses of IDH2R172 and BRAFV600E mutations. The present analytical method enabled an unequivocal and objective HRM analysis and is suitable for reliable mutation scanning in surgically obtained glioma tissues. This approach could facilitate molecular diagnostics in clinical environments. PMID:27529619

  6. Development of Novel High-Resolution Melting-Based Assays for Genotyping Two Alu Insertion Polymorphisms (FXIIIB and PV92).

    PubMed

    González-Giraldo, Yeimy; Rodríguez-Dueñas, Marisol; Forero, Diego A

    2016-03-01

    Insertion/Deletion polymorphisms (InDels) are a common type of genetic variation, with a growing role in population genetics and applied genomics. There is the need for the development of novel cost-effective assays for genotyping InDels of high importance. The main objective of this study was to develop high-resolution melting-based assays for genotyping two commonly studied Alu insertion polymorphisms: FXIIIB and PV92 (rs70942849 and rs3138523). Three primers (two forward and one reverse) were designed for each marker, and high-resolution melting (HRM) analyses in a qPCR platform were performed, using EvaGreen fluorescent dye. For each one of the two Alu insertion polymorphisms, HRM analyses identified distinguishable peaks for the three genotypes, allowing a robust genotyping. Results were validated using 96 DNA samples previously genotyped and the assays worked with different DNA concentrations. In this study, we developed novel cost-effective assays, using qPCR, for genotyping two Alu insertion polymorphisms (widely used as ancestry markers). Our results highlight the feasibility of using HRM analyses for genotyping InDel polymorphisms of medical and biotechnological importance. PMID:26843017

  7. High-resolution melt analysis for species identification of coagulase-negative staphylococci derived from bovine milk.

    PubMed

    Ajitkumar, Praseeda; Barkema, Herman W; Zadoks, Ruth N; Morck, Douglas W; van der Meer, Frank J U M; De Buck, Jeroen

    2013-03-01

    Coagulase-negative staphylococci (CNS) are the most frequently isolated pathogens isolated from bovine milk. In this study, we report a rapid assay for species identification of CNS using high-resolution melt analysis (HRMA) of 16S rDNA sequences. Real-time polymerase chain reaction amplification of 16S rRNA gene fragment, spanning the variable region V1 and V2, was performed with a resulting amplicon of 215 bp. A library of distinct melt curves of reference strains of 13 common CNS species was created using HRMA. Sequencing of 16S rRNA and rpoB genes, and, when needed, tuf gene, of 100 CNS isolates obtained from Canadian Bovine Mastitis Research Network was done to determine their species identity, allowing for subsequent evaluation of the performance of HRMA for field isolates of bovine CNS. A combination of HRMA and sequencing revealed that Staphylococcus chromogenes, S. xylosus, S. simulans, and S. sciuri had multiple genotypes, complicating their resolution by HRMA. As the 3 genotypes of S. chromogenes had distinct melt curves, the 3 distinct genotypes were employed as reference strains in a blinded trial of 156 CNS isolates to identify S. chromogenes. HRMA correctly identified all S. chromogenes isolates which were later confirmed by sequencing. Staphylococcus chromogenes (68%) was most frequently found among the CNS isolates, followed by S. haemolyticus (10%) and S. xylosus (6%). The present study revealed that HRMA of 16S rRNA gene (V1-V2) could be used as a rapid, efficient, low-cost, and minimally cumbersome technique for S. chromogenes identification, the most common CNS derived from bovine milk. PMID:23273337

  8. Viscosity of Carbonate-Silicate Melts Using Ultra-High Resolution Falling Sphere Viscometry

    NASA Astrophysics Data System (ADS)

    Hummer, D. R.; Kavner, A.; Manning, C. E.; Park, C.; Kono, Y.; Kenney-Benson, C.

    2014-12-01

    Carbonatites are carbon-rich magmas that participate in the deep-Earth carbon cycle, and may be precursors to many types of terrestrial magmatism. [1] Viscosity is a crucial parameter in determining migration rates and behavior of melts from the upper mantle to Earth's surface, but very little is known about the viscosity of carbonate-silicate liquids at conditions relevant to Earth's interior. To examine the viscosity of carbonate-silicate liquids as a function of composition, we performed in situ falling sphere viscosity experiments using a high speed X-ray camera and Paris-Edinburgh press at the HPCAT beamline (Advanced Photon Source, Argonne National Laboratory). Mixtures from the CaCO3-CaSiO3 (calcite-wollastonite) binary system were used to simulate mantle silicate carbonatites. Samples were loaded using the experimental setup of Yamada et al [2], held at 3 GPa, and heated until the sample was fully molten (between 1350-1650 oC). The high speed camera recorded the falling rate of a platinum sphere placed near the top of the sample chamber, enabling the calculation of terminal velocity and hence viscosity. Results indicate that pure CaCO3 at upper mantle conditions has a very low viscosity of ~0.006 Pa-s, only a little higher than that of water. This viscosity is 2-6 times lower than that of potassium carbonates at similar pressures (2.5-4.0 GPa) but at somewhat lower temperatures (800-1200 oC). [3] Our measured viscosity as a function of increasing silicate content increases along a log-linear trend, reaching 0.256 Pa-s for CaSiO3 liquid. This heavy dependence of viscosity on composition has implications for melt migration processes at different depths, suggesting either viscosity-driven or porosity-driven migration depending on both extent of melting and carbonate content. [1] Dasgupta, R. et al. (2013) Nature 493, 211-215. [2] Yamada, A. et al. (2011) Rev. Sci. Instr. 82, 015103. [3] Dobson, D. et al. (1996) Earth Plan. Sci. Lett. 143, 207-215.

  9. High resolution melting curve analysis as a new tool for rapid identification of canine parvovirus type 2 strains.

    PubMed

    Bingga, Gali; Liu, Zhicheng; Zhang, Jianfeng; Zhu, Yujun; Lin, Lifeng; Ding, Shuangyang; Guo, Pengju

    2014-01-01

    A high resolution melting (HRM) curve method was developed to identify canine parvovirus type 2 (CPV-2) strains by nested PCR. Two sets of primers, CPV-426F/426R and CPV-87R/87F, were designed that amplified a 52 bp and 53 bp product from the viral VP2 capsid gene. The region amplified by CPV-426F/426R included the A4062G and T4064A mutations in CPV-2a, CPV-2b and CPV-2c. The region amplified by CPV-87F/87R included the A3045T mutation in the vaccine strains of CPV-2 and CPV-2a, CPV-2b and CPV-2c. Faecal samples were obtained from 30 dogs that were CPV antigen-positive. The DNA was isolated from the faecal samples and PCR-amplified using the two sets of primers, and genotyped by HRM curve analysis. The PCR-HRM assay was able to distinguish single nucleotide polymorphisms between CPV-2a, CPV-2b and CPV-2c using CPV-426F/426R. CPV-2a was distinguished from CPV-2b and CPV-2c by differences in the melting temperature. CPV-2b and CPV-2c could be distinguished based on the shape of the melting curve after generating heteroduplexes using a CPV-2b reference sample. The vaccine strains of CPV-2 were identified using CPV-87F/87R. Conventional methods for genotyping CPV strains are labor intensive, expensive or time consuming; the present PCR-based HRM assay might be an attractive alternative. PMID:25159576

  10. Melt Infiltrated Ceramic Composites (Hipercomp) for Gas Turbine Engine Applications

    SciTech Connect

    Gregory Corman; Krishan Luthra

    2005-09-30

    This report covers work performed under the Continuous Fiber Ceramic Composites (CFCC) program by GE Global Research and its partners from 1994 through 2005. The processing of prepreg-derived, melt infiltrated (MI) composite systems based on monofilament and multifilament tow SiC fibers is described. Extensive mechanical and environmental exposure characterizations were performed on these systems, as well as on competing Ceramic Matrix Composite (CMC) systems. Although current monofilament SiC fibers have inherent oxidative stability limitations due to their carbon surface coatings, the MI CMC system based on multifilament tow (Hi-Nicalon ) proved to have excellent mechanical, thermal and time-dependent properties. The materials database generated from the material testing was used to design turbine hot gas path components, namely the shroud and combustor liner, utilizing the CMC materials. The feasibility of using such MI CMC materials in gas turbine engines was demonstrated via combustion rig testing of turbine shrouds and combustor liners, and through field engine tests of shrouds in a 2MW engine for >1000 hours. A unique combustion test facility was also developed that allowed coupons of the CMC materials to be exposed to high-pressure, high-velocity combustion gas environments for times up to {approx}4000 hours.

  11. Ecological applications of high resolution spectrometry

    NASA Technical Reports Server (NTRS)

    Lawrence, William T.

    1989-01-01

    Future directions of NASA's space program plans include a significant effort at studying the Earth as a system of interrelated ecosystems. As part of NASA's Earth Observing System (Eos) Program a series of space platforms will be launched and operated to study the Earth with a variety of active and passive instruments. Several of the Eos instruments will be capable of imaging the planet's surface reflectance on a large number of very narrow portions of the solar spectrum. After the development of appropriate algorithms, this reflectance information will be used to determine key parameters about the structure and function of terrestrial and aquatic ecosystems and the pattern and processes of those systems across large areas of the globe. Algorithm development applicable to terrestrial systems will permit the inference of ecological processes from high resolution spectrometry data, similar to that to be forthcoming from the Eos mission. The first summer was spent working with tropical soils and relating their reflectance characteristics to particle size, iron content, and color. This summer the emphasis is on vegetation and work was begun with the Forest Ecosystems Dynamics Project in the Earth Resources Branch where both optical and radar characteristics of a mixed conifer/hardwood forest in Maine are being studied for use in a ecological modeling effort. A major series of aircraft overflights will take place throughout the summer. Laboratory and field spectrometers are used to measure the spectral reflectance of a hierarchy of vegetation from individual leaves to whole canopies for eventual modeling of their nutrient content using reflectance data. Key leaf/canopy parameters are being approximated including chlorophyll, nitrogen, phosphorus, water content, and leaf specific weight using high resolution spectrometry alone. Measurements are made of carbon exchange across the landscape for input to a spatial modeling effort to gauge production within the forest. A

  12. Impact of Mutation Type and Amplicon Characteristics on Genetic Diversity Measures Generated Using a High-Resolution Melting Diversity Assay

    PubMed Central

    Cousins, Matthew M.; Donnell, Deborah; Eshleman, Susan H.

    2013-01-01

    We adapted high-resolution melting (HRM) technology to measure genetic diversity without sequencing. Diversity is measured as a single numeric HRM score. Herein, we determined the impact of mutation types and amplicon characteristics on HRM diversity scores. Plasmids were generated with single-base changes, insertions, and deletions. Different primer sets were used to vary the position of mutations within amplicons. Plasmids and plasmid mixtures were analyzed to determine the impact of mutation type, position, and concentration on HRM scores. The impact of amplicon length and G/C content on HRM scores was also evaluated. Different mutation types affected HRM scores to varying degrees (1-bp deletion < 1-bp change < 3-bp insertion < 9-bp insertion). The impact of mutations on HRM scores was influenced by amplicon length and the position of the mutation within the amplicon. Mutations were detected at concentrations of 5% to 95%, with the greatest impact at 50%. The G/C content altered melting temperature values of amplicons but had no impact on HRM scores. These data are relevant to the design of assays that measure genetic diversity using HRM technology. PMID:23178437

  13. A high-resolution melting (HRM) assay for the differentiation between Israeli field and Neethling vaccine lumpy skin disease viruses.

    PubMed

    Menasherow, Sophia; Erster, Oran; Rubinstein-Giuni, Marisol; Kovtunenko, Anita; Eyngor, Evgeny; Gelman, Boris; Khinich, Evgeny; Stram, Yehuda

    2016-06-01

    Lumpy skin disease (LSD) is a constant threat to the Middle East including the State of Israel. During vaccination programs it is essential for veterinary services and farmers to be able to distinguish between animals affected by the cattle-borne virulent viruses and vaccinated animals, subsequently affected by the vaccine strain. This study describes an improved high resolution-melting (HRM) test that exploits a 27 base pair (bp) fragment of the LSDV126 extracellular enveloped virion (EEV) gene that is present in field viruses but is absent from the Neethling vaccine strain. This difference leads to ∼0.5 °C melting point change in the HRM assay, when testing the quantitative PCR (qPCR) products generated from the virulent field viruses compared to the attenuated vaccine. By exploiting this difference, it could be shown using the newly developed HRM assay that virus isolated from vaccinated cattle that developed disease symptoms behave similarly to vaccine virus control, indicating that the vaccine virus can induce disease symptoms. This assay is not only in full agreement with the previously published PCR gradient and restriction fragment length polymorphism (RFLP) tests but it is faster with, fewer steps, cheaper and dependable. PMID:26902159

  14. Differentiation of Campylobacter jejuni and Campylobacter coli Using Multiplex-PCR and High Resolution Melt Curve Analysis

    PubMed Central

    Banowary, Banya; Dang, Van Tuan; Sarker, Subir; Connolly, Joanne H.; Chenu, Jeremy; Groves, Peter; Ayton, Michelle; Raidal, Shane; Devi, Aruna; Vanniasinkam, Thiru; Ghorashi, Seyed A.

    2015-01-01

    Campylobacter spp. are important causes of bacterial gastroenteritis in humans in developed countries. Among Campylobacter spp. Campylobacter jejuni (C. jejuni) and C. coli are the most common causes of human infection. In this study, a multiplex PCR (mPCR) and high resolution melt (HRM) curve analysis were optimized for simultaneous detection and differentiation of C. jejuni and C. coli isolates. A segment of the hippuricase gene (hipO) of C. jejuni and putative aspartokinase (asp) gene of C. coli were amplified from 26 Campylobacter isolates and amplicons were subjected to HRM curve analysis. The mPCR-HRM was able to differentiate between C. jejuni and C. coli species. All DNA amplicons generated by mPCR were sequenced. Analysis of the nucleotide sequences from each isolate revealed that the HRM curves were correlated with the nucleotide sequences of the amplicons. Minor variation in melting point temperatures of C. coli or C. jejuni isolates was also observed and enabled some intraspecies differentiation between C. coli and/or C. jejuni isolates. The potential of PCR-HRM curve analysis for the detection and speciation of Campylobacter in additional human clinical specimens and chicken swab samples was also confirmed. The sensitivity and specificity of the test were found to be 100% and 92%, respectively. The results indicated that mPCR followed by HRM curve analysis provides a rapid (8 hours) technique for differentiation between C. jejuni and C. coli isolates. PMID:26394042

  15. High Resolution Melting Analysis for Rapid Mutation Screening in Gyrase and Topoisomerase IV Genes in Quinolone-Resistant Salmonella enterica

    PubMed Central

    Thong, Kwai Lin

    2014-01-01

    The increased Salmonella resistance to quinolones and fluoroquinolones is a public health concern in the Southeast Asian region. The objective of this study is to develop a high resolution melt curve (HRM) assay to rapidly screen for mutations in quinolone-resistant determining region (QRDR) of gyrase and topoisomerase IV genes. DNA sequencing was performed on 62 Salmonella strains to identify mutations in the QRDR of gyrA, gyrB, parC, and parE genes. Mutations were detected in QRDR of gyrA (n = 52; S83F, S83Y, S83I, D87G, D87Y, and D87N) and parE (n = 1; M438I). Salmonella strains with mutations within QRDR of gyrA are generally more resistant to nalidixic acid (MIC 16 > 256 μg/mL). Mutations were uncommon within the QRDR of gyrB, parC, and parE genes. In the HRM assay, mutants can be distinguished from the wild-type strains based on the transition of melt curves, which is more prominent when the profiles are displayed in difference plot. In conclusion, HRM analysis allows for rapid screening for mutations at the QRDRs of gyrase and topoisomerase IV genes in Salmonella. This assay markedly reduced the sequencing effort involved in mutational studies of quinolone-resistance genes. PMID:25371903

  16. High resolution melting analysis for rapid mutation screening in gyrase and Topoisomerase IV genes in quinolone-resistant Salmonella enterica.

    PubMed

    Ngoi, Soo Tein; Thong, Kwai Lin

    2014-01-01

    The increased Salmonella resistance to quinolones and fluoroquinolones is a public health concern in the Southeast Asian region. The objective of this study is to develop a high resolution melt curve (HRM) assay to rapidly screen for mutations in quinolone-resistant determining region (QRDR) of gyrase and topoisomerase IV genes. DNA sequencing was performed on 62 Salmonella strains to identify mutations in the QRDR of gyrA, gyrB, parC, and parE genes. Mutations were detected in QRDR of gyrA (n = 52; S83F, S83Y, S83I, D87G, D87Y, and D87N) and parE (n = 1; M438I). Salmonella strains with mutations within QRDR of gyrA are generally more resistant to nalidixic acid (MIC 16 > 256 μg/mL). Mutations were uncommon within the QRDR of gyrB, parC, and parE genes. In the HRM assay, mutants can be distinguished from the wild-type strains based on the transition of melt curves, which is more prominent when the profiles are displayed in difference plot. In conclusion, HRM analysis allows for rapid screening for mutations at the QRDRs of gyrase and topoisomerase IV genes in Salmonella. This assay markedly reduced the sequencing effort involved in mutational studies of quinolone-resistance genes. PMID:25371903

  17. A method to distinguish morphologically similar Peromyscus species using extracellular RNA and high-resolution melt analysis.

    PubMed

    Seifert, Veronica A; Clarke, Benjamin L; Crossland, Janet P; Bemis, Lynne T

    2016-09-01

    A method applying high-resolution melt (HRM) analysis to PCR products copied and amplified from extracellular RNA (exRNA) has been developed to distinguish two morphologically similar Peromyscus species: Peromyscus leucopus and Peromyscus maniculatus. P. leucopus is considered the primary reservoir host of Borrelia burgdorferi, the causative agent for Lyme disease in North America. In northern Minnesota the habitat ranges of P. leucopus overlaps with that of P. maniculatus. Serum samples from live mice of both species were collected from cheek bleeds, total extracellular RNA (exRNA) was extracted, copied using reverse transcription and amplified by PCR followed by HRM analysis. A circulating ribosomal RNA (rRNA) was identified which differed at seven nucleotides between the two species and a method of HRM analysis was developed allowing rapid species confirmation. In the future, this HRM based method may be adapted for additional species. PMID:27349513

  18. Melt spreading code assessment, modifications, and application to the EPR core catcher design.

    SciTech Connect

    Farmer, M. T .; Nuclear Engineering Division

    2009-03-30

    The Evolutionary Power Reactor (EPR) is under consideration by various utilities in the United States to provide base load electrical production, and as a result the design is undergoing a certification review by the U.S. Nuclear Regulatory Commission (NRC). The severe accident design philosophy for this reactor is based upon the fact that the projected power rating results in a narrow margin for in-vessel melt retention by external cooling of the reactor vessel. As a result, the design addresses ex-vessel core melt stabilization using a mitigation strategy that includes: (1) an external core melt retention system to temporarily hold core melt released from the vessel; (2) a layer of 'sacrificial' material that is admixed with the melt while in the core melt retention system; (3) a melt plug in the lower part of the retention system that, when failed, provides a pathway for the mixture to spread to a large core spreading chamber; and finally, (4) cooling and stabilization of the spread melt by controlled top and bottom flooding. The overall concept is illustrated in Figure 1.1. The melt spreading process relies heavily on inertial flow of a low-viscosity admixed melt to a segmented spreading chamber, and assumes that the melt mass will be distributed to a uniform height in the chamber. The spreading phenomenon thus needs to be modeled properly in order to adequately assess the EPR design. The MELTSPREAD code, developed at Argonne National Laboratory, can model segmented, and both uniform and nonuniform spreading. The NRC is thus utilizing MELTSPREAD to evaluate melt spreading in the EPR design. MELTSPREAD was originally developed to support resolution of the Mark I containment shell vulnerability issue. Following closure of this issue, development of MELTSPREAD ceased in the early 1990's, at which time the melt spreading database upon which the code had been validated was rather limited. In particular, the database that was utilized for initial validation consisted

  19. Detection of Sequence Polymorphism in Rubus Occidentalis L. Monomorphic Microsatellite Markers by High Resolution Melting

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. Development of microsatellite primers through the identification of appropriate repeate...

  20. High resolution melting detects sequence polymorphism in rubus occidentalis L. monomorphic microsatellite markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. However, primer pairs designed from the regions that flank SSRs often generate fragment...

  1. High resolution SAR applications and instrument design

    NASA Technical Reports Server (NTRS)

    Dionisio, C.; Torre, A.

    1993-01-01

    The Synthetic Aperture Radar (SAR) has viewed, in the last two years, a huge increment of interest from many preset and potential users. The good spatial resolution associated to the all weather capability lead to considering SAR not only a scientific instrument but a tool for verifying and controlling the daily human relationships with the Earth Environment. New missions were identified for SAR as spatial resolution became lower than three meters: disasters, pollution, ships traffic, volcanic eruptions, earthquake effect are only a few of the possible objects which can be effectively detected, controlled and monitored by SAR mounted on satellites. High resolution radar design constraints and dimensioning are discussed.

  2. High Resolution Melting Analysis: A Rapid Screening and Typing Tool for Common β-Thalassemia Mutation in Chinese Population

    PubMed Central

    Lin, Min; Jiao, Ji-Wei; Zhan, Xiu-Hui; Zhan, Xiao-Fen; Pan, Mei-Chen; Wang, Jun-Li; Wang, Chun-Fang; Zhong, Tian-Yu; Zhang, Qin; Yu, Xia; Wu, Jiao-Ren; Yang, Hui-Tian; Lin, Fen; Tong, Xin; Yang, Hui; Zha, Guang-Cai; Wang, Qian; Zheng, Lei; Wen, Ying-Fang; Yang, Li-Ye

    2014-01-01

    β-thalassemia is a common inherited disorder worldwide including southern China, and at least 45 distinct β-thalassemia mutations have been identified in China. High-resolution melting (HRM) assay was recently introduced as a rapid, inexpensive and effective method for genotyping. However, there was no systemic study on the diagnostic capability of HRM to identify β-thalassemia. Here, we used an improved HRM method to screen and type 12 common β-thalassemia mutations in Chinese, and the rapidity and reliability of this method was investigated. The whole PCR and HRM procedure could be completed in 40 min. The heterozygous mutations and 4 kinds of homozygous mutations could be readily differentiated from the melting curve except c.-78A>G heterozygote and c.-79A>G heterozygote. The diagnostic reliability of this HRM assay was evaluated on 756 pre-typed genomic DNA samples and 50 cases of blood spots on filter paper, which were collected from seven high prevalent provinces in southern China. If c.-78A>G heterozygote and c.-79A>G heterozygote were classified into the same group (c.-78&79 A>G heterozygote), the HRM method was in complete concordance with the reference method (reverse dot blot/DNA-sequencing). In a conclusion, the HRM method appears to be an accurate and sensitive method for the rapid screening and identification of β-thalassemia mutations. In the future, we suggest this technology to be used in neonatal blood spot screening program. It could enlarge the coverage of β-thalassemia screening program in China. At the same time, its value should be confirmed in prospectively clinical and epidemiological studies. PMID:25089872

  3. Detection of Schistosoma mansoni and Schistosoma haematobium by Real-Time PCR with High Resolution Melting Analysis

    PubMed Central

    Sady, Hany; Al-Mekhlafi, Hesham M.; Ngui, Romano; Atroosh, Wahib M.; Al-Delaimy, Ahmed K.; Nasr, Nabil A.; Dawaki, Salwa; Abdulsalam, Awatif M.; Ithoi, Init; Lim, Yvonne A. L.; Chua, Kek Heng; Surin, Johari

    2015-01-01

    The present study describes a real-time PCR approach with high resolution melting-curve (HRM) assay developed for the detection and differentiation of Schistosoma mansoni and S. haematobium in fecal and urine samples collected from rural Yemen. The samples were screened by microscopy and PCR for the Schistosoma species infection. A pair of degenerate primers were designed targeting partial regions in the cytochrome oxidase subunit I (cox1) gene of S. mansoni and S. haematobium using real-time PCR-HRM assay. The overall prevalence of schistosomiasis was 31.8%; 23.8% of the participants were infected with S. haematobium and 9.3% were infected with S. mansoni. With regards to the intensity of infections, 22.1% and 77.9% of S. haematobium infections were of heavy and light intensities, respectively. Likewise, 8.1%, 40.5% and 51.4% of S. mansoni infections were of heavy, moderate and light intensities, respectively. The melting points were distinctive for S. mansoni and S. haematobium, categorized by peaks of 76.49 ± 0.25 °C and 75.43 ± 0.26 °C, respectively. HRM analysis showed high detection capability through the amplification of Schistosoma DNA with as low as 0.0001 ng/µL. Significant negative correlations were reported between the real-time PCR-HRM cycle threshold (Ct) values and microscopic egg counts for both S. mansoni in stool and S. haematobium in urine (p < 0.01). In conclusion, this closed-tube HRM protocol provides a potentially powerful screening molecular tool for the detection of S. mansoni and S. haematobium. It is a simple, rapid, accurate, and cost-effective method. Hence, this method is a good alternative approach to probe-based PCR assays. PMID:26193254

  4. Genotyping single-nucleotide polymorphisms of human genes involved in organophosphate detoxification by high-resolution melting.

    PubMed

    Kurdyukov, Ivan; Rodionov, Gennady; Radilov, Andrey; Babakov, Vladimir

    2014-08-01

    Paraoxonase-1 (PON1) and butyrylcholinesterase (BCHE) are natural bioscavengers of organophosphate acetylcholinesterase inhibitors in the human body, which can determine individual sensitivity to organophosphate toxicity. Interindividual differences in activity of PON1 (catalytic bioscavenger) and substrate specificity are strongly associated with the substitution of two amino acids: Leu/Met (L/M) at position 55 (rs854560) and Gln/Arg (Q/R) at position 192 (rs662). In the case of BCHE (stoichiometric bioscavenger) substitution, Ala/Thr (A/T) at position 539 produces the so-called "K-variant" of the enzyme (rs1803274). Threonine allele is often co-inherited with an atypical BCHE allele (rs1799807). The atypical variant of BCHE displays a lower affinity for cholinesterase inhibitors. Genotyping rs662 and rs1803274 single-nucleotide polymorphisms (SNP) by high-resolution melting (HRM) is facilitated by the nucleotide substitution A>G (G>A), which resulted in a changed number of hydrogen bonds in the PCR product and, consequently, shifted T m. In the case of rs854560, genotyping is complicated by the nucleotide substitution T>A, which has no significant effect on the T m of the PCR product. An addition of a small quantity of LL homozygote DNA into the reaction mixture before PCR discriminates the three genotypes by the melt curves due to different amounts of heteroduplexes formed in the LM and MM samples. HRM analysis can be applied for genotyping human rs854560, rs662, and rs1803274 SNPs. PMID:24705954

  5. Detection of Schistosoma mansoni and Schistosoma haematobium by Real-Time PCR with High Resolution Melting Analysis.

    PubMed

    Sady, Hany; Al-Mekhlafi, Hesham M; Ngui, Romano; Atroosh, Wahib M; Al-Delaimy, Ahmed K; Nasr, Nabil A; Dawaki, Salwa; Abdulsalam, Awatif M; Ithoi, Init; Lim, Yvonne A L; Chua, Kek Heng; Surin, Johari

    2015-01-01

    The present study describes a real-time PCR approach with high resolution melting-curve (HRM) assay developed for the detection and differentiation of Schistosoma mansoni and S. haematobium in fecal and urine samples collected from rural Yemen. The samples were screened by microscopy and PCR for the Schistosoma species infection. A pair of degenerate primers were designed targeting partial regions in the cytochrome oxidase subunit I (cox1) gene of S. mansoni and S. haematobium using real-time PCR-HRM assay. The overall prevalence of schistosomiasis was 31.8%; 23.8% of the participants were infected with S. haematobium and 9.3% were infected with S. mansoni. With regards to the intensity of infections, 22.1% and 77.9% of S. haematobium infections were of heavy and light intensities, respectively. Likewise, 8.1%, 40.5% and 51.4% of S. mansoni infections were of heavy, moderate and light intensities, respectively. The melting points were distinctive for S. mansoni and S. haematobium, categorized by peaks of 76.49 ± 0.25 °C and 75.43 ± 0.26 °C, respectively. HRM analysis showed high detection capability through the amplification of Schistosoma DNA with as low as 0.0001 ng/µL. Significant negative correlations were reported between the real-time PCR-HRM cycle threshold (Ct) values and microscopic egg counts for both S. mansoni in stool and S. haematobium in urine (p < 0.01). In conclusion, this closed-tube HRM protocol provides a potentially powerful screening molecular tool for the detection of S. mansoni and S. haematobium. It is a simple, rapid, accurate, and cost-effective method. Hence, this method is a good alternative approach to probe-based PCR assays. PMID:26193254

  6. Evaluation of low melting halide systems for battery applications

    NASA Astrophysics Data System (ADS)

    Mamantov, G.; Perrovic, C.

    1981-03-01

    This three year program involves evaluation of selected low temperature molten salt solvent systems containing inorganic and/or organic chlorides and bromides for battery applications. The research involves determination of the liquidus temperatures, the specific electrical conductivity, and the electrochemical span of selected halide systems. Characterization of the solvent species by Raman spectroscopy, vapor pressure measurements, and the electrochemical study of a few cathode and anode systems will be undertaken for the most promising solvent systems. The research during the second year of this project involved the determination of liquidus temperatures and/or specific electrical conductivities for a number of binary and ternary molten salt systems containing AlCl3, AlBr3, SbCl3, FeCl3, and GaCl3.

  7. Molecular simultaneous detection of Cherry necrotic rusty mottle virus and Cherry green ring mottle virus by real-time RT-PCR and high resolution melting analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, real-time RT-PCR assays were combined with high resolution melting (HRM) analysis for the simultaneous detection of Cherry necrotic rusty mottle virus (CNRMV) and Cherry green ring mottle virus (CGRMV) infection in sweet cherry trees. Detection of CNRMV and CGRMV was performed using a...

  8. Recovery of zinc and lead from fly ash from ash-melting and gasification-melting processes of MSW--comparison and applicability of chemical leaching methods.

    PubMed

    Okada, T; Tojo, Y; Tanaka, N; Matsuto, T

    2007-01-01

    Fly ash generated from MSW ash-melting and gasification-melting plants, known as Melting Furnace Fly Ash (MFA), contains considerable amounts of heavy metals such as Pb and Zn. These metals can be recovered using a smelting furnace after "pre-treatment" for removal of unnecessary elements such as Cl, Sn and Si. Chemical methods have been studied for pretreatment in the past. However, they have been discussed only with regard to treatment cost and the concentration of Pb and Zn recovered, but neither applicability to various types of MFA nor the environmental impact have been considered. In this study, acid, alkaline and ammonia/chloride leaching methods were compared from the standpoints of: (1) applicability to MFA, (2) concentration of Pb and Zn recovered, (3) treatment cost, and (4) environmental impact. Twenty-three samples of MFAs were collected and classified into 4 types based on element contents. A Pb and Zn recovery experiment was conducted for the representative MFA of those types. The results showed: (1) MFA from gasification-melting plants cannot be treated by chemical methods; (2) the other MFA can be treated to an acceptable quality by existing smelting furnaces; (3) only MFA from electric resistance ash-melting plants can be treated easily by the water washing method; and (4) alkaline and ammonia/chloride leaching methods were more effective than acid leaching. PMID:16488594

  9. High-resolution melting curve analysis for genotyping of common SNP in MTHFR gene using fixed-cell suspension.

    PubMed

    Sinthuwiwat, Thivaratana; Poowasanpetch, Phanasit; Wongngamrungroj, Angsana; Promso, Somying; Auewarakul, Chirayu; Mooney, Sean; Tocharoentanaphol, Chintana

    2008-01-01

    Genetic variation in MTHFR might explain the interindividual differences in both therapeutic and toxic responses to the treatment of cancer and rheumatoid arthritis with methotrexate, and can be involved in the sensitivity of developing diseases like cancer and congenital anomalies. We investigated the common sequence variation, C677T, in the MTHFR gene in fixed-cell specimens archived after chromosomal analysis using a novel gene scanning method based on post PCR analysis of high-resolution melting curves (HRM). These fixed specimens were stored after routine chromosomal analysis for 1 year at -20 degrees C in a 3:1 methanol:acetic acid solution. The method revealed a distinct pattern between homozygous and heterozygous alleles. Sensitivity and specificity of the HRM based method were comparable to that obtained by a hybridization probe. While the success rate for genotyping of a common SNP in MTHFR was similar to the hybridization probe approach, the HRM based method was more cost-effective and had a shorter turnaround time. PMID:18725286

  10. Probe-free and sensitive detection of diarrhea-causing pathogens using RT-PCR combined high resolution melting analysis.

    PubMed

    Wang, Hai-Bo; Mo, Qiu-Hua; Wang, Qi; Wu, Bi-Mei; Feng, Zi-Li; Lin, Ji-Can; Yang, Ze

    2016-09-01

    Rapid and sensitive diagnostic methods are needed to help physicians make faster and better treatment decision for patients suffered from diarrhea. In the present study, a probe-free and sensitive RT-PCR combined high resolution melting analysis (HRMA) assay was established successfully for the detection of four major diarrhea-causing pathogens. The lower limit of detection of the assay were 10(0), 10(2), 10(0) and 10(3) copies/reaction for rotaviruses group A, astroviruses serotype 1, noroviruses genogroup II, and sapoviruses genegroup I, respectively, which were 1000-fold, 10-fold, 1000-fold and 10-fold more sensitive than conventional RT-PCR assay developed in parallel and comparable to or higher than commercially available real-time RT-PCR assay. Blinded sample evaluation showed that the assay was 100% concordant to both conventional RT-PCR and commercial real-time RT-PCR, indicating high reliability of the new assay. Therefore, the assay could provide a valuable platform for the probe-free and sensitive diagnosis of these pathogens. PMID:27461241

  11. Combined Use of Molecular Markers and High-Resolution Melting (HRM) to Assess Chromosome Dosage in Potato Hybrids.

    PubMed

    Villano, Clizia; Miraglia, Valeria; Iorizzo, Massimo; Aversano, Riccardo; Carputo, Domenico

    2016-03-01

    In plants, the most widely used cytological techniques to assess parental genome contributions are based on in situ hybridization (FISH and GISH), but they are time-consuming and need specific expertise and equipment. Recent advances in genomics and molecular biology have made PCR-based markers a straightforward, affordable technique for chromosome typing. Here, we describe the development of a molecular assay that uses single-copy conserved ortholog set II (COSII)-based single nucleotide polymorphisms (SNPs) and the high-resolution melting (HRM) technique to assess the chromosome dosage of interspecific hybrids between a Solanum phureja-S. tuberosum diploid (2n = 2x = 24) hybrid and its wild relative S. commersonii. Screening and analysis of 45 COSII marker sequences allowed S. commersonii-specific SNPs to be identified for all 12 chromosomes. Combining the HRM technique with the establishment of synthetic DNA hybrids, SNP markers were successfully used to predict the expected parental chromosome ratio of 5 interspecific triploid hybrids. These results demonstrate the ability of this strategy to distinguish diverged genomes from each other, and to estimate chromosome dosage. The method could potentially be applied to any species as a tool to assess paternal to maternal ratios in the framework of a breeding program or following transformation techniques. PMID:26663623

  12. Identification of Molecular Markers Associated with Verticillium Wilt Resistance in Alfalfa (Medicago Sativa L.) Using High-Resolution Melting

    PubMed Central

    Zhang, Tiejun; Yu, Long-Xi; McCord, Per; Miller, David; Bhamidimarri, Suresh; Johnson, David; Monteros, Maria J.; Ho, Julie; Reisen, Peter; Samac, Deborah A.

    2014-01-01

    Verticillium wilt, caused by the soilborne fungus, Verticillium alfalfae, is one of the most serious diseases of alfalfa (Medicago sativa L.) worldwide. To identify loci associated with resistance to Verticillium wilt, a bulk segregant analysis was conducted in susceptible or resistant pools constructed from 13 synthetic alfalfa populations, followed by association mapping in two F1 populations consisted of 352 individuals. Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were used for genotyping. Phenotyping was done by manual inoculation of the pathogen to replicated cloned plants of each individual and disease severity was scored using a standard scale. Marker-trait association was analyzed by TASSEL. Seventeen SNP markers significantly associated with Verticillium wilt resistance were identified and they were located on chromosomes 1, 2, 4, 7 and 8. SNP markers identified on chromosomes 2, 4 and 7 co-locate with regions of Verticillium wilt resistance loci reported in M. truncatula. Additional markers identified on chromosomes 1 and 8 located the regions where no Verticillium resistance locus has been reported. This study highlights the value of SNP genotyping by high resolution melting to identify the disease resistance loci in tetraploid alfalfa. With further validation, the markers identified in this study could be used for improving resistance to Verticillium wilt in alfalfa breeding programs. PMID:25536106

  13. High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species

    PubMed Central

    Zampieri, Ricardo Andrade; Laranjeira-Silva, Maria Fernanda; Muxel, Sandra Marcia; Stocco de Lima, Ana Carolina; Shaw, Jeffrey Jon; Floeter-Winter, Lucile Maria

    2016-01-01

    Background Protozoan parasites of the genus Leishmania cause a large spectrum of clinical manifestations known as Leishmaniases. These diseases are increasingly important public health problems in many countries both within and outside endemic regions. Thus, an accurate differential diagnosis is extremely relevant for understanding epidemiological profiles and for the administration of the best therapeutic protocol. Methods/Principal Findings Exploring the High Resolution Melting (HRM) dissociation profiles of two amplicons using real time polymerase chain reaction (real-time PCR) targeting heat-shock protein 70 coding gene (hsp70) revealed differences that allowed the discrimination of genomic DNA samples of eight Leishmania species found in the Americas, including Leishmania (Leishmania) infantum chagasi, L. (L.) amazonensis, L. (L.) mexicana, L. (Viannia) lainsoni, L. (V.) braziliensis, L. (V.) guyanensis, L. (V.) naiffi and L. (V.) shawi, and three species found in Eurasia and Africa, including L. (L.) tropica, L. (L.) donovani and L. (L.) major. In addition, we tested DNA samples obtained from standard promastigote culture, naturally infected phlebotomines, experimentally infected mice and clinical human samples to validate the proposed protocol. Conclusions/Significance HRM analysis of hsp70 amplicons is a fast and robust strategy that allowed for the detection and discrimination of all Leishmania species responsible for the Leishmaniases in Brazil and Eurasia/Africa with high sensitivity and accuracy. This method could detect less than one parasite per reaction, even in the presence of host DNA. PMID:26928050

  14. Genotyping of the C742T mutation of the FGFR3 gene causing type 1 thanatophoric dysplasia by high-resolution melting analysis.

    PubMed

    Liu, Ying-Na; Li, Ru; Li, Dong-Zhi

    2011-01-01

    Type 1 thanatophoric dysplasia (TD) is typically a lethal dwarfism. It is not always possible to distinguish fetuses with TD from other skeletal dysplasia in utero by ultrasonography. A definite diagnosis should be established by molecular genetic analysis to find out the abnormal mutations in the fibroblast growth factor receptor 3 (FGFR 3) gene. Among the known mutations of this gene, the C742T (R248C) mutation is the most common one associated with type 1 TD. Exon 7 of the FGFR3 gene was analyzed in 10 prenatal samples with type 1 TD, as well as in 30 control individuals for the presence of the c.742 C > T variant using melting curve analysis with a high-resolution melting instrument. The high-resolution melting curve analysis successfully genotyped this mutation in all 10 samples with type 1 TD without the need of further assays. The technique had a sensitivity and specificity of 100%. This study suggest that high-resolution melting analysis is a simple, rapid, and sensitive one tube assay for genotyping the FGFR3 gene. PMID:20569165

  15. Detection and characterization of Leishmania (Leishmania) and Leishmania (Viannia) by SYBR green-based real-time PCR and high resolution melt analysis targeting kinetoplast minicircle DNA.

    PubMed

    Ceccarelli, Marcello; Galluzzi, Luca; Migliazzo, Antonella; Magnani, Mauro

    2014-01-01

    Leishmaniasis is a neglected disease with a broad clinical spectrum which includes asymptomatic infection. A thorough diagnosis, able to distinguish and quantify Leishmania parasites in a clinical sample, constitutes a key step in choosing an appropriate therapy, making an accurate prognosis and performing epidemiological studies. Several molecular techniques have been shown to be effective in the diagnosis of leishmaniasis. In particular, a number of PCR methods have been developed on various target DNA sequences including kinetoplast minicircle constant regions. The first aim of this study was to develop a SYBR green-based qPCR assay for Leishmania (Leishmania) infantum detection and quantification, using kinetoplast minicircle constant region as target. To this end, two assays were compared: the first used previously published primer pairs (qPCR1), whereas the second used a nested primer pairs generating a shorter PCR product (qPCR2). The second aim of this study was to evaluate the possibility to discriminate among subgenera Leishmania (Leishmania) and Leishmania (Viannia) using the qPCR2 assay followed by melting or High Resolution Melt (HRM) analysis. Both assays used in this study showed good sensitivity and specificity, and a good correlation with standard IFAT methods in 62 canine clinical samples. However, the qPCR2 assay allowed to discriminate between Leishmania (Leishmania) and Leishmania (Viannia) subgenera through melting or HRM analysis. In addition to developing assays, we investigated the number and genetic variability of kinetoplast minicircles in the Leishmania (L.) infantum WHO international reference strain (MHOM/TN/80/IPT1), highlighting the presence of minicircle subclasses and sequence heterogeneity. Specifically, the kinetoplast minicircle number per cell was estimated to be 26,566±1,192, while the subclass of minicircles amplifiable by qPCR2 was estimated to be 1,263±115. This heterogeneity, also observed in canine clinical samples

  16. High time-resolution photodetectors for PET applications

    SciTech Connect

    Ronzhin, Anatoly

    2015-11-27

    This paper describes recent developments aiming at the improvement of the time resolution of photodetectors used in positron emission tomography (PET). Promising photodetector candidates for future PET-time-of-flight (TOF) applications are also discussed.

  17. High time-resolution photodetectors for PET applications

    DOE PAGESBeta

    Ronzhin, Anatoly

    2016-02-01

    This paper describes recent developments aiming at the improvement of the time resolution of photodetectors used in positron emission tomography (PET). Promising photodetector candidates for future PET-time-of-flight (TOF) applications are also discussed.

  18. Applications of high-resolution remote sensing image data

    NASA Technical Reports Server (NTRS)

    Strome, W. M.; Leckie, D.; Miller, J.; Buxton, R.

    1990-01-01

    There are many situations in which the image resolution of satellite data is insufficient to provide the detail required for resource management and environmental monitoring. This paper will focus on applications of high-resolution (0.4 to 10 m) airborne multispectral and imaging spectrometer data acquired in Canada using the MEIS II multispectral line imager and the PMI imaging spectrometer. Applications discussed will include forestry, mapping, and geobotany.

  19. Multiplex Real-Time PCR Assay with High-Resolution Melting Analysis for Characterization of Antimicrobial Resistance in Neisseria gonorrhoeae.

    PubMed

    Donà, Valentina; Kasraian, Sara; Lupo, Agnese; Guilarte, Yuvia N; Hauser, Christoph; Furrer, Hansjakob; Unemo, Magnus; Low, Nicola; Endimiani, Andrea

    2016-08-01

    Resistance to antibiotics used against Neisseria gonorrhoeae infections is a major public health concern. Antimicrobial resistance (AMR) testing relies on time-consuming culture-based methods. Development of rapid molecular tests for detection of AMR determinants could provide valuable tools for surveillance and epidemiological studies and for informing individual case management. We developed a fast (<1.5-h) SYBR green-based real-time PCR method with high-resolution melting (HRM) analysis. One triplex and three duplex reactions included two sequences for N. gonorrhoeae identification and seven determinants of resistance to extended-spectrum cephalosporins (ESCs), azithromycin, ciprofloxacin, and spectinomycin. The method was validated by testing 39 previously fully characterized N. gonorrhoeae strains, 19 commensal Neisseria species strains, and an additional panel of 193 gonococcal isolates. Results were compared with results of culture-based AMR determination. The assay correctly identified N. gonorrhoeae and the presence or absence of the seven AMR determinants. There was some cross-reactivity with nongonococcal Neisseria species, and the detection limit was 10(3) to 10(4) genomic DNA (gDNA) copies/reaction. Overall, the platform accurately detected resistance to ciprofloxacin (sensitivity and specificity, 100%), ceftriaxone (sensitivity, 100%; specificity, 90%), cefixime (sensitivity, 92%; specificity, 94%), azithromycin (sensitivity and specificity, 100%), and spectinomycin (sensitivity and specificity, 100%). In conclusion, our methodology accurately detects mutations that generate resistance to antibiotics used to treat gonorrhea. Low assay sensitivity prevents direct diagnostic testing of clinical specimens, but this method can be used to screen collections of gonococcal isolates for AMR more quickly than current culture-based AMR testing. PMID:27225407

  20. Comparison of a High-Resolution Melting Assay to Next-Generation Sequencing for Analysis of HIV Diversity

    PubMed Central

    Cousins, Matthew M.; Ou, San-San; Wawer, Maria J.; Munshaw, Supriya; Swan, David; Magaret, Craig A.; Mullis, Caroline E.; Serwadda, David; Porcella, Stephen F.; Gray, Ronald H.; Quinn, Thomas C.; Donnell, Deborah; Eshleman, Susan H.

    2012-01-01

    Next-generation sequencing (NGS) has recently been used for analysis of HIV diversity, but this method is labor-intensive, costly, and requires complex protocols for data analysis. We compared diversity measures obtained using NGS data to those obtained using a diversity assay based on high-resolution melting (HRM) of DNA duplexes. The HRM diversity assay provides a single numeric score that reflects the level of diversity in the region analyzed. HIV gag and env from individuals in Rakai, Uganda, were analyzed in a previous study using NGS (n = 220 samples from 110 individuals). Three sequence-based diversity measures were calculated from the NGS sequence data (percent diversity, percent complexity, and Shannon entropy). The amplicon pools used for NGS were analyzed with the HRM diversity assay. HRM scores were significantly associated with sequence-based measures of HIV diversity for both gag and env (P < 0.001 for all measures). The level of diversity measured by the HRM diversity assay and NGS increased over time in both regions analyzed (P < 0.001 for all measures except for percent complexity in gag), and similar amounts of diversification were observed with both methods (P < 0.001 for all measures except for percent complexity in gag). Diversity measures obtained using the HRM diversity assay were significantly associated with those from NGS, and similar increases in diversity over time were detected by both methods. The HRM diversity assay is faster and less expensive than NGS, facilitating rapid analysis of large studies of HIV diversity and evolution. PMID:22785188

  1. High resolution melting analysis of the NR1I3 genetic variants: Is there an association with neonatal hyperbilirubinemia?

    PubMed

    Cheung, Tian Pei; Van Rostenberghe, Hans; Ismail, Rosliza; Nawawi, Noor Namirah; Abdullah, Nurul Amierah; Ramli, Noraida; Ibrahim, Nor Rosidah; Hj Abd Majid, Noorizan; Mohd Yusoff, Narazah; Nishio, Hisahide; Yusoff, Surini

    2015-12-01

    Constitutive androstane receptor (CAR) encoded by the nuclear receptor subfamily 1, group I, member 3 (NR1I3) gene regulates the elimination of bilirubin through activating the components of the bilirubin clearance pathway. Hence, NR1I3 genetic variants may affect bilirubin metabolism and result in neonatal hyperbilirubinemia. Thus far, research which investigates the association between NR1I3 variants and neonatal hyperbilirubinemia has not been undertaken in any population. The present study aimed to evaluate the influence of MPJ6_1I3008 (rs10157822), IVS8+116T>G (rs4073054) and 540A>G (rs2307424) on neonatal hyperbilirubinemia development in the Malay population. Buccal swabs were collected from 232 hyperbilirubinemia and 277 control term newborns with gestational age ≥37weeks and birth weight ≥2500g. The NR1I3 variants were genotyped by using high resolution melting (HRM) assays and verified by DNA sequencing. Gender, mode of delivery and birth weight did not differ between hyperbilirubinemia and control groups. The genotypic and allelic frequencies of MPJ6_1I3008, IVS8+116T>G and 540A>G were not significantly different between the groups. However, stratification by gender revealed a significant inverse association between homozygous variant genotype of MPJ6_1I3008 and risk of neonatal hyperbilirubinemia in the females (OR, 0.44; 95% CI, 0.20-0.95; p=0.034). This study demonstrates that the homozygous variant genotype of MPJ6_1I3008 was associated with a significant reduced risk of neonatal hyperbilirubinemia in the females. PMID:26188155

  2. Identifying the last bloodmeal of questing sheep tick nymphs (Ixodes ricinus L.) using high resolution melting analysis.

    PubMed

    Collini, Margherita; Albonico, Francesca; Hauffe, Heidi C; Mortarino, Michele

    2015-06-15

    The sheep tick, Ixodes ricinus L., is an important hematophagous vector of zoonotic disease of both veterinary and public health importance in Europe. Risk models for tick-borne diseases can be improved by identifying the main hosts of this species in any given area. However, this generalist tick stays on a host for only a few days a year over its life cycle, making the study of its feeding ecology difficult. In contrast, ticks can easily be collected from vegetation when they are questing. Molecular methods have proved to be a reliable alternative to field observation, but most current methods have low sensitivity and/or low identification success (i.e. hosts are only identified to taxonomic levels higher than species). In this study we use Real-time PCR coupled with High Resolution Melting Analysis (HRMA) to identify the source of the last bloodmeal in questing tick nymphs. Twenty of the most important tick hosts were grouped taxonomically and six group-specific primer sets, targeting short mitochondrial DNA regions, were designed de novo. Firstly, we show that these primers successfully amplify target host DNA (from host tissue or engorged ticks), and that HRMA can be used to reliably identify hosts to species (or genera in the case of Sorex and Apodemus). Secondly, the new protocol was tested on field-collected questing nymphs. Bloodmeal source was identified in 65.4% of 52 individuals. In 83.3% of these, the host was identified to species or genera using HRMA alone. Moreover, the primer sets designed here can unequivocally identify mixed bloodmeals. The combination of sensitivity and identification success together with the closed-tube and single step approach that minimizes contamination, make Real-time HRMA a good alternative to current methods for bloodmeal identification. PMID:25941127

  3. Application of Markov Chain Monte Carlo Method to Mantle Melting: An Example from REE Abundances in Abyssal Peridotites

    NASA Astrophysics Data System (ADS)

    LIU, B.; Liang, Y.

    2015-12-01

    Markov chain Monte Carlo (MCMC) simulation is a powerful statistical method in solving inverse problems that arise from a wide range of applications, such as nuclear physics, computational biology, financial engineering, among others. In Earth sciences applications of MCMC are primarily in the field of geophysics [1]. The purpose of this study is to introduce MCMC to geochemical inverse problems related to trace element fractionation during concurrent melting, melt transport and melt-rock reaction in the mantle. MCMC method has several advantages over linearized least squares methods in inverting trace element patterns in basalts and mantle rocks. First, MCMC can handle equations that have no explicit analytical solutions which are required by linearized least squares methods for gradient calculation. Second, MCMC converges to global minimum while linearized least squares methods may be stuck at a local minimum or converge slowly due to nonlinearity. Furthermore, MCMC can provide insight into uncertainties of model parameters with non-normal trade-off. We use MCMC to invert for extent of melting, amount of trapped melt, and extent of chemical disequilibrium between the melt and residual solid from REE data in abyssal peridotites from Central Indian Ridge and Mid-Atlantic Ridge. In the first step, we conduct forward calculation of REE evolution with melting models in a reasonable model space. We then build up a chain of melting models according to Metropolis-Hastings algorithm to represent the probability of specific model. We show that chemical disequilibrium is likely to play an important role in fractionating LREE in residual peridotites. In the future, MCMC will be applied to more realistic but also more complicated melting models in which partition coefficients, diffusion coefficients, as well as melting and melt suction rates vary as functions of temperature, pressure and mineral compositions. [1]. Sambridge & Mosegarrd [2002] Rev. Geophys.

  4. Applications of high resolution inverse Raman spectroscopy

    SciTech Connect

    Owyoung, A.; Esherick, P.

    1980-01-01

    The use of high-power, narrow-band lasers has significantly improved the resolving power and sensitivity of inverse Raman spectroscopy of gases. In this paper we shall describe this technique, illustrate its capabilities by showing some Q-branch spectra of heavy spherical tops, and survey some possible future applications.

  5. Sensitive Detection and Serovar Differentiation of Typhoidal and Nontyphoidal Salmonella enterica Species Using 16S rRNA Gene PCR Coupled with High-Resolution Melt Analysis

    PubMed Central

    Masek, Billie J.; Hardick, Justin; Won, Helen; Yang, Samuel; Hsieh, Yu-Hsiang; Rothman, Richard E.; Gaydos, Charlotte A.

    2015-01-01

    Salmonella enterica species infections are a significant public health problem causing high morbidity rates worldwide and high mortality rates in the developing world. These infections are not always rapidly diagnosed as a cause of bloodstream infections because of the limitations of blood culture, which greatly affects clinical care as a result of treatment delays. A molecular diagnostic assay that could rapidly detect and identify S. enterica species infections as a cause of sepsis is needed. Nine typhoidal and nontyphoidal S. enterica serovars were used to establish the limit of detection (LOD) of a previously published 16S rRNA gene PCR (16S PCR) in mock whole blood specimens. In addition, 16 typhoidal and nontyphoidal S. enterica serovars were used to evaluate the serovar differentiation capability of 16S PCR coupled with high-resolution melt analysis. The overall LOD of 16S PCR for the nine typhoidal and nontyphoidal S. enterica serovars analyzed was <10 colony-forming units per milliliter (CFU/mL) in mock whole blood specimens, with the lowest and highest LOD at <1 CFU/mL and 9 CFU/mL, respectively. By high-resolution melt analysis, the typhoidal and nontyphoidal S. enterica serovar groups analyzed each generated a unique grouping code, allowing for serovar-level identification. 16S PCR coupled with high-resolution melt analysis could be a useful molecular diagnostic that could enhance the current diagnostic, treatment, and surveillance methods of S. enterica bloodstream infections. PMID:24365382

  6. High-resolution melting analysis of the spa locus reveals significant diversity within sequence type 93 methicillin-resistant Staphylococcus aureus from northern Australia.

    PubMed

    Tong, S Y C; Lilliebridge, R A; Holt, D C; McDonald, M I; Currie, B J; Giffard, P M

    2009-12-01

    High-resolution melting analysis is an inherently robust, easy and inexpensive approach to the examination of genomic regions containing single-nucleotide polymorphisms and hypervariable loci. Staphylococcus aureus sequence type (ST) 93 is a singleton, Panton-Valentine leukocidin-positive clone unique to Australia. A high-resolution melting-based method for the identification of ST93 was developed, and a similar approach was used to reveal diversity within the spa locus of this lineage. Statistical and graphical methods that account for instrumental and operator-dependent variation in high-resolution melting curves were developed, to allow greater confidence and reproducibility in deciding whether another curve is truly different from the baseline curve of an amplicon with known sequence. The data support a very early acquisition, or multiple independent acquisitions, of SCCmec by ST93 methicillin-susceptible S. aureus (MSSA), and the coexistence of MSSA and methicillin-resistant S. aureus versions of the same lineage within northern Australia. PMID:19392885

  7. Towards a Pathogenic Escherichia coli Detection Platform Using Multiplex SYBR®Green Real-Time PCR Methods and High Resolution Melting Analysis

    PubMed Central

    Kagkli, Dafni-Maria; Folloni, Silvia; Barbau-Piednoir, Elodie; Van den Eede, Guy; Van den Bulcke, Marc

    2012-01-01

    Escherichia coli is a group of bacteria which has raised a lot of safety concerns in recent years. Five major intestinal pathogenic groups have been recognized amongst which the verocytotoxin or shiga-toxin (stx1 and/or stx2) producing E. coli (VTEC or STEC respectively) have received a lot of attention recently. Indeed, due to the high number of outbreaks related to VTEC strains, the European Food Safety Authority (EFSA) has requested the monitoring of the “top-five” serogroups (O26, O103, O111, O145 and O157) most often encountered in food borne diseases and addressed the need for validated VTEC detection methods. Here we report the development of a set of intercalating dye Real-time PCR methods capable of rapidly detecting the presence of the toxin genes together with intimin (eae) in the case of VTEC, or aggregative protein (aggR), in the case of the O104:H4 strain responsible for the outbreak in Germany in 2011. All reactions were optimized to perform at the same annealing temperature permitting the multiplex application in order to minimize the need of material and to allow for high-throughput analysis. In addition, High Resolution Melting (HRM) analysis allowing the discrimination among strains possessing similar virulence traits was established. The development, application to food samples and the flexibility in use of the methods are thoroughly discussed. Together, these Real-time PCR methods facilitate the detection of VTEC in a new highly efficient way and could represent the basis for developing a simple pathogenic E. coli platform. PMID:22761753

  8. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis

    PubMed Central

    Hong, Yanbin; Pandey, Manish K.; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K.; Liang, Xuanqiang; Huang, Shangzhi

    2015-01-01

    The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut. PMID:26697032

  9. Identification and Evaluation of Single-Nucleotide Polymorphisms in Allotetraploid Peanut (Arachis hypogaea L.) Based on Amplicon Sequencing Combined with High Resolution Melting (HRM) Analysis.

    PubMed

    Hong, Yanbin; Pandey, Manish K; Liu, Ying; Chen, Xiaoping; Liu, Hong; Varshney, Rajeev K; Liang, Xuanqiang; Huang, Shangzhi

    2015-01-01

    The cultivated peanut (Arachis hypogaea L.) is an allotetraploid (AABB) species derived from the A-genome (Arachis duranensis) and B-genome (Arachis ipaensis) progenitors. Presence of two versions of a DNA sequence based on the two progenitor genomes poses a serious technical and analytical problem during single nucleotide polymorphism (SNP) marker identification and analysis. In this context, we have analyzed 200 amplicons derived from expressed sequence tags (ESTs) and genome survey sequences (GSS) to identify SNPs in a panel of genotypes consisting of 12 cultivated peanut varieties and two diploid progenitors representing the ancestral genomes. A total of 18 EST-SNPs and 44 genomic-SNPs were identified in 12 peanut varieties by aligning the sequence of A. hypogaea with diploid progenitors. The average frequency of sequence polymorphism was higher for genomic-SNPs than the EST-SNPs with one genomic-SNP every 1011 bp as compared to one EST-SNP every 2557 bp. In order to estimate the potential and further applicability of these identified SNPs, 96 peanut varieties were genotyped using high resolution melting (HRM) method. Polymorphism information content (PIC) values for EST-SNPs ranged between 0.021 and 0.413 with a mean of 0.172 in the set of peanut varieties, while genomic-SNPs ranged between 0.080 and 0.478 with a mean of 0.249. Total 33 SNPs were used for polymorphism detection among the parents and 10 selected lines from mapping population Y13Zh (Zhenzhuhei × Yueyou13). Of the total 33 SNPs, nine SNPs showed polymorphism in the mapping population Y13Zh, and seven SNPs were successfully mapped into five linkage groups. Our results showed that SNPs can be identified in allotetraploid peanut with high accuracy through amplicon sequencing and HRM assay. The identified SNPs were very informative and can be used for different genetic and breeding applications in peanut. PMID:26697032

  10. Strong thermodynamic coupling between sub-ice-shelf melting and sea ice in a high-resolution global sea-ice-ocean isopycnal model

    NASA Astrophysics Data System (ADS)

    Sergienko, O. V.

    2015-12-01

    Sub-ice-shelf melting(freezing) of the Antarctic ice shelves acts as a source(sink) of freshwater, therefore, affects ocean water properties and circulation. In its turn, sub-ice-shelf melting/freezing is controlled by the ocean water properties that reach the sub-ice-shelf cavities. The properties of these water masses are determined by heat and fresh-water exchange with sea ice and atmosphere. Simulations of a high-resolution (1/8 deg) global sea-ice-ocean isopycnal model capable to resolve the ocean circulation in sub-ice-shelf cavities of Antarctic ice shelves and account for the thermodynamic interaction of the circulation with ice shelves show that melting/freezing rates have a strong seasonal cycle with highest melting rates observed in the Austral Fall. On the continental shelf, subsurface ocean temperatures (100-300 m) have a similar seasonal cycle which is lagged with respect to the surface. Shelf temperatures peak in the summertime, followed by rapid cooling towards the freezing point as seasonal ice cover increases. The lagged warming in the subsurface is attributable to reduced heat loss to the atmosphere in the presence of seasonal sea ice. This suggests that the seasonal cycle in melt rates is controlled by the phasing of subsurface temperatures on the continental shelf, which is in turn dominated by sea ice. The outflowing fresh, cold and light meltwater formed in sub-ice-shelf cavities remains in the mixed layer and promotes formation of sea ice and its longer persistence into the Austral Summer. These processes suggest the presence of strong mutual feedbacks between sub-ice-shelf melting and sea ice formation around Antarctic ice shelves.

  11. High-resolution melting analysis (HRM) for differentiation of four major Taeniidae species in dogs Taenia hydatigena, Taenia multiceps, Taenia ovis, and Echinococcus granulosus sensu stricto.

    PubMed

    Dehghani, Mansoureh; Mohammadi, Mohammad Ali; Rostami, Sima; Shamsaddini, Saeedeh; Mirbadie, Seyed Reza; Harandi, Majid Fasihi

    2016-07-01

    Tapeworms of the genus Taenia include several species of important parasites with considerable medical and veterinary significance. Accurate identification of these species in dogs is the prerequisite of any prevention and control program. Here, we have applied an efficient method for differentiating four major Taeniid species in dogs, i.e., Taenia hydatigena, T. multiceps, T. ovis, and Echinococcus granulosus sensu stricto. High-resolution melting (HRM) analysis is simpler, less expensive, and faster technique than conventional DNA-based assays and enables us to detect PCR amplicons in a closed system. Metacestode samples were collected from local abattoirs from sheep. All the isolates had already been identified by PCR-sequencing, and their sequence data were deposited in the GenBank. Real-time PCR coupled with HRM analysis targeting mitochondrial cox1 and ITS1 genes was used to differentiate taeniid species. Distinct melting curves were obtained from ITS1 region enabling accurate differentiation of three Taenia species and E. granulosus in dogs. The HRM curves of Taenia species and E .granulosus were clearly separated at Tm of 85 to 87 °C. In addition, double-pick melting curves were produced in mixed infections. Cox1 melting curves were not decisive enough to distinguish four taeniids. In this work, the efficiency of HRM analysis to differentiate four major taeniid species in dogs has been demonstrated using ITS1 gene. PMID:27008188

  12. Detection of plant oil DNA using high resolution melting (HRM) post PCR analysis: a tool for disclosure of olive oil adulteration.

    PubMed

    Vietina, Michelangelo; Agrimonti, Caterina; Marmiroli, Nelson

    2013-12-15

    Extra virgin olive oil is frequently subjected to adulterations with addition of oils obtained from plants other than olive. DNA analysis is a fast and economic tool to identify plant components in oils. Extraction and amplification of DNA by PCR was tested in olives, in milled seeds and in oils, to investigate its use in olive oil traceability. DNA was extracted from different oils made of hazelnut, maize, sunflower, peanut, sesame, soybean, rice and pumpkin. Comparing the DNA melting profiles in reference plant materials and in the oils, it was possible to identify any plant components in oils and mixtures of oils. Real-Time PCR (RT-PCR) platform has been added of the new methodology of high resolution melting (HRM), both were used to analyse olive oils mixed with different percentage of other oils. Results showed HRM a cost effective method for efficient detection of adulterations in olive oils. PMID:23993554

  13. The utility of high-resolution melting analysis of SNP nucleated PCR amplicons--an MLST based Staphylococcus aureus typing scheme.

    PubMed

    Lilliebridge, Rachael A; Tong, Steven Y C; Giffard, Philip M; Holt, Deborah C

    2011-01-01

    High resolution melting (HRM) analysis is gaining prominence as a method for discriminating DNA sequence variants. Its advantage is that it is performed in a real-time PCR device, and the PCR amplification and HRM analysis are closed tube, and effectively single step. We have developed an HRM-based method for Staphylococcus aureus genotyping. Eight single nucleotide polymorphisms (SNPs) were derived from the S. aureus multi-locus sequence typing (MLST) database on the basis of maximized Simpson's Index of Diversity. Only G↔A, G↔T, C↔A, C↔T SNPs were considered for inclusion, to facilitate allele discrimination by HRM. In silico experiments revealed that DNA fragments incorporating the SNPs give much higher resolving power than randomly selected fragments. It was shown that the predicted optimum fragment size for HRM analysis was 200 bp, and that other SNPs within the fragments contribute to the resolving power. Six DNA fragments ranging from 83 bp to 219 bp, incorporating the resolution optimized SNPs were designed. HRM analysis of these fragments using 94 diverse S. aureus isolates of known sequence type or clonal complex (CC) revealed that sequence variants are resolved largely in accordance with G+C content. A combination of experimental results and in silico prediction indicates that HRM analysis resolves S. aureus into 268 "melt types" (MelTs), and provides a Simpson's Index of Diversity of 0.978 with respect to MLST. There is a high concordance between HRM analysis and the MLST defined CCs. We have generated a Microsoft Excel key which facilitates data interpretation and translation between MelT and MLST data. The potential of this approach for genotyping other bacterial pathogens was investigated using a computerized approach to estimate the densities of SNPs with unlinked allelic states. The MLST databases for all species tested contained abundant unlinked SNPs, thus suggesting that high resolving power is not dependent upon large numbers of SNPs

  14. Hybrid analysis (barcode-high resolution melting) for authentication of Thai herbal products, Andrographis paniculata (Burm.f.) Wall.ex Nees

    PubMed Central

    Osathanunkul, Maslin; Suwannapoom, Chatmongkon; Khamyong, Nuttaluck; Pintakum, Danupol; Lamphun, Santisuk Na; Triwitayakorn, Kanokporn; Osathanunkul, Kitisak; Madesis, Panagiotis

    2016-01-01

    Background: Andrographis paniculata Nees is a medicinal plant with multiple pharmacological properties. It has been used over many centuries as a household remedy. A. paniculata products sold on the markets are in processed forms so it is difficult to authenticate. Therefore buying the herbal products poses a high-risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed. Materials and Methods: High resolution melting analysis coupled with DNA barcoding (Bar-HRM) was applied to detect adulteration in commercial herbal products. The rbcL barcode was selected to use in primers design for HRM analysis to produce standard melting profile of A. paniculata species. DNA of the tested commercial products was isolated and their melting profiles were then generated and compared with the standard A. paniculata. Results: The melting profiles of the rbcL amplicons of the three closely related herbal species (A. paniculata, Acanthus ebracteatus and Rhinacanthus nasutus) are clearly separated so that they can be distinguished by the developed method. The method was then used to authenticate commercial herbal products. HRM curves of all 10 samples tested are similar to A. paniculata which indicated that all tested products were contained the correct species as labeled. Conclusion: The method described in this study has been proved to be useful in aiding identification and/or authenticating A. paniculata. This Bar-HRM analysis has allowed us easily to determine the A. paniculata species in herbal products on the markets even they are in processed forms. SUMMARY We propose the use of DNA barcoding combined with High Resolution Melting analysis for authenticating of Andrographis paniculata products.The developed method can be used regardless of the type of the DNA template (fresh or dried tissue, leaf, and stem).rbcL region was chosen for the analysis and work well with our samplesWe can easily

  15. Hot-melt extrusion of polyvinyl alcohol for oral immediate release applications.

    PubMed

    De Jaeghere, W; De Beer, T; Van Bocxlaer, J; Remon, J P; Vervaet, C

    2015-08-15

    The primary purpose of this study was to process partially hydrolyzed PVOH grades (degree of hydroxylation (DH): 33-88%) via HME and to evaluate them as carrier for oral immediate release dosage forms in order to improve the release rate of poorly water soluble drugs (i.e., HCT and CEL) via the formulation of solid dispersions. PVOH grades (DH >70%) were able to solubilize HCT and CEL up to 15%, but required higher extrusion temperature, due to the crystalline nature of PVOH. The highest drug release rate was observed from hot-melt extruded PVOH samples with a high DH. While drug release from extrudates consisting of PVOH with a low DH was affected by ionic strength, there was no influence of pH and ionic strength on HCT release from PVOH samples with a higher DH. However, PVOH (DH >70%) required higher extrusion temperatures, which could hamper its application for thermosensitive drugs. Therefore, the secondary purpose was to investigate the effect of sorbitol, a water-soluble plasticizer, on the thermal properties of hot-melt extruded PVOH (DH >70%). The melting of PVOH/sorbitol mixture was required to establish molecular interactions between PVOH and sorbitol. These molecular interactions were reflected in the HME behavior: whereas an extrusion temperature of 180 °C was necessary to process physical mixtures of PVOH (DH >70%) and sorbitol, only 140 °C was necessary during re-extrusion (after quench cooling and cryomilling) of the PVOH/sorbitol mixture. In addition, the in vitro and in vivo dug release of plasticized PVOH was examined; whereas the CEL/PVO/sorbitol system was able to maintain supersaturation during in vitro dissolution (0.1N HCl) compared to Celebrex(®), the in vivo pharmacokinetic parameters (AUC0-24h, Cmax and Tmax) were highly comparable. PMID:26160667

  16. Hot-Melt Extrusion: from Theory to Application in Pharmaceutical Formulation.

    PubMed

    Patil, Hemlata; Tiwari, Roshan V; Repka, Michael A

    2016-02-01

    Hot-melt extrusion (HME) is a promising technology for the production of new chemical entities in the developmental pipeline and for improving products already on the market. In drug discovery and development, industry estimates that more than 50% of active pharmaceutical ingredients currently used belong to the biopharmaceutical classification system II (BCS class II), which are characterized as poorly water-soluble compounds and result in formulations with low bioavailability. Therefore, there is a critical need for the pharmaceutical industry to develop formulations that will enhance the solubility and ultimately the bioavailability of these compounds. HME technology also offers an opportunity to earn intellectual property, which is evident from an increasing number of patents and publications that have included it as a novel pharmaceutical formulation technology over the past decades. This review had a threefold objective. First, it sought to provide an overview of HME principles and present detailed engineered extrusion equipment designs. Second, it included a number of published reports on the application of HME techniques that covered the fields of solid dispersions, microencapsulation, taste masking, targeted drug delivery systems, sustained release, films, nanotechnology, floating drug delivery systems, implants, and continuous manufacturing using the wet granulation process. Lastly, this review discussed the importance of using the quality by design approach in drug development, evaluated the process analytical technology used in pharmaceutical HME monitoring and control, discussed techniques used in HME, and emphasized the potential for monitoring and controlling hot-melt technology. PMID:26159653

  17. Applications of super-resolution and deblurring to practical sensors

    NASA Astrophysics Data System (ADS)

    Young, S. Susan; Sims, Richard; Kraples, Keith; Waterman, James; Smith, Leslie; Jacobs, Eddie; Corbin, Ted; Larsen, Louis; Driggers, Ronald G.

    2008-04-01

    In image formation and recording process, there are many factors that affect sensor performance and image quality that result in loss of high-frequency information. Two of these common factors are undersampled sensors and sensor's blurring function. Two image processing algorithms, including super-resolution image reconstruction and deblur filtering, have been developed based on characterizing the sources of image degradation from image formation and recording process. In this paper, we discuss the applications of these two algorithms to three practical thermal imaging systems. First, super-resolution and deblurring are applied to a longwave uncooled sensor in a missile seeker. Target resolution is improved in the flight phase of the seeker operation. Second, these two algorithms are applied to a midwave target acquisition sensor for use in long-range target identification. Third, the two algorithms are applied to a naval midwave distributed aperture sensor (DAS) for infrared search and track (IRST) system that is dual use in missile detection and force protection/anti-terrorism applications. In this case, super-resolution and deblurring are used to improve the resolution of on-deck activity discrimination.

  18. Allele-specific extension allows base-pair neutral homozygotes to be discriminated by high-resolution melting of small amplicons.

    PubMed

    Cai, Yanning; Yuan, Yanpeng; Lin, Qingling; Chan, Piu

    2010-11-01

    Not all single-nucleotide polymorphisms (SNPs) can be determined using high-resolution melting (HRM) of small amplicons, especially class 3 and 4 SNPs. This is due mainly to the small shift in the melting temperature (Tm) between two types of homozygote. Choosing rs1869458 (a class 4 SNP) as a sample, we developed a modified small amplicon HRM assay. An allele-specific extension (ASE) primer, which ended at an SNP site and matched only one of the alleles, was added to the reaction as well as additional thermal steps for ASE. Following asymmetric polymerase chain reaction and melting curve analysis, heterozygotes were easily identified. Two types of homozygote were also distinguishable, indicating that extension primers 11 to 13 bases in length worked efficiently in an allele-specific way. Modification of the limiting amplification primer with locked nucleic acid increased the Tm difference between extension and amplification peaks and facilitated subsequent genotyping. In addition, 194 human genomic DNA samples were genotyped with the developed assay and by direct sequencing, with the different methods providing identical genotyping results. In conclusion, ASE-HRM is a simple, inexpensive, closed-tube genotyping method that can be used to examine all types of SNP. PMID:20599636

  19. Rapid detection and identification of Wuchereria bancrofti, Brugia malayi, B. pahangi, and Dirofilaria immitis in mosquito vectors and blood samples by high resolution melting real-time PCR.

    PubMed

    Thanchomnang, Tongjit; Intapan, Pewpan M; Tantrawatpan, Chairat; Lulitanond, Viraphong; Chungpivat, Sudchit; Taweethavonsawat, Piyanan; Kaewkong, Worasak; Sanpool, Oranuch; Janwan, Penchom; Choochote, Wej; Maleewong, Wanchai

    2013-12-01

    A simple, rapid, and high-throughput method for detection and identification of Wuchereria bancrofti, Brugia malayi, Brugia pahangi, and Dirofilaria immitis in mosquito vectors and blood samples was developed using a real-time PCR combined with high-resolution melting (HRM) analysis. Amplicons of the 4 filarial species were generated from 5S rRNA and spliced leader sequences by the real-time PCR and their melting temperatures were determined by the HRM method. Melting of amplicons from W. bancrofti, B. malayi, D. immitis, and B. pahangi peaked at 81.5±0.2℃, 79.0±0.3℃, 76.8±0.1℃, and 79.9±0.1℃, respectively. This assay is relatively cheap since it does not require synthesis of hybridization probes. Its sensitivity and specificity were 100%. It is a rapid and technically simple approach, and an important tool for population surveys as well as molecular xenomonitoring of parasites in vectors. PMID:24516268

  20. Rapid Detection and Identification of Wuchereria bancrofti, Brugia malayi, B. pahangi, and Dirofilaria immitis in Mosquito Vectors and Blood Samples by High Resolution Melting Real-Time PCR

    PubMed Central

    Thanchomnang, Tongjit; Intapan, Pewpan M.; Tantrawatpan, Chairat; Lulitanond, Viraphong; Chungpivat, Sudchit; Taweethavonsawat, Piyanan; Kaewkong, Worasak; Sanpool, Oranuch; Janwan, Penchom; Choochote, Wej

    2013-01-01

    A simple, rapid, and high-throughput method for detection and identification of Wuchereria bancrofti, Brugia malayi, Brugia pahangi, and Dirofilaria immitis in mosquito vectors and blood samples was developed using a real-time PCR combined with high-resolution melting (HRM) analysis. Amplicons of the 4 filarial species were generated from 5S rRNA and spliced leader sequences by the real-time PCR and their melting temperatures were determined by the HRM method. Melting of amplicons from W. bancrofti, B. malayi, D. immitis, and B. pahangi peaked at 81.5±0.2℃, 79.0±0.3℃, 76.8±0.1℃, and 79.9±0.1℃, respectively. This assay is relatively cheap since it does not require synthesis of hybridization probes. Its sensitivity and specificity were 100%. It is a rapid and technically simple approach, and an important tool for population surveys as well as molecular xenomonitoring of parasites in vectors. PMID:24516268

  1. Polymeric formulations for drug release prepared by hot melt extrusion: application and characterization.

    PubMed

    Stanković, Milica; Frijlink, Henderik W; Hinrichs, Wouter L J

    2015-07-01

    Over the past few decades hot melt extrusion (HME) has emerged as a powerful processing technology for the production of pharmaceutical solid dosage forms in which an active pharmaceutical ingredient (API) is dispersed into polymer matrices. It has been shown that formulations using HME can provide time-controlled, sustained and targeted drug delivery, and improved bioavailability of poorly soluble drugs. In this review, the basic principles of the HME process are described together with an overview of some of the most common biodegradable and nonbiodegradable polymers used for the preparation of different formulations using this method. Further, the applications of HME in drug delivery and analytical techniques employed to characterize HME products are addressed. PMID:25660507

  2. Application of hot melt extrusion for poorly water-soluble drugs: limitations, advances and future prospects.

    PubMed

    Lu, Ming; Guo, Zhefei; Li, Yongcheng; Pang, Huishi; Lin, Ling; Liu, Xu; Pan, Xin; Wu, Chuanbin

    2014-01-01

    Hot melt extrusion (HME) is a powerful technology to enhance the solubility and bioavailability of poorly water-soluble drugs by producing amorphous solid dispersions. Although the number of articles and patents about HME increased dramatically in the past twenty years, there are very few commercial products by far. The three main obstacles limiting the commercial application of HME are summarized as thermal degradation of heat-sensitive drugs at high process temperature, recrystallization of amorphous drugs during storage and dissolving process, and difficulty to obtain products with reproducible physicochemical properties. Many efforts have been taken in recent years to understand the basic mechanism underlying these obstacles and then to overcome them. This article reviewed and summarized the limitations, recent advances, and future prospects of HME. PMID:23651401

  3. Rapid Detection and Statistical Differentiation of KPC Gene Variants in Gram-Negative Pathogens by Use of High-Resolution Melting and ScreenClust Analyses

    PubMed Central

    Roth, Amanda L.

    2013-01-01

    In the United States, the production of the Klebsiella pneumoniae carbapenemase (KPC) is an important mechanism of carbapenem resistance in Gram-negative pathogens. Infections with KPC-producing organisms are associated with increased morbidity and mortality; therefore, the rapid detection of KPC-producing pathogens is critical in patient care and infection control. We developed a real-time PCR assay complemented with traditional high-resolution melting (HRM) analysis, as well as statistically based genotyping, using the Rotor-Gene ScreenClust HRM software to both detect the presence of blaKPC and differentiate between KPC-2-like and KPC-3-like alleles. A total of 166 clinical isolates of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii with various β-lactamase susceptibility patterns were tested in the validation of this assay; 66 of these organisms were known to produce the KPC β-lactamase. The real-time PCR assay was able to detect the presence of blaKPC in all 66 of these clinical isolates (100% sensitivity and specificity). HRM analysis demonstrated that 26 had KPC-2-like melting peak temperatures, while 40 had KPC-3-like melting peak temperatures. Sequencing of 21 amplified products confirmed the melting peak results, with 9 isolates carrying blaKPC-2 and 12 isolates carrying blaKPC-3. This PCR/HRM assay can identify KPC-producing Gram-negative pathogens in as little as 3 h after isolation of pure colonies and does not require post-PCR sample manipulation for HRM analysis, and ScreenClust analysis easily distinguishes blaKPC-2-like and blaKPC-3-like alleles. Therefore, this assay is a rapid method to identify the presence of blaKPC enzymes in Gram-negative pathogens that can be easily integrated into busy clinical microbiology laboratories. PMID:23077125

  4. A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β0-thalassaemia deletion

    PubMed Central

    Leng Kho, Siew; Heng Chua, Kek; George, Elizabeth; Tan, Jin Ai Mary Anne

    2015-01-01

    Homozygosity for the α-thalassaemia Southeast Asian (α-SEA) and Filipino β0-thalassaemia (β-FIL) deletions can cause serious complications leading to foetal death or life-long blood transfusions. A rapid and accurate molecular detection assay is essential in populations where the deletions are common. In this study, gap-polymerase chain reaction (PCR) with high resolution melting (HRM) analysis was developed to detect both the large deletions. Melting curves at 86.9 ± 0.1 °C were generated by normal individuals without the α-SEA deletion, 84.7 ± 0.1 °C by homozygous α-SEA deletion individuals and two melting curves at 84.7 ± 0.1 °C and 86.9 ± 0.1 °C by α-SEA deletion carriers. Normal individuals without the β-FIL deletion produce amplicons with a melting temperature (Tm) at 74.6 ± 0.1 °C, homozygous β-FIL individuals produce amplicons with Tm at 73.6 ± 0.1 °C and heterozygous β-FIL individuals generate two amplicons with Tm at 73.6 ± 0.1 °C and 74.6 ± 0.1 °C. Evaluation using blinded tests on 220 DNA samples showed 100% sensitivity and specificity. The developed assays are sensitive and specific for rapid molecular and prenatal diagnosis for the α-SEA and β-FIL deletions. PMID:26365497

  5. A novel gap-PCR with high resolution melting analysis for the detection of α-thalassaemia Southeast Asian and Filipino β°-thalassaemia deletion.

    PubMed

    Kho, Siew Leng; Chua, Kek Heng; George, Elizabeth; Tan, Jin Ai Mary Anne

    2015-01-01

    Homozygosity for the α-thalassaemia Southeast Asian (α-SEA) and Filipino β°-thalassaemia (β-FIL) deletions can cause serious complications leading to foetal death or life-long blood transfusions. A rapid and accurate molecular detection assay is essential in populations where the deletions are common. In this study, gap-polymerase chain reaction (PCR) with high resolution melting (HRM) analysis was developed to detect both the large deletions. Melting curves at 86.9 ± 0.1 °C were generated by normal individuals without the α-SEA deletion, 84.7 ± 0.1 °C by homozygous α-SEA deletion individuals and two melting curves at 84.7 ± 0.1 °C and 86.9 ± 0.1 °C by α-SEA deletion carriers. Normal individuals without the β-FIL deletion produce amplicons with a melting temperature (Tm) at 74.6 ± 0.1 °C, homozygous β-FIL individuals produce amplicons with Tm at 73.6 ± 0.1 °C and heterozygous β-FIL individuals generate two amplicons with Tm at 73.6 ± 0.1 °C and 74.6 ± 0.1 °C. Evaluation using blinded tests on 220 DNA samples showed 100% sensitivity and specificity. The developed assays are sensitive and specific for rapid molecular and prenatal diagnosis for the α-SEA and β-FIL deletions. PMID:26365497

  6. Melt-growth bulk superconductors and application to an axial-gap-type rotating machine

    NASA Astrophysics Data System (ADS)

    Zhang, Yufeng; Zhou, Difan; Ida, Tetsuya; Miki, Motohiro; Izumi, Mitsuru

    2016-04-01

    The present manuscript addresses key issues in the course of our study of materials processing of bulk high-temperature superconductors, trapped flux and its application to a prototype axial-gap-type rotating machine. The TUMSAT group has conducted a series of studies since 2003 on the growth of GdBa2Cu3O7-δ bulk material and its application in a compact low-speed high-torque rotating machine. In the stage of material growth, gaining the advantage of a large motive torque density requires large integrated flux in the motor/generators. A large grain surface might be required with sophisticated techniques for the melt-growth texture in the bulk with optimal flux pinning. In the second stage, the in situ magnetization procedure for bulk superconductors in the applied machine is a crucial part of the technology. Pulsed current excitation by using an armature copper winding has magnetized field pole bulks on the rotor. The axial-gap flux synchronous machine studied in the past decade is a condensed technology and indicates that further scientific development is required for a future compact machine to be superior to conventional ones in accordance with the cryogenic periphery and flux stabilization.

  7. Amundsen Sea sector ice shelf thickness, melt rates, and inland response from annual high-resolution DEM mosaics

    NASA Astrophysics Data System (ADS)

    Shean, D. E.; Joughin, I. R.; Smith, B. E.; Alexandrov, O.; Moratto, Z.; Porter, C. C.; Morin, P. J.

    2014-12-01

    Significant grounding line retreat, acceleration, and thinning have occurred along the Amundsen Sea sector of West Antarctica in recent decades. These changes are driven primarily by ice-ocean interaction beneath ice shelves, but existing observations of the spatial distribution, timing, and magnitude of ice shelf melt are limited. Using the NASA Ames Stereo Pipeline, we generated digital elevation models (DEMs) with ~2 m posting from all ~450 available WorldView-1/2 along-track stereopairs for the Amundsen Sea sector. A novel iterative closest point algorithm was used to coregister DEMs to filtered Operation IceBridge ATM/LVIS data and ICESat-1 GLAS data, offering optimal sub-meter horizontal/vertical accuracy. The corrected DEMs were used to produce annual mosaics for the entire ~500x700 km region with focused, sub-annual products for ice shelves and grounding zones. These mosaics provide spatially-continuous measurements of ice shelf topography with unprecedented detail. Using these data, we derive estimates of ice shelf thickness for regions in hydrostatic equilibrium and map networks of sub-shelf melt channels for the Pine Island (PIG), Thwaites, Crosson, and Dotson ice shelves. We also document the break-up of the Thwaites ice shelf and PIG rift evolution leading up to the 2013 calving event. Eulerian difference maps document 2010-2014 thinning over fast-flowing ice streams and adjacent grounded ice. These data reveal the greatest thinning rates over the Smith Glacier ice plain and slopes beyond the margins of the fast-flowing PIG trunk. Difference maps also highlight the filling of at least two subglacial lakes ~30 km upstream of the PIG grounding line in 2011. Lagrangian difference maps reveal the spatial distribution of ice shelf thinning, which can primarily be attributed to basal melt. Preliminary results show focused ice shelf thinning within troughs and large basal channels, especially along the western margin of the Dotson ice shelf. These new data

  8. Impact of melt segregation on chemical composition with application to deep crustal hot zones

    NASA Astrophysics Data System (ADS)

    Solano, J.; Jackson, M.; Sparks, R. S.; Blundy, J. D.

    2010-12-01

    Models of heat transfer during the emplacement of mantle-derived basaltic sills in the mid- to lower crust demonstrate that large volumes of evolved melt may be generated in deep crustal hot zones (DCHZ). These models consider only the thermal evolution of a DCHZ, yet melt must also segregate from along the grain boundaries where it initially resides to form a magma which leaves the DCHZ. However, models which include melt migration describe phase change using simple melt fraction-temperature relations, which do not capture the impact of melt segregation on the chemical evolution of melt and residual solid. We present a model of melting and buoyancy-driven melt segregation in which phase change is described using a phase diagram and the chemical evolution of the melt and residual solid is properly captured. Melt migration is assumed to occur along grain boundaries so local thermodynamic equilibrium is maintained. We begin by using a simple binary phase diagram and model a 1-D column with several different initial compositions and thermal boundary conditions. We investigate this simple case because it could be closely replicated in the laboratory, and allows aspects of the physics which hitherto have been poorly understood to be clearly observed and explained. It is trivial to extend our model to more complex systems. For an initially homogenous column, in which the fraction of component A is less than the eutectic composition, we find that the melt fraction at the base decreases and the bulk composition becomes enriched in component A, while the melt fraction at the top increases and the bulk composition tends towards the eutectic composition. Melt segregation provides a mechanism for accumulating melt of (or close to) the eutectic composition, but at much higher melt fractions than predicted by purely thermal models; for example, static melting to 10% may yield the eutectic composition, but melt segregation allows that composition to accumulate to 100%. For a

  9. Clinical applications of high-resolution ocular magnetic resonance imaging.

    PubMed

    Tanitame, Keizo; Sone, Takashi; Kiuchi, Yoshiaki; Awai, Kazuo

    2012-11-01

    Magnetic resonance imaging (MRI) using fast sequences with subjects staring at a target can provide motion-free ocular images, and small receiver surface coils make it possible to produce ocular images with high spatial resolution. MRI using half-Fourier single-shot rapid acquisition with a relaxation enhancement sequence as a fast T2-weighted imaging yields useful images for the morphologic diagnosis of ocular diseases, and MRI using a fast spoiled gradient-recalled-echo sequence as a T1-weighted imaging yields additional information by the administration of gadolinium-based contrast material for assessing the vascularity of intraocular tumors. These ocular imaging techniques are useful for the evaluation of patients with angle closure glaucoma, congenital abnormality of ocular globes, intraocular tumors and several types of detachments, as well as patients after ocular surgery. In this pictorial essay, we demonstrate the clinical applications of fast high-resolution ocular MRI with fixation of the subjects' visual foci. PMID:22923185

  10. High-resolution adaptive holographic interferometer for biomedical applications

    NASA Astrophysics Data System (ADS)

    Dovgalenko, George; Dagdanova, Ayuna

    2007-07-01

    We realized new adaptive holographic sensor and interferometer, which allows to visualize high-resolution 3D images of diffuse reflected objects in Continue Hologram Registration Regime- CHRR. The coupled laser wave nonlinear theory was applied for optimization of hologram recording in crystals symmetry 23 and optimized experimental set up. Experimentally demonstrated dynamical holographic image sensors on doped 23 symmetry photosensitive crystals, with resolution 7900-lines/mm at 632 nm and 11641 lines/mm at 440 nm for 15 mW CW HeNe and He-Cd lasers. The results are presented for holographic visualization of Cryogenic and Ultrasonic near field images of Surgical Medical Instrument. Application of CHRR interferometer for hologram registration of moving biological object in "vivo" is illustrated.

  11. Application of the Billet Casting Method to Determine the Onset of Incipient Melting of 319 Al Alloy Engine Blocks

    NASA Astrophysics Data System (ADS)

    Lombardi, A.; Ravindran, C.; MacKay, R.

    2015-06-01

    The increased use of Al for automotive applications has resulted from the need to improve vehicle fuel efficiency. Aluminum alloy engine blocks fulfil the need of lightweighting. However, there are many challenges associated with thermo-mechanical mismatch between Al and the gray cast iron cylinder liners, which result in large tensile residual stress along the cylinder bores. This requires improced mechanical properties in this region to prevent premature engine failure. In this study, replicating billet castings were used to simulate the engine block solution heat treatment process and determine the onset of incipient melting. Microstructural changes during heat treatment were assessed with SEM and EDX, while thermal analysis was carried out using differential scanning calorimetry. The results suggest that solution heat treatment at 500 °C was effective in dissolving secondary phase particles, while solutionizing at 515 or 530 °C caused incipient melting of Al2Cu and Al5Mg8Cu2Si6. Incipient melting caused the formation ultra-fine eutectic clusters consisting of Al, Al2Cu, and Al5Mg8Cu2Si6 on quenching. In addition, DSC analysis found that incipient melting initiated at 507 °C for all billets, although the quantity of local melting reduced with microstructural refinement as evidenced by smaller endothermic peaks and energy absorption. The results from this study will assist in improving engine block casting integrity and process efficiency.

  12. Identification and Differentiation of Monilinia Species Causing Brown Rot of Pome and Stone Fruit using High-Resolution Melting (HRM) Analysis.

    PubMed

    Papavasileiou, Antonios; Madesis, Panagiotis B; Karaoglanidis, George S

    2016-09-01

    Brown rot is a devastating disease of stone fruit caused by Monilinia spp. Among these species, Monilinia fructicola is a quarantine pathogen in Europe but has recently been detected in several European countries. Identification of brown rot agents relies on morphological differences or use of molecular methods requiring fungal isolation. The current study was initiated to develop and validate a high-resolution melting (HRM) method for the identification of the Monilinia spp. and for the detection of M. fructicola among other brown rot pathogens. Based on the sequence of the cytb intron from M. laxa, M. fructicola, M. fructigena, M. mumecola, M. linhartiana, and M. yunnanensis isolates originating from several countries, a pair of universal primers for species identification and a pair of primers specific to M. fructicola were designed. The specificity of the primers was verified to ensure against cross-reaction with other fungal species. The melting curve analysis using the universal primers generated six different HRM curve profiles, each one specific for each species. Τhe HRM analysis primers specific to M. fructicola amplified a 120-bp region with a distinct melt profile corresponding to the presence of M. fructicola, regardless of the presence of other species. HRM analysis can be a useful tool for rapid identification and differentiation of the six Monilinia spp. using a single primer pair. This novel assay has the potential for simultaneous identification and differentiation of the closely related Monilinia spp. as well as for the differentiation of M. fructicola from other common pathogens or saprophytes that may occur on the diseased fruit. PMID:27247082

  13. Application of MODIS snow cover products: wildfire impacts on snow and melt in the Sierra Nevada

    NASA Astrophysics Data System (ADS)

    Micheletty, P. D.; Kinoshita, A. M.; Hogue, T. S.

    2014-07-01

    The current work evaluates the spatial and temporal variability in snow after a large forest fire in northern California with Moderate Resolution Imaging Spectroradiometer (MODIS) snow covered area and grain size (MODSCAG) algorithm. MODIS MOD10A1 fractional snow covered area and MODSCAG fractional snow cover products are utilized to detect spatial and temporal changes in snowpack after the 2007 Moonlight Fire and an unburned basin, Grizzly Ridge, for water years (WY) 2002-2012. Estimates of canopy adjusted and non-adjusted MODSCAG fractional snow covered area (fSCA) are smoothed and interpolated to provide a continuous timeseries of daily basin average snow extent over the two basins. The removal of overstory canopy by wildfire exposes more snow cover; however, elemental pixel comparisons and statistical analysis show that the MOD10A1 product has a tendency to overestimate snow coverage pre-fire, muting the effects of wildfire. The MODSCAG algorithm better distinguishes sub-pixel snow coverage in forested areas and is highly correlated to soil burn severity after the fire. Annual MODSCAG fSCA estimates show statistically significant increased fSCA in the Moonlight Fire study area after the fire (WY 2008-2011; P < 0.01) compared to pre-fire averages and the control basin. After the fire, the number of days exceeding a pre-fire high snow cover threshold increased by 81%. Canopy reduction increases exposed viewable snow area and the amount of solar radiation that reaches the snowpack leading to earlier basin average melt-out dates compared to the nearby unburned basin. There is also a significant increase in MODSCAG fSCA post-fire regardless of slope or burn severity. Alteration of regional snow cover has significant implications for both short and long-term water supplies for downstream communities and resource managers.

  14. Application of MODIS snow cover products: wildfire impacts on snow and melt in the Sierra Nevada

    NASA Astrophysics Data System (ADS)

    Micheletty, P. D.; Kinoshita, A. M.; Hogue, T. S.

    2014-11-01

    The current work evaluates the spatial and temporal variability in snow after a large forest fire in northern California using Moderate Resolution Imaging Spectroradiometer (MODIS) snow-covered area and grain size (MODSCAG). MODIS MOD10A1 fractional snow-covered area and MODSCAG fractional snow cover products are utilized to detect spatial and temporal changes in snowpack after the 2007 Moonlight Fire and an unburned basin, Grizzly Ridge, for water years (WY) 2002-2012. Estimates of canopy-adjusted and non-adjusted MODSCAG fractional snow-covered area (fSCA) are smoothed and interpolated to provide a continuous time series of average daily snow extent over the two basins. The removal of overstory canopy by wildfire exposes more snow cover; however, elemental pixel comparisons and statistical analysis show that the MOD10A1 product has a tendency to overestimate snow coverage pre-fire, muting the observed effects of wildfire. The MODSCAG algorithm better distinguishes subpixel snow coverage in forested areas and is highly correlated to soil burn severity after the fire. Annual MODSCAG fSCA estimates show statistically significant increased fSCA in the Moonlight Fire study area after the fire (P < 0.01 for WY 2008-2011) compared to pre-fire averages and the control basin. After the fire, the number of days exceeding a pre-fire high snow-cover threshold increased by 81%. Canopy reduction increases exposed viewable snow area and the amount of solar radiation that reaches the snowpack, leading to earlier basin average melt-out dates compared to the nearby unburned basin. There is also a significant increase in MODSCAG fSCA post-fire regardless of slope or burn severity. Regional snow cover change has significant implications for both short- and long-term water supply for impacted ecosystems, downstream communities, and resource managers.

  15. Duplex High-Resolution Melting Assay for the Simultaneous Genotyping of IL28B rs12979860 and PNPLA3 rs738409 Polymorphisms in Chronic Hepatitis C Patients

    PubMed Central

    Enache, Elena L.; Sin, Anca; Bancu, Ligia; Ramière, Christophe; Diaz, Olivier; André, Patrice; Enache, Liviu S.

    2015-01-01

    Chronic hepatitis C (CHC) is a major burden for public health worldwide. Although newer direct-acting antivirals show good efficacy, their cost precludes their wide adoption in resource-limited regions. Thus, strategies are being developed to help identify patients with high susceptibility to response to classic PEG-interferon + ribavirin therapy. IL28B polymorphism rs12979860 C/T is an important predictor for an efficient response to interferon-based therapy. A genetic variant in adiponutrin (PNPLA3) gene, rs738409 C/G, is associated with steatosis, severity, and progression of liver fibrosis in CHC patients, and predicts treatment outcome in difficult-to-cure HCV-infected patients with advanced fibrosis. We developed a rapid and inexpensive assay based on duplex high-resolution melting (HRM) for the simultaneous genotyping of these two polymorphisms. The assay validation was performed on synthetic DNA templates and 132 clinical samples from CHC patients. When compared with allele-specific PCR and sequencing, our assay showed 100% (95% CI: 0.9724–1) accuracy, with 100% sensitivity and specificity. Our assay was robust against concentration and quality of DNA samples, melting curve normalization intervals, HRM analysis algorithm, and sequence variations near the targeted SNPs (single nucleotide polymorphism). This duplex assay should provide useful information for patient-oriented management and clinical decision-making in CHC. PMID:26389885

  16. Rapid and Reliable Detection of Glucose-6-Phosphate Dehydrogenase (G6PD) Gene Mutations in Han Chinese Using High-Resolution Melting Analysis

    PubMed Central

    Yan, Jing-bin; Xu, Hong-ping; Xiong, Can; Ren, Zhao-rui; Tian, Guo-li; Zeng, Fanyi; Huang, Shu-zhen

    2010-01-01

    Glucose-6-phosphate dehydrogenase (G6PD) deficiency, an X-linked inherited disease, is one of the most common enzymopathies and affects over 400 million people worldwide. In China at least 21 distinct point mutations have been identified so far. In this study high-resolution melting (HRM) analysis was used to screen for G6PD mutations in 260 unrelated Han Chinese individuals, and the rapidity and reliability of this method was investigated. The mutants were readily differentiated by using HRM analysis, which produced distinct melting curves for each tested mutation. Interestingly, G1388A and G1376T, the two most common variants accounting for 50% to 60% of G6PD deficiency mutations in the Chinese population, could be differentiated in a single reaction. Further, two G6PD mutations not previously reported in the Chinese population were identified in this study. One of these mutations, designated “G6PD Jiangxi G1340T,” involved a G1340T substitution in exon 11, predicting a Gly447Val change in the protein. The other mutation involved a C406T substitution in exon 5. The frequencies of the common polymorphism site C1311T/IVS (intervening sequence) XI t93c between patients with G6PD and healthy volunteers were not significantly different. Thus, HRM analysis will be a useful alternative for screening G6PD mutations. PMID:20203002

  17. Rapid and reliable detection of glucose-6-phosphate dehydrogenase (G6PD) gene mutations in Han Chinese using high-resolution melting analysis.

    PubMed

    Yan, Jing-bin; Xu, Hong-ping; Xiong, Can; Ren, Zhao-rui; Tian, Guo-li; Zeng, Fanyi; Huang, Shu-zhen

    2010-05-01

    Glucose-6-phosphate dehydrogenase (G6PD) deficiency, an X-linked inherited disease, is one of the most common enzymopathies and affects over 400 million people worldwide. In China at least 21 distinct point mutations have been identified so far. In this study high-resolution melting (HRM) analysis was used to screen for G6PD mutations in 260 unrelated Han Chinese individuals, and the rapidity and reliability of this method was investigated. The mutants were readily differentiated by using HRM analysis, which produced distinct melting curves for each tested mutation. Interestingly, G1388A and G1376T, the two most common variants accounting for 50% to 60% of G6PD deficiency mutations in the Chinese population, could be differentiated in a single reaction. Further, two G6PD mutations not previously reported in the Chinese population were identified in this study. One of these mutations, designated "G6PD Jiangxi G1340T," involved a G1340T substitution in exon 11, predicting a Gly447Val change in the protein. The other mutation involved a C406T substitution in exon 5. The frequencies of the common polymorphism site C1311T/IVS (intervening sequence) XI t93c between patients with G6PD and healthy volunteers were not significantly different. Thus, HRM analysis will be a useful alternative for screening G6PD mutations. PMID:20203002

  18. Development of a High-Resolution Melting Approach for Scanning Beta Globin Gene Point Mutations in the Greek and Other Mediterranean Populations.

    PubMed

    Chassanidis, Christos; Boutou, Effrossyni; Voskaridou, Ersi; Balassopoulou, Angeliki

    2016-01-01

    Beta-thalassaemia is one of the most common autosomal recessive disorders worldwide. The disease's high incidence, which is observed in the broader Mediterranean area has led to the establishment of molecular diagnostics' assays to prevent affected births. Therefore, the development of a reliable, cost-effective and rapid scanning method for β globin gene point mutations, easily adapted to a routine laboratory, is absolutely essential. Here, we describe, for the first time, the development of a High-Resolution Melting Analysis (HRMA) approach, suitable for scanning the particularly heterogeneous beta globin gene mutations present in the Greek population, and thus adaptable to the Mediterranean and other areas where these mutations have been identified. Within this context, β globin gene regions containing mutations frequently identified in the Greek population were divided in ten overlapping amplicons. Our reactions' setup allowed for the simultaneous amplification of multiple primer sets and partial multiplexing, thereby resulting in significant reduction of the experimental time. DNA samples from β-thalassaemia patients/carriers with defined genotypes were tested. Distinct genotypes displayed distinguishable melting curves, enabling accurate detection of mutations. The described HRMA can be adapted to a high-throughput level. It represents a rapid, simple, cost-effective, reliable, highly feasible and sensitive method for β-thalassaemia gene scanning. PMID:27351925

  19. Development of a high-resolution melting analysis assay for rapid and high-throughput identification of clinically important dermatophyte species.

    PubMed

    Didehdar, M; Khansarinejad, B; Amirrajab, N; Shokohi, T

    2016-07-01

    Accurate identification of dermatophyte species is important both for epidemiological studies and for implementing antifungal treatment strategies. Although nucleic acid amplification-based assays have several advantages over conventional mycological methods, a major disadvantage is their high cost. The aim of this study was to develop a rapid and accurate real-time PCR-based high-resolution melting (HRM) assay for differentiation of the most common dermatophyte species. The oligonucleotide primers were designed to amplify highly conserved regions of the dermatophyte ribosomal DNA. Analysis of a panel containing potentially interfering fungi demonstrated no cross reactivity with the assay. To evaluate the performance characteristics of the method, a total of 250 clinical isolates were tested in comparison with the long-established PCR-RFLP method and the results were reassessed using DNA sequencing, as the reference standard method. The assay is able to type dermatophytes using normalised melting peak, difference plot analysis or electrophoresis on agarose gel methods. The results showed that, in comparison to PCR-RFLP, the developed HRM assay was able to differentiate at least 10 common dermatophytes species with a higher speed, throughput and accuracy. These results indicate that the HRM assay will be a useful sensitive, high throughput and cost-effective method for differentiating the most common dermatophyte species. PMID:26991756

  20. Duplex High-Resolution Melting Assay for the Simultaneous Genotyping of IL28B rs12979860 and PNPLA3 rs738409 Polymorphisms in Chronic Hepatitis C Patients.

    PubMed

    Enache, Elena L; Sin, Anca; Bancu, Ligia; Ramière, Christophe; Diaz, Olivier; André, Patrice; Enache, Liviu S

    2015-01-01

    Chronic hepatitis C (CHC) is a major burden for public health worldwide. Although newer direct-acting antivirals show good efficacy, their cost precludes their wide adoption in resource-limited regions. Thus, strategies are being developed to help identify patients with high susceptibility to response to classic PEG-interferon + ribavirin therapy. IL28B polymorphism rs12979860 C/T is an important predictor for an efficient response to interferon-based therapy. A genetic variant in adiponutrin (PNPLA3) gene, rs738409 C/G, is associated with steatosis, severity, and progression of liver fibrosis in CHC patients, and predicts treatment outcome in difficult-to-cure HCV-infected patients with advanced fibrosis. We developed a rapid and inexpensive assay based on duplex high-resolution melting (HRM) for the simultaneous genotyping of these two polymorphisms. The assay validation was performed on synthetic DNA templates and 132 clinical samples from CHC patients. When compared with allele-specific PCR and sequencing, our assay showed 100% (95% CI: 0.9724-1) accuracy, with 100% sensitivity and specificity. Our assay was robust against concentration and quality of DNA samples, melting curve normalization intervals, HRM analysis algorithm, and sequence variations near the targeted SNPs (single nucleotide polymorphism). This duplex assay should provide useful information for patient-oriented management and clinical decision-making in CHC. PMID:26389885

  1. Development of a High-Resolution Melting Approach for Scanning Beta Globin Gene Point Mutations in the Greek and Other Mediterranean Populations

    PubMed Central

    Chassanidis, Christos; Boutou, Effrossyni; Voskaridou, Ersi; Balassopoulou, Angeliki

    2016-01-01

    Beta-thalassaemia is one of the most common autosomal recessive disorders worldwide. The disease’s high incidence, which is observed in the broader Mediterranean area has led to the establishment of molecular diagnostics’ assays to prevent affected births. Therefore, the development of a reliable, cost-effective and rapid scanning method for β globin gene point mutations, easily adapted to a routine laboratory, is absolutely essential. Here, we describe, for the first time, the development of a High-Resolution Melting Analysis (HRMA) approach, suitable for scanning the particularly heterogeneous beta globin gene mutations present in the Greek population, and thus adaptable to the Mediterranean and other areas where these mutations have been identified. Within this context, β globin gene regions containing mutations frequently identified in the Greek population were divided in ten overlapping amplicons. Our reactions’ setup allowed for the simultaneous amplification of multiple primer sets and partial multiplexing, thereby resulting in significant reduction of the experimental time. DNA samples from β-thalassaemia patients/carriers with defined genotypes were tested. Distinct genotypes displayed distinguishable melting curves, enabling accurate detection of mutations. The described HRMA can be adapted to a high-throughput level. It represents a rapid, simple, cost-effective, reliable, highly feasible and sensitive method for β-thalassaemia gene scanning. PMID:27351925

  2. Method for site-specific detection of m6A nucleoside presence in RNA based on high-resolution melting (HRM) analysis.

    PubMed

    Golovina, Anna Y; Dzama, Margarita M; Petriukov, Kirill S; Zatsepin, Timofei S; Sergiev, Petr V; Bogdanov, Alexey A; Dontsova, Olga A

    2014-02-01

    Chemical landscape of natural RNA species is decorated with the large number of modified nucleosides. Some of those could easily be detected by reverse transcription, while others permit only high-performance liquid chromatography or mass-spectrometry detection. Presence of m(6)A nucleoside at a particular position of long RNA molecule is challenging to observe. Here we report an easy and high-throughput method for detection of m(6)A nucleosides in RNA based on high-resolution melting analysis. The method relies on the previous knowledge of the modified nucleoside position at a particular place of RNA and allows rapid screening for conditions or genes necessary for formation of that modification. PMID:24265225

  3. A new identification method for five species of oysters in genus Crassostrea from China based on high-resolution melting analysis

    NASA Astrophysics Data System (ADS)

    Wang, Jiafeng; Xu, Fei; Li, Li; Zhang, Guofan

    2014-03-01

    The high phenotypic plasticity in the shell of oysters presents a challenge during taxonomic and phylogenetic studies of these economically important bivalves. However, because DNA can exhibit marked differences among morphologically similar species, DNA barcoding offers a potential means for oyster identification. We analyzed the complete sequences of the cytochrome oxidase subunit I (COI) of five common Crassostrea species in China (including Hong Kong oyster C. hongkongensis, Jinjiang oyster C. ariakensis, Portuguese oyster C. angulata, Kumamoto oyster C. sikamea, and Pacific oyster C. gigas) and screened for distinct fragments. Using these distinct fragments on a high-resolution melting analysis platform, we developed an identification method that does not rely on species-specific PCR or fragment length polymorphism and is efficient, reliable, and easy to visualize. Using a single pair of primers (Oyster-COI-1), we were able to successfully distinguish among the five oyster species. This new method provides a simple and powerful tool for the identification of oyster species.

  4. Specific heat treatment of selective laser melted Ti-6Al-4V for biomedical applications

    NASA Astrophysics Data System (ADS)

    Huang, Qianli; Liu, Xujie; Yang, Xing; Zhang, Ranran; Shen, Zhijian; Feng, Qingling

    2015-12-01

    The ductility of as-fabricated Ti-6Al-4V falls far short of the requirements for biomedical titanium alloy implants and the heat treatment remains the only applicable option for improvement of their mechanical properties. In the present study, the decomposition of as-fabricated martensite was investigated to provide a general understanding on the kinetics of its phase transformation. The decomposition of asfabricated martensite was found to be slower than that of water-quenched martensite. It indicates that specific heat treatment strategy is needed to be explored for as-fabricated Ti-6Al-4V. Three strategies of heat treatment were proposed based on different phase transformation mechanisms and classified as subtransus treatment, supersolvus treatment and mixed treatment. These specific heat treatments were conducted on selective laser melted samples to investigate the evolutions of microstructure and mechanical properties. The subtransus treatment leaded to a basket-weave structure without changing the morphology of columnar prior β grains. The supersolvus treatment resulted in a lamellar structure and equiaxed β grains. The mixed treatment yielded a microstructure that combines both features of the subtransus treatment and supersolvus treatment. The subtransus treatment is found to be the best choice among these three strategies for as-fabricated Ti-6Al-4V to be used as biomedical implants.

  5. Unraveling Host-Vector-Arbovirus Interactions by Two-Gene High Resolution Melting Mosquito Bloodmeal Analysis in a Kenyan Wildlife-Livestock Interface

    PubMed Central

    Omondi, David; Masiga, Daniel K.; Ajamma, Yvonne Ukamaka; Fielding, Burtram C.; Njoroge, Laban; Villinger, Jandouwe

    2015-01-01

    The blood-feeding patterns of mosquitoes are directly linked to the spread of pathogens that they transmit. Efficient identification of arthropod vector bloodmeal hosts can identify the diversity of vertebrate species potentially involved in disease transmission cycles. While molecular bloodmeal analyses rely on sequencing of cytochrome b (cyt b) or cytochrome oxidase 1 gene PCR products, recently developed bloodmeal host identification based on high resolution melting (HRM) analyses of cyt b PCR products is more cost-effective. To resolve the diverse vertebrate hosts that mosquitoes may potentially feed on in sub-Saharan Africa, we utilized HRM profiles of both cyt b and 16S ribosomal RNA genes. Among 445 blood-fed Aedeomyia, Aedes, Anopheles, Culex, Mansonia, and Mimomyia mosquitoes from Kenya’s Lake Victoria and Lake Baringo regions where many mosquito-transmitted pathogens are endemic, we identified 33 bloodmeal hosts including humans, eight domestic animal species, six peridomestic animal species and 18 wildlife species. This resolution of vertebrate host species was only possible by comparing profiles of both cyt b and 16S markers, as melting profiles of some pairs of species were similar for either marker but not both. We identified mixed bloodmeals in a Culex pipiens from Mbita that had fed on a goat and a human and in two Mansonia africana mosquitoes from Baringo that each had fed on a rodent (Arvicanthis niloticus) in addition to a human or baboon. We further detected Sindbis and Bunyamwera viruses in blood-fed mosquito homogenates by Vero cell culture and RT-PCR in Culex, Aedeomyia, Anopheles and Mansonia mosquitoes from Baringo that had fed on humans and livestock. The observed mosquito feeding on both arbovirus amplifying hosts (including sheep and goats) and possible arbovirus reservoirs (birds, porcupine, baboons, rodents) informs arbovirus disease epidemiology and vector control strategies. PMID:26230507

  6. Application of the high resolution return beam vidicon

    NASA Technical Reports Server (NTRS)

    Cantella, M. J.

    1977-01-01

    The Return Beam Vidicon (RBV) is a high-performance electronic image sensor and electrical storage component. It can accept continuous or discrete exposures. Information can be read out with a single scan or with many repetitive scans for either signal processing or display. Resolution capability is 10,000 TV lines/height, and at 100 lp/mm, performance matches or exceeds that of film, particularly with low-contrast imagery. Electronic zoom can be employed effectively for image magnification and data compression. The high performance and flexibility of the RBV permit wide application in systems for reconnaissance, scan conversion, information storage and retrieval, and automatic inspection and test. This paper summarizes the characteristics and performance parameters of the RBV and cites examples of feasible applications.

  7. Enhancing the resolution of gpr spectra for pavement engineering applications

    NASA Astrophysics Data System (ADS)

    Benedetto, F.; Benedetto, A.

    2012-04-01

    Ground Penetrating Radar (GPR) is a geophysical method that uses radar pulses to image the subsurface. This non-destructive method uses electromagnetic radiation and detects the reflected signals from subsurface structures. It can detect objects, changes in material, and voids and cracks. GPR has many applications in a number of fields. In the field of civil engineering one of the most advanced technologies used for road pavement monitoring is based on the deployment of advanced GPR systems. One of the most relevant causes of road pavement damage is often referable to water intrusion in structural layers. In this context, GPR has been recently proposed as a method to estimate moisture content in a porous medium without preventive calibration. Hence, the development of methods to obtain an estimate of the moisture content is a crucial research field involving economic, social and strategic aspects in road safety for a great number of public and private Agencies. In particular, a recent new approach was proposed to estimate moisture content in a porous medium basing on the theory of Rayleigh scattering, showing a shift of the frequency peak of the GPR spectrum towards lower frequencies as the moisture content increases in the soil. The weakness characterizing this approach is represented by the needs of high resolution signals, whereas GPR spectra are affected by low resolution. Hence, the rising requirement for high resolution leads to specific demands for improved prediction methods. Recently, a new technique combining the response of the conventional fast Fourier transform (FFT, well known for its high-precision receiving signal level) with that of the MUSIC (multiple signal classification) algorithm, well known for its super-resolution capacity has been proposed. This combined method has been proved to obtain a high precision level in quantifying the shift of the frequency peak of the GPR spectrum. This combined method can perform a reliable coarse estimate of

  8. Analysis of impact melt and vapor production in CTH for planetary applications

    DOE PAGESBeta

    Quintana, S. N.; Crawford, D. A.; Schultz, P. H.

    2015-05-19

    This study explores impact melt and vapor generation for a variety of impact speeds and materials using the shock physics code CTH. The study first compares the results of two common methods of impact melt and vapor generation to demonstrate that both the peak pressure method and final temperature method are appropriate for high-speed impact models (speeds greater than 10 km/s). However, for low-speed impact models (speeds less than 10 km/s), only the final temperature method is consistent with laboratory analyses to yield melting and vaporization. Finally, a constitutive model for material strength is important for low-speed impacts because strengthmore » can cause an increase in melting and vaporization.« less

  9. Analysis of impact melt and vapor production in CTH for planetary applications

    SciTech Connect

    Quintana, S. N.; Crawford, D. A.; Schultz, P. H.

    2015-05-19

    This study explores impact melt and vapor generation for a variety of impact speeds and materials using the shock physics code CTH. The study first compares the results of two common methods of impact melt and vapor generation to demonstrate that both the peak pressure method and final temperature method are appropriate for high-speed impact models (speeds greater than 10 km/s). However, for low-speed impact models (speeds less than 10 km/s), only the final temperature method is consistent with laboratory analyses to yield melting and vaporization. Finally, a constitutive model for material strength is important for low-speed impacts because strength can cause an increase in melting and vaporization.

  10. Machine learning with systematic density-functional theory calculations: Application to melting temperatures of single- and binary-component solids

    NASA Astrophysics Data System (ADS)

    Seko, Atsuto; Maekawa, Tomoya; Tsuda, Koji; Tanaka, Isao

    2014-02-01

    A combination of systematic density-functional theory (DFT) calculations and machine learning techniques has a wide range of potential applications. This study presents an application of the combination of systematic DFT calculations and regression techniques to the prediction of the melting temperature for single and binary compounds. Here we adopt the ordinary least-squares regression, partial least-squares regression, support vector regression, and Gaussian process regression. Among the four kinds of regression techniques, SVR provides the best prediction. The inclusion of physical properties computed by the DFT calculation to a set of predictor variables makes the prediction better. In addition, limitation of the predictive power is shown when extrapolation from the training dataset is required. Finally, a simulation to find the highest melting temperature toward the efficient materials design using kriging is demonstrated. The kriging design finds the compound with the highest melting temperature much faster than random designs. This result may stimulate the application of kriging to efficient materials design for a broad range of applications.

  11. Wide genetic variations at 18S ribosomal RNA locus of Cyclospora cayetanensis isolated from Egyptian patients using high resolution melting curve.

    PubMed

    Hussein, Eman M; El-Moamly, Amal A; Mahmoud, Moushira A; Ateek, Nayera S

    2016-07-01

    A variable clinical picture of cyclosporiasis including gastrointestinal tract (GIT) symptomatic or asymptomatic beside extraintestinal consequences suggests a possibility of heterogenicity of Cyclospora cayetanensis. The present work aimed to explore the possibility of genetic variation of C. cayetanensis using high-resolution melting (HRM) curve of polymerase chain reaction (PCR) amplified 18S rRNA genes. DNAs extracted from the stool samples of 70 cyclosporiasis patients were amplified and scanned by PCR/HRM curve. The results showed that there are four different genotypic profiles of C. cayetanensis with presence of mixed ones. Although Tm of all profiles was within the same range, they were discerned by plotting of the temperature-shifted florescence difference between normalized melting curves (dF/dT). Genotypic profile I was found alone in 40 % of patients and mixed with genotypic profile II and/or III in 25.7 % of patients, followed by genotypic profile II in 14.3 % then genotypic profile III and IV (10 % each). A significant relation was found between genotypic profiles and GIT symptomatic status as profile I and profile II were mostly detected in patients with acute GIT symptoms without or with chronic illness, respectively, while profile IV cases only were GIT asymptomatic. Statistical significance relations between genotypic profiles and age, gender, residence and oocyst shape index were determined. In conclusion, PCR/HRM proved a wide variation on C. cayetanensis genes that could be reflected on its pathogenic effects and explaining the variability of the clinical manifestations presented by cyclosporiasis patients. PMID:27041342

  12. Shear melting and high temperature embrittlement: theory and application to machining titanium.

    PubMed

    Healy, Con; Koch, Sascha; Siemers, Carsten; Mukherji, Debashis; Ackland, Graeme J

    2015-04-24

    We describe a dynamical phase transition occurring within a shear band at high temperature and under extremely high shear rates. With increasing temperature, dislocation deformation and grain boundary sliding are supplanted by amorphization in a highly localized nanoscale band, which allows for massive strain and fracture. The mechanism is similar to shear melting and leads to liquid metal embrittlement at high temperature. From simulation, we find that the necessary conditions are lack of dislocation slip systems, low thermal conduction, and temperature near the melting point. The first two are exhibited by bcc titanium alloys, and we show that the final one can be achieved experimentally by adding low-melting-point elements: specifically, we use insoluble rare earth metals (REMs). Under high shear, the REM becomes mixed with the titanium, lowering the melting point within the shear band and triggering the shear-melting transition. This in turn generates heat which remains localized in the shear band due to poor heat conduction. The material fractures along the shear band. We show how to utilize this transition in the creation of new titanium-based alloys with improved machinability. PMID:25955055

  13. A review of melt and vapor growth techniques for polydiacetylene thin films for nonlinear optical applications

    NASA Technical Reports Server (NTRS)

    Penn, B. G.; Shields, A.; Frazier, D. O.

    1988-01-01

    Methods for the growth of polydiacetylene thin films by melt and vapor growth and their subsequent polymerization are summarized. Films with random orientations were obtained when glass or quartz were used as substrates in the vapor growth process. Oriented polydiacetylene films were fabricated by the vapor deposition of diacetylene monomer onto oriented polydiacetylene on a glass substrate and its subsequent polymerization by UV light. A method for the growth of oriented thin films by a melt-shear growth process as well as a method of film growth by seeded recrstallization from the melt between glass plates, that may be applied to the growth of polydiacetylene films, are described. Moreover, a method is presented for the fabrication of single crystal thin films of polyacetylenes by irradiation of the surface of diacetylene single crystals to a depth between 100 and 2000 angstroms.

  14. An electrochemical series of redox couples in silicate melts - A review and applications to geochemistry

    NASA Technical Reports Server (NTRS)

    Schreiber, Henry D.

    1987-01-01

    An electrochemical series for redox couples in a glass-forming oxide melt is developed. This series is a quantitative numerical scale of reference reduction potentials of the redox couples in a silicate melt that is a model for basaltic magmas. The redox couples are ordered in terms of their reference reduction potentials; the order appears to be relatively independent of the exact melt composition and temperature. Thus, upon calibration to a desired composition, oxygen fugacity, and temperature, this electrochemical series can provide estimates of redox state proportions in basaltic magmas on different planetary bodies. The geochemical electrochemical series can also be used to understand the interrelationship of the redox state of the magma and the presence of volatile species such as oxygen, water, sulfur gases, and carbon gases.

  15. Application of rock melting to construction of storage holes for nuclear waste

    SciTech Connect

    Neudecker, J.W. Jr.

    1988-12-31

    Rock melting technology can provide in-situ glass liners in nuclear waste package emplacement holes to reduce permeability and increase borehole stability. Reduction of permeability would reduce the time and probability of groundwater contacting the waste packages. Increasing the stability of the storage boreholes would enhance the retrievability of the nuclear waste packages. The rock melting hole forming technology has already been tested in volcanic tuff similar to the geology at the proposed nuclear waste repository at Yucca Mountain, Nevada. 6 refs., 5 figs., 2 tabs.

  16. Nickel and Cobalt Partitioning Between Spinel and Basaltic Melt: Applications to Planetary Basalt Suites

    NASA Technical Reports Server (NTRS)

    Righter, K.

    2002-01-01

    New experimental spinel/melt partition coefficients for Ni and Co have been measured in basalt samples with natural levels of Ni and Co, are lower than previous high doping experiments, and are applied to several planetary basalt suites. Additional information is contained in the original extended abstract.

  17. Predicting Melting Points of Organic Molecules: Applications to Aqueous Solubility Prediction Using the General Solubility Equation.

    PubMed

    McDonagh, J L; van Mourik, T; Mitchell, J B O

    2015-11-01

    In this work we make predictions of several important molecular properties of academic and industrial importance to seek answers to two questions: 1) Can we apply efficient machine learning techniques, using inexpensive descriptors, to predict melting points to a reasonable level of accuracy? 2) Can values of this level of accuracy be usefully applied to predicting aqueous solubility? We present predictions of melting points made by several novel machine learning models, previously applied to solubility prediction. Additionally, we make predictions of solubility via the General Solubility Equation (GSE) and monitor the impact of varying the logP prediction model (AlogP and XlogP) on the GSE. We note that the machine learning models presented, using a modest number of 2D descriptors, can make melting point predictions in line with the current state of the art prediction methods (RMSE≥40 °C). We also find that predicted melting points, with an RMSE of tens of degrees Celsius, can be usefully applied to the GSE to yield accurate solubility predictions (log10 S RMSE<1) over a small dataset of drug-like molecules. PMID:27491032

  18. Thermodynamics of Oligonucleotide Duplex Melting

    ERIC Educational Resources Information Center

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-01-01

    Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply…

  19. Macroscopic coupling of deformation and melt migration at continental interiors, with applications to the Colorado Plateau

    NASA Astrophysics Data System (ADS)

    Roy, Mousumi; Gold, Stav; Johnson, Alex; Osuna Orozco, Rodrigo; Holtzman, Benjamin K.; Gaherty, James

    2016-05-01

    Within continental interiors far from plate boundaries, we hypothesize that the architecture of the lithosphere will influence dynamic pressure gradients produced as the lithosphere moves relative to the underlying asthenosphere. We investigate how these dynamic pressure gradients affect melt migration by percolative flow within the mantle beneath continental interiors. Our models show that for a lithospheric keel that protrudes into the "mantle wind," the behavior of the system can be classified into three categories: (1) small-scale convective instabilities modify both the geometry of the lithosphere-asthenophere boundary (LAB) and associated dynamic pressure gradients so that the surface flux of melt is largest above a narrow downwelling at the center of the keel; (2) weak convection does not substantially modify the keel and persistent gradients at the LAB at margins of the keel control dynamic pressure gradients so that surface melt flux is elevated within the keel relative to its surroundings; and (3) when convective instabilities are suppressed due to sufficiently high viscosity in the asthenosphere, asymmetric dynamic pressure gradients due to mantle shear beneath the keel focus melt streamlines toward the upwind flank of the keel and direct melt away from the downwind flank. We interpret surface patterns of Cenozoic magmatism at the Colorado Plateau, particularly the "upwind-downwind" asymmetry relative to the direction of motion of North America over the underlying asthenosphere, in terms of category (3) above. Our models quantitatively assess the viability of spatially variable dynamic pressure gradients as a physical mechanism to explain disparate observations at the Colorado Plateau, such as surface magmatism, heat flow, xenolith data, and seismic structure.

  20. Differentiation of four strains of Chinese soft-shelled turtle (Pelodiscus sinensis) based on high-resolution melting analysis of single nucleotide polymorphism sites in mitochondrial DNA.

    PubMed

    Zhang, H Q; Zhang, C; Xu, X J; Zhu, J J; He, Z Y; Shao, J Z

    2015-01-01

    The Chinese soft-shelled turtle (Pelodiscus sinensis) has been one of the most economically important aquatic animals in China for thousands of years, and several breeding strains have been formed. Since the morphological characteristics of some strains are similar, a rapid and accurate molecular method to differentiate between strains is required. In this study, partial sequences of mitochondrial DNA from four turtle strains, Taihu Lake Strain, Taiwan Strain, Japanese Strain, and Yellow River Strain, were amplified and sequenced based on selected strain-specific single nucleotide polymorphism (SNP) sites. The corresponding primers were designed and a high-resolution melting (HRM) technique was employed for genotyping these SNPs. The results indicated that a total of seven SNPs can be detected by HRM. Among these SNPs, one can be used for identifying the Taihu Lake Strain, one for the Japanese Strain, two for the Taiwan Strain, and three for the Yellow River Strain. This method is rapid and convenient, which offers technical support for strain identification and selective breeding in Chinese soft-shelled turtles. PMID:26535627

  1. Screening of the BRCA1 gene in Brazilian patients with breast and/or ovarian cancer via high-resolution melting reaction analysis.

    PubMed

    de Oliveira, Eneida Santos; Soares, Bárbara Luisa; Lemos, Sara; Rosa, Reginaldo Cruz Alves; Rodrigues, Angélica Nogueira; Barbosa, Leandro Augusto; de Oliveira Lopes, Débora; dos Santos, Luciana Lara

    2016-04-01

    The aim of this study was to evaluate the profile of BRCA1 mutations among cancer-affected Brazilian women from the Midwest region of Minas Gerais state with clearly defined risk factors for hereditary breast and ovarian cancer (HBOC) syndrome. In this Brazilian region, the first Center for Hereditary Cancer Control began operation in 2011, and 90% of patients receive assistance from the public health service. Eighteen patients at high risk for HBOC were subjected to molecular analysis. Primers were designed for 22 coding exons of the gene; DNA was extracted; and real-time PCR followed by high-resolution melting reaction was performed. The amplicons were sequenced to confirm the identified profiles. Only exon 11 was directly sequenced due its length. Multiplex ligation-dependent probe amplification (MLPA) was performed for those patients in whom no pathogenic mutations were found. Among the 14 alterations identified in this study, the c.5263_5264insC pathogenic mutation was present in two patients (11.1%). Four alterations showed no clinical relevance; one exhibited inconclusive clinical relevance according to the examined databases; and eight alterations presented a divergent classification between the databases. No deletions or duplications were found using the MLPA technique. The HRM methodology was highly sensitive in identifying variants in the BRCA1 gene and can dramatically reduce the amount of sequencing required to identify germline mutations in BRCA genes, enabling cheaper tests and increasing their availability to Brazilian women assisted by the public health service. PMID:26666763

  2. Rapid Identification of Echinococcus granulosus and E. canadensis Using High-Resolution Melting (HRM) Analysis by Focusing on a Single Nucleotide Polymorphism.

    PubMed

    Safa, Ahmad Hosseini; Harandi, Majid Fasihi; Tajaddini, Mohammadhasan; Rostami-Nejad, Mohammad; Mohtashami-Pour, Mehdi; Pestehchian, Nader

    2016-07-22

    High-resolution melting (HRM) is a reliable and sensitive scanning method to detect variation in DNA sequences. We used this method to better understand the epidemiology and transmission of Echinococcus granulosus. We tested the use of HRM to discriminate the genotypes of E. granulosus and E. canadensis. One hundred forty-one hydatid cysts were collected from slaughtered animals in different parts of Isfahan-Iran in 2013. After DNA extraction, the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was amplified using PCR coupled with the HRM curve. The result of HRM analysis using partial the sequences of cox1 gene revealed that 93, 35, and 2 isolates were identified as G1, G3, and G6 genotypes, respectively. A single nucleotide polymorphism (SNP) was found in locus 9867 of the cox1 gene. This is a critical locus for the differentiation between the G6 and G7 genotypes. In the phylogenic tree, the sample with a SNP was located between the G6 and G7 genotypes, which suggest that this isolate has a G6/G7 genotype. The HRM analysis developed in the present study provides a powerful technique for molecular and epidemiological studies on echinococcosis in humans and animals. PMID:26567833

  3. Detection of NPM1 exon 12 mutations and FLT3 – internal tandem duplications by high resolution melting analysis in normal karyotype acute myeloid leukemia

    PubMed Central

    Tan, Angela YC; Westerman, David A; Carney, Dennis A; Seymour, John F; Juneja, Surender; Dobrovic, Alexander

    2008-01-01

    Background Molecular characterisation of normal karyotype acute myeloid leukemia (NK-AML) allows prognostic stratification and potentially can alter treatment choices and pathways. Approximately 45–60% of patients with NK-AML carry NPM1 gene mutations and are associated with a favourable clinical outcome when FLT3-internal tandem duplications (ITD) are absent. High resolution melting (HRM) is a novel screening method that enables rapid identification of mutation positive DNA samples. Results We developed HRM assays to detect NPM1 mutations and FLT3-ITD and tested diagnostic samples from 44 NK-AML patients. Eight were NPM1 mutation positive only, 4 were both NPM1 mutation and FLT3-ITD positive and 4 were FLT3-ITD positive only. A novel point mutation Y572C (c.1715A>G) in exon 14 of FLT3 was also detected. In the group with de novo NK-AML, 40% (12/29) were NPM1 mutation positive whereas NPM1 mutations were observed in 20% (3/15) of secondary NK-AML cases. Sequencing was performed and demonstrated 100% concordance with the HRM results. Conclusion HRM is a rapid and efficient method of screening NK-AML samples for both novel and known NPM1 and FLT3 mutations. NPM1 mutations can be observed in both primary and secondary NK-AML cases. PMID:18664261

  4. Rapid Detection and Identification of Mucormycetes in Bronchoalveolar Lavage Samples from Immunocompromised Patients with Pulmonary Infiltrates by Use of High-Resolution Melt Analysis

    PubMed Central

    Racil, Zdenek; Hrncirova, Kristyna; Kocmanova, Iva; Volfova, Pavlina; Ricna, Dita; Bejdak, Petr; Moulis, Mojmir; Pavlovsky, Zdenek; Weinbergerova, Barbora; Toskova, Martina; Mayer, Jiri

    2014-01-01

    Rapid differential diagnostics of pulmonary infiltrates suspected of invasive fungal disease in an immunocompromised host and early initiation of effective antifungal therapy are crucial for patient outcomes. There are no serological tests available to detect mucormycetes; therefore, PCR-based methods are highly suitable. We validated our previously published PCR followed by high-resolution melt analysis (PCR/HRMA) to detect Rhizopus spp., Rhizomucor pusillus, Lichtheimia corymbifera, and Mucor spp. in bronchoalveolar lavage (BAL) samples from immunocompromised patients who were at risk of invasive fungal disease. All PCR/HRMA-positive samples were retested using novel real-time quantitative PCR (RQ PCR) assays specific to the species identified. In total, between January 2009 and December 2012 we analyzed 99 BAL samples from 86 patients with pulmonary abnormalities using PCR/HRMA. Ninety (91%) BAL samples were negative, and 9 (9%) samples were positive. The sensitivity and specificity of PCR/HRMA were 100% and 93%, respectively. By combining the positive results of PCR/HRMA with positive RQ PCR results, the specificity was raised to 98%. PCR/HRMA, due to its high negative predictive value (99%), represents a fast and reliable tool for routine BAL sample screening for the differential diagnosis of pulmonary infiltrates in immunocompromised patients for the four most clinically important mucormycetes. PMID:24850354

  5. Rapid detection and identification of mucormycetes in bronchoalveolar lavage samples from immunocompromised patients with pulmonary infiltrates by use of high-resolution melt analysis.

    PubMed

    Lengerova, Martina; Racil, Zdenek; Hrncirova, Kristyna; Kocmanova, Iva; Volfova, Pavlina; Ricna, Dita; Bejdak, Petr; Moulis, Mojmir; Pavlovsky, Zdenek; Weinbergerova, Barbora; Toskova, Martina; Mayer, Jiri

    2014-08-01

    Rapid differential diagnostics of pulmonary infiltrates suspected of invasive fungal disease in an immunocompromised host and early initiation of effective antifungal therapy are crucial for patient outcomes. There are no serological tests available to detect mucormycetes; therefore, PCR-based methods are highly suitable. We validated our previously published PCR followed by high-resolution melt analysis (PCR/HRMA) to detect Rhizopus spp., Rhizomucor pusillus, Lichtheimia corymbifera, and Mucor spp. in bronchoalveolar lavage (BAL) samples from immunocompromised patients who were at risk of invasive fungal disease. All PCR/HRMA-positive samples were retested using novel real-time quantitative PCR (RQ PCR) assays specific to the species identified. In total, between January 2009 and December 2012 we analyzed 99 BAL samples from 86 patients with pulmonary abnormalities using PCR/HRMA. Ninety (91%) BAL samples were negative, and 9 (9%) samples were positive. The sensitivity and specificity of PCR/HRMA were 100% and 93%, respectively. By combining the positive results of PCR/HRMA with positive RQ PCR results, the specificity was raised to 98%. PCR/HRMA, due to its high negative predictive value (99%), represents a fast and reliable tool for routine BAL sample screening for the differential diagnosis of pulmonary infiltrates in immunocompromised patients for the four most clinically important mucormycetes. PMID:24850354

  6. Taxonomic Identification of Mediterranean Pines and Their Hybrids Based on the High Resolution Melting (HRM) and trnL Approaches: From Cytoplasmic Inheritance to Timber Tracing

    PubMed Central

    Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

    2013-01-01

    Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

  7. Characterization of Genetic Diversity of Bacillus anthracis in France by Using High-Resolution Melting Assays and Multilocus Variable-Number Tandem-Repeat Analysis ▿ †

    PubMed Central

    Derzelle, S.; Laroche, S.; Le Flèche, P.; Hauck, Y.; Thierry, S.; Vergnaud, G.; Madani, N.

    2011-01-01

    Using high-resolution melting (HRM) analysis, we developed a cost-effective method to genotype a set of 13 phylogenetically informative single-nucleotide polymorphisms (SNPs) within the genome of Bacillus anthracis. SNP discrimination assays were performed in monoplex or duplex and applied to 100 B. anthracis isolates collected in France from 1953 to 2009 and a few reference strains. HRM provided a reliable and cheap alternative to subtype B. anthracis into one of the 12 major sublineages or subgroups. All strains could be correctly positioned on the canonical SNP (canSNP) phylogenetic tree, except the divergent Pasteur vaccine strain ATCC 4229. We detected the cooccurrence of three canSNP subgroups in France. The dominant B.Br.CNEVA sublineage was found to be prevalent in the Alps, the Pyrenees, the Auvergne region, and the Saône-et-Loire department. Strains affiliated with the A.Br.008/009 subgroup were observed throughout most of the country. The minor A.Br.001/002 subgroup was restricted to northeastern France. Multiple-locus variable-number tandem-repeat analysis using 24 markers further resolved French strains into 60 unique profiles and identified some regional patterns. Diversity found within the A.Br.008/009 and B.Br.CNEVA subgroups suggests that these represent old, ecologically established clades in France. Phylogenetic relationships with strains from other parts of the world are discussed. PMID:21998431

  8. Mutation scanning in a single and a stacked genetically modified (GM) event by real-time PCR and high resolution melting (HRM) analysis.

    PubMed

    Ben Ali, Sina-Elisabeth; Madi, Zita Erika; Hochegger, Rupert; Quist, David; Prewein, Bernhard; Haslberger, Alexander G; Brandes, Christian

    2014-01-01

    Genetic mutations must be avoided during the production and use of seeds. In the European Union (EU), Directive 2001/18/EC requires any DNA construct introduced via transformation to be stable. Establishing genetic stability is critical for the approval of genetically modified organisms (GMOs). In this study, genetic stability of two GMOs was examined using high resolution melting (HRM) analysis and real-time polymerase chain reaction (PCR) employing Scorpion primers for amplification. The genetic variability of the transgenic insert and that of the flanking regions in a single oilseed rape variety (GT73) and a stacked maize (MON88017×MON810) was studied. The GT73 and the 5' region of MON810 showed no instabilities in the examined regions. However; two out of 100 analyzed samples carried a heterozygous point mutation in the 3' region of MON810 in the stacked variety. These results were verified by direct sequencing of the amplified PCR products as well as by sequencing of cloned PCR fragments. The occurrence of the mutation suggests that the 5' region is more suitable than the 3' region for the quantification of MON810. The identification of the single nucleotide polymorphism (SNP) in a stacked event is in contrast to the results of earlier studies of the same MON810 region in a single event where no DNA polymorphism was found. PMID:25365178

  9. Mutation Scanning in a Single and a Stacked Genetically Modified (GM) Event by Real-Time PCR and High Resolution Melting (HRM) Analysis

    PubMed Central

    Ben Ali, Sina-Elisabeth; Madi, Zita Erika; Hochegger, Rupert; Quist, David; Prewein, Bernhard; Haslberger, Alexander G.; Brandes, Christian

    2014-01-01

    Genetic mutations must be avoided during the production and use of seeds. In the European Union (EU), Directive 2001/18/EC requires any DNA construct introduced via transformation to be stable. Establishing genetic stability is critical for the approval of genetically modified organisms (GMOs). In this study, genetic stability of two GMOs was examined using high resolution melting (HRM) analysis and real-time polymerase chain reaction (PCR) employing Scorpion primers for amplification. The genetic variability of the transgenic insert and that of the flanking regions in a single oilseed rape variety (GT73) and a stacked maize (MON88017 × MON810) was studied. The GT73 and the 5' region of MON810 showed no instabilities in the examined regions. However; two out of 100 analyzed samples carried a heterozygous point mutation in the 3' region of MON810 in the stacked variety. These results were verified by direct sequencing of the amplified PCR products as well as by sequencing of cloned PCR fragments. The occurrence of the mutation suggests that the 5' region is more suitable than the 3' region for the quantification of MON810. The identification of the single nucleotide polymorphism (SNP) in a stacked event is in contrast to the results of earlier studies of the same MON810 region in a single event where no DNA polymorphism was found. PMID:25365178

  10. Integrated Microfluidic Card with TaqMan Probes and High-Resolution Melt Analysis To Detect Tuberculosis Drug Resistance Mutations across 10 Genes

    PubMed Central

    Pholwat, Suporn; Liu, Jie; Stroup, Suzanne; Gratz, Jean; Banu, Sayera; Rahman, S. M. Mazidur; Ferdous, Sara Sabrina; Foongladda, Suporn; Boonlert, Duangjai; Ogarkov, Oleg; Zhdanova, Svetlana; Kibiki, Gibson; Heysell, Scott

    2015-01-01

    ABSTRACT Genotypic methods for drug susceptibility testing of Mycobacterium tuberculosis are desirable to speed the diagnosis and proper therapy of tuberculosis (TB). However, the numbers of genes and polymorphisms implicated in resistance have proliferated, challenging diagnostic design. We developed a microfluidic TaqMan array card (TAC) that utilizes both sequence-specific probes and high-resolution melt analysis (HRM), providing two layers of detection of mutations. Twenty-seven primer pairs and 40 probes were designed to interrogate 3,200 base pairs of critical regions of the inhA, katG, rpoB, embB, rpsL, rrs, eis, gyrA, gyrB, and pncA genes. The method was evaluated on 230 clinical M. tuberculosis isolates from around the world, and it yielded 96.1% accuracy (2,431/2,530) in comparison to that of Sanger sequencing and 87% accuracy in comparison to that of the slow culture-based susceptibility testing. This TAC-HRM method integrates assays for 10 genes to yield fast, comprehensive, and accurate drug susceptibility results for the 9 major antibiotics used to treat TB and could be deployed to improve treatment outcomes. PMID:25714709

  11. rpoB gene high-resolution melt curve analysis: a rapid approach for diagnosis and screening of drug resistance in tuberculous meningitis.

    PubMed

    Sharma, Kusum; Modi, Manish; Kaur, Harsimran; Sharma, Aman; Ray, Pallab; Varma, Subhash

    2015-10-01

    Timely and rapid diagnosis of multidrug resistance in tuberculous meningitis (TBM) is a challenge both for a microbiologist and neurologist. The present study was conducted to evaluate role of real-time polymerase chain reaction (PCR) using rpoB, IS6110, and MPB64 as targets in diagnosis of TBM in 110 patients and subsequent high-resolution melt (HRM) curve analysis of rpoB gene amplicons for screening of drug resistance. The sensitivity of smear, culture, and real-time PCR was 1.8%, 10.9%, and 83.63%, respectively. All 120 control patients showed negative results. With HRM rpoB analysis, rifampicin resistance was detected in 3 out of 110 cases of TBM (3.33%). Subsequently, results of HRM analysis were confirmed by rpoB gene sequencing, and mutations were observed at 516 (2 patients) and 531 (1 patient) codons, respectively. rpoB HRM analysis can be a promising tool for rapid diagnosis and screening of drug resistance in TBM patients in 90minutes. PMID:26254140

  12. Taxonomic identification of mediterranean pines and their hybrids based on the high resolution melting (HRM) and trnL approaches: from cytoplasmic inheritance to timber tracing.

    PubMed

    Ganopoulos, Ioannis; Aravanopoulos, Filippos; Madesis, Panagiotis; Pasentsis, Konstantinos; Bosmali, Irene; Ouzounis, Christos; Tsaftaris, Athanasios

    2013-01-01

    Fast and accurate detection of plant species and their hybrids using molecular tools will facilitate the assessment and monitoring of local biodiversity in an era of climate and environmental change. Herein, we evaluate the utility of the plastid trnL marker for species identification applied to Mediterranean pines (Pinus spp.). Our results indicate that trnL is a very sensitive marker for delimiting species biodiversity. Furthermore, High Resolution Melting (HRM) analysis was exploited as a molecular fingerprint for fast and accurate discrimination of Pinus spp. DNA sequence variants. The trnL approach and the HRM analyses were extended to wood samples of two species (Pinus nigra and Pinus sylvestris) with excellent results, congruent to those obtained using leaf tissue. Both analyses demonstrate that hybrids from the P. brutia (maternal parent) × P. halepensis (paternal parent) cross, exhibit the P. halepensis profile, confirming paternal plastid inheritance in Group Halepensis pines. Our study indicates that a single one-step reaction method and DNA marker are sufficient for the identification of Mediterranean pines, their hybrids and the origin of pine wood. Furthermore, our results underline the potential for certain DNA regions to be used as novel biological information markers combined with existing morphological characters and suggest a relatively reliable and open taxonomic system that can link DNA variation to phenotype-based species or hybrid assignment status and direct taxa identification from recalcitrant tissues such as wood samples. PMID:23577179

  13. Use of a High Resolution Melting (HRM) Assay to Compare Gag, Pol, and Env Diversity in Adults with Different Stages of HIV Infection

    PubMed Central

    Cousins, Matthew M.; Laeyendecker, Oliver; Beauchamp, Geetha; Brookmeyer, Ronald; Towler, William I.; Hudelson, Sarah E.; Khaki, Leila; Koblin, Beryl; Chesney, Margaret; Moore, Richard D.; Kelen, Gabor D.; Coates, Thomas; Celum, Connie; Buchbinder, Susan P.; Seage, George R.; Quinn, Thomas C.; Donnell, Deborah; Eshleman, Susan H.

    2011-01-01

    Background Cross-sectional assessment of HIV incidence relies on laboratory methods to discriminate between recent and non-recent HIV infection. Because HIV diversifies over time in infected individuals, HIV diversity may serve as a biomarker for assessing HIV incidence. We used a high resolution melting (HRM) diversity assay to compare HIV diversity in adults with different stages of HIV infection. This assay provides a single numeric HRM score that reflects the level of genetic diversity of HIV in a sample from an infected individual. Methods HIV diversity was measured in 203 adults: 20 with acute HIV infection (RNA positive, antibody negative), 116 with recent HIV infection (tested a median of 189 days after a previous negative HIV test, range 14–540 days), and 67 with non-recent HIV infection (HIV infected >2 years). HRM scores were generated for two regions in gag, one region in pol, and three regions in env. Results Median HRM scores were higher in non-recent infection than in recent infection for all six regions tested. In multivariate models, higher HRM scores in three of the six regions were independently associated with non-recent HIV infection. Conclusions The HRM diversity assay provides a simple, scalable method for measuring HIV diversity. HRM scores, which reflect the genetic diversity in a viral population, may be useful biomarkers for evaluation of HIV incidence, particularly if multiple regions of the HIV genome are examined. PMID:22073290

  14. High Resolution Reconstruction of the Ionosphere for SAR Applications

    NASA Astrophysics Data System (ADS)

    Minkwitz, David; Gerzen, Tatjana; Hoque, Mainul

    2014-05-01

    Caused by ionosphere's strong impact on radio signal propagation, high resolution and highly accurate reconstructions of the ionosphere's electron density distribution are demanded for a large number of applications, e.g. to contribute to the mitigation of ionospheric effects on Synthetic Aperture Radar (SAR) measurements. As a new generation of remote sensing satellites the TanDEM-L radar mission is planned to improve the understanding and modelling ability of global environmental processes and ecosystem change. TanDEM-L will operate in L-band with a wavelength of approximately 24 cm enabling a stronger penetration capability compared to X-band (3 cm) or C-band (5 cm). But accompanied by the lower frequency of the TanDEM-L signals the influence of the ionosphere will increase. In particular small scale irregularities of the ionosphere might lead to electron density variations within the synthetic aperture length of the TanDEM-L satellite and in turn might result into blurring and azimuth pixel shifts. Hence the quality of the radar image worsens if the ionospheric effects are not mitigated. The Helmholtz Alliance project "Remote Sensing and Earth System Dynamics" (EDA) aims in the preparation of the HGF centres and the science community for the utilisation and integration of the TanDEM-L products into the study of the Earth's system. One significant point thereby is to cope with the mentioned ionospheric effects. Therefore different strategies towards achieving this objective are pursued: the mitigation of the ionospheric effects based on the radar data itself, the mitigation based on external information like global Total Electron Content (TEC) maps or reconstructions of the ionosphere and the combination of external information and radar data. In this presentation we describe the geostatistical approach chosen to analyse the behaviour of the ionosphere and to provide a high resolution 3D electron density reconstruction. As first step the horizontal structure of

  15. E-beam GIDC resolution enhancement technology in practical applications

    NASA Astrophysics Data System (ADS)

    Martens, S.; Butschke, J.; Galler, R.; Krüger, M.; Sailer, H.; Sülzle, M.

    2013-09-01

    For nearly all relevant applications of e-beam lithography the resolution and pattern quality requirements are approaching or exceeding the limits of the available process. On one hand, for shrinking feature dimensions, the e-beam proximity effect and process effects such as photo acid diffusion limit the pattern contrast and process window. On the other hand, e-beam process related parasitic effects such as shot noise, fogging, developer loading, heating, charging, and inhomogeneous bake introduce some significant errors. Even though e-beam tool and process tool suppliers continue to implement new or improve current strategies to avoid or correct these effects, the amount of residual errors requires some reasonable e-beam process window, in particular for high end applications. For some patterns the undersize-overdose approach (SIZE) improves the pattern fidelity and process window. However, for patterns with high fill factors this approach increases the overall deposited electron dose, which due to the increased backscattering diminishes or even eliminates the advantages. The geometrically induced dose correction (GIDC) method overcomes this issue by combining the SIZE concept with a short range framing technique, which reduces the deposited dose in large filled pattern areas. This paper provides a comparison of the standard, SIZE, and GIDC correction approaches for 1D test patterns as well as production patterns. For a broad comparison, patterns were printed onto negative and positive chemically amplified resists and on wafer and mask substrates using a Vistec SB352HR variable shape e-beam writer. Both wafers were also etched. The outcome of the study is that the SIZE and GIDC approaches often outperform the standard proximity effect correction. For dense patterns, GIDC still provides a better pattern quality and process window, while the SIZE approach suffers from the increased overall deposited electron dose and clearly falls behind GIDC in terms of process

  16. High spatial resolution geochemistry and textural characteristics of 'microtektite' glass spherules in proximal Cretaceous-Paleogene sections: Insights into glass alteration patterns and precursor melt lithologies

    NASA Astrophysics Data System (ADS)

    Belza, Joke; Goderis, Steven; Smit, Jan; Vanhaecke, Frank; Baert, Kitty; Terryn, Herman; Claeys, Philippe

    2015-03-01

    Using laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), we have conducted spatially resolved trace element analysis on fresh, unaltered microtektite glasses linked to the Cretaceous-Paleogene (K-Pg) boundary Chicxulub crater and on their surrounding alteration phases. This unique approach offers the opportunity to study in situ and at high spatial resolution both the mixing of different target lithologies and the variation of the major and trace element budget during the alteration process. In addition, two-dimensional element distribution maps reveal important geochemical information beyond the capabilities of single spot laser drilling. Glasses from two localities in opposite quadrants from the source crater were studied. At the Beloc locality (Haiti), the glass population is dominated by the presence of yellow high-Ca glass and black andesitic glass formed by admixture of carbonate/dolomite/anhydrite platform lithologies with crystalline basement. These glasses alter according to the well-established hydration-palagonitization model postulated for mafic volcanic glasses. REEs become progressively leached from the glass to below the detection limit for the applied spot size, while immobile Zr, Hf, Nb, and Ta passively accumulate in the process exhibiting both inter-element ratios and absolute concentrations similar to those for the original glass. In contrast, The Arroyo El Mimbral locality (NE Mexico) is characterized by abundant green glass fragments high in Si, Al and alkalis, and low in Mg, Ca, Fe. Low Si black glass is less abundant though similar in composition to the black glass variety at Beloc. The alteration pattern of high-Si, Al green glass at the Mimbral locality is more complex, including numerous competing reaction processes (ion-exchange, hydration, dissolution, and secondary mineral precipitation) generally controlled by the pH and composition of the surrounding fluid. All green, high-Si, Al glasses are hydrated and

  17. Melting-point measurements at high static pressures from laser heating methods: Application to uranium

    SciTech Connect

    Sitaud, B.; Thevenin, T.

    1999-07-01

    Two experimental approaches dealing with the determination of melting at high static pressures are described and analyzed. With the sample squeezed inside a diamond anvil cell, high temperatures up to the solid-liquid transition are obtained using Nd:YAG laser heating. Two methods have been investigated. In the first technique, the heating is accomplished with a pulsed laser and the brief radiation variations (t {lt} 10 ms) emitted from the sample are recorded with two high-speed infrared detectors. The melting location is defined by a plateau or changes of slope of the signals, and the temperatures are calculated by assuming a constant value of emissivity factor at the end of the transition over the studied pressure range. The second system employs a continuous laser and a two-dimensional CCD detector to measure temperatures using multispectral pyrometry. Melting is detected from criteria related either to textural change in the sample involving interference contrast under a laser illumination or to the specific variations of temperatures and emissivity as a function of laser power. Thermal radiation is fitted to Planck's law with temperature and emissivity as the free parameters. Advantages and drawbacks are presented from results obtained on pure uranium.

  18. Application of a hot-melt granulation process to enhance fenofibrate solid dose manufacturing.

    PubMed

    Chaudhary, Rakesh Singh; Amankwaa, Edward; Kumar, Sandeep; Hu, Tom; Chan, Mohamed; Sanghvi, Pradeep

    2016-07-01

    Evaluation of hot-melt granulation of fenofibrate and croscarmellose sodium and its cooling time for the molten mass in a ratio of 55:45 was conducted to assess the manufacturing process capability to produce an acceptable granulation which flows well on Korsch PH300 tablet compression machine. The formation of the drug-polymer eutectic mixture was investigated by differential scanning calorimetry, scanning electron microscopy and X-ray powder diffraction. The physical properties of the hot-melt was determined by examining the milled blocks after solidification and milling after cooling periods of 10, 20 and 30 d. The milled material was assessed for the effect of hold time of the blend on the solid dose compression characteristics. The impact of cooling on the processing of the blocks was assessed after 10, 20 and 30 d of cooling. The study suggests that after the hot-melt formed the fenofibrate crystallized independently and a solid solution with croscarmellose sodium was not formed. The age of the blocks determined the hardness of the crystals, changing the processing nature of the granules with respect to compression and powder flow characteristics. The blocks processed after 20 d and beyond produced granules with a characteristic suitable for holding the blend for 14 d in the bin with no impact on flow properties and compressibility of the blend. There was no chipping, capping, sticking or picking observed and a higher compression speed was achieved. PMID:26552938

  19. Application of Aerosondes to melt-pond observation over Arctic sea ice

    NASA Astrophysics Data System (ADS)

    Inoue, J.; Curry, J. A.

    2006-12-01

    Continuous observation of sea ice using a small robotic aircraft called the Aerosonde was made over the Arctic Ocean from Barrow, Alaska, on 20-21 July 2003. Over a region of 350 km off the coast of Barrow, ice concentration data that consists of ice and ponded areas was made using images taken by the aircraft. Melt- pond fraction (A_p) increased northward from 15 % to 30 % as the ice fraction (A_i) increased. However, the fraction of the ice that is ponded (A_p/(A_i+A_p)) was over 30 % in the perennial ice zone while about 25 % in the first year ice zone, suggesting the different stages of melt-pond evolution in each regions. AMSRE-derived ice concentration was underestimated 7% as compared with the observed one (A_i+A_p). These analyses demonstrate new technology for monitoring the spatial variations in the sea ice with melt ponds that would be very difficult to measure using satellites.

  20. Thermal Assessment of a Latent-Heat Energy Storage Module During Melting and Freezing for Solar Energy Applications

    NASA Astrophysics Data System (ADS)

    Ramos Archibold, Antonio

    Capital investment reduction, exergetic efficiency improvement and material compatibility issues have been identified as the primary techno-economic challenges associated, with the near-term development and deployment of thermal energy storage (TES) in commercial-scale concentrating solar power plants. Three TES techniques have gained attention in the solar energy research community as possible candidates to reduce the cost of solar-generated electricity, namely (1) sensible heat storage, (2) latent heat (tank filled with phase change materials (PCMs) or encapsulated PCMs packed in a vessel) and (3) thermochemical storage. Among these the PCM macro-encapsulation approach seems to be one of the most-promising methods because of its potential to develop more effective energy exchange, reduce the cost associated with the tank and increase the exergetic efficiency. However, the technological barriers to this approach arise from the encapsulation techniques used to create a durable capsule, as well as an assessment of the fundamental thermal energy transport mechanisms during the phase change. A comprehensive study of the energy exchange interactions and induced fluid flow during melting and solidification of a confined storage medium is reported in this investigation from a theoretical perspective. Emphasis has been placed on the thermal characterization of a single constituent storage module rather than an entire storage system, in order to, precisely capture the energy exchange contributions of all the fundamental heat transfer mechanisms during the phase change processes. Two-dimensional, axisymmetric, transient equations for mass, momentum and energy conservation have been solved numerically by the finite volume scheme. Initially, the interaction between conduction and natural convection energy transport modes, in the absence of thermal radiation, is investigated for solar power applications at temperatures (300--400°C). Later, participating thermal radiation

  1. Applications of web produced by hot air assisted melt differential electrospinning method

    NASA Astrophysics Data System (ADS)

    Bubakir, Mahmoud M.; Li, Haoyi; Wu, Weifeng; Li, Xiaohu; Ma, Shuai; Yang, Weimin

    2014-08-01

    Melt electrospinning, a technique that has gained increasing attention since it easily can generate continuous ultrafine fibers directly from polymer melts without the use of any solvent. Therefore, it is considered as a safe, cost effective, and environmental friendly technique. However, with all those great advantages, the technique still suffers some drawbacks such as: large fiber diameter and low throughput. The hot air assisted melt differential electrospinning (MDES) is a new technique invented by our research team that can solve or eliminate those drawbacks. The most important features of our used apparatus are: Needleless nozzle that could generate multiple Taylor cones around the bottom edge of the nozzle, which can result in a high throughput. The stretching force acting on the jets can be further strengthened by an air current provided by an air pressure gun. Interference between the high voltage supply and temperature sensors could be prevented through the grounding of the nozzle. The ultrafine pp webs produced using the same apparatus was in the micro/nano scale with a diameter of 600nm-6um and a smooth surface. Porosity of the webs ranges from 86.5%-99.4% when different collecting devices are used. The resultant ultrafine webs were applied in three areas: oil sorption, water treatment, and hydrophilic PP membrane. The results were very promising as for oil the sorption capacity was 129.0g/g; for water treatment, the rejection rate for 3um particles was 95%. And for the hydrophilic PP membrane, the water sorption capacity was 12.3 g/g.

  2. Rapid detection of multidrug-resistant Mycobacterium tuberculosis by use of real-time PCR and high-resolution melt analysis.

    PubMed

    Ramirez, Melissa V; Cowart, Kelley C; Campbell, Patricia J; Morlock, Glenn P; Sikes, David; Winchell, Jonas M; Posey, James E

    2010-11-01

    The current study describes the development of a unique real-time PCR assay for the detection of mutations conferring drug resistance in Mycobacterium tuberculosis. The rifampicin resistance determinant region (RRDR) of rpoB and specific regions of katG and the inhA promoter were targeted for the detection of rifampin (RIF) and isoniazid (INH) resistance, respectively. Additionally, this assay was multiplexed to discriminate Mycobacterium tuberculosis complex (MTC) strains from nontuberculous Mycobacteria (NTM) strains by targeting the IS6110 insertion element. High-resolution melting (HRM) analysis following real-time PCR was used to identify M. tuberculosis strains containing mutations at the targeted loci, and locked nucleic acid (LNA) probes were used to enhance the detection of strains containing specific single-nucleotide polymorphism (SNP) transversion mutations. This method was used to screen 252 M. tuberculosis clinical isolates, including 154 RIF-resistant strains and 174 INH-resistant strains based on the agar proportion method of drug susceptibility testing (DST). Of the 154 RIF-resistant strains, 148 were also resistant to INH and therefore classified as multidrug resistant (MDR). The assay demonstrated sensitivity and specificity of 91% and 98%, respectively, for the detection of RIF resistance and 87% and 100% for the detection of INH resistance. Overall, this assay showed a sensitivity of 85% and a specificity of 98% for the detection of MDR strains. This method provides a rapid, robust, and inexpensive way to detect the dominant mutations known to confer MDR in M. tuberculosis strains and offers several advantages over current molecular and culture-based techniques. PMID:20810777

  3. Hypervariable pili and flagella genes provide suitable new targets for DNA high-resolution melt-based genotyping of dairy Geobacillus spp.

    PubMed

    Chauhan, Kanika; Seale, R Brent; Deeth, Hilton C; Turner, Mark S

    2014-10-01

    Although nonpathogenic in nature, spores of Geobacillus are able to attach to surfaces, germinate, and form biofilms, allowing rapid multiplication and persistence within milk powder processing plants, causing final product contamination, and eventually leading to a loss of revenue in terms of downgraded product quality. As a result, Geobacillus spp. have been found to be common contaminants of milk powder worldwide. Genotyping methods can help in gaining insight into the ecology and transmission of these thermophilic bacteria within and between dairy processing plants. The objective of this study was to use the assembled draft genomes of two Geobacillus spp. to identify and test new hypervariable genotyping targets for differentiating closely related dairy Geobacillus isolates. The two Geobacillus spp. strains obtained from high spore count powders were obtained in 2010 (isolate 7E) and in 1995 (isolate 126) and were previously shown to be of same genotype based on a variable number tandem repeat genotyping method. Significant nucleotide sequence variation was found in genes encoding pili and flagella, which were further investigated as suitable loci for a new high-resolution melt analysis (HRMA)-based genotyping method. Three genes encoding pulG (containing prepilin-type N-terminal cleavage domain), pilT (pili retraction protein), and fliW (flagellar assembly protein) were selected as targets for the new pili/flagella gene (PilFla) HRMA genotyping method. The three-gene-based PilFla-HRMA genotyping method differentiated 35 milk powder Geobacillus spp. isolates into 19 different genotype groups (D = 0.93), which compared favorably to the previous method (which used four variable number tandem repeat loci) that generated 16 different genotype groups (D = 0.90). In conclusion, through comparative genomics of two closely related dairy Geobacillus strains, we have identified new hypervariable regions that prove to be useful targets for highly discriminatory genotyping

  4. Evaluation of the Capacity of PCR and High-Resolution Melt Curve Analysis for Identification of Mixed Infection with Mycoplasma gallisepticum Strains.

    PubMed

    Ghorashi, Seyed A; Kanci, Anna; Noormohammadi, Amir H

    2015-01-01

    Pathogenicity and presentation of Mycoplasma gallisepticum (MG) infection may differ from one strain to another and this may have implications on control measures. Infection of individual birds with more than one MG strain has been reported. A PCR followed by high resolution melt (HRM) curve analysis has been developed in our laboratory and routinely used for detection and differentiation of MG strains. However the potential of this test for identification of MG strains in a mixed specimen has not been evaluated. In the present study, the capability of PCR-HRM curve analysis technique, targeting vlhA and pvpA genes was assessed for identification of individual MG strains in a mixed population. Different DNA ratios of two MG strains from 1 to 10(-4) ng were tested with some generated conventional and normalized curves distinct from those of individual strains alone. Using genotype confidence percentages (GCP) generated from HRM curve analysis, it was found that vlhA PCR-HRM was more consistent than pvpA PCR-HRM for the detection of MG ts-11 vaccine strain mixed with any of the MG strains 6/85, F, S6 or a field isolate. The potential of vlhA PCR-HRM to detect mixed MG strains in a specimen was found to be primarily dependent on quantity and proportion of the target DNAs in the mixture. This is the first study examining the capacity of PCR-HRM technique for identification of individual MG strains in a mixed strain population. PMID:25970590

  5. Evaluation of the Capacity of PCR and High-Resolution Melt Curve Analysis for Identification of Mixed Infection with Mycoplasma gallisepticum Strains

    PubMed Central

    Ghorashi, Seyed A.; Kanci, Anna; Noormohammadi, Amir H.

    2015-01-01

    Pathogenicity and presentation of Mycoplasma gallisepticum (MG) infection may differ from one strain to another and this may have implications on control measures. Infection of individual birds with more than one MG strain has been reported. A PCR followed by high resolution melt (HRM) curve analysis has been developed in our laboratory and routinely used for detection and differentiation of MG strains. However the potential of this test for identification of MG strains in a mixed specimen has not been evaluated. In the present study, the capability of PCR-HRM curve analysis technique, targeting vlhA and pvpA genes was assessed for identification of individual MG strains in a mixed population. Different DNA ratios of two MG strains from 1 to 10-4 ng were tested with some generated conventional and normalized curves distinct from those of individual strains alone. Using genotype confidence percentages (GCP) generated from HRM curve analysis, it was found that vlhA PCR-HRM was more consistent than pvpA PCR-HRM for the detection of MG ts-11 vaccine strain mixed with any of the MG strains 6/85, F, S6 or a field isolate. The potential of vlhA PCR-HRM to detect mixed MG strains in a specimen was found to be primarily dependent on quantity and proportion of the target DNAs in the mixture. This is the first study examining the capacity of PCR-HRM technique for identification of individual MG strains in a mixed strain population. PMID:25970590

  6. Quantitation of CDH1 promoter methylation in formalin-fixed paraffin-embedded tissues of breast cancer patients using differential high resolution melting analysis

    PubMed Central

    Naghitorabi, Mojgan; Mohammadi-Asl, Javad; Sadeghi, Hamid Mir Mohammad; Rabbani, Mohammad; Jafarian-Dehkordi, Abbas; Javanmard, Shaghayegh Haghjooy

    2016-01-01

    Background: E-cadherin (CDH1) plays an important role in cell–cell adhesion of epithelial tissues. Loss of E-cadherin expression can lead to loss of tissue integrity, metastasis, and cancer progression. Also loss of E-cadherin expression might be related to aberrant promoter methylation of the CDH1 gene. Many studies have been performed on CDH1 promoter methylation, especially in breast cancer. Although most of the studies have used qualitative methods for methylation analysis, this study is designed to quantitatively investigate CDH1 promoter methylation in breast cancer and its correlation with patients’ clinicopathological features. Materials and Methods: Using differential high resolution melting analysis (D-HRMA), the methylation level of the CDH1 gene promoter was quantified in 98 breast cancer formalin-fixed paraffin-embedded (FFPE) tissues and also 10 fresh frozen normal breast tissues. Results: All samples were detected to be methylated at the CDH1 promoter region. About 74.5% of the breast cancer samples were hypermethylated with an average methylation level of around 60%, while 25.5% of the patients were methylated with the mean methylation level of about 33%, and 90% of the normal samples had a mean methylation level of about 18%. Statistical analyses represented a significant correlation between CDH1 promoter methylation and cancer progression hallmarks, such as, clinical stage, nodal involvement, tumor size, and histological grade. Conclusion: In summary, quantitation of CDH1 promoter methylation can serve as a diagnostic and prognostic tool in breast cancer. Also D-HRMA can be used as a fast and reliable method for quantitation of promoter methylation. PMID:27308263

  7. Real-Time PCR and High-Resolution Melt Analysis for Rapid Detection of Mycobacterium leprae Drug Resistance Mutations and Strain Types

    PubMed Central

    Li, Wei; Matsuoka, Masanori; Kai, Masanori; Thapa, Pratibha; Khadge, Saraswoti; Hagge, Deanna A.; Brennan, Patrick J.

    2012-01-01

    Drug resistance surveillance and strain typing of Mycobacterium leprae are necessary to investigate ongoing transmission of leprosy in regions of endemicity. To enable wider implementation of these molecular analyses, novel real-time PCR–high-resolution melt (RT-PCR-HRM) assays without allele-specific primers or probes and post-PCR sample handling were developed. For the detection of mutations within drug resistance-determining regions (DRDRs) of folP1, rpoB, and gyrA, targets for dapsone, rifampin, and fluoroquinolones, real-time PCR-HRM assays were developed. Wild-type and drug-resistant mouse footpad-derived strains that included three folP1, two rpoB, and one gyrA mutation types in a reference panel were tested. RT-PCR-HRM correctly distinguished the wild type from the mutant strains. In addition, RT-PCR-HRM analyses aided in recognizing samples with mixed or minor alleles and also a mislabeled sample. When tested in 121 sequence-characterized clinical strains, HRM identified all the folP1 mutants representing two mutation types, including one not within the reference panel. The false positives (<5%) could be attributed to low DNA concentration or PCR inhibition. A second set of RT-PCR-HRM assays for identification of three previously reported single nucleotide polymorphisms (SNPs) that have been used for strain typing were developed and validated in 22 reference and 25 clinical strains. Real-time PCR-HRM is a sensitive, simple, rapid, and high-throughput tool for routine screening known DRDR mutants in new and relapsed cases, SNP typing, and detection of minor mutant alleles in the wild-type background at lower costs than current methods and with the potential for quality control in leprosy investigations. PMID:22170923

  8. Al-Fe-Zr alloys for high temperature applications produced by rapid quenching from the melt

    SciTech Connect

    Okazaki, K.; Skinner, D.J.

    1984-09-01

    The melt-spinning technique to produce microstructure for high temperature-high strength Al-Fe-Zr alloys, meeting aerospace structural requirements, is presented, including the investigations for the improvement of the thermal stability of iron aluminide dispersoids by addition of Zr. The alloys containing about 27 to 30 percent volume fraction of dispersoids would be the optimum to meet the requirements from the strength and ductility viewpoint. The thermal stability of the alloys was determined by measuring the microvickers hardness on the isochronally annealed ribbons. 9 references.

  9. Sulfur in vacuum - Sublimation effects on frozen melts, and applications to Io's surface and torus

    NASA Technical Reports Server (NTRS)

    Nash, Douglas B.

    1987-01-01

    Vacuum sublimation effects on solid sulfur yield a form of the element that is white at room temperature, is fluffy in texture, and forms on frozen sulfur in vacuum through differential evaporation of molecular species in the solid. This vacuum sulfur should exist in large quantity on Io, if the solid free sulfur there has solidified from a melt; a sulfur volcanism model for Io is accordingly developed on this basis which implies that the color and spectra of different sulfur regions of Io could indicate their relative crystallization ages and cooling histories. The flux of sublimating hotspot sulfur appears consistent with estimated turnover rates of the Io surface.

  10. Application of mixtures of polymeric carriers for dissolution enhancement of fenofibrate using hot-melt extrusion.

    PubMed

    Kalivoda, Adela; Fischbach, Matthias; Kleinebudde, Peter

    2012-06-15

    Hot-melt extrusion was applied to improve dissolution behavior of poorly soluble model drug fenofibrate. Blends of polymers were used as carrier: copovidone (COP), polyvinyl caprolactam-polyvinyl acetate-polyethylene glycol copolymer (PVCL-PVAc-PEG) and hypromellose 2910/5 (HPMC). The ratio of fenofibrate to COP remained constantly 1+3 (weighted parts) with varying amounts of PVCL-PVAc-PEG and HPMC. Solid state of fenofibrate was characterized by X-ray diffractometry and differential scanning calorimetry. Dissolution performance was compared to marketed formulations Lipidil and Lipidil-Ter. Stability studies were conducted at 25°C/60%rH. The dissolution rate from extrudates was significantly increased when compared to pure fenofibrate powder or physical mixture of the components. A supersaturation of 7.6-12.1 was reached with the pelletized extrudates. All extrudates were superior to marketed formulations. No recrystallization was observed after 26 weeks of storage for fenofibrate-COP extrudates 1+3 (weighted parts) with or without polymeric additives. Even so, both degree and duration of supersaturation decreased with increasing storage periods with the exception of fenofibrate-HPMC extrudates. Of particular interest is the finding that by adding polymers with differing release characteristics to the drug-carrier mixture, the dissolution performance of hot-melt extruded solid dosage forms can be readily adapted to meet specific requirements. PMID:22440149

  11. Ground state of two-dimensional Yukawa bosons: Applications to vortex melting

    NASA Astrophysics Data System (ADS)

    Magro, W. R.; Ceperley, D. M.

    1993-07-01

    Using variational and diffusion Monte Carlo techniques, we investigate the ground state of bosons interacting in the continuum through a repulsive modified-Bessel-function potential, ɛK0(r/σ), in two dimensions. This is a simplified model for flux lines in high-Tc superconductors. A pair-product trial function is first optimized so that its variational energy is very near the ground-state energy, then the diffusion Monte Carlo technqiue is used to calculate the exact ground-state energy. As a function of mass and density, we calculate the region of stability of the solid for densities greater than 0.01/σ2. The quantum crystal melts at high density, due to the potential's soft core, and at low density, due to the exponentially weak interaction. Bosons with ħ2/2mσ2ɛ>0.09 do not crystallize at any density. Within the flux model, we compute the flux-line phase diagram for Bi2Sr2CaCu2O8. Pair-correlation functions, structure factors, and Lindemann ratios at melting are also comptued.

  12. Full Spatial Resolution Infrared Sounding Application in the Preconvection Environment

    NASA Astrophysics Data System (ADS)

    Liu, C.; Liu, G.; Lin, T.

    2013-12-01

    Advanced infrared (IR) sounders such as the Atmospheric Infrared Sounder (AIRS) and Infrared Atmospheric Sounding Interferometer (IASI) provide atmospheric temperature and moisture profiles with high vertical resolution and high accuracy in preconvection environments. The derived atmospheric stability indices such as convective available potential energy (CAPE) and lifted index (LI) from advanced IR soundings can provide critical information 1 ; 6 h before the development of severe convective storms. Three convective storms are selected for the evaluation of applying AIRS full spatial resolution soundings and the derived products on providing warning information in the preconvection environments. In the first case, the AIRS full spatial resolution soundings revealed local extremely high atmospheric instability 3 h ahead of the convection on the leading edge of a frontal system, while the second case demonstrates that the extremely high atmospheric instability is associated with the local development of severe thunderstorm in the following hours. The third case is a local severe storm that occurred on 7-8 August 2010 in Zhou Qu, China, which caused more than 1400 deaths and left another 300 or more people missing. The AIRS full spatial resolution LI product shows the atmospheric instability 3.5 h before the storm genesis. The CAPE and LI from AIRS full spatial resolution and operational AIRS/AMSU soundings along with Geostationary Operational Environmental Satellite (GOES) Sounder derived product image (DPI) products were analyzed and compared. Case studies show that full spatial resolution AIRS retrievals provide more useful warning information in the preconvection environments for determining favorable locations for convective initiation (CI) than do the coarser spatial resolution operational soundings and lower spectral resolution GOES Sounder retrievals. The retrieved soundings are also tested in a regional data assimilation WRF 3D-var system to evaluate the

  13. A new perturbation theory of solids and fluids and its applications to high-pressure melting problems

    SciTech Connect

    Ree, F.H.

    1990-05-01

    A statistical mechanical theory that can describe both solids and fluids in a self-consistent way is described. This theory utilizes a optimized reference potential whose repulsive range shrinks with density. A unique feature of the new theory is that solid- and fluid-phase thermodynamic properties are both computed within a single theoretical framework. Hence, it allows us to study melting phenomena in a self-consistent manner. For solids, the new theory treats both harmonic and anharmonic effects in thermodynamic properties on equal footing. Applications to several model and rare gas systems show that the new theory can accurately predict fluid, solid, and fluid-solid transition properties. Effective pair potentials inferred from the analysis of krypton and xenon isotherms contain short- and long-range modifications to the Aziz-Slaman pair potential. The long-range correction is repulsive and originates from the Axilrod-Teller three-body force, while the short-range correction probably originates from many-body forces. Using the computed melting curves of krypton and neon, we discuss the range of validity of the corresponding states principle for rare gas systems. 68 refs., 8 figs., 6 tabs.

  14. Miniature high-resolution thermometer for low-temperature applications

    NASA Astrophysics Data System (ADS)

    Welander, Paul B.; Hahn, Inseob

    2001-09-01

    We report on a new miniature, high-resolution, susceptibility thermometer that employs LaxGd1-xCl3 as the paramagnetic material for temperature measurement below 4 K. The thermometer utilizes small permanent disk magnets to provide the required magnetic field, and has a total mass of only 2 g. The thermometer shows a resolution of 0.2 nK in a 1 Hz bandwidth and an absolute drift rate less than 50 fK/s at 2.2 K. In this article, we describe the thermometer design, assembly procedure, and experimental test results, including its thermal time constant and susceptibility to external magnetic fields.

  15. Identification of BRCA1/2 Founder Mutations in Southern Chinese Breast Cancer Patients Using Gene Sequencing and High Resolution DNA Melting Analysis

    PubMed Central

    Kwong, Ava; Ng, Enders Kai On; Wong, Chris Lei Po; Law, Fian Bic Fai; Au, Tommy; Wong, Hong Nei; Kurian, Allison W.; West, Dee W.; Ford, James M.; Ma, Edmond Siu Kwan

    2012-01-01

    Background Ethnic variations in breast cancer epidemiology and genetics have necessitated investigation of the spectra of BRCA1 and BRCA2 mutations in different populations. Knowledge of BRCA mutations in Chinese populations is still largely unknown. We conducted a multi-center study to characterize the spectra of BRCA mutations in Chinese breast and ovarian cancer patients from Southern China. Methodology/Principal Findings A total of 651 clinically high-risk breast and/or ovarian cancer patients were recruited from the Hong Kong Hereditary Breast Cancer Family Registry from 2007 to 2011. Comprehensive BRCA1 and BRCA2 mutation screening was performed using bi-directional sequencing of all coding exons of BRCA1 and BRCA2. Sequencing results were confirmed by in-house developed full high resolution DNA melting (HRM) analysis. Among the 451 probands analyzed, 69 (15.3%) deleterious BRCA mutations were identified, comprising 29 in BRCA1 and 40 in BRCA2. The four recurrent BRCA1 mutations (c.470_471delCT, c.3342_3345delAGAA, c.5406+1_5406+3delGTA and c.981_982delAT) accounted for 34.5% (10/29) of all BRCA1 mutations in this cohort. The four recurrent BRCA2 mutations (c.2808_2811delACAA, c.3109C>T, c.7436_7805del370 and c.9097_9098insA) accounted for 40% (16/40) of all BRCA2 mutations. Haplotype analysis was performed to confirm 1 BRCA1 and 3 BRCA2 mutations are putative founder mutations. Rapid HRM mutation screening for a panel of the founder mutations were developed and validated. Conclusion In this study, our findings suggest that BRCA mutations account for a substantial proportion of hereditary breast/ovarian cancer in Southern Chinese population. Knowing the spectrum and frequency of the founder mutations in this population will assist in the development of a cost-effective rapid screening assay, which in turn facilitates genetic counseling and testing for the purpose of cancer risk assessment. PMID:22970155

  16. Kawai-type apparatus equipped with sintered diamond and its application to melting of mantle materials

    NASA Astrophysics Data System (ADS)

    Ito, E.; Kubo, A.; Katsura, T.; Walter, M. J.

    2003-12-01

    Kawai-type (the 6-8 type) of multi-anvil apparatus has been widely used in the mineral physics because of its versatile abilities such as large volume and pressure environment of high hydrostacity. However, it has been realized for last two decades that the maximum attainable pressure is limited to ca. 27 GPa when using tungsten carbide (WC) as anvil material. We have tried to extend capability of Kawai-type apparatus by adopting sintered diamond (SD) cubes of 14 mm edge length with 1.5 or 2.0 mm truncations together with an octahedral magnesia pressure medium. Recently generated pressures of 54 GPa and 40 GPa were confirmed for 1.5 and 2.0 mm truncations, respectively, at room temperature based on the MgO pressure scale. Following above technical innovation, we have carried out melting experiments on peridotite and CI model mantle material up to 35 GPa to examine the hypothesis for crystal fractionation in deep magma ocean in early stage of the Earth's history. Powdered starting material was put directly into a small cylindrical Re heater, which was set in the octahedron with a LaCrO3 sleeve. The sample was heated to ca. 2500° C for 2-3 min at the prescribed load. The quenched products were made to polished sections, which were examined by electron microscopy and then analyzed by the electron probe micro analyzer. In peridotite, ferropericlase (Fp) is the liquidus phase up to about 30 GPa. Both Fp and Mg-perovskite (Mg-Pv), however, coexist on the liquidus at 31 GPa, indicating multiple saturation of these phases. At higher than 32 GPa the front of Fp grains moves back from the liquidus to the slightly lower temperature region and Mg-Pv becomes the liquidus phase. Ca-perovskite (Ca-Pv) crystallizes at a fairly lower temperature than Fp and Mg-Pv at pressures up to ca. 29 GPa. However the crystallization temperatures of Fp and Ca-Pv become closer with increasing pressure, and the former might be only a few degrees higher than the latter at 33 GPa. In CI mantle, on

  17. Application of Classification Models to Pharyngeal High-Resolution Manometry

    ERIC Educational Resources Information Center

    Mielens, Jason D.; Hoffman, Matthew R.; Ciucci, Michelle R.; McCulloch, Timothy M.; Jiang, Jack J.

    2012-01-01

    Purpose: The authors present 3 methods of performing pattern recognition on spatiotemporal plots produced by pharyngeal high-resolution manometry (HRM). Method: Classification models, including the artificial neural networks (ANNs) multilayer perceptron (MLP) and learning vector quantization (LVQ), as well as support vector machines (SVM), were…

  18. Astrophysical applications of high angular resolution array-telescopes

    NASA Technical Reports Server (NTRS)

    Linsley, J.

    1985-01-01

    The air shower array-telescopes which are currently being used to search for and study point sources of UHE gamma-rays have angular resolution similar to 1 deg, limited by either the small total area of particle detectors or poor timing resolution. As the signal to noise ratio depends sensitively on the angular resolution, it seems certain that this figure will quickly be surpassed when second generation instruments come into operation. Since the trajectories of galactic cosmic rays with E 100,000 GeV are practically straight lines on scales of 1 A.U. or less, these new instruments will be able to observe a shadow cast by the Moon (angular diameter 0.5 deg). Although the angular diameter of the Sun is practically the same, its shadow will be more complex because of its magnetic field. Thus, high angular resolution observations of the Sun afford a means of investigating the solar magnetic field, and also the charge composition of cosmic rays, including the ratio of antiprotons to protons.

  19. Experiments on flow focusing in soluble porous media, with applications to melt extraction from the mantle

    SciTech Connect

    Kelemen, P.B.; Whitehead, J.A.; Aharonov, E.; Jordahl, K.A.

    1995-01-01

    We demonstrate finite strucutres formed as a consequence of the `reactive infiltration instability` in a series of laboratory and numerical experiments with growth of solution channels parallel to the fluid flow direction. Our experiments demonstrate channel growth in the presence of an initial solution front and without an initial solution front where there is a gradient in the solubility of the solid matrix. In the gradient case, diffuse flow is unstable everywhere, channels can form and grow at any point, and channels may extend over the length scale of the gradient. As a consequence of the gradient results, we suggest that the reactive infiltration instability is important in the Earth`s mantle, where partial melts in the mantle ascend adiabatically. This hypothesis represents an important alternative to mid-oceanic ridge basalts (MORB) extraction in fractures, since fractures may not form in weak, viscously deforming asthenospheric mantle. We also briefly consider the effects of crystallization, rather than dissolution reactions, on the morphology of porous flow via a second set of experiments where fluid becomes supersaturated in a solid phase. This process may produce a series of walled conduits, as in our experiments. Development of a low-porosity cap overlying high porosity conduits may create hydrostatic overpressure sufficient to cause fracture and magma transport to the surface in dikes.

  20. Collimator application for microchannel plate image intensifier resolution improvement

    DOEpatents

    Thomas, S.W.

    1996-02-27

    A collimator is included in a microchannel plate image intensifier (MCPI). Collimators can be useful in improving resolution of MCPIs by eliminating the scattered electron problem and by limiting the transverse energy of electrons reaching the screen. Due to its optical absorption, a collimator will also increase the extinction ratio of an intensifier by approximately an order of magnitude. Additionally, the smooth surface of the collimator will permit a higher focusing field to be employed in the MCP-to-collimator region than is currently permitted in the MCP-to-screen region by the relatively rough and fragile aluminum layer covering the screen. Coating the MCP and collimator surfaces with aluminum oxide appears to permit additional significant increases in the field strength, resulting in better resolution. 2 figs.

  1. Collimator application for microchannel plate image intensifier resolution improvement

    DOEpatents

    Thomas, Stanley W.

    1996-02-27

    A collimator is included in a microchannel plate image intensifier (MCPI). Collimators can be useful in improving resolution of MCPIs by eliminating the scattered electron problem and by limiting the transverse energy of electrons reaching the screen. Due to its optical absorption, a collimator will also increase the extinction ratio of an intensifier by approximately an order of magnitude. Additionally, the smooth surface of the collimator will permit a higher focusing field to be employed in the MCP-to-collimator region than is currently permitted in the MCP-to-screen region by the relatively rough and fragile aluminum layer covering the screen. Coating the MCP and collimator surfaces with aluminum oxide appears to permit additional significant increases in the field strength, resulting in better resolution.

  2. High-resolution electron microscopy and its applications.

    PubMed

    Li, F H

    1987-12-01

    A review of research on high-resolution electron microscopy (HREM) carried out at the Institute of Physics, the Chinese Academy of Sciences, is presented. Apart from the direct observation of crystal and quasicrystal defects for some alloys, oxides, minerals, etc., and the structure determination for some minute crystals, an approximate image-contrast theory named pseudo-weak-phase object approximation (PWPOA), which shows the image contrast change with crystal thickness, is described. Within the framework of PWPOA, the image contrast of lithium ions in the crystal of R-Li2Ti3O7 has been observed. The usefulness of diffraction analysis techniques such as the direct method and Patterson method in HREM is discussed. Image deconvolution and resolution enhancement for weak-phase objects by use of the direct method are illustrated. In addition, preliminary results of image restoration for thick crystals are given. PMID:3505590

  3. Vacuum Shear Force Microscopy Application to High Resolution Work

    NASA Astrophysics Data System (ADS)

    Polonski, Vitali; Yamamoto, Yoh; White, Jonathon; Kourogi, Motonobu; Ohtsu, Motoichi

    1999-07-01

    A new technique—Vacuum Shear Force Microscopy (VSFM)—is introduced as a reliable method for maintaining a constant separation between a probe and sample. Elimination of many of the instabilities observed when applying the shear force mechanism to imaging under ambient conditions, allows for routine nanometer lateral and sub-nanometer normal resolution. In this paper this technique is applied, firstly, to the imaging of microtubules (biology) and, secondly, to the patterning and subsequent imaging of nanoscale metal lines (nanofabrication).

  4. High resolution frequency analysis techniques with application to the redshift experiment

    NASA Technical Reports Server (NTRS)

    Decher, R.; Teuber, D.

    1975-01-01

    High resolution frequency analysis methods, with application to the gravitational probe redshift experiment, are discussed. For this experiment a resolution of .00001 Hz is required to measure a slowly varying, low frequency signal of approximately 1 Hz. Major building blocks include fast Fourier transform, discrete Fourier transform, Lagrange interpolation, golden section search, and adaptive matched filter technique. Accuracy, resolution, and computer effort of these methods are investigated, including test runs on an IBM 360/65 computer.

  5. High-Resolution Melting Is a Sensitive, Cost-Effective, Time-Saving Technique for BRAF V600E Detection in Thyroid FNAB Washing Liquid: A Prospective Cohort Study

    PubMed Central

    Marino, Marco; Monzani, Maria Laura; Brigante, Giulia; Cioni, Katia; Madeo, Bruno; Santi, Daniele; Maiorana, Antonino; Bettelli, Stefania; Moriondo, Valeria; Pignatti, Elisa; Bonacini, Lara; Carani, Cesare; Rochira, Vincenzo; Simoni, Manuela

    2015-01-01

    Objective The diagnostic accuracy of thyroid fine needle aspiration biopsy (FNAB) can be improved by the combination of cytological and molecular analysis. In this study, washing liquids of FNAB (wFNAB) were tested for the BRAF V600E mutation, using the sensitive and cost-effective technique called high-resolution melting (HRM). The aim was to demonstrate the feasibility of BRAF analysis in wFNAB and its diagnostic utility, combined with cytology. Design Prospective cohort study. Methods 481 patients, corresponding to 648 FNAB samples, were subjected to both cytological (on cells smeared onto a glass slide) and molecular analysis (on fluids obtained washing the FNAB needle with 1 ml of saline) of the same aspiration. BRAF V600E analysis was performed by HRM after methodological validation for application to wFNAB (technique sensitivity: 5.4%). Results The cytological results of the FNAB were: 136 (21%) nondiagnostic (THY1); 415 (64%) benign (THY2); 80 (12.4%) indeterminate (THY3); 9 (1.4%) suspicious for malignancy (THY4); 8 (1.2%) diagnostic of malignancy (THY5). The BRAF V600E mutation was found in 5 THY2, 2 THY3, 6 THY4 and 6 THY5 samples. Papillary carcinoma diagnosis was histologically confirmed in all BRAF+ thyroidectomized patients. BRAF combined with cytology improved the diagnostic value compared to cytology alone in a subgroup of 74 operated patients. Conclusions HRM was demonstrated to be a feasible method for BRAF analysis in wFNAB. Thanks to its sensitivity and cost-effectiveness, it might be routinely used on a large scale in clinical practice. In perspective, standby wFNAB samples could be analyzed a posteriori in case of indeterminate cytology and/or suspicious findings on ultrasound. PMID:26279992

  6. Application and evaluation of high-resolution WRF-CMAQ with simple urban parameterization

    EPA Science Inventory

    The 2-way coupled WRF-CMAQ meteorology and air quality modeling system is evaluated for high-resolution applications by comparing to a regional air quality field study (Discover-AQ). The model was modified to better account for the effects of urban environments. High-resolution...

  7. Application and evaluation of high-resolution WRF-CMAQ with simple urban parameterization.

    EPA Science Inventory

    The 2-way coupled WRF-CMAQ meteorology and air quality modeling system is evaluated for high-resolution applications by comparing to a regional air quality field study (Discover-AQ). The model was modified to better account for the effects of urban environments. High-resolution...

  8. High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics.

    PubMed

    Dulin, David; Cui, Tao Ju; Cnossen, Jelmer; Docter, Margreet W; Lipfert, Jan; Dekker, Nynke H

    2015-11-17

    The observation of biological processes at the molecular scale in real time requires high spatial and temporal resolution. Magnetic tweezers are straightforward to implement, free of radiation or photodamage, and provide ample multiplexing capability, but their spatiotemporal resolution has lagged behind that of other single-molecule manipulation techniques, notably optical tweezers and AFM. Here, we present, to our knowledge, a new high-resolution magnetic tweezers apparatus. We systematically characterize the achievable spatiotemporal resolution for both incoherent and coherent light sources, different types and sizes of beads, and different types and lengths of tethered molecules. Using a bright coherent laser source for illumination and tracking at 6 kHz, we resolve 3 Å steps with a 1 s period for surface-melted beads and 5 Å steps with a 0.5 s period for double-stranded-dsDNA-tethered beads, in good agreement with a model of stochastic bead motion in the magnetic tweezers. We demonstrate how this instrument can be used to monitor the opening and closing of a DNA hairpin on millisecond timescales in real time, together with attendant changes in the hairpin dynamics upon the addition of deoxythymidine triphosphate. Our approach opens up the possibility of observing biological events at submillisecond timescales with subnanometer resolution using camera-based detection. PMID:26588570

  9. 77 FR 70433 - Resolute Marine Energy, Inc.; Notice of Preliminary Permit Application Accepted for Filing and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-26

    ... Alaska Wave Energy Project No. 14438. Resolute supplemented its application on September 19, 2012. The...) Between 7 and 15 Surge Wave Energy Converters for a maximum total installed capacity of 750 kilowatts;...

  10. High Resolution Atmospheric Modeling for Wind Energy Applications

    SciTech Connect

    Simpson, M; Bulaevskaya, V; Glascoe, L; Singer, M

    2010-03-18

    The ability of the WRF atmospheric model to forecast wind speed over the Nysted wind park was investigated as a function of time. It was found that in the time period we considered (August 1-19, 2008), the model is able to predict wind speeds reasonably accurately for 48 hours ahead, but that its forecast skill deteriorates rapidly after 48 hours. In addition, a preliminary analysis was carried out to investigate the impact of vertical grid resolution on the forecast skill. Our preliminary finding is that increasing vertical grid resolution does not have a significant impact on the forecast skill of the WRF model over Nysted wind park during the period we considered. Additional simulations during this period, as well as during other time periods, will be run in order to validate the results presented here. Wind speed is a difficult parameter to forecast due the interaction of large and small length scale forcing. To accurately forecast the wind speed at a given location, the model must correctly forecast the movement and strength of synoptic systems, as well as the local influence of topography / land use on the wind speed. For example, small deviations in the forecast track or strength of a large-scale low pressure system can result in significant forecast errors for local wind speeds. The purpose of this study is to provide a preliminary baseline of a high-resolution limited area model forecast performance against observations from the Nysted wind park. Validating the numerical weather prediction model performance for past forecasts will give a reasonable measure of expected forecast skill over the Nysted wind park. Also, since the Nysted Wind Park is over water and some distance from the influence of terrain, the impact of high vertical grid spacing for wind speed forecast skill will also be investigated.

  11. Application of the Plagioclase-Liquid Hygrometer to the Bishop Tuff: Consistency with Melt Inclusion H2O Contents

    NASA Astrophysics Data System (ADS)

    Jolles, J.; Lange, R. A.

    2015-12-01

    High-silica (74-77 wt% SiO2) rhyolites are the most evolved magmas on Earth and constitute some of the largest eruptions (1000s of km3). Of these, one classic example is the Bishop Tuff, a 760 ka eruption of >670 km3 of high-silica rhyolite erupted from Long Valley caldera, CA. Documenting dissolved H2O contents is crucial for understanding its origin and evolution. Analyses of water contents measured in quartz-hosted melt inclusions from the Bishop Tuff (Wallace et al. 1999; Anderson et al. 2000) show that the Early and Middle Bishop Tuff (Ig1Eb, Ig2Ea) have higher water contents (≤ 6.3 wt% H2O) than the Late Bishop Tuff (Ig2NWa; ≤ 5.2 wt%). Our work utilizes the revised plagioclase-liquid hygrometer (Waters & Lange, 2015), which is applicable to rhyolite, to evaluate internal consistency between Fe-Ti oxide temperatures, the plagioclase hygrometer, and melt inclusion H2O analyses. Two-oxide thermometry (Ghiorso & Evans, 2008), using all possible Fe-Ti oxide pairs (between 56 and 1500 pairs for individual samples), was carried out on 2-3 pumice clasts for each sampled eruptive unit. Resulting temperatures (°C ± 1σ) for individual clasts are: 705 ± 12, 728 ± 10 for unit Ig1Eb; 710 ± 12, 728 ± 11 for unit Ig2Ea; 752 ±10, 776 ± 8, 778 ± 7 for unit Ig2NWa; 791 ± 7, 795 ± 8 for unit Ig2Nb. The compositions of the most calcic plagioclase phenocrysts in the Early and Middle units are An17-19, whereas in the Late units they are An29-30. When the Fe-Ti oxide temperatures, whole rock analyses, and plagioclase compositions are incorporated into the plagioclase hygrometer, they give water contents at the onset of plagioclase crystallization of 6.6-6.9 wt% for the Early and Middle units and 4.8-4.9 wt % for the Late units. These results show internal consistency between melt inclusion analyses of water, Fe-Ti oxide thermometry, and the plagioclase-liquid hygrometer; they further support a temperature gradient across the Early, Middle, and Late Bishop Tuff units.

  12. Real-time RT-PCR high-resolution melting curve analysis and multiplex RT-PCR to detect and differentiate grapevine leafroll-associated virus 3 variant groups I, II, III and VI

    PubMed Central

    2012-01-01

    Background Grapevine leafroll-associated virus 3 (GLRaV-3) is the main contributing agent of leafroll disease worldwide. Four of the six GLRaV-3 variant groups known have been found in South Africa, but their individual contribution to leafroll disease is unknown. In order to study the pathogenesis of leafroll disease, a sensitive and accurate diagnostic assay is required that can detect different variant groups of GLRaV-3. Methods In this study, a one-step real-time RT-PCR, followed by high-resolution melting (HRM) curve analysis for the simultaneous detection and identification of GLRaV-3 variants of groups I, II, III and VI, was developed. A melting point confidence interval for each variant group was calculated to include at least 90% of all melting points observed. A multiplex RT-PCR protocol was developed to these four variant groups in order to assess the efficacy of the real-time RT-PCR HRM assay. Results A universal primer set for GLRaV-3 targeting the heat shock protein 70 homologue (Hsp70h) gene of GLRaV-3 was designed that is able to detect GLRaV-3 variant groups I, II, III and VI and differentiate between them with high-resolution melting curve analysis. The real-time RT-PCR HRM and the multiplex RT-PCR were optimized using 121 GLRaV-3 positive samples. Due to a considerable variation in melting profile observed within each GLRaV-3 group, a confidence interval of above 90% was calculated for each variant group, based on the range and distribution of melting points. The intervals of groups I and II could not be distinguished and a 95% joint confidence interval was calculated for simultaneous detection of group I and II variants. An additional primer pair targeting GLRaV-3 ORF1a was developed that can be used in a subsequent real-time RT-PCR HRM to differentiate between variants of groups I and II. Additionally, the multiplex RT-PCR successfully validated 94.64% of the infections detected with the real-time RT-PCR HRM. Conclusion The real-time RT-PCR HRM

  13. Dynamics in Polymer Melts and Nanocomposites

    NASA Astrophysics Data System (ADS)

    Schneider, Gerald

    Intense research has led to substantial progress in the field of polymer melts and nanocomposites, both regarding the fundamental understanding and the relationship to applications. From a fundamental point of view, knowing the microscopic single chain dynamics is important. It may even lead to optimized materials ranging from the classical car tire to battery or fuel cell applications. In polymer melts, different processes, such as diffusion, reptation, contour length fluctuations, etc. occur and determine the macroscopic results, e.g. obtained by rheology. In nanocomposites confinement effects and interactions of chains with surfaces play an important role. High resolution techniques, such as small-angle neutron scattering or neutron spin echo spectroscopy are suited to explore the structure and dynamics of chains. The presentation illuminates the fundamental relationship between the microscopic dynamics and the mesoscopic properties, exploiting different experimental techniques, such as dielectric spectroscopy, rheology, neutron scattering and neutron spin echo spectroscopy.

  14. Application of high-resolution EFTEM SI in an AEM.

    PubMed

    Schaffer, Bernhard; Grogger, Werner; Kothleitner, Gerald; Hofer, Ferdinand

    2008-03-01

    In this work we show how energy-filtered imaging can be used to obtain spectrum images of electron energy-loss spectrometric data. Focus is placed on improved energy resolution within these data sets. Using two multilayer samples (GaN/AlN and InP/InAs), we demonstrate the advantages of spectrum-imaging and its extended mapping capabilities. Plasmon-ratio maps are used to quickly create high-contrast material maps with high signal-to-noise ratio, ratio-contrast plots are used to gain optimum settings for the ratio maps, and plasmon-position maps are used to map small shifts of the energy position of bulk plasmon peaks. PMID:17874077

  15. Monitoring the melt-extrusion transesterification of ethylene-vinylacetate copolymer by self-modeling curve resolution analysis of on-line near-infrared spectra.

    PubMed

    Sasić, S; Kita, Y; Furukawa, T; Watari, M; Siesler, H W; Ozaki, Y

    2000-12-01

    The transesterification of molten ethylene-vinylacetate (EVA) copolymers by octanol with sodium methoxide as catalyst in an extruder has been monitored by on-line near infrared (NIR) spectroscopy. A total of 60 NIR spectra were acquired for 37 min with the last spectrum recorded 31 min after the addition of octanol and catalyst was stopped. The experimental spectra show strong baseline fluctuations which are corrected for by multiplicative scatter correction (MSC). The chemometric methods of the orthogonal projection approach (OPA) and multivariate curve resolution (MCR) were used to resolve the spectra and to derive concentration profiles of the species. The detailed analysis reveals the absence of completely pure variables which leads to small errors in the calculation of pure spectra. The initial estimation of a concentration that is necessary as an input parameter for MCR also presents a non-trivial task. We obtained results that were not ideal but applicable for practical concentration control. They enable a fast monitoring of the process in real-time and resolve the spectra of the EVA copolymer and the ethylene-vinyl alcohol (EVAL) copolymer to be very close to the reference spectra. The chemometric methods used and the decomposed spectra are discussed in detail. PMID:11219074

  16. High Spatial Resolution 40Ar/39Ar Geochronology of Impact Melt Breccias from Apollo 17 Boulders at Stations 2, 6, and 7

    NASA Astrophysics Data System (ADS)

    Mercer, C. M.; Hodges, K. V.; Jolliff, B. L.; Van Soest, M. C.; Wartho, J. A.; Weirich, J. R.

    2015-12-01

    Several boulders located at the bases of the North and South Massifs were among the primary field targets of the Apollo 17 mission to the Taurus-Littrow Valley on the Moon [1]. Some boulders are polylithologic, including Boulder 1 at Station 2 and the boulders at Stations 6 and 7. These boulders were the subjects of consortium studies [2, 3] that included 40Ar/39Ar geochronology to determine the ages of distinct lithologies within each boulder [e.g., 4-6]. We report new 40Ar/39Ar data for the impact melt breccias 72255, 76315, 77075, and 77135 obtained using the UV laser ablation microprobe (UVLAMP) methods of [7]. For 72255, we obtained a preliminary isochron date ca. 3814 Ma from 22 melt analyses, which is younger than published plateau dates (e.g., 3951-3835 Ma [4, 8]). Fifteen melt analyses of 76315 yield a preliminary isochron date ca. 3850 Ma, younger than the 3900 ± 16 Ma date reported by [8]. Melt analyses of 77075 yield preliminary dates between ca. 3797-3584 Ma, possibly reflecting partial loss of 40Ar. In this case, the oldest date may provide a minimum age for the formation of melt in 77075. Finally, the UVLAMP dates for the 77135 melt range from 3810-3361 Ma and corresponding Ca/K ratios range from ca. 100-6. Electron microprobe analyses of small (ca. 10s of microns wide) pockets of K-rich materials show that both K-rich glass and K-feldspar are present. The UVLAMP dates for 77135 likely reflect spatially variable 40Ar loss, consistent with published step heating results [e.g., 6]. References: [1] Schmitt (1973) Science, 182, 681-690. [2] Ryder (1993). Catalog of Apollo 17 Rocks: Volume 1 - Stations 2 and 3 (South Massif). LPI. [3] Ryder (1993). Catalog of Apollo 17 Rocks: Volume 4 - North Massif. LPI. [4] Leich et al. (1975) The Moon, 14, 407-444. [5] Cadogan & Turner (1976). LPSC, 7, 2267-2285. [6] Stettler et al. (1978). LPSC, 9, 1113-1115. [7] Mercer et al. (2015) Sci. Adv., 1, e1400050. [8] Dalrymple & Ryder (1996). JGR, 101, 26069-26084.

  17. Application of Metabolomics for High Resolution Phenotype Analysis

    PubMed Central

    Fukusaki, Eiichiro

    2014-01-01

    Metabolome, a total profile of whole metabolites, is placed on downstream of proteome. Metabolome is thought to be results of implementation of genomic information. In other words, metabolome can be called as high resolution phenotype. The easiest operation of metabolomics is the integration to the upstream ome information including transcriptome and/or proteome. Those trials have been reported at a certain scientific level. In addition, metabolomics can be operated in stand-alone mode without any other ome information. Among metabolomics tactics, the author’s group is particularly focusing on metabolic fingerprinting, in which metabolome information is employed as explanatory variant to evaluate response variant. Metabolic fingerprinting technique is expected not only for analyzing slight difference depending on genotype difference but also for expressing dynamic variation of living organisms. The author introduces several good examples which he performed. Those are useful for easy understanding of the power of metabolomics. In addition, the author mentions the latest technology for analysis of metabolic dynamism. The author’s group developed a facile analytical method for semi-quantitative metabolic dynamism. The author introduces the novel method that uses time dependent variation of isotope distribution based on stable isotope dilution. PMID:26819889

  18. Applications of High-Resolution Observations at Millimeter Wavelengths

    NASA Astrophysics Data System (ADS)

    Rosenfeld, Katherine

    Interferometric observations at millimeter wavelengths provide a precious, detailed view of certain astrophysical objects. This thesis is composed of studies that both rely on and enable this technique to study the structure of planet-forming disks and soon image the closest regions around super-massive black holes. Young stars form out of a cloud of gas and dust that, before its eventual dissipation, flattens to a disk. However the disk population is diverse and recent high-resolution images have revealed a wide variety of interesting features. To understand these observations we use detailed radiative transfer models to motivate various physical scenarios. First we identify a set of traits in the disk around V4046 Sgr that marks the coupled progression of the gas and dust distributions in the presence of at least one embedded companion. Next, we investigate how the vertical temperature structure of a disk can be spatially resolved and apply our framework to observations of the disk around HD163296. Lastly, we show how large-scale radial flows of gas may be observable and question how this phenomenon might be distinguished from other scenarios such as warps or outflows. The last chapter summarizes the APHIDS project which changes the sampling rate of data taken at the SMA so that it may be used for VLBI campaigns.

  19. Multivariate curve resolution: a review of advanced and tailored applications and challenges.

    PubMed

    Ruckebusch, C; Blanchet, L

    2013-02-26

    Multivariate curve resolution (MCR) is a widespread methodology for the analysis of process data in many different application fields. This article intends to propose a critical review of the recently published works. Particular attention will be paid to situations requiring advanced and tailored applications of multivariate curve resolution, dealing with improvements in preprocessing methods, multi-set data arrangements, tailored constraints, issues related to non-ideal noise structure and deviation to linearity. These analytical issues are tackling the limits of applicability of MCR methods and, therefore, they can be considered as the most challenging ones. PMID:23410623

  20. Ultra high resolution stepper motors design, development, performance and application

    NASA Technical Reports Server (NTRS)

    Moll, H.; Roeckl, G.

    1979-01-01

    The design and development of stepper motors with steps in the 10 arc sec to 2 arc min range is described. Some of the problem areas, e.g. rotor suspension, tribology aspects and environmental conditions are covered. A summary of achieved test results and the employment in different mechanisms already developed and tested is presented to give some examples of the possible use of this interesting device. Adaptations to military and commercial requirements are proposed and show the wide range of possible applications.

  1. Microstructures and mechanical properties of Co-29Cr-6Mo alloy fabricated by selective laser melting process for dental applications.

    PubMed

    Takaichi, Atsushi; Suyalatu; Nakamoto, Takayuki; Joko, Natsuka; Nomura, Naoyuki; Tsutsumi, Yusuke; Migita, Satoshi; Doi, Hisashi; Kurosu, Shingo; Chiba, Akihiko; Wakabayashi, Noriyuki; Igarashi, Yoshimasa; Hanawa, Takao

    2013-05-01

    The selective laser melting (SLM) process was applied to a Co-29Cr-6Mo alloy, and its microstructure, mechanical properties, and metal elution were investigated to determine whether the fabrication process is suitable for dental applications. The microstructure was evaluated using scanning electron microscopy with energy-dispersed X-ray spectroscopy (SEM-EDS), X-ray diffractometry (XRD), and electron back-scattered diffraction pattern analysis. The mechanical properties were evaluated using a tensile test. Dense builds were obtained when the input energy of the laser scan was higher than 400 J mm⁻³, whereas porous builds were formed when the input energy was lower than 150 J mm⁻³. The microstructure obtained was unique with fine cellular dendrites in the elongated grains parallel to the building direction. The γ phase was dominant in the build and its preferential <001> orientation was confirmed along the building direction, which was clearly observed for the builds fabricated at lower input energy. Although the mechanical anisotropy was confirmed in the SLM builds due to the unique microstructure, the yield strength, UTS, and elongation were higher than those of the as-cast alloy and satisfied the type 5 criteria in ISO22764. Metal elution from the SLM build was smaller than that of the as-cast alloy, and thus, the SLM process for the Co-29Cr-6Mo alloy is a promising candidate for fabricating dental devices. PMID:23500549

  2. New melt-processable thermoplastic polyimides for opto-electronic applications

    NASA Astrophysics Data System (ADS)

    Narayanan, Aditya; Haralur, Gurulingamurthy

    2012-10-01

    The rapid development and adoption of digital technology is leading to an increase in demand for smaller, faster digital data devices and faster digital telecommunication networks. This trend requires increased network bandwidth to handle large amounts of data and seamless integration of network devices with compatible end-user devices. This need is being met by using fiber-optic and photonics technology, infra-red (IR) signals to transmit information, and is fundamental changing the communication industry, thereby creating a need for new polymeric materials. New ULTEM* polyetherimide (PEI) and EXTEM* thermoplastic polyimide (TPI) resins meet the material requirements for the optoelectronics industry. These resins have building blocks enabling IR light transmission without degrading signal quality. They can be injection-molded into thin, precision optical lenses and connectors. ULTEM* resins are been widely used in this industry as fiber-optic components in trans-receivers. EXTEM* resins are amenable to lead-free soldering (LFS), a greener industrial assembly process. While still being IR-transparent, EXTEM* resin is an ideal material for LFS capable substrates, connectors and lenses. An optical product portfolio has been developed and is being presented as a solution to the opto-electronics component industry and some of the successful applications therein.

  3. Melt pool dynamics during selective electron beam melting

    NASA Astrophysics Data System (ADS)

    Scharowsky, T.; Osmanlic, F.; Singer, R. F.; Körner, C.

    2014-03-01

    Electron beam melting is a promising additive manufacturing technique for metal parts. Nevertheless, the process is still poorly understood making further investigations indispensable to allow a prediction of the part's quality. To improve the understanding of the process especially the beam powder interaction, process observation at the relevant time scale is necessary. Due to the difficult accessibility of the building area, the high temperatures, radiation and the very high scanning speeds during the melting process the observation requires an augmented effort in the observation equipment. A high speed camera in combination with an illumination laser, band pass filter and mirror system is suitable for the observation of the electron beam melting process. The equipment allows to observe the melting process with a high spatial and temporal resolution. In this paper the adjustment of the equipment and results of the lifetime and the oscillation frequencies of the melt pool for a simple geometry are presented.

  4. Advances in super-resolution technology and application in biomedical research

    NASA Astrophysics Data System (ADS)

    O'Connell, Christopher B.; Ross, Stephen T.

    2012-02-01

    The diffraction limit of the conventional light microscope establishes a barrier that limits resolution and prevents observation of fine structural details within biological specimens. A number of commercially available systems now enable researchers to beat diffraction and achieve up to ten-fold improvements in resolution. These super resolution systems generally rely on one of two strategies. They either add optical elements in order to overcome the diffraction limit or they implement computational power and fitting algorithms to circumvent it. We have now entered the next phase in the development of super resolution systems, where probes, hardware, and software are gaining the refinements necessary to facilitate their application to a range of biological problems. Here, we highlight the recent developments in these areas for two types of super resolution imaging systems, structured illumination microscopy (SIM) and stochastic optical reconstruction microscopy (STORM). These improvements are promoting the fast acquisition and processing speeds needed for live cell imaging beyond the diffraction limit.

  5. Minimizing the grid-resolution dependence of flow-routing algorithms for geomorphic applications

    NASA Astrophysics Data System (ADS)

    Pelletier, Jon D.

    2010-10-01

    The results of flow-routing methods currently used in the geomorphic literature depend on grid resolution. This poses a problem for landscape evolution models, which must be independent of grid resolution to the greatest extent possible. Here I illustrate a refinement of currently-used flow-routing algorithms that yields unit contributing areas (i.e. contributing areas per unit width of flow) with minimal grid-resolution effects. I illustrate the application of this method in idealized topography, in high-resolution Digital Elevation Models (DEMs) of real-world topography, and by integration into a landscape evolution model for ridge-and-valley topography. The landscape evolution model produces grid-resolution-independent results in a more straightforward way than previous models for this type of landscape.

  6. A Survey on Large High-Resolution Display Technologies, Techniques, and Applications

    SciTech Connect

    Ni, Tao; Schmidt, Greg S.; Staadt, Oliver G.; Livingston, Mark A.; Ball, Robert; May, Richard A.

    2006-03-27

    Continued advances in display hardware, computing power, networking, and rendering algorithms have all converged to dramatically improve large high-resolution display capabilities. We present a survey on prior research with large high-resolution displays. In the hardware configurations section we examine systems including multi-monitor workstations, recon*gurable projector arrays, and others. Rendering and the data pipeline are addressed with an overview of current technologies. We discuss many applications for large high-resolution displays such as automotive design, scientific visualization, control centers, and others. Quantifying the effect of large high-resolution displays on human performance and other aspects is important as we look toward future advances in display technology and how it is applied in different situations. Interacting with these displays brings a different set of challenges for HCI professionals, so an overview of some of this work is provided. Finally, we present our view of the top ten greatest challenges in large high-resolution displays.

  7. High resolution mesospheric sodium properties for adaptive optics applications

    NASA Astrophysics Data System (ADS)

    Pfrommer, T.; Hickson, P.

    2014-05-01

    Context. The performance of laser guide star adaptive optics (AO) systems for large optical and infrared telescopes is affected by variability of the sodium layer, located at altitudes between 80 and 120 km in the upper mesosphere and lower thermosphere. The abundance and density structure of the atomic sodium found in this region is subject to local and global weather effects, planetary and gravity waves and magnetic storms, and is variable on time scales down to tens of milliseconds, a range relevant to AO. Aims: It is therefore important to characterize the structure and dynamical evolution of the sodium region on small, as well as large spatial and temporal scales. Parameters of particular importance for AO are the mean sodium altitude, sodium layer width and the temporal power spectrum of the centroid altitude. Methods: We have conducted a three-year campaign employing a high-resolution lidar system installed on the 6-m Large Zenith Telescope (LZT) located near Vancouver, Canada. During this period, 112 nights of useful data were obtained. Results: The vertical density profile of atomic sodium shows remarkable structure and variability. Smooth Gaussian-shaped profiles rarely occur. Multiple internal layers are frequently found. These layers often have sharp lower edges, with scale heights of just a few hundred meters, and tend to drift downwards at a typical rate of one kilometer every two to three hours. Individual layers can persist for many hours, but their density and internal structure can be highly variable. Sporadic layers are seen reaching peak densities several times the average, often in just a few minutes. Coherent vertical oscillations are often found, typically extending over tens of kilometers in altitude. Regions of turbulence are evident and Kelvin-Helmholtz instability are sometimes seen. The mean value of the centroid altitude is found to be 90.8 ± 0.1 km. The sodium layer width was determined by computing the altitude range that contains a

  8. Calculating Freshwater Input from Iceberg Melt in Greenlandic Fjords by Combining In Situ Observations of Iceberg Movement with High Resolution Satellite Imagery

    NASA Astrophysics Data System (ADS)

    Sulak, D. J.; Sutherland, D.; Stearns, L. A.; Hamilton, G. S.

    2015-12-01

    Understanding fjord circulation in Greenland's outlet glacial fjords is crucial to explaining recent temporal and spatial variability in glacier dynamics, as well as freshwater transport on the continental shelf. The fjords are commonly assumed to exhibit a plume driven circulation that draws in warmer and saltier Atlantic-origin water toward the glacier at depth. Freshwater input at glacier termini directly drives this circulation and significantly influences water column stratification, which indirectly feeds back on the plume driven circulation. Previous work has focused on freshwater inputs from surface runoff and submarine melting, but the contribution from iceberg melt, a potentially important freshwater source, has not been quantified. Here, we develop a new technique combining in situ observations of movement from iceberg-mounted GPS units with multispectral satellite imagery from Landsat 8. The combination of datasets allows us to examine the details of iceberg movement and quantify mean residence times in a given fjord. We then use common melt rate parameterizations to estimate freshwater input for a given iceberg, utilizing novel satellite-derived iceberg distributions to scale up to a fjord-wide freshwater contribution. We apply this technique to Rink Isbræ and Kangerlussuup Sermia in west Greenland, and Helheim Glacier in southeast Greenland. The analysis can be rapidly expanded to look at other systems as well as seasonal and interannual changes in how icebergs affect the circulation and stratification of Greenland's outlet glacial fjords. Ultimately, this work will lead to a more complete understanding of the wide range of factors that control the observed regional variability in Greenland's glaciers.

  9. Chloride-bearing liquids and partial melting of mantle eclogites: experimental study and application to the diamond-forming processes.

    NASA Astrophysics Data System (ADS)

    Safonov, Oleg

    2010-05-01

    Recent studies prove that the partial melting in some eclogite xenoliths in kimberlites is closely related to formation of diamonds in these rocks at 4-6 GPa and 1150-12500C [e.g. 1, 2]. Along with specific mineral assemblages, the products of the eclogite partial melting commonly include relics of potassium-rich silicic melts (45-65 wt. % of SiO2, 4-14 wt. % of K2O and K2O/Na2O > 1.0) [1, 2]. Available experimental data, however, demonstrate that such melts can not be produced by 'dry' or hydrous melting of a common eclogite. It implies that partial melting and conjugate diamond formation in mantle eclogites was triggered by infiltration of potassic fluids/melts. Assemblages of Cl-bearing phases and carbonates in eclogite xenoliths [1], and eclogitic diamonds [3-6] suggest that these agents were chloride-carbonate-H2O melts or/and chloride-H2O-CO2 fluids. In order to characterize interaction of both types of liquids with eclogites and their minerals, experiments in the eclogite-related systems with participation of CaCO3-Na2CO3-KCl-H2O or H2O-CO2-KCl are reviewed. Melting relations in the system eclogite-CaCO3-Na2CO3-KCl-H2O follow the general scheme proposed earlier for chloride-carbonate-silicate systems [7]. Below 12000C, Grt, Cpx and phlogopite (Phl) coexist with LCC only. Formation of Phl and Ca-rich Grt after Cpx indicate active reactions of Cpx with LCC accompanied by CO2 degassing and depletion of the clinopyroxene in jadeite. Subsequent dissolution of silicates in LCC at >1200OC results in formation of potassic silica-undersaturated carbonate and Cl-bearing melt (LCS) (37-40 wt. % of SiO2, 10-12 wt. % of K2O, ~3.5 wt. % of Cl) immiscible with the LCC. Compositional feature of this melt is very comparable to those of low-Mg carbonate-silicate melt inclusions in diamonds [6]. However, it is not relevant to the melt relics preserved in the partially molten eclogite xenoliths. Melting of eclogites with participation of the H2O-CO2-KCl fluid at 5 GPa at 1200

  10. Experimental investigation of the electrical behavior of olivine during partial melting under pressure and application to the lunar mantle

    NASA Astrophysics Data System (ADS)

    Pommier, A.; Leinenweber, K.; Tasaka, M.

    2015-09-01

    Electrical conductivity measurements were performed during melting experiments of olivine compacts (dry and hydrous Fo77 and Fo90) at 4 and 6 GPa in order to investigate melt transport properties and quantify the effect of partial melting on electrical properties. Experiments were performed in the multi-anvil apparatus and electrical measurements were conducted using the impedance spectroscopy technique with the two-electrode method. Changes in impedance spectra were used to identify the transition from an electrical response controlled by the solid matrix to an electrical response controlled by the melt phase. This transition occurs slightly above the solidus temperature and lasts until Tsolidus + 75 °C (±25). At higher temperature, a significant increase in conductivity (corresponding to an increase in conductivity values by a factor ranging from ∼30 to 100) is observed, consistent with the transition from a tube-dominated network to a structure in which melt films and pools become prominent features. This increase in conductivity corresponds to an abrupt jump for all dry samples and to a smoother increase for the hydrous sample. It is followed by a plateau at higher temperature, suggesting that the electrical response of the investigated samples lacks sensitivity to temperature at an advanced stage of partial melting. Electron microprobe analyses on quenched products indicated an increase in Mg# (molar Mg / (Mg +Fe)) of olivine during experiments (∼77-93 in the quenched samples with an initial Fo77 composition and ∼92-97 in the quenched samples with an initial Fo90 composition) due to the partitioning of iron to the melt phase. Assuming a respective melt fraction of 0.10 and 0.20 before and after the phase of significant increase in conductivity, in agreement with previous electrical and permeability studies, our results can be reproduced satisfactorily by two-phase electrical models (the Hashin and Shtrikman bounds and the modified brick layer model

  11. Sub-7-second genotyping of single-nucleotide polymorphism by high-resolution melting curve analysis on a thermal digital microfluidic device.

    PubMed

    Chen, Tianlan; Jia, Yanwei; Dong, Cheng; Gao, Jie; Mak, Pui-In; Martins, Rui P

    2016-02-21

    We developed a thermal digital microfluidic (T-DMF) device enabling ultrafast DNA melting curve analysis (MCA). Within 7 seconds, the T-DMF device succeeded in differentiating a melting point difference down to 1.6 °C with a variation of 0.3 °C in a tiny droplet sample (1.2 μL), which was 300 times faster and with 20 times less sample spending than the standard MCA (35 minutes, 25 μL) run in a commercial qPCR machine. Such a performance makes it possible for a rapid discrimination of single-nucleotide mutation relevant to prompt clinical decision-making. Also, aided by electronic intelligent control, the T-DMF device facilitates sample handling and pipelining in an automatic serial manner. An optimized oval-shaped thermal electrode is introduced to achieve high thermal uniformity. A device-sealing technique averts sample contamination and permits uninterrupted chemical/biological reactions. Simple fabrication using a single chromium layer fulfills both the thermal and typical transport electrode requirements. Capable of thermally modulating DNA samples with ultrafast MCA, this T-DMF device has the potential for a wide variety of life science analyses, especially for disease diagnosis and prognosis. PMID:26781669

  12. The Human Genomic Melting Map

    PubMed Central

    Liu, Fang; Tøstesen, Eivind; Sundet, Jostein K; Jenssen, Tor-Kristian; Bock, Christoph; Jerstad, Geir Ivar; Thilly, William G; Hovig, Eivind

    2007-01-01

    In a living cell, the antiparallel double-stranded helix of DNA is a dynamically changing structure. The structure relates to interactions between and within the DNA strands, and the array of other macromolecules that constitutes functional chromatin. It is only through its changing conformations that DNA can organize and structure a large number of cellular functions. In particular, DNA must locally uncoil, or melt, and become single-stranded for DNA replication, repair, recombination, and transcription to occur. It has previously been shown that this melting occurs cooperatively, whereby several base pairs act in concert to generate melting bubbles, and in this way constitute a domain that behaves as a unit with respect to local DNA single-strandedness. We have applied a melting map calculation to the complete human genome, which provides information about the propensities of forming local bubbles determined from the whole sequence, and present a first report on its basic features, the extent of cooperativity, and correlations to various physical and biological features of the human genome. Globally, the melting map covaries very strongly with GC content. Most importantly, however, cooperativity of DNA denaturation causes this correlation to be weaker at resolutions fewer than 500 bps. This is also the resolution level at which most structural and biological processes occur, signifying the importance of the informational content inherent in the genomic melting map. The human DNA melting map may be further explored at http://meltmap.uio.no. PMID:17511513

  13. Development of a double-stage DDIA apparatus and its application to in-situ melting experiments at high pressures

    NASA Astrophysics Data System (ADS)

    Jing, Z.; Wang, Y.; Tange, Y.; Hilairet, N.; Yu, T.; Sakamaki, T.

    2010-12-01

    Melting experiments at high pressures are critical to our studies on the chemical evolution and dynamics of Earth and other terrestrial planets. A large volume press can generate a homogeneous and stable high-temperature environment, which is the key to melting experiments. However, previous in-situ melting experiments using a large volume press were often restricted to relatively low pressures. In order to expand the P-T conditions, a double-stage 6-8 configuration (6 first-stage anvils and 8 second stage-anvils) has been developed in a DDIA apparatus (DDIA-30), recently installed at the GSECARS Beamline 13-ID-D at the Advanced Photon Source. 27 mm DIA-type first-stage anvils and 14 mm second-stage anvils with the truncation edge length (TEL) of 1.5 mm are employed. A cell assembly that is suitable for synchrotron X-ray studies developed by Tange et al. (2008) has been adopted for melting experiments. High pressure and temperature conditions are generated up to 27 GPa and 2473 K by using tungsten carbide anvils, and up to 35 GPa and 1773 K by using sintered diamond anvils. Both LaCrO3 and TiB2 heater materials have been successfully applied for high-temperature generation. Although TiB2 shows a decrease of resistance at temperatures higher than 2000 K at 20 GPa, we are able to achieve 2473 K with temperature fluctuations in the range of ±30 K. Using tungsten carbide anvils and TiB2 heaters, we have determined the melting curve of gold up to 20 GPa. We constrain the melting temperature based on the disappearance of the gold peaks in energy dispersive X-ray diffraction patterns and the change of sample shape in the radiographic images. The combination of these two observations can reduce the uncertainties in melting temperatures to within 100 K. The measured melting temperatures of gold at 8, 13, and 20 GPa are consistent with the low-pressure results (up to 6 GPa) such as Mirwald and Kennedy (1979). Melting experiments with sintered diamond anvils are currently

  14. Fundamental study of a refractory-based carbon fiber reinforced composite made by reactive melt infiltration for hypersonic applications

    NASA Astrophysics Data System (ADS)

    Wali, Natalie Alice

    Ceramic matrix composites are excellent candidates for ultrahigh temperature applications due their good physical properties, which are a combination of a chemically stable matrix and tough fiber reinforcement. This work is a fundamental study of a carbon fiber reinforced zirconium carbide composite (Cf/ZrC). The background chapter reviews reactive melt infiltration, which is the processing method used to make the Cf/ZrC composite. The first chapter discusses the microstructural characterization and development of Cf/ZrC. A formation mechanism of the unique matrix microstructure is proposed based on the characterization results. In the second chapter the mechanical properties of Cf/ZrC were determined. The fracture toughness at room temperature is obtained with a standard four point bend test, while flexural strength of Cf/ZrC is obtained to the ultra high temperature regime. For high temperatures a testing rig was modified to operate in inert atmosphere and tests were conducted at 1100 °C, 1350 °C and 1650 °C. Correlation is made between the flexural strength and fiber coatings of two different composite types. In situ compression tests were performed a modified SEM. Digital image correlation was used to monitor strains during compression. The stress-strain information is correlated to surface deformation. The environmental durability and oxidation behavior of Cf/ZrC and ZrC is detailed in the third and fourth chapters. The oxidation and shock behavior of Cf/ZrC were observed under both slow and rapid heating rates to ultra high temperatures. For rapid heating rates a panel was subjected to heating at steady-state and non-steady state heat flux. For slow heating rates specimen coupons were heated at 2000 °C in a bottom-loading furnace. Specimens were characterized post-test by x-ray diffraction, electron microscopy, electron probe microanalysis, and optical microscopy. The oxidation kinetics of Cf/ZrC composites and ZrC powders (45 micron and 60 nanometer

  15. Effect of surface conditioning on the flowability of Ti6Al7Nb powder for selective laser melting applications

    NASA Astrophysics Data System (ADS)

    Marcu, T.; Todea, M.; Gligor, I.; Berce, P.; Popa, C.

    2012-01-01

    Porous metallic implants have been developed to provide a good implant-tissue mechanical attachment and an as close as possible elastic modulus to that of human bone, by the means of a proper porosity. A viable manufacturing technology for personalized implants is rapid prototyping (RP), which employs fine feeding powders which usually display a poor flow behaviour. In the present work, the required flowability of Ti6Al7Nb powder aimed for selective laser melting (SLM) applications was improved by applying a simple heat treatment in air, at temperatures higher than 500 °C. As flowability depends on the powder surface condition, the surface chemical composition before and after heat treatment was characterized by X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) analysis. The results indicated that the amount of basic and acidic -OH groups is almost the same for powders treated at 400 °C, which do not flow, and powders treated at 500 °C, which display flowability. An increase of the Al2O3 amount in the TiO2-based surface layer on the powder particles with the treatment temperature was noticed. Based on the results, the temperature of 500 °C was selected for the further research. The conditioned powder displayed a very good technological behaviour, being successfully used for obtaining specimens with both cellular and fully dense structures through SLM. The microstructure of the manufactured samples, characterized by optical microscopy and scanning electron microscopy (SEM), has shown mainly α‧ martensite, with columnar grains.

  16. Vitis vinifera L. Single-Nucleotide Polymorphism Detection with High-Resolution Melting Analysis Based on the UDP-Glucose:Flavonoid 3-O-Glucosyltransferase Gene.

    PubMed

    Pereira, Leonor; Martins-Lopes, Paula

    2015-10-21

    Vitis vinifera L. is a species with a large number of varieties, which differ in terms of anthocyanin content. The genes involved in the anthocyanin biosynthesis pathway have a direct effect in the anthocyanin profile of each variety, being potentially interesting for varietal identification. The current study aimed at the design of an assay suitable for the discrimination of the largest number of grapevine varieties. Two genes of the anthocyanin pathway, chalcone isomerase (CHI) and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT), were sequenced in 22 grapevine varieties. The CHI gene presented 5 SNPs within the sequence. A total of 58 SNPs and 1 INDEL were found among the UFGT gene, allowing the discrimination of 18 different genotypes within the 22 grapevine varieties. A HRM assay designed for UFGT, containing 704 bp, produced differentiated melting curves for each of the 18 haplotypes. The developed HRM assay is efficient in grapevine varietal discrimination. PMID:26422991

  17. IR super-resolution microspectroscopy and its application to single cells.

    PubMed

    Sakai, Makoto; Inoue, Keiichi; Fujii, Masaaki

    2013-01-01

    For many years, spatial resolution is the most critical problem in IR microspectroscopy. This is because the spatial resolution of a conventional infrared microscope is restricted by the diffraction limit, which is almost the same as the wavelength of IR light, ranging from 2.5 to 25 μm. In the recent years, we have developed two novel types of far-field IR super-resolution microscopes using 2-color laser spectroscopies, those are transient fluorescence detected IR (TFD-IR) spectroscopy and vibrational sum-frequency generation (VSFG) spectroscopy. In these ways, because both transient fluorescence and VSFG signal have a wavelength in the visible region, the image is observed at the resolution of visible light, which is about 10 times smaller than that of IR light (that is, IR super-resolution). By using these techniques, we can map the specific IR absorption band with sub-micrometer spatial resolution, visualization of the molecular structure and reaction dynamics in a non-uniform environment such as a cell becomes a possibility. In the present reviews, we introduce our novel IR super-resolution microspectroscopy and its application to single cells in detail. PMID:22356113

  18. Regional Studies and Applications with a Variable Resolution Stretched Grid Data Assimilation System

    NASA Technical Reports Server (NTRS)

    Fox-Rabinovitz, Michael; Dee, Dick; Takacs, Lawrence

    1999-01-01

    The variable resolution stretched grid (SG) version of the Goddard Earth Observing System (GEOS) Data Assimilation System (DAS) incorporating the GEOS SG-GCM, is used for regional analysis, forecast, and climate applications. The region of interest with enhanced horizontal resolution, mostly used in experiments, is a rectangle over the U.S. The SG-DAS is capable of reproducing regional mesoscale fields, patterns and diagnostics that are not produced by the medium uniform resolution run with the same amount of grid points as for the SG. The SG-DAS regional analyses and diagnostics are used for: validation of regional climate simulation experiments produced with the SG-GCM for the U.S. 1988 summer drought; and are planned to be used for atmospheric chemistry transport experiments. Also, a case study is conducted on a super-typhoon development in December 1997. The SG-DAS appears to be a viable candidate for a variety of regional studies and applications.

  19. Architecture and applications of a high resolution gated SPAD image sensor

    PubMed Central

    Burri, Samuel; Maruyama, Yuki; Michalet, Xavier; Regazzoni, Francesco; Bruschini, Claudio; Charbon, Edoardo

    2014-01-01

    We present the architecture and three applications of the largest resolution image sensor based on single-photon avalanche diodes (SPADs) published to date. The sensor, fabricated in a high-voltage CMOS process, has a resolution of 512 × 128 pixels and a pitch of 24 μm. The fill-factor of 5% can be increased to 30% with the use of microlenses. For precise control of the exposure and for time-resolved imaging, we use fast global gating signals to define exposure windows as small as 4 ns. The uniformity of the gate edges location is ∼140 ps (FWHM) over the whole array, while in-pixel digital counting enables frame rates as high as 156 kfps. Currently, our camera is used as a highly sensitive sensor with high temporal resolution, for applications ranging from fluorescence lifetime measurements to fluorescence correlation spectroscopy and generation of true random numbers. PMID:25090572

  20. Super-resolution imaging with stochastic single-molecule localization: concepts, technical developments, and biological applications.

    PubMed

    Oddone, Anna; Vilanova, Ione Verdeny; Tam, Johnny; Lakadamyali, Melike

    2014-07-01

    Light microscopy has undergone a revolution with the advent of super-resolution microscopy methods that can surpass the diffraction limit. These methods have generated much enthusiasm, in particular with regards to the new possibilities they offer for biological imaging. The recent years have seen a great advancement both in terms of new technological developments and exciting biological applications. Here, we review some of the important milestones in the field and highlight some recent biological applications. PMID:24616244

  1. Phase-equilibrium geobarometers for silicic rocks based on rhyolite-MELTS. Part 2: application to Taupo Volcanic Zone rhyolites

    NASA Astrophysics Data System (ADS)

    Bégué, Florence; Gualda, Guilherme A. R.; Ghiorso, Mark S.; Pamukcu, Ayla S.; Kennedy, Ben M.; Gravley, Darren M.; Deering, Chad D.; Chambefort, Isabelle

    2014-11-01

    Constraining the pressure of crystallisation of large silicic magma bodies gives important insight into the depth and vertical extent of magmatic plumbing systems; however, it is notably difficult to constrain pressure at the level of detail necessary to understand shallow magmatic systems. In this study, we use the recently developed rhyolite-MELTS geobarometer to constrain the crystallisation pressures of rhyolites from the Taupo Volcanic Zone (TVZ). As sanidine is absent from the studied deposits, we calculate the pressures at which quartz and feldspar are found to be in equilibrium with melt now preserved as glass (the quartz +1 feldspar constraint of Gualda and Ghiorso, Contrib Mineral Petrol 168:1033. doi:10.1007/s00410-014-1033-3. 2014). We use glass compositions (matrix glass and melt inclusions) from seven eruptive deposits dated between ~320 and 0.7 ka from four distinct calderas in the central TVZ, and we discuss advantages and limitations of the rhyolite-MELTS geobarometer in comparison with other geobarometers applied to the same eruptive deposits. Overall, there is good agreement with other pressure estimates from the literature (amphibole geobarometry and H2O-CO2 solubility models). One of the main advantages of this new geobarometer is that it can be applied to both matrix glass and melt inclusions—regardless of volatile saturation. The examples presented also emphasise the utility of this method to filter out spurious glass compositions. Pressure estimates obtained with the new rhyolite-MELTS geobarometer range between ~250 to ~50 MPa, with a large majority at ~100 MPa. These results confirm that the TVZ hosts some of the shallowest rhyolitic magma bodies on the planet, resulting from the extensional tectonic regime and thinning of the crust. Distinct populations with different equilibration pressures are also recognised, which is consistent with the idea that multiple batches of eruptible magma can be present in the crust at the same time and

  2. Partial crystallization of picritic melt and its applications for the genesis of high-Ti and low-Ti basalts

    NASA Astrophysics Data System (ADS)

    Yang, J.; WANG, C.; Jin, Z.; Jin, S.; Yan, S.

    2015-12-01

    Geochemical and petrological studies have revealed the existence of high-Ti and low-Ti basalts in large igneous provinces (LIPs). However the originate of these high-Ti and low-Ti magmas are still under debate. Several different mechanisms have been proposed: (1) the high-Ti basalts are formed by the melting of mantle plume containing recycled oceanic crust (Spandler et al., 2008) while low-Ti basalts are formed by the melting of subcontinental lithospheric mantle (Xiao et al., 2004); (2) both high-Ti and low-Ti basalts are from mantle plume source, but the production of high-Ti basalts are associated with the thick lithosphere while the low-Ti basalts are controlled by the thin lithosphere (Arndt et al., 1993); (3) they are derived from the different degrees of melting, with high-Ti basalts representing low degree of partial melting of mantle plume (Xu et al., 2004). The low Mg# (below 0.7) of high-Ti and low-Ti basalts provides that they are far away from direct melting of mantle peridotite. In addition, seismic data indicate unusually high seismic velocities bodies beneath the LIPs which explained by the fractionated cumulates from picritic magmas (Farnetani et al., 1996). Therefore, we believed that the crystallization differentiation process might play a more significant role in the genesis of high-Ti and low-Ti basalts.In order to investigate the generation of high-Ti and low-Ti basalts, a series of high pressure and high temperature partial crystallization experiments were performed at pressures of 1.5, 3.0 and 5.0 GPa and a temperature range of 1200-1700℃. The starting material is picrate glass with relative high TiO2 (2.7 wt %), which is synthesized according to the chemical composition of primary magmas of Emeishan LIP (Xu et al., 2001). The experimental results show that: (1) At a given pressure, the TiO2 content is decreased with increasing melt fraction; (2) At a given melt fraction, the TiO2 content of melts is increased with increasing pressure. On

  3. Optimal Spatial Resolution of Omnidirectional Imaging Systems for Pipe Inspection Applications

    NASA Astrophysics Data System (ADS)

    Dehghan Tezerjani, Abbasali; Mehrandezh, Mehran; Paranjape, Raman

    2015-10-01

    Achieving optimal spatial resolution in imaging systems plays a major role in the design of vision-based industrial inspection tools. Single-view omnidirectional imaging systems provide a cost-effective and computationally-traceable solution for real-time inspection of infrastructure with a favorable size factor. We formulate, for the first time, the spatial cylindrical resolution of omnidirectional Catadioptric and Dioptric imaging systems with the focus on pipe inspection applications. We also provide a design guideline to achieve the highest resolution in these systems. First, we deliver a comprehensive study on optimal resolution in Catadioptric imaging systems which consist of a perspective pinhole camera, a collimated laser as the light source, and a reflective surface (i.e., hyperbolic mirror). Variation of the spatial resolution in terms of the camera's focal length, the mirror curvature, and the relative position between the laser projector and the camera is fully investigated via simulation and experiments. Also, the optimal resolution in Dioptric systems, which consist of a camera with compound refractive lenses (i.e., fish-eye lens) is studied and compared with that in Catadioptric systems. Tests were conducted on a 40-cm-diameter PVC pipe in a controlled laboratory environment.

  4. On the Utility of High-Resolution InSAR Data for Geodynamic Applications

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Amelung, F.

    2014-12-01

    High-spatial and high-temporal resolution InSAR data acquired by the TerraSAR-X and Cosmo-Skymed satellites is becoming increasingly available for geodynamic applications, including volcanic crises, the arctic ice sheets and land subsidence problems. The advantage of these second-generation SAR systems is that processes can be resolved that were not visible by the low-resolution first-generation systems, such as pre-eruptive deformation of a volcanic dome and uplift or subsidence of the bedrock in response to a glacial surge. The drawback is the limited temporal coherence because these satellites operate at X-Band, which makes them suitable only for particular environments. In this poster we present a variety of applications. Our purpose is to better define the potential of these systems for geodynamic applications.

  5. Application of temporal moments and other signal processing algorithms to analysis of ultrasonic signals through melting wax

    NASA Astrophysics Data System (ADS)

    Lau, Sarah J.; Moore, David G.; Stair, Sarah L.; Nelson, Ciji L.

    2016-02-01

    Ultrasonic analysis is being explored as a way to capture events during melting of highly dispersive wax. Typical events include temperature changes in the material, phase transition of the material, surface flows and reformations, and void filling as the material melts. Melt tests are performed with wax to evaluate the usefulness of different signal processing algorithms in capturing event data. Several algorithm paths are being pursued. The first looks at changes in the velocity of the signal through the material. This is only appropriate when the changes from one ultrasonic signal to the next can be represented by a linear relationship, which is not always the case. The second tracks changes in the frequency content of the signal. The third algorithm tracks changes in the temporal moments of a signal over a full test. This method does not require that the changes in the signal be represented by a linear relationship, but attaching changes in the temporal moments to physical events can be difficult. This paper describes the algorithm paths applied to experimental data from ultrasonic signals as wax melts and explores different ways to display the results.

  6. Additive Manufacturing by selective laser melting the realizer desktop machine and its application for the dental industry

    NASA Astrophysics Data System (ADS)

    Gebhardt, Andreas; Schmidt, Frank-Michael; Hötter, Jan-Steffen; Sokalla, Wolfgang; Sokalla, Patrick

    Additive Manufacturing of metal parts by Selective Laser Melting has become a powerful tool for the direct manufacturing of complex parts mainly for the aerospace and medical industry. With the introduction of its desktop machine, Realizer targeted the dental market. The contribution describes the special features of the machine, discusses details of the process and shows manufacturing results focused on metal dental devices.

  7. The application of tubes produced by the electroslag melting process in tubing of thermal power plants and boilers

    NASA Astrophysics Data System (ADS)

    Nemykina, T. I.; Koz'minskii, A. N.

    2013-06-01

    The results of a chemical analysis to determine the short-term mechanical and metallographic properties of boiler tubes manufactured by the electroslag melting process are presented. The paper also contains the data on the long-term strength of the above tubes.

  8. Experimental investigation of low temperature garnet-melt partitioning in CMASH, with application to subduction zone processes.

    NASA Astrophysics Data System (ADS)

    Morizet, Y.; Blundy, J.; McDade, P.

    2003-04-01

    During subduction, the slab undergoes several processes such as dehydration and partial melting at pressures of 2-3 GPa and temperatures of 600-900^oC. Under these conditions, there is little or no distinction between melt and fluid phases (Bureau &Keppler, 1999, EPSL 165, 187-196). To investigate the behaviour of trace elements under these conditions we have carried out partitioning experiments in the system CMASH at 2.2 GPa, 700-920^oC. CMAS starting compositions were doped with trace elements, and loaded together with quartz and water into a Pt capsule, which was in turn contained within a Ni-lined Ti capsule. Run durations were 3-7 days. A run at 810^oC produced euhedral calcic garnet, zoisite, quartz, hydrous melt and tiny clinopyroxene interpreted as quench crystals. LA-ICPMS and SIMS were used to quantify trace element concentrations of the phases. Garnet-melt D's for the HREE decrease from ˜300 for Lu to less than 0.2 for La. DSc and D_V are less than 5, consistent with the large X-site dimension in the garnet. DLi DSr and DBa are considerably less than the adjacent REE. There is a very slight negative partitioning anomaly for Zr and Hf relative to Nd and Sm; DHf is slightly greater than DZr. D_U < DTh, due largely to the oxidizing conditions of the experiment (NNO). The most striking result is very high D's for Nb and Ta: 18±10 and 5.4±1.9 (LA-ICPMS), 25.8±11.9 and 6.6±1.3 (SIMS) for Nb and Ta respectively. These are considerably larger than any previously measured (at much higher temperatures). The observed partitioning behaviour is consistent with the large temperature dependence for DREE proposed by Van Westrenen et al. (2001, Contrib Min Pet, 142, 219-234), and an even larger temperature dependence for DNb and DTa. These preliminary results suggest that garnet (rather than rutile) may play the key role in controlling the Nb and Ta budget of arc magmas and the Nb/Ta ratio of residual eclogites. For example, modelling of eclogite melting, using a N

  9. Resolution enhancement in long pulse OTDR for application in structural health monitoring

    NASA Astrophysics Data System (ADS)

    Bahrampour, Ali Reza; Maasoumi, Fatemeh

    2010-08-01

    To improve the range resolution in inexpensive conventional long pulse optical time domain reflectometer (OTDR) for application in structural health monitoring (SHM) and robotic neural network, the Fourier Wavelet Regularized Deconvolution (ForWaRD) based on the adaptive wavelet method is employed. Since Deconvolution is a noise sensitive process, employing the (ForWaRD) method enhances the signal to noise ratio. Simulation for long pulse OTDR system is done and ForWaRD method is employed to improve the resolution of the OTDR system to the order of several centimeters. In this method the resolution is limited by the bandwidth of detector, bandwidth of electronic circuit, and the sampling rate of analog to digital convertor.

  10. Development and biological applications of high-resolution ion beam induced fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Zhaohong, Mi

    High-resolution fluorescence microscopy has become an essential tool in both biological and biomedical sciences, to directly visualize biological processes at the cellular and subcellular levels through specific fluorescence labeling. Among the fluorescence microscopy techniques, mega-electron-volt (MeV) ion-induced fluorescence microscopy has unique advantages because MeV ions can penetrate through biological cells with little deflection in their trajectories. The state-of-the-art bioimaging facility in the Centre for Ion Beam Applications, National University of Singapore can achieve sub-30 nm spatial resolutions for structural imaging of biological cells, which is well below the diffraction limits imposed by optical microscopy. Our aim is to achieve similar spatial resolutions for Ion Beam Induced Fluorescence Imaging. (Abstract shortened by UMI.).

  11. Low-cost high-resolution diffractive position sensors for X-by-wire applications

    NASA Astrophysics Data System (ADS)

    Tupinier, L.; Marroux, O.; Ndao, M.; Kress, B.; Meyrueis, P.

    2006-04-01

    We are proposing a novel method to implement high resolution optical position sensors for automotive and other applications. Grating diffractive incremental encoders (both linear and rotation) are already becoming commodity products now, and include a read-out grating and a ruling grating [3]. We are implementing out high resolution incremental and/or absolute position encoders with a single diffractive substrate, replicated in mass in plastic. The diffractive structures are here much more complex than standard linear gratings. These new optical position sensors can achieve high absolute resolution without need of electronic interpolation, therefore being potentially very fast and accurate. Furthermore, due to the nature of these diffractive optical elements (surface relief elements), they are very cheaply replicated in mass by either polymers embossing or injection moulding.

  12. Surface Melt Magnitude Retrieval Over Ross Ice Shelf, Antarctica Using Coupled MODIS Optical and Thermal Satellite Measurements During the 2002-03 Melt Season

    NASA Astrophysics Data System (ADS)

    Karmosky, C. C.; Lampkin, D. J.

    2008-12-01

    Ice shelf stability is of crucial importance in the Antarctic because shelves serve as buttresses to glacial ice advancing from the Antarctic Ice Sheet. Surface melt has been increasing over recent years, especially over the Antarctic Peninsula, contributing to disintegration of shelves such as Larsen. Unfortunately, we are not realistically able to quantify surface snowmelt from ground-based methods because there is sparse coverage in automatic weather stations. Satellite based assessments of melt from passive microwave systems are limited in that they only provide an indication of melt occurrence and have coarse resolution. Though this is useful in tracking the duration of melt, melt amount of magnitude is still unknown. Coupled optical/thermal surface measurements from MODIS were calibrated by estimates of liquid water fraction (LWF) in the upper 1cm of the firn derived from a one-dimensional thermal snowmelt model (SNTHERM). SNTHERM was forced by hourly meteorological data from automatic weather station data at reference sites spanning a range of melt conditions across the Ross Ice Shelf during a particularly intense melt season. Melt intensities or LWF were derived for satellite composite periods covering the Antarctic summer months at a 4km resolution over the entire Ross Ice Shelf, ranging from 0-2 percent LWF in early December to areas along the coast with upwards of 10 percent LWF during the time of peak surface melt. Spatial and temporal variations in the amount of surface melt are seen to be related to both katabatic wind strength and wind shifts due to the progression of cyclones along the circumpolar vortex. Sea ice concentration along the ice shelf front, specifically the formation of polynyas, are also thought to be driving factors for surface melt as latent and sensible heat fluxes increase by one to three orders of magnitude as polynyas form. A future application of surface melt mapping using this empirical retrieval model is to determine melt

  13. High energy resolution x-ray spectrometer for high count rate XRF applications

    SciTech Connect

    Rossington, C.S.; Madden, N.W.; Chapman, K.

    1993-08-01

    A new x-ray spectrometer has been constructed which incorporates a novel large area, low capacitance Si(Li) detector and a low noise JFET (junction field effect transistor) pr- eamplifier. The spectrometer operates at high count rates without the conventional compromise in energy resolution. For example, at an amplifier peaking time of 1 {mu}sec and a throughput count rate of 145,000 counts sec{sup {minus}1}, the energy resolution at 5.9 key is 220 eV FWHM. Commercially available spectrometers utilizing conventional geometry Si(Li) detectors with areas equivalent to the new detector have resolutions on the order of 540 eV under the same conditions. Conventional x-ray spectrometers offering high energy resolution must employ detectors with areas one-tenth the size of the new LBL detector (20 mm{sup 2} compared with 200 mm{sup 2}). However, even with the use of the smaller area detectors, the energy resolution of a commercial system is typically limited to approximately 300 eV (again, at 1 {mu}sec and 5.9 keV) due to the noise of the commercially available JFET`S. The new large area detector is useful in high count rate applications, but is also useful in the detection of weak photon signals, in which it is desirable to subtend as large an angle of the available photon flux as possible, while still maintaining excellent energy resolution. X-ray fluorescence data from the new spectrometer is shown in comparison to a commercially available system in the analysis of a dilute multi-element material, and also in conjunction with high count rate synchrotron EXAMS applications.

  14. Study of the shape of an optical window in a super-resolution state by electromagnetic-thermal coupled simulation: Effects of melting of an active layer in an optical disc

    SciTech Connect

    Sano, Haruyuki; Shima, Takayuki; Kuwahara, Masashi; Fujita, Yoshiya; Uchiyama, Munehisa; Aono, Yoshiyuki

    2014-04-21

    We performed a multi-physics simulation for the propagation of electromagnetic waves and heat conduction in a super-resolution optical disc that includes an active layer of InSb. Because the change in the optical constant of InSb due to the phase transition is taken into account, the melting of the active layer can be realistically simulated in our calculation. It was found that in the case of an incident light power (P) of 2 mW, a profile of the electric field intensity transmitted through the InSb layer has an asymmetric shape with a narrow peak. This beam-narrowing was suggested to be an essential mechanism of the super-resolution, because a narrower light beam allows the detection of a smaller pit structure than the optical diffraction limit. This beam-narrowing was found to be originating from a small molten region produced in the InSb layer, which works as a mask for light exposure.

  15. Resolution in QCM Sensors for the Viscosity and Density of Liquids: Application to Lead Acid Batteries

    PubMed Central

    Cao-Paz, Ana María; Rodríguez-Pardo, Loreto; Fariña, José; Marcos-Acevedo, Jorge

    2012-01-01

    In battery applications, particularly in automobiles, submarines and remote communications, the state of charge (SoC) is needed in order to manage batteries efficiently. The most widely used physical parameter for this is electrolyte density. However, there is greater dependency between electrolyte viscosity and SoC than that seen for density and SoC. This paper presents a Quartz Crystal Microbalance (QCM) sensor for electrolyte density-viscosity product measurements in lead acid batteries. The sensor is calibrated in H2SO4 solutions in the battery electrolyte range to obtain sensitivity, noise and resolution. Also, real-time tests of charge and discharge are conducted placing the quartz crystal inside the battery. At the same time, the present theoretical “resolution limit” to measure the square root of the density-viscosity product (ρη) of a liquid medium or best resolution achievable with a QCM oscillator is determined. Findings show that the resolution limit only depends on the characteristics of the liquid to be studied and not on frequency. The QCM resolution limit for ρη measurements worsens when the density-viscosity product of the liquid is increased, but it cannot be improved by elevating the work frequency. PMID:23112618

  16. Resolution in QCM sensors for the viscosity and density of liquids: application to lead acid batteries.

    PubMed

    Cao-Paz, Ana María; Rodríguez-Pardo, Loreto; Fariña, José; Marcos-Acevedo, Jorge

    2012-01-01

    In battery applications, particularly in automobiles, submarines and remote communications, the state of charge (SoC) is needed in order to manage batteries efficiently. The most widely used physical parameter for this is electrolyte density. However, there is greater dependency between electrolyte viscosity and SoC than that seen for density and SoC. This paper presents a Quartz Crystal Microbalance (QCM) sensor for electrolyte density-viscosity product measurements in lead acid batteries. The sensor is calibrated in H(2)SO(4) solutions in the battery electrolyte range to obtain sensitivity, noise and resolution. Also, real-time tests of charge and discharge are conducted placing the quartz crystal inside the battery. At the same time, the present theoretical "resolution limit" to measure the square root of the density-viscosity product [Formula: see text] of a liquid medium or best resolution achievable with a QCM oscillator is determined. Findings show that the resolution limit only depends on the characteristics of the liquid to be studied and not on frequency. The QCM resolution limit for [Formula: see text] measurements worsens when the density-viscosity product of the liquid is increased, but it cannot be improved by elevating the work frequency. PMID:23112618

  17. Super-resolution fluorescent materials: an insight into design and bioimaging applications.

    PubMed

    Yang, Zhigang; Sharma, Amit; Qi, Jing; Peng, Xiao; Lee, Dong Yeop; Hu, Rui; Lin, Danying; Qu, Junle; Kim, Jong Seung

    2016-08-22

    Living organisms are generally composed of complex cellular processes which persist only within their native environments. To enhance our understanding of the biological processes lying within complex milieus, various techniques have been developed. Specifically, the emergence of super-resolution microscopy has generated a renaissance in cell biology by redefining the existing dogma towards nanoscale cell dynamics, single synaptic vesicles, and other complex bioprocesses by overcoming the diffraction-imposed resolution barrier that is associated with conventional microscopy techniques. Besides the typical technical reliance on the optical framework and computational algorithm, super-resolution imaging microscopy resorts largely to fluorescent materials with special photophysical properties, including fluorescent proteins, organic fluorophores and nanomaterials. In this tutorial review article, with the emphasis on cell biology, we summarize the recent developments in fluorescent materials being utilized in various super-resolution techniques with successful integration into bio-imaging applications. Fluorescent proteins (FP) applied in super-resolution microscopy will not be covered herein as it has already been well summarized; additionally, we demonstrate the breadth of opportunities offered from a future perspective. PMID:27296269

  18. One-step Melt Synthesis of Water Soluble, Photoluminescent, Surface-Oxidized Silicon Nanoparticles for Cellular Imaging Applications

    PubMed Central

    Manhat, Beth A.; Brown, Anna L.; Black, Labe A.; Ross, J.B. Alexander; Fichter, Katye; Vu, Tania; Richman, Erik

    2012-01-01

    We have developed a versatile, one-step melt synthesis of water-soluble, highly emissive silicon nanoparticles using bi-functional, low-melting solids (such as glutaric acid) as reaction media. Characterization through transmission electron microscopy, selected area electron diffraction, X-ray photoelectron spectroscopy, and Raman spectroscopy shows that the one-step melt synthesis produces nanoscale Si cores surrounded by a silicon oxide shell. Analysis of the nanoparticle surface using FT-IR, zeta potential, and gel electrophoresis indicates that the bi-functional ligand used in the one-step synthesis is grafted onto the nanoparticle, which allows for tuning of the particle surface charge, solubility, and functionality. Photoluminescence spectra of the as-prepared glutaric acid-synthesized silicon nanoparticles show an intense blue-green emission with a short (ns) lifetime suitable for biological imaging. These nanoparticles are found to be stable in biological media and have been used to examine cellular uptake and distribution in live N2a cells. PMID:23139440

  19. A melt route for the synthesis of activated carbon derived from carton box for high performance symmetric supercapacitor applications

    NASA Astrophysics Data System (ADS)

    Wang, Dewei; Fang, Guoli; Xue, Tong; Ma, Jinfu; Geng, Guihong

    2016-03-01

    Activated carbon materials have been playing a significant role in addressing the challenges posed with the ever-increasing demand for alternative clean and sustainable energy technologies. In the present study, a facile strategy is proposed for generating porosity in porous carbons by using carton box as the precursor and eutectic NaOH-KOH melt as the activating agent. The prepared carbon materials have a very high specific surface area up to 2731 m2 g-1 with large pore volume of 1.68 cm3 g-1, which is greater than that of only KOH was used at the same mass ratio. Electrochemical studies based on symmetric supercapacitor devices demonstrating that the NaOH-KOH melt activated porous carbon exhibits significantly improved rate capability in the range of 0.5-75 A g-1 despite of the similar specific capacitance with respect to KOH activated carbon at a low current density of 0.5 A g-1. The remarkable deviations in capacitive behavior at high current density for the NaOH-KOH melt activated porous carbon and KOH activated samples highlighting the specific surface area is not the only parameter that determines the capacitive performance especially at high charge-discharge rate.

  20. Application and Refinement of a Method to Achieve Uniform Convective Response on Variable-Resolution Meshes

    NASA Astrophysics Data System (ADS)

    Walko, R. L.; Medvigy, D.; Avissar, R.

    2013-12-01

    Variable-resolution computational grids can substantially improve the benefit-to-cost ratio in many environmental modeling applications, but they can also introduce unwanted and unrealistic numerical anomalies if not properly utilized. For example, we showed in previous studies that resolved (non-parameterized) atmospheric convection develops more quickly as resolution increases. Furthermore, on variable grids that transition from resolved to parameterized convection, timing and intensity of the convection in both regimes is generally disparate unless special care is taken to tune the parameterization. In both cases, the convection that develops first (due to purely numerical reasons) tends to suppress convection elsewhere by inducing subsidence in the surrounding environment. This highly nonlinear competition, while desirable when induced by natural causes such as surface inhomogeneity, is highly undesirable when it is a numerical artifact of variable grid resolution and/or selective application of convective parameterization. Our current research is aimed at leveling the playing field for convection across a variable resolution grid so that the above problems are avoided. The underlying idea is to apply the same or very similar 'convective machinery' to all areas of the grid. For convection-resolving regions of the grid, this machinery is simply the model grid itself, along with explicit representation of dynamics and a bulk microphysics parameterization. For coarser regions of the grid, the local environment is sampled from one or more grid columns (depending on local resolution) and fed to a separate 'convective processor', which determines the convective response to that environment and feeds the result back to the host grid. The convective processor chooses to either (1) explicitly resolve convective activity in the given environment on a separate (independent) limited-area 3D computational grid of comparable resolution to the convection-resolving part of the

  1. High-resolution melting analysis of the single nucleotide polymorphism hot-spot region in the rpoB gene as an indicator of reduced susceptibility to rifaximin in Clostridium difficile.

    PubMed

    Pecavar, Verena; Blaschitz, Marion; Hufnagl, Peter; Zeinzinger, Josef; Fiedler, Anita; Allerberger, Franz; Maass, Matthias; Indra, Alexander

    2012-06-01

    Clostridium difficile, a Gram-positive, spore-forming, anaerobic bacterium, is the main causative agent of hospital-acquired diarrhoea worldwide. In addition to metronidazole and vancomycin, rifaximin, a rifamycin derivative, is a promising antibiotic for the treatment of recurring C. difficile infections (CDI). However, exposure of C. difficile to this antibiotic has led to the development of rifaximin-resistance due to point mutations in the β-subunit of the RNA polymerase (rpoB) gene. In the present study, 348 C. difficile strains with known PCR-ribotypes were investigated for respective single nucleotide polymorphisms (SNPs) within the proposed rpoB hot-spot region by using high-resolution melting (HRM) analysis. This method allows the detection of SNPs by comparing the altered melting behaviour of dsDNA with that of wild-type DNA. Discrimination between wild-type and mutant strains was enhanced by creating heteroduplexes by mixing sample DNA with wild-type DNA, leading to characteristic melting curve shapes from samples containing SNPs in the respective rpoB section. In the present study, we were able to identify 16 different rpoB sequence-types (ST) by sequencing analysis of a 325 bp fragment. The 16 PCR STs displayed a total of 24 different SNPs. Fifteen of these 24 SNPs were located within the proposed 151 bp SNP hot-spot region, resulting in 11 different HRM curve profiles (CP). Eleven SNPs (seven of which were within the proposed hot-spot region) led to amino acid substitutions associated with reduced susceptibility to rifaximin and 13 SNPs (eight of which were within the hot-spot region) were synonymous. This investigation clearly demonstrates that HRM analysis of the proposed SNP hot-spot region in the rpoB gene of C. difficile is a fast and cost-effective method for the identification of C. difficile samples with reduced susceptibility to rifaximin and even allows simultaneous SNP subtyping of the respective C. difficile isolates. PMID:22361457

  2. Applications of High-Resolution LiDAR Data for the Christina River Basin CZO

    NASA Astrophysics Data System (ADS)

    Hicks, N. S.; Aufdenkampe, A. K.; Hicks, S. D.

    2011-12-01

    High-resolution LiDAR data allows for fine scale geomorphic assessment over relatively large spatial extents. Previously available DEMs with a resolution of ten meters or more did not provide adequate resolution for geomorphic characterization of small streams and watersheds or the identification of changes in stream morphology over time. High-resolution LiDAR data for a portion of the Christina River Basin Critical Zone Observatory (CRB-CZO) was obtained during both leaf-off and leaf-on time periods in 2010. Topographic data from these flights is being analyzed with the intent of geomorphic applications such as stream morphology, sediment transport studies, and the evaluation of alluvial deposits. These data and resultant products will also be used in hydrologic and biogeochemical modeling and in biologic and biogeochemical studies of these streams, which are long-term study sites. The LiDAR data also facilitate informed instrument placement and will be used for vegetation studies. The LiDAR data for the CRB-CZO has been used to create a variety of LiDAR based topographic data products including TINs and 0.5-m DEMs. LiDAR derived slope and elevation products were combined with LiDAR intensity images to identify stream channel boundaries and stream centerlines for third through first-order streams. High-resolution slope data also aided in floodplain characterization of these small streams. These high precision stream channel and floodplain characterizations would not have been otherwise possible without extensive field surveying. Future LiDAR flights will allow for the identification of changes in channel morphology over time in low order basins. These characterizations are of particular interest in comparisons between forested and meadow reaches, and in studying the effects of changes in land-use on channel morphology. High-resolution LiDAR data allow for the generation of surface characterizations of importance to a wide range of interdisciplinary researchers.

  3. Fault rheology beyond frictional melting.

    PubMed

    Lavallée, Yan; Hirose, Takehiro; Kendrick, Jackie E; Hess, Kai-Uwe; Dingwell, Donald B

    2015-07-28

    During earthquakes, comminution and frictional heating both contribute to the dissipation of stored energy. With sufficient dissipative heating, melting processes can ensue, yielding the production of frictional melts or "pseudotachylytes." It is commonly assumed that the Newtonian viscosities of such melts control subsequent fault slip resistance. Rock melts, however, are viscoelastic bodies, and, at high strain rates, they exhibit evidence of a glass transition. Here, we present the results of high-velocity friction experiments on a well-characterized melt that demonstrate how slip in melt-bearing faults can be governed by brittle fragmentation phenomena encountered at the glass transition. Slip analysis using models that incorporate viscoelastic responses indicates that even in the presence of melt, slip persists in the solid state until sufficient heat is generated to reduce the viscosity and allow remobilization in the liquid state. Where a rock is present next to the melt, we note that wear of the crystalline wall rock by liquid fragmentation and agglutination also contributes to the brittle component of these experimentally generated pseudotachylytes. We conclude that in the case of pseudotachylyte generation during an earthquake, slip even beyond the onset of frictional melting is not controlled merely by viscosity but rather by an interplay of viscoelastic forces around the glass transition, which involves a response in the brittle/solid regime of these rock melts. We warn of the inadequacy of simple Newtonian viscous analyses and call for the application of more realistic rheological interpretation of pseudotachylyte-bearing fault systems in the evaluation and prediction of their slip dynamics. PMID:26124123

  4. Fault rheology beyond frictional melting

    PubMed Central

    Lavallée, Yan; Hirose, Takehiro; Kendrick, Jackie E.; Hess, Kai-Uwe; Dingwell, Donald B.

    2015-01-01

    During earthquakes, comminution and frictional heating both contribute to the dissipation of stored energy. With sufficient dissipative heating, melting processes can ensue, yielding the production of frictional melts or “pseudotachylytes.” It is commonly assumed that the Newtonian viscosities of such melts control subsequent fault slip resistance. Rock melts, however, are viscoelastic bodies, and, at high strain rates, they exhibit evidence of a glass transition. Here, we present the results of high-velocity friction experiments on a well-characterized melt that demonstrate how slip in melt-bearing faults can be governed by brittle fragmentation phenomena encountered at the glass transition. Slip analysis using models that incorporate viscoelastic responses indicates that even in the presence of melt, slip persists in the solid state until sufficient heat is generated to reduce the viscosity and allow remobilization in the liquid state. Where a rock is present next to the melt, we note that wear of the crystalline wall rock by liquid fragmentation and agglutination also contributes to the brittle component of these experimentally generated pseudotachylytes. We conclude that in the case of pseudotachylyte generation during an earthquake, slip even beyond the onset of frictional melting is not controlled merely by viscosity but rather by an interplay of viscoelastic forces around the glass transition, which involves a response in the brittle/solid regime of these rock melts. We warn of the inadequacy of simple Newtonian viscous analyses and call for the application of more realistic rheological interpretation of pseudotachylyte-bearing fault systems in the evaluation and prediction of their slip dynamics. PMID:26124123

  5. On the application of ENO scheme with subcell resolution to conservation laws with stiff source terms

    NASA Technical Reports Server (NTRS)

    Chang, Shih-Hung

    1991-01-01

    Two approaches are used to extend the essentially non-oscillatory (ENO) schemes to treat conservation laws with stiff source terms. One approach is the application of the Strang time-splitting method. Here the basic ENO scheme and the Harten modification using subcell resolution (SR), ENO/SR scheme, are extended this way. The other approach is a direct method and a modification of the ENO/SR. Here the technique of ENO reconstruction with subcell resolution is used to locate the discontinuity within a cell and the time evolution is then accomplished by solving the differential equation along characteristics locally and advancing in the characteristic direction. This scheme is denoted ENO/SRCD (subcell resolution - characteristic direction). All the schemes are tested on the equation of LeVeque and Yee (NASA-TM-100075, 1988) modeling reacting flow problems. Numerical results show that these schemes handle this intriguing model problem very well, especially with ENO/SRCD which produces perfect resolution at the discontinuity.

  6. Analytic system matrix resolution modeling in PET: an application to Rb-82 cardiac imaging

    PubMed Central

    Rahmim, A; Tang, J; Lodge, M A; Lashkari, S; Ay, M R; Lautamäki, R; Tsui, B M W; Bengel, F M

    2011-01-01

    This work explores application of a novel resolution modeling technique based on analytic physical models which individually models the various resolution degrading effects in PET (positron range, photon non-collinearity, inter-crystal scattering and inter-crystal penetration) followed by their combination and incorporation within the image reconstruction task. In addition to phantom studies, the proposed technique was particularly applied to and studied in the task of clinical Rb-82 myocardial perfusion imaging, which presently suffers from poor statistics and resolution properties in the reconstructed images. Overall, the approach is able to produce considerable enhancements in image quality. The reconstructed FWHM for a Discovery RX PET/CT scanner was seen to improve from 5.1 mm to 7.7 mm across the field-of-view (FoV) to ~3.5 mm nearly uniformly across the FoV. Furthermore, extended-source phantom studies indicated clearly improved images in terms of contrast versus noise performance. Using Monte Carlo simulations of clinical Rb-82 imaging, the resolution modeling technique was seen to significantly outperform standard reconstructions qualitatively, and also quantitatively in terms of contrast versus noise (contrast between the myocardium and other organs, as well as between myocardial defects and the left ventricle). PMID:18836219

  7. Imaging live cells at high spatiotemporal resolution for lab-on-a-chip applications.

    PubMed

    Chin, Lip Ket; Lee, Chau-Hwang; Chen, Bi-Chang

    2016-05-24

    Conventional optical imaging techniques are limited by the diffraction limit and difficult-to-image biomolecular and sub-cellular processes in living specimens. Novel optical imaging techniques are constantly evolving with the desire to innovate an imaging tool that is capable of seeing sub-cellular processes in a biological system, especially in three dimensions (3D) over time, i.e. 4D imaging. For fluorescence imaging on live cells, the trade-offs among imaging depth, spatial resolution, temporal resolution and photo-damage are constrained based on the limited photons of the emitters. The fundamental solution to solve this dilemma is to enlarge the photon bank such as the development of photostable and bright fluorophores, leading to the innovation in optical imaging techniques such as super-resolution microscopy and light sheet microscopy. With the synergy of microfluidic technology that is capable of manipulating biological cells and controlling their microenvironments to mimic in vivo physiological environments, studies of sub-cellular processes in various biological systems can be simplified and investigated systematically. In this review, we provide an overview of current state-of-the-art super-resolution and 3D live cell imaging techniques and their lab-on-a-chip applications, and finally discuss future research trends in new and breakthrough research areas of live specimen 4D imaging in controlled 3D microenvironments. PMID:27121367

  8. Partitioning of Se, As, Sb, Te and Bi between monosulfide solid solution and sulfide melt - Application to magmatic sulfide deposits

    NASA Astrophysics Data System (ADS)

    Helmy, Hassan M.; Ballhaus, Chris; Wohlgemuth-Ueberwasser, Cora; Fonseca, Raúl O. C.; Laurenz, Vera

    2010-11-01

    The chalcogenes (S, Se, Te), semimetals (As, Sb) and the metal Bi are important ligands for noble metals and form a wide range of compositionally diverse minerals with the platinum-group elements (PGE). With the exception of S, few experimental data exist to quantify the behavior of these elements in magmatic sulfide systems. Here we report experimental partition coefficients for Se, Te, As, Sb, and Bi between monosulfide solid solution (mss) and sulfide melt, determined at 950 °C at a range of sulfur fugacities ( fS2) bracketed by the Fe-FeS (metal-troilite) and the Fe 1-×S-S x (mss-sulfur) equilibria. Selenium is shown to partition in mss-saturated sulfide melt as an anion replacing S 2-. Arsenic changes its oxidation state with fS 2 from predominantly anionic speciation at low fS 2, to cationic speciation at high fS 2. The elements Sb, Te, and Bi are so highly incompatible with mss that they can only be present in sulfide melt as cations and/or as neutral metallic species. The partition coefficients derived fall with increasing atomic radius of the element. They also reflect the positions of the respective elements in the Periodic Table: within a group (e.g., As, Sb, Bi) the partition coefficients fall with increasing atomic radius, and within a period the elements of the 15th group are more incompatible with mss than the neighboring elements of the 16th group.

  9. X-ray characterization of CMOS imaging detector with high resolution for fluoroscopic imaging application

    NASA Astrophysics Data System (ADS)

    Cha, Bo Kyung; Kim, Cho Rong; Jeon, Seongchae; Kim, Ryun Kyung; Seo, Chang-Woo; Yang, Keedong; Heo, Duchang; Lee, Tae-Bum; Shin, Min-Seok; Kim, Jong-Boo; Kwon, Oh-Kyung

    2013-12-01

    This paper introduces complementary metal-oxide semiconductor (CMOS) active pixel sensor (APS)-based X-ray imaging detectors with high spatial resolution for medical imaging application. In this study, our proposed X-ray CMOS imaging sensor has been fabricated by using a 0.35 μm 1 Poly 4 Metal CMOS process. The pixel size is 100 μm×100 μm and the pixel array format is 24×96 pixels, which provide a field-of-view (FOV) of 9.6 mm×2.4 mm. The 14.3-bit extend counting analog-to digital converter (ADC) with built-in binning mode was used to reduce the area and simultaneously improve the image resolution. Both thallium-doped CsI (CsI:Tl) and Gd2O2S:Tb scintillator screens were used as converters for incident X-rays to visible light photons. The optical property and X-ray imaging characterization such as X-ray to light response as a function of incident X-ray exposure dose, spatial resolution and X-ray images of objects were measured under different X-ray energy conditions. The measured results suggest that our developed CMOS-based X-ray imaging detector has the potential for fluoroscopic imaging and cone-beam computed tomography (CBCT) imaging applications.

  10. Superheating of Crystalline Solids: Theory, Experiment, Simulation and Applications to Static and Dynamic High-pressure Melting

    NASA Astrophysics Data System (ADS)

    Luo, S.; Ahrens, T. J.; Cagin, T.; Strachan, A.; Goddard, W. A.

    2002-12-01

    Systematics of superheating (Θ =Δ T/Tm, where Δ T is the amount of superheating and Tm melting temperature) of crystalline solids as a function of heating rate (Q) are established by defining a dimensionless energy barrier for nucleation, β=16π γsl3/(3kTmΔ Hm2) where γsl is the solid-liquid interfacial energy, Δ Hm is the heat of fusion and k Boltzmann constant. Under conditions that lead to homogeneous nucleation (e.g., ultrafast internal heating), superheating is more pronounced. Sound speed and shock temperature measurements on various materials (Fe, V, Mo, Ta, W, CsBr, KBr, SiO2, and Mg2SiO4) under planar impact (Q~ 1012 K/s) leads to superheating of Θ =0.2-0.6. Comparable superheating was achieved during intense laser irradiation (Q~ 1012-1015 K/s) on Al, Pb and GaAs. These observations are captured by the Θ -β-Q systematics. Homogeneous nucleation is inherent in molecular dynamics simulations of perfect bulk crystals with typical heating rates Q (~ 1012-1013 K/s) similar to those in shock wave loading and intense laser irradiation. Single-phase and two-phase simulations of melting of fcc metals (Al, Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au), a bcc metal (Ta), oxides (MgO and SiO2) with various types of force field (FF) such as embedded atom method potential, first-principle potential and Morse-stretch charge equilibrium FF etc., have demonstrated superheating consistent with the superheating systematics. Despite of the large range of melting temperatures observed, the extrapolation of melting curves from diamond-anvil-cell experiments on V, Mo, Ta and W remain discrepant with shock wave results even when superheating and experiment uncertainties are taken into account. In the case of Fe, the discrepancy is less pronounced. This may result from a not yet explored solid-solid phase transition.

  11. High resolution applications of laser-induced breakdown spectroscopy for environmental and forensic applications

    NASA Astrophysics Data System (ADS)

    Martin, Madhavi Z.; Labbé, Nicole; André, Nicolas; Harris, Ronny; Ebinger, Michael; Wullschleger, Stan D.; Vass, Arpad A.

    2007-12-01

    Laser-induced breakdown spectroscopy (LIBS) has been used in the elemental analysis for a variety of environmental samples and as a proof of concept for a host of forensic applications. In the first application, LIBS was used for the rapid detection of carbon from a number of different soil types. In this application, a major breakthrough was achieved by using a multivariate analytical approach that has brought us closer towards a "universal calibration curve". In a second application, it has been demonstrated that LIBS in combination with multivariate analysis can be employed to analyze the chemical composition of annual tree growth rings and correlate them to external parameters such as changes in climate, forest fires, and disturbances involving human activity. The objectives of using this technology in fire scar determinations are: 1) To determine the characteristic spectra of wood exposed to forest fires and 2) To examine the viability of this technique for detecting fire occurrences in stems that did not develop fire scars. These examples demonstrate that LIBS-based techniques are inherently well suited for diverse environmental applications. LIBS was also applied to a variety of proof of concept forensic applications such as the analysis of cremains (human cremation remains) and elemental composition analysis of prosthetic implants.

  12. High Resolution Applications of Laser-Induced Breakdown Spectroscopy for Environmental and Forensic Applications

    SciTech Connect

    Martin, Madhavi Z; Labbe, Nicole; Andre, Nicolas O; Harris, Ronny D; Ebinger, Michael H; Wullschleger, Stan D; Vass, Arpad Alexander

    2007-01-01

    Laser-induced breakdown spectroscopy (LIBS) has been used in the elemental analysis for a variety of environmental samples and as a proof of concept for a host of forensic applications. In the first application, LIBS was used for the rapid detection of carbon from a number of different soil types. In this application, a major breakthrough was achieved by using a multivariate analytical approach that has brought us closer towards a "universal calibration curve". In a second application, it has been demonstrated that LIBS in combination with multivariate analysis can be employed to analyze the chemical composition of annual tree growth rings and correlate them to external parameters such as changes in climate, forest fires, and disturbances involving human activity. The objectives of using this technology in fire scar determinations are: 1) To determine the characteristic spectra of wood exposed to forest fires and 2) To examine the viability of this technique for detecting fire occurrences in stems that did not develop fire scars. These examples demonstrate that LIBS-based techniques are inherently well suited for diverse environmental applications. LIBS was also applied to a variety of proof of concept forensic applications such as the analysis of cremains (human cremation remains) and elemental composition analysis of prosthetic implants.

  13. Characterisation of LSO:Tb scintillator films for high resolution X-ray imaging applications

    NASA Astrophysics Data System (ADS)

    Cecilia, A.; Rack, A.; Douissard, P.-A.; Martin, T.; Dos Santos Rolo, T.; Vagovič, P.; Pelliccia, D.; Couchaud, M.; Dupré, K.; Baumbach, T.

    2011-05-01

    Within the framework of an FP6 project (SCINTAX)1The Project SCINTAX is funded by the European Community (STRP 033 427), . we developed a new thin film single crystal scintillator for high resolution X-ray imaging based on a layer of modified LSO (Lu2SiO5) grown by liquid phase epitaxy (LPE) on a dedicated substrate. In this work we present the characterisation of the scintillating LSO films in terms of optical and scintillation properties as well as spatial resolution performances. The obtained results are discussed and compared with the performances of the thin scintillating films commonly used in synchrotron-based micro-imaging applications.

  14. High resolution gamma ray tomography scanner for flow measurement and non-destructive testing applications

    SciTech Connect

    Hampel, U.; Bieberle, A.; Hoppe, D.; Kronenberg, J.; Schleicher, E.; Suehnel, T.; Zimmermann, F.; Zippe, C.

    2007-10-15

    We report on the development of a high resolution gamma ray tomography scanner that is operated with a Cs-137 isotopic source at 662 keV gamma photon energy and achieves a spatial image resolution of 0.2 line pairs/mm at 10% modulation transfer function for noncollimated detectors. It is primarily intended for the scientific study of flow regimes and phase fraction distributions in fuel element assemblies, chemical reactors, pipelines, and hydrodynamic machines. Furthermore, it is applicable to nondestructive testing of larger radiologically dense objects. The radiation detector is based on advanced avalanche photodiode technology in conjunction with lutetium yttrium orthosilicate scintillation crystals. The detector arc comprises 320 single detector elements which are operated in pulse counting mode. For measurements at fixed vessels or plant components, we built a computed tomography scanner gantry that comprises rotational and translational stages, power supply via slip rings, and data communication to the measurement personal computer via wireless local area network.

  15. Subnanometer-Resolution Frequency Modulation Atomic Force Microscopy in Liquid for Biological Applications

    NASA Astrophysics Data System (ADS)

    Fukuma, Takeshi

    2009-08-01

    The spatial resolution and force sensitivity of frequency modulation atomic force microscopy (FM-AFM) in liquid have been dramatically improved in the last a few years. It is now possible to image individual atoms and molecules at a solid/liquid interface with a subnanometer-scale resolution and a piconewton-order loading force. This capability enabled the direct visualization of hydration layers and mobile ions on a lipid bilayer and β-strands constituting an amyloid fibril. These striking results highlighted the significant potential of FM-AFM in biological research. Here, I summarize the technological innovation that brought about this progress and review biological applications of FM-AFM in liquid.

  16. Accuracy and Resolution of Kinect Depth Data for Indoor Mapping Applications

    PubMed Central

    Khoshelham, Kourosh; Elberink, Sander Oude

    2012-01-01

    Consumer-grade range cameras such as the Kinect sensor have the potential to be used in mapping applications where accuracy requirements are less strict. To realize this potential insight into the geometric quality of the data acquired by the sensor is essential. In this paper we discuss the calibration of the Kinect sensor, and provide an analysis of the accuracy and resolution of its depth data. Based on a mathematical model of depth measurement from disparity a theoretical error analysis is presented, which provides an insight into the factors influencing the accuracy of the data. Experimental results show that the random error of depth measurement increases with increasing distance to the sensor, and ranges from a few millimeters up to about 4 cm at the maximum range of the sensor. The quality of the data is also found to be influenced by the low resolution of the depth measurements. PMID:22438718

  17. High-resolution detectors for medical applications and synchrotron radiation research

    NASA Astrophysics Data System (ADS)

    Babichev, E. A.; Baru, S. E.; Grigoriev, D. N.; Groshev, V. R.; Leonov, V. V.; Papushev, P. A.; Porosev, V. V.; Savinov, G. A.; Shayakhmetov, V. R.; Shekhtman, L. I.; Tikhonov, Yu. A.; Ukraintsev, Yu. G.; Yurchenko, Yu. B.

    2011-02-01

    In the present report, we summarize our experience in the development of high-resolution position sensitive gas detectors for medicine and synchrotron radiation experiments at Budker Institute of Nuclear Physics for the last years. We have designed several versions of Multistrip Ionisation Chambers with a channel pitch varying from 0.4 down to 0.1 mm. The high quantum efficiency (>65%) of these detectors allow its application in high quality diagnostic imaging. The detector with 0.1 mm strip pitch and 20 atm pressure of Xe demonstrates the best possible DQE and spatial resolution for gaseous detectors in a wide range of X-ray energies. Additionally, the initial results of feasibility study of the detector for beam position monitoring for Heavy Ion Therapy System are presented too.

  18. High resolution gamma ray tomography scanner for flow measurement and non-destructive testing applications

    NASA Astrophysics Data System (ADS)

    Hampel, U.; Bieberle, A.; Hoppe, D.; Kronenberg, J.; Schleicher, E.; Sühnel, T.; Zimmermann, F.; Zippe, C.

    2007-10-01

    We report on the development of a high resolution gamma ray tomography scanner that is operated with a Cs-137 isotopic source at 662keV gamma photon energy and achieves a spatial image resolution of 0.2linepairs/mm at 10% modulation transfer function for noncollimated detectors. It is primarily intended for the scientific study of flow regimes and phase fraction distributions in fuel element assemblies, chemical reactors, pipelines, and hydrodynamic machines. Furthermore, it is applicable to nondestructive testing of larger radiologically dense objects. The radiation detector is based on advanced avalanche photodiode technology in conjunction with lutetium yttrium orthosilicate scintillation crystals. The detector arc comprises 320 single detector elements which are operated in pulse counting mode. For measurements at fixed vessels or plant components, we built a computed tomography scanner gantry that comprises rotational and translational stages, power supply via slip rings, and data communication to the measurement personal computer via wireless local area network.

  19. A Solvent-Free Surface Suspension Melt Technique for Making Biodegradable PCL Membrane Scaffolds for Tissue Engineering Applications.

    PubMed

    Suntornnond, Ratima; An, Jia; Tijore, Ajay; Leong, Kah Fai; Chua, Chee Kai; Tan, Lay Poh

    2016-01-01

    In tissue engineering, there is limited availability of a simple, fast and solvent-free process for fabricating micro-porous thin membrane scaffolds. This paper presents the first report of a novel surface suspension melt technique to fabricate a micro-porous thin membrane scaffolds without using any organic solvent. Briefly, a layer of polycaprolactone (PCL) particles is directly spread on top of water in the form of a suspension. After that, with the use of heat, the powder layer is transformed into a melted layer, and following cooling, a thin membrane is obtained. Two different sizes of PCL powder particles (100 µm and 500 µm) are used. Results show that membranes made from 100 µm powders have lower thickness, smaller pore size, smoother surface, higher value of stiffness but lower ultimate tensile load compared to membranes made from 500 µm powder. C2C12 cell culture results indicate that the membrane supports cell growth and differentiation. Thus, this novel membrane generation method holds great promise for tissue engineering. PMID:27007364

  20. Building optimal regression tree by ant colony system-genetic algorithm: application to modeling of melting points.

    PubMed

    Hemmateenejad, Bahram; Shamsipur, Mojtaba; Zare-Shahabadi, Vali; Akhond, Morteza

    2011-10-17

    The classification and regression trees (CART) possess the advantage of being able to handle large data sets and yield readily interpretable models. A conventional method of building a regression tree is recursive partitioning, which results in a good but not optimal tree. Ant colony system (ACS), which is a meta-heuristic algorithm and derived from the observation of real ants, can be used to overcome this problem. The purpose of this study was to explore the use of CART and its combination with ACS for modeling of melting points of a large variety of chemical compounds. Genetic algorithm (GA) operators (e.g., cross averring and mutation operators) were combined with ACS algorithm to select the best solution model. In addition, at each terminal node of the resulted tree, variable selection was done by ACS-GA algorithm to build an appropriate partial least squares (PLS) model. To test the ability of the resulted tree, a set of approximately 4173 structures and their melting points were used (3000 compounds as training set and 1173 as validation set). Further, an external test set containing of 277 drugs was used to validate the prediction ability of the tree. Comparison of the results obtained from both trees showed that the tree constructed by ACS-GA algorithm performs better than that produced by recursive partitioning procedure. PMID:21907021

  1. Evaluation and development of a high resolution wind model for wildfire applications in complex terrain

    NASA Astrophysics Data System (ADS)

    Wagenbrenner, Natalie Suzanne

    Accurate modeling of near-surface winds is important for wildfire applications, including wildfire behavior and spread as well as post-fire processes, including wind-driven dust and ash emissions from burned soils. The work presented in this dissertation investigates a high resolution wind model for use in wildfire applications in complex terrain and includes (1) an observational field study to collect high resolution surface wind data from two types of complex terrain features; (2) use of these observed data to evaluate a suite of Numerical Weather Prediction (NWP) model near surface wind predictions and dynamical downscaling of those predictions with a high resolution wind model; and (3) field quantification of wind erosion from soils burned by wildfire. Unique flow features, including upslope, downslope, and synoptically-driven flow events were presented for an isolated mountain and a steep river canyon. Evaluations with these observed datasets indicated that NWP surface winds can be improved in complex terrain via dynamic downscaling with a high resolution wind model, WindNinja, so long as the average approach flow to the area of interest can be reasonably defined (i.e., the initial wind field must be appropriately defined). The biggest improvements occurred during periods of synoptically-driven events when observed winds speeds exceeded 10 m s-1. Results from the post-fire field campaign demonstrated that post-fire landscapes can be significant sources of particulates and that dust emissions can persist for up to a year post-fire. Data collected during this study represents the first real-time measurements of PM10 fluxes from a burned landscape. These data will be useful in evaluating windblown dust emissions algorithms applied to burned landscapes.

  2. Improved Edge Directed Super-Resolution (EDSR) with hardware realization for surveillance, transportation, and multimedia applications

    NASA Astrophysics Data System (ADS)

    Wang, Yue; de Lima, Osborn; Saber, Eli; Bengtson, Kurt R.

    2014-03-01

    In this paper, we present an improved Edge Directed Super Resolution (EDSR) technique to produce enhanced edge definition and improved image quality in the resulting high resolution image. The basic premise behind this algorithm remains, like its predecessor, to utilize gradient and spatial information and interpolate along the edge direction in a multiple pass iterative fashion. The edge direction map generated from horizontal and vertical gradients and resized to the target resolution is quantized into eight directions over a 5 × 5 block compared to four directions over a 3 × 3 block in the previous algorithm. This helps reduce the noise caused in part due to the quantization error and the super resolved results are significantly improved. In addition, an appropriate weighting encompassing the degree of similarity between the quantized edge direction and the actual edge direction is also introduced. In an attempt to determine the optimal super resolution parameters for the case of still image capture, a hardware setup was utilized to investigate and evaluate those factors. In particular, the number of images captured as well as the amount of sub pixel displacement that yield a high quality result was studied. This is done by utilizing a XY stage capable of sub-pixel movement. Finally, an edge preserving smoothing algorithm contributes to improved results by reducing the high frequency noise introduced by the super resolution process. The algorithm showed favorable results on a wide variety of datasets obtained from transportation to multimedia based print/scan application in addition to images captured with the aforementioned hardware setup.

  3. High-resolution solid-state NMR study of the effect of composition on network connectivity and structural disorder in multi-component glasses in the diopside and jadeite join: Implications for structure of andesitic melts

    NASA Astrophysics Data System (ADS)

    Park, Sun Young; Lee, Sung Keun

    2014-12-01

    The structural evolution of andesitic melts with varying compositions remains one of the unsolved questions in high-temperature geochemistry and petrology. In this article, we report the structural details of model andesitic glasses [CaO-MgO-Na2O-Al2O3-SiO2 (CMNAS)] in the diopside (CaMgSi2O6) and jadeite (NaAlSi2O6) join using high-resolution, multi-nuclear, solid-state nuclear magnetic resonance (NMR). The 27Al NMR spectra of CMNAS glasses confirm that [4]Al is dominant. While a minor fraction of [5]Al is observed, its presence is only prevalent in the glasses with higher Ca-Mg content. Topological disorder in the glass network also tends to increase with Ca-Mg content as evidenced by the increase in the quadrupolar coupling constant (Cq) of [4]Al for glasses with increasing diopside contents (XDiopside). Despite the complex nature of the glasses studied here (with five oxide components), the 17O 3QMAS NMR spectra resolve diverse bridging oxygens (BOs) and non-bridging oxygens (NBOs), from which the degree of Al avoidance among framework cations (Si and Al) and preferential proximity among non-network cations (Ca2+, Mg2+, and Na+) and each oxygen site can be estimated: presence of Al-O-Al in jadeite glass implies a violation of the Al-avoidance rule in the glasses and the decrease in the fraction of NBOs with increasing XDiopside is consistent with a decrease in their viscosity. Analysis of the peak position of {Ca, Mg}-mixed NBOs, along with the absence of Na-NBO peak, and the peak shape of Si-O-Al reveals preferential partitioning of Ca2+ and Mg2 into NBOs and the proximity of Na+ to BOs. The fraction of highly coordinated Al has been linked to thermodynamic and transport properties of the melts. Considering all the experimental Al coordination environments available in the literature, together with the current experimental studies, we attempt to establish the relationship between the fractions of highly coordinated Al and composition, particularly average

  4. Ice shelf melt rates and 3D imaging

    NASA Astrophysics Data System (ADS)

    Lewis, Cameron Scott

    Ice shelves are sensitive indicators of climate change and play a critical role in the stability of ice sheets and oceanic currents. Basal melting of ice shelves plays an important role in both the mass balance of the ice sheet and the global climate system. Airborne- and satellite based remote sensing systems can perform thickness measurements of ice shelves. Time separated repeat flight tracks over ice shelves of interest generate data sets that can be used to derive basal melt rates using traditional glaciological techniques. Many previous melt rate studies have relied on surface elevation data gathered by airborne- and satellite based altimeters. These systems infer melt rates by assuming hydrostatic equilibrium, an assumption that may not be accurate, especially near an ice shelf's grounding line. Moderate bandwidth, VHF, ice penetrating radar has been used to measure ice shelf profiles with relatively coarse resolution. This study presents the application of an ultra wide bandwidth (UWB), UHF, ice penetrating radar to obtain finer resolution data on the ice shelves. These data reveal significant details about the basal interface, including the locations and depth of bottom crevasses and deviations from hydrostatic equilibrium. While our single channel radar provides new insight into ice shelf structure, it only images a small swatch of the shelf, which is assumed to be an average of the total shelf behavior. This study takes an additional step by investigating the application of a 3D imaging technique to a data set collected using a ground based multi channel version of the UWB radar. The intent is to show that the UWB radar could be capable of providing a wider swath 3D image of an ice shelf. The 3D images can then be used to obtain a more complete estimate of the bottom melt rates of ice shelves.

  5. High resolution melting analysis (HRM) as a new tool for the identification of species belonging to the Lactobacillus casei group and comparison with species-specific PCRs and multiplex PCR.

    PubMed

    Iacumin, Lucilla; Ginaldi, Federica; Manzano, Marisa; Anastasi, Veronica; Reale, Anna; Zotta, Teresa; Rossi, Franca; Coppola, Raffaele; Comi, Giuseppe

    2015-04-01

    The correct identification and characterisation of bacteria is essential for several reasons: the classification of lactic acid bacteria (LAB) has changed significantly over the years, and it is important to distinguish and define them correctly, according to the current nomenclature, avoiding problems in the interpretation of literature, as well as mislabelling when probiotic are used in food products. In this study, species-specific PCR and HRM (high-resolution melting) analysis were developed to identify strains belonging to the Lactobacillus casei group and to classify them into L. casei, Lactobacillus paracasei and Lactobacillus rhamnosus. HRM analysis confirmed to be a potent, simple, fast and economic tool for microbial identification. In particular, 201 strains, collected from International collections and attributed to the L. casei group, were examined using these techniques and the results were compared with consolidated molecular methods, already published. Seven of the tested strains don't belong to the L. casei group. Among the remaining 194 strains, 6 showed inconsistent results, leaving identification undetermined. All the applied techniques were congruent for the identification of the vast majority of the tested strains (188). Notably, for 46 of the strains, the identification differed from the previous attribution. PMID:25475306

  6. Pseudomonas aeruginosa Outbreak Linked to Mineral Water Bottles in a Neonatal Intensive Care Unit: Fast Typing by Use of High-Resolution Melting Analysis of a Variable-Number Tandem-Repeat Locus▿ †

    PubMed Central

    Naze, F.; Jouen, E.; Randriamahazo, R. T.; Simac, C.; Laurent, P.; Blériot, A.; Chiroleu, F.; Gagnevin, L.; Pruvost, O.; Michault, A.

    2010-01-01

    Pseudomonas aeruginosa is an opportunistic pathogen that causes nosocomial infections in intensive care units. Determining a system of typing that is discriminatory is essential for epidemiological surveillance of P. aeruginosa. We developed a method for the typing of Pseudomonas aeruginosa, namely, multiple-locus variable-number tandem-repeat (VNTR) typing with high-resolution melting analysis (HRMA). The technology was used to genotype a collection of 43 environmental and clinical strains isolated during an outbreak in a neonatal intensive care unit (NICU) that we report. Nineteen strains isolated in other departments or outside the hospital were also tested. The genetic diversity of this collection was determined using VNTR-HRMA, with amplified fragment length polymorphism (AFLP) analysis as a reference. Twenty-five and 28 genotypes were identified, respectively, and both techniques produced congruent data. VNTR-HRMA established clonal relationships between the strains of P. aeruginosa isolated during the outbreak in the NICU and proved, for the first time, the role of mineral water as the inoculum source. VNTR typing with one primer pair in association with HRMA is highly reproducible and discriminative, easily portable among laboratories, fast, and inexpensive, and it demonstrated excellent typeability in this study. VNTR-HRMA represents a promising tool for the molecular surveillance of P. aeruginosa and perhaps for molecular epidemiologic analysis of other hospital infections. PMID:20573865

  7. MECP2 mutations in Czech patients with Rett syndrome and Rett-like phenotypes: novel mutations, genotype-phenotype correlations and validation of high-resolution melting analysis for mutation scanning.

    PubMed

    Zahorakova, Daniela; Lelkova, Petra; Gregor, Vladimir; Magner, Martin; Zeman, Jiri; Martasek, Pavel

    2016-07-01

    Rett syndrome (RTT) is an X-linked neurodevelopmental disorder characterized by developmental regression with loss of motor, communication and social skills, onset of stereotypic hand movements and often seizures. RTT is primarily caused by de novo mutations in the methyl-CpG-binding protein 2 gene (MECP2). We established a high-resolution melting (HRM) technique for mutation scanning of the MECP2 gene and performed analyses in Czech patients with RTT, autism spectrum conditions and intellectual disability with Rett-like features. In the cases with confirmed MECP2 mutations, we determined X-chromosome inactivation (XCI), examined the relationships between genotype and clinical severity and evaluated the modifying influence of XCI. Our results demonstrate that HRM analysis is a reliable method for the detection of point mutations, small deletions and duplications in the MECP2 gene. We identified 29 pathogenic mutations in 75 girls, including four novel mutations: c.155_1189del1035;909_932inv;insC, c.573delC, c.857_858dupAA and c.1163_1200del38. Skewed XCI (ratio >75%) was found in 19.3% of the girls, but no gross divergence in clinical severity was observed. Our findings confirm a high mutation frequency in classic RTT (92%) and a correlation between the MECP2 mutation type and clinical severity. We also demonstrate limitations of XCI in explaining all of the phenotypic differences in RTT. PMID:26984561

  8. Detection of EGFR mutation in supernatant, cell pellets of pleural effusion and tumor tissues from non-small cell lung cancer patients by high resolution melting analysis and sequencing

    PubMed Central

    Lin, Jie; Gu, Ye; Du, Rui; Deng, Min; Lu, Yaodan; Ding, Yanqing

    2014-01-01

    To determine epidermal growth factor receptor (EGFR) mutation in advanced non-small cell lung cancer (NSCLC) patients and compare the detection efficiency between different sample resources, both high resolution melting (HRM) analysis and direct sequencing method were used to analyze 36 pleural effusion samples and 22 matched biopsy tumor tissues collected from NSCLC patients. For each pleural effusion sample, the supernatant and the cell pellets were examined separately. Among all the 36 cases of pleural effusion samples, 18 mutations of EGFR were found in cell-free supernatant while 13 mutations were found in the cell pellets as detected by HRM analysis. In the 22 matched samples, 13 cases of EGFR mutations were identified in paraffin-embedded biopsy tissue samples, 12 cases in the cell-free supernatant and 9 cases in the cell pellets of pleural effusion. EGFR mutations in 15 cases out of the total 36 pleural effusion samples detected by direct sequencing were also identified by HRM analysis, giving 100% efficiency for HRM method. The results established the important role of HRM as a reliable and efficient method to determine EGFR mutation status and indicated the feasibility of using pleural effusion in replacement of biopsy tissues in particular clinical cases. Furthermore, the cell-free supernatant of pleural effusion might be a better resource for mutation detection than cell pellets. PMID:25674250

  9. Scaleable Clean Aluminum Melting Systems

    SciTech Connect

    Han, Q.; Das, S.K.

    2008-02-15

    The project entitled 'Scaleable Clean Aluminum Melting Systems' was a Cooperative Research and Development Agreements (CRADAs) between Oak Ridge National Laboratory (ORNL) and Secat Inc. The three-year project was initially funded for the first year and was then canceled due to funding cuts at the DOE headquarters. The limited funds allowed the research team to visit industrial sites and investigate the status of using immersion heaters for aluminum melting applications. Primary concepts were proposed on the design of furnaces using immersion heaters for melting. The proposed project can continue if the funding agency resumes the funds to this research. The objective of this project was to develop and demonstrate integrated, retrofitable technologies for clean melting systems for aluminum in both the Metal Casting and integrated aluminum processing industries. The scope focused on immersion heating coupled with metal circulation systems that provide significant opportunity for energy savings as well as reduction of melt loss in the form of dross. The project aimed at the development and integration of technologies that would enable significant reduction in the energy consumption and environmental impacts of melting aluminum through substitution of immersion heating for the conventional radiant burner methods used in reverberatory furnaces. Specifically, the program would couple heater improvements with furnace modeling that would enable cost-effective retrofits to a range of existing furnace sizes, reducing the economic barrier to application.

  10. Microscale application of column theory for high resolution force and displacement sensing

    NASA Astrophysics Data System (ADS)

    Samuel, B. A.; Desai, A. V.; Haque, M. A.

    2005-07-01

    We present the design, fabrication, and experimental validation of a device which exploits the amplification of displacement and attenuation of structural stiffness in the post-buckling deformation of slender columns to obtain pico-Newton force and nanometer displacement resolution, even under an optical microscope. The extremely small size, purely mechanical sensing scheme and vacuum compatibility of the instrument makes it compatible with existing visualization tools of nanotechnology. The instrument has a wide variety of potential applications ranging from electro-mechanical characterization of one dimensional solids to single biological cells.

  11. Application of Multiframe High-Resolution Image Reconstruction to Digital Microscopy

    NASA Astrophysics Data System (ADS)

    Baxley, Frank O.; Hardie, Russell C.

    1999-04-01

    A high-resolution image reconstruction algorithm previously used to improve undersampled infrared airborne imagery was applied to two different sets of digital microscopy images. One set is that of medical pap smear images, and the second set contains metallurgical micrographs. Both the pap smear images and the metallurgical micrographs are undersampled, thus causing loss of detail and aliasing artifacts. The algorithm minimizes the effects of aliasing and restores detail unobtainable through simple interpolation techniques. Both applications demonstrate improvement by use of the image reconstruction algorithm.

  12. Quantifying melting and mobilistaion of interstitial melts in crystal mushes

    NASA Astrophysics Data System (ADS)

    Veksler, Ilya; Dobson, Katherine; Hess, Kai-Uwe; Ertel-Ingrisch, Werner; Humphreys, Madeleine

    2015-04-01

    The deformation of crystals mushes and separation of melts and crystals in is critical to understanding the development of physical and chemical heterogeneity in magma chambers and has been invoked as an eruption trigger mechanism. Here we investigate the behaviour of the melt in the well characterised, classic crystal mush system of the Skaergaard intrusion by combining experimental petrology and the non-destructive 3D imaging methods. Starting materials for partial melting experiments were four samples from the upper Middle Zone of the Layered Series. Cylinders, 15 mm in diameter and 20 mm in length, were drilled out of the rock samples, placed in alumina crucibles and held for 5 days in electric furnaces at atmospheric pressure and 1050-1100 °C. Redox conditions set by the CO-CO2 gas mixture were kept close to those of the FMQ buffer. We then use spatially registered 3D x-ray computed tomography images, collected before and after the experiment, to determine the volume and distribution of the crystal framework and interstitial phases, and the volume, distribution and connectivity the interstitial phases that undergo melting and extraction while at elevated temperature. Image analysis has allowed us to quantify these physical changes with high spatial resolution. Our work is a first step towards quantitative understanding of the melt mobilisation and migration processes operating in notionally locked crystal rich magmatic systems.

  13. Application of film-casting technique to investigate drug-polymer miscibility in solid dispersion and hot-melt extrudate.

    PubMed

    Parikh, Tapan; Gupta, Simerdeep Singh; Meena, Anuprabha K; Vitez, Imre; Mahajan, Nidhi; Serajuddin, Abu T M

    2015-07-01

    Determination of drug-polymer miscibility is critical for successful development of solid dispersions. This report details a practical method to predict miscibility and physical stability of drug with various polymers in solid dispersion and, especially, in melt extrudates by applying a film-casting technique. Mixtures of itraconazole (ITZ) with hydroxypropylmethylcellulose phthalate (HPMCP), Kollidon(®) VA 64, Eudragit(®) E PO, and Soluplus(®) were film-casted, exposed to 40°C/75% RH for 1 month and then analyzed using differential scanning calorimetry (DSC), powder X-ray diffractometry, and polarized light microscopy (PLM). ITZ had the highest miscibility with HPMCP, being miscible at drug to polymer ratio of 6:4 (w/w). There was a downward trend of lower miscibility with Soluplus(®) (miscible at 3:7, w/w, and a few microcrystals present at 4:6, w/w), Kollidon(®) VA 64 (2:8, w/w) and Eudragit(®) E PO (<1:9, w/w). PLM was found more sensitive to detect drug crystallization than DSC and powder X-ray diffractometry. There was general correlation between results of film casting and hot-melt extrusion (HME) using a twin screw extruder. For ITZ-Soluplus(®) mixtures, HME at 4:6 (w/w) resulted in a single phase, whereas drug crystallization was observed at higher drug load. HME of ITZ-Kollidon(®) VA 64 mixtures also correlated well with the miscibility predicted by film casting. PMID:25917333

  14. Applications of high resolution ICP-AES in the nuclear industry

    SciTech Connect

    Johnson, S.G.; Giglio, J.J.; Goodall, P.S.; Cummings, D.G.

    1998-07-01

    Application of high resolution ICP-AES to selected problems of importance in the nuclear industry is a growing field. The advantages in sample preparation time, waste minimization and equipment cost are considerable. Two examples of these advantages are presented in this paper, burnup analysis of spent fuel and analysis of major uranium isotopes. The determination of burnup, an indicator of fuel cycle efficiency, has been accomplished by the determination of {sup 139}La by high resolution inductively coupled plasma atomic emission spectroscopy (HR-ICP-AES). Solutions of digested samples of reactor fuel rods were introduced into a shielded glovebox housing an inductively coupled plasma (ICP) and the resulting atomic emission transmitted to a high resolution spectrometer by a 31 meter fiber optic bundle. Total and isotopic U determination by thermal ionization mass spectrometry (TIMS) is presented to allow for the calculation of burnup for the samples. This method of burnup determination reduces the time, material, sample handling and waste generated associated with typical burnup determinations which require separation of lanthanum from the other fission products with high specific activities. Work concerning an alternative burnup indicator, {sup 236}U, is also presented for comparison. The determination of {sup 235}U:{sup 238}U isotope ratios in U-Zr fuel alloys is also presented to demonstrate the versatility of HR-ICP-AES.

  15. High-resolution stochastic generation of extreme rainfall intensity for urban drainage modelling applications

    NASA Astrophysics Data System (ADS)

    Peleg, Nadav; Blumensaat, Frank; Molnar, Peter; Fatichi, Simone; Burlando, Paolo

    2016-04-01

    Urban drainage response is highly dependent on the spatial and temporal structure of rainfall. Therefore, measuring and simulating rainfall at a high spatial and temporal resolution is a fundamental step to fully assess urban drainage system reliability and related uncertainties. This is even more relevant when considering extreme rainfall events. However, the current space-time rainfall models have limitations in capturing extreme rainfall intensity statistics for short durations. Here, we use the STREAP (Space-Time Realizations of Areal Precipitation) model, which is a novel stochastic rainfall generator for simulating high-resolution rainfall fields that preserve the spatio-temporal structure of rainfall and its statistical characteristics. The model enables a generation of rain fields at 102 m and minute scales in a fast and computer-efficient way matching the requirements for hydrological analysis of urban drainage systems. The STREAP model was applied successfully in the past to generate high-resolution extreme rainfall intensities over a small domain. A sub-catchment in the city of Luzern (Switzerland) was chosen as a case study to: (i) evaluate the ability of STREAP to disaggregate extreme rainfall intensities for urban drainage applications; (ii) assessing the role of stochastic climate variability of rainfall in flow response and (iii) evaluate the degree of non-linearity between extreme rainfall intensity and system response (i.e. flow) for a small urban catchment. The channel flow at the catchment outlet is simulated by means of a calibrated hydrodynamic sewer model.

  16. The Silicon Photomultiplier for application to high-resolution Positron Emission Tomography

    NASA Astrophysics Data System (ADS)

    Herbert, D. J.; Moehrs, S.; D'Ascenzo, N.; Belcari, N.; Del Guerra, A.; Morsani, F.; Saveliev, V.

    2007-04-01

    Positron Emission Tomography (PET) for small animal studies requires high-resolution gamma cameras with high sensitivity. Traditionally, inorganic scintillators are used and, in recent times, coupled to position sensitive PMTs to achieve a higher resolution. Such PSPMTs are costly, operated at high voltage and have a relatively low packing fraction. However, their advantage, compared to current solid state photodetectors, is their high signal-to-noise ratio. The Silicon Photomultiplier (SiPM) is a silicon diode detector that shows great promise as a photodetector for scintillators and hence application in nuclear medicine imaging applications. The microcell MRS (Metal-Resistor-Semiconductor) structure of the SiPM leads to a self-quenching, Geiger-mode avalanche photodiode (GAPD), that produces a large gain (5×105) at low bias voltage (50 V) and proportional output for moderate photon flux. Such a compact silicon detector, with a performance similar to a PMT, is obviously well disposed to being developed into a close-packed array in order to have a position-sensitive detection surface. We propose a miniature, high-resolution camera for a small-animal PET imaging system that is based on such an array of SiPM. The design is based upon the classic Anger camera principle; each detector module consists of a continuous slab of scintillator, viewed by a matrix of SiPM. A detector head of 4×4 cm2 in area is proposed, constructed from three such modules of the continuous camera described above. The stacked layers would give the system intrinsic depth of interaction (DOI) information. A summary of measured SiPM performance and results of a simulation of the proposed camera, using the Monte Carlo package GEANT4, are presented. It is shown that using three layers of 5 mm thick LSO, gives an efficiency of 68% with maximum count rates in the front layers. Intrinsic spatial resolution of <0.4 mm FWHM was found although this is degraded at the edges. Although the inclusion of DOI

  17. Digital Light Processing for high-brightness high-resolution applications

    NASA Astrophysics Data System (ADS)

    Hornbeck, Larry J.

    1997-05-01

    Electronic projection display technology for high-brightness applications had its origins in the Gretag Eidophor, an oil film-based projection system developed in the early 1940s. A number of solid state technologies have challenged the Eidophor, including CRT-addressed LCD light valves and active-matrix-addressed LCD panels. More recently, in response to various limitations of the LCD technologies, high-brightness systems have been developed based on Digital Light Processing technology. At the heart of the DLP projection display is the Digital Micromirror Device, a semiconductor-based array of fast, reflective digital light switches that precisely control a light source using a binary pulsewidth modulation technique. This paper describes the design, operation, performance, and advantages of DLP- based projection systems for high-brightness, high- resolution applications. It also presents the current status of high-brightness products that will soon be on the market.

  18. The Resolution Function of Triple-Crystal X-Ray Diffractometer and its Applications

    NASA Astrophysics Data System (ADS)

    Gu, Tianqu

    Based on the dynamical theory of X-ray scattering, the resolution function of a triple-crystal X-ray diffractometer is studied with particular emphasis on high-resolution setups. A general form describing the intensity distribution of a Bragg peak in reciprocal space is derived. The dynamical streaks associated with a Bragg peak and the width of the resolution function under the Gaussian approximation are studied in detail. The theory of absolute integrated intensity measurement by means of a triple-crystal diffractometer is developed. X-ray diffraction with synchrotron sources and multi-reflection collimators are studied briefly. Most aspects of the theory are verified by experiments. Extensive measurements are conducted in vast 2theta range to test the width distribution of the resolution function. The streak structure in reciprocal space is also measured experimentally. The absolute integrated intensity measurements are conducted over a GaAs single crystal sample. All these results agree reasonably well with the theory. As an example of application, the atomic concentration difference of Ga and In atoms in Ga_ {0.5}In_{0.5}P superstructure is obtained through the absolute integrated intensity measurement, and the correlation length of the superstructure is estimated, with the help of Hendricks-Teller's model. X-ray reflectivity is a special case of a Bragg peak. By using X-ray reflectivity measurements, the interface and its subsequent evolution of Ti/Fe bilayer over SiO _2 substrate under various annealing stages are studied. The electron density profiles of the structures are acquired.

  19. Viking High-Resolution Topography and Mars '01 Site Selection: Application to the White Rock Area

    NASA Astrophysics Data System (ADS)

    Tanaka, K. L.; Kirk, Randolph L.; Mackinnon, D. J.; Howington-Kraus, E.

    1999-06-01

    Definition of the local topography of the Mars '01 Lander site is crucial for assessment of lander safety and rover trafficability. According to Golombek et al., steep surface slopes may (1) cause retro-rockets to be fired too early or late for a safe landing, (2) the landing site slope needs to be < 1deg to ensure lander stability, and (3) a nearly level site is better for power generation of both the lander and the rover and for rover trafficability. Presently available datasets are largely inadequate to determine surface slope at scales pertinent to landing-site issues. Ideally, a topographic model of the entire landing site at meter-scale resolution would permit the best assessment of the pertinent topographic issues. MOLA data, while providing highly accurate vertical measurements, are inadequate to address slopes along paths of less than several hundred meters, because of along-track data spacings of hundreds of meters and horizontal errors in positioning of 500 to 2000 m. The capability to produce stereotopography from MOC image pairs is not yet in hand, nor can we necessarily expect a suitable number of stereo image pairs to be acquired. However, for a limited number of sites, high-resolution Viking stereo imaging is available at tens of meters horizontal resolution, capable of covering landing-ellipse sized areas. Although we would not necessarily suggest that the chosen Mars '01 Lander site should be located where good Viking stereotopography is available, an assessment of typical surface slopes at these scales for a range of surface types may be quite valuable in landing-site selection. Thus this study has a two-fold application: (1) to support the proposal of White Rock as a candidate Mars '01 Lander site, and (2) to evaluate how Viking high resolution stereotopography may be of value in the overall Mars '01 Lander site selection process.

  20. High-resolution infrared detector and its electronic unit for space application

    NASA Astrophysics Data System (ADS)

    Meftah, M.; Montmessin, F.; Korablev, O.; Trokhimovsky, A.; Poiet, G.; Bel, J.-B.

    2015-05-01

    High-resolution infrared detector is used extensively for military and civilian purposes. Military applications include target acquisition, surveillance, night vision, and tracking. Civilian applications include, among others, scientific observations. For our space systems, we want to use the products developed by SOFRADIR Company. Thus, we have developed a space electronic unit that is used to control the high-resolution SCORPIO-MW infrared detector, which has a format of 640×512 pixels with 15μm×15μm pixel pitch. The detector within microelectronics based on infrared mid-wave (MW) complementary metal oxide semiconductors (CMOS) uses a micro-cooler in order to keep its temperature around 100 K. The standard wavelength range (3 to 5μm) is adapted to the 2.2 to 4.3μm wavelength range thanks to adaptation of the optical interface of the detector and with an antireflection coating. With our electronic system, we can acquire 3 images per second. To increase the signal to noise ratio, we have the opportunity to make a summation of 15 frames per image. Through this article, we will describe the space electronic system that we have developed in order to achieve space observations (e.g. Atmospheric Chemistry Suite package for ExoMars Trace Gas Orbiter).

  1. Enhancing resolution properties of array antennas via field extrapolation: application to MIMO systems

    NASA Astrophysics Data System (ADS)

    Reggiannini, Ruggero

    2015-12-01

    This paper is concerned with spatial properties of linear arrays of antennas spaced less than half wavelength. Possible applications are in multiple-input multiple-output (MIMO) wireless links for the purpose of increasing the spatial multiplexing gain in a scattering environment, as well as in other areas such as sonar and radar. With reference to a receiving array, we show that knowledge of the received field can be extrapolated beyond the actual array size by exploiting the finiteness of the interval of real directions from which the field components impinge on the array. This property permits to increase the performance of the array in terms of angular resolution. A simple signal processing technique is proposed allowing formation of a set of beams capable to cover uniformly the entire horizon with an angular resolution better than that achievable by a classical uniform-weighing half-wavelength-spaced linear array. Results are also applicable to active arrays. As the above approach leads to arrays operating in super-directive regime, we discuss all related critical aspects, such as sensitivity to external and internal noises and to array imperfections, and bandwidth, so as to identify the basic design criteria ensuring the array feasibility.

  2. Applications of High Resolution Laser: Induced Breakdown Spectroscopy for Environmental and Biological Samples

    NASA Astrophysics Data System (ADS)

    Martin, Madhavi Z.; Labbe, Nicole; Wagner, Rebekah J.

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  3. Applications of High Resolution Laser Induced Breakdown Spectroscopy for Environmental and Biological Samples

    SciTech Connect

    Martin, Madhavi Z; Labbe, Nicole; Wagner, Rebekah J.

    2013-01-01

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  4. Surface chemistry of Ti6Al4V components fabricated using selective laser melting for biomedical applications.

    PubMed

    Vaithilingam, Jayasheelan; Prina, Elisabetta; Goodridge, Ruth D; Hague, Richard J M; Edmondson, Steve; Rose, Felicity R A J; Christie, Steven D R

    2016-10-01

    Selective laser melting (SLM) has previously been shown to be a viable method for fabricating biomedical implants; however, the surface chemistry of SLM fabricated parts is poorly understood. In this study, X-ray photoelectron spectroscopy (XPS) was used to determine the surface chemistries of (a) SLM as-fabricated (SLM-AF) Ti6Al4V and (b) SLM fabricated and mechanically polished (SLM-MP) Ti6Al4V samples and compared with (c) traditionally manufactured (forged) and mechanically polished Ti6Al4V samples. The SLM-AF surface was observed to be porous with an average surface roughness (Ra) of 17.6±3.7μm. The surface chemistry of the SLM-AF was significantly different to the FGD-MP surface with respect to elemental distribution and their existence on the outermost surface. Sintered particles on the SLM-AF surface were observed to affect depth profiling of the sample due to a shadowing effect during argon ion sputtering. Surface heterogeneity was observed for all three surfaces; however, vanadium was witnessed only on the mechanically polished (SLM-MP and FGD-MP) surfaces. The direct and indirect 3T3 cell cytotoxicity studies revealed that the cells were viable on the SLM fabricated Ti6Al4V parts. The varied surface chemistry of the SLM-AF and SLM-MP did not influence the cell behaviour. PMID:27287125

  5. Osteogenic differentiation of human bone marrow mesenchymal stem cells seeded on melt based chitosan scaffolds for bone tissue engineering applications.

    PubMed

    Costa-Pinto, Ana R; Correlo, Vitor M; Sol, Paula C; Bhattacharya, Mrinal; Charbord, Pierre; Delorme, Bruno; Reis, Rui L; Neves, Nuno M

    2009-08-10

    The purpose of this study was to evaluate the growth patterns and osteogenic differentiation of human bone marrow mesenchymal stem cells (hBMSCs) when seeded onto new biodegradable chitosan/polyester scaffolds. Scaffolds were obtained by melt blending chitosan with poly(butylene succinate) in a proportion of 50% (wt) each and further used to produce a fiber mesh scaffold. hBMSCs were seeded on those structures and cultured for 3 weeks under osteogenic conditions. Cells were able to reduce MTS and demonstrated increasing metabolic rates over time. SEM observations showed cell colonization at the surface as well as within the scaffolds. The presence of mineralized extracellular matrix (ECM) was successfully demonstrated by peaks corresponding to calcium and phosphorus elements detected in the EDS analysis. A further confirmation was obtained when carbonate and phosphate group peaks were identified in Fourier Transformed Infrared (FTIR) spectra. Moreover, by reverse transcriptase (RT)-PCR analysis, it was observed the expression of osteogenic gene markers, namely, Runt related transcription factor 2 (Runx2), type 1 collagen, bone sialoprotein (BSP), and osteocalcin. Chitosan-PBS (Ch-PBS) biodegradable scaffolds support the proliferation and osteogenic differentiation of hBMSCs cultured at their surface in vitro, enabling future in vivo testing for the development of bone tissue engineering therapies. PMID:19621927

  6. Effects of Mg and Zn on the surface of doped melt-derived glass for biomaterials applications

    NASA Astrophysics Data System (ADS)

    Dietrich, E.; Oudadesse, H.; Lucas-Girot, A.; Le Gal, Y.; Jeanne, S.; Cathelineau, G.

    2008-11-01

    Bioactive glasses in the system SiO 2-CaO-Na 2O-P 2O 5 were synthesized pure and doped with magnesium or zinc by melt-derived method. The bioactivity was studied during in vitro assays: the ability of hydroxycarbonate apatite (HCA) layer to form on the glass surface was examined after contact with simulated body fluid (SBF). The X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) studies were performed before and after immersion in vitro assays. The SBF solutions were also analyzed using inductively coupled plasma-optical emission spectroscopy (ICP-OES). Introduction of magnesium and zinc as trace element induces several modifications on the observed phenomena at the glass surface and in SBF solution after immersion of the samples. The chemical durability of the glasses, the formation of the silica-rich layer and the crystallization of the HCA layer were affected, but not present the same modifications as the introduced doping element.

  7. Thermodynamics of gas-metal-slag equilibria for applications in in situ and ex situ vitrification melts

    SciTech Connect

    Miller, R.L.; Reimann, G.A.

    1993-05-01

    An equilibrium thermodynamic model for melting mixed waste was evaluated using the STEPSOL computer code. STEPSOL uses free energy minimization techniques to predict equilibrium composition from input species and user selected species in the output. The model assumes equilibrium between gas, slag, and metallic phases. Input for the model was developed using compositional data from Pit 9 of the Subsurface Disposal Area at the Idaho National Engineering Laboratory. Thermodynamic data were primarily from compilations published by the US Government. The results of model evaluation indicate that the amount of plutonium chloride or plutonium oxyhydroxide that would be evaporated into the vapor phase would be minor. Relatively more uranium chloride and uranium oxyhydroxide would be vaporized. However, a hazards analysis was not part of the present task. Minor amounts of plutonium and uranium would be reduced to the metallic state, but these amounts should alloy with the iron-chromium-nickel metallic phase. The vast majority of the plutonium and uranium are in the slag phase as oxides. Results of the calculations show that silica and silicates dominate the products and that the system is very reducing. The major gases are carbon monoxide and hydrogen, with lesser amounts of carbon dioxide and water. High vapor pressure metals are considered but were not analyzed using STEPSOL. STEPSOL does not make predictions of distribution of species between phases.

  8. Development of dual scale scaffolds via direct polymer melt deposition and electrospinning for applications in tissue regeneration.

    PubMed

    Park, Suk Hee; Kim, Taek Gyoung; Kim, Hyo Chan; Yang, Dong-Yol; Park, Tae Gwan

    2008-09-01

    The objective of this study was the fabrication of highly functionalized polymeric three-dimensional (3D) structures characterized by nano and microfibers for use as an extracellular matrix-like tissue engineering scaffold. A hybrid process utilizing direct polymer melt deposition (DPMD) and an electrospinning method were employed to obtain the structure. Each microfibrous layer of the scaffold was built using the DPMD process in accordance with computer-aided design modeling data considering some structural points such as pore size, pore interconnectivity and fiber diameter. Between the layers of the three-dimensional structure, polycaprolactone/collagen nanofiber matrices were deposited via an electrospinning process. To evaluate the fabricated scaffolds, chondrocytes were seeded and cultured within the developed scaffolds for 10 days, and the levels of cell adhesion and proliferation were monitored. The results showed that the polymeric scaffolds with nanofiber matrices fabricated using the proposed hybrid process provided favorable conditions for cell adhesion and proliferation. These conditions can be attributed to enhanced cytocompatibility of the scaffold due to surficial nanotopography in the scaffold, chemical composition by use of a functional biocomposite, and an enlarged inner surface of the structure for cell attachment and growth. PMID:18458008

  9. Advanced flat top laser heating system for high pressure research at GSECARS: application to the melting behavior of germanium

    SciTech Connect

    Prakapenka, V.B.; Kubo, A.; Kuznetzov, A.; Laskin, A.; Shkurkhin, O.; Dera, P.; Rivers, M.L.; Sutton, S.R.

    2008-09-29

    Laser heating plays an essential role for in-situ high pressure high temperature studies into the physical and chemical properties of materials in the diamond anvil cell (DAC) and minerals at conditions relevant to the Earth's deep interior. High temperature experiments in the multi-Mbar (over 100 GPa) pressure range require the use of very small samples and consequently the utmost stability and controllability of the laser heating is crucial. To accomplish this, we have modified the laser heating system at GSECARS employing newly developed beam shaping optics combined with two diode-pumped, single mode fiber lasers. Varying the settings of the laser heating system, we were able to shape the beam to almost any desired intensity profile and size on the surface of the sample in the DAC, including tight focus, flat top, trident and doughnut types. The advantages and excellent performance of the flat top laser heating (FTLH) technique were demonstrated in melting experiments on germanium in the DAC at pressures up to 40 GPa.

  10. Kinetic processes in supercooled monosaccharides upon melting: Application of dielectric spectroscopy in the mutarotation studies of D-ribose

    NASA Astrophysics Data System (ADS)

    Wlodarczyk, P.; Kaminski, K.; Haracz, S.; Dulski, M.; Paluch, M.; Ziolo, J.; Wygledowska-Kania, M.

    2010-05-01

    Dielectric spectroscopy has been recently used to monitor mutarotation in undercooled D-fructose. This method can be viewed as a universal method to study mutarotation phenomenon in the whole family of monosaccharides. In this paper, we studied kinetics of mutaration of anhydrous D-ribose at ambient pressure as well as pressure effect on the rate constant of this process. Ribose mutarotation behavior is compared to the one obtained for D-fructose. In addition, we attempted to determine the "direction" of mutarotation in undercooled monosaccharides after quenching the melted sample. To this end, analysis of dipole moments of different tautomers of D-fructose and D-ribose have been performed. Conformational analysis of studied carbohydrates was done with use of density functional theory. Geometry optimizations as well as calculations of dipole moments were done on the 6-311++G(d,p)/B3LYP level. Finally, it turned out that data obtained from the mutarotation experiment might be helpful in understanding the origin of γ-process occurring in the whole family of carbohydrates.

  11. High resolution transmission electron microscopy study of the hardening mechanism through phase separation in a beta-Ti-35Nb-7Zr-5Ta alloy for implant applications.

    PubMed

    Afonso, Conrado R M; Ferrandini, Peterson L; Ramirez, Antonio J; Caram, Rubens

    2010-04-01

    beta-Ti alloys are highly attractive metallic materials for biomedical applications due to their high specific strength, high corrosion resistance and excellent biocompatibility, including low elastic modulus. This work aims to clarify the hardening mechanism of a beta-Ti-Nb-Zr-Ta alloy using different characterization techniques. Ingots (50 g) of Ti-35Nb-7Zr-5Ta (wt.%) alloy were arc furnace melted in an Ar((g)) atmosphere, homogenized, hot rolled, solubilized and finally aged at several temperatures from 200 to 700 degrees C for 4 h. Microstructure characterization was performed using X-ray diffraction, optical microscopy, scanning and high resolution transmission electron microscopy (HR-TEM). The 4 h aging showed that the highest hardness values were found when aged at 400 degrees C and the HR-TEM images confirmed splitting of spots on the Fourier space map, which indicated the presence of a coherent interface between separated phases (beta and beta') and explains the hardening mechanism of the alloy. Through geometric phase analysis analysis, using the HR-TEM image, the localized strain map showed 5-10 nm domains of the beta and beta' phases. The combination of suitable values of yield strength, hardness and low Young's modulus makes Ti-35Nb-7Zr-5Ta alloy suitable for medical applications as a metallic orthopedic implant. PMID:19913645

  12. Development of a Novel Real-Time PCR Assay with High-Resolution Melt Analysis To Detect and Differentiate OXA-48-Like β-Lactamases in Carbapenem-Resistant Enterobacteriaceae

    PubMed Central

    Hemarajata, Peera; Yang, Shangxin; Hindler, Janet A.

    2015-01-01

    The rapid global spread of carbapenem-resistant Enterobacteriaceae (CRE) poses an urgent threat to public health. More than 250 class D β-lactamases (OXAs) have been described in recent years, with variations in hydrolytic activity for β-lactams. The plasmid-borne OXA-48 β-lactamase and its variants are identified only sporadically in the United States but are common in Europe. Recognition of these OXA-48-like carbapenemases is vital in order to control their dissemination. We developed a real-time PCR assay based on high-resolution melt analysis, using blaOXA-48-like-specific primers coupled with an unlabeled 3′-phosphorylated oligonucleotide probe (LunaProbe) homologous to OXA-48-like carbapenemase genes. The assay was validated using genomic DNA from 48 clinical isolates carrying a variety of carbapenemase genes, including blaKPC, blaSME, blaIMP, blaNDM-1, blaVIM, blaOXA-48, blaOXA-162, blaOXA-181, blaOXA-204, blaOXA-244, blaOXA-245, and blaOXA-232. Our assay identified the presence of blaOXA-48-like β-lactamase genes and clearly distinguished between blaOXA-48 and its variants in control strains, including between blaOXA-181 and blaOXA-232, which differ by only a single base pair in the assay target region. This approach has potential for use in epidemiological investigations and continuous surveillance to help control the spread of CRE strains producing OXA-48-like enzymes. PMID:26124164

  13. Detection of BRAF Mutations Using a Fully Automated Platform and Comparison with High Resolution Melting, Real-Time Allele Specific Amplification, Immunohistochemistry and Next Generation Sequencing Assays, for Patients with Metastatic Melanoma

    PubMed Central

    Harlé, Alexandre; Salleron, Julia; Franczak, Claire; Dubois, Cindy; Filhine-Tressarieu, Pierre; Leroux, Agnès; Merlin, Jean-Louis

    2016-01-01

    Background Metastatic melanoma is a severe disease with one of the highest mortality rate in skin diseases. Overall survival has significantly improved with immunotherapy and targeted therapies. Kinase inhibitors targeting BRAF V600 showed promising results. BRAF genotyping is mandatory for the prescription of anti-BRAF therapies. Methods Fifty-nine formalin-fixed paraffin-embedded melanoma samples were assessed using High-Resolution-Melting (HRM) PCR, Real-time allele-specific amplification (RT-ASA) PCR, Next generation sequencing (NGS), immunohistochemistry (IHC) and the fully-automated molecular diagnostics platform IdyllaTM. Sensitivity, specificity, positive predictive value and negative predictive value were calculated using NGS as the reference standard to compare the different assays. Results BRAF mutations were found in 28(47.5%), 29(49.2%), 31(52.5%), 29(49.2%) and 27(45.8%) samples with HRM, RT-ASA, NGS, IdyllaTM and IHC respectively. Twenty-six (81.2%) samples were found bearing a c.1799T>A (p.Val600Glu) mutation, three (9.4%) with a c.1798_1799delinsAA (p.Val600Lys) mutation and one with c.1789_1790delinsTC (p.Leu597Ser) mutation. Two samples were found bearing complex mutations. Conclusions HRM appears the less sensitive assay for the detection of BRAF V600 mutations. The RT-ASA, IdyllaTM and IHC assays are suitable for routine molecular diagnostics aiming at the prescription of anti-BRAF therapies. IdyllaTM assay is fully-automated and requires less than 2 minutes for samples preparation and is the fastest of the tested assays. PMID:27111917

  14. High-resolution melting-curve analysis of obg gene to differentiate the temperature-sensitive Mycoplasma synoviae vaccine strain MS-H from non-temperature-sensitive strains.

    PubMed

    Shahid, Muhammad A; Markham, Philip F; Marenda, Marc S; Agnew-Crumpton, Rebecca; Noormohammadi, Amir H

    2014-01-01

    Temperature-sensitive (ts+) vaccine strain MS-H is the only live attenuated M. synoviae vaccine commercially available for use in poultry. With increasing use of this vaccine to control M. synoviae infections, differentiation of MS-H from field M. synoviae strains and from rarely occurring non-temperature-sensitive (ts-) MS-H revertants has become important, especially in countries where local strains are indistinguishable from MS-H by sequence analysis of variable lipoprotein haemagglutinin (vlhA) gene. Single nucleotide polymorphisms (SNPs) in the obg of MS-H have been found to associate with ts phenotype. In this study, four PCRs followed by high-resolution melting (HRM)-curve analysis of the regions encompassing these SNPs were developed and evaluated for their potential to differentiate MS-H from 36 M. synoviae strains/isolates. The nested-obg PCR-HRM differentiated ts+ MS-H vaccine not only from field M. synoviae strains/isolates but also from ts- MS-H revertants. The mean genotype confidence percentages, 96.9±3.4 and 8.8±11.2 for ts+ and ts- strains, respectively, demonstrated high differentiating power of the nested-obg PCR-HRM. Using a combination of nested-obg and obg-F3R3 PCR-HRM, 97% of the isolates/strains were typed according to their ts phenotype with all MS-H isolates typed as MS-H. A set of respiratory swabs from MS-H vaccinated specific pathogen free chickens and M. synoviae infected commercial chicken flocks were tested using obg PCR-HRM system and results were consistent with those of vlhA genotyping. The PCR-HRM system developed in this study, proved to be a rapid and reliable tool using pure M. synoviae cultures as well as direct clinical specimens. PMID:24643035

  15. Comparison of high resolution melting analysis, pyrosequencing, next generation sequencing and immunohistochemistry to conventional Sanger sequencing for the detection of p.V600E and non-p.V600E BRAF mutations

    PubMed Central

    2014-01-01

    Background The approval of vemurafenib in the US 2011 and in Europe 2012 improved the therapy of not resectable or metastatic melanoma. Patients carrying a substitution of valine to glutamic acid at codon 600 (p.V600E) or a substitution of valine to leucine (p.V600K) in BRAF show complete or partial response. Therefore, the precise identification of the underlying somatic mutations is essential. Herein, we evaluate the sensitivity, specificity and feasibility of six different methods for the detection of BRAF mutations. Methods Samples harboring p.V600E mutations as well as rare mutations in BRAF exon 15 were compared to wildtype samples. DNA was extracted from formalin-fixed paraffin-embedded tissues by manual micro-dissection and automated extraction. BRAF mutational analysis was carried out by high resolution melting (HRM) analysis, pyrosequencing, allele specific PCR, next generation sequencing (NGS) and immunohistochemistry (IHC). All mutations were independently reassessed by Sanger sequencing. Due to the limited tumor tissue available different numbers of samples were analyzed with each method (82, 72, 60, 72, 49 and 82 respectively). Results There was no difference in sensitivity between the HRM analysis and Sanger sequencing (98%). All mutations down to 6.6% allele frequency could be detected with 100% specificity. In contrast, pyrosequencing detected 100% of the mutations down to 5% allele frequency but exhibited only 90% specificity. The allele specific PCR failed to detect 16.3% of the mutations eligible for therapy with vemurafenib. NGS could analyze 100% of the cases with 100% specificity but exhibited 97.5% sensitivity. IHC showed once cross-reactivity with p.V600R but was a good amendment to HRM. Conclusion Therefore, at present, a combination of HRM and IHC is recommended to increase sensitivity and specificity for routine diagnostic to fulfill the European requirements concerning vemurafenib therapy of melanoma patients. PMID:24410877

  16. Comparison of multiple genes and 16S-23S rRNA intergenic space region for their capacity in high resolution melt curve analysis to differentiate Mycoplasma gallisepticum vaccine strain ts-11 from field strains.

    PubMed

    Ghorashi, Seyed A; Bradbury, Janet M; Ferguson-Noel, Naola M; Noormohammadi, Amir H

    2013-12-27

    Mycoplasma gallisepticum (MG) is an important avian pathogen causing significant economic losses in the global poultry industry. In an attempt to compare and evaluate existing genotyping methods for differentiation of MG strains/isolates, high resolution melt (HRM) curve analysis was applied to 5 different PCR methods targeting vlhA, pvpA, gapA, mgc2 genes and 16S-23S rRNA intergenic space region (IGSR). To assess the discriminatory power of PCR-HRM of examined genes and IGSR, MG strains ts-11, F, 6/85 and S6, and, initially, 8 field isolates were tested. All MG strains/isolates were differentiated using PCR-HRM curve analysis and genotype confidence percentage (GCP) values of vlhA and pvpA genes, while only 0, 3 and 4 out of 12 MG strains/isolates were differentiated using gapA, mgc2 genes and IGSR, respectively. The HRM curve analysis of vlhA and pvpA genes was found to be highly correlated with the genetic diversity of the targeted genes confirmed by sequence analysis of amplicons generated from MG strains. The potential of the vlhA and pvpA genes was also demonstrated for genotyping of 12 additional MG strains from Europe and the USA. Results from this study provide a direct comparison between genes previously used in sequencing-based genotyping methods for MG strain identification and highlight the usefulness of vlhA and pvpA HRM curve analyses as rapid and reliable tools specially for diagnosis and differentiation of MG strains used here. PMID:24238667

  17. Association between the p73 gene G4C14-to-A4T14 single nucleotide polymorphism and risk of cervical cancer by high resolution melting and PCR with confronting two-pair primers in a Chinese population

    PubMed Central

    GUO, HAIYAN; YANG, SHAODI; XU, LIJIAN; LI, DING; TANG, JIANXIN; WANG, SHUANGSHAUNG; WEI, BENJIE; LIU, ZHENGCHUN

    2016-01-01

    As a member of the p53 gene family, the p73 gene can affect an individual's susceptibility to cancer through a p53-like manner. DNA sequence variation in the p73 gene has been reported to be associated with cancer risk. The present study aimed to identify whether the p73 gene G4C14-to-A4T14 single nucleotide polymorphism (SNP) is associated with risk of cervical cancer in a Chinese population. The p73 G4C14-to-A4T14 polymorphism was genotyped in 175 cervical cancer and 189 healthy control peripheral blood DNA samples using high resolution melting, polymerase chain reaction with confronting two-pair primers and direct DNA sequencing. The results demonstrated that carriers of the AT/AT genotype were associated with a significantly increased risk of cervical cancer (P=0.042; χ2=4.122; odds ratio = 2.241; 95% confidence interval = 1.013–4.956) compared with the GC/GC genotype carriers. In addition, there was a significant association between p73 genotypes and tumor size in patients with cervical cancer (P=0.014; χ2=8.607). However, no association was identified between p73 genotypes and tumor stage, histological type or lymph node metastasis in patients with cervical cancer. These results suggest that the p73 G4C14-to-A4T14 SNP may function as a marker of genetic susceptibility to cervical cancer in the Chinese population. PMID:27347206

  18. Assessment of high resolution melt analysis feasibility for evaluation of beta-globin gene mutations as a reproducible, cost-efficient and fast alternative to the present conventional method

    PubMed Central

    Ramezanzadeh, Mahboubeh; Salehi, Mansour; Salehi, Rasoul

    2016-01-01

    Background: Beta-thalassemia is the most prevalent monogenic disease throughout the world. It was the first genetic disorder nominated for nation-wide prevention programs involving population screening for heterozygotes and prenatal diagnosis (PND) in Iran. Due to the high prevalence of beta-thalassemia, the shift from conventional mutation detection methods to more recently developed techniques based on novel innovative technologies are essential. We aimed to develop a real-time polymerase chain reaction (PCR) based protocol using high resolution melting (HRM) analysis for diagnosis of common beta-thalassemia mutations. Materials and Methods: Forty DNA samples extracted from peripheral blood of suspected beta-thalassemia carriers participated in this study were subjected to amplification refractory mutation system (ARMS). We then used 20 of these samples for HRM optimization. When 100% sensitivity and specificity was obtained with HRM procedure, we applied the technique for mutation detection on another remaining 20 samples as thalassemia cases with unknown mutations (detected mutations with ARMS-PCR kept confidential). Finally, the HRM procedure applied on 2 chorionic villous sample (CVS) biopsied from 12 weeks gestational age pregnant women for routine PND analysis. Results: In the first step of study, Fr 8/9 (+G), IVSI-1 (G > A), IVSI-5 (G > C), IVSI-110 (G > A), and CD44 (−C) mutations were diagnosed in samples under study using ARMS-PCR technique. Finally, the HRM procedure applied on 20 unknown samples and 2 CVS The results of HRM were in complete concordance with ARMS and confirmed by sequencing. Conclusions: The advantages of HRM analysis over conventional methods is high throughput, rapid, accurate, cost-effective, and reproducible. PMID:27169102

  19. Application and correlation of nano resolution microscopy techniques to viral protein localization

    NASA Astrophysics Data System (ADS)

    Hodges, Jeffery Allen

    This dissertation is primarily focused on the application of super-resolution microscopy techniques to localization of viral proteins within envelope viruses. Advances in optical super-resolution microscopy techniques have enabled scientists to observe phenomena much smaller than the Abbe diffraction limit by stochastically limiting the number of molecules excited at a given instance and localizing their positions one at a time. Additionally, methods such as Atomic Force Microscopy (AFM) allow scientists to measure the topological features and material properties of samples through contact with a force probe. This dissertation describes the application of these two techniques to virology in order to localize internal viral proteins of enveloped virions, and measure their effect on the elastic properties of the virion. By utilizing super-resolution microscopy techniques such as Fluorescent Photo-Activated Localization Microscopy (fPALM) on virions, which have had their surface glycoproteins labeled with a photo-switchable label, the viral envelope may be accurately recovered. This dissertation describes the development and application of this technique as it applies to envelope recovery of Vesicular Stomatitis Virus (VSV) and Human Immunodeficiency Virus-1 (HIV-1). By fluorescently labeling proteins, which are internal to each of these viruses, I have been able to localize a variety of viral proteins within their recovered envelopes. This is done without significant damage to the virion, making this method a highly effective in vivo technique. In the case of VSV, an asymmetric localization along the central axis towards the blunt 5' end was found to exist for both the polymerase and phosphoproteins. These have been determined to occupy a region in the central cavity of ˜57 +/- 12 nm on the 5' end. This inhomogeneity of the underlying proteins such an asymmetry would predict that the Young's modulus would vary along the central axis of the virion. This dissertation

  20. Flood and Landslide Applications of High Time Resolution Satellite Rain Products

    NASA Technical Reports Server (NTRS)

    Adler, Robert F.; Hong, Yang; Huffman, George J.

    2006-01-01

    Experimental, potentially real-time systems to detect floods and landslides related to heavy rain events are described. A key basis for these applications is high time resolution satellite rainfall analyses. Rainfall is the primary cause for devastating floods across the world. However, in many countries, satellite-based precipitation estimation may be the best source of rainfall data due to insufficient ground networks and absence of data sharing along many trans-boundary river basins. Remotely sensed precipitation from the NASA's TRMM Multi-satellite Precipitation Analysis (TMPA) operational system (near real-time precipitation at a spatial-temporal resolution of 3 hours and 0.25deg x 0.25deg) is used to monitor extreme precipitation events. Then these data are ingested into a macro-scale hydrological model which is parameterized using spatially distributed elevation, soil and land cover datasets available globally from satellite remote sensing. Preliminary flood results appear reasonable in terms of location and frequency of events, with implementation on a quasi-global basis underway. With the availability of satellite rainfall analyses at fine time resolution, it has also become possible to assess landslide risk on a near-global basis. Early results show that landslide occurrence is closely associated with the spatial patterns and temporal distribution of TRMM rainfall characteristics. Particularly, the number of landslides triggered by rainfall is related to rainfall climatology, antecedent rainfall accumulation, and intensity-duration of rainstorms. For the purpose of prediction, an empirical TMPA-based rainfall intensity-duration threshold is developed and shown to have skill in determining potential areas of landslides. These experimental findings, in combination with landslide surface susceptibility information based on satellite-based land surface information, form a starting point towards a potential operational landslide monitoring/warning system

  1. Development and Applications of a New, High-Resolution, Operational MISR Aerosol Product

    NASA Astrophysics Data System (ADS)

    Garay, M. J.; Diner, D. J.; Kalashnikova, O.

    2014-12-01

    Since early 2000, the Multi-angle Imaging SpectroRadiometer (MISR) instrument on NASA's Terra satellite has been providing aerosol optical depth (AOD) and particle property retrievals at 17.6 km spatial resolution. Capitalizing on the capabilities provided by multi-angle viewing, the operational MISR algorithm performs well, with about 75% of MISR AOD retrievals falling within 0.05 or 20% × AOD of the paired validation data from the ground-based Aerosol Robotic Network (AERONET), and is able to distinguish aerosol particles by size and sphericity, over both land and water. These attributes enable a variety of applications, including aerosol transport model validation and global air quality assessment. Motivated by the adverse impacts of aerosols on human health at the local level, and taking advantage of computational speed advances that have occurred since the launch of Terra, we have implemented an operational MISR aerosol product with 4.4 km spatial resolution that maintains, and sometimes improves upon, the quality of the 17.6 km resolution product. We will describe the performance of this product relative to the heritage 17.6 km product, the global AERONET validation network, and high spatial density AERONET-DRAGON sites. Other changes that simplify product content, and make working with the data much easier for users, will also be discussed. Examples of how the new product demonstrates finer spatial variability of aerosol fields than previously retrieved, and ways this new dataset can be used for studies of local aerosol effects, will be shown.

  2. Effects of melt aging and off-stoichiometric melts on CsSrI3:Eu(2+) single crystal scintillators.

    PubMed

    Wu, Yuntao; Zhuravleva, Mariya; Johnson, Jesse Ashby; Wei, Hua; Koschan, Merry; Melcher, Charles L

    2016-03-28

    Ternary halide scintillators are commonly prepared from a mixture of commercially available binary halides. The initial binary halides may contain excess halogen ions or have different volatilities, which could lead to loss of stoichiometry of the resulting ternary halide crystals and potentially negatively affect optical and scintillation properties. In this work, the effects of vacuum aging of the melt (melt aging) and use of off-stoichiometric melts via introduction of excess CsI on the crystal quality and scintillation properties of CsSrI3:Eu(2+), a promising scintillator for gamma-ray detection applications, are investigated. The phase purity of the grown samples was confirmed by powder X-ray diffraction and differential scanning calorimeter measurements, and the existence of matrix composition variations is revealed by energy-dispersive X-ray spectroscopy analyses. An abnormal relationship between the full energy peak and the shaping time, i.e. full energy peak broadening or existence of two full energy peaks, in the melt-aged and off-stoichiometric samples is observed. It is ascribed to a slow scintillation decay event in a time scale between 15 and 50 μs. For the CsSrI3:Eu(2+) single crystal grown from a stoichiometric melt without melt aging treatment, an energy resolution of 5.0% at 662 keV and a light yield of 48,000 ± 2000 photons per MeV can be achieved at a size of 1.4 cm(3). PMID:26934721

  3. Rate-gyro-integral constraint for ambiguity resolution in GNSS attitude determination applications.

    PubMed

    Zhu, Jiancheng; Li, Tao; Wang, Jinling; Hu, Xiaoping; Wu, Meiping

    2013-01-01

    In the field of Global Navigation Satellite System (GNSS) attitude determination, the constraints usually play a critical role in resolving the unknown ambiguities quickly and correctly. Many constraints such as the baseline length, the geometry of multi-baselines and the horizontal attitude angles have been used extensively to improve the performance of ambiguity resolution. In the GNSS/Inertial Navigation System (INS) integrated attitude determination systems using low grade Inertial Measurement Unit (IMU), the initial heading parameters of the vehicle are usually worked out by the GNSS subsystem instead of by the IMU sensors independently. However, when a rotation occurs, the angle at which vehicle has turned within a short time span can be measured accurately by the IMU. This measurement will be treated as a constraint, namely the rate-gyro-integral constraint, which can aid the GNSS ambiguity resolution. We will use this constraint to filter the candidates in the ambiguity search stage. The ambiguity search space shrinks significantly with this constraint imposed during the rotation, thus it is helpful to speeding up the initialization of attitude parameters under dynamic circumstances. This paper will only study the applications of this new constraint to land vehicles. The impacts of measurement errors on the effect of this new constraint will be assessed for different grades of IMU and current average precision level of GNSS receivers. Simulations and experiments in urban areas have demonstrated the validity and efficacy of the new constraint in aiding GNSS attitude determinations. PMID:23793044

  4. A high-resolution integrated optical spectrometer with applications to fibre sensor signal processing

    NASA Astrophysics Data System (ADS)

    Varasi, M.; Signorazzi, M.; Vannucci, A.; Dunphy, Jim

    1996-02-01

    An integrated optical device has been developed to realize the instrumentation for the processing of the optical signal such as those from fibre optic Bragg grating sensors (FBG) embedded in composite materials. The optical circuit integrates on X-cut 0957-0233/7/2/009/img7 an acousto-optical TE - TM converter included between two crossed polarizers, in order to realize a tunable high-resolution optical filter. The design and fabrication process parameters and solutions adopted with the aim of obtaining very-high-resolution filters ( FWHM < 0.45 nm at 1300 nm) are discussed. The device has been demonstrated to allow the polarization-independent spectrum analysis of in-fibre optical radiation, exploiting the heterodyne detection of the optical signals from the output of the acousto-optical tunable filter. The application as instrumentation for the processing of optical signals from such sensors is described and the experimental results are presented for the monitoring of static and dynamic deformations of composite material structures such as those in which the FBG sensors have been embedded.

  5. Continuous wave terahertz wave spectrometer based on diode laser pumping: potential applications in high resolution spectroscopy.

    PubMed

    Tanabe, Tadao; Ragam, Srinivasa; Oyama, Yutaka

    2009-11-01

    We constructed a high resolution terahertz (THz) spectroscopic system with an automatic scanning control using a continuous wave (cw) THz wave generator based on difference frequency generation method by excitation of phonon-polariton mode in GaP. The pump and signals lasers were compact, tunable external cavity laser, and distributed feedback (DFB) lasers, respectively. The generated THz waves were tuned automatically by changing the temperature of the DFB laser using a system control. We present the water vapor transmission characteristics of the THz wave and also absorption spectrum of a white polyethylene in the frequency range of 1.97-2.45 THz. The spectroscopic measurements performed at an output power level of 2 nW, which was obtained with a 15-mm-long GaP crystal at 2 THz. The advantage of this cw THz spectrometer is wide frequency tuning range (0.7-4.42 THz) with an estimated linewidth of full width at quarter maximum <8 MHz and this system has a potential application in high resolution spectroscopy. PMID:19947715

  6. Sensitivity and resolution enhancement of oriented solid-state NMR: application to membrane proteins.

    PubMed

    Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi

    2013-11-01

    Oriented solid-state NMR (O-ssNMR) spectroscopy is a major technique for the high-resolution analysis of the structure and topology of transmembrane proteins in native-like environments. Unlike magic angle spinning (MAS) techniques, O-ssNMR spectroscopy requires membrane protein preparations that are uniformly oriented (mechanically or magnetically) so that anisotropic NMR parameters, such as dipolar and chemical shift interactions, can be measured to determine structure and orientation of membrane proteins in lipid bilayers. Traditional sample preparations involving mechanically aligned lipids often result in short relaxation times which broaden the (15)N resonances and encumber the manipulation of nuclear spin coherences. The introduction of lipid bicelles as membrane mimicking systems has changed this scenario, and the more favorable relaxation properties of membrane protein (15)N and (13)C resonances make it possible to develop new, more elaborate pulse sequences for higher spectral resolution and sensitivity. Here, we describe our recent progress in the optimization of O-ssNMR pulse sequences. We explain the theory behind these experiments, demonstrate their application to small and medium size proteins, and describe the technical details for setting up these new experiments on the new generation of NMR spectrometers. PMID:24160761

  7. The online application of binding condition B in native and non-native pronoun resolution

    PubMed Central

    Patterson, Clare; Trompelt, Helena; Felser, Claudia

    2014-01-01

    Previous research has shown that anaphor resolution in a non-native language may be more vulnerable to interference from structurally inappropriate antecedents compared to native anaphor resolution. To test whether previous findings on reflexive anaphors generalize to non-reflexive pronouns, we carried out an eye-movement monitoring study investigating the application of binding condition B during native and non-native sentence processing. In two online reading experiments we examined when during processing local and/or non-local antecedents for pronouns were considered in different types of syntactic environment. Our results demonstrate that both native English speakers and native German-speaking learners of English showed online sensitivity to binding condition B in that they did not consider syntactically inappropriate antecedents. For pronouns thought to be exempt from condition B (so-called “short-distance pronouns”), the native readers showed a weak preference for the local antecedent during processing. The non-native readers, on the other hand, showed a preference for the matrix subject even where local coreference was permitted, and despite demonstrating awareness of short-distance pronouns' referential ambiguity in a complementary offline task. This indicates that non-native comprehenders are less sensitive during processing to structural cues that render pronouns exempt from condition B, and prefer to link a pronoun to a salient subject antecedent instead. PMID:24611060

  8. High resolution interrogation system for fiber Bragg grating (FBG) sensor application using radio frequency spectrum analyser

    NASA Astrophysics Data System (ADS)

    Muhammad, F. D.; Zulkifli, M. Z.; Harun, S. W.; Ahmad, H.

    2013-05-01

    In this paper, we propose a fiber Bragg grating (FBG) interrogation system for high resolution sensor application based on radio frequency (RF) generation technique by beating a single longitudinal mode (SLM) fiber ring laser with an external tunable laser source (TLS). The external TLS provides a constant wavelength (CW), functioning as the reference signal for the frequency beating technique. The TLS used has a constant output power and wavelength over time. The sensor signal is provided by the reflected wavelength of a typical fiber Bragg grating (FBG) in the SLM fiber ring laser, which consists of a 1 m long highly doped Erbium doped fiber as the gain medium. The key to ensure the SLM laser oscillation is the role of graphene as saturable absorber which is opposed to the commonly used unpumped erbiumdoped fiber and this consequently contributes to the simple and short cavity design of our proposed system. The signal from the SLM fiber ring laser, which is generated by the FBG in response to external changes, such as temperature, strain, air humidity and air movement, is heterodyned with the CW signal from the TLS at a 6 GHz photodetector using a 3-dB fused coupler to generate the frequency beating. This proposed system is experimentally demonstrated as a temperature sensor and the results shows that the frequency response of the system towards the changes in temperature is about 1.3 GHz/°C, taking into account the resolution bandwidth of 3 MHz of the radio frequency spectrum analyzer (RFSA).

  9. MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay

    PubMed Central

    Nagy, Alexander; Černíková, Lenka; Vitásková, Eliška; Křivda, Vlastimil; Dán, Ádám; Dirbáková, Zuzana; Jiřincová, Helena; Procházka, Bohumír; Sedlák, Kamil; Havlíčková, Martina

    2016-01-01

    In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence. PMID:27031831

  10. Valence state partitioning of V between pyroxene-melt: Effects of pyroxene and melt composition, and direct determination of V valence states by XANES. Application to Martian basalt QUE 94201 composition

    SciTech Connect

    Karner, J.M.; Papike, J.J.; Sutton, S.R.; Shearer, C.K.; Burger, P.; McKay, G.; Le, L.

    2009-01-13

    Experiments on a Martian basalt composition show that D{sub V} augite/melt is greater than D{sub V} pigeonite/melt in samples equilibrated under the same fO{sub 2} conditions. This increase is due to the increased availability of elements for coupled substitution with the V{sup 3+} or V{sup 4+} ions, namely Al and Na. for this bulk composition, both Al and Na are higher in concentration in augite compared with pigeonite; therefore more V can enter augite than pigeonite. Direct valence state determination by XANES shows that the V{sup 3+} and V{sup 4+} are the main V species in the melt at fO{sub 2} conditions of IW-1 to IW+3.5, whereas pyroxene grains at IW-1, IW, and IW+1 contain mostly V{sup 3+}. This confirms the idea that V{sup 3+} is more compatible in pyroxene than V{sup 4+}. The Xanes data also indicates that a small percentage of V{sup 2+} may exist in melt and pyroxene at IW-1. The similar valence of V in glass and pyroxene at IW-1 suggests that V{sup 2+} and V{sup 3+} may have similar compatibilities in pyroxene.

  11. Clinical applications of esophageal impedance monitoring and high-resolution manometry.

    PubMed

    Kessing, Boudewijn F; Smout, André J P M; Bredenoord, Albert J

    2012-06-01

    Esophageal impedance monitoring and high-resolution manometry (HRM) are useful tools in the diagnostic work-up of patients with upper gastrointestinal complaints. Impedance monitoring increases the diagnostic yield for gastroesophageal reflux disease in adults and children and has become the gold standard in the diagnostic work-up of reflux symptoms. Its role in the work-up for belching disorders and rumination seems promising. HRM is superior to other diagnostic tools for the evaluation of achalasia and contributes to a more specific classification of esophageal disorders in patients with non-obstructive dysphagia. The role of HRM in patients with dysphagia after laparoscopic placement of an adjustable gastric band seems promising. Future studies will further determine the clinical implications of the new insights which have been acquired with these techniques. This review aims to describe the clinical applications of impedance monitoring and HRM. PMID:22350944

  12. Assessing spatial resolution versus sensitivity from laser speckle contrast imaging: application to frequency analysis.

    PubMed

    Bricq, Stéphanie; Mahé, Guillaume; Rousseau, David; Humeau-Heurtier, Anne; Chapeau-Blondeau, François; Varela, Julio Rojas; Abraham, Pierre

    2012-10-01

    For blood perfusion monitoring, laser speckle contrast (LSC) imaging is a recent non-contact technique that has the characteristic of delivering noise-like speckled images. To exploit LSC images for quantitative physiological measurements, we developed an approach that implements controlled spatial averaging to reduce the detrimental impact of the noise and improve measurement sensitivity. By this approach, spatial resolution and measurement sensitivity can be traded-off in a flexible way depending on the quantitative prospect of the study. As an application, detectability of the cardiac activity from LSC images of forearm using power spectrum analysis is studied through the construction of spatial activity maps offering a window on the blood flow perfusion and its regional distribution. Comparisons with results obtained with signals of laser Doppler flowmetry probes are performed. PMID:22644256

  13. Clinical Application of Esophageal High-resolution Manometry in the Diagnosis of Esophageal Motility Disorders

    PubMed Central

    van Hoeij, Froukje B; Bredenoord, Albert J

    2016-01-01

    Esophageal high-resolution manometry (HRM) is replacing conventional manometry in the clinical evaluation of patients with esophageal symptoms, especially dysphagia. The introduction of HRM gave rise to new objective metrics and recognizable patterns of esophageal motor function, requiring a new classification scheme: the Chicago classification. HRM measurements are more detailed and more easily performed compared to conventional manometry. The visual presentation of acquired data improved the analysis and interpretation of esophageal motor function. This led to a more sensitive, accurate, and objective analysis of esophageal motility. In this review we discuss how HRM changed the way we define and categorize esophageal motility disorders. Moreover, we discuss the clinical applications of HRM for each esophageal motility disorder separately. PMID:26631942

  14. Clinical Application of Esophageal High-resolution Manometry in the Diagnosis of Esophageal Motility Disorders.

    PubMed

    van Hoeij, Froukje B; Bredenoord, Albert J

    2016-01-31

    Esophageal high-resolution manometry (HRM) is replacing conventional manometry in the clinical evaluation of patients with esophageal symptoms, especially dysphagia. The introduction of HRM gave rise to new objective metrics and recognizable patterns of esophageal motor function, requiring a new classification scheme: the Chicago classification. HRM measurements are more detailed and more easily performed compared to conventional manometry. The visual presentation of acquired data improved the analysis and interpretation of esophageal motor function. This led to a more sensitive, accurate, and objective analysis of esophageal motility. In this review we discuss how HRM changed the way we define and categorize esophageal motility disorders. Moreover, we discuss the clinical applications of HRM for each esophageal motility disorder separately. PMID:26631942

  15. Application of high-resolution stereo satellite images to detailed landslide hazard assessment

    NASA Astrophysics Data System (ADS)

    Nichol, Janet E.; Shaker, Ahmed; Wong, Man-Sing

    2006-06-01

    This study investigates and demonstrates the state of the art in remote sensing techniques for detailed landslide hazard assessment applicable to large areas. Since the most common methods of landslide hazard assessment using simple inventories and weighted overlays are heavily dependent on three-dimensional terrain visualization and analysis, stereo satellite images from the IKONOS Very High Resolution (VHR) sensor are used for this study. The DEMs created from IKONOS stereo images appear to be much more accurate and sensitive to micro-scale terrain features than a DEM created from digital contour data with a 2 m contour interval. Pan-sharpened stereo IKONOS images permit interpretation of recent landslides as small as 2-3 m in width as well as relict landslides older than 50 years. A cost-benefit analysis comparing stereo air photo interpretation with stereo satellite image interpretation suggests that stereo satellite imagery is usually more cost-effective for detailed landslide hazard assessment over large areas.

  16. Efficient generalized cross-validation with applications to parametric image restoration and resolution enhancement.

    PubMed

    Nguyen, N; Milanfar, P; Golub, G

    2001-01-01

    In many image restoration/resolution enhancement applications, the blurring process, i.e., point spread function (PSF) of the imaging system, is not known or is known only to within a set of parameters. We estimate these PSF parameters for this ill-posed class of inverse problem from raw data, along with the regularization parameters required to stabilize the solution, using the generalized cross-validation method (GCV). We propose efficient approximation techniques based on the Lanczos algorithm and Gauss quadrature theory, reducing the computational complexity of the GCV. Data-driven PSF and regularization parameter estimation experiments with synthetic and real image sequences are presented to demonstrate the effectiveness and robustness of our method. PMID:18255545

  17. Application of the high-resolution Godunov method to the multi-fluid flow calculations

    NASA Astrophysics Data System (ADS)

    Bai, Jin-Song; Li, Ping; Zhang, Zhan-Ji; Hua, Jin-Song; Tan, Hua

    2004-12-01

    In this paper, we have numerically solved the multi-fluid problems using an operator-split two-step high-resolution Godunov PPM (parabolic piecewise method) for the flow in complex geometries. By using the front capturing method, the PPM integrator captures the interface in the solution process. The basic multi-fluid integrator is coupled to a Cartesian grid algorithm where a VOF (volume of fluid) representation of the fluid interface is also used. As an application of this method, we test the 2D interfacial advection example and simulate an experimental hypervelocity launcher model from Sandia National Laboratories. The computational design of the hypervelocity launcher is also given in the paper.

  18. High resolution combat simulations to support training for close combat light applications

    SciTech Connect

    Toms, R.M.; Dobbs, L.A.; Pimper, J.E.

    1990-06-14

    Superior tactical planning and maneuver synchronization are essential to fight and win on the CCL battlefield. This superiority can be achieved by the use of a combination of field exercises and high-resolution, computerized, combat simulation systems designed to support training. Computerized simulation systems provide a cost effective capability to promote learning through repetition and permit the exploration of scenarios that are impractical or dangerous to apply to live exercises. Man-in-the-loop, real-time, and force-on-force simulation systems with interactive color graphics interfaces are now available to support CCL training. Combat simulations have been developed specifically for this environment within the Conflict Simulation Laboratory (CSL) at the Lawrence Livermore National Laboratory (LLNL). Research and development efforts are underway that will greatly improve these capabilities. Applications are envisioned in training support, mission planning, analysis of new tactics and weapons, real-time display, and real-time operational support. 32 refs.

  19. High resolution remote sensing image processing technology and its application to uranium geology

    NASA Astrophysics Data System (ADS)

    Zhang, Jie-lin

    2008-12-01

    Hyperspectral and high spatial resolution remote sensing technology take important role in uranium geological application, data mining and knowledge discovery methods are key to character spectral and spatial information of uranium mineralization factors. Based on curvelet transform algorithm, this paper developed the image fusion technology of hyperspectral (Hyperion) and high spatial data (SPOT5), and results demonstrated that fusion image had advantage in denoising, enhancing and information identification. Used discrete wavelet transform, the spectral parameters of uranium mineralization factors were acquired, the spectral identification pedigrees of typical quadrivalence and hexavalence uranium minerals were established. Furthermore, utilizing hyperspectral remote sensing observation technology, this paper developed hyperspectral logging of drill cores and trench, it can quickly processed lots of geological and spectral information, and the relationship between radioactive intensity and abnormal spectral characteristics of Fe3+ was established. All those provided remote sensing technical bases to uranium geology, and the better results have been achieved in Taoshan uranium deposits in south China.

  20. Stabilizing Crystal Oscillators With Melting Metals

    NASA Technical Reports Server (NTRS)

    Stephens, J. B.; Miller, C. G.

    1984-01-01

    Heat of fusion provides extended period of constant temperature and frequency. Crystal surrounded by metal in spherical container. As outside temperature rises to melting point of metal, metal starts to liquefy; but temperature stays at melting point until no solid metal remains. Potential terrestrial applications include low-power environmental telemetering transmitters and instrumentation transmitters for industrial processes.

  1. Influences of composition, melt viscosity and crystallization on the color strength and stability of multioxide glass frit/zircon-vanadium pigment systems for ceramic whitewares coatings applications

    NASA Astrophysics Data System (ADS)

    Earl, David Alonzo

    Color control is becoming increasingly important in the industrial processing of ceramics coatings. Multi-oxide glass frits are the predominant materials in ceramic whitewares coatings, and zircon doped pigments are the most commonly used colorants. The primary objective of this research was to determine if glass frits could be formulated to improve the fired color strength and high-temperature stability of ceramic coatings colored with zircon-vanadium (Zr-V) blue pigments. The results would also be applicable to other ceramic pigments that utilize the same zircon structure to incorporate colorant metal ions. A secondary goal was to relate the frit oxide composition, pigment content, firing temperature, melt viscosity and microstructural development to the fired color. A ceramic tile process was applied to fabricate sample coatings for the study. A coating's color was quantified and related to human perception with CIE L*, a* and b* values and pigment absorption factors (K/S), calculated based on spectral reflectance data. The research was successful in quantifying the influence of individual glass frit oxides on the fired color strength and high-temperature stability of the coatings. Opaque and transparent glossy frit compositions which yield excellent color strength and stability were formulated. Mathematical models for predicting a coating's color strength and stability given the frit oxide composition, Zr-V pigment loading and peak firing temperature were derived. Frit oxides of ZrO2, SrO, ZnO, Al2O3, Na 2O and K2O were found to have a significant influence on crystallization, pigment dissolution and color development. The properties, sizes, morphologies and quantities of crystalline phases that precipitated in the coatings during firing were related to the color. A technique for producing uniquely light yet high chroma colors through control of zircon precipitate particle size was demonstrated. In addition, a statistical model was developed for calculating the

  2. Methods for Melting Temperature Calculation

    NASA Astrophysics Data System (ADS)

    Hong, Qi-Jun

    Melting temperature calculation has important applications in the theoretical study of phase diagrams and computational materials screenings. In this thesis, we present two new methods, i.e., the improved Widom's particle insertion method and the small-cell coexistence method, which we developed in order to capture melting temperatures both accurately and quickly. We propose a scheme that drastically improves the efficiency of Widom's particle insertion method by efficiently sampling cavities while calculating the integrals providing the chemical potentials of a physical system. This idea enables us to calculate chemical potentials of liquids directly from first-principles without the help of any reference system, which is necessary in the commonly used thermodynamic integration method. As an example, we apply our scheme, combined with the density functional formalism, to the calculation of the chemical potential of liquid copper. The calculated chemical potential is further used to locate the melting temperature. The calculated results closely agree with experiments. We propose the small-cell coexistence method based on the statistical analysis of small-size coexistence MD simulations. It eliminates the risk of a metastable superheated solid in the fast-heating method, while also significantly reducing the computer cost relative to the traditional large-scale coexistence method. Using empirical potentials, we validate the method and systematically study the finite-size effect on the calculated melting points. The method converges to the exact result in the limit of a large system size. An accuracy within 100 K in melting temperature is usually achieved when the simulation contains more than 100 atoms. DFT examples of Tantalum, high-pressure Sodium, and ionic material NaCl are shown to demonstrate the accuracy and flexibility of the method in its practical applications. The method serves as a promising approach for large-scale automated material screening in which

  3. Modeling of DFT quality neural network potential for sodium clusters: Application to melting of sodium clusters (Na20 to Na40)

    NASA Astrophysics Data System (ADS)

    Chiriki, Siva; Bulusu, Satya S.

    2016-05-01

    The present work demonstrates the use of computationally inexpensive neural network (NN) potential for studying global optimizations and phase transitions in small to medium sized sodium clusters with DFT accuracy. Accuracy of NN potential has been tested by performing global optimizations in the size range of 16-40 atoms. We performed Monte Carlo (MC) simulations using NN potential to study the melting behaviour. Melting study in the size range of 20-40 atoms shows a characteristic premelting peak and a main melting peak. Our results using NN potentials support the idea of stepwise melting in small Na clusters (Aguado, 2011).

  4. Variable high-resolution color CCD camera system with online capability for professional photo studio application

    NASA Astrophysics Data System (ADS)

    Breitfelder, Stefan; Reichel, Frank R.; Gaertner, Ernst; Hacker, Erich J.; Cappellaro, Markus; Rudolf, Peter; Voelk, Ute

    1998-04-01

    Digital cameras are of increasing significance for professional applications in photo studios where fashion, portrait, product and catalog photographs or advertising photos of high quality have to be taken. The eyelike is a digital camera system which has been developed for such applications. It is capable of working online with high frame rates and images of full sensor size and it provides a resolution that can be varied between 2048 by 2048 and 6144 by 6144 pixel at a RGB color depth of 12 Bit per channel with an also variable exposure time of 1/60s to 1s. With an exposure time of 100 ms digitization takes approx. 2 seconds for an image of 2048 by 2048 pixels (12 Mbyte), 8 seconds for the image of 4096 by 4096 pixels (48 Mbyte) and 40 seconds for the image of 6144 by 6144 pixels (108 MByte). The eyelike can be used in various configurations. Used as a camera body most commercial lenses can be connected to the camera via existing lens adaptors. On the other hand the eyelike can be used as a back to most commercial 4' by 5' view cameras. This paper describes the eyelike camera concept with the essential system components. The article finishes with a description of the software, which is needed to bring the high quality of the camera to the user.

  5. Multivariate curve resolution for hyperspectral image analysis :applications to microarray technology.

    SciTech Connect

    Van Benthem, Mark Hilary; Sinclair, Michael B.; Haaland, David Michael; Martinez, M. Juanita (University of New Mexico, Albuquerque, NM); Timlin, Jerilyn Ann; Werner-Washburne, Margaret C. (University of New Mexico, Albuquerque, NM); Aragon, Anthony D. (University of New Mexico, Albuquerque, NM)

    2003-01-01

    Multivariate curve resolution (MCR) using constrained alternating least squares algorithms represents a powerful analysis capability for a quantitative analysis of hyperspectral image data. We will demonstrate the application of MCR using data from a new hyperspectral fluorescence imaging microarray scanner for monitoring gene expression in cells from thousands of genes on the array. The new scanner collects the entire fluorescence spectrum from each pixel of the scanned microarray. Application of MCR with nonnegativity and equality constraints reveals several sources of undesired fluorescence that emit in the same wavelength range as the reporter fluorphores. MCR analysis of the hyperspectral images confirms that one of the sources of fluorescence is due to contaminant fluorescence under the printed DNA spots that is spot localized. Thus, traditional background subtraction methods used with data collected from the current commercial microarray scanners will lead to errors in determining the relative expression of low-expressed genes. With the new scanner and MCR analysis, we generate relative concentration maps of the background, impurity, and fluorescent labels over the entire image. Since the concentration maps of the fluorescent labels are relatively unaffected by the presence of background and impurity emissions, the accuracy and useful dynamic range of the gene expression data are both greatly improved over those obtained by commercial microarray scanners.

  6. Applications and Advancements in the use of High-Resolution Microendoscopy for Detection of Gastrointestinal Neoplasia

    PubMed Central

    Louie, Justin S.; Richards-Kortum, Rebecca; Anandasabapathy, Sharmila

    2014-01-01

    The high-resolution microendoscope (HRME) is a novel imaging modality that allows real-time epithelial imaging at subcellular resolution. Used in concert with any standard endoscope, this portable, low cost, ‘optical biopsy’ technology has the ability to provide images of cellular morphology during a procedure. This technology has been the subject of a number of studies investigating its use in screening and surveillance of a range of gastrointestinal neoplasia, including esophageal adenocarcinoma(EAC), esophageal squamous cell cancer(ESCC), colorectal neoplasia(CRC) and anal neoplasia. These studies have shown that HRME is a modality that consistently provides high specificity, negative predictive value, and accuracy across different diseases. In addition, they have illustrated that HRME users can be relatively easily trained in a short period of time and that users have demonstrated solid inter-rater reliability. These features make HRME a potential complement to high definition white light imaging, narrow band imaging and other ‘red flag technologies’ in facilitating real-time clinical diagnosis, endoscopic therapy and margin determination. Further clinical validation is needed to determine whether this translates to reduced procedure times, pathology costs, and follow up procedures. Finally, the HRME has a relatively simple design compared to other similar technologies, making it portable, simple to maintain, and low cost. This may allow the HRME device to function in both advanced care settings as well as in places with less resources and specialized support systems. As a whole, the HRME device has shown good performance along with low-cost and portable construction, and its application in different conditions and settings has been promising. PMID:25108219

  7. Validation of High Resolution Melting Analysis (HRM) of the Amplified ITS2 Region for the Detection and Identification of Yeasts from Clinical Samples: Comparison with Culture and MALDI-TOF Based Identification

    PubMed Central

    Duyvejonck, Hans; Cools, Piet; Decruyenaere, Johan; Roelens, Kristien; Noens, Lucien; Vermeulen, Stefan; Claeys, Geert; Decat, Ellen; Van Mechelen, Els; Vaneechoutte, Mario

    2015-01-01

    Aim Candida species are known as opportunistic pathogens, and a possible cause of invasive infections. Because of their species-specific antimycotic resistance patterns, reliable techniques for their detection, quantification and identification are needed. We validated a DNA amplification method for direct detection of Candida spp. from clinical samples, namely the ITS2-High Resolution Melting Analysis (direct method), by comparing it with a culture and MALDI-TOF Mass Spectrometry based method (indirect method) to establish the presence of Candida species in three different types of clinical samples. Materials and Methods A total of 347 clinical samples, i.e. throat swabs, rectal swabs and vaginal swabs, were collected from the gynaecology/obstetrics, intensive care and haematology wards at the Ghent University Hospital, Belgium. For the direct method, ITS2-HRM was preceded by NucliSENS easyMAG DNA extraction, directly on the clinical samples. For the indirect method, clinical samples were cultured on Candida ID and individual colonies were identified by MALDI-TOF. Results For 83.9% of the samples there was complete concordance between both techniques, i.e. the same Candida species were detected in 31.1% of the samples or no Candida species were detected in 52.8% of the samples. In 16.1% of the clinical samples, discrepant results were obtained, of which only 6.01% were considered as major discrepancies. Discrepancies occurred mostly when overall numbers of Candida cells in the samples were low and/or when multiple species were present in the sample. Discussion Most of the discrepancies could be decided in the advantage of the direct method. This is due to samples in which no yeast could be cultured whereas low amounts could be detected by the direct method and to samples in which high quantities of Candida robusta according to ITS2-HRM were missed by culture on Candida ID agar. It remains to be decided whether the diagnostic advantages of the direct method

  8. AB161. High resolution melting analysis of buccal DNA revealed a significant association between UGT1A1 c.211G>A and neonatal hyperbilirubinemia development in Malay population

    PubMed Central

    Cheung, Tian Pei; Van Rostenberghe, Hans; Ismail, Rosliza; Nawawi, Noor Namirah; Abdullah, Nurul Amierah; Ramli, Noraida; Ibrahim, Nor Rosidah; Hj Abd Majid, Noorizan; Mohd Yusoff, Narazah; Nishio, Hisahide; Yusoff, Surini

    2015-01-01

    Background Severe neonatal hyperbilirubinemia or neonatal jaundice (NNJ) characterised by an elevated total serum bilirubin (TSB) level may result in kernicterus or even death. Uridine diphosphate glucuronosyltransferase 1A1 (UGT1A1) is the key enzyme which conjugates bilirubin with glucuronic acid for the subsequent bilirubin excretion. Conversely, constitutive androstane receptor (CAR), encoded by nuclear receptor subfamily 1, group I, member 3 (NR1I3) gene, regulates bilirubin excretion by activating the components of the bilirubin clearance pathway. Thus, genetic variants in UGT1A1 and NR1I3 genes may modulate bilirubin excretion and lead to NNJ. This study aimed to determine the association between UGT1A1 and NR1I3 genetic variants and NNJ development in Malay population by genotyping the DNA isolated from buccal swabs. The accuracy and reliability of the genotyping results produced by buccal DNA was also compared with that of the whole blood DNA. Methods Buccal swabs were collected from 232 hyperbilirubinemia and 232 non-hyperbilirubinemia newborns admitted to and/or born in Hospital Universiti Sains Malaysia (HUSM). Hyperbilirubinemia subjects were those with TSB levels ≥250 µmol/L within the first week after birth while non-hyperbilirubinemia subjects were newborns without significant hyperbilirubinemia. The UGT1A1 (c.211G>A) and NR1I3 [MPJ6_1I3008 (G>A), IVS8+116T>G and 540A>G] variants were genotyped by using high resolution melting (HRM) analysis. Binary logistic regression was used to assess the association between variant genotypes and risk of NNJ. Whole blood samples were also collected from 60 subjects and genotyped to compare the HRM genotyping results with that of the buccal swabs. Results When compared with wild-type genotype, both heterozygous and homozygous variant genotypes of MPJ6_1I3008 (G>A), IVS8+116T>G and 540A>G were not significantly associated with NNJ. However, the heterozygous genotype (GA) of c.211G>A was found to increase the

  9. Sierra Nevada snow melt from SMS-2

    NASA Technical Reports Server (NTRS)

    Breaker, L. C.; Mcmillan, M. C.

    1975-01-01

    A film loop from SMS-2 imagery shows snow melt over the Sierra Nevadas from May 10 to July 8, 1975. The sequence indicates a successful application of geostationary satellite data for monitoring dynamic hydrologic conditions.

  10. UT-CT: A National Resource for Applications of High-Resolution X-ray Computed Tomography in the Geological Sciences

    NASA Astrophysics Data System (ADS)

    Carlson, W. D.; Ketcham, R. A.; Rowe, T. B.

    2002-12-01

    An NSF-sponsored (EAR-IF) shared multi-user facility dedicated to research applications of high-resolution X-ray computed tomography (CT) in the geological sciences has been in operation since 1997 at the University of Texas at Austin. The centerpiece of the facility is an industrial CT scanner custom-designed for geological applications. Because the instrument can optimize trade-offs among penetrating ability, spatial resolution, density discrimination, imaging modes, and scan times, it can image a very broad range of geological specimens and materials, and thus offers significant advantages over medical scanners and desktop microtomographs. Two tungsten-target X-ray sources (200-kV microfocal and 420-kV) and three X-ray detectors (image-intensifier, high-sensitivity cadmium tungstate linear array, and high-resolution gadolinium-oxysulfide radiographic line scanner) can be used in various combinations to meet specific imaging goals. Further flexibility is provided by multiple imaging modes: second-generation (translate-rotate), third-generation (rotate-only; centered and variably offset), and cone-beam (volume CT). The instrument can accommodate specimens as small as about 1 mm on a side, and as large as 0.5 m in diameter and 1.5 m tall. Applications in petrology and structural geology include measuring crystal sizes and locations to identify mechanisms governing the kinetics of metamorphic reactions; visualizing relationships between alteration zones and abundant macrodiamonds in Siberian eclogites to elucidate metasomatic processes in the mantle; characterizing morphologies of spiral inclusion trails in garnet to test hypotheses of porphyroblast rotation during growth; measuring vesicle size distributions in basaltic flows for determination of elevation at the time of eruption to constrain timing and rates of continental uplift; analysis of the geometry, connectivity, and tortuosity of migmatite leucosomes to define the topology of melt flow paths, for numerical

  11. Improving the Transparency of Ultra-Drawn Melt-Crystallized Polyethylenes: Toward High-Modulus/High-Strength Window Application.

    PubMed

    Shen, Lihua; Nickmans, Koen; Severn, John; Bastiaansen, Cees W M

    2016-07-13

    Highly transparent, ultradrawn high-density polyethylene (HDPE) films were successfully prepared using compression molding and solid-state drawing techniques. The low optical transmittance (<50%) of the pure drawn HDPE films can be drastically improved (>90%) by incorporating a small amount (>1 wt %/wt) of specific additives to HDPE materials prior to drawing. It is shown that additives with relatively high refractive index result in an increased optical transmittance in the visible light wavelength which illustrates that the improvement in optical characteristics probably originates from refractive index matching between the crystalline and noncrystalline regions in the drawn films. Moreover, the optically transparent drawn HDPE films containing additives maintain their physical and mechanical properties, especially their high modulus and high strength, which make these films potentially useful in a variety of applications, such as high-impact windows. PMID:27314927

  12. A high-resolution and one-cycle conversion time-to-digital converter architecture for PET image applications.

    PubMed

    Sheng, Duo; Chung, Ching-Che; Huang, Chih-Chung; Jian, Jia-Wei

    2013-01-01

    In this paper, a high-resolution and one-cycle conversion time-to-digital converter (TDC) architecture with cell-based design for positron emission tomography (PET) applications is presented. The proposed TDC employs a cascade-stage structure to achieve high timing resolution and wide sampling range at the same time. Besides, based on the proposed two-level conversion structure, the proposed TDC not only can achieve single cycle latency and high speed of operation, but also have low circuit complexity as compared with conventional approaches. Simulation results show that operation frequency of the proposed TDC can be improved to 200 MHz with 50 ps resolution. In addition, the proposed TDC can be implemented with standard cells, making it easily portable to different processes and very suitable for biomedical chip applications. PMID:24110225

  13. LPE grown LSO:Tb scintillator films for high-resolution X-ray imaging applications at synchrotron light sources

    NASA Astrophysics Data System (ADS)

    Cecilia, A.; Rack, A.; Douissard, P.-A.; Martin, T.; Dos Santos Rolo, T.; Vagovič, P.; Hamann, E.; van de Kamp, T.; Riedel, A.; Fiederle, M.; Baumbach, T.

    2011-08-01

    Within the project ScinTAX of the 6th framework program (FP6) of the European Commission (SCINTAX—STRP 033 427) we have developed a new thin single crystal scintillator for high-resolution X-ray imaging. The scintillator is based on a Tb-doped Lu2SiO5 (LSO) film epitaxially grown on an adapted substrate. The high density, effective atomic number and light yield of the scintillating LSO significantly improves the efficiency of the X-ray imaging detectors currently used in synchrotron micro-imaging applications. In this work we present the characterization of the scintillating LSO films in terms of their spatial resolution performance and we provide two examples of high spatial and high temporal resolution applications.

  14. 'Structure-from-Motion': a high resolution, low-cost photogrammetric tool for geoscience applications

    NASA Astrophysics Data System (ADS)

    Westoby, M. J.; Glasser, N. F.; Brasington, J.; Hambrey, M.; Reynolds, J. M.

    2011-12-01

    Presently, the majority of methods capable of surveying, at high resolution, often complex landforms and landscapes are accompanied by high costs and difficult portability. Furthermore, the relative remoteness and inaccessibility of many field sites renders these approaches impractical. The 'Structure-from-Motion' (SfM) method operates under the same basic assumption of stereoscopic photogrammetry, namely that 3D structure can be resolved from two or more overlapping, offset images. Using only a consumer-grade digital camera and a network of ground control targets, the user moves through the environment, acquiring photographs of the feature or area of interest from as many locations and perspectives as possible. Freely-available, automated feature extraction and bundle adjustment software is used to reconstruct scene geometry. Results from example applications of the technique to two moraine dam complexes in the Nepal Himalaya will be presented. Both sites have produced catastrophic glacial lake outburst floods, and as a result possess impressive breaches through their moraine dams. DTMs of the moraine complexes were constructed, facilitating the extraction of precise metric data pertaining to breach dimensions, volumes of released water from the lake basin, and amounts of material removed from the moraine complexes during the outburst. Such data are invaluable for detailed hydrodynamic modelling and subsequent hazard assessments. To conclude, SfM output will be directly compared with that obtained from a Terrestrial Laser Scanning system.

  15. Development of high-resolution cathodoluminescence system for STEM and application to plasmonic nanostructures.

    PubMed

    Yamamoto, Naoki

    2016-08-01

    A high-resolution cathodoluminescence (CL) system for scanning transmission electron microscope (STEM) has been developed by employing a field emission gun and a spherical aberration corrector, which realizes a probe size of 1 nm even at an accelerating voltage of 80 kV and beam current of the order of 1 nA. Angle resolved measurement of light emission from a sample in the STEM is possible by combining a parabolic mirror and position-controlled pinhole. CL spectra are successively acquired by a highly sensitive charge-coupled device while scanning the incident electron beam or pinhole, which enables various detection modes, i.e. (i) angle resolved spectral pattern, (ii) beam scan spectral image and (iii) photon map. In order to calibrate the acquired spectrum, the correction function is created from the comparison between the observed and theoretical spectra of the transition radiation. Furthermore, the modification of polarization by the parabolic mirror is discussed. Some examples of the applications of the STEM-CL system to plasmonics are presented to demonstrate the unique measurement features of the CL system, i.e. (i) multipole modes in silver nanoparticles, (ii) surface plasmon polariton modes in a 2D plasmonic crystal and (iii) localized surface plasmon modes in a gold bow tie nano-antenna. PMID:27473259

  16. Trace element mineral/melt partitioning for basaltic and basaltic andesitic melts: An experimental and laser ICP-MS study with application to the oxidation state of mantle source regions

    NASA Astrophysics Data System (ADS)

    Laubier, Muriel; Grove, Timothy L.; Langmuir, Charles H.

    2014-04-01

    Understanding magmatic processes such as crystallization and melting recorded in natural samples requires calibration of mineral-melt trace element partition coefficients (D) and their dependence on temperature, pressure, oxygen fugacity (fO2) and chemical composition. However, few experimental studies have focused on measuring trace element partition coefficients for a large number of trace elements, in the various minerals present in basaltic rocks, and under diverse conditions, particularly of variable fO2. Twenty-seven 0.1 MPa experiments provide partition coefficients for major elements and Sc, Ti, V, Mn, Co, Ni, Ga, Sr, Y, Nb, Ba, Ce, Nd, Eu, Gd, and Yb for the mineral phases olivine, plagioclase, orthopyroxene and clinopyroxene. The experimental conditions range from 1150 to 1190 °C with oxygen fugacities from QFM to NNO+2. Run products were analyzed by laser-ablation ICP-MS. The new partition coefficients, combined with previously published data, can be used to model crystallization processes at low pressure. Partitioning of multivalent cations V, Fe and Eu varies as a function of the redox conditions, consistent with previous work, and can be used to constrain oxidation states of magmatic source regions. The V/Yb ratio is shown to be a useful proxy for oxidation state. The V/Yb ratio varies during mantle melting as a function of oxidation state of the mantle source, and it is not modified during fractional crystallization of olivine ± plag ± cpx. V/Yb increases from MORB, BABB to arc lavas, suggesting a progressive increase of fO2 from QFM to NNO+2. Apparent fO2 of arc lavas, however, is quite variable. These results demonstrate that sub-arc mantle displays a larger range of redox conditions toward a more oxidized mantle than the MORB mantle.

  17. Investigation on the microstructure, mechanical property and corrosion behavior of the selective laser melted CoCrW alloy for dental application.

    PubMed

    Lu, Yanjin; Wu, Songquan; Gan, Yiliang; Li, Junlei; Zhao, Chaoqian; Zhuo, Dongxian; Lin, Jinxin

    2015-04-01

    In this study, an experimental investigation on fabricating Ni-free CoCrW alloys by selective laser melting (SLM) for dental application was conducted in terms of microstructure, hardness, mechanical property, electrochemical behavior, and metal release; and line and island scanning strategy were applied to determine whether these strategies are able to obtain expected CoCrW parts. The XRD revealed that the γ-phase and ε-phase coexisted in the as-SLM CoCrW alloys; The OM and SEM images showed that the microstructure of CoCrW alloys appeared square-like pattern with the fine cellular dendrites at the borders; tensile test suggested that the difference of mechanical properties of line- and island-formed specimens was very small; whilst the outcomes from the electrochemical and metal release tests indicated that the island-formed alloys showed slightly better corrosion resistance than line-formed ones in PBS and Hanks solutions. Considering that the mechanical properties and corrosion resistance of line-formed and island-formed specimens meet the standards of ISO 22674:2006 and EN ISO 10271, CoCrW dental alloys can be successfully fabricated by line and island scanning strategies in the SLM process. PMID:25686979

  18. Selective Laser Melting: a regular unit cell approach for the manufacture of porous, titanium, bone in-growth constructs, suitable for orthopedic applications.

    PubMed

    Mullen, Lewis; Stamp, Robin C; Brooks, Wesley K; Jones, Eric; Sutcliffe, Christopher J

    2009-05-01

    In this study, a novel porous titanium structure for the purpose of bone in-growth has been designed, manufactured and evaluated. The structure was produced by Selective Laser Melting (SLM); a rapid manufacturing process capable of producing highly intricate, functionally graded parts. The technique described utilizes an approach based on a defined regular unit cell to design and produce structures with a large range of both physical and mechanical properties. These properties can be tailored to suit specific requirements; in particular, functionally graded structures with bone in-growth surfaces exhibiting properties comparable to those of human bone have been manufactured. The structures were manufactured and characterized by unit cell size, strand diameter, porosity, and compression strength. They exhibited a porosity (10-95%) dependant compression strength (0.5-350 Mpa) comparable to the typical naturally occurring range. It is also demonstrated that optimized structures have been produced that possesses ideal qualities for bone in-growth applications and that these structures can be applied in the production of orthopedic devices. PMID:18837456

  19. Preparation of three-dimensional nanoporous Si using dealloying by metallic melt and application as a lithium-ion rechargeable battery negative electrode

    NASA Astrophysics Data System (ADS)

    Wada, Takeshi; Yamada, Junpei; Kato, Hidemi

    2016-02-01

    Silicon is a promising material for negative electrode in Li-ion batteries because of high gravimetric capacity. A Si nanomaterial that can accommodate volume expansion accompanied by lithiation is needed for practical application in Li-ion batteries. We prepare three-dimensional nanoporous interconnected silicon material with controlled pore and ligament sizes by dealloying using an Mg-Si precursor and Bi melt. The Mg atoms in the precursor selectively dissolve into Bi, and the remaining Si atoms self-organize into a nanoporous structure with characteristic length ranging from several ten to hundred nanometer. The Li-ion battery electrodes made from nanoporous silicon exhibit higher capacities, increased cycle lives, and improved rate performances compared with those made from commercial Si nanoparticles. Measurements on the electrical resistivity and electrode thickness change by lithiation/delithiation suggest that the superior performance of nanoporous Si electrode originates from the following: (1) The nanoporous Si has much lower electrical resistivity compared with that of the nanoparticle Si owing to the n-type dopant incorporated during dealloying. (2) The nanoporous Si-based electrode has higher porosity owing to the presence of intra-particle pores, which can accommodate Si expansion up to higher levels of lithiation.

  20. A Honeycomb-Structured Ti-6Al-4V Oil-Gas Separation Rotor Additively Manufactured by Selective Electron Beam Melting for Aero-engine Applications

    NASA Astrophysics Data System (ADS)

    Tang, H. P.; Wang, Q. B.; Yang, G. Y.; Gu, J.; Liu, N.; Jia, L.; Qian, M.

    2016-03-01

    Oil -gas separation is a key process in an aero-engine lubrication system. This study reports an innovative development in oil -gas separation. A honeycomb-structured rotor with hexagonal cone-shaped pore channels has been designed, additively manufactured from Ti-6Al-4V using selective electron beam melting (SEBM) and assessed for oil -gas separation for aero-engine application. The Ti-6Al-4V honeycomb structure showed a high compressive strength of 110 MPa compared to less than 20 MPa for metal foam structures. The oil -gas separation efficiency of the honeycomb-structured separation rotor achieved 99.8% at the rotation speed of 6000 rpm with much lower ventilation resistance (17.3 kPa) than that of the separator rotor constructed using a Ni-Cr alloy foam structure (23.5 kPa). The honeycomb-structured Ti-6Al-4V separator rotor produced by SEBM provides a promising solution to more efficient oil -gas separation in the aero-engine lubrication system.

  1. A multi-resolution method for climate system modeling: application of Spherical Centroidal A multi-resolution method for climate system modeling: Application of Spherical Centroidal Voroni Tessellations

    SciTech Connect

    Ringler, Todd D; Gunzburger, Max; Ju, Lili

    2008-01-01

    During the next decade and beyond, climate system models will be challenged to resolve scales and processes that are far beyond their current scope. Each climate system component has its prototypical example of an unresolved process that may strongly influence the global climate system, ranging from eddy activity within ocean models, to ice streams within ice sheet models, to surface hydrological processes within land system models, to cloud processes within atmosphere models. These new demands will almost certainly result in the develop of multi-resolution schemes that are able, at least regional to faithfully simulate these fine-scale processes. Spherical Centroidal Voronoi Tessellations (SCVTs) offer one potential path toward the development of robust, multi-resolution climate system component models, SCVTs allow for the generation of high quality Voronoi diagrams and Delaunay triangulations through the use of an intuitive, user-defined density function, each of the examples provided, this method results in high-quality meshes where the quality measures are guaranteed to improve as the number of nodes is increased. Real-world examples are developed for the Greenland ice sheet and the North Atlantic ocean. Idealized examples are developed for ocean-ice shelf interaction and for regional atmospheric modeling. In addition to defining, developing and exhibiting SCVTs, we pair this mesh generation technique with a previously developed finite-volume method. Our numerical example is based on the nonlinear shallow-water equations spanning the entire surface of the sphere. This example is used to elucidate both the potential benefits of this multi-resolution method and the challenges ahead.

  2. A partial melting study of an ordinary (H) chondrite composition with application to the unique achondrite Graves Nunataks 06128 and 06129

    NASA Astrophysics Data System (ADS)

    Usui, Tomohiro; Jones, John H.; Mittlefehldt, David W.

    2015-04-01

    Melting experiments of a synthesized, alkali-bearing, H-chondrite composition were conducted at ambient pressure with three distinct oxygen fugacity conditions (IW-1, IW, and IW+2). Oxygen fugacity conditions significantly influence the compositions of partial melts. Partial melts at IW-1 are distinctly enriched in SiO2 relative to those of IW and IW+2 melts. The silica-enriched, reduced (IW-1) melts are characterized by high alkali contents and have silica-oversaturated compositions. In contrast, the silica-depleted, oxidized (≥IW) melts, which are also enriched in alkali contents, have distinctly silica-undersaturated compositions. These experimental results suggest that alkali-rich, felsic, asteroidal crusts as represented by paired achondrites Graves Nunataks 06128 and 06129 should originate from a low-degree, relatively reduced partial melt from a parent body having near-chondritic compositions. Based on recent chronological constraints and numerical considerations as well as our experimental results, we propose that such felsic magmatism should have occurred in a parent body that is smaller in size and commenced accreting later than those highly differentiated asteroids having basaltic crusts and metallic cores.

  3. Finding the best resolution for the Kingman-Tajima coalescent: theory and applications.

    PubMed

    Sainudiin, Raazesh; Stadler, Tanja; Véber, Amandine

    2015-05-01

    Many summary statistics currently used in population genetics and in phylogenetics depend only on a rather coarse resolution of the underlying tree (the number of extant lineages, for example). Hence, for computational purposes, working directly on these resolutions appears to be much more efficient. However, this approach seems to have been overlooked in the past. In this paper, we describe six different resolutions of the Kingman-Tajima coalescent together with the corresponding Markov chains, which are essential for inference methods. Two of the resolutions are the well-known n-coalescent and the lineage death process due to Kingman. Two other resolutions were mentioned by Kingman and Tajima, but never explicitly formalized. Another two resolutions are novel, and complete the picture of a multi-resolution coalescent. For all of them, we provide the forward and backward transition probabilities, the probability of visiting a given state as well as the probability of a given realization of the full Markov chain. We also provide a description of the state-space that highlights the computational gain obtained by working with lower-resolution objects. Finally, we give several examples of summary statistics that depend on a coarser resolution of Kingman's coalescent, on which simulations are usually based. PMID:24825079

  4. Cloud screening and melt water detection over melting sea ice using AATSR/SLSTR

    NASA Astrophysics Data System (ADS)

    Istomina, Larysa; Heygster, Georg

    2014-05-01

    With the onset of melt in the Arctic Ocean, the fraction of melt water on sea ice, the melt pond fraction, increases. The consequences are: the reduced albedo of sea ice, increased transmittance of sea ice and affected heat balance of the system with more heat passing through the ice into the ocean, which facilitates further melting. The onset of melt, duration of melt season and melt pond fraction are good indicators of the climate state of the Arctic and its change. In the absence of reliable sea ice thickness retrievals in summer, melt pond fraction retrieval from satellite is in demand as input for GCM as an indicator of melt state of the sea ice. The retrieval of melt pond fraction with a moderate resolution radiometer as AATSR is, however, a non-trivial task due to a variety of subpixel surface types with very different optical properties, which give non-unique combinations if mixed. In this work this has been solved by employing additional information on the surface and air temperature of the pixel. In the current work, a concept of melt pond detection on sea ice is presented. The basis of the retrieval is the sensitivity of AATSR reflectance channels 550nm and 860nm to the amount of melt water on sea ice. The retrieval features extensive usage of a database of in situ surface albedo spectra. A tree of decisions is employed to select the feasible family of in situ spectra for the retrieval, depending on the melt stage of the surface. Reanalysis air temperature at the surface and brightness temperature measured by the satellite sensor are analyzed in order to evaluate the melting status of the surface. Case studies for FYI and MYI show plausible retrieved melt pond fractions, characteristic for both of the ice types. The developed retrieval can be used to process the historical AATSR (2002-2012) dataset, as well as for the SLSTR sensor onboard the future Sentinel-3 mission (scheduled for launch in 2015), to keep the continuity and obtain longer time sequence

  5. Application of high resolution images from unmanned aerial vehicles for hydrology and rangeland science

    NASA Astrophysics Data System (ADS)

    Rango, A.; Vivoni, E. R.; Anderson, C. A.; Perini, N. A.; Saripalli, S.; Laliberte, A.

    2012-12-01

    A common problem in many natural resource disciplines is the lack of high-enough spatial resolution images that can be used for monitoring and modeling purposes. Advances have been made in the utilization of Unmanned Aerial Vehicles (UAVs) in hydrology and rangeland science. By utilizing low flight altitudes and velocities, UAVs are able to produce high resolution (5 cm) images as well as stereo coverage (with 75% forward overlap and 40% sidelap) to extract digital elevation models (DEM). Another advantage of flying at low altitude is that the potential problems of atmospheric haze obscuration are eliminated. Both small fixed-wing and rotary-wing aircraft have been used in our experiments over two rangeland areas in the Jornada Experimental Range in southern New Mexico and the Santa Rita Experimental Range in southern Arizona. The fixed-wing UAV has a digital camera in the wing and six-band multispectral camera in the nose, while the rotary-wing UAV carries a digital camera as payload. Because we have been acquiring imagery for several years, there are now > 31,000 photos at one of the study sites, and 177 mosaics over rangeland areas have been constructed. Using the DEM obtained from the imagery we have determined the actual catchment areas of three watersheds and compared these to previous estimates. At one site, the UAV-derived watershed area is 4.67 ha which is 22% smaller compared to a manual survey using a GPS unit obtained several years ago. This difference can be significant in constructing a watershed model of the site. From a vegetation species classification, we also determined that two of the shrub types in this small watershed(mesquite and creosote with 6.47 % and 5.82% cover, respectively) grow in similar locations(flat upland areas with deep soils), whereas the most predominant shrub(mariola with 11.9% cover) inhabits hillslopes near stream channels(with steep shallow soils). The positioning of these individual shrubs throughout the catchment using

  6. Melt containment member

    SciTech Connect

    Rieken, Joel R.; Heidloff, Andrew J.

    2014-09-09

    A tubular melt containment member for transient containment of molten metals and alloys, especially reactive metals and alloys, includes a melt-contacting layer or region that comprises an oxygen-deficient rare earth oxide material that is less reactive as compared to the counterpart stoichiometric rare earth oxide. The oxygen-deficient (sub-stoichiometric) rare earth oxide can comprise oxygen-deficient yttria represented by Y.sub.2O.sub.3-x wherein x is from 0.01 to 0.1. Use of the oxygen-deficient rare earth oxide as the melt-contacting layer or region material reduces reaction with the melt for a given melt temperature and melt contact time.

  7. Nanotexturing of surfaces to reduce melting point.

    SciTech Connect

    Garcia, Ernest J.; Zubia, David; Mireles, Jose; Marquez, Noel; Quinones, Stella

    2011-11-01

    This investigation examined the use of nano-patterned structures on Silicon-on-Insulator (SOI) material to reduce the bulk material melting point (1414 C). It has been found that sharp-tipped and other similar structures have a propensity to move to the lower energy states of spherical structures and as a result exhibit lower melting points than the bulk material. Such a reduction of the melting point would offer a number of interesting opportunities for bonding in microsystems packaging applications. Nano patterning process capabilities were developed to create the required structures for the investigation. One of the technical challenges of the project was understanding and creating the specialized conditions required to observe the melting and reshaping phenomena. Through systematic experimentation and review of the literature these conditions were determined and used to conduct phase change experiments. Melting temperatures as low as 1030 C were observed.

  8. Olivine-FeS Partial-Melt

    SciTech Connect

    Roberts, J; Siebert, J; Ryerson, F J; Kinney, J

    2006-10-02

    The figure shows Fe-S-filled melt channels in olivine created at high temperature and pressure. The 3D image was obtained on Beamline 8.3.2 at the Advanced Light Source, Lawrence Berkeley Laboratory, with a spatial resolution of better than two microns (bar is 10 microns). Permeability of Fe-S melts in olivine at high temperatures and pressures provides an important constraint on models of planetary core formation. Permeability must be inferred from empirical relationships based on microstructure. To date, estimates of permeability have varied by more than five orders of magnitude. To provide more accurate constraints, we used high-resolution synchrotron radiation computed tomography to image the three-dimensional network of melt-containing pores in an olivine matrix, and calculated the permeability directly by solving the equations of Stokes flow through the actual pore network using a lattice-Boltzmann approach. These calculations provide an independent constraint on models of planetary core formation.

  9. Continuum model of tensile fracture of metal melts and its application to a problem of high-current electron irradiation of metals

    SciTech Connect

    Mayer, Alexander E. E-mail: mayer.al.evg@gmail.com; Mayer, Polina N.

    2015-07-21

    A continuum model of the metal melt fracture is formulated on the basis of the continuum mechanics and theory of metastable liquid. A character of temperature and strain rate dependences of the tensile strength that is predicted by the continuum model is verified, and parameters of the model are fitted with the use of the results of the molecular dynamics simulations for ultra-high strain rates (≥1–10/ns). A comparison with experimental data from literature is also presented for Al and Ni melts. Using the continuum model, the dynamic tensile strength of initially uniform melts of Al, Cu, Ni, Fe, Ti, and Pb within a wide range of strain rates (from 1–10/ms to 100/ns) and temperatures (from melting temperature up to 70–80% of critical temperature) is calculated. The model is applied to numerical investigation of a problem of the high-current electron irradiation of Al, Cu, and Fe targets.

  10. Understanding Super-Resolution Nanoscopy and Its Biological Applications in Cell Imaging

    SciTech Connect

    Hu, Dehong; Zhao, Baoming; Xie, Yumei; Orr, Galya; Li, Alexander D.

    2013-01-01

    Optical microscopy has been an ideal tool to study phenomena in live cells because visible light at reasonable intensity does not perturb much of the normal biological functions. However, optical resolution using visible light is significantly limited by the wavelength. Overcoming this diffraction-limit barrier will reveal biological mechanisms, cellular structures, and physiological processes at nanometer scale, orders of magnitude lower than current optical microscopy. Although this appears to be a daunting task, recently developed photoswitchable probes enable reconstruction of individual images into a super-resolution image, thus the emergence of nanoscopy. Harnessing the resolution power of nanoscopy, we report here nano-resolution fluorescence imaging of microtubules and their network structures in biological cells. The super-resolution nanoscopy successfully resolved nanostructures of microtubule network—a daunting task that cannot be completed using conventional wide-field microscopy.

  11. High-resolution computational ghost diffraction with shaped incoherent sources and its applicability in coherent diffraction imaging

    NASA Astrophysics Data System (ADS)

    Luo, Chun-Ling

    2016-01-01

    Computational ghost diffraction (CGD) with a higher-order cosh-Gaussian modulated incoherent source is investigated theoretically. The corresponding numerical simulations are given to see clearly the effects of the parameters of the higher-order cosh-Gaussian source on the imaging quality. Our results show that the resolution of the CGD patterns can be significantly improved by properly varying the source parameters. In addition, we numerically study the effect of the propagation distances in the CGD system and explore the CGD applicability in coherent diffraction imaging. These results may be helpful for implementation of high-resolution x-ray diffraction.

  12. Ultra high resolution molecular beam cars spectroscopy with application to planetary atmospheric molecules

    NASA Technical Reports Server (NTRS)

    Byer, R. L.

    1982-01-01

    The measurement of high resolution pulsed and continuous wave (CW) coherent anti-Stokes Raman spectroscopy (CARS) measurements in pulsed and steady state supersonic expansions were demonstrated. Pulsed molecular beam sources were characterized, and saturation of a Raman transition and, for the first time, the Raman spectrum of a complex molecular cluster were observed. The observation of CW CARS spectra in a molecular expansion and the effects of transit time broadening is described. Supersonic expansion is established as a viable technique for high resolution Raman spectroscopy of cold molecules with resolutions of 100 MH2.

  13. Application of the MAP estimation model to hyperspectral resolution image enhancement

    NASA Astrophysics Data System (ADS)

    Dong, Guangjun; Zhou, Haifang; Ji, Song; Shu, Rong

    2009-10-01

    This paper makes a study of maximum a posteriori (MAP) estimation method for enhancing the spatial resolution of a hyperspectral image using a higher resolution coincident panchromatic image. Here, the mathematical formulation of the proposed MAP method is described and the detail process step is introduced. Then, enhancement results using PHI hyperspectral image datasets are provided. In general, it is found that the MAP method is able to obtain high-resolution hyperspectral data. Experiment shows that the method is effective while the enhancement for conventional methods, like average estimation, is limited primarily to fuse spectral information.

  14. Melting enthalpies of mantle peridotite: calorimetric determinations in the system CaO-MgO-Al 2O 3-SiO 2 and application to magma generation

    NASA Astrophysics Data System (ADS)

    Kojitani, Hiroshi; Akaogi, Masaki

    1997-12-01

    High-temperature drop calorimetry in the temperature range of 1398-1785 K was performed for the samples of mixtures of synthetic anorthite (An), diopside (Di), enstatite (En) and forsterite (Fo) with the same compositions as those of primary melts generated at 1.1, 3 and 4 GPa at most 10° above the solidus of anhydrous mantle peridotite in the CaO-MgO-Al 2O 3-SiO 2 system. From the differences between the heat contents ( H T-H 298) of liquid and that of crystal mixture at the liquidus temperature, melting enthalpies of the samples of 1.1, 3 and 4 GPa-primary melt compositions were determined at 1 atm to be 531 ± 39 J · g -1 at 1583 K, 604 ± 21 J · g -1 at 1703 K, 646 ± 21 J · g -1 at 1753 K, respectively. These heat of fusion values suggest that mixing enthalpy of the melt in the An-Di-En-Fo system is approximately zero within the experimental errors when we use the heat of fusion of Fo by Richet et al. (P. Richet, F. Leclerc, L. Benoist, Melting of forsterite and spinel, with implications for the glass transition of Mg 2SiO 4 liquid, Geophys. Res. Lett. 20 (1993) 1675-1678). The measured enthalpies of melting at 1 atm were converted into those for melting reactions which occur under high pressures by correcting enthalpy changes associated with solid-state mineral reactions. Correcting the effects of pressure, temperature and FeO and Na 2O components on the melting enthalpies at 1 atm, heat of fusion values of a representative mantle peridotite just above the solidus under high pressure were estimated to be 590 J at 1.1 GPa and 1523 K, 692 J at 3 GPa and 1773 K, and 807 J at 4 GPa and 1923 K for melting reactions producing liquid of 1 g, with uncertainties of 50 J. By applying these melting enthalpies to a mantle diapir model which generates present MORBs, a potential mantle temperature of 1533 K has been estimated, assuming an eruption temperature of magma of 1473 K.

  15. A Variable Resolution Stretched Grid Data Assimilation System for Regional Studies and Applications

    NASA Technical Reports Server (NTRS)

    Fox-Rabinovitz, Michael S.; Takacs, Lawrence L.; Dee, Dick P.

    1999-01-01

    The variable resolution stretched grid (SG) version of the Goddard Earth Observing System (GEOS) Data Assimilation System (DAS) incorporating the GEOS SG-GCM, has been developed and tested. The area/region of interest used in experiments is a rectangle over the U.S. with -60 km horizontal resolution and 70 layers extending from the surface to 0.1 hPa. The forecast error statistics has been reassessed for finer regional resolution. The experiments are performed for winter and summer seasons. The SG-GCM and SG-DAS experiments show that a definite down-scaling takes place over the area of interest. The SG-DAS is capable of reproducing regional mesoscale patterns and diagnostics that are not produced by coarser uniform resolution runs. The SG-DAS fields and diagnostics are used for regional forecasting, new instrument impact studies, and for validation of regional climate simulation experiments.

  16. Matching Observations to Model Resolution for Future Weather and Climate Applications

    NASA Technical Reports Server (NTRS)

    Pagano, Thomas S.

    2008-01-01

    High spatial resolution sounding observations will improve initialization and assimilation into the next generation forecast models and validation of the next generation of climate models. One such advanced sounder concept for low earth orbit is the Advanced Remote-sensing Imaging Emission Spectrometer (ARIES) which proposes to provide highvspatial hyperspectral resolution observations in the mid to longwave infrared. This paper explores the effects of spatial resolution on the errors expected from the combined use of models and observations for representing scene information. We calculate the frequency response of the instrument and model and determine the error at any given spatial frequency. The results show that it is vital to have observations match the spatial resolution of models to minimize the uncertainty in the representation of the scene contents.

  17. Coreference resolution: A review of general methodologies and applications in the clinical domain

    PubMed Central

    Zheng, Jiaping; Chapman, Wendy W.; Crowley, Rebecca S.; Savova, Guergana K.

    2011-01-01

    Coreference resolution is the task of determining linguistic expressions that refer to the same real-world entity in natural language. Research on coreference resolution in the general English domain dates back to 1960s and 1970s. However, research on coreference resolution in the clinical free text has not seen major development. The recent US government initiatives that promote the use of electronic health records (EHRs) provide opportunities to mine patient notes as more and more health care institutions adopt EHR. Our goal was to review recent advances in general purpose coreference resolution to lay the foundation for methodologies in the clinical domain, facilitated by the availability of a shared lexical resource of gold standard coreference annotations, the Ontology Development and Information Extraction (ODIE) corpus. PMID:21856441

  18. Application of High Resolution Multispectral Imagery for Levee Slide Detection and Monitoring

    NASA Technical Reports Server (NTRS)

    Hossain, A. K. M. Azad; Easson, Greg

    2007-01-01

    The objective is to develop methods to detect and monitor levee slides using commercially available high resolution multispectral imagery. High resolution multispectral imagery like IKONOS and QuickBird are suitable for detecting and monitoring levee slides. IKONOS is suitable for visual inspection, image classification and Tasseled Cap transform based slide detection. Tasseled Cap based model was found to be the best method for slide detection. QuickBird was suitable for visual inspection and image classification.

  19. Melt inclusions: Chapter 6

    USGS Publications Warehouse

    Audétat A.; Lowenstern, J. B.

    2014-01-01

    Melt inclusions are small droplets of silicate melt that are trapped in minerals during their growth in a magma. Once formed, they commonly retain much of their initial composition (with some exceptions) unless they are re-opened at some later stage. Melt inclusions thus offer several key advantages over whole rock samples: (i) they record pristine concentrations of volatiles and metals that are usually lost during magma solidification and degassing, (ii) they are snapshots in time whereas whole rocks are the time-integrated end products, thus allowing a more detailed, time-resolved view into magmatic processes (iii) they are largely unaffected by subsolidus alteration. Due to these characteristics, melt inclusions are an ideal tool to study the evolution of mineralized magma systems. This chapter first discusses general aspects of melt inclusions formation and methods for their investigation, before reviewing studies performed on mineralized magma systems.

  20. Glass Melt Stability

    NASA Astrophysics Data System (ADS)

    Schaeffer, Helmut A.; Müller-Simon, Hayo

    The employment of sensors during glass melting represents a major prerequisite for an improved process control leading to higher production yields. In situ sensoring techniques can be divided into two groups: on the one hand, techniques which extract information of glass melt properties, e.g., oxidation state and concentrations of relevant polyvalent species (such as iron, sulfur, chromium) and on the other hand, techniques which monitor the furnace atmosphere with respect to toxic emissions (e.g., SO2, NO x ) and combustion species (e.g., CO, CO2, H2O). Nowadays it is feasible not only to install early warning systems indicating deviations from target glass properties, but also to implement process control systems which enforce a stable and reproducible glass melting. Examples are given for the redox control of green glass melting utilizing high portions of recycled cullet and the redox control of amber glass melting.

  1. Thermodynamics of Glass Melting

    NASA Astrophysics Data System (ADS)

    Conradt, Reinhard

    First, a model based on linear algebra is described by which the thermodynamic properties of industrial multi-component glasses and glass melts can be accurately predicted from their chemical composition. The model is applied to calculate the heat content of glass melts at high temperatures, the standard heat of formation of glasses from the elements, and the vapor pressures of individual oxides above the melt. An E-fiber glass composition is depicted as an example. Second, the role of individual raw materials in the melting process of E-glass is addressed, with a special focus on the decomposition kinetics and energetic situation of alkaline earth carriers. Finally, the heat of the batch-to-melt conversion is calculated. A simplified reaction path model comprising heat turnover, content of residual solid matter, and an approach to batch viscosity is outlined.

  2. Spatial resolution and noise in organic light-emitting diode displays for medical imaging applications.

    PubMed

    Yamazaki, Asumi; Wu, Chih-Lei; Cheng, Wei-Chung; Badano, Aldo

    2013-11-18

    We report on the resolution and noise characteristics of handheld and workstation organic light-emitting diode (OLED) displays in comparison with liquid crystal displays (LCDs). The results demonstrate advantages, in terms of sharpness, of handheld OLED displays with modulation transfer function (MTF) values exceeding 0.60 at the Nyquist frequencies. The OLED workstation included in this study exhibits significant signal contamination among adjacent pixels resulting in degraded resolution performance indicated by horizontal and vertical MTF values of 0.13 and 0.24 at the Nyquist frequency. On the other hand, its noise characteristics are superior to the LCD workstation tested. While the noise power spectral (NPS) values of the OLED workstation are 8.0×10(-6) mm2 at 1 mm(-1), the LCD workstation has NPS values of 2.6×10(-5) mm2. Although phone-size OLED displays have superior resolution and noise per pixel, the perceived resolution characteristics at appropriate viewing distances are inferior to tablet-size and workstation LCDs. In addition, our results show some degree of dependency of the resolution and noise on luminance level and viewing orientation. We also found a slightly degraded resolution and increased low-frequency noise at off-normal orientations in the handheld displays. PMID:24514325

  3. Congruent Melting Kinetics: Constraints on Chondrule Formation

    NASA Technical Reports Server (NTRS)

    Greenwood, James P.; Hess, Paul C.

    1995-01-01

    The processes and mechanisms of melting and their applications to chondrule formation are discussed A model for the kinetics of congruent melting is developed and used to place constraints on the duration and maximum temperature experienced by the interiors of relict-bearing chondrules. Specifically, chondrules containing relict forsteritic olivine or enstatitic pyroxene cannot have been heated in excess of 1901 C or 1577 C, respectively, for more than a few seconds.

  4. Commercial Zone Melting Ingots

    NASA Astrophysics Data System (ADS)

    Zheng, Yun; Xie, Hongyao; Shu, Shengcheng; Yan, Yonggao; Li, Han; Tang, Xinfeng

    2014-06-01

    Bismuth telluride-based compounds have been extensively utilized for commercial application. However, thermoelectric materials must suffer numerous mechanical vibrations and thermal stresses while in service, making it equally important to discuss the mechanical properties, especially at high temperature. In this study, the compressive and bending strengths of Bi0.5Sb1.5Te3 commercial zone melting (ZM) ingots were investigated at 25, 100, and 200 °C, respectively. Due to the obvious anisotropy of materials prepared by ZM method, the effect of anisotropy on the strengths was also explored. Two-parameter Weibull distribution was employed to fit a series of values acquired by a universal testing machine. And digital speckle photography was applied to record the strain field evolution, providing visual observation of surface strain. The compressive and bending strengths along ZM direction were approximately three times as large as those perpendicular to the ZM direction independent of the temperature, indicating a weak van der Waals bond along the c axis.

  5. A High Resolution, Light-Weight, Synthetic Aperture Radar for UAV Application

    SciTech Connect

    Doerry, A.W.; Hensley, W.H.; Stence, J.; Tsunoda, S.I. Pace, F.; Walker, B,C.; Woodring, M.

    1999-05-27

    (U) Sandia National Laboratories in collaboration with General Atomics (GA) has designed and built a high resolution, light-weight, Ku-band Synthetic Aperture Radar (SAR) known as "Lynx". Although Lynx can be operated on a wide variety of manned and unmanned platforms, its design is optimized for use on medium altitude Unmanned Aerial Vehicles (UAVS). In particular, it can be operated on the Predator, I-GNAT, and Prowler II platforms manufactured by GA. (U) The radar production weight is less than 120 lb and operates within a 3 GHz band from 15.2 GHz to 18.2 GHz with a peak output power of 320 W. Operating range is resolution and mode dependent but can exceed 45 km in adverse weather (4 mm/hr rain). Lynx has operator selectable resolution and is capable of 0.1 m resolution in spotlight mode and 0.3 m resolution in stripmap mode, over substantial depression angles (5 to 60 deg) and squint angles (broadside ±45 deg). Real-time Motion Compensation is implemented to allow high-quality image formation even during vehicle turns and other maneuvers.

  6. Exo-Melt{trademark} process for intermetallic powders

    SciTech Connect

    Sikka, V.K.; Deevi, S.C.

    1996-06-01

    The methods of powder production for intermetallics are reviewed. An innovative method known as Exo-Melt{trademark} is described for producing molten aluminides for gas- and water-atomization processes that require a molten metal stream. The Exo-Melt{trademark} process is based on the effective utilization of the heats of formation of aluminides from their constituent elements. The Exo-Melt{trademark} process principles are discussed along with a description of a furnace-loading sequence that uses the principles for practical applications. The benefits of the Exo-Melt{trademark} process are compared with the problems associated with the conventional melting process.

  7. Portable and cost-effective pixel super-resolution on-chip microscope for telemedicine applications.

    PubMed

    Bishara, Waheb; Sikora, Uzair; Mudanyali, Onur; Su, Ting-Wei; Yaglidere, Oguzhan; Luckhart, Shirley; Ozcan, Aydogan

    2011-01-01

    We report a field-portable lensless on-chip microscope with a lateral resolution of <1 μm and a large field-of-view of ~24 mm(2). This microscope is based on digital in-line holography and a pixel super-resolution algorithm to process multiple lensfree holograms and obtain a single high-resolution hologram. In its compact and cost-effective design, we utilize 23 light emitting diodes butt-coupled to 23 multi-mode optical fibers, and a simple optical filter, with no moving parts. Weighing only ~95 grams, we demonstrate the performance of this field-portable microscope by imaging various objects including human malaria parasites in thin blood smears. PMID:22256247

  8. A Versatile Medium-Resolution X-ray Emission Spectrometer for Diamond Anvil Cell Applications

    SciTech Connect

    Mortensen, Devon R.; Seidler, G. T.; Bradley, J. A.; Lipp, M. J.; Evans, W. J.; Chow, P.; Xiao, Y. M.; Boman, G.; Bowden, Mark E.

    2013-08-28

    We present design and performance details for a polycapillary-coupled x-ray spectrometer that provides very high collection efficiency at a moderate energy resolution suitable for many studies of nonresonant x-ray emission spectroscopy, especially for samples of heavy elements under high pressures. Using a single Bragg analyzer operating close to a backscattering so as to minimize the effect of the weak divergence of the quasicollimated exit beam from the polycapillary optic, this instrument can maintain a typical energy resolution of 5 eV over photon energies from 5 keV to 10 keV. We find dramatically improved count rates as compared to a traditional higher-resolution instrument based on a single spherically-bent crystal analyzer.

  9. A versatile medium-resolution x-ray emission spectrometer for diamond anvil cell applications

    SciTech Connect

    Mortensen, D. R.; Seidler, G. T.; Bradley, J. A.; Lipp, M. J.; Evans, W. J.; Chow, P.; Xiao, Y.-M.; Boman, G.; Bowden, M. E.

    2013-08-15

    We present design and performance details for a polycapillary-coupled x-ray spectrometer that provides very high collection efficiency at a moderate energy resolution suitable for many studies of nonresonant x-ray emission spectroscopy, especially for samples of heavy elements under high pressures. Using a single Bragg analyzer operating close to backscattering geometry so as to minimize the effect of the weak divergence of the quasicollimated exit beam from the polycapillary optic, this instrument can maintain a typical energy resolution of 5 eV over photon energies from 5 keV to 10 keV. We find dramatically improved count rates as compared to a traditional higher-resolution instrument based on a single spherically bent crystal analyzer.

  10. Crystal chemical effects on the partitioning of trace elements between mineral and melt - An experimental study of melilite with applications to refractory inclusions from carbonaceous chondrites

    NASA Technical Reports Server (NTRS)

    Beckett, John R.; Spivack, Arthur J.; Hutcheon, Ian D.; Wasserburg, G. J.; Stolper, Edward M.

    1990-01-01

    Results are presented on the partitioning experiments for trace elements Be, Sc, Ba, La, Ce, and Tm between melilite and melt for a bulk composition relevant to Type B inclusions, using a technique, described by Brody and Flemings (1966), by which distributon coeffecients can be obtained over the entire range of crystallization from trace element analysis of a single zoned crystal. Zoned crystals of melilite were grown during controlled cooling rate experiments, and trace element concentrations were determined by SIMS. At each step in the crystal growth, trace element concentrations in the coexisting melt were determined by mass balance, using stepwise integration of a Rayleigh fractionation equation.

  11. Crystal chemical effects on the partitioning of trace elements between mineral and melt - an experimental study of melilite with applications to refractory inclusions from carbonaceous chondrites

    NASA Astrophysics Data System (ADS)

    Beckett, J. R.; Spivack, A. J.; Hutcheon, I. D.; Wasserburg, G. J.; Stolper, E. M.

    1990-06-01

    Results are presented on the partitioning experiments for trace elements Be, Sc, Ba, La, Ce, and Tm between melilite and melt for a bulk composition relevant to Type B inclusions, using a technique, described by Brody and Flemings (1966), by which distributon coeffecients can be obtained over the entire range of crystallization from trace element analysis of a single zoned crystal. Zoned crystals of melilite were grown during controlled cooling rate experiments, and trace element concentrations were determined by SIMS. At each step in the crystal growth, trace element concentrations in the coexisting melt were determined by mass balance, using stepwise integration of a Rayleigh fractionation equation.

  12. Signatures of nonthermal melting.

    PubMed

    Zier, Tobias; Zijlstra, Eeuwe S; Kalitsov, Alan; Theodonis, Ioannis; Garcia, Martin E

    2015-09-01

    Intense ultrashort laser pulses can melt crystals in less than a picosecond but, in spite of over thirty years of active research, for many materials it is not known to what extent thermal and nonthermal microscopic processes cause this ultrafast phenomenon. Here, we perform ab-initio molecular-dynamics simulations of silicon on a laser-excited potential-energy surface, exclusively revealing nonthermal signatures of laser-induced melting. From our simulated atomic trajectories, we compute the decay of five structure factors and the time-dependent structure function. We demonstrate how these quantities provide criteria to distinguish predominantly nonthermal from thermal melting. PMID:26798822

  13. Signatures of nonthermal melting

    PubMed Central

    Zier, Tobias; Zijlstra, Eeuwe S.; Kalitsov, Alan; Theodonis, Ioannis; Garcia, Martin E.

    2015-01-01

    Intense ultrashort laser pulses can melt crystals in less than a picosecond but, in spite of over thirty years of active research, for many materials it is not known to what extent thermal and nonthermal microscopic processes cause this ultrafast phenomenon. Here, we perform ab-initio molecular-dynamics simulations of silicon on a laser-excited potential-energy surface, exclusively revealing nonthermal signatures of laser-induced melting. From our simulated atomic trajectories, we compute the decay of five structure factors and the time-dependent structure function. We demonstrate how these quantities provide criteria to distinguish predominantly nonthermal from thermal melting. PMID:26798822

  14. Applications of high resolution NMR to geochemistry: crystalline, glass, and molten silicates

    SciTech Connect

    Schneider, E.

    1985-11-01

    The nuclear spin interactions and the associated quantum mechanical dynamics which are present in solid state NMR are introduced. A brief overview of aluminosilicate structure is presented and crystalline structure is then reviewed, with emphasis on the contributions made by /sup 29/Si NMR spectroscopy. The local structure of glass aluminosilicates as observed by NMR, is presented with analysis of the information content of /sup 29/Si spectra. A high-temperature (to 1300/sup 0/C) NMR spectroscopic investigation of the local environment and dynamics of molecular motion in molten aluminosilicates is described. A comparison is made of silicate liquid, glass, and crystalline local structure. The atomic and molecular motions present in a melt are investigated through relaxation time (T/sub 1/ and T/sub 2/) measurements as a function of composition and temperature for /sup 23/Na and /sup 29/Si.

  15. Theory and application of optimal linear resolution to MRI truncation artifacts, multiexponential decays and in vivo multiple sclerosis pathology

    NASA Astrophysics Data System (ADS)

    Cover, Keith S.

    It is widely believed that one of the best way to proceed when analysing data is to generate estimates which fit the data. However, when the relationship between the unknown model and data is linear for highly underdetermined systems, is it common practice to find estimates with good linear resolution with no regard for fitting the data. For example, windowed Fourier transforms produces estimates that have good linear resolution but do not fit the data. Surprisingly, many researchers do not seem to be explicitly aware of this fact. This thesis presents a theoretical basis for the linear resolution which demonstrates that, for a wide range of problems, algorithms which produce estimates with good linear resolution can be a more powerful and convenient way of presenting the information in the data, than models that fit the data. Linear resolution was also applied to two outstanding problems in linear inverse theory. The first was the problem of truncation artifacts in magnetic resonance imaging (MRI). Truncation artifacts were heavily suppressed or eliminated by the choice of one of two novel Fourier transform windows. Complete elimination of truncation artifacts generally led to unexpectedly blurry images. Heavy suppression seemed to be the best compromise between truncation artifacts and blurriness. The second problem was estimating the relaxation distribution of a multiexponential system from its decay curve. This is an example where hundreds of papers have been written on the subject, yet almost no one has made a substantial effort to apply linear resolution. I found the application to be very successful. As an example, the algorithm was applied to the decay of MRI data from multiple sclerosis patients in an attempt to differentiate between various pathologies.

  16. Applications and Innovations for Use of High Definition and High Resolution Digital Motion Imagery in Space Operations

    NASA Technical Reports Server (NTRS)

    Grubbs, Rodney

    2016-01-01

    The first live High Definition Television (HDTV) from a spacecraft was in November, 2006, nearly ten years before the 2016 SpaceOps Conference. Much has changed since then. Now, live HDTV from the International Space Station (ISS) is routine. HDTV cameras stream live video views of the Earth from the exterior of the ISS every day on UStream, and HDTV has even flown around the Moon on a Japanese Space Agency spacecraft. A great deal has been learned about the operations applicability of HDTV and high resolution imagery since that first live broadcast. This paper will discuss the current state of real-time and file based HDTV and higher resolution video for space operations. A potential roadmap will be provided for further development and innovations of high-resolution digital motion imagery, including gaps in technology enablers, especially for deep space and unmanned missions. Specific topics to be covered in the paper will include: An update on radiation tolerance and performance of various camera types and sensors and ramifications on the future applicability of these types of cameras for space operations; Practical experience with downlinking very large imagery files with breaks in link coverage; Ramifications of larger camera resolutions like Ultra-High Definition, 6,000 [pixels] and 8,000 [pixels] in space applications; Enabling technologies such as the High Efficiency Video Codec, Bundle Streaming Delay Tolerant Networking, Optical Communications and Bayer Pattern Sensors and other similar innovations; Likely future operations scenarios for deep space missions with extreme latency and intermittent communications links.

  17. Photon-counting imaging camera for high-resolution X-ray and γ-ray applications

    NASA Astrophysics Data System (ADS)

    Hall, D. J.; Holland, A.

    2011-01-01

    Standard X-ray imaging techniques using CCDs require the integration of thousands of X-ray photons into a single image frame. Through the addition of a scintillating layer to the CCD it is possible to greatly increase the X-ray detection efficiency at high energies. Using standard imaging techniques with the inclusion of the scintillating layer does, however, leave serious limitations on the spatial resolution achievable due to the spreading of the light generated in the scintillator. The Electron-Multiplying CCD (EM-CCD) shares much of the common architecture of the standard CCD but for the inclusion of a supplementary readout register. This additional high-voltage register allows the signal electrons to be `multiplied' before reaching the readout node of the CCD, increasing the signal before any significant noise is introduced. The increase in the signal-to-noise ratio allows very low signals to be extracted above the noise floor, leading to the common use of EM-CCDs in night-vision and security applications. Through the coupling of a scintillator to an EM-CCD it is possible to resolve individual X-ray photon interactions in the scintillator above the noise floor. Without this extra gain these low signals would be lost beneath the noise floor. Using various centroiding techniques it is possible to locate the interaction position of the incident X-ray photon in the scintillator to the sub-pixel level, with measurements here at 59.5 keV giving an initial FWHM of the line spread function of 31μm. This high-resolution, hard X-ray imager has many potential applications in medical and biological imaging, where energy discrimination at a high resolution is desired. Further applications include synchrotron-based research, an area in which high-resolution imaging is essential.

  18. Greenland Ice Sheet Melt from MODIS and Associated Atmospheric Variability

    NASA Technical Reports Server (NTRS)

    Hakkinen, Sirpa; Hall, Dorothy K.; Shuman, Christopher A.; Worthen, Denise L.; DiGirolamo, Nicolo E.

    2014-01-01

    Daily June-July melt fraction variations over the Greenland Ice Sheet (GIS) derived from the MODerate-resolution Imaging Spectroradiometer (MODIS) (2000-2013) are associated with atmospheric blocking forming an omega-shape ridge over the GIS at 500hPa height (from NCEPNCAR). Blocking activity with a range of time scales, from synoptic waves breaking poleward ( 5 days) to full-fledged blocks (5 days), brings warm subtropical air masses over the GIS controlling daily surface temperatures and melt. The temperature anomaly of these subtropical air mass intrusions is also important for melting. Based on the largest MODIS melt years (2002 and 2012), the area-average temperature anomaly of 2 standard deviations above the 14-year June-July mean, results in a melt fraction of 40 or more. Summer 2007 had the most blocking days, however atmospheric temperature anomalies were too small to instigate extreme melting.

  19. High-Resolution Surface Reconstruction from Imagery for Close Range Cultural Heritage Applications

    NASA Astrophysics Data System (ADS)

    Wenzel, K.; Abdel-Wahab, M.; Cefalu, A.; Fritsch, D.

    2012-07-01

    The recording of high resolution point clouds with sub-mm resolution is a demanding and cost intensive task, especially with current equipment like handheld laser scanners. We present an image based approached, where techniques of image matching and dense surface reconstruction are combined with a compact and affordable rig of off-the-shelf industry cameras. Such cameras provide high spatial resolution with low radiometric noise, which enables a one-shot solution and thus an efficient data acquisition while satisfying high accuracy requirements. However, the largest drawback of image based solutions is often the acquisition of surfaces with low texture where the image matching process might fail. Thus, an additional structured light projector is employed, represented here by the pseudo-random pattern projector of the Microsoft Kinect. Its strong infrared-laser projects speckles of different sizes. By using dense image matching techniques on the acquired images, a 3D point can be derived for almost each pixel. The use of multiple cameras enables the acquisition of a high resolution point cloud with high accuracy for each shot. For the proposed system up to 3.5 Mio. 3D points with sub-mm accuracy can be derived per shot. The registration of multiple shots is performed by Structure and Motion reconstruction techniques, where feature points are used to derive the camera positions and rotations automatically without initial information.

  20. Application of high resolution images from unmanned aerial vehicles for hydrology and range science

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A common problem in many natural resource disciplines is the lack of high-enough spatial resolution images that can be used for monitoring and modeling purposes. Advances have been made in the utilization of Unmanned Aerial Vehicles (UAVs) in hydrology and rangeland science. By utilizing low fligh...

  1. Application of high resolution images from unmanned aircraft systems for watershed and rangeland science

    Technology Transfer Automated Retrieval System (TEKTRAN)

    UAS provide a new way to acquire hyperspatial data with a resolution of 6 cm that has not been available in the past. This hyperspatial data can be used to obtain detailed 1-m DEMs, mosaics of entire watersheds, detailed vegetation classification of bare soils and vegetation type, and input to mode...

  2. Potential Errors in the Application of Thermal-based Energy Balance Models with Coarse Resolution Data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A thermal sharpening algorithm (TsHARP) providing fine resolution land surface temperature (LST) to the Two-Source-Model (TSM) for mapping evapotranspiration (ET) was applied over two agricultural regions in the U.S. One site is a rainfed corn and soybean production region in central Iowa, while th...

  3. Accurate Atmospheric Parameters at Moderate Resolution Using Spectral Indices: Preliminary Application to the MARVELS Survey

    NASA Astrophysics Data System (ADS)

    Ghezzi, Luan; Dutra-Ferreira, Letícia; Lorenzo-Oliveira, Diego; Porto de Mello, Gustavo F.; Santiago, Basílio X.; De Lee, Nathan; Lee, Brian L.; da Costa, Luiz N.; Maia, Marcio A. G.; Ogando, Ricardo L. C.; Wisniewski, John P.; González Hernández, Jonay I.; Stassun, Keivan G.; Fleming, Scott W.; Schneider, Donald P.; Mahadevan, Suvrath; Cargile, Phillip; Ge, Jian; Pepper, Joshua; Wang, Ji; Paegert, Martin

    2014-12-01

    Studies of Galactic chemical, and dynamical evolution in the solar neighborhood depend on the availability of precise atmospheric parameters (effective temperature T eff, metallicity [Fe/H], and surface gravity log g) for solar-type stars. Many large-scale spectroscopic surveys operate at low to moderate spectral resolution for efficiency in observing large samples, which makes the stellar characterization difficult due to the high degree of blending of spectral features. Therefore, most surveys employ spectral synthesis, which is a powerful technique, but relies heavily on the completeness and accuracy of atomic line databases and can yield possibly correlated atmospheric parameters. In this work, we use an alternative method based on spectral indices to determine the atmospheric parameters of a sample of nearby FGK dwarfs and subgiants observed by the MARVELS survey at moderate resolving power (R ~ 12,000). To avoid a time-consuming manual analysis, we have developed three codes to automatically normalize the observed spectra, measure the equivalent widths of the indices, and, through a comparison of those with values calculated with predetermined calibrations, estimate the atmospheric parameters of the stars. The calibrations were derived using a sample of 309 stars with precise stellar parameters obtained from the analysis of high-resolution FEROS spectra, permitting the low-resolution equivalent widths to be directly related to the stellar parameters. A validation test of the method was conducted with a sample of 30 MARVELS targets that also have reliable atmospheric parameters derived from the high-resolution spectra and spectroscopic analysis based on the excitation and ionization equilibria method. Our approach was able to recover the parameters within 80 K for T eff, 0.05 dex for [Fe/H], and 0.15 dex for log g, values that are lower than or equal to the typical external uncertainties found between different high-resolution analyses. An additional test was

  4. Application of high-resolution thermal infrared sensors for geothermal exploration at the Salton Sea, California

    NASA Astrophysics Data System (ADS)

    Reath, K. A.; Ramsey, M.; Tratt, D. M.

    2010-12-01

    The Salton Sea geothermal field straddles the southeast margin of the Salton Sea in California, USA. This field includes approximately 20km2 of mud volcanoes and mud pots and centered on the Mullet Island thermal anomaly. The area has been previously exploited for geothermal power; there are currently seven power plants in the area that produce 1000 MW. The field itself is relatively un-vegetated, which provides for unfettered detection of the surface mineralogy, radiant heat, and emitted gases using air and spaceborne thermal infrared (TIR) sensors. On March 26, 2009, the airborne Spatially Enhanced Broadband Array Spectrograph System (SEBASS) sensor was flown over the Salton Sea-Mullet Island area. SEBASS has a spectral resolution of 128 bands in the 7.5-14.5 micron spectral region and a spatial resolution of 1m/pixel from the 3000-ft altitude flown for this study. A large portion of the Calipatria Fault, a NW/SE-trending geothermally active fault that bisects the Mullet Island thermal anomaly, was imaged during this flight and several thermal/mineralogical anomalies were noted. The orbital Advanced Spaceborne Thermal Emission Reflection Radiometer (ASTER) has only 5 spectral bands at 90m/pixel resolution, but has acquired dozens of visible and TIR datasets over the geothermal field in the 10-year history of the instrument. The thermal-temporal trend of this dataset has been analyzed, and the November 2008 image studied in detail for comparison to SEBASS. The land-leaving TIR radiance data were separated into brightness temperature and surface emissivity. TIR emissivity data are unique to each mineral and a TIR mineral spectral library was used to determine their presence on the ground. Various mineral maps were created showing the distribution surrounding the most active geothermal features. The higher spectral/spatial resolution SEBASS data were used to validate the lower spectral/spatial resolution ASTER data (as well as the higher resolution laboratory TIR

  5. Accurate atmospheric parameters at moderate resolution using spectral indices: Preliminary application to the marvels survey

    SciTech Connect

    Ghezzi, Luan; Da Costa, Luiz N.; Maia, Marcio A. G.; Ogando, Ricardo L. C.; Dutra-Ferreira, Letícia; Lorenzo-Oliveira, Diego; Porto de Mello, Gustavo F.; Santiago, Basílio X.; De Lee, Nathan; Lee, Brian L.; Ge, Jian; Wisniewski, John P.; González Hernández, Jonay I.; Stassun, Keivan G.; Cargile, Phillip; Pepper, Joshua; Fleming, Scott W.; Schneider, Donald P.; Mahadevan, Suvrath; Wang, Ji; and others

    2014-12-01

    Studies of Galactic chemical, and dynamical evolution in the solar neighborhood depend on the availability of precise atmospheric parameters (effective temperature T {sub eff}, metallicity [Fe/H], and surface gravity log g) for solar-type stars. Many large-scale spectroscopic surveys operate at low to moderate spectral resolution for efficiency in observing large samples, which makes the stellar characterization difficult due to the high degree of blending of spectral features. Therefore, most surveys employ spectral synthesis, which is a powerful technique, but relies heavily on the completeness and accuracy of atomic line databases and can yield possibly correlated atmospheric parameters. In this work, we use an alternative method based on spectral indices to determine the atmospheric parameters of a sample of nearby FGK dwarfs and subgiants observed by the MARVELS survey at moderate resolving power (R ∼ 12,000). To avoid a time-consuming manual analysis, we have developed three codes to automatically normalize the observed spectra, measure the equivalent widths of the indices, and, through a comparison of those with values calculated with predetermined calibrations, estimate the atmospheric parameters of the stars. The calibrations were derived using a sample of 309 stars with precise stellar parameters obtained from the analysis of high-resolution FEROS spectra, permitting the low-resolution equivalent widths to be directly related to the stellar parameters. A validation test of the method was conducted with a sample of 30 MARVELS targets that also have reliable atmospheric parameters derived from the high-resolution spectra and spectroscopic analysis based on the excitation and ionization equilibria method. Our approach was able to recover the parameters within 80 K for T {sub eff}, 0.05 dex for [Fe/H], and 0.15 dex for log g, values that are lower than or equal to the typical external uncertainties found between different high-resolution analyses. An

  6. Matrix-assisted diffusion-ordered spectroscopy: application of surfactant solutions to the resolution of isomer spectra.

    PubMed

    Tormena, Cláudio F; Evans, Robert; Haiber, Stephan; Nilsson, Mathias; Morris, Gareth A

    2012-06-01

    The component spectra of a mixture of isomers with nearly identical diffusion coefficients cannot normally be distinguished in a standard diffusion-ordered spectroscopy (DOSY) experiment but can often be easily resolved using matrix-assisted DOSY, in which diffusion behaviour is manipulated by the addition of a co-solute such as a surfactant. Relatively little is currently known about the conditions required for such a separation, for example, how the choice between normal and reverse micelles affects separation or how the isomer structures themselves affect the resolution. The aim of this study was to explore the application of sodium dodecyl sulfate (SDS) normal micelles in aqueous solution and sodium 1,4-bis(2-ethylhexyl)sulfosuccinate (AOT) aggregates in chloroform, at a range of concentrations, to the diffusion resolution of some simple model sets of isomers such as monomethoxyphenols and short chain alcohols. It is shown that SDS micelles offer better resolution where these isomers differ in the position of a hydroxyl group, whereas AOT aggregates are more effective for isomers differing in the position of a methyl group. For both the normal SDS micelles and the less well-defined AOT aggregates, differences in the resolution of the isomers can in part be rationalised in terms of differing degrees of hydrophobicity, amphiphilicity and steric effects. PMID:22549888

  7. High-resolution EEG techniques for brain-computer interface applications.

    PubMed

    Cincotti, Febo; Mattia, Donatella; Aloise, Fabio; Bufalari, Simona; Astolfi, Laura; De Vico Fallani, Fabrizio; Tocci, Andrea; Bianchi, Luigi; Marciani, Maria Grazia; Gao, Shangkai; Millan, Jose; Babiloni, Fabio

    2008-01-15

    High-resolution electroencephalographic (HREEG) techniques allow estimation of cortical activity based on non-invasive scalp potential measurements, using appropriate models of volume conduction and of neuroelectrical sources. In this study we propose an application of this body of technologies, originally developed to obtain functional images of the brain's electrical activity, in the context of brain-computer interfaces (BCI). Our working hypothesis predicted that, since HREEG pre-processing removes spatial correlation introduced by current conduction in the head structures, by providing the BCI with waveforms that are mostly due to the unmixed activity of a small cortical region, a more reliable classification would be obtained, at least when the activity to detect has a limited generator, which is the case in motor related tasks. HREEG techniques employed in this study rely on (i) individual head models derived from anatomical magnetic resonance images, (ii) distributed source model, composed of a layer of current dipoles, geometrically constrained to the cortical mantle, (iii) depth-weighted minimum L(2)-norm constraint and Tikhonov regularization for linear inverse problem solution and (iv) estimation of electrical activity in cortical regions of interest corresponding to relevant Brodmann areas. Six subjects were trained to learn self modulation of sensorimotor EEG rhythms, related to the imagination of limb movements. Off-line EEG data was used to estimate waveforms of cortical activity (cortical current density, CCD) on selected regions of interest. CCD waveforms were fed into the BCI computational pipeline as an alternative to raw EEG signals; spectral features are evaluated through statistical tests (r(2) analysis), to quantify their reliability for BCI control. These results are compared, within subjects, to analogous results obtained without HREEG techniques. The processing procedure was designed in such a way that computations could be split into a

  8. Rainfall resolution from weather radars and their application in urban drainage modelling

    NASA Astrophysics Data System (ADS)

    Bruni, G.; ten Veldhuis, J. A. E.; Otto, T.; Leijnse, H.

    2012-04-01

    Urban hydrological modelling requires high resolution rainfall data to be able to simulate fast runoff processes and related short response times. Over the last three decades, rainfall input into urban hydrological and hydrodynamic models has often been restricted to a single rain gauge in or near the catchment, rendering rainfall input one of the main sources of uncertainty in model calculations. In recent years, rainfall data from weather radars that provide space-time estimates of rainfall are becoming increasingly available. C-band and S-band radars have been used for operational precipitation measurements and offer spatial resolutions of 1km2 to several km2. This resolution is still insufficient to meet the relevant scales of urban hydrology (e.g. Berne et al. 2004; Emmanuel et al., 2011, Schellart et al., in press). Higher spatial resolution rainfall measurements can be provided by X-band radars, especially at short range where attenuation is not yet a major factor. At the Cabauw Experimental Site for Atmospheric Research (CESAR), an X-band Doppler polarimetric radar has been installed as well as a dense network of rain gauges (Leijnse et al., 2010). Data from the C-band Doppler radar at 25 km distance are also available for this site. A network of 11 rain gauges is to be installed in the city area as well as a network of water level sensors in the stormwater sewers. A selection of rain events is analysed based on the available rainfall measurement instruments for this site. The events are used as input into a hydrodynamic model of the sewer system of the city of Utrecht, located between CESAR and the C-band radar site. The effect of different spatial rainfall data resolutions and of rainfall data uncertainty on hydrological response will be analysed for various sizes of catchments within the Utrecht sewer system.

  9. Free-energy calculations using classical molecular simulation: application to the determination of the melting point and chemical potential of a flexible RDX model.

    PubMed

    Sellers, Michael S; Lísal, Martin; Brennan, John K

    2016-03-21

    We present an extension of various free-energy methodologies to determine the chemical potential of the solid and liquid phases of a fully-flexible molecule using classical simulation. The methods are applied to the Smith-Bharadwaj atomistic potential representation of cyclotrimethylene trinitramine (RDX), a well-studied energetic material, to accurately determine the solid and liquid phase Gibbs free energies, and the melting point (Tm). We outline an efficient technique to find the absolute chemical potential and melting point of a fully-flexible molecule using one set of simulations to compute the solid absolute chemical potential and one set of simulations to compute the solid-liquid free energy difference. With this combination, only a handful of simulations are needed, whereby the absolute quantities of the chemical potentials are obtained, for use in other property calculations, such as the characterization of crystal polymorphs or the determination of the entropy. Using the LAMMPS molecular simulator, the Frenkel and Ladd and pseudo-supercritical path techniques are adapted to generate 3rd order fits of the solid and liquid chemical potentials. Results yield the thermodynamic melting point Tm = 488.75 K at 1.0 atm. We also validate these calculations and compare this melting point to one obtained from a typical superheated simulation technique. PMID:26661376

  10. Application of an ultra-high-resolution FBG strain sensor for crustal deformation measurements at the Aburatsubo Bay, Japan

    NASA Astrophysics Data System (ADS)

    Tokunaga, T.; Liu, Q.; He, Z.; Mogi, K.; Matsui, H.; Wang, H. F.; Kato, T.

    2011-12-01

    For crustal deformation measurements, high-resolution strain sensors on the order of tens of nano-strains are desirable. Current sensors for this purpose include quartz-tube extensometers, free-space laser interferometers, and borehole strainmeters. The former two sensors show quite high strain resolution, however, these are large in size, from tens to hundreds of meter long, and hence, are difficult to measure spatial strain distribution. The optical fiber strain sensors have advantages of multiplexing capability and relatively low cost, and are widely adopted in the applications for structural health monitoring of civil structures such as bridges and buildings. Thus, as long as the strain resolution can be high enough to meet the requirement of crustal deformation measurements, fiber strain sensors can be an attractive tool. We have been developing an ultra-high strain-resolution fiber Bragg grating (FBG) sensor for static strain measurement, interrogated by a narrow line-width tunable laser. The sensor consists of a pair of FBGs, one for strain sensing and the other for temperature compensation. The Bragg wavelength difference between the two FBGs is evaluated using a cross-correlation algorithm. We already demonstrated that an ultra-high resolution corresponding to 2.6 nano-strain was obtained in the case where no strain was applied to the sensor, which was considered to be the ultimate performance of our measurement system. By directly applying variable strains to the developed sensor with a piezo-stage, a resolution of 17.6 nano-strain was demonstrated. This time, the sensor was installed into the vault at Aburatsubo, Japan, to measure crustal deformation caused by ocean tide, and the measured data were compared with the results obtained by a quartz-tube extensometer at the site, which has been measured by the University of Tokyo's Earthquake Research Institute. The deformation induced by oceanic tide was measured by the FBG sensor with the resolution about

  11. Melt fracture revisited

    SciTech Connect

    Greenberg, J. M.

    2003-07-16

    In a previous paper the author and Demay advanced a model to explain the melt fracture instability observed when molten linear polymer melts are extruded in a capillary rheometer operating under the controlled condition that the inlet flow rate was held constant. The model postulated that the melts were a slightly compressible viscous fluid and allowed for slipping of the melt at the wall. The novel feature of that model was the use of an empirical switch law which governed the amount of wall slip. The model successfully accounted for the oscillatory behavior of the exit flow rate, typically referred to as the melt fracture instability, but did not simultaneously yield the fine scale spatial oscillations in the melt typically referred to as shark skin. In this note a new model is advanced which simultaneously explains the melt fracture instability and shark skin phenomena. The model postulates that the polymer is a slightly compressible linearly viscous fluid but assumes no slip boundary conditions at the capillary wall. In simple shear the shear stress {tau}and strain rate d are assumed to be related by d = F{tau} where F ranges between F{sub 2} and F{sub 1} > F{sub 2}. A strain rate dependent yield function is introduced and this function governs whether F evolves towards F{sub 2} or F{sub 1}. This model accounts for the empirical observation that at high shears polymers align and slide more easily than at low shears and explains both the melt fracture and shark skin phenomena.

  12. Application of lanthanum halide scintillators and low-resolution dense plastics for modern MC&A needs.

    SciTech Connect

    Chung, K.; Belian, A. P.; McKigney E. A.; Russo, P. A.

    2004-01-01

    Recent developments in lanthanum halide scintillators and low-resolution dense plastics give breadth to gamma-ray methods of nuclear material detection suitable for modern MC and A needs. Demanding goals for modernization of MC and A cover both portable and continuous on-line measurement applications that are quantitative for inventory/verification, and that serve those quantitative measurement needs plant-wide. Improved performance (sensitivity and reoslution) is important for portable applications in which a single detector must measure many types of materials. Budget is a major issue for continuous inventory measurements with hundreds or even thousands of detectors placed throughout a facility. Experimentally proven resolution of under 4% for 662 keV {sup 137}Cs gamma rays measured with large cerium-doped LaCl{sub 3} (lanthanum chloride) crystals set a new performance standard for versatile, efficient portable applications comparable in price to NaI(Tl), which has been dominant for decades. While the relatively high cost of crystals remains an obstacle for the application of very large numbers of lanthanum halide scintillators as distributed networked detectors, scintillators made from high-density plastic offer a different type of solution for these gamma-ray measurements. Compared to lanthanum halide crystals they are inexpensive and can be larger in size. Despite lower resolution than NaI(Tl), a quantitative interpretation of the photopeak response of the low-cost dense plastic detectors can be tailored to the unique mechanical and spectral properties of different materials at each of hundreds of fixed on-line locations in a plant. This paper describes the properties and presents experimental results for the two new spectrometer types that, together, bracket NaI(Tl) detectors in both performance and cost, fulfilling modern demands for portable and continuous on-line accountability of uranium and plutonium.

  13. Analysis of Picosecond Pulsed Laser Melted Graphite

    DOE R&D Accomplishments Database

    Steinbeck, J.; Braunstein, G.; Speck, J.; Dresselhaus, M. S.; Huang, C. Y.; Malvezzi, A. M.; Bloembergen, N.

    1986-12-01

    A Raman microprobe and high resolution TEM have been used to analyze the resolidified region of liquid carbon generated by picosecond pulse laser radiation. From the relative intensities of the zone center Raman-allowed mode for graphite at 1582 cm{sup -1} and the disorder-induced mode at 1360 cm{sup -1}, the average graphite crystallite size in the resolidified region is determined as a function of position. By comparison with Rutherford backscattering spectra and Raman spectra from nanosecond pulsed laser melting experiments, the disorder depth for picosecond pulsed laser melted graphite is determined as a function of irradiating energy density. Comparisons of TEM micrographs for nanosecond and picosecond pulsed laser melting experiments show that the structure of the laser disordered regions in graphite are similar and exhibit similar behavior with increasing laser pulse fluence.

  14. A Multi-Resolution Nonlinear Mapping Technique for Design and Analysis Applications

    NASA Technical Reports Server (NTRS)

    Phan, Minh Q.

    1998-01-01

    This report describes a nonlinear mapping technique where the unknown static or dynamic system is approximated by a sum of dimensionally increasing functions (one-dimensional curves, two-dimensional surfaces, etc.). These lower dimensional functions are synthesized from a set of multi-resolution basis functions, where the resolutions specify the level of details at which the nonlinear system is approximated. The basis functions also cause the parameter estimation step to become linear. This feature is taken advantage of to derive a systematic procedure to determine and eliminate basis functions that are less significant for the particular system under identification. The number of unknown parameters that must be estimated is thus reduced and compact models obtained. The lower dimensional functions (identified curves and surfaces) permit a kind of "visualization" into the complexity of the nonlinearity itself.

  15. New developments in high resolution borehole seismology and their applications to reservoir development and management

    SciTech Connect

    Paulsson, B.N.P.

    1997-08-01

    Single-well seismology, Reverse Vertical Seismic Profiles (VSP`s) and Crosswell seismology are three new seismic techniques that we jointly refer to as borehole seismology. Borehole seismic techniques are of great interest because they can obtain much higher resolution images of oil and gas reservoirs than what is obtainable with currently used seismic techniques. The quality of oil and gas reservoir management decisions depend on the knowledge of both the large and the fine scale features in the reservoirs. Borehole seismology is capable of mapping reservoirs with an order of magnitude improvement in resolution compared with currently used technology. In borehole seismology we use a high frequency seismic source in an oil or gas well and record the signal in the same well, in other wells, or on the surface of the earth.

  16. A Multi-Resolution Nonlinear Mapping Technique for Design and Analysis Application

    NASA Technical Reports Server (NTRS)

    Phan, Minh Q.

    1997-01-01

    This report describes a nonlinear mapping technique where the unknown static or dynamic system is approximated by a sum of dimensionally increasing functions (one-dimensional curves, two-dimensional surfaces, etc.). These lower dimensional functions are synthesized from a set of multi-resolution basis functions, where the resolutions specify the level of details at which the nonlinear system is approximated. The basis functions also cause the parameter estimation step to become linear. This feature is taken advantage of to derive a systematic procedure to determine and eliminate basis functions that are less significant for the particular system under identification. The number of unknown parameters that must be estimated is thus reduced and compact models obtained. The lower dimensional functions (identified curves and surfaces) permit a kind of "visualization" into the complexity of the nonlinearity itself.

  17. On the application of subcell resolution to conservation laws with stiff source terms

    NASA Technical Reports Server (NTRS)

    Chang, Shih-Hung

    1989-01-01

    LeVeque and Yee recently investigated a one-dimensional scalar conservation law with stiff source terms modeling the reacting flow problems and discovered that for the very stiff case most of the current finite difference methods developed for non-reacting flows would produce wrong solutions when there is a propagating discontinuity. A numerical scheme, essentially nonoscillatory/subcell resolution - characteristic direction (ENO/SRCD), is proposed for solving conservation laws with stiff source terms. This scheme is a modification of Harten's ENO scheme with subcell resolution, ENO/SR. The locations of the discontinuities and the characteristic directions are essential in the design. Strang's time-splitting method is used and time evolutions are done by advancing along the characteristics. Numerical experiment using this scheme shows excellent results on the model problem of LeVeque and Yee. Comparisons of the results of ENO, ENO/SR, and ENO/SRCD are also presented.

  18. Ultra-high-resolution alpha spectrometry for nuclear forensics and safeguards applications

    SciTech Connect

    Bacrania, Minesh K; Croce, Mark; Bond, Evelyn; Dry, Donald; Moody, W. Allen; Lamont, Stephen; Rabin, Michael; Rim, Jung; Smith, Audrey; Beall, James; Bennett, Douglas; Kotsubo, Vincent; Horansky, Robert; Hilton, Gene; Schmidt, Daniel; Ullom, Joel; Cantor, Robin

    2010-01-01

    We will present our work on the development of ultra-high-resolution detectors for alpha particle spectrometry. These detectors, based on superconducting transition-edge sensors, offer energy resolution that is five to ten times better than conventional silicon detectors. Using these microcalorimeter detectors, the isotopic composition of mixed-actinide samples can be determined rapidly without the need for actinide separation chemistry to isolate each element, or mass spectrometry to separate isotopic signatures that can not be resolved using traditional alpha spectrometry (e.g. Pu-239/Pu-240, or Pu-238/Am-241). This paper will cover the detector and measurement system, actinide source preparation, and the quantitative isotopic analysis of a number of forensics- and safeguards-relevant radioactive sources.

  19. Application of modulation transfer function in high-resolution image fusion

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoping; Jia, Yonghong; Chen, Xiaoyan; Pan, Delu; Chen, Jianyu; Hao, Zengzhou

    2011-11-01

    Modulation transfer function (MTF) is applied to the high frequency modulation fusion in this paper. Firstly, MTFs are calculated using the edge method, and 2-dimension MTF-filters are properly designed. Secondly, MTF-filters are used for degrading original high resolusion images. High frequency modulation fusion parameters are then obtained under the minimum mean square error criterion. The results show that fusion images derived from the improved high frequency modulation based on MTF method have spatial resolution close to non-degraded pan images. Compared with fusion methods of weighted high-pass filtering (w-HPF), MTF general image fusion framework (MTF-GIF), the improved method performs well in terms of preservation of spectral information and spatial resolution.

  20. The Application of Synthetically Focused Imaging Techniques for High Resolution Guided Wave Pipe Inspection

    NASA Astrophysics Data System (ADS)

    Davies, J.; Cawley, P.

    2007-03-01

    Synthetically focused guided wave imaging techniques have previously been employed for plate like structures. Much work has been has been done using algorithms such as the synthetic aperture focusing technique (SAFT), the total focusing method (TFM) and common source method (CSM) using both linear and circular arrays. The resolutions for such algorithms for the plate case are well known. We have attempted to use these algorithms for imaging defects in pipes using an array of piezoelectric shear transducers clamped around the pipe circumference. We show that the SAFT and the TFM methods both suffer from coherent noise in the image caused by circumferentially propagating wave modes. It is shown that the common source method (CSM) method does not suffer from this problem though the resolution obtained is poorer. Results from the different imaging algorithms are presented for an 8 inch pipe using 50 kHz excitation, both from finite element simulations and laboratory experiments.

  1. Demonstration of high-resolution inverse VSP for reservoir characterization applications

    SciTech Connect

    Parra, J.O.

    1991-01-01

    The objective of this project is the determination of inverse vertical seismic profiling (VSP) measurements using new experimental field instrumentation capable of providing at least an order of magnitude improvement in the resolution of structural details in comparison with conventional seismic images. This two-year project will entail instrumentation tests under controlled field conditions during the first year followed by full-scale field demonstration tests in a representative oil-bearing reservoir formation during the second year. An automatic time-picking program and a tomographic inversion program developed for processing interwell seismic data were generalized for processing reverse VSP data. A technical paper was submitted for publication to Geophysics. The paper is entitled; A Wax-Embedded Borehole Seismic Detector for High-Resolution Measurements.'' A copy of this manuscript is enclosed in the Appendix. 3 figs., 1 tab.

  2. Direct contact melting process on a porous heating wall

    SciTech Connect

    Oka, M.; Hasegawa, E.

    1995-12-31

    Direct contact melting process takes place in many natural and technological processes. One of the important application of this process is thermal storage system. Phase change material (PCM) is stored in a small capsule. It melts by heating peripherally. This paper presents a theoretical study of direct contact melting process in a capsule. Inner wall surface of the capsule is made of porous material. In this melting process, melting rate is important factor for the efficiency of the system. In this paper, the authors propose utilization of porous material as a heating wall. This is one of the effective way to accelerate melting rate. Melted liquid goes through into the porous heating wall. As a result, the solid PCM can reach closer to the heating wall. The authors also discussed conductivity of the porous wall.

  3. The moderate resolution imaging spectrometer: An EOS facility instrument candidate for application of data compression methods

    NASA Technical Reports Server (NTRS)

    Salomonson, Vincent V.

    1991-01-01

    The Moderate Resolution Imaging Spectrometer (MODIS) observing facility will operate on the Earth Observing System (EOS) in the late 1990's. It is estimated that this observing facility will produce over 200 gigabytes of data per day requiring a storage capability of just over 300 gigabytes per day. Archiving, browsing, and distributing the data associated with MODIS represents a rich opportunity for testing and applying both lossless and lossy data compression methods.

  4. Application of high-resolution laser spectroscopy to the monitoring of vapor-phase metals

    SciTech Connect

    Lipert, R.J.; Wang, Z.M.; Schuler, R.; Edelson, M.C.

    1992-10-01

    Research conducted in the Ames Laboratory Nuclear Safeguards and Security Program is reviewed. Progress in applying high-resolution laser spectroscopy to the monitoring of vapor-phase metals is described. The spectroscopic techniques employed include fluorescence excitation in an atomic beam, laser atomic absorption in a heat-pipe oven and atomic beam, Doppler-free saturated absorption in a heat-pipe oven, and Doppler-free polarization spectroscopy for the stabilization of the laser wavelength.

  5. High-resolution linear CCD application in the recognition of cuttings' lithology category

    NASA Astrophysics Data System (ADS)

    Mu, Bing; Li, Wen-Dong; Cheng, Kai; Ding, Ming-Ming; Sun, Zheng; Ren, Lihui; Ci, Xing-Hua; Zheng, Rong-Er

    2009-11-01

    It is difficult in the description of rock cuttings' lithology category with a traditional manual method since PDC bits have been widely used in the process of drilling. To recognize the tiny cuttings' lithology category effectively, a digital compact system based on high-resolution color linear CCD and microphotography is established and introduced in this paper. The system is mainly constructed by high resolution color linear CCD, micro lens, white LED light sources and conveyor. The Color linear CCD with up to 4080 pixels per line combined with micro lens leads to a resultant reproduction ratio of 1:1. It ensures that tiny cuttings' images can be captured clearly, and hence the detailed information of cuttings' color and texture can be obtained. With the linear scanning, we can get images with both high-resolution and larger field of view than array CCD. Optimal parameter configuration is determined by the experiments of hardware control program and optical parameter adjustment. The software to recognize cuttings' lithology category is developed by extracting multi-character values from the image information and by using the LIBSVM classifier. With the optimal parameter configuration and the developed recognition software, the cuttings' lithology category has been well described with a average recognition rate about 95% for mudstones and about 90% for sandstones, which proves that the cuttings' images captured by the high-resolution linear CCD meet the requirement of the subsequent recognition algorithm. The obtained results show that the digital compact system is greatly potential to be used in oil field logging.

  6. Application of high resolution synchrotron micro-CT radiation in dental implant osseointegration.

    PubMed

    Neldam, Camilla Albeck; Lauridsen, Torsten; Rack, Alexander; Lefolii, Tore Tranberg; Jørgensen, Niklas Rye; Feidenhans'l, Robert; Pinholt, Else Marie

    2015-06-01

    The purpose of this study was to describe a refined method using high-resolution synchrotron radiation microtomography (SRmicro-CT) to evaluate osseointegration and peri-implant bone volume fraction after titanium dental implant insertion. SRmicro-CT is considered gold standard evaluating bone microarchitecture. Its high resolution, high contrast, and excellent high signal-to-noise-ratio all contribute to the highest spatial resolutions achievable today. Using SRmicro-CT at a voxel size of 5 μm in an experimental goat mandible model, the peri-implant bone volume fraction was found to quickly increase to 50% as the radial distance from the implant surface increased, and levelled out to approximately 80% at a distance of 400 μm. This method has been successful in depicting the bone and cavities in three dimensions thereby enabling us to give a more precise answer to the fraction of the bone-to-implant contact compared to previous methods. PMID:25957106

  7. In-vivo high resolution corneal imaging and analysis on animal models for clinical applications

    NASA Astrophysics Data System (ADS)

    Hong, Jesmond; Shinoj, V. K.; Murukeshan, V. M.; Baskaran, M.; Aung, Tin

    2015-07-01

    A simple and low cost optical probe system for the high resolution imaging of the cornea is proposed, based on a Gaussian beam epi-illumination configuration. Corneal topography is obtained by moving the scanning spot across the eye in a raster fashion whereas pachymetry data is achieved by reconstructing the images obtained at different depths. The proposed prototype has been successfully tested on porcine eye samples ex vivo and subsequently on laboratory animals, such as the New Zealand White Rabbit, in vivo. This proposed system and methodology pave the way for realizing a simple and inexpensive optical configuration for pachymetry and keratometry readings, with achievable resolution up to the cellular level. This novel and non-contact high resolution imaging modality demonstrates high intraobserver reproducibility and repeatability. Together with its sophisticated data analysis strategies and safety profile, it is believed to complement existing imaging modalities in the assessment and evaluation of corneal diseases, which enable a decrease in morbidity and improvement in the effectiveness of subsequent treatment.

  8. A compact high resolution flat panel PET detector based on the new 4-side buttable MPPC for biomedical applications

    NASA Astrophysics Data System (ADS)

    Wang, Qiang; Wen, Jie; Ravindranath, Bosky; O`Sullivan, Andrew W.; Catherall, David; Li, Ke; Wei, Shouyi; Komarov, Sergey; Tai, Yuan-Chuan

    2015-09-01

    Compact high-resolution panel detectors using virtual pinhole (VP) PET geometry can be inserted into existing clinical or pre-clinical PET systems to improve regional spatial resolution and sensitivity. Here we describe a compact panel PET detector built using the new Though Silicon Via (TSV) multi-pixel photon counters (MPPC) detector. This insert provides high spatial resolution and good timing performance for multiple bio-medical applications. Because the TSV MPPC design eliminates wire bonding and has a package dimension which is very close to the MPPC's active area, it is 4-side buttable. The custom designed MPPC array (based on Hamamatsu S12641-PA-50(x)) used in the prototype is composed of 4×4 TSV-MPPC cells with a 4.46 mm pitch in both directions. The detector module has 16×16 lutetium yttrium oxyorthosilicate (LYSO) crystal array, with each crystal measuring 0.92×0.92×3 mm3 with 1.0 mm pitch. The outer diameter of the detector block is 16.8×16.8 mm2. Thirty-two such blocks will be arranged in a 4×8 array with 1 mm gaps to form a panel detector with detection area around 7 cm×14 cm in the full-size detector. The flood histogram acquired with 68Ge source showed excellent crystal separation capability with all 256 crystals clearly resolved. The detector module's mean, standard deviation, minimum (best) and maximum (worst) energy resolution were 10.19%, ±0.68%, 8.36% and 13.45% FWHM, respectively. The measured coincidence time resolution between the block detector and a fast reference detector (around 200 ps single photon timing resolution) was 0.95 ns. When tested with Siemens Cardinal electronics the performance of the detector blocks remain consistent. These results demonstrate that the TSV-MPPC is a promising photon sensor for use in a flat panel PET insert composed of many high resolution compact detector modules.

  9. The microwave properties of simulated melting precipitation particles: sensitivity to initial melting

    NASA Astrophysics Data System (ADS)

    Johnson, B. T.; Olson, W. S.; Skofronick-Jackson, G.

    2015-06-01

    A simplified approach is presented for assessing the microwave response to the initial melting of realistically-shaped ice particles. This paper is divided into two parts: (1) a description of the Single Particle Melting Model (SPMM): a heuristic melting simulation for ice-phase precipitation particles of any shape or size. SPMM is applied to two simulated aggregate snow particles, simulating melting up to 0.15 melt fraction by mass; and (2) the computation of the single-particle microwave scattering and extinction properties these hydrometeors, using the discrete dipole approximation (via DDSCAT), at the following selected frequencies: 13.4, 35.6, 94.0 GHz for radar applications; and 89, 165.0 and 183.31 GHz for radiometer applications. These selected frequencies are consistent with current microwave remote sensing platforms, such as CloudSat and the Global Precipitation Measurement (GPM) mission. Comparisons with calculations using variable-density spheres indicate significant deviations in scattering and extinction properties throughout the initial range of melting (liquid volume fractions less than 0.15). Integration of the single-particle properties over an exponential particle-size distribution provides additional insight into idealized radar reflectivity and passive microwave brightness temperature sensitivity to variations in size/mass, shape, melt fraction, and particle orientation.

  10. The microwave properties of simulated melting precipitation particles: sensitivity to initial melting

    NASA Astrophysics Data System (ADS)

    Johnson, B. T.; Olson, W. S.; Skofronick-Jackson, G.

    2016-01-01

    A simplified approach is presented for assessing the microwave response to the initial melting of realistically shaped ice particles. This paper is divided into two parts: (1) a description of the Single Particle Melting Model (SPMM), a heuristic melting simulation for ice-phase precipitation particles of any shape or size (SPMM is applied to two simulated aggregate snow particles, simulating melting up to 0.15 melt fraction by mass), and (2) the computation of the single-particle microwave scattering and extinction properties of these hydrometeors, using the discrete dipole approximation (via DDSCAT), at the following selected frequencies: 13.4, 35.6, and 94.0 GHz for radar applications and 89, 165.0, and 183.31 GHz for radiometer applications. These selected frequencies are consistent with current microwave remote-sensing platforms, such as CloudSat and the Global Precipitation Measurement (GPM) mission. Comparisons with calculations using variable-density spheres indicate significant deviations in scattering and extinction properties throughout the initial range of melting (liquid volume fractions less than 0.15). Integration of the single-particle properties over an exponential particle size distribution provides additional insight into idealized radar reflectivity and passive microwave brightness temperature sensitivity to variations in size/mass, shape, melt fraction, and particle orientation.

  11. Kinetics of anorthite dissolution in basaltic melt

    NASA Astrophysics Data System (ADS)

    Yu, Yi; Zhang, Youxue; Chen, Yang; Xu, Zhengjiu

    2016-04-01

    We report convection-free anorthite dissolution experiments in a basaltic melt at 1280-1500 °C and 0.5 GPa on two different crystallographic surfaces, (1 2 1 bar) and (3 bar 0 2) to investigate dissolution kinetics. The anisotropy of the anorthite dissolution rate along these two surfaces is negligible. Time series experiments at ∼1280 °C show that anorthite dissolution is mainly controlled by diffusion in the melt within experimental uncertainty. Analytical solutions were used to model the dissolution and diffusion processes, and to obtain the diffusivities and the saturation concentrations of the equilibrium-determining component (Al2O3) for anorthite dissolution into the basaltic melt. For the first time, we are able to show the physical and chemical characteristics of quench growth effect on the near-interface melt using high spatial resolution (0.3 μm) EDS analyses. For anorthite (An# ⩾ 90) saturation in a melt with 39-53 wt% SiO2 and ⩽0.4 wt% H2O, the concentration of Al2O3 in wt% depends on temperature as follows:

  12. Application of the maximum entropy method to spectral-domain optical coherence tomography for enhancing axial resolution

    NASA Astrophysics Data System (ADS)

    Takahashi, Yoshiyuki; Watanabe, Yuuki; Sato, Manabu

    2007-08-01

    For the first time we applied the maximum entropy method (MEM) to spectral domain optical coherence tomography to enhance axial resolution (AR). The MEM estimates the power spectrum by fitting. For an onion with optimization of M = 70, the AR of 18.8 μm by discrete Fourier transform (DFT) was improved three times compared with peak widths. The calculation time by the MEM with M = 70 was 20 times longer than that of DFT. However, further studies are needed for practical applications, because the validity of the MEM depends on the sample structures.

  13. Low drift and high resolution miniature optical fiber combined pressure- and temperature sensor for cardio-vascular and urodynamic applications

    NASA Astrophysics Data System (ADS)

    Poeggel, Sven; Tosi, Daniele; Duraibabu, Dineshbabu; Sannino, Simone; Lupoli, Laura; Ippolito, Juliet; Fusco, Fernando; Mirone, Vincenzo; Leen, Gabriel; Lewis, Elfed

    2014-05-01

    The all-glass optical fibre pressure and temperature sensor (OFPTS), present here is a combination of an extrinsic Fabry Perot Interferometer (EFPI) and an fiber Bragg gratings (FBG), which allows a simultaneously measurement of both pressure and temperature. Thermal effects experienced by the EFPI can be compensated by using the FBG. The sensor achieved a pressure measurement resolution of 0.1mmHg with a frame-rate of 100Hz and a low drift rate of < 1 mmHg/hour drift. The sensor has been evaluated using a cardiovascular simulator and additionally has been evaluated in-vivo in a urodynamics application under medical supervision.

  14. TanDEM-X high resolution DEMs and their applications to flow modeling

    NASA Astrophysics Data System (ADS)

    Wooten, Kelly M.

    Lava flow modeling can be a powerful tool in hazard assessments; however, the ability to produce accurate models is usually limited by a lack of high resolution, up-to-date Digital Elevation Models (DEMs). This is especially obvious in places such as Kilauea Volcano (Hawaii), where active lava flows frequently alter the terrain. In this study, we use a new technique to create high resolution DEMs on Kilauea using synthetic aperture radar (SAR) data from the TanDEM-X (TDX) satellite. We convert raw TDX SAR data into a geocoded DEM using GAMMA software [Werner et al., 2000]. This process can be completed in several hours and permits creation of updated DEMs as soon as new TDX data are available. To test the DEMs, we use the Harris and Rowland [2001] FLOWGO lava flow model combined with the Favalli et al. [2005] DOWNFLOW model to simulate the 3-15 August 2011 eruption on Kilauea's East Rift Zone. Results were compared with simulations using the older, lower resolution 2000 SRTM DEM of Hawaii. Effusion rates used in the model are derived from MODIS thermal infrared satellite imagery. FLOWGO simulations using the TDX DEM produced a single flow line that matched the August 2011 flow almost perfectly, but could not recreate the entire flow field due to the relatively high DEM noise level. The issues with short model flow lengths can be resolved by filtering noise from the DEM. Model simulations using the outdated SRTM DEM produced a flow field that followed a different trajectory to that observed. Numerous lava flows have been emplaced at Kilauea since the creation of the SRTM DEM, leading the model to project flow lines in areas that have since been covered by fresh lava flows. These results show that DEMs can quickly become outdated on active volcanoes, but our new technique offers the potential to produce accurate, updated DEMs for modeling lava flow hazards.

  15. Compound classification by computer treatment of low resolution mass spectra - Application to geochemical and environmental problems.

    NASA Technical Reports Server (NTRS)

    Smith, D. H.; Eglinton, G.

    1972-01-01

    A description is given of a development of computer analysis of low-resolution chromatographic-mass spectrometric data, which provides a preliminary classification of an unknown spectrum as a listing of candidate classes of compounds. This procedure, referred to as COMSOC (Classification of Mass Spectra on Computers), operates by converting an incoming unknown mass spectrum into a simplified key word which is then compared with each of the key words held in its reference file. The advantages of COMSOC in characterizing complex mixtures are emphasized.

  16. Development and application of the High resolution VOC Atmospheric Chemistry in Canopies (Hi-VACC) model

    NASA Astrophysics Data System (ADS)

    Kenny, W.; Bohrer, G.; Chatziefstratiou, E.

    2013-12-01

    We have been working to develop a new post-processing model - High resolution VOC Atmospheric Chemistry in Canopies (Hi-VACC) - which will be able to resolve the dispersion and chemistry of reacting chemical species given their emission rates from the vegetation and soil, driven by high resolution meteorological forcing and wind fields from various high resolution atmospheric regional and large-eddy simulations. Hi-VACC reads in fields of pressure, temperature, humidity, air density, short-wave radiation, wind (3-D u, v and w components) and sub-grid-scale turbulence that were simulated by a high resolution atmospheric model. This meteorological forcing data is provided as snapshots of 3-D fields. Presently, the advection-diffusion portion of the model is fully developed, and we have tested it using a number of RAMS-based Forest Large Eddy Simulation (RAFLES) runs. Here, we present results from utilizing Hi-VACC in a few different contexts where it performs smoke and particle dispersion well. These include simulations of smoke dispersion from a theoretical forest fire in a domain in The Pine Barrens in New Jersey, as well as simulations to test the effects of heat flux on a scalar plume dispersing over a vegetative windbreak in an agricultural setting. Additional, we show initial results from testing the coupled chemistry component of Hi-VACC. One of the primary benefits of Hi-VACC is that users of other models can utilize this tool with only minimal work on their part -- processing their output fields into the appropriate HI-VACC input format. We have developed our model such that for whatever atmospheric model is being used with it, a MATLAB function must be written to extract the necessary information from the output files of that model and shape it into the proper format. This is the only model-specific work required. As such, this sort of smoke dispersion modeling performed by Hi-VACC - as well as its other capabilities - can be easily performed in other

  17. Application of the Lucy–Richardson Deconvolution Procedure to High Resolution Photoemission Spectra

    SciTech Connect

    Rameau, J.; Yang, H.-B.; Johnson, P.D.

    2010-07-01

    Angle-resolved photoemission has developed into one of the leading probes of the electronic structure and associated dynamics of condensed matter systems. As with any experimental technique the ability to resolve features in the spectra is ultimately limited by the resolution of the instrumentation used in the measurement. Previously developed for sharpening astronomical images, the Lucy-Richardson deconvolution technique proves to be a useful tool for improving the photoemission spectra obtained in modern hemispherical electron spectrometers where the photoelectron spectrum is displayed as a 2D image in energy and momentum space.

  18. A multichannel, high-resolution, UV spectrometer for laser-fusion applications

    SciTech Connect

    Donaldson, W.R.; Millecchia, M.; Keck, R.

    2005-07-15

    A 63-channel, ultraviolet (UV) spectrometer has been designed and tested. With an input energy of 1 {mu}J per channel, 63 spectra can be acquired simultaneously on a single, multibeam laser shot. The spectrometer has a dispersion at the detector plane of 8.6x10{sup -2} pm/{mu}m and a spectral window of 2.4 nm at {lambda}=351 nm. The wavelength resolution varies from 2.5 pm at the center of the field of view to 6 pm at the edge.

  19. Application of high-resolution single-channel recording to functional studies of cystic fibrosis mutants.

    PubMed

    Cai, Zhiwei; Sohma, Yoshiro; Bompadre, Silvia G; Sheppard, David N; Hwang, Tzyh-Chang

    2011-01-01

    The patch-clamp technique is a powerful and versatile method to investigate the cystic fibrosis transmembrane conductance regulator (CFTR) Cl- channel, its malfunction in disease and modulation by small molecules. Here, we discuss how the molecular behaviour of CFTR is investigated using high-resolution single-channel recording and kinetic analyses of channel gating. We review methods used to quantify how cystic fibrosis (CF) mutants perturb the biophysical properties and regulation of CFTR. By explaining the relationship between macroscopic and single-channel currents, we demonstrate how single-channel data provide molecular explanations for changes in CFTR-mediated transepithelial ion transport elicited by CF mutants. PMID:21594800

  20. Application of High-Resolution Single-Channel Recording to Functional Studies of Cystic Fibrosis Mutants

    PubMed Central

    Cai, Zhiwei; Sohma, Yoshiro; Bompadre, Silvia G.; Sheppard, David N.; Hwang, Tzyh-Chang

    2016-01-01

    The patch-clamp technique is a powerful and versatile method to investigate the cystic fibrosis transmem-brane conductance regulator (CFTR) Cl− channel, its malfunction in disease and modulation by small molecules. Here, we discuss how the molecular behaviour of CFTR is investigated using high-resolution single-channel recording and kinetic analyses of channel gating. We review methods used to quantify how cystic fibrosis (CF) mutants perturb the biophysical properties and regulation of CFTR. By explaining the relationship between macroscopic and single-channel currents, we demonstrate how single-channel data provide molecular explanations for changes in CFTR-mediated transepithelial ion transport elicited by CF mutants. PMID:21594800

  1. Computer-controlled High Resolution Arbitrary Waveform Generator (HRAWG) for Focusing Beamforming Applications

    NASA Astrophysics Data System (ADS)

    Assef, Amauri Amorin; Maia, Joaquim Miguel; Costa, Eduardo Tavares

    In advanced ultrasound imaging systems, expensive high-end integrated analog front-ends have been traditionally used to support generation of arbitrary transmit waveforms, in addition to transmit focusing and apodization control. In this paper, we present a cost-effective computer-controlled reconfigurable high-resolution arbitrary waveform generator (HRAWG) that has been designed for ultrasound research, development and teaching at the Federal University of Technology (UTFPR), Brazil. The 8-channel transmit beamformer is fully controlled by a host computer in which a Matlab GUI with the Field II simulation program, allows easy and accurate control over the transmission parameters such as waveform, amplitude apodization and timing.

  2. InfraRed Standards Used for Spectrophotometric Calibration - Application to the Medium Resolution Spectrometer of {MIRI}

    NASA Astrophysics Data System (ADS)

    Decin, L.; Bauwens, E.; Blommaert, J. A. D. L.

    2007-04-01

    One of the main ingredients in establishing the relation between input signal and output flux from a spectrometer, is the accurate determination of the {spectrophotometric calibration}. In case of spectrometers onboard satellites, the accuracy of this part of the calibration pedigree is ultimately linked to the reliability of the candidate calibrators as being fiducial. In this contribution, we deal with the spectrophotometric calibration of {infrared} spectrometers in the 2-200 μm wavelength range. We outline a general selection procedure to arrive at a set of fiducial IR calibrators, and apply the method to the Medium Resolution Spectrometer of MIRI which will be onboard the James Webb Space Telescope.

  3. Multi-Resolution Markov-Chain-Monte-Carlo Approach for System Identification with an Application to Finite-Element Models

    SciTech Connect

    Johannesson, G; Glaser, R E; Lee, C L; Nitao, J J; Hanley, W G

    2005-02-07

    Estimating unknown system configurations/parameters by combining system knowledge gained from a computer simulation model on one hand and from observed data on the other hand is challenging. An example of such inverse problem is detecting and localizing potential flaws or changes in a structure by using a finite-element model and measured vibration/displacement data. We propose a probabilistic approach based on Bayesian methodology. This approach does not only yield a single best-guess solution, but a posterior probability distribution over the parameter space. In addition, the Bayesian approach provides a natural framework to accommodate prior knowledge. A Markov chain Monte Carlo (MCMC) procedure is proposed to generate samples from the posterior distribution (an ensemble of likely system configurations given the data). The MCMC procedure proposed explores the parameter space at different resolutions (scales), resulting in a more robust and efficient procedure. The large-scale exploration steps are carried out using coarser-resolution finite-element models, yielding a considerable decrease in computational time, which can be a crucial for large finite-element models. An application is given using synthetic displacement data from a simple cantilever beam with MCMC exploration carried out at three different resolutions.

  4. User Friendly Processing of Sediment CT Data: Software and Application in High Resolution Non-Destructive Sediment Core Data Sets

    NASA Astrophysics Data System (ADS)

    Reilly, B. T.; Stoner, J. S.; Wiest, J.; Abbott, M. B.; Francus, P.; Lapointe, F.

    2015-12-01

    Computed Tomography (CT) of sediment cores allow for high resolution images, three dimensional volumes, and down core profiles, generated through the attenuation of X-rays as a function of density and atomic number. When using a medical CT-Scanner, these quantitative data are stored in pixels using the Hounsfield scale, which are relative to the attenuation of X-rays in water and air at standard temperature and pressure. Here we present MATLAB based software specifically designed for sedimentary applications with a user friendly graphical interface to process DICOM files and stitch overlapping CT scans. For visualization, the software allows easy generation of core slice images with grayscale and false color relative to a user defined Hounsfield number range. For comparison to other high resolution non-destructive methods, down core Hounsfield number profiles are extracted using a method robust to coring imperfections, like deformation, bowing, gaps, and gas expansion. We demonstrate the usefulness of this technique with lacustrine sediment cores from the Western United States and Canadian High Arctic, including Fish Lake, Oregon, and Sawtooth Lake, Ellesmere Island. These sites represent two different depositional environments and provide examples for a variety of common coring defects and lithologies. The Hounsfield profiles and images can be used in combination with other high resolution data sets, including sediment magnetic parameters, XRF core scans and many other types of data, to provide unique insights into how lithology influences paleoenvironmental and paleomagnetic records and their interpretations.

  5. Applications of shallow high-resolution seismic reflection to various environmental problems

    USGS Publications Warehouse

    Miller, R.D.; Steeples, D.W.

    1994-01-01

    Shallow seismic reflection has been successfully applied to environmental problems in a variety of geologic settings. Increased dynamic range of recording equipment and decreased cost of processing hardware and software have made seismic reflection a cost-effective means of imaging shallow geologic targets. Seismic data possess sufficient resolution in many areas to detect faulting with displacement of less than 3 m and beds as thin as 1 m. We have detected reflections from depths as shallow as 2 m. Subsurface voids associated with abandoned coal mines at depths of less than 20 m can be detected and mapped. Seismic reflection has been successful in mapping disturbed subsurface associated with dissolution mining of salt. A graben detected and traced by seismic reflection was shown to be a preferential pathway for leachate leaking from a chemical storage pond. As shown by these case histories, shallow high-resolution seismic reflection has the potential to significantly enhance the economics and efficiency of preventing and/or solving many environmental problems. ?? 1994.

  6. Interactive desktop analysis of high resolution simulations: application to turbulent plume dynamics and current sheet formation

    NASA Astrophysics Data System (ADS)

    Clyne, John; Mininni, Pablo; Norton, Alan; Rast, Mark

    2007-08-01

    The ever increasing processing capabilities of the supercomputers available to computational scientists today, combined with the need for higher and higher resolution computational grids, has resulted in deluges of simulation data. Yet the computational resources and tools required to make sense of these vast numerical outputs through subsequent analysis are often far from adequate, making such analysis of the data a painstaking, if not a hopeless, task. In this paper, we describe a new tool for the scientific investigation of massive computational datasets. This tool (VAPOR) employs data reduction, advanced visualization, and quantitative analysis operations to permit the interactive exploration of vast datasets using only a desktop PC equipped with a commodity graphics card. We describe VAPORs use in the study of two problems. The first, motivated by stellar envelope convection, investigates the hydrodynamic stability of compressible thermal starting plumes as they descend through a stratified layer of increasing density with depth. The second looks at current sheet formation in an incompressible helical magnetohydrodynamic flow to understand the early spontaneous development of quasi two-dimensional (2D) structures embedded within the 3D solution. Both of the problems were studied at sufficiently high spatial resolution, a grid of 5042 by 2048 points for the first and 15363 points for the second, to overwhelm the interactive capabilities of typically available analysis resources.

  7. Multiscale seismic attributes: source-corrected wavelet response and application to high-resolution seismic data

    NASA Astrophysics Data System (ADS)

    Ker, Stephan; Le Gonidec, Yves; Gibert, Dominique

    2012-09-01

    A wavelet-based method was presented in a previous work to introduce multiscale seismic attributes for high-resolution seismic data. Because of the limited frequency bandwidth of the seismic source, we observed distortions in the seismic attributes based on the wavelet response of the subsurface discontinuities (Le Gonidec et al.). In this paper, we go further in the seismic source-correction by considering Lévy alpha-stable distributions introduced in the formalism of the continuous wavelet transform (CWT). The wavelets are Gaussian derivative functions (GDF), characterized by a derivative order. We show that a high-resolution seismic source, after a classical signature processing, can be taken into account with a GDF. We demonstrate that in the framework of the Born approximation, the CWT of a seismic trace involving such a finite frequency bandwidth can be made equivalent to the CWT of the impulse response of the subsurface and is defined for a reduced range of dilations. We apply the method for the SYSIF seismic device (Marsset et al.; Ker et al.) and show that the source-corrections allow to define seismic attributes for layer thicknesses in the range [24; 115 cm]. We present the analysis for two seismic reflectors identified on a SYSIF profile, and we show that the source-corrected multiscale analysis quantifies their complex geometries.

  8. Power asymmetry in conflict resolution with application to a water pollution dispute in China

    NASA Astrophysics Data System (ADS)

    Yu, Jing; Kilgour, D. Marc; Hipel, Keith W.; Zhao, Min

    2015-10-01

    The concept of power asymmetry is incorporated into the framework of the Graph Model for Conflict Resolution (GMCR) and then applied to a water pollution dispute in China in order to show how it can provide strategic insights into courses of action. In a new definition of power asymmetry, one of the decision makers (DMs) in a conflict can influence the preferences of other DMs by taking advantage of additional options reflecting the particular DM's more powerful position. The more powerful DM may have three different kinds of power: direct positive, direct negative, or indirect. It is useful to analyze a model of a conflict without power asymmetry, and then to analyze a power-asymmetric model. As demonstrated by analysis of the water quality controversy that took place at the border separating the Chinese provinces of Jiangsu and Zhejiang, this novel conflict resolution methodology can be readily applied to real-world strategic conflicts to gain an enhanced understanding of the effects of asymmetric power.

  9. High Speed High Resolution Current Comparator and its Application to Analog to Digital Converter

    NASA Astrophysics Data System (ADS)

    Sridhar, Ranjana; Pandey, Neeta; Bhattacharyya, Asok; Bhatia, Veepsa

    2016-06-01

    This paper introduces a high speed high resolution current comparator which includes the current differencing stage and employs non linear feedback in the gain stage. The usefulness of the proposed comparator is demonstrated by implementing a 3-bit current mode flash analog-to-digital converter (ADC). Simulation program with integrated circuit emphasis (SPICE) simulations have been carried out to verify theoretical proposition and performance parameters of both comparator and ADC are obtained using TSMC 0.18 µm CMOS technology parameters. The current comparator shows a resolution of ±5 nA and a delay of 0.86 ns for current difference of ±1 µA. The impact of process variation on proposed comparator propagation delay has been studied through Monte Carlo simulation and it is found that percentage change in propagation delay in best case is 1.3 % only and in worst case is 9 % only. The ADC exhibits an offset, gain error, differential nonlinearity (DNL) and integral nonlinearity (INL) of 0.102 µA, 0.99, -0.34 LSB and 0.0267 LSB, respectively. The impact of process variation on ADC has also been studied at different process corners.

  10. High Speed High Resolution Current Comparator and its Application to Analog to Digital Converter

    NASA Astrophysics Data System (ADS)

    Sridhar, Ranjana; Pandey, Neeta; Bhattacharyya, Asok; Bhatia, Veepsa

    2015-04-01

    This paper introduces a high speed high resolution current comparator which includes the current differencing stage and employs non linear feedback in the gain stage. The usefulness of the proposed comparator is demonstrated by implementing a 3-bit current mode flash analog-to-digital converter (ADC). Simulation program with integrated circuit emphasis (SPICE) simulations have been carried out to verify theoretical proposition and performance parameters of both comparator and ADC are obtained using TSMC 0.18 µm CMOS technology parameters. The current comparator shows a resolution of ±5 nA and a delay of 0.86 ns for current difference of ±1 µA. The impact of process variation on proposed comparator propagation delay has been studied through Monte Carlo simulation and it is found that percentage change in propagation delay in best case is 1.3 % only and in worst case is 9 % only. The ADC exhibits an offset, gain error, differential nonlinearity (DNL) and integral nonlinearity (INL) of 0.102 µA, 0.99, -0.34 LSB and 0.0267 LSB, respectively. The impact of process variation on ADC has also been studied at different process corners.

  11. Image resolution enhancement using edge extraction and sparse representation in wavelet domain for real-time application

    NASA Astrophysics Data System (ADS)

    Ponomaryov, Volodymyr I.; Chavez-Roman, Herminio; Gonzalez-Huitron, Victor

    2014-05-01

    The paper presents the design and hardware implementation of novel framework for image resolution enhancement employing the wavelet domain. The principal idea of resolution enhancement consists of using edge preservation procedure and mutual interpolation between the input low-resolution (LR) image and the HF sub-band images performed via the Discrete Wavelet Transform (DWT). The LR image is used in the sparse representation for the resolutionenhancement process, employing a 1-D interpolation in set of angle directions; following, the computations of the new samples are found, estimating the missing samples. Finally, pixels are performed via the Lanczos interpolation. To preserve more edge information additional edge extraction in HF sub-bands is performed in the DWT decomposition of input image. The differences between the LL sub-band image and LR input image is used to correct the HF component, generating a significantly sharper reconstructed image. All sub-band images are used to generate the new HR image applying the inverse DWT (IDWT). Additionally, the novel framework employs a denoising procedure by using the Non-Local Means for the input LR image. An efficiency analysis of the designed and other state-of-the-art filters have been performed on the DSP TMS320DM648 by Texas Instruments through MATLAB's Simulink module and on the video card (NVIDIA®Quadro® K2000), showing that novel SR procedure can be used in real-time processing applications. Experimental results have confirmed that implemented framework outperforms existing SR algorithms in terms of objective criteria (PSNR, MAE and SSIM) as well as in subjective perception, justifying better image resolution.

  12. Partial Ambiguity Resolution for Ground and Space-Based Applications in a GPS+Galileo scenario: A simulation study

    NASA Astrophysics Data System (ADS)

    Nardo, A.; Li, B.; Teunissen, P. J. G.

    2016-01-01

    Integer Ambiguity Resolution (IAR) is the key to fast and precise GNSS positioning. The proper diagnostic metric for successful IAR is provided by the ambiguity success rate being the probability of correct integer estimation. In this contribution we analyse the performance of different GPS+Galileo models in terms of number of epochs needed to reach a pre-determined success rate, for various ground and space-based applications. The simulation-based controlled model environment enables us to gain insight into the factors contributing to the ambiguity resolution strength of the different GPS+Galileo models. Different scenarios of modernized GPS+Galileo are studied, encompassing the long baseline ground case as well as the medium dynamics case (airplane) and the space-based Low Earth Orbiter (LEO) case. In our analyses of these models the capabilities of partial ambiguity resolution (PAR) are demonstrated and compared to the limitations of full ambiguity resolution (FAR). The results show that PAR is generally a more efficient way than FAR to reduce the time needed to achieve centimetre-level positioning precision. For long single baselines, PAR can achieve time reductions of fifty percent to achieve such precision levels, while for multiple baselines it even becomes more effective, reaching reductions up to eighty percent for four station networks. For a LEO, the rapidly changing observation geometry does not even allow FAR, while PAR is then still possible for both dual- and triple-frequency scenarios. With the triple-frequency GPS+Galileo model the availability of precise positioning improves by fifteen percent with respect to the dual-frequency scenario.

  13. Greenland ice sheet melt from MODIS and associated atmospheric variability

    PubMed Central

    Häkkinen, Sirpa; Hall, Dorothy K; Shuman, Christopher A; Worthen, Denise L; DiGirolamo, Nicolo E

    2014-01-01

    Daily June-July melt fraction variations over the Greenland ice sheet (GIS) derived from the Moderate Resolution Imaging Spectroradiometer (MODIS) (2000–2013) are associated with atmospheric blocking forming an omega-shape ridge over the GIS at 500 hPa height. Blocking activity with a range of time scales, from synoptic waves breaking poleward (<5 days) to full-fledged blocks (≥5 days), brings warm subtropical air masses over the GIS controlling daily surface temperatures and melt. The temperature anomaly of these subtropical air mass intrusions is also important for melting. Based on the years with the greatest melt (2002 and 2012) during the MODIS era, the area-average temperature anomaly of 2 standard deviations above the 14 year June-July mean results in a melt fraction of 40% or more. Though the summer of 2007 had the most blocking days, atmospheric temperature anomalies were too small to instigate extreme melting. Key Points Short-term atmospheric blocking over Greenland contributes to melt episodes Associated temperature anomalies are equally important for the melt Duration and strength of blocking events contribute to surface melt intensity PMID:25821277

  14. High-Resolution Laser-Induced Breakdown Spectroscopy used in Homeland Security and Forensic Applications

    SciTech Connect

    Martin, Madhavi Z; Wullschleger, Stan D; Vass, Arpad Alexander; Martin, Rodger Carl; Grissino-Mayer, Henri

    2006-01-01

    The technique of laser-induced breakdown spectroscopy (LIBS) to detect elements for a variety of homeland security applications such as nuclear materials identification and inventory,and forensic applications has been demonstrated. For nuclear materials applications, we detected and profiled metals in coatings that were used to encapsulate nuclear fuel. Multivariate analysis has been successfully employed in the quantification of elements present in treated wood and engineered wood composites. These examples demonstrate that LIBS-based techniques are inherently well suited for diverse environmental applications related to homeland security. Three key advantages are evident: (1) small samples (mg) are sufficient; (2) samples can be analyzed by LIBS very rapidly, and (3) biological materials such as human and animal bones and wood can be analyzed with minimal sample preparation. For forensic applications they have used LIBS to determine differences in animal and human bones. They have also applied this technique in the determination of counterfeit and non-counterfeit currency. They recently applied LIBS in helping to solve a murder case.

  15. Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and application

    NASA Astrophysics Data System (ADS)

    Agarwal, Animesh; Delle Site, Luigi

    2016-09-01

    We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution Simulation Molecular Dynamics (GC-AdResS) method. We have tested the implementation on two different systems, liquid parahydrogen at extreme thermodynamic conditions and liquid water at ambient conditions; the reproduction of structural as well as dynamical results of reference systems are highly satisfactory. The capability of performing GC-AdResS CMD simulations allows for the treatment of a system characterized by some quantum features and open boundaries. This latter characteristic not only is of computational convenience, allowing for equivalent results of much larger and computationally more expensive systems, but also suggests a tool of analysis so far not explored, that is the unambiguous identification of the essential degrees of freedom required for a given property.

  16. Compact, high-resolution, gamma ray imaging for scintimammography and other medical diagostic applications

    DOEpatents

    Majewski, Stanislaw; Weisenberger, Andrew G.; Wojcik, Randolph F.; Steinbach, Daniela

    1999-01-01

    A high resolution gamma ray imaging device includes an aluminum housing, a lead screen collimator at an opened end of the housing, a crystal scintillator array mounted behind the lead screen collimator, a foam layer between the lead screen collimator and the crystal scintillator array, a photomultiplier window coupled to the crystal with optical coupling grease, a photomultiplier having a dynode chain body and a base voltage divider with anodes, anode wire amplifiers each connected to four anodes and a multi pin connector having pin connections to each anode wire amplifier. In one embodiment the crystal scintillator array includes a yttrium aluminum perovskite (YAP) crystal array. In an alternate embodiment, the crystal scintillator array includes a gadolinium oxyorthosilicate (GSO) crystal array.

  17. Application of LES Technique to Diagnosis of Wind Farm by Using High Resolution Elevation Data

    NASA Astrophysics Data System (ADS)

    Uchida, Takanori; Ohya, Yuji

    We are developing the numerical model called the RIAM-COMPACT (Research Institute for Applied Mechanics, Kyushu University, Computational Prediction of Airflow over Complex Terrain). The object domain of this numerical model is from several m to several km, and can predict the airflow and the gas diffusion over complex terrain with high precision. The RIAM-COMPACT has already been marketed by certain tie-up companies. The estimation of the annual electrical power output is also possible now based on the field observation data. In the present study, wind simulation of an actual wind farm was executed using the high resolution elevation data. As a result, an appropriate point and an inappropriate point for locating a wind turbine generator were shown based on the numerical results obtained. This cause was found to be a topographical irregularity in front of the wind turbine generator.

  18. High resolution applications of the Osher upwind scheme for the Euler equations

    NASA Technical Reports Server (NTRS)

    Chakravarthy, S. R.; Osher, S.

    1983-01-01

    The 'Osher' scheme was introduced by Osher (1981). It represents an upwind finite-difference method for hyperbolic systems of conservation laws, including the Euler equations. In studies conducted by Osher (1981) and Osher and Solomon (1982), the method was applied to the nonisentropic form of the Euler equations in one dimension and the isentropically restricted form in two spatial dimensions, both in Cartesian coordinates. Chakravarthy and Osher (1982) have shown an approach for extending the Osher scheme to the Euler equations written for general geometries, taking into account the use of mappings to arbitrary curvilinear coordinate systems. The present investigation is concerned with the high resolution extension of the Osher scheme to second-order accuracy. Results are presented for several example problems, giving attention to quasi-one-dimensional Laval nozzle flow, a one-dimensional shock tube problem, and supersonic flow over a cylinder.

  19. High-resolution Earth-based lunar radar studies: Applications to lunar resource assessment

    NASA Technical Reports Server (NTRS)

    Stacy, N. J. S.; Campbell, D. B.

    1992-01-01

    The lunar regolith will most likely be a primary raw material for lunar base construction and resource extraction. High-resolution radar observations of the Moon provide maps of radar backscatter that have intensity variations generally controlled by the local slope, material, and structural properties of the regolith. The properties that can be measured by the radar system include the dielectric constant, density, loss tangent, and wavelength scale roughness. The radar systems currently in operation at several astronomical observatories provide the ability to image the lunar surface at spatial resolutions approaching 30 m at 3.8 cm and 12.6 cm wavelengths and approximately 500 m at 70 cm wavelength. The radar signal penetrates the lunar regolith to a depth of 10-20 wavelengths so the measured backscatter contains contributions from the vacuum-regolith interface and from wavelength-scale heterogeneities in the electrical properties of the subsurface material. The three wavelengths, which are sensitive to different scale structures and scattering volumes, provide complementary information on the regolith properties. Aims of the previous and future observations include (1) analysis of the scattering properties associated with fresh impact craters, impact crater rays, and mantled deposits; (2) analysis of high-incidence-angle observations of the lunar mare to investigate measurement of the regolith dielectric constant and hence porosity; (3) investigation of interferometric techniques using two time-delayed observations of the same site, observations that require a difference in viewing geometry less than 0.05 deg and, hence, fortuitous alignment of the Earth-Moon system when visible from Arecibo Observatory.

  20. Reference Standardization for Mass Spectrometry and High-resolution Metabolomics Applications to Exposome Research.

    PubMed

    Go, Young-Mi; Walker, Douglas I; Liang, Yongliang; Uppal, Karan; Soltow, Quinlyn A; Tran, ViLinh; Strobel, Frederick; Quyyumi, Arshed A; Ziegler, Thomas R; Pennell, Kurt D; Miller, Gary W; Jones, Dean P

    2015-12-01

    The exposome is the cumulative measure of environmental influences and associated biological responses throughout the lifespan, including exposures from the environment, diet, behavior, and endogenous processes. A major challenge for exposome research lies in the development of robust and affordable analytic procedures to measure the broad range of exposures and associated biologic impacts occurring over a lifetime. Biomonitoring is an established approach to evaluate internal body burden of environmental exposures, but use of biomonitoring for exposome research is often limited by the high costs associated with quantification of individual chemicals. High-resolution metabolomics (HRM) uses ultra-high resolution mass spectrometry with minimal sample preparation to support high-throughput relative quantification of thousands of environmental, dietary, and microbial chemicals. HRM also measures metabolites in most endogenous metabolic pathways, thereby providing simultaneous measurement of biologic responses to environmental exposures. The present research examined quantification strategies to enhance the usefulness of HRM data for cumulative exposome research. The results provide a simple reference standardization protocol in which individual chemical concentrations in unknown samples are estimated by comparison to a concurrently analyzed, pooled reference sample with known chemical concentrations. The approach was tested using blinded analyses of amino acids in human samples and was found to be comparable to independent laboratory results based on surrogate standardization or internal standardization. Quantification was reproducible over a 13-month period and extrapolated to thousands of chemicals. The results show that reference standardization protocol provides an effective strategy that will enhance data collection for cumulative exposome research. In principle, the approach can be extended to other types of mass spectrometry and other analytical methods. PMID

  1. Application of high-resolution transmission electron microscopy to the study of aragonite crystallography and diagenesis

    SciTech Connect

    Haywick, D.W. . Geology Dept.); Ness, S.E. . Instrumentation Centre)

    1993-03-01

    High-resolution transmission electron microscopy (HRTEM) is a valuable technique by which to study the ultrastructure of various organic and inorganic compounds. Some biogeological minerals, including skeletal aragonite, have proven to be relatively unstable under an electron beam. Nevertheless, these compounds can be examined by HRTEM provided that minimal exposure techniques are employed. The authors have successfully applied HRTEM to examine diagenetically altered Plio-Pleistocene aragonitic faunas from New Zealand. To date, they have obtained high-resolution images of lattice-fringes with a spacing of 3.7 [angstrom] using a defocused, low-intensity electron beam. At least two of the samples imaged revealed clusters of lattice planes which together, form an interlocking mosaic of variably oriented micro-domains between 5 and 100 nm across. These micro-domains suggest that at least some of the aragonite is heterogeneous at a nm-scale; however, the individual micro-domains, when averaged together, generate single crystal electron diffraction patterns typical of well-ordered aragonite. The origin of the micro-domains is presently unclear. They may be an artifact of diagenetic alteration of an ultrastructurally homogeneous crystal. It is more likely, however, that the micro-domains were produced during aragonite precipitation. If this scenario is correct, it could have major implications for carbonate diagenesis, particularly if micro-domains prove to be ubiquitous within biogenic carbonate minerals. Inter-domains boundaries would be zones of comparative weakness and may provide nucleation points for diagenetic alteration. The intent now is to apply HRTEM in conjunction with other analytical techniques (e.g. x-ray diffraction, electron microprobe, stable isotope geochemistry) to characterize crystallographic changes during progressive diagenesis of aragonite, especially the aragonite-calcite transformation.

  2. Estimates of olivine-basaltic melt electrical conductivity using a digital rock physics approach

    NASA Astrophysics Data System (ADS)

    Miller, Kevin J.; Montési, Laurent G. J.; Zhu, Wen-lu

    2015-12-01

    Estimates of melt content beneath fast-spreading mid-ocean ridges inferred from magnetotelluric tomography (MT) vary between 0.01 and 0.10. Much of this variation may stem from a lack of understanding of how the grain-scale melt geometry influences the bulk electrical conductivity of a partially molten rock, especially at low melt fraction. We compute bulk electrical conductivity of olivine-basalt aggregates over 0.02 to 0.20 melt fraction by simulating electric current in experimentally obtained partially molten geometries. Olivine-basalt aggregates were synthesized by hot-pressing San Carlos olivine and high-alumina basalt in a solid-medium piston-cylinder apparatus. Run conditions for experimental charges were 1.5 GPa and 1350 °C. Upon completion, charges were quenched and cored. Samples were imaged using synchrotron X-ray micro-computed tomography (μ-CT). The resulting high-resolution, 3-dimensional (3-D) image of the melt distribution constitutes a digital rock sample, on which numerical simulations were conducted to estimate material properties. To compute bulk electrical conductivity, we simulated a direct current measurement by solving the current continuity equation, assuming electrical conductivities for olivine and melt. An application of Ohm's Law yields the bulk electrical conductivity of the partially molten region. The bulk electrical conductivity values for nominally dry materials follow a power-law relationship σbulk = Cσmeltϕm with fit parameters m = 1.3 ± 0.3 and C = 0.66 ± 0.06. Laminar fluid flow simulations were conducted on the same partially molten geometries to obtain permeability, and the respective pathways for electrical current and fluid flow over the same melt geometry were compared. Our results indicate that the pathways for flow fluid are different from those for electric current. Electrical tortuosity is lower than fluid flow tortuosity. The simulation results are compared to existing experimental data, and the potential

  3. Comparison of high resolution terrestrial laser scanning and terrestrial photogrammetry for modeling applications

    NASA Astrophysics Data System (ADS)

    Özdemir, Samed; Bayrak, Temel

    2016-04-01

    3D documentation of cultural heritage and engineering projects is an important matter. These documentation applications, requires highest possible accuracy and detail to represent the actual surface correctly. Terrestrial photogrammetric method which is employed to produce 3D models to day, now can obtain dense point clouds thanks to advancements in computer technology. Terrestrial laser scanners gained popularity in the last decade because of their high capacity and today they are being widely used in many applications. However every application has its own requirements that depend on the type of application, modeling environment, accuracy and budget limitations. This means, for every application highest accuracy instruments are not always best, considering the facts that mentioned before. In this study, laser scanner and terrestrial photogrammetric methods' spatial and model accuracies investigated under various conditions which include measuring targets at different instrument to object distances then investigating the accuracy of these measurements, modeling an irregular shaped surface to compare two surfaces volume and surface areas, at last comparing dimensions of known geometrical shaped small objects. Also terrestrial laser scanners and terrestrial photogrammetric methods most suitable application conditions investigated in terms of cost, time, mobility and accuracy. Terrestrial laser scanner has the ability to, measure distances under cm accuracy and directly measuring 3D world but there is also some drawbacks like sensitive, bulky and expensive equipment. When it comes to terrestrial photogrammetry, it has above cm accuracy, comparatively fast (considering the image acquisition stage), inexpensive but it can be affected by the coarse geometry, surface texture and the environmental lighting. Key Words: Accuracy, Comparison, Model, Terrestrial Photogrammetry, Terrestrial Laser Scanning,.

  4. Complexation of Sr in aqueous fluids equilibrated with silicate melts: effect of melt and fluid composition

    NASA Astrophysics Data System (ADS)

    Borchert, Manuela; Wilke, Max; Schmidt, Christian; Kvashnina, Kristina

    2010-05-01

    At crustal conditions, the fluid-melt partitioning of Sr is mainly controlled by the salinity of the fluid and the composition of the melt (Borchert et al., 2010). The data show a sharp increase in the Sr partition coefficient with the alumina saturation index (ASI) to a maximum of 0.3 at an ASI of 1.05. Because fluid-melt partitioning of a given element depends on its complexation in the fluid and its incorporation in the melt, these data imply a change in the Sr speciation at least one of the two phases. For silicate melts, Kohn et al. (1990) found only small changes in the first coordination shell of Sr in a suite of melts with various degrees of polymerization, and argued that incorporation of Sr in the melt should not play a major role in controlling Sr partitioning. For the aqueous fluid, Bai and Koster van Groos (1999) and Webster et al. (1989) suggested a control of the Sr partition coefficient by SrCl2 complexes based on the correlation between partition coefficient and Cl concentration in the fluid after quenching. Both hypotheses cannot explain our partitioning data. Thus, new information on Sr complexation is required. Here, we studied the complexation of Sr in peraluminous or peralkaline melt dissolved in aqueous fluids in-situ at elevated PT conditions using hydrothermal diamond-anvil cells (HDAC) and X-ray absorption near edge structure (XANES) spectroscopy. The starting materials were peraluminous or peralkaline glass and H2O or a chloridic solution. The glass was doped with high concentrations of 5000 or 10000 ppm Sr. We used bulk compositions with 10 to 15 wt.% glass to ensure that the melt was completely dissolved in the fluid at high PT conditions. For qualitative evaluation, we analyzed the starting glasses and various crystalline compounds and standard solutions. The experiments were performed at beamline ID26 at ESRF (Grenoble, France) using a high resolution emission spectrometer and Si(311) monochromator crystals for high resolution and Si

  5. Melting scenarios for three-dimensional dusty plasma clusters

    NASA Astrophysics Data System (ADS)

    Schella, André; Miksch, Tobias; Melzer, André; Schablinski, Jan; Block, Dietmar; Piel, Alexander; Thomsen, Hauke; Ludwig, Patrick; Bonitz, Michael

    2011-11-01

    The melting transition of finite three-dimensional dust clouds (Yukawa balls) from a solid-like to a liquid-like state is systematically studied with high spatial and temporal resolution of the individual grains by means of stereoscopy. Two different melting scenarios are reported: Melting is induced first by an increase of plasma power, and second by laser-induced heating. The experiments confirm that melting starts with a loss of orientational correlation, followed by a loss of the radial order upon further heating. While the plasma-power melting is driven via the ion wakefield, laser heating provides a more equilibrium scenario. The internal loss of correlations is well captured by the triple correlation function (TCF) which is insensitive to particle exchanges and the rotation of the cluster as a whole. The critical Coulomb coupling parameter for N=35 is determined as Γcrit≈570. The experimental findings are in good agreement with thermodynamic Monte Carlo simulations.

  6. Note: Measurement method for sound velocity of melts in large volume press and its application to liquid sodium up to 2.0 GPa.

    PubMed

    Song, Wei; Liu, Yonggang; Wang, Zhigang; Gong, Chaoying; Guo, Jie; Zhou, Wenge; Xie, Hongsen

    2011-08-01

    Based on large volume press and conventional pulse-echo ultrasonic technique, we have overcome the difficulty in determining the length of liquid specimen under high pressure, and the sound velocity in liquid Na has been measured up to 2 GPa. The P-V data deduced by our sound velocity results through equation of state is in an excellent agreement with previous data directly determined by piezometer method. This new experimental technique is convenient and ready for use, being expected to advance investigation on thermodynamic properties of liquid metals and other melts under high pressure. PMID:21895286

  7. Predicting natural-convection-dominated phase change problems by control volume unstructured triangular grid: Applications to the melting of pure metal

    SciTech Connect

    Hong, Z.C.; Liou, J.H.

    1998-02-20

    Control volume methods have recently been developed for fluid flow and heat transfer on unstructured meshes. In this study, the authors extend these methods to implement the solution of natural-convection-dominated melting of gallium by a fixed-grid method. A simple, robust, and reliable explicit numerical method (MAC method) is applied for an unstructured triangular grid. This investigation also applies the implicit SIMPLER method for an unstructured triangular grid. Results obtained from the unstructured triangular grid correlate well with the structured mesh computations and experimental data. Also, the feasibility of applying the triangular grid to complex geometric problems is demonstrated by calculating two different triangular domains.

  8. Viscosity Measurement for Tellurium Melt

    NASA Technical Reports Server (NTRS)

    Lin, Bochuan; Li, Chao; Ban, Heng; Scripa, Rosalia N.; Su, Ching-Hua; Lehoczky, Sandor L.

    2006-01-01

    The viscosity of high temperature Te