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Sample records for resolution melting application

  1. 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

  2. Application of PCR and High-Resolution Melting for Rapid Identification of Yeasts Routinely Isolated in a Clinical Microbiology Laboratory.

    PubMed

    Ninghui, Guo; Bing, Wang; Wei, Ren; Mengmeng, Liu; Meiling, Chu; Dongya, Meng; Liqiong, Yao; Wencheng, Xue

    2015-01-01

    This study aimed to develop a method for rapid and accurate identification of yeasts obtained in the clinic, especially from immunocompromised patients, in order to provide a timely and appropriate antifungal therapy. A total of 112 Candida isolates were analyzed in this study; 28 of them were used to validate the PCR-HRM method in species identification in a blinded manner. Strains were identified by conventional techniques that use VITEK 2 YST cards and Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). These methods were compared to the newly developed technique based on real-time polymerase-chain reaction high-resolution melting (PCR-HRM). Discordant results were resolved with internal transcribed spacer (ITS) gene sequencing, the "golden standard" used to evaluate the reliability of all methods in identifying yeasts at the species level. PCR-HRM sensitivity was assessed with the isolated strains. VITEK 2, MALDI-TOF-MS, and PCR-HRM accurately identified 89.2% (74/83), 97.6% (81/83), 100% (83/83) of the isolates, respectively. PCR-HRM detection limit was 1fg/μl of yeasts. In validation assays, a 100% accuracy rate was achieved by the use of PCR-HRM. Therefore, the PCR-HRM method is a rapid, sensitive, and specific diagnostic approach, which provides a cost-effective and more suitable alternative for yeast identification in a clinical laboratory. Future research is needed for automation of data acquisition.

  3. Application of High-Resolution DNA Melting for Genotyping in Lepidopteran Non-Model Species: Ostrinia furnacalis (Crambidae)

    PubMed Central

    Li, FengBo; Niu, BaoLong; Huang, YongPing; Meng, ZhiQi

    2012-01-01

    Development of an ideal marker system facilitates a better understanding of the genetic diversity in lepidopteran non-model organisms, which have abundant species, but relatively limited genomic resources. Single nucleotide polymorphisms (SNPs) discovered within single-copy genes have proved to be desired markers, but SNP genotyping by current techniques remain laborious and expensive. High resolution melting (HRM) curve analysis represents a simple, rapid and inexpensive genotyping method that is primarily confined to clinical and diagnostic studies. In this study, we evaluated the potential of HRM analysis for SNP genotyping in the lepidopteran non-model species Ostrinia furnacalis (Crambidae). Small amplicon and unlabeled probe assays were developed for the SNPs, which were identified in 30 females of O. furnacalis from 3 different populations by our direct sequencing. Both assays were then applied to genotype 90 unknown female DNA by prior mixing with known wild-type DNA. The genotyping results were compared with those that were obtained using bi-directional sequencing analysis. Our results demonstrated the efficiency and reliability of the HRM assays. HRM has the potential to provide simple, cost-effective genotyping assays and facilitates genotyping studies in any non-model lepidopteran species of interest. PMID:22253755

  4. Applications of the method of high resolution melting analysis for diagnosis of Leber's disease and the three primary mutation spectrum of LHON in the Han Chinese population.

    PubMed

    Cui, Guanglin; Ding, Hu; Xu, Yujun; Li, Bin; Wang, Dao Wen

    2013-01-01

    Current screening methods, such as single strand conformational polymorphism (SSCP), denaturing high performance liquid chromatography (dHPLC) and direct DNA sequencing that are used for detecting mutation in Leber's hereditary optic neuropathy (LHON) subjects are time consuming and costly. Here we tested high-resolution melt (HRM) analysis for mtDNA primary mutations in LHON patients. In this study, we applied the high resolution melting (HRM) technology to screen mtDNA primary mutations in 50 LHON patients from their peripheral blood. In order to evaluate the reliability of this technique, we compared the results obtained by HRM and direct mtDNA sequencing. We also investigated the spectrum of three most common mtDNA mutations implicated in LHON in the Han Chinese population. The results showed HRM analysis differentiated all of the mtDNA primary mutations and identified 4 additional mtDNA mutations from 50 patients in the blind study. The prevalence of three primary mutations were 11778G>A (87.9%), 14484T>C (6.5%) and 3460G>A (1.7%) in the Han Chinese population. In conclusion, HRM analysis is a rapid, reliable, and low-cost tool for detecting mtDNA primary mutations and has practical applications in molecular genetics.

  5. 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.

  6. 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

  7. Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.).

    PubMed

    Kamel, Katarzyna A; Kroc, Magdalena; Święcicki, Wojciech

    2015-01-01

    Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

  8. 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

  9. Establishment of a simple and rapid identification method for Listeria spp. by using high-resolution melting analysis, and its application in food industry.

    PubMed

    Ohshima, Chihiro; Takahashi, Hajime; Phraephaisarn, Chirapiphat; Vesaratchavest, Mongkol; Keeratipibul, Suwimon; Kuda, Takashi; Kimura, Bon

    2014-01-01

    Listeria monocytogenes is the causative bacteria of listeriosis, which has a higher mortality rate than that of other causes of food poisoning. Listeria spp., of which L. monocytogenes is a member, have been isolated from food and manufacturing environments. Several methods have been published for identifying Listeria spp.; however, many of the methods cannot identify newly categorized Listeria spp. Additionally, they are often not suitable for the food industry, owing to their complexity, cost, or time consumption. Recently, high-resolution melting analysis (HRMA), which exploits DNA-sequence differences, has received attention as a simple and quick genomic typing method. In the present study, a new method for the simple, rapid, and low-cost identification of Listeria spp. has been presented using the genes rarA and ldh as targets for HRMA. DNA sequences of 9 Listeria species were first compared, and polymorphisms were identified for each species for primer design. Species specificity of each HRM curve pattern was estimated using type strains of all the species. Among the 9 species, 7 were identified by HRMA using rarA gene, including 3 new species. The remaining 2 species were identified by HRMA of ldh gene. The newly developed HRMA method was then used to assess Listeria isolates from the food industry, and the method efficiency was compared to that of identification by 16S rDNA sequence analysis. The 2 methods were in coherence for 92.6% of the samples, demonstrating the high accuracy of HRMA. The time required for identifying Listeria spp. was substantially low, and the process was considerably simplified, providing a useful and precise method for processing multiple samples per day. Our newly developed method for identifying Listeria spp. is highly valuable; its use is not limited to the food industry, and it can be used for the isolates from the natural environment.

  10. Differentiation of Staphylococcus spp. by high-resolution melting analysis.

    PubMed

    Slany, Michal; Vanerkova, Martina; Nemcova, Eva; Zaloudikova, Barbora; Ruzicka, Filip; Freiberger, Tomas

    2010-12-01

    High-resolution melting analysis (HRMA) is a fast (post-PCR) high-throughput method to scan for sequence variations in a target gene. The aim of this study was to test the potential of HRMA to distinguish particular bacterial species of the Staphylococcus genus even when using a broad-range PCR within the 16S rRNA gene where sequence differences are minimal. Genomic DNA samples isolated from 12 reference staphylococcal strains (Staphylococcus aureus, Staphylococcus capitis, Staphylococcus caprae, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus intermedius, Staphylococcus saprophyticus, Staphylococcus sciuri, Staphylococcus simulans, Staphylococcus warneri, and Staphylococcus xylosus) were subjected to a real-time PCR amplification of the 16S rRNA gene in the presence of fluorescent dye EvaGreen™, followed by HRMA. Melting profiles were used as molecular fingerprints for bacterial species differentiation. HRMA of S. saprophyticus and S. xylosus resulted in undistinguishable profiles because of their identical sequences in the analyzed 16S rRNA region. The remaining reference strains were fully differentiated either directly or via high-resolution plots obtained by heteroduplex formation between coamplified PCR products of the tested staphylococcal strain and phylogenetically unrelated strain.

  11. 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.

  12. 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

  13. 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.

  14. The WAIS Melt Monitor: An automated ice core melting system for meltwater sample handling and the collection of high resolution microparticle size distribution data

    NASA Astrophysics Data System (ADS)

    Breton, D. J.; Koffman, B. G.; Kreutz, K. J.; Hamilton, G. S.

    2010-12-01

    Paleoclimate data are often extracted from ice cores by careful geochemical analysis of meltwater samples. The analysis of the microparticles found in ice cores can also yield unique clues about atmospheric dust loading and transport, dust provenance and past environmental conditions. Determination of microparticle concentration, size distribution and chemical makeup as a function of depth is especially difficult because the particle size measurement either consumes or contaminates the meltwater, preventing further geochemical analysis. Here we describe a microcontroller-based ice core melting system which allows the collection of separate microparticle and chemistry samples from the same depth intervals in the ice core, while logging and accurately depth-tagging real-time electrical conductivity and particle size distribution data. This system was designed specifically to support microparticle analysis of the WAIS Divide WDC06A deep ice core, but many of the subsystems are applicable to more general ice core melting operations. Major system components include: a rotary encoder to measure ice core melt displacement with 0.1 millimeter accuracy, a meltwater tracking system to assign core depths to conductivity, particle and sample vial data, an optical debubbler level control system to protect the Abakus laser particle counter from damage due to air bubbles, a Rabbit 3700 microcontroller which communicates with a host PC, collects encoder and optical sensor data and autonomously operates Gilson peristaltic pumps and fraction collectors to provide automatic sample handling, melt monitor control software operating on a standard PC allowing the user to control and view the status of the system, data logging software operating on the same PC to collect data from the melting, electrical conductivity and microparticle measurement systems. Because microparticle samples can easily be contaminated, we use optical air bubble sensors and high resolution ice core density

  15. High-resolution melt analysis of the minisatellite D1S80: a potential forensic screening tool.

    PubMed

    Pomeroy, Robert S; Balamurugan, Kuppareddi; Wong, Helena; Duncan, George

    2014-11-01

    High-resolution melt (HRM) analysis of the VNTR region of the human D1S80 locus, a 16-bp repeat minisatellite from approximately 400 to over 700 bp in length, was investigated. A Qiagen Rotor-Gene Q using the Type-it PCR HRM kit was used to acquire HRM curves for 14 single, and 16 biallelic, dsDNA samples. The HRM analysis was applicable over a range of DNA concentrations; however the characteristics of the melt curve did depend on the forward and reverse primer ratio. Despite the large amplicon size and the similarities of the repeat sequences, it was possible to discriminate different genotypes. Heterozygotes were clearly different from the homozygous variants and even small differences in the repeat sequence could be differentiated. However, the melt analysis requires a high-resolution system with temperature resolution of 0.02°C or better in order to sort out differences in these large amplicons of near identical GC content (in this case 56%). HRM analysis of amplicons with large repeat sequences can be used as a means of comparing DNA fragments. Examination of multiple sequences can be used to differentiate DNA samples and demonstrate the potential of HRM analysis as a rapid and inexpensive prescreening technique in forensic applications.

  16. 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.

  17. Hot-melt extrusion--basic principles and pharmaceutical applications.

    PubMed

    Lang, Bo; McGinity, James W; Williams, Robert O

    2014-09-01

    Originally adapted from the plastics industry, the use of hot-melt extrusion has gained favor in drug delivery applications both in academia and the pharmaceutical industry. Several commercial products made by hot-melt extrusion have been approved by the FDA, demonstrating its commercial feasibility for pharmaceutical processing. A significant number of research articles have reported on advances made regarding the pharmaceutical applications of the hot-melt extrusion processing; however, only limited articles have been focused on general principles regarding formulation and process development. This review provides an in-depth analysis and discussion of the formulation and processing aspects of hot-melt extrusion. The impact of physicochemical properties of drug substances and excipients on formulation development using a hot-melt extrusion process is discussed from a material science point of view. Hot-melt extrusion process development, scale-up, and the interplay of formulation and process attributes are also discussed. Finally, recent applications of hot-melt extrusion to a variety of dosage forms and drug substances have also been addressed.

  18. Identification of gene mutation in patients with osteogenesis imperfect using high resolution melting analysis

    PubMed Central

    Wang, Jianhai; Ren, Xiuzhi; Bai, Xue; Zhang, Tianke; Wang, Yi; Li, Keqiu; Li, Guang

    2015-01-01

    Osteogenesis imperfecta (OI), a congenital bone disorder, is caused by mutations in COL1A1 and COL1A2 genes, leading to deficiency of type I collagen. The high resolution melting (HRM) analysis has been used for detecting mutations, polymorphisms and epigenetic alteration in double-stranded DNAs. This study was to evaluate the potential application of HRM analysis for identifying gene mutations in patients with OI. This study included four children with OI and their parents and fifty normal people as controls. Blood samples were collected for HRM analysis of PCR-amplified exons and flanking DNA sequences of COL1A1 and COL1A2 genes. Direct gene sequencing was performed to validate HRM-identified gene mutations. As compared to controls, HRM analysis of samples form children with OI showed abnormal melting curves in exons 11 and 33–34 of the COL1A1 gene and exons 19 and 48 of the COL1A2 gene, which indicates the presence of heterozygous mutations in COL1A1 and COL1A2 genes. In addition to two known mutations in the COL1A2 gene, c.982G > A and c.3197G > T, sequencing analysis identified two novel mutations in the COL1A1 gene, c.2321delC and c.768dupC mutations, which function as premature stop codons. These results support future studies of applying HRM analysis as a diagnostic approach for OI. PMID:26307460

  19. Identification of gene mutation in patients with osteogenesis imperfect using high resolution melting analysis.

    PubMed

    Wang, Jianhai; Ren, Xiuzhi; Bai, Xue; Zhang, Tianke; Wang, Yi; Li, Keqiu; Li, Guang

    2015-01-01

    Osteogenesis imperfecta (OI), a congenital bone disorder, is caused by mutations in COL1A1 and COL1A2 genes, leading to deficiency of type I collagen. The high resolution melting (HRM) analysis has been used for detecting mutations, polymorphisms and epigenetic alteration in double-stranded DNAs. This study was to evaluate the potential application of HRM analysis for identifying gene mutations in patients with OI. This study included four children with OI and their parents and fifty normal people as controls. Blood samples were collected for HRM analysis of PCR-amplified exons and flanking DNA sequences of COL1A1 and COL1A2 genes. Direct gene sequencing was performed to validate HRM-identified gene mutations. As compared to controls, HRM analysis of samples form children with OI showed abnormal melting curves in exons 11 and 33-34 of the COL1A1 gene and exons 19 and 48 of the COL1A2 gene, which indicates the presence of heterozygous mutations in COL1A1 and COL1A2 genes. In addition to two known mutations in the COL1A2 gene, c.982G > A and c.3197G > T, sequencing analysis identified two novel mutations in the COL1A1 gene, c.2321delC and c.768dupC mutations, which function as premature stop codons. These results support future studies of applying HRM analysis as a diagnostic approach for OI. PMID:26307460

  20. 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.

  1. Automated DNA extraction, quantification, dilution, and PCR preparation for genotyping by high-resolution melting.

    PubMed

    Seipp, Michael T; Herrmann, Mark; Wittwer, Carl T

    2010-12-01

    Genotyping by high-resolution amplicon melting uses only two PCR primers per locus and a generic, saturating DNA dye that detects heteroduplexes as well as homoduplexes. Heterozygous genotypes have a characteristic melting curve shape and a broader width than homozygous genotypes, which are usually differentiated by their melting temperature (T(m)). The H63D mutation, associated with hemochromatosis, is a single nucleotide polymorphism, which is impossible to genotype based on T(m), as the homozygous WT and mutant amplicons melt at the same temperature. To distinguish such homozygous variants, WT DNA can be added to controls and unknown samples to create artificial heterozygotes with all genotypes distinguished by quantitative heteroduplex analysis. By automating DNA extraction, quantification, and PCR preparation, a hands-off integrated solution for genotyping is possible. A custom Biomek® NX robot with an onboard spectrophotometer and custom programming was used to extract DNA from whole blood, dilute the DNA to appropriate concentrations, and add the sample DNA to preprepared PCR plates. Agencourt® Genfind™ v.2 chemistry was used for DNA extraction. PCR was performed on a plate thermocycler, high-resolution melting data collected on a LightScanner-96, followed by analysis and automatic genotyping using custom software. In a blinded study of 42 H63D samples, 41 of the 42 sample genotypes were concordant with dual hybridization probe genotyping. The incorrectly assigned genotype was a heterozygote that appeared to be a homozygous mutant as a result of a low sample DNA concentration. Automated DNA extraction from whole blood with quantification, dilution, and PCR preparation was demonstrated using quantitative heteroduplex analysis. Accuracy is critically dependent on DNA quantification.

  2. 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

  3. Rapid fingerprinting of methanogenic communities by high-resolution melting analysis.

    PubMed

    Kim, Jaai; Lee, Changsoo

    2014-12-01

    Characterizing microbial community structure using molecular techniques is becoming a popular approach in studies of waste/wastewater treatment processes. A rapid and robust tool to analyze microbial communities is required for efficient process monitoring and control. In this study, a new community fingerprinting method based on high-resolution melting (HRM) analysis was developed and applied to compare methanogenic community structures of five different anaerobic digesters. The new method produced robust community clustering and ordination results comparable to the results from the commonly used denaturing gradient gel electrophoresis (DGGE) performed in parallel. This method transforms melting peak plots (MPs) of community DNA samples generated by HRM analysis to molecular fingerprints and estimates the relationships between the communities based on the fingerprints. The MP-based fingerprinting would provide a good alternative to monitor variations in microbial community structure especially when handling large sample numbers due to its high-throughput capacity and short analysis time.

  4. Pharmaceutical applications of hot-melt extrusion: part I.

    PubMed

    Crowley, Michael M; Zhang, Feng; Repka, Michael A; Thumma, Sridhar; Upadhye, Sampada B; Battu, Sunil Kumar; McGinity, James W; Martin, Charles

    2007-09-01

    Interest in hot-melt extrusion techniques for pharmaceutical applications is growing rapidly with well over 100 papers published in the pharmaceutical scientific literature in the last 12 years. Hot-melt extrusion (HME) has been a widely applied technique in the plastics industry and has been demonstrated recently to be a viable method to prepare several types of dosage forms and drug delivery systems. Hot-melt extruded dosage forms are complex mixtures of active medicaments, functional excipients, and processing aids. HME also offers several advantages over traditional pharmaceutical processing techniques including the absence of solvents, few processing steps, continuous operation, and the possibility of the formation of solid dispersions and improved bioavailability. This article, Part I, reviews the pharmaceutical applications of hot-melt extrusion, including equipment, principles of operation, and process technology. The raw materials processed using this technique are also detailed and the physicochemical properties of the resultant dosage forms are described. Part II of this review will focus on various applications of HME in drug delivery such as granules, pellets, immediate and modified release tablets, transmucosal and transdermal systems, and implants.

  5. Rapid Genetic Analysis of X-Linked Chronic Granulomatous Disease by High-Resolution Melting

    PubMed Central

    Hill, Harry R.; Augustine, Nancy H.; Pryor, Robert J.; Reed, Gudrun H.; Bagnato, Joshua D.; Tebo, Anne E.; Bender, Jeffrey M.; Pasi, Brian M.; Chinen, Javier; Hanson, I. Celine; de Boer, Martin; Roos, Dirk; Wittwer, Carl T.

    2010-01-01

    High-resolution melting analysis was applied to X-linked chronic granulomatous disease, a rare disorder resulting from mutations in CYBB. Melting curves of the 13 PCR products bracketing CYBB exons were predicted by Poland's algorithm and compared with observed curves from 96 normal individuals. Primer plates were prepared robotically in batches and dried, greatly simplifying the 3- to 6-hour workflow that included DNA isolation, PCR, melting, and cycle sequencing of any positive products. Small point mutations or insertions/deletions were detected by mixing the hemizygous male DNA with normal male DNA to produce artificial heterozygotes, whereas detection of gross deletions was performed on unmixed samples. Eighteen validation samples and 22 clinical kindreds were analyzed for CYBB mutations. All blinded validation samples were correctly identified. The clinical probands were identified after screening for neutrophil oxidase activity. Nineteen different mutations were found, including seven near intron-exon boundaries predicting splicing defects, five substitutions within exons, three small deletions predicting premature termination, and four gross deletions of multiple exons. Ten novel mutations were found, including (c.) two missense (730T>A, 134T>G), one nonsense (90C>A), four splice site defects (45 + 1G>T, 674 + 4A>G, 1461 + 2delT, and 1462-2A>C), two small deletions (636delT, 1661_1662delCT), and one gross deletion of exons 6 to 8. High-resolution melting can provide timely diagnosis at low cost for effective clinical management of rare, genetic primary immunodeficiency disorders. PMID:20228266

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. Identification of forensically important blowfly species (Diptera: Calliphoridae) by high-resolution melting PCR analysis.

    PubMed

    Malewski, Tadeusz; Draber-Mońko, Agnieszka; Pomorski, Jan; Łoś, Marta; Bogdanowicz, Wiesław

    2010-07-01

    We describe here the successful coupling of real-time polymerase chain reaction (PCR) and high-resolution melting (HRM) analysis to rapidly identify 15 forensically important species of blowfly from the family Calliphoridae (Diptera), which occur in Poland. Two short regions (119 and 70 base pairs, respectively) of cytochrome oxidase gene subunit I with sufficient sequence diversity were selected. In the case of lacking taxa (e.g., reference species) these amplicons can be synthesized using sequences deposited in gene banks. The technique utilizes low template DNA concentration and is highly reproducible. The melting profile was not altered up to a 10,000-fold difference in DNA template concentration (ranging from 5 pg to 50 ng). The several HRM runs performed on different specimens from Poland belonging to the same species and on different days resulted in only minor variations in the amplification curves and in melting temperatures of the peaks. Intraspecific variation in a larger scale was tested using synthesized oligonucleotides from cosmopolitan Lucilia illustris originating from Poland, France, Great Britain, India, and USA. As HRM PCR analysis is sensitive to even single base changes, all geographic variants of this species were identified. This technique is also cost-effective and simple, and it may even be used by non-geneticists. A working protocol was ultimately constructed for the purpose of rapid and accurate species identification in most countries in Europe regardless of which stage or which part of a blowfly was collected.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. High-resolution DNA melt curve analysis of the clustered, regularly interspaced short-palindromic-repeat locus of Campylobacter jejuni.

    PubMed

    Price, Erin P; Smith, Helen; Huygens, Flavia; Giffard, Philip M

    2007-05-01

    A novel method for genotyping the clustered, regularly interspaced short-palindromic-repeat (CRISPR) locus of Campylobacter jejuni is described. Following real-time PCR, CRISPR products were subjected to high-resolution melt (HRM) analysis, a new technology that allows precise melt profile determination of amplicons. This investigation shows that the CRISPR HRM assay provides a powerful addition to existing C. jejuni genotyping methods and emphasizes the potential of HRM for genotyping short sequence repeats in other species.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. Genotyping of beta thalassemia trait by high-resolution DNA melting analysis.

    PubMed

    Saetung, Rattika; Ongchai, Siriwan; Charoenkwan, Pimlak; Sanguansermsri, Torpong

    2013-11-01

    Beta thalassemia is a common hereditary hemalogogical disease in Thailand, with a prevalence of 5-8%. In this study, we evaluated the high resolution DNA melting (HRM) assay to identify beta thalassemia mutation in samples from 143 carriers of the beta thalassemia traits in at risk couples. The DNA was isolated from venous blood samples and tested for mutation under a series of 5 PCR-HRM (A, B, C, D and E primers) protocols. The A primers were for detection of beta thalassemia mutations in the HBB promoter region, the B primers for mutations in exon I, the C primers for exon II, the D primers for exon III and the E primers for the 3.4 kb deletion mutation. The mutations were diagnosed by comparing the complete melting curve profiles of a wild type control with those for each mutant sample. With the PCR-HRM technique, fourteen types of beta thalassemia mutations were detected. Each mutation had a unique and specific melting profile. The mutations included 36.4% (52 cases) codon 41/42-CTTT, 26.6% (38 cases) codon 17 A-T, 11.2% (16 cases) IVS1-1 G-T, 8.4% (12 cases) codon 71/72 +A, 8.4% (12 cases) of the 3.4 kb deletion and 3.5% (5 cases) -28 A-G. The remainder included one instance each of -87 C-A, -31 A-C, codon 27/28 +C, codon 30 G-A, IVS1-5 G-C, codon 35 C-A, codon 41-C and IVSII -654 C-T. Of the total cases, 85.8% of the mutations could be detected by primers B and C. The PCR-HRM method provides a rapid, simple and highly feasible strategy for mutation screening of beta thalassemia traits. PMID:24450243

  3. 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

  4. 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

  5. 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

  6. 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.

  7. Applying high-resolution melting (HRM) technology to identify five commonly used Artemisia species

    PubMed Central

    Song, Ming; Li, Jingjian; Xiong, Chao; Liu, Hexia; Liang, Junsong

    2016-01-01

    Many members of the genus Artemisia are important for medicinal purposes with multiple pharmacological properties. Often, these herbal plants sold on the markets are in processed forms so it is difficult to authenticate. Routine testing and identification of these herbal materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. In this study, five commonly used Artemisia species included Artemisia argyi, Artemisia annua, Artemisia lavandulaefolia, Artemisia indica, and Artemisia atrovirens were analyzed using high resolution melting (HRM) analysis based on the internal transcribed spacer 2 (ITS2) sequences. The melting profiles of the ITS2 amplicons of the five closely related herbal species are clearly separated so that they can be differentiated by HRM method. The method was further applied to authenticate commercial products in powdered. HRM curves of all the commercial samples tested are similar to the botanical species as labeled. These congeneric medicinal products were also clearly separated using the neighbor-joining (NJ) tree. Therefore, HRM method could provide an efficient and reliable authentication system to distinguish these commonly used Artemisia herbal products on the markets and offer a technical reference for medicines quality control in the drug supply chain. PMID:27698485

  8. 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.

  9. Melt processing of bulk high Tc superconductors and their application

    NASA Astrophysics Data System (ADS)

    Murakami, M.; Oyama, T.; Fujimoto, H.; Gotoh, S.; Yamaguchi, K.

    1991-03-01

    The authors report a melt-powder-melt-growth (MPMG) process which results in high Jc for bulk Y-Ba-Cu-O superconductors. The Y-Ba-Cu-O pellets or powders are melt quenched. The quenched plates are crushed into powder and mixed well. The powder is then compacted into desired shapes, remelted, and slowly cooled in a thermal gradient. When the starting composition is changed from the 1:2:3 stoichiometry toward the Y2BaCuO5(211) rich region, the 211 inclusions can be dispersed in the YBa2Cu3O(x) matrix, which contributes to increases in both flux pinning force and fracture toughness. A Jc value exceeding 3 x 108 A/sq m has been achieved at 77 K and 1 T. Another attractive feature of the MPMG process is that other components such as fine Ag powders can be added during solid-state mixing. Fine dispersion of Ag particles can effectively reduce the amount of cracking. MPMG-processed Y-Ba-Cu-O with Ag doping can levitate a mass of 3-kg at 1-mm height using a repulsive force against a 0.4-T magnet. A noncontacting rotation device such as a magnetic bearing can be made utilizing bulk high-Jc materials. A superconducting permanent magnet is also a promising candidate for future application. MPMG-processed Y-Ba-Cu-O can generate 0.25 T at 77 K.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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

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

    PubMed

    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.

  16. 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

  17. High resolution melt analysis to track infections due to ribotype 027 Clostridium difficile.

    PubMed

    Grando, Danilla; Said, Mohamed M; Mayall, Barrie C; Gurtler, Volker

    2012-05-01

    The increased prevalence of hypervirulent ribotype 027 Clostridium difficile requires rapid identification of isolates in order to implement timely infection control strategies. High resolution melt (HRM) analysis of PCR products can identify strain variation amongst genera of bacteria. The intergenic (16S-23S rDNA) spacer region contains sequence regions conserved within genera and other sequence region variables between species within genera. We wished to investigate whether HRM analysis of PCR ribotyping products could identify ribotype 027 C. difficile. Ribotyping was performed on 93 clinical isolates and five control strains and band patterns were analysed using GelCompar II (Applied Maths, USA). Real-time PCR using ribotyping primers was performed and normalised melt curves were generated. The HRM data was then imported into ScreenClust software (QIAGEN) to generate principal component analysis graphs depicting clustered relationships of strains. Ribotyping produced clear PCR bands for 88/98 isolates tested. Dendrograms generated by GelCompar showed a diversity of ribotype patterns amongst these 88 isolates with 18 groups identified with 70% homology. One clinical isolate showed 100% homology with the control 027 strains. ScreenClust analysis of the same 88 HRM results showed clustering of isolates, with 027 strains identifiable as a unique cluster. HRM analysis correctly identified the control 027 stains and the clinical isolate shown to be 027. HRM combined with ScreenClust analysis of real-time PCR products of the 16S-23S rDNA spacer region successfully identified ribotype 027 strains. For infection control purposes this was achieved within 2-3 h of colony isolation.

  18. 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.

  19. Validation of a blood group genotyping method based on high-resolution melting curve analysis.

    PubMed

    Gong, Tianxiang; Hong, Ying; Wang, Naihong; Fu, Xuemei; Zhou, Changhua

    2014-01-01

    The detection of polymorphism is the basis of blood group genotyping and phenotype prediction. Genotyping may be useful to determine blood groups when serologic results are unclear. The development and application of different methods for blood group genotyping may be needed as a substitute for blood group typing. The purpose of this study is to establish an approach for blood group genotyping based on a melting curve analysis of real-time polymerase chain reaction (PCR). Using DNA extracted from whole blood, we developed and validated a DNA typing method for detecting DO*01/DO*02, DO*01/DI*02, LU*01/LU*02, and GYPB*03/GYBP*04 alleles using a melting curve analysis. All assays were confirmed with a commercial reagent containing sequence-specific primers (PCR-SSP), and a cohort of the samples was confirmed with sequencing. Results for all blood groups were within the range of specificity and assay variability. Genotypes of 300 blood donors were fully consistent with PCR-SSP data. The obtained genotype distribution is in complete concordance with existing data for the Chinese population. There are several advantages for this approach of blood group genotyping: lower contamination rates with PCR products in this laboratory, ease of performance, automation potential, and rapid cycling time.

  20. 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

  1. Analysis of bla(SHV) codon 238 and 240 allele mixtures using Sybr green high-resolution melting analysis.

    PubMed

    Andersson, Patiyan; Harris, Tegan; Tong, Steven Y C; Giffard, Philip M

    2009-06-01

    Klebsiella pneumoniae isolates frequently contain complex mixtures of bla(SHV) alleles. A high-resolution melting-based method for interrogating the extended-spectrum activity conferring codon 238 and 240 polymorphisms was developed. This detects minority extended-spectrum beta-lactamase-encoding alleles, allows estimation of allele ratios, and discriminates between single and double mutants.

  2. [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

  3. Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping

    PubMed Central

    Fraley, Stephanie I.; Athamanolap, Pornpat; Masek, Billie J.; Hardick, Justin; Carroll, Karen C.; Hsieh, Yu-Hsiang; Rothman, Richard E.; Gaydos, Charlotte A.; Wang, Tza-Huei; Yang, Samuel

    2016-01-01

    High Resolution Melt (HRM) is a versatile and rapid post-PCR DNA analysis technique primarily used to differentiate sequence variants among only a few short amplicons. We recently developed a one-vs-one support vector machine algorithm (OVO SVM) that enables the use of HRM for identifying numerous short amplicon sequences automatically and reliably. Herein, we set out to maximize the discriminating power of HRM + SVM for a single genetic locus by testing longer amplicons harboring significantly more sequence information. Using universal primers that amplify the hypervariable bacterial 16 S rRNA gene as a model system, we found that long amplicons yield more complex HRM curve shapes. We developed a novel nested OVO SVM approach to take advantage of this feature and achieved 100% accuracy in the identification of 37 clinically relevant bacteria in Leave-One-Out-Cross-Validation. A subset of organisms were independently tested. Those from pure culture were identified with high accuracy, while those tested directly from clinical blood bottles displayed more technical variability and reduced accuracy. Our findings demonstrate that long sequences can be accurately and automatically profiled by HRM with a novel nested SVM approach and suggest that clinical sample testing is feasible with further optimization. PMID:26778280

  4. Differential effect of three base modifications on DNA thermostability revealed by high resolution melting.

    PubMed

    López, Carlos M Rodríguez; Lloyd, Amanda J; Leonard, Kate; Wilkinson, Mike J

    2012-09-01

    High resolution melting (HRM) can detect and quantify the presence of 5-methylcytosine (5mC) in DNA samples, but the ability of HRM to diagnose other DNA modifications remains unexplored. The DNA bases N6-methyladenine and 5-hydroxymethylcytosine occur across almost all phyla. While their function remains controversial, their presence perturbs DNA structure. Such modifications could affect gene regulation, chromatin condensation and DNA packaging. Here, we reveal that DNA containing N6-methyladenine or 5-hydroxymethylcytosine exhibits reduced thermal stability compared to cytosine-methylated DNA. These thermostability changes are sufficiently divergent to allow detection and quantification by HRM analysis. Thus, we report that HRM distinguishes between sequence-identical DNA differing only in the modification type of one base. This approach is also able to distinguish between two DNA fragments carrying both N6-methyladenine and 5-methylcytosine but differing only in the distance separating the modified bases. This finding provides scope for the development of new methods to characterize DNA chemically and to allow for low cost screening of mutant populations of genes involved in base modification. More fundamentally, contrast between the thermostabilizing effects of 5mC on dsDNA compared with the destabilizing effects of N6-methyladenine (m6A) and 5-hydroxymethylcytosine (5hmC) raises the intriguing possibility of an antagonistic relationship between modification types with functional significance.

  5. Nested Machine Learning Facilitates Increased Sequence Content for Large-Scale Automated High Resolution Melt Genotyping.

    PubMed

    Fraley, Stephanie I; Athamanolap, Pornpat; Masek, Billie J; Hardick, Justin; Carroll, Karen C; Hsieh, Yu-Hsiang; Rothman, Richard E; Gaydos, Charlotte A; Wang, Tza-Huei; Yang, Samuel

    2016-01-01

    High Resolution Melt (HRM) is a versatile and rapid post-PCR DNA analysis technique primarily used to differentiate sequence variants among only a few short amplicons. We recently developed a one-vs-one support vector machine algorithm (OVO SVM) that enables the use of HRM for identifying numerous short amplicon sequences automatically and reliably. Herein, we set out to maximize the discriminating power of HRM + SVM for a single genetic locus by testing longer amplicons harboring significantly more sequence information. Using universal primers that amplify the hypervariable bacterial 16 S rRNA gene as a model system, we found that long amplicons yield more complex HRM curve shapes. We developed a novel nested OVO SVM approach to take advantage of this feature and achieved 100% accuracy in the identification of 37 clinically relevant bacteria in Leave-One-Out-Cross-Validation. A subset of organisms were independently tested. Those from pure culture were identified with high accuracy, while those tested directly from clinical blood bottles displayed more technical variability and reduced accuracy. Our findings demonstrate that long sequences can be accurately and automatically profiled by HRM with a novel nested SVM approach and suggest that clinical sample testing is feasible with further optimization. PMID:26778280

  6. 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

  7. High Resolution Melting Analysis: A Rapid and Accurate Method to Detect CALR Mutations

    PubMed Central

    Moreno, Melania; Torres, Laura; Santana-Lopez, Gonzalo; Rodriguez-Medina, Carlos; Perera, María; Bellosillo, Beatriz; de la Iglesia, Silvia; Molero, Teresa; Gomez-Casares, Maria Teresa

    2014-01-01

    Background The recent discovery of CALR mutations in essential thrombocythemia (ET) and primary myelofibrosis (PMF) patients without JAK2/MPL mutations has emerged as a relevant finding for the molecular diagnosis of these myeloproliferative neoplasms (MPN). We tested the feasibility of high-resolution melting (HRM) as a screening method for rapid detection of CALR mutations. Methods CALR was studied in wild-type JAK2/MPL patients including 34 ET, 21 persistent thrombocytosis suggestive of MPN and 98 suspected secondary thrombocytosis. CALR mutation analysis was performed through HRM and Sanger sequencing. We compared clinical features of CALR-mutated versus 45 JAK2/MPL-mutated subjects in ET. Results Nineteen samples showed distinct HRM patterns from wild-type. Of them, 18 were mutations and one a polymorphism as confirmed by direct sequencing. CALR mutations were present in 44% of ET (15/34), 14% of persistent thrombocytosis suggestive of MPN (3/21) and none of the secondary thrombocytosis (0/98). Of the 18 mutants, 9 were 52 bp deletions, 8 were 5 bp insertions and other was a complex mutation with insertion/deletion. No mutations were found after sequencing analysis of 45 samples displaying wild-type HRM curves. HRM technique was reproducible, no false positive or negative were detected and the limit of detection was of 3%. Conclusions This study establishes a sensitive, reliable and rapid HRM method to screen for the presence of CALR mutations. PMID:25068507

  8. Limitation of high-resolution melting curve analysis for genotyping simple sequence repeats in sheep.

    PubMed

    Yang, M; Yue, Y J; Guo, T T; Han, J L; Liu, J B; Guo, J; Sun, X P; Feng, R L; Wu, Y Y; Wang, C F; Wang, L P; Yang, B H

    2014-04-08

    Variation in microsatellite or simple sequence repeat (SSR) loci has, until recently, relied heavily on the use of gel-based methods that can be both time consuming and difficult to genotype. Non gel-based systems are therefore important to increase simplicity and improve turn-around time without compromising assay sensitivity and accuracy. In this report, we assessed the latest of the non-gel-based methods, high-resolution melting (HRM) curve analysis. HRM is a technique that monitors exactly the decreasing fluorescence of intercalating dye in the process of dissociation of double-stranded DNA. The measurement immediately follows polymerase chain reaction in a one-step, closed-tube method. Four SSR loci of different complexity in sheep, namely MAF209, MCM140, CB226, and SRCRSP5, were assessed using the LightScanners System with LC Greens PLUS DNA binding dye. In order to improve the accuracy of genotyping, we applied internal oligo nucleotide calibrators while performing HRM. DNA polymorphisms were previously identified using capillary electrophoresis analysis (CE). The result showed that CE detected more genotypes than HRM in the same loci regardless of the level of polymorphism at the SSR loci. We demonstrate current limitations of the HRM method for the analysis of SSR loci.

  9. High-resolution melt analysis of DNA methylation to discriminate semen in biological stains.

    PubMed

    Antunes, Joana; Silva, Deborah S B S; Balamurugan, Kuppareddi; Duncan, George; Alho, Clarice S; McCord, Bruce

    2016-02-01

    The goal of this study was to develop a method for the detection of semen in biological stains using high-resolution melt (HRM) analysis and DNA methylation. To perform this task, we used an epigenetic locus that targets a tissue-specific differentially methylated region for semen. This specific locus, ZC3H12D, contains methylated CpG sites that are hypomethylated in semen and hypermethylated in blood and saliva. Using this procedure, DNA from forensic stains can be isolated, processed using bisulfite-modified polymerase chain reaction (PCR), and detected by real-time PCR with HRM capability. The method described in this article is robust; we were able to obtain results from samples with as little as 1 ng of genomic DNA. Samples inhibited by humic acid still produced reliable results. Furthermore, the procedure is specific and will not amplify non-bisulfite-modified DNA. Because this process can be performed using real-time PCR and is quantitative, it fits nicely within the workflow of current forensic DNA laboratories. As a result, it should prove to be a useful technique for processing trace evidence samples for serological analysis.

  10. 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

  11. 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.

  12. Development of a high-resolution melting-based approach for efficient differentiation among Bacillus cereus group isolates.

    PubMed

    Antolinos, Vera; Fernández, Pablo S; Ros-Chumillas, María; Periago, Paula M; Weiss, Julia

    2012-09-01

    Strains belonging to Bacillus cereus Group include six different species, among which are Bacillus thuringiensis, Bacillus weihenstephanensis, and Bacillus cereus sensu stricto, a causative agent of food poisoning. Sequence of the panC-housekeeping gene is used for B. cereus Group affiliation to seven major phylogenetic groups (I-VII) with different ecological niches and variations in thermal growth range and spore heat resistance of B. cereus Group microorganisms varies among phylogenetic groups. We assigned a selection of B. cereus sensu stricto strains related to food poisoning from the Spanish cultivar Collection (Valencia) to Group IV strains based on panC gene sequence. Thermal inactivation assays revealed variability of spore heat resistance within these Group IV strains. Adequate food sanitizing treatments therefore require fast and reliable identification of particular strains. In the present study, feasibility of genotyping via high-resolution melting (HRM) analysis was examined. HRM analysis of amplified polymorphic 16S-23 intergenic spacer region (ISR) region proved to be discriminatory for B. cereus sensu stricto strain typing, while two other polymorphic regions within the bacterial rRNA operon allowed differentiation between Bacillus species, demonstrating its applicability for discrimination on the species and strain level within B. cereus Group.

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. Rapid and high throughput molecular identification of diverse mosquito species by high resolution melting analysis

    PubMed Central

    Ajamma, Yvonne Ukamaka; Mararo, Enock; Omondi, David; Onchuru, Thomas; Muigai, Anne W. T.; Masiga, Daniel; Villinger, Jandouwe

    2016-01-01

    Mosquitoes are a diverse group of invertebrates, with members that are among the most important vectors of diseases. The correct identification of mosquitoes is paramount to the control of the diseases that they transmit. However, morphological techniques depend on the quality of the specimen and often unavailable taxonomic expertise, which may still not be able to distinguish mosquitoes among species complexes (sibling and cryptic species). High resolution melting (HRM) analyses, a closed-tube, post-polymerase chain reaction (PCR) method used to identify variations in nucleic acid sequences, has been used to differentiate species within the Anopheles gambiae and Culex pipiens complexes. We validated the use of PCR-HRM analyses to differentiate species within Anopheles and within each of six genera of culicine mosquitoes, comparing primers targeting cytochrome b ( cyt b), NADH dehydrogenase subunit 1 (ND1), intergenic spacer region (IGS) and cytochrome c oxidase subunit 1 ( COI) gene regions. HRM analyses of amplicons from all the six primer pairs successfully differentiated two or more mosquito species within one or more genera ( Aedes ( Ae. vittatus from Ae. metallicus), Culex ( Cx. tenagius from Cx. antennatus, Cx. neavei from Cx. duttoni, cryptic Cx. pipiens species), Anopheles ( An. gambiae s.s. from An. arabiensis) and Mansonia ( Ma. africana from Ma. uniformis)) based on their HRM profiles. However, PCR-HRM could not distinguish between species within Aedeomyia ( Ad. africana and Ad. furfurea), Mimomyia ( Mi. hispida and Mi. splendens) and Coquillettidia ( Cq. aurites, Cq. chrysosoma, Cq. fuscopennata, Cq. metallica, Cq. microannulatus, Cq. pseudoconopas and Cq. versicolor) genera using any of the primers. The IGS and COI barcode region primers gave the best and most definitive separation of mosquito species among anopheline and culicine mosquito genera, respectively, while the other markers may serve to confirm identifications of closely related sub

  19. 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

  20. Rapid and high throughput molecular identification of diverse mosquito species by high resolution melting analysis

    PubMed Central

    Ajamma, Yvonne Ukamaka; Mararo, Enock; Omondi, David; Onchuru, Thomas; Muigai, Anne W. T.; Masiga, Daniel; Villinger, Jandouwe

    2016-01-01

    Mosquitoes are a diverse group of invertebrates, with members that are among the most important vectors of diseases. The correct identification of mosquitoes is paramount to the control of the diseases that they transmit. However, morphological techniques depend on the quality of the specimen and often unavailable taxonomic expertise, which may still not be able to distinguish mosquitoes among species complexes (sibling and cryptic species). High resolution melting (HRM) analyses, a closed-tube, post-polymerase chain reaction (PCR) method used to identify variations in nucleic acid sequences, has been used to differentiate species within the Anopheles gambiae and Culex pipiens complexes. We validated the use of PCR-HRM analyses to differentiate species within Anopheles and within each of six genera of culicine mosquitoes, comparing primers targeting cytochrome b ( cyt b), NADH dehydrogenase subunit 1 (ND1), intergenic spacer region (IGS) and cytochrome c oxidase subunit 1 ( COI) gene regions. HRM analyses of amplicons from all the six primer pairs successfully differentiated two or more mosquito species within one or more genera ( Aedes ( Ae. vittatus from Ae. metallicus), Culex ( Cx. tenagius from Cx. antennatus, Cx. neavei from Cx. duttoni, cryptic Cx. pipiens species), Anopheles ( An. gambiae s.s. from An. arabiensis) and Mansonia ( Ma. africana from Ma. uniformis)) based on their HRM profiles. However, PCR-HRM could not distinguish between species within Aedeomyia ( Ad. africana and Ad. furfurea), Mimomyia ( Mi. hispida and Mi. splendens) and Coquillettidia ( Cq. aurites, Cq. chrysosoma, Cq. fuscopennata, Cq. metallica, Cq. microannulatus, Cq. pseudoconopas and Cq. versicolor) genera using any of the primers. The IGS and COI barcode region primers gave the best and most definitive separation of mosquito species among anopheline and culicine mosquito genera, respectively, while the other markers may serve to confirm identifications of closely related sub

  1. Putative hybrids between two Anisakis cryptic species: molecular genotyping using High Resolution Melting.

    PubMed

    Cavallero, S; Costa, A; Caracappa, S; Gambetta, B; D'Amelio, S

    2014-11-01

    The genus Anisakis includes nine recognized species and the complex of cryptic species Anisakis simplex s. l. is often associated with the human disease known as anisakiasis. During the last decades the use of nuclear ribosomal ITS allowed the identification and description of numerous anisakid nematodes and the discovery of recombinant genotypes or putative hybrids even in other parasitic helminths, such as those between A. simplex sensu stricto and A. pegreffii. The existence of pure hybrids of the two sibling species has been long debated due to the large recovery of larval forms from sympatric areas and the rare observation of adult hybrids. The aims of the present report were to identify anisakid nematodes collected from Stenella coeruleoalba using PCR-RFLP of ITS and to focus the interest on hybrid forms using a High Resolution Melting (HRM) and direct sequencing analyses, since the new record of putative hybrid at adult stage. The PCR-RFLP analysis enabled to identify A. simplex s.s., A. pegreffii, the heterozygous genotype of the two species and A. physeteris. The use of the genotyping approach based on HRM confirmed the profiles of the two species A. simplex s.s. and A. pegreffii, and of the hybrid individuals. The new record of adult hybrids in definitive hosts rekindles the long debate about their existence and their evolutionary meaning. Since the reproductive isolation between A. simplex s.s. and A. pegreffii is the assumption for their existence as separated species, the use of alternative molecular markers and population genetic studies on adult anisakids are recommended. PMID:25241034

  2. 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

  3. 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.

  4. Primate genotyping via high resolution melt analysis: rapid and reliable identification of color vision status in wild lemurs.

    PubMed

    Jacobs, Rachel L; Spriggs, Amanda N; MacFie, Tammie S; Baden, Andrea L; Irwin, Mitchell T; Wright, Patricia C; Louis, Edward E; Lawler, Richard R; Mundy, Nicholas I; Bradley, Brenda J

    2016-10-01

    Analyses of genetic polymorphisms can aid our understanding of intra- and interspecific variation in primate sociality, ecology, and behavior. Studies of primate opsin genes are prime examples of this, as single nucleotide variants (SNVs) in the X-linked opsin gene underlie variation in color vision. For primate species with polymorphic trichromacy, genotyping opsin SNVs can generally indicate whether individual primates are red-green color-blind (denoted homozygous M or homozygous L) or have full trichromatic color vision (heterozygous ML). Given the potential influence of color vision on behavior and fitness, characterizing the color vision status of study subjects is becoming commonplace for many primate field projects. Such studies traditionally involve a multi-step sequencing-based method that can be costly and time-consuming. Here we present a new reliable, rapid, and relatively inexpensive method for characterizing color vision in primate populations using high resolution melt analysis (HRMA). Using lemurs as a case study, we characterized variation at exons 3 and/or 5 of the X-linked opsin gene for 87 individuals representing nine species. We scored opsin genotypes and color vision status using both traditional sequencing-based methods as well as our novel melting-curve based HRMA protocol. For each species, the melting curves of varying genotypes (homozygous M, homozygous L, heterozygous ML) differed in melting temperature and/or shape. Melting curves for each sample were consistent across replicates, and genotype-specific melting curves were consistent across DNA sources (blood vs. feces). We show that opsin genotypes can be quickly and reliably scored using HRMA once lab-specific reference curves have been developed based on known genotypes. Although the protocol presented here focuses on genotyping lemur opsin loci, we also consider the larger potential for applying this approach to various types of genetic studies of primate populations. PMID:27271303

  5. Primate genotyping via high resolution melt analysis: rapid and reliable identification of color vision status in wild lemurs.

    PubMed

    Jacobs, Rachel L; Spriggs, Amanda N; MacFie, Tammie S; Baden, Andrea L; Irwin, Mitchell T; Wright, Patricia C; Louis, Edward E; Lawler, Richard R; Mundy, Nicholas I; Bradley, Brenda J

    2016-10-01

    Analyses of genetic polymorphisms can aid our understanding of intra- and interspecific variation in primate sociality, ecology, and behavior. Studies of primate opsin genes are prime examples of this, as single nucleotide variants (SNVs) in the X-linked opsin gene underlie variation in color vision. For primate species with polymorphic trichromacy, genotyping opsin SNVs can generally indicate whether individual primates are red-green color-blind (denoted homozygous M or homozygous L) or have full trichromatic color vision (heterozygous ML). Given the potential influence of color vision on behavior and fitness, characterizing the color vision status of study subjects is becoming commonplace for many primate field projects. Such studies traditionally involve a multi-step sequencing-based method that can be costly and time-consuming. Here we present a new reliable, rapid, and relatively inexpensive method for characterizing color vision in primate populations using high resolution melt analysis (HRMA). Using lemurs as a case study, we characterized variation at exons 3 and/or 5 of the X-linked opsin gene for 87 individuals representing nine species. We scored opsin genotypes and color vision status using both traditional sequencing-based methods as well as our novel melting-curve based HRMA protocol. For each species, the melting curves of varying genotypes (homozygous M, homozygous L, heterozygous ML) differed in melting temperature and/or shape. Melting curves for each sample were consistent across replicates, and genotype-specific melting curves were consistent across DNA sources (blood vs. feces). We show that opsin genotypes can be quickly and reliably scored using HRMA once lab-specific reference curves have been developed based on known genotypes. Although the protocol presented here focuses on genotyping lemur opsin loci, we also consider the larger potential for applying this approach to various types of genetic studies of primate populations.

  6. 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.

  7. 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

  8. 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.

  9. Rapid Identification of Biothreat and Other Clinically Relevant Bacterial Species by Use of Universal PCR Coupled with High-Resolution Melting Analysis▿

    PubMed Central

    Yang, Samuel; Ramachandran, Padmini; Rothman, Richard; Hsieh, Yu-Hsiang; Hardick, Andrew; Won, Helen; Kecojevic, Aleksandar; Jackman, Joany; Gaydos, Charlotte

    2009-01-01

    A rapid assay for eubacterial species identification is described using high-resolution melt analysis to characterize PCR products. Unique melt profiles generated from multiple hypervariable regions of the 16S rRNA gene for 100 clinically relevant bacterial pathogens, including category A and B biothreat agents and their surrogates, allowed highly specific species identification. PMID:19458181

  10. 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

  11. Molecular Differentiation of Schistosoma japonicum and Schistosoma mekongi by Real-Time PCR with High Resolution Melting Analysis

    PubMed Central

    Kongklieng, Amornmas; Kaewkong, Worasak; Intapan, Pewpan M.; Sanpool, Oranuch; Janwan, Penchom; Thanchomnang, Tongjit; Lulitanond, Viraphong; Sri-Aroon, Pusadee; Limpanont, Yanin

    2013-01-01

    Human schistosomiasis caused by Schistosoma japonicum and Schistosoma mekongi is a chronic and debilitating helminthic disease still prevalent in several countries of Asia. Due to morphological similarities of cercariae and eggs of these 2 species, microscopic differentiation is difficult. High resolution melting (HRM) real-time PCR is developed as an alternative tool for the detection and differentiation of these 2 species. A primer pair was designed for targeting the 18S ribosomal RNA gene to generate PCR products of 156 base pairs for both species. The melting points of S. japonicum and S. mekongi PCR products were 84.5±0.07℃ and 85.7±0.07℃, respectively. The method permits amplification from a single cercaria or an egg. The HRM real-time PCR is a rapid and simple tool for differentiation of S. japonicum and S. mekongi in the intermediate and final hosts. PMID:24516269

  12. 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

  13. High-resolution melting analysis for the detection of two erythromycin-resistant Bordetella pertussis strains carried by healthy schoolchildren in China.

    PubMed

    Zhang, Q; Li, M; Wang, L; Xin, T; He, Q

    2013-06-01

    Two erythromycin-resistant strains of Bordetella pertussis were isolated from nasopharyngeal specimens of two asymptomatic schoolchildren in China. High-resolution melting and sequencing analyses confirmed the homogeneous A2047G mutation in 23S rRNA genes of the two isolates. High-resolution melting (HRM) analysis is a useful assay for the rapid detection of erythromycin-resistant B. pertussis. The appearance of erythromycin-resistant B. pertussis strains in China is alarming.

  14. 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.

  15. High Resolution Melting Analysis Is a More Sensitive and Effective Alternative to Gel-Based Platforms in Analysis of SSR – An Example in Citrus

    PubMed Central

    Distefano, Gaetano; Caruso, Marco; La Malfa, Stefano; Gentile, Alessandra; Wu, Shu-Biao

    2012-01-01

    High resolution melting curve analysis (HRM) has been used as an efficient, accurate and cost-effective tool to detect single nucleotide polymorphisms (SNPs) or insertions or deletions (INDELs). However, its efficiency, accuracy and applicability to discriminate microsatellite polymorphism have not been extensively assessed. The traditional protocols used for SSR genotyping include PCR amplification of the DNA fragment and the separation of the fragments on electrophoresis-based platform. However, post-PCR handling processes are laborious and costly. Furthermore, SNPs present in the sequences flanking repeat motif cannot be detected by polyacrylamide-gel-electrophoresis based methods. In the present study, we compared the discriminating power of HRM with the traditional electrophoresis-based methods and provided a panel of primers for HRM genotyping in Citrus. The results showed that sixteen SSR markers produced distinct polymorphic melting curves among the Citrus spp investigated through HRM analysis. Among those, 10 showed more genotypes by HRM analysis than capillary electrophoresis owing to the presence of SNPs in the amplicons. For the SSR markers without SNPs present in the flanking region, HRM also gave distinct melting curves which detected same genotypes as were shown in capillary electrophoresis (CE) analysis. Moreover, HRM analysis allowed the discrimination of most of the 15 citrus genotypes and the resulting genetic distance analysis clustered them into three main branches. In conclusion, it has been approved that HRM is not only an efficient and cost-effective alternative of electrophoresis-based method for SSR markers, but also a method to uncover more polymorphisms contributed by SNPs present in SSRs. It was therefore suggested that the panel of SSR markers could be used in a variety of applications in the citrus biodiversity and breeding programs using HRM analysis. Furthermore, we speculate that the HRM analysis can be employed to analyse SSR

  16. Barcode High Resolution Melting (Bar-HRM) analysis for detection and quantification of PDO "Fava Santorinis" (Lathyrus clymenum) adulterants.

    PubMed

    Ganopoulos, Ioannis; Madesis, Panagiotis; Darzentas, Nikos; Argiriou, Anagnostis; Tsaftaris, Athanasios

    2012-07-15

    Legumes considered as one of the most important crops worldwide. Due to high price as a PDO product, commercial products of "Fava Santorinis" are often subjected to adulterations from other legume products coming from other Lathyrus or Vicia and Pisum species. Using plant DNA barcoding regions (trnL and rpoC) coupled with High Resolution Melting (Bar-HRM) we have developed a method allowing us to detect and authenticate PDO "Fava Santorinis". Bar-HRM proved to be a very sensitive tool able to genotype Lathyrus and its closed relative species and to detect admixtures, being sensitive enough to as low as 1:100 of non-"Fava Santorinis" in "Fava Santorinis" commercial products. In conclusion, Bar-HRM analysis can be a faster, with higher resolution and cost effectiveness alternative method to authenticate PDO "Fava Santorinis" and to quantitatively detect adulterations in "Fava Santorinis" with other relative commercial "Fava" food products. PMID:25683426

  17. Application of a SeaWinds/QuikSCAT sea ice melt algorithm for assessing melt dynamics in the Canadian Arctic Archipelago

    NASA Astrophysics Data System (ADS)

    Howell, Stephen E. L.; Tivy, Adrienne; Yackel, John J.; Scharien, Randall K.

    2006-07-01

    A remotely sensed sea ice melt algorithm utilizing SeaWinds/QuikSCAT (QuikSCAT) data is developed and applied to sea ice the Canadian Arctic Archipelago (CAA) from 2000 to 2004. The extended advanced very high resolution radiometer Polar Pathfinder (APP-x) data set is used to identify spatially coupled relationships between sea ice melt and radiative forcings. In situ data from the Collaborative Interdisciplinary Cryospheric Experiment (C-ICE) (2000, 2001, and 2002) and the Canadian Arctic Shelf Exchange Study (CASES) (2004) are used to validate APP-x data during the melt period. QuikSCAT-detected maps of melt onset, pond onset, and drainage are created from 2000 to 2004, and results indicate considerable interannual variability of melt dynamics within the CAA. In some years, melt stages are positively spatially autocorrelated, whereas other years exhibit a negative or no spatial autocorrelation. QuikSCAT-detected stages of melt are found to be influenced by interannual varying amounts and timing of radiative forcing making prediction difficult. The spatiotemporal variability of ice melt also influences the distribution of ice within the CAA. The lower-latitude regions of the CAA are shown to have accumulated increasing concentrations of multiyear ice from 2000 to 2005. This paper concludes with a discussion of the interplay between thermodynamic and dynamic sea ice processes likely to have contributed to this trend.

  18. 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

  19. 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.

  20. 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

  1. High-resolution melting analysis using unlabeled probe and amplicon scanning simultaneously detects several lactase persistence variants.

    PubMed

    Janukonyté, Jurgita; Vestergaard, Else M; Ladefoged, Søren A; Nissen, Peter H

    2010-12-01

    Lactase persistence and thereby tolerance to lactose is a common trait in people of Northern European descent. It is linked to the LCT -13910C>T variant located in intron 13 of the MCM6 gene 13.9 kb upstream of the lactase (LCT) gene. In people of African and Middle Eastern descent, lactase persistence can be associated with other variants nearby the -13910C>T variant, limiting the use of the -13910C>T-based SNP analysis, e.g. TaqMan assays for the diagnosis of lactose intolerance. Using high-resolution melting analysis, we identified five samples that were heterozygous for the -13915T>G variant among 78 patients genotyped as -13910C/C by a TaqMan assay. All samples originated from patients of probable Middle Eastern descent. In order to detect the -13910 and -13915 variants simultaneously, we developed a new high-resolution melting (HRM) analysis assay based on unlabeled probe genotyping and simultaneous amplicon scanning analysis. By using this assay we were able to distinguish the -13910 and -13915 genotypes clearly. Furthermore, we identified two rare variants, the -13907C>G and -13913T>C. With this method, based on an inexpensive unlabeled probe, it is possible to simultaneously detect the -13910C>T and -13915T>G variants in addition to rarer variants surrounding the -13910 site. This new method may contribute to improve the diagnostic performance of the genetic analysis for lactose intolerance.

  2. 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

  3. Rapid identification of bovine mastitis pathogens by high-resolution melt analysis of 16S rDNA sequences.

    PubMed

    Ajitkumar, Praseeda; Barkema, Herman W; De Buck, Jeroen

    2012-03-23

    Accurate identification of mastitis pathogens is often compromised when using conventional culture-based methods. Here, we report a novel, rapid assay tested for speciation of bacterial mastitis pathogens using high-resolution melt analysis (HRMA) of 16S rDNA sequences. Real-time PCR amplification of 16S rRNA gene fragment, spanning the variable region V5 and V6 was performed with a resulting amplicon of 290bp. First, a library was generated of melt curves of 9 common pathogens that are implicated in bovine mastitis. Six of the isolates, Escherichia coli, Streptococcus agalactiae, Klebsiella pneumoniae, Streptococcus uberis, Staphylococcus aureus and Mycoplasma bovis, were type strains while the other 3, Arcanobacterium pyogenes, Corynebacterium bovis and Streptococcus dysgalactiae, were bovine mastitis field isolates. Four of the type strains, E. coli, S. agalactiae, K. pneumoniae and S. aureus, were found to be of human origin, while the other 3 type strains were isolated from bovine infections. Secondly, the melt curves and corresponding amplicon sequences of A. pyogenes, E. coli, S. agalactiae, S. dysgalactiae, K. pneumoniae, S. uberis and S. aureus were compared with 10 bovine mastitis field isolates of each pathogen. Based on the distinct differences in melt curves and sequences between human and bovine isolates of E. coli and K. pneumoniae, it was deemed necessary to select a set of bovine strains for these pathogens to be used as reference strains in the HRMA. Next, the HRMA was validated by three interpreters analyzing the differential clustering pattern of melt curves of 60 bacterial cultures obtained from mastitis milk samples. The three test interpreters were blinded to the culture and sequencing results of the isolates. Overall accuracy of the validation assay was 95% as there was difficulty in identifying the streptococci due to heterogeneity observed in the PCR amplicons of S. uberis. The present study revealed that broad-range real-time PCR with

  4. 24 CFR 3286.705 - Applicability of dispute resolution program.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 5 2010-04-01 2010-04-01 false Applicability of dispute resolution...-Administered States § 3286.705 Applicability of dispute resolution program. (a) Generally. Regardless of any... available under the HUD dispute resolution program, as implemented in part 3288 of this chapter, continue...

  5. 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

  6. 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.

  7. Molecular Differentiation of Opisthorchis viverrini and Clonorchis sinensis Eggs by Multiplex Real-Time PCR with High Resolution Melting Analysis

    PubMed Central

    Kaewkong, Worasak; Intapan, Pewpan M.; Sanpool, Oranuch; Janwan, Penchom; Thanchomnang, Tongjit; Laummaunwai, Porntip; Lulitanond, Viraphong; Doanh, Pham Ngoc

    2013-01-01

    Opisthorchis viverrini and Clonorchis sinensis are parasites known to be carcinogenic and causative agents of cholangiocarcinoma in Asia. The standard method for diagnosis for those parasite infections is stool examination to detect parasite eggs. However, the method has low sensitivity, and eggs of O. viverrini and C. sinensis are difficult to distinguish from each other and from those of some other trematodes. Here, we report a multiplex real-time PCR coupled with high resolution melting (HRM) analysis for the differentiation of O. viverrini and C. sinensis eggs in fecal samples. Using 2 pairs of species-specific primers, DNA sequences from a portion of the mitochondrial NADH dehydrogenase subunit 2 (nad 2) gene, were amplified to generate 209 and 165 bp products for O. viverrini and C. sinensis, respectively. The distinct characteristics of HRM patterns were analyzed, and the melting temperatures peaked at 82.4±0.09℃ and 85.9±0.08℃ for O. viverrini and C. sinensis, respectively. This technique was able to detect as few as 1 egg of O. viverrini and 2 eggs of C. sinensis in a 150 mg fecal sample, which is equivalent to 7 and 14 eggs per gram of feces, respectively. The method is species-specific, rapid, simple, and does not require fluorescent probes or post-PCR processing for discrimination of eggs of the 2 species. It offers a new tool for differentiation and detection of Asian liver fluke infections in stool specimens. PMID:24516275

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

    PubMed

    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.

  9. Rapid molecular identification of Listeria species by use of real-time PCR and high-resolution melting analysis.

    PubMed

    Jin, Dazhi; Luo, Yun; Zhang, Zheng; Fang, Weijia; Ye, Julian; Wu, Fang; Ding, Gangqiang

    2012-05-01

    Identification of Listeria species via a molecular method is critical for food safety and clinical diagnosis. In this study, an assay integrating real-time quantitative PCR (Q-PCR) with high-resolution melting (HRM) curve analysis was developed and assessed for rapid identification of six Listeria species. The ssrA gene, which encodes a transfer-messenger RNA (tmRNA) is conserved and common to all bacterial phyla, contains a variable domain in Listeria spp. Therefore, Q-PCR and a HRM profile were applied to characterize this gene. Fifty-three Listeria species and 45 non-Listeria species were detected using one primer set, with an accuracy of 100% in reference to conventional methods. There was a 93.3% correction rate to 30 artificially contaminated samples. Thus, Q-PCR with melting profiling analysis proved able to identify Listeria species accurately. Consequently, this study demonstrates that the assay we developed is a functional tool for rapidly identifying six Listeria species, and has the potential for discriminating novel species food safety and epidemiological research.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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...

  17. High resolution melting method to detect single nucleotide polymorphism of VKORC1 and CYP2C9.

    PubMed

    Chen, Chunxia; Li, Siyue; Lu, Xiaojun; Tan, Bin; Huang, Chunyan; Qin, Li

    2014-01-01

    Single nucleotide polymorphisms (SNPs) of VKORC (1173T/C, rs9934438) and CYP2C9 (1075A/C, rs1057910) are major contributory factors on the sensitivity of warfarin in Chinese. Analysis of the two genomic loci could help warfarin treatment individual from bleeding or thrombosis events. An assay with the advantages of simplicity, speed, high sensitivity and low cost for genotyping is calling for clinical laboratories. High resolution method (HRM) meets these callings, but no study with large sample tested its performance in genotyping of rs9934438 and rs1057910. In this study, we identified polymorphisms of rs9934438 and rs1057910 in 255 unrelated Chinese heart valve replacement patients of Han ethnic group from West China Hospital. The two genomic loci were genotyped by HRM using LightCycler® 480 High Resolution Melting Master on LightCycler® 480 Real-Time PCR instruments (Roche Diagnostics), and all amplified PCR products were sent for direct DNA sequencing. The genotyping of rs1057910 between HRM and sequencing showed perfect 100% concordance. While the concordance of rs9934438 between HRM and sequencing was 99.2%. Unexpected mutation interfered genotyping results of HRM when genotyping rs9934438. HRM is a valuable technique for genotype detection of rs9934438 and rs1057910 to assess individual sensitivity to warfarin, where DNA sequencing is added inevitably sometimes.

  18. 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...

  19. 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

  20. 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

  1. Melt electrospinning.

    PubMed

    Hutmacher, Dietmar W; Dalton, Paul D

    2011-01-01

    Melt electrospinning is relatively under-investigated compared to solution electrospinning but provides opportunities in numerous areas, in which solvent accumulation or toxicity are a concern. These applications are diverse, and provide a broad set of challenges to researchers involved in electrospinning. In this context, melt electrospinning provides an alternative approach that bypasses some challenges to solution electrospinning, while bringing new issues to the forefront, such as the thermal stability of polymers. This Focus Review describes the literature on melt electrospinning, as well as highlighting areas where both melt and solution are combined, and potentially merge together in the future.

  2. Rapid identification of bacterial pathogens in positive blood culture bottles by use of a broad-based PCR assay coupled with high-resolution melt analysis.

    PubMed

    Won, Helen; Rothman, Richard; Ramachandran, Padmini; Hsieh, Yu-Hsiang; Kecojevic, Aleksandar; Carroll, Karen C; Aird, Deborah; Gaydos, Charlotte; Yang, Samuel

    2010-09-01

    We evaluated a broad-based PCR assay coupled with high-resolution melt analysis for rapid bacterial identification in patients with bacterial sepsis. With a reference library of 60 clinically relevant bacterial species, 52 positive blood culture samples were tested. Our assay identified 46/52 samples at the species level, with 100% concordance to culture findings.

  3. High-resolution melt PCR analysis for rapid identification of Chlamydia abortus live vaccine strain 1B among C. abortus strains and field isolates.

    PubMed

    Vorimore, Fabien; Cavanna, Noémie; Vicari, Nadia; Magnino, Simone; Willems, Hermann; Rodolakis, Annie; Siarkou, Victoria I; Laroucau, Karine

    2012-09-01

    We describe a novel high-resolution melt assay that clearly differentiates Chlamydia abortus live vaccine strain 1B from field C. abortus strains and field wild-type isolates based on previously described single nucleotide polymorphisms. This modern genotyping technique is inexpensive, easy to use, and less time-consuming than PCR-RFLP.

  4. 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.

  5. Rapid molecular typing of Prototheca zopfii by high resolution melting real-time PCR (PCR-HRM).

    PubMed

    Sobukawa, Hideto; Ibaraki, Masato; Kano, Rui; Ito, Takaaki; Suzuki, Kazuyuki; Kamata, Hiroshi; Hasegawa, Atsuhiko

    2013-01-01

    Prototheca zopfii is an achlorophyllic alga that is ubiquitous around cow sheds. The alga is associated with bovine mastitis, which causes a reduction in milk production and secretion of thin watery milk containing white flakes. Isolates of P. zopfii from bovine mastitis were almost all identified as P. zopfii genotype 2, suggesting that it is the main causative agent of bovine protothecal mastitis. The ability to differentiate between genotype 1 and genotype 2 is therefore very important for preventing bovine mastitis. In this study, high resolution melting real-time PCR (PCR-HRM) analysis of the protothecal 18S rDNA domain successfully differentiated between genotypes of P. zopfii in less than 3 hours, while conventional sequence analysis requires more than 48 hours to differentiate between genotypes. PCR-HRM analysis clustered P. zopfii genotype 1 isolates separately from P. zopfii genotype 2 isolates, indicating that this molecular typing method is an effective tool for rapidly diagnosing bovine protothecal mastitis. PMID:24292136

  6. Rapid Detection and Differentiation of Clonorchis sinensis and Opisthorchis viverrini Using Real-Time PCR and High Resolution Melting Analysis

    PubMed Central

    Cai, Xian-Quan; Yu, Hai-Qiong; Li, Rong; Yue, Qiao-Yun; Liu, Guo-Hua; Bai, Jian-Shan; Deng, Yan; Qiu, De-Yi; Zhu, Xing-Quan

    2014-01-01

    Clonorchis sinensis and Opisthorchis viverrini are both important fish-borne pathogens, causing serious public health problem in Asia. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis for the specific detection and rapid identification of C. sinensis and O. viverrini. Primers targeting COX1 gene were highly specific for these liver flukes, as evidenced by the negative amplification of closely related trematodes. Assays using genomic DNA extracted from the two flukes yielded specific amplification and their identity was confirmed by sequencing, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit below 1 pg of purified genomic DNA, 5 EPG, or 1 metacercaria of C. sinensis. Moreover, C. sinensis and O. viverrini were able to be differentiated by their HRM profiles. The method can reduce labor of microscopic examination and the contamination of agarose electrophoresis. Moreover, it can differentiate these two flukes which are difficult to be distinguished using other methods. The established method provides an alternative tool for rapid, simple, and duplex detection of C. sinensis and O. viverrini. PMID:25386621

  7. 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

  8. Development of a high-resolution melting marker for selecting Fusarium crown and root rot resistance in tomato.

    PubMed

    Kim, Bichseam; Kim, Nahui; Kim, Jun Young; Kim, Byung Sup; Jung, Hee-Jeong; Hwang, Indoek; Noua, Ill-Sup; Sim, Sung-Chur; Park, Younghoon

    2016-03-01

    Fusarium crown and root rot is a severe fungal disease of tomato caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL). In this study, the genomic location of the FORL-resistance locus was determined using a set of molecular markers on chromosome 9 and an F2 population derived from FORL-resistant inbred 'AV107-4' (Solanum lycopersicum) × susceptible 'L3708' (Solanum pimpinellifolium). Bioassay performed using Korean FORL strain KACC 40031 showed single dominant inheritance of FORL resistance in the F2 population. In all, 13 polymerase chain reaction-based markers encompassing approximately 3.6-72.0 Mb of chromosome 9 were developed based on the Tomato-EXPEN 2000 map and SolCAP Tomato single nucleotide polymorphism array analysis. These markers were genotyped on 345 F2 plants, and the FORL-resistance locus was found to be present on a pericentromeric region of suppressed chromosomal recombination in chromosome 9. The location of the FORL-resistance locus was further confirmed by testing these markers against diverse commercial tomato and stock cultivars resistant to FORL. A restriction fragment length polymorphism marker, PNU-D4, located at approximately 6.1 Mb of chromosome 9 showed the highest match with the resistance locus and was used for conducting high-resolution melting analysis for marker-assisted selection of FORL resistance.

  9. Diagnostic accuracy of high resolution melting analysis for detection of KRAS mutations: a systematic review and meta-analysis.

    PubMed

    Liu, Yue-Ping; Wu, Hai-Yan; Yang, Xiang; Xu, Han-Qing; Chen, Dong; Huang, Qing; Fu, Wei-Ling

    2014-01-01

    Increasing evidence points to a negative correlation between KRAS mutations and patients' responses to anti-EGFR monoclonal antibody treatment. Therefore, patients must undergo KRAS mutation detection to be eligible for treatment. High resolution melting analysis (HRM) is gaining increasing attention in KRAS mutation detection. However, its accuracy has not been systematically evaluated. We conducted a meta-analysis of published articles, involving 13 articles with 1,520 samples, to assess its diagnostic accuracy compared with DNA sequencing. The quality of included articles was assessed using the revised Quality Assessment for Studies of Diagnostic Accuracy (QUADAS-2) tools. Random effects models were applied to analyze the performance of pooled characteristics. The overall sensitivity and specificity of HRM were 0.99 (95% confidence interval [CI]: 0.98-1.00) and 0.96 (95%CI: 0.94-0.97), respectively. The area under the summary receiver operating characteristic curve was 0.996. High sensitivity and specificity, less labor, rapid turn-around and the closed-tube format of HRM make it an attractive choice for rapid detection of KRAS mutations in clinical practice. The burden of DNA sequencing can be reduced dramatically by the implementation of HRM, but positive results still need to be sequenced for diagnostic confirmation. PMID:25515911

  10. Forensic age prediction for dead or living samples by use of methylation-sensitive high resolution melting.

    PubMed

    Hamano, Yuya; Manabe, Sho; Morimoto, Chie; Fujimoto, Shuntaro; Ozeki, Munetaka; Tamaki, Keiji

    2016-07-01

    Age prediction with epigenetic information is now edging closer to practical use in forensic community. Many age-related CpG (AR-CpG) sites have proven useful in predicting age in pyrosequencing or DNA chip analyses. In this study, a wide range methylation status in the ELOVL2 and FHL2 promoter regions were detected with methylation-sensitive high resolution melting (MS-HRM) in a labor-, time-, and cost-effective manner. Non-linear-distributions of methylation status and chronological age were newly fitted to the logistic curve. Notably, these distributions were revealed to be similar in 22 living blood samples and 52 dead blood samples. Therefore, the difference of methylation status between living and dead samples suggested to be ignorable by MS-HRM. Additionally, the information from ELOVL2 and FHL2 were integrated into a logistic curve fitting model to develop a final predictive model through the multivariate linear regression of logit-linked methylation rates and chronological age with adjusted R(2)=0.83. Mean absolute deviation (MAD) was 7.44 for 74 training set and 7.71 for 30 additional independent test set, indicating that the final predicting model is accurate. This suggests that our MS-HRM-based method has great potential in predicting actual forensic age.

  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

    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.

  13. 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

  14. 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

  15. 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

  16. Forensic age prediction for dead or living samples by use of methylation-sensitive high resolution melting.

    PubMed

    Hamano, Yuya; Manabe, Sho; Morimoto, Chie; Fujimoto, Shuntaro; Ozeki, Munetaka; Tamaki, Keiji

    2016-07-01

    Age prediction with epigenetic information is now edging closer to practical use in forensic community. Many age-related CpG (AR-CpG) sites have proven useful in predicting age in pyrosequencing or DNA chip analyses. In this study, a wide range methylation status in the ELOVL2 and FHL2 promoter regions were detected with methylation-sensitive high resolution melting (MS-HRM) in a labor-, time-, and cost-effective manner. Non-linear-distributions of methylation status and chronological age were newly fitted to the logistic curve. Notably, these distributions were revealed to be similar in 22 living blood samples and 52 dead blood samples. Therefore, the difference of methylation status between living and dead samples suggested to be ignorable by MS-HRM. Additionally, the information from ELOVL2 and FHL2 were integrated into a logistic curve fitting model to develop a final predictive model through the multivariate linear regression of logit-linked methylation rates and chronological age with adjusted R(2)=0.83. Mean absolute deviation (MAD) was 7.44 for 74 training set and 7.71 for 30 additional independent test set, indicating that the final predicting model is accurate. This suggests that our MS-HRM-based method has great potential in predicting actual forensic age. PMID:27497326

  17. High-resolution imagery applications in the littorals

    NASA Astrophysics Data System (ADS)

    Abileah, Ronald

    2001-12-01

    We focus on three applications of high-resolution imagery in the littorals: mapping bathymetry, monitoring the health of coral reefs, and taking censuses of marine mammals. All three applications show the importance and potential benefits of higher-resolution imagery. Increased radiometric sensitivity and the simultaneous collection of panchromatic and multispectral imagery are also important. An Ikonos image of Maui is used to demonstrate these applications. We also briefly explain some important differences between multispectral remote sensing over water and land.

  18. A Melting-Layer Model for Passive/Active Microwave Remote Sensing Applications. Part I: Model Formulation and Comparison with Observations.

    NASA Astrophysics Data System (ADS)

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

    2001-07-01

    In this study, a 1D steady-state microphysical model that 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 grid points of `parent' 3D 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 (10.65-85.5 GHz) are enhanced greatly for relatively small (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 with 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 that do not contain mixed

  19. A novel method for simultaneous Enterococcus species identification/typing and van genotyping by high resolution melt analysis.

    PubMed

    Gurtler, Volker; Grando, Danilla; Mayall, Barrie C; Wang, Jenny; Ghaly-Derias, Shahbano

    2012-09-01

    In order to develop a typing and identification method for van gene containing Enterococcus faecium, two multiplex PCR reactions were developed for use in HRM-PCR (High Resolution Melt-PCR): (i) vanA, vanB, vanC, vanC23 to detect van genes from different Enterococcus species; (ii) ISR (intergenic spacer region between the 16S and 23S rRNA genes) to detect all Enterococcus species and obtain species and isolate specific HRM curves. To test and validate the method three groups of isolates were tested: (i) 1672 Enterococcus species isolates from January 2009 to December 2009; (ii) 71 isolates previously identified and typed by PFGE (pulsed-field gel electrophoresis) and MLST (multi-locus sequence typing); and (iii) 18 of the isolates from (i) for which ISR sequencing was done. As well as successfully identifying 2 common genotypes by HRM from the Austin Hospital clinical isolates, this study analysed the sequences of all the vanB genes deposited in GenBank and developed a numerical classification scheme for the standardised naming of these vanB genotypes. The identification of Enterococcus faecalis from E. faecium was reliable and stable using ISR PCR. The typing of E. faecium by ISR PCR: (i) detected two variable peaks corresponding to different copy numbers of insertion sequences I and II corresponding to peak I and II respectively; (ii) produced 7 melt profiles for E. faecium with variable copy numbers of sequences I and II; (iii) demonstrated stability and instability of peak heights with equal frequency within the patient sample (36.4±4.5 days and 38.6±5.8 days respectively for 192 patients); (iv) detected ISR-HRM types with as much discrimination as PFGE and more than MLST; and (v) detected ISR-HRM types that differentiated some isolates that were identical by PFGE and MLST. In conjunction with the rapid and accurate van genotyping method described here, this ISR-HRM typing and identification method can be used as a stable identification and typing method with

  20. Chalcophile element partitioning between sulfide phases and hydrous mantle melt: Applications to mantle melting and the formation of ore deposits

    NASA Astrophysics Data System (ADS)

    Li, Yuan

    2014-11-01

    Understanding the geochemical behavior of chalcophile elements in magmatic processes is hindered by the limited partition coefficients between sulfide phases and silicate melt, in particular at conditions relevant to partial melting of the hydrated, metasomatized upper mantle. In this study, the partitioning of elements Co, Ni, Cu, Zn, As, Mo, Ag, and Pb between sulfide liquid, monosulfide solid solution (MSS), and hydrous mantle melt has been investigated at 1200 °C/1.5 GPa and oxygen fugacity ranging from FMQ-2 to FMQ+1 in a piston-cylinder apparatus. The determined partition coefficients between sulfide liquid and hydrous mantle melt are: 750-1500 for Cu; 600-1200 for Ni; 35-42 for Co; 35-53 for Pb; and 1-2 for Zn, As, and Mo. The partition coefficients between MSS and hydrous mantle melt are: 380-500 for Cu; 520-750 for Ni; ∼50 for Co; <0.5 for Zn; 0.3-6 for Pb; 0.1-2 for As; 1-2 for Mo; and >34 for Ag. The variation of the data is primarily due to differences in oxygen fugacity. These partitioning data in conjunction with previous data are applied to partial melting of the upper mantle and the formation of magmatic-hydrothermal Cu-Au deposits and magmatic sulfide deposits. I show that the metasomatized arc mantle may no longer contain sulfide after >10-14% melt extraction but is still capable of producing the Cu concentrations in the primitive arc basalts, and that the comparable Cu concentrations in primitive arc basalts and in MORB do not necessarily imply similar oxidation states in their source regions. Previous models proposed for producing Cu- and/or Au-rich magmas have been reassessed, with the conclusions summarized as follows. (1) Partial melting of the oxidized (fO2 > FMQ), metasomatized arc mantle with sulfide exhaustion at degrees >10-14% may not generate Cu-rich, primitive arc basalts. (2) Partial melting of sulfide-bearing cumulates in the root of thickened lower continental crust or lithospheric mantle does not typically generate Cu- and

  1. High resolution melting technique for molecular epidemiological studies of cystic echinococcosis: differentiating G1, G3, and G6 genotypes of Echinococcus granulosus sensu lato.

    PubMed

    Rostami, Sima; Talebi, Saeed; Babaei, Zahra; Sharbatkhori, Mitra; Ziaali, Naser; Rostami, Habib; Harandi, Majid Fasihi

    2013-10-01

    Reliable and rapid genotyping of large number of Echinococcus granulosus sensu lato isolates is crucial for understanding the epidemiology and transmission of cystic echinococcosis. We have developed a method for distinguishing and discriminating common genotypes of E. granulosus s.l. (G1, G3, and G6) in Iran. This method is based on polymerase chain reaction coupled with high resolution melting curve (HRM), ramping from 70 to 86 °C with fluorescence data acquisition set at 0.1 °C increments and continuous fluorescence monitoring. Consistency of this technique was assessed by inter- and intra-assays. Assessment of intra- and inter-assay variability showed low and acceptable coefficient of variations ranging from 0.09 to 0.17 %. Two hundred and eighty E. granulosus s.l. isolates from sheep, cattle, and camel were used to evaluate the applicability and accuracy of the method. The isolates were categorized as G1 (93, 94, and 25%), G3 (7, 4, and 4%), and G6 (0, 2, and 71%) for sheep, cattle, and camel, respectively. HRM results were completely compatible with those obtained from sequencing and rostellar hook measurement. This method proved to be a valuable screening tool for large-scale molecular epidemiological studies. PMID:23832641

  2. Preliminary validation of a novel high-resolution melt-based typing method based on the multilocus sequence typing scheme of Streptococcus pyogenes.

    PubMed

    Richardson, L J; Tong, S Y C; Towers, R J; Huygens, F; McGregor, K; Fagan, P K; Currie, B J; Carapetis, J R; Giffard, P M

    2011-09-01

    The major limitation of current typing methods for Streptococcus pyogenes, such as emm sequence typing and T typing, is that these are based on regions subject to considerable selective pressure. Multilocus sequence typing (MLST) is a better indicator of the genetic backbone of a strain but is not widely used due to high costs. The objective of this study was to develop a robust and cost-effective alternative to S. pyogenes MLST. A 10-member single nucleotide polymorphism (SNP) set that provides a Simpson's Index of Diversity (D) of 0.99 with respect to the S. pyogenes MLST database was derived. A typing format involving high-resolution melting (HRM) analysis of small fragments nucleated by each of the resolution-optimized SNPs was developed. The fragments were 59-119 bp in size and, based on differences in G+C content, were predicted to generate three to six resolvable HRM curves. The combination of curves across each of the 10 fragments can be used to generate a melt type (MelT) for each sequence type (ST). The 525 STs currently in the S. pyogenes MLST database are predicted to resolve into 298 distinct MelTs and the method is calculated to provide a D of 0.996 against the MLST database. The MelTs are concordant with the S. pyogenes population structure. To validate the method we examined clinical isolates of S. pyogenes of 70 STs. Curves were generated as predicted by G+C content discriminating the 70 STs into 65 distinct MelTs.

  3. Self-consistent models for REE partitioning among high-Ca pyroxene, low-Ca pyroxene, and basaltic melts with applications to REE distribution during adiabatic mantle melting and pyroxenite-derived melt and mantle interaction

    NASA Astrophysics Data System (ADS)

    Yao, L.; Sun, C.; Liang, Y.

    2011-12-01

    compositions during near-fractional melting of lherzolite. Application of our two pyroxene-portioning models shows that DREE for cpx and opx exhibit small variations during anhydrous adiabatic melting, Hence constant DREE between pyroxenes and basaltic melt can be used to model adiabatic mantle melting. Reaction between pyroxenite-derived melts and peridotites often dissolves olivine and precipitates opx or pigeonite , which is important for melting of a heterogeneous mantle. Compositions of the precipitated or reacted low-Ca pyroxene vary considerably (0.2~9% CaO, 0.3~9% Al2O320~37% MgO), but DREE for these low-Ca pyroxenes have not been reported. Application of our low-Ca pyroxene model to the melt-rock reaction experiments show large variations in DREE (DLa = 0.0001~0.023, DNd = 0.015~0.1, DLu = 0.07~0.35). Hence composition-dependent DREE for low-Ca pyroxene needs to be considered for melting of a pyroxenite-veined mantle. [1] Wood & Blundy (1997) CMP, 129, 166-181. [2] Sun & Liang (2011) CMP, submitted. [3] Witt-Eickschen and O'Neil (2005) CG, 221,65-101. [4] Asimow et al. (2004) G3, doi: 10.1029/2003GC000568.

  4. 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

  5. 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

  6. Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity.

    PubMed

    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; Redd, Andrew D

    2012-09-01

    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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Structure and disorder in iron-bearing sodium silicate glasses and melts: High-resolution 29Si and 17O solid-state NMR study

    NASA Astrophysics Data System (ADS)

    Kim, H.; Lee, S.

    2012-12-01

    Understanding of the effect of iron content on the structure (Si coordination environment and the degree of polymerization) of iron-bearing silicate melts and glasses is essential for studying their macroscopic properties and diverse geological processes in Earth's interior. Although the recent advances in high-resolution solid-state NMR techniques provide detailed structural information of a diverse iron-free oxide glasses with varying composition (e.g., Lee, P. Natl. Acad. Sci. USA., 2011, 108, 6847; Lee and Sung, Chem. Geol., 2008, 256, 326; Park and Lee, Geochim. Cosmochim. Acta, 2012, 80, 125; Lee et al., Phys. Rev., 103, 095501, 2009), their application to iron-bearing silicate glasses has a limited usefulness in resolving atomic configurations due to the effect of paramagnetic cation (i.e., Fe) on the NMR spectra. Here, we report the first ^{29}Si and ^{17}O NMR spectra for sodium-iron silicate glasses with varying iron content (Na_{2}O-Fe_{2}O_{3}-SiO_{2} glasses, up to 34.60 wt% Fe_{2}O_{3}), revealing previously unknown details of iron-induced changes in structure and disorder. While signal intensity decreases and peak width increases exponentially with increasing iron content [=Fe_{2}O_{3}/(Na_{2}O+Fe_{2}O_{3})], ^{29}Si MAS NMR spectra for sodium-iron silicate glasses present the slight peak shift and an asymmetrical peak broadening toward higher Q^{n} species with increasing iron content. This result implies an increase in the degree of polymerization with increasing iron content. Additionally, ^{29}Si spin-relaxation time (T_{1}) for the glasses decreases with increasing of iron content by several orders of magnitude. ^{17}O 3QMAS NMR spectra for the glasses show well-resolved non-bridging oxygen (NBO, Na-O-Si) and bridging oxygen (BO, Si-O-Si) even at relatively high iron content, providing the first direct experimental estimation of the degree of polymerization. In sodium-iron silicate glasses, the fraction of NBO decreases with increasing iron

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. Comparative study of IDH1 mutations in gliomas by high resolution melting analysis, immunohistochemistry and direct DNA sequencing.

    PubMed

    Li, Juan; Zhang, Haiyan; Wang, Li; Yang, Chuanhong; Lai, Huangwen; Zhang, Wei; Chen, Xiaodong; Wang, Jie

    2015-09-01

    Patients with glioblastomas with a specific mutation in the isocitrate dehydrogenase 1 (IDH1) gene have a better prognosis than those with gliomas with wild‑type IDH1. IDH1 analysis has become part of the standard diagnostic procedure and a promising tool used for stratification in clinical trials. The present study aimed to compare high resolution melting (HRM) analysis, immunohistochemistry (IHC) and direct DNA sequencing for the detection of IDH mutations in gliomas. Fifty‑one formalin‑fixed paraffin‑embedded tumor samples were selected. For the HRM analysis and direct DNA sequencing, DNA was extracted from the tissues. For IHC, sections were stained with an anti‑IDH1‑R132H specific antibody. The HRM analysis method identified 33 cases of IDH1 gene mutations, and all mutations occurred at the R132H site. There were 33 cases of IDH1 gene mutations found by IHC, which was consistent with that identified using the HRM analysis method. However, only 30 IDH1 samples were confirmed by sequencing, in which mutations occurred at the IDH1 exon 4 R132H site. No mutation was detected in the other three of these 33 cases (two grade II oligodendroglioma and one grade II diffuse astrocytoma) by sequencing, while IHC was positive for IDH1‑R132H. The results showed that the mutation detection rate was not identified to be significantly different (P=0.250) when determined by the HRM analysis method or by direct DNA sequencing, as the concordant rate between the two methods was high (κ=0.866). The HRM analysis method in glioma IDH1 gene mutation detection has advantages of high sensitivity, good repeatability, simple operation and accurate results. It provides a novel method for detecting mutations of the IDH1 gene in paraffin embedded tissue samples of clinical glioma. Related to a small amount of sample, there was no evidence showing that HRM analysis method is superior to IHC. Direct DNA sequencing, HRM analysis and IHC results were consistent; however, HRM and

  17. 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

  18. A real-time ARMS PCR/high-resolution melt curve assay for the detection of the three primary mitochondrial mutations in Leber’s hereditary optic neuropathy

    PubMed Central

    Ryan, Fergus; O’Dwyer, Veronica; Neylan, Derek

    2016-01-01

    Purpose Approximately 95% of patients who are diagnosed with Leber’s hereditary optic neuropathy (LHON) have one of three mitochondrial point mutations responsible for the disease, G3460A, G11778A, and T14484C. The purpose of this study was to develop a novel multiplex real-time amplification-refractory mutation system (ARMS) PCR combined with high-resolution melt curves to identify the individual mutations involved. The study aimed to provide a more robust, cost- and time-effective mutation detection strategy than that offered with currently available methods. The assay reported in this study will allow diagnostic laboratories to avoid costly next-generation sequencing (NGS) assays for most patients with LHON and to focus resources on patients with unknown mutations that require further analysis. Methods The test uses a combination of multiplex allele-specific PCR (ARMS PCR) in combination with a high-resolution melt curve analysis to detect the presence of the mutations in G3460A, G11778A, and T14484C. PCR primer sets were designed to produce a control PCR product and PCR products only in the presence of the mutations in 3460A, 11778A, and 14484C in a multiplex single tube format. Products produce discrete well-separated melt curves to clearly detect the mutations. Results This novel real-time ARMS PCR/high-resolution melt curve assay accurately detected 95% of the mutations that cause LHON. The test has proved to be robust, cost- and time-effective with the real-time closed tube system taking approximately 1 h to complete. Conclusions A novel real-time ARMS PCR/high-resolution melt curve assay is described for the detection of the three primary mitochondrial mutations in LHON. This test provides a simple, robust, easy-to-read output that is cost- and time-effective, thus providing an alternative method to individual endpoint PCR-restriction fragment length polymorphism (RFLP), PCR followed by Sanger sequencing or pyrosequencing, and next-generation sequencing

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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

  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. Probing the structural disorder of basalts and slab-driven andesite melts: Insights from high-resolution solid-state NMR study

    NASA Astrophysics Data System (ADS)

    Park, S.; Lee, S.

    2012-12-01

    Whereas the structure of multi-component silicate melts has strong implication for the properties of natural silicate melts and relevant magmatic processes in Earth's mantle and crust, little is known about their atomic structures due to lack of suitable experimental probes of multi-component amorphous oxides. Although most of the progress in melt structure has been made for relatively simple binary and ternary silicate glasses, recent advances in high-resolution solid-state NMR (nuclear magnetic resonance) unveil previously unknown structural details of multi-component silicate melts (Lee, S. K. and Sung, S., Chem. Geol., 2008, 256, 326; Lee et al., P. Natl. Acad. Sci. USA., 2011, 108, 6847; Park and Lee, Geochim. Cosmochim. Acta, 2012, 80, 125). In this study we report experimental results on the effects of composition. atomic structure of CaO-MgO-Al_{2} O_{3} -SiO_{2} (CMAS) glasses in diopside (CaMgSi_{2}O_{6}) and Ca-tschermakite (CaAl_{2}SiO_{6}) join and glass in the diopside-anorthite eutectic composition (Di_{64}An_{36})—model systems for basaltic melts—using solid-state NMR. We also report the first high-resolution experimental results on the atomic structure of CaO-MgO-Na_{2}O-Al_{2}O_{3}-SiO_{2} (CMNAS) glasses in diopside and jadeite (NaAlSi_{2}O_{6}) join, and glass in the natural phonolite composition (CaO: MgO: Na_{2}O: K_{2}O: Al_{2}O_{3}: SiO_{2}= 1.4: 8.0: 9.0: 3.8: 13: 64 mol%), a model system for slab driven andesite melts. The Al-27 3QMAS (triple quantum magic angle spinning) NMR spectra of CMAS glasses in diopside-Ca-tschermakite join show predominant ^{[4]}Al and a non-negligible fraction of ^{[5]}Al. Approximately 3.3% of ^{[5]}Al is observed for Di_{64}An_{36} glass. The Al-27 3QMAS NMR spectra of CMNAS glasses in diopside and jadeite join show mostly ^{[4]}Al and a non-negligible fraction of ^{[5]}Al (X_{Diopside}=0.75, the mole fraction of diopside content). While the C_{q} (quadrupolar coupling constant) of ^{[4]}Al for glasses in

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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.

  15. Rapid and specific detection of Salmonella in water samples using real-time PCR and High Resolution Melt (HRM) curve analysis.

    PubMed

    van Blerk, G N; Leibach, L; Mabunda, A; Chapman, A; Louw, D

    2011-01-01

    A real-time PCR assay combined with a pre-enrichment step for the specific and rapid detection of Salmonella in water samples is described. Following amplification of the invA gene target, High Resolution Melt (HRM) curve analysis was used to discriminate between products formed and to positively identify invA amplification. The real-time PCR assay was evaluated for specificity and sensitivity. The assay displayed 100% specificity for Salmonella and combined with a 16-18 h non-selective pre-enrichment step, the assay proved to be highly sensitive with a detection limit of 1.0 CFU/ml for surface water samples. The detection assay also demonstrated a high intra-run and inter-run repeatability with very little variation in invA amplicon melting temperature. When applied to water samples received routinely by the laboratory, the assay showed the presence of Salmonella in particularly surface water and treated effluent samples. Using the HRM based assay, the time required for Salmonella detection was drastically shortened to less than 24 h compared to several days when using standard culturing methods. This assay provides a useful tool for routine water quality monitoring as well as for quick screening during disease outbreaks.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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

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

    PubMed

    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.

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

    PubMed

    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

  3. 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.

  4. 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.

  5. 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.

  6. Alternative high-resolution lithographic technologies for optical applications

    NASA Astrophysics Data System (ADS)

    Zeitner, Uwe D.; Weichelt, Tina; Bourgin, Yannick; Kinder, Robert

    2016-03-01

    Modern optical applications have special demands on the lithographic fabrication technologies. This relates to the lateral shape of the structures as well as to their three dimensional surface profile. On the other hand optical nano-structures are often periodic which allows for the use of dedicated lithographic exposure principles. The paper briefly reviews actual developments in the field of optical nano-structure generation. Special emphasis will be given to two technologies: electron-beam lithography based on a flexible cell-projection method and the actual developments in diffractive mask aligner lithography. Both offer a cost effective fabrication alternative for high resolution structures or three-dimensional optical surface profiles.

  7. 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.

  8. An innovative energy-saving in-flight melting technology and its application to glass production

    NASA Astrophysics Data System (ADS)

    Yao, Yaochun; Watanabe, Takayuki; Yano, Tetsuji; Iseda, Toru; Sakamoto, Osamu; Iwamoto, Masanori; Inoue, Satoru

    2008-04-01

    The conventional method used for glass melting is air-fuel firing, which is inefficient, energy-intensive and time-consuming. In this study, an innovative in-flight melting technology was developed and applied to glass production for the purposes of energy conservation and environmental protection. Three types of heating sources, radio-frequency (RF) plasma, a 12-phase alternating current (ac) arc and an oxygen burner, were used to investigate the in-flight melting behavior of granulated powders. Results show that the melted particles are spherical with a smooth surface and compact structure. The diameter of the melted particles is about 50% of that of the original powders. The decomposition and vitrification degrees of the prepared powders decrease in the order of powders prepared by RF plasma, the 12-phase ac arc and the oxygen burner. The largest heat transfer is from RF plasma to particles, which results in the highest particle temperature (1810 °C) and the greatest vitrification degree of the raw material. The high decomposition and vitrification degrees, which are achieved in milliseconds, shorten the melting and fining times of the glass considerably. Our results indicate that the proposed in-flight melting technology is a promising method for use in the glass industry.

  9. 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

  10. A novel closed-tube method based on high resolution melting (HRM) analysis for authenticity testing and quantitative detection in Greek PDO Feta cheese.

    PubMed

    Ganopoulos, Ioannis; Sakaridis, Ioannis; Argiriou, Anagnostis; Madesis, Panagiotis; Tsaftaris, Athanasios

    2013-11-15

    Animal species identification of milk and dairy products has received increasing attention concerning food composition, traceability, allergic pathologies and accurate consumer information. Here we sought to develop an easy to use and robust method for species identification in cheese with emphasis on an authenticity control of PDO Feta cheese products. We used specific mitochondrial DNA regions coupled with high resolution melting (HRM) a closed-tube method allowing us to detect bovine, ovine and caprine species and authenticate Greek PDO Feta cheese. The primers successfully amplified DNA isolated from milk and cheese and showed a high degree of specificity. HRM was proven capable of accurately identifying the presence of bovine milk (not allowed in Feta) down to 0.1% and also of quantifying the ratio of sheep to goat milk mixture in different Feta cheese commercial products. In conclusion, HRM analysis can be a faster, with higher resolution and a more cost effective alternative method to authenticate milk and dairy products including PDO Feta cheese and to quantitatively detect its sheep milk adulterations.

  11. 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.

  12. 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

  13. Trace metal imaging with high spatial resolution: applications in biomedicine.

    PubMed

    Qin, Zhenyu; Caruso, Joseph A; Lai, Barry; Matusch, Andreas; Becker, J Sabine

    2011-01-01

    New generations of analytical techniques for imaging of metals are pushing hitherto boundaries of spatial resolution and quantitative analysis in biology. Because of this, the application of these imaging techniques described herein to the study of the organization and dynamics of metal cations and metal-containing biomolecules in biological cell and tissue is becoming an important issue in biomedical research. In the current review, three common metal imaging techniques in biomedical research are introduced, including synchrotron X-ray fluorescence (SXRF) microscopy, secondary ion mass spectrometry (SIMS), and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). These are exemplified by a demonstration of the dopamine-Fe complexes, by assessment of boron distribution in a boron neutron capture therapy cell model, by mapping Cu and Zn in human brain cancer and a rat brain tumor model, and by the analysis of metal topography within neuromelanin. These studies have provided solid evidence that demonstrates that the sensitivity, spatial resolution, specificity, and quantification ability of metal imaging techniques is suitable and highly desirable for biomedical research. Moreover, these novel studies on the nanometre scale (e.g., of individual single cells or cell organelles) will lead to a better understanding of metal processes in cells and tissues.

  14. A Non-Arrhenian Viscosity Model for Natural Silicate Melts with Applications to Volcanology

    NASA Astrophysics Data System (ADS)

    Russell, J. K.; Giordano, D.; Dingwell, D. B.

    2005-12-01

    Silicate melt viscosity is the most important physical property in volcanic systems. It governs styles and rates of flow, velocity distributions in flowing magma, rates of vesiculation, and, ultimately, sets limits on coherent(vs. fragmented or disrupted) flow. The prediction of melt viscosity over the range of conditions found on terrestrial planets remains a challenge. However, the extraordinary increase in number and quality of published measurements of melt viscosity suggests the possibility of new models. Here we review the attributes of previous models for silicate melt viscosity and, then, present a new predictive model natural silicate melts. The importance of silicate melt viscosity was recognized early [1] and culminated in 2 models for predicting silicate melt viscosity [2,3]. These models used an Arrhenian T-dependence; they were limited by a limited experimental database dominated by high-T measurements. Subsequent models have aimed to: i) extend the compositional range of Arrhenian T-dependent models [4,5]; ii) to develop non-Arrhenian models for limited ranges of composition [6,7,8], iii) to develop new strategies for modelling the composition and T-dependence of viscosity [9,10,11], and, finally, to create chemical models for the non-Arrhenian T-dependence of natural melts [12]. We present a multicomponent model for the compositional and T dependence of silicate melt viscosity based on data spanning a wide range of anhydrous melt compositions. The experimental data include micropenetration and concentric cylinder viscometry measurements covering a viscosity range of 10-1 to 1012 Pa s and a T-range from 700 to 1650°C. These published data provide a high- quality database comprising ~ 800 experimental data on 44 well-characterized melt compositions. Our model uses the Adam-Gibbs equation to capture T-dependence: log η = A + B/[T · log (T/C)] where A, B, and C are adjustable parameters that vary for different melt compositions. We assume that all

  15. A high resolution capacitive imaging sensor for manufacturing applications

    SciTech Connect

    Novak, J.L.; Wiczer, J.J.

    1990-09-06

    A high resolution capacitive image sensing technique for measuring edge and surface profiles during manufacturing processes has been invented. A prototype device utilizing this technique consists of two 0.020 in. (500 {mu}m) diameter electrodes fabricated on a printed circuit board with a 0.010 in. (250 {mu}m) gap between them. As the device is mechanically scanned over the workpiece, the spatial variations in the edge or surface to be measured interfere with an electric field imposed between the electrodes, altering the mutual capacitance. The sensor functions as a near field proximity sensor producing range images of surface imperfections. This sensor has been used in applications requiring a preview image of burrs on the edge of a machined part and other processes requiring an inspection image after automated deburring operations. 10 refs., 8 figs.

  16. 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.

  17. Shear Melting and High Temperature Embrittlement: Theory and Application to Machining Titanium

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  18. 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

  19. 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

  20. 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

  1. 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

  2. Assessment of the MAR regional climate model over the Antarctic Peninsula (1999 - 2009) through spaceborne enhanced spatial resolution melting maps and near-surface observations

    NASA Astrophysics Data System (ADS)

    Datta, R.; Tedesco, M.; Alexander, P. M.; Fettweis, X.; Steiner, N.; Gallee, H.

    2012-12-01

    We report results assessing the outputs of the regional climate model Modèle Atmosphérique Régionale (MAR) over the Antarctic peninsula for the period 1999 - 2009. Specifically, we compare maps of melt extent and duration generated by MAR with those obtained from the enhanced spatial resolution product (~ 5 km) distributed by the NASA Scatterometer Climate Record Pathfinder (SCP), at Brigham Young University (Utah, USA). Snowmelt is estimated from remote sensing observations using both a canonical threshold-based approach and a novel method based on wavelet methodology. MAR outputs are also evaluated against available surface observations (e.g., near-surface temperature, wind speed and direction, etc.). The additional effects of blowing snow upon the surface and energy balance can be uniquely explored by simulations in Antarctica (as compared to Greenland, for example). Because of this, as of the time of abstract submission, MAR is set up to run for a scenario with blowing snow as well as a scenario without blowing snow. Our final assessment will present the results of both, providing insight into the sensitivity of MAR outputs to the blowing snow model.

  3. Rapid Detection and Simultaneous Genotyping of Cronobacter spp. (formerly Enterobacter sakazakii) in Powdered Infant Formula Using Real-time PCR and High Resolution Melting (HRM) Analysis

    PubMed Central

    Cai, Xian-Quan; Yu, Hai-Qiong; Ruan, Zhou-Xi; Yang, Lei-Liang; Bai, Jian-Shan; Qiu, De-Yi; Jian, Zhi-Hua; Xiao, Yi-Qian; Yang, Jie-Yang; Le, Thanh Hoa; Zhu, Xing-Quan

    2013-01-01

    Cronobacter spp. is an emerging pathogen that causes meningitis, sepsis, bacteremia, and necrotizing enterocolitis in neonates and children. The present study developed an assay integrating real-time PCR and high resolution melting (HRM) analysis targeting the OmpA gene for the specific detection and rapid identification of Cronobacter spp. (formerly Enterobacter sakazakii) in powdered infant formula. Eleven Cronobacter field isolates and 25 reference strains were examined using one pair of primers, having the accuracy of 100% in reference to conventional methods. The assay was proved to be highly sensitive with a detection limit of 102 CFU/ml without pre-enrichment, and highly concordant (100%) when compared with ISO-IDF 22964 in 89 actual samples. The method performed for Cronobacter spp. detection was less than 24 h, drastically shortened, compared to several days using standard culturing method, it is probe-free and reduces a risk of PCR carryover. Moreover, all Cronobacter strains examined in this study were genotyped into two species according to their HRM profiles. The established method should provide a molecular tool for direct detection and simultaneous genotyping of Cronobacter spp. in powdered infant formula. PMID:23825624

  4. Rapid detection and non-subjective characterisation of infectious bronchitis virus isolates using high-resolution melt curve analysis and a mathematical model.

    PubMed

    Hewson, Kylie; Noormohammadi, Amir H; Devlin, Joanne M; Mardani, Karim; Ignjatovic, Jagoda

    2009-01-01

    Infectious bronchitis virus (IBV) is a coronavirus that causes upper respiratory, renal and/or reproductive diseases with high morbidity in poultry. Classification of IBV is important for implementation of vaccination strategies to control the disease in commercial poultry. Currently, the lengthy process of sequence analysis of the IBV S1 gene is considered the gold standard for IBV strain identification, with a high nucleotide identity (e.g. > or =95%) indicating related strains. However, this gene has a high propensity to mutate and/or undergo recombination, and alone it may not be reliable for strain identification. A real-time polymerase chain reaction (RT-PCR) combined with high-resolution melt (HRM) curve analysis was developed based on the 3'UTR of IBV for rapid detection and classification of IBV from commercial poultry. HRM curves generated from 230 to 435-bp PCR products of several IBV strains were subjected to further analysis using a mathematical model also developed during this study. It was shown that a combination of HRM curve analysis and the mathematical model could reliably group 189 out of 190 comparisons of pairs of IBV strains in accordance with their 3'UTR and S1 gene identities. The newly developed RT-PCR/HRM curve analysis model could detect and rapidly identify novel and vaccine-related IBV strains, as confirmed by S1 gene and 3'UTR nucleotide sequences. This model is a rapid, reliable, accurate and non-subjective system for detection of IBVs in poultry flocks.

  5. 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

  6. Molecular identification of Mycobacterium avium subsp. silvaticum by duplex high-resolution melt analysis and subspecies-specific real-time PCR.

    PubMed

    Rónai, Zsuzsanna; Csivincsik, Ágnes; Dán, Ádám

    2015-05-01

    Accurate identification of mycobacterial species and subspecies is essential to evaluate their significance and to perform epidemiological studies. The subspecies of Mycobacterium avium have different attributes but coincide in their zoonotic potential. Our knowledge about M. avium subsp. silvaticum is limited, since its identification is uncertain. Mycobacterium avium subsp. avium and M. avium subsp. silvaticum can be discriminated from each other based only on phenotypic characteristics, as they have almost identical genome sequences. Here we describe the development of a diagnostic method which enables the molecular identification of M. avium subsp. silvaticum and discrimination from M. avium subsp. avium based on genomic differences in a duplex high-resolution melt and M. avium subsp. silvaticum-specific mismatch real-time PCR. The developed assay was tested on reference strains and 199 field isolates, which were analyzed by phenotypic methods previously. This assay not only identified all 63 M. avium subsp. silvaticum and 138 M. avium subsp. avium strains correctly but also enabled the detection of mixed M. avium subsp. avium-M. avium subsp. silvaticum cultures. This is the first time that such a large panel of strains has been analyzed, and we also report the first isolation of M. avium subsp. silvaticum from red fox, red deer, wild boar, cattle, and badger. This assay is reliable, rapid, simple, inexpensive, and robust. It eliminates the long-existing problem of ambiguous phenotypic identification and opens up the possibility for detailed and comprehensive strain studies.

  7. 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

    2014-10-31

    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.

  8. A refined, rapid and reproducible high resolution melt (HRM)-based method suitable for quantification of global LINE-1 repetitive element methylation

    PubMed Central

    2011-01-01

    Background The methylation of DNA is recognized as a key mechanism in the regulation of genomic stability and evidence for its role in the development of cancer is accumulating. LINE-1 methylation status represents a surrogate measure of genome-wide methylation. Findings Using high resolution melt (HRM) curve analysis technology, we have established an in-tube assay that is linear (r > 0.9986) with a high amplification efficiency (90-105%), capable of discriminating between partcipant samples with small differences in methylation, and suitable for quantifying a wide range of LINE-1 methylation levels (0-100%)--including the biologically relevant range of 50-90% expected in human DNA. We have optimized this procedure to perform using 2 μg of starting DNA and 2 ng of bisulfite-converted DNA for each PCR reaction. Intra- and inter-assay coefficients of variation were 1.44% and 0.49%, respectively, supporting the high reproducibility and precision of this approach. Conclusions In summary, this is a completely linear, quantitative HRM PCR method developed for the measurement of LINE-1 methylation. This cost-efficient, refined and reproducible assay can be performed using minimal amounts of starting DNA. These features make our assay suitable for high throughput analysis of multiple samples from large population-based studies. PMID:22204640

  9. Plasmid-based controls to detect rpoB mutations in Mycobacterium tuberculosis by quantitative polymerase chain reaction-high-resolution melting

    PubMed Central

    da Silva, Joas Lucas; Leite, Gabriela Guimaraes Sousa; Bastos, Gisele Medeiros; Lucas, Beatriz Cacciacarro; Shinohara, Daniel Keniti; Takinami, Joice Sayuri; Miyata, Marcelo; Fajardo, Cristina Moreno; Luchessi, André Ducati; Leite, Clarice Queico Fujimura; Cardoso, Rosilene Fressatti; Hirata, Rosario Dominguez Crespo; Hirata, Mario Hiroyuki

    2013-01-01

    Quantitative polymerase chain reaction-high-resolution melting (qPCR-HRM) analysis was used to screen for mutations related to drug resistance in Mycobacterium tuberculosis. We detected the C526T and C531T mutations in the rifampicin resistance-determining region (RRDR) of the rpoB gene with qPCR-HRM using plasmid-based controls. A segment of the RRDR region from M. tuberculosis H37Rv and from strains carrying C531T or C526T mutations in the rpoB were cloned into pGEM-T vector and these vectors were used as controls in the qPCR-HRM analysis of 54 M. tuberculosis strains. The results were confirmed by DNA sequencing and showed that recombinant plasmids can replace genomic DNA as controls in the qPCR-HRM assay. Plasmids can be handled outside of biosafety level 3 facilities, reducing the risk of contamination and the cost of the assay. Plasmids have a high stability, are normally maintained in Escherichia coli and can be extracted in large amounts. PMID:23440123

  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. 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

  12. Genotyping of Salmonella enterica serovar Typhimurium isolates by multilocus variable number of tandem repeat high-resolution melting analysis (MLV-HRMA).

    PubMed

    Keeratipibul, Suwimon; Silamat, Panusanun; Phraephaisarn, Chirapiphat; Srisitthinam, Daranee; Takahashi, Hajime; Chaturongkasumrit, Yuphakhun; Vesaratchavest, Mongkol

    2015-01-01

    Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) is one of the most important virulent foodborne pathogens in industrialized countries. The ability to type bacterial strains is essential for surveillance, investigation of outbreaks, and epidemiological studies. Multilocus variable number tandem repeat combined with high-resolution melting analysis (MLV-HRMA) is a fast, cost-efficient, and easy sample genotyping method. In this study, MLV-HRMA and multilocus variable number tandem repeat analysis (MLVA) were used to differentiate between the allelic variants in 5 tandem repeat (TR) loci in 117 Salmonella Typhimurium isolates derived from various farms, slaughterhouses, market, and humans in Thailand. Both MLV-HRMA and MLVA analyses resulted in the identification of a total of 43 different genotypes, but slight differences were observed in cluster analysis results between the 2 methods. The unweighted pair-group method with arithmetic mean-based cluster analysis showed the same core clades; some small differences in the placement of sister-clades and subgrouping were observed due to the inability to reliably type the polymorphic STTR3 locus in the MLV-HRMA. The results of this study show that the MLV-HRMA, following the selection of suitable TR loci, is a relatively reliable and rapid screening method capable of differentiating between Salmonella Typhimurium isolates on the basis of allelic diversity at TR loci. As such, MLV-HRMA can be potentially used to investigate and track sources of contamination in order to effectively control Salmonella contamination in the food supply chain. PMID:25457374

  13. 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.

  14. 3D Compressible Melt Transport with Mesh Adaptivity

    NASA Astrophysics Data System (ADS)

    Dannberg, J.; Heister, T.

    2015-12-01

    Melt generation and migration have been the subject of numerous investigations. However, their typical time and length scales are vastly different from mantle convection, and the material properties are highly spatially variable and make the problem strongly non-linear. These challenges make it difficult to study these processes in a unified framework and in three dimensions. We present our extension of the mantle convection code ASPECT that allows for solving additional equations describing the behavior of melt percolating through and interacting with a viscously deforming host rock. One particular advantage is ASPECT's adaptive mesh refinement, as the resolution can be increased in areas where melt is present and viscosity gradients are steep, whereas a lower resolution is sufficient in regions without melt. Our approach includes both melt migration and melt generation, allowing for different melting parametrizations. In contrast to previous formulations, we consider the individual compressibilities of the solid and fluid phases in addition to compaction flow. This ensures self-consistency when linking melt generation to processes in the deeper mantle, where the compressibility of the solid phase becomes more important. We evaluate the functionality and potential of this method using a series of benchmarks and applications, including solitary waves, magmatic shear bands and melt generation and transport in a rising mantle plume. We compare results of the compressible and incompressible formulation and find melt volume differences of up to 15%. Moreover, we demonstrate that adaptive mesh refinement has the potential to reduce the runtime of a computation by more than one order of magnitude. Our model of magma dynamics provides a framework for investigating links between the deep mantle and melt generation and migration. This approach could prove particularly useful applied to modeling the generation of komatiites or other melts originating in greater depths.

  15. 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…

  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. 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.

  19. 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

  20. 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.

  1. 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

  2. Differentiation between pathogenic serotype 1 isolates of Marek's disease virus and the Rispens CVI988 vaccine in Australia using real-time PCR and high resolution melt curve analysis.

    PubMed

    Renz, K G; Cheetham, B F; Walkden-Brown, S W

    2013-01-01

    Two real-time PCR assays were developed which enable quantitation and differentiation between pathogenic Australian isolates of Marek's disease virus (MDV) serotype 1 and the serotype 1 vaccine strain Rispens CVI988. The assays are based on a DNA sequence variation in the meq gene between pathogenic and vaccinal MDV1 which has been confirmed by sequencing of 20 Australian field strains of MDV. Complete specificity has been demonstrated in samples containing pathogenic MDV (n=20), Rispens (3 commercial vaccine strains), or both. The limit of detection of both the Rispens-specific and the pathogenic MDV1-specific assays was 10 viral copies/reaction. The tests successfully differentiated and quantified MDV in mixtures of pathogenic and vaccinal Rispens virus. A high resolution melt curve analysis targeting the same SNP used for the real-time PCR assays was also developed which successfully detected sequence variation between Md5, six Australian MDV1 isolates and the three Rispens vaccines. However it was ineffective at differentiating mixtures of pathogenic and vaccinal MDV1. The real-time PCR assays have both diagnostic and epidemiological applications as they enable differentiation and quantitation of Rispens CVI988 and pathogenic MDV1 in co-infected chickens in Australia.

  3. A screening method for the detection of the 35S promoter and the nopaline synthase terminator in genetically modified organisms in a real-time multiplex polymerase chain reaction using high-resolution melting-curve analysis.

    PubMed

    Akiyama, Hiroshi; Nakamura, Fumi; Yamada, Chihiro; Nakamura, Kosuke; Nakajima, Osamu; Kawakami, Hiroshi; Harikai, Naoki; Furui, Satoshi; Kitta, Kazumi; Teshima, Reiko

    2009-11-01

    To screen for unauthorized genetically modified organisms (GMO) in the various crops, we developed a multiplex real-time polymerase chain reaction high-resolution melting-curve analysis method for the simultaneous qualitative detection of 35S promoter sequence of cauliflower mosaic virus (35SP) and the nopaline synthase terminator (NOST) in several crops. We selected suitable primer sets for the simultaneous detection of 35SP and NOST and designed the primer set for the detection of spiked ColE1 plasmid to evaluate the validity of the polymerase chain reaction (PCR) analyses. In addition, we optimized the multiplex PCR conditions using the designed primer sets and EvaGreen as an intercalating dye. The contamination of unauthorized GMO with single copy similar to NK603 maize can be detected as low as 0.1% in a maize sample. Furthermore, we showed that the present method would be applicable in identifying GMO in various crops and foods like authorized GM soybean, authorized GM potato, the biscuit which is contaminated with GM soybeans and the rice which is contaminated with unauthorized GM rice. We consider this method to be a simple and reliable assay for screening for unauthorized GMO in crops and the processing food products.

  4. Novel application of hot-melt extrusion for the preparation of monolithic matrices containing enteric-coated particles.

    PubMed

    Schilling, Sandra U; McGinity, James W

    2010-11-15

    The objective was to investigate a novel application of hot-melt extrusion for the preparation of multiparticulate matrices comprising delayed-release particles. Multiparticulates of different mechanical strengths (theophylline granules, wet-mass extruded/spheronized pellets and drug-layered microcrystalline cellulose spheres) were coated with Eudragit(®) L30D-55 and characterized regarding potency, moisture content, dissolution properties and tensile strength. The coated particles were incorporated into a water-soluble matrix using hot-melt extrusion. Six hydrophilic polymers including polyethylene glycols, poloxamers and polyethylene oxides were studied as the carrier material for the extrusion. Dissolution testing showed that the maintenance of the delayed-release properties of the incorporated particles was independent of the particle tensile strength, but influenced by the nature of the carrier polymer. High miscibility between the carrier and the coating polymer correlated with increased film permeability and higher drug release in acidic media. Of the materials tested, poloxamer 407 exhibited lower miscibility with the Eudragit(®) L polymer and matrices containing up to 40% enteric pellets were compliant with the USP dissolution requirements for delayed-release dosage forms. The potential advantages of hot-melt extrusion over direct compression for the processing of soft drug granules coated with Eudragit(®) L polymer were demonstrated.

  5. 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

    2016-01-01

    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.

  6. Bartonellae in domestic and stray cats from Israel: comparison of bacterial cultures and high-resolution melt real-time PCR as diagnostic methods.

    PubMed

    Gutiérrez, Ricardo; Morick, Danny; Gross, Ifat; Winkler, Ronen; Abdeen, Ziad; Harrus, Shimon

    2013-12-01

    To determine the occurrence of feline bartonellosis in Israel, blood samples were collected from 179 stray and 155 domestic cats from 18 cities or villages in central and northcentral Israel. Samples were screened for Bartonella infection by culture isolation and molecular detection using high-resolution melt (HRM) real-time PCR assay targeting the 16S-23S rRNA internal transcribed spacer (ITS). All positive samples were confirmed by two additional HRM real-time PCR assays targeting two fragments of the β-subunit of RNA polymerase (rpoB) and the 16S rRNA genes. The prevalence of Bartonella spp. infection in the general tested population was 25.1% (84/334). A higher prevalence was detected in the stray (30.7%; 55/179) than the domestic cats (18.7%; 29/155). Bartonella henselae, Bartonella clarridgeiae, and Bartonella koehlerae were highly prevalent in both cat populations, however their distribution among the two populations varied significantly (p=0.016). B. clarridgeiae and B. koehlerae were found to be more prevalent in stray than domestic cats, whereas B. henselae was evenly distributed. Co-infection with two or more different Bartonella spp. was determined in 2.1% (7) of the cats. The ITS HRM real-time PCR assay used in this study was shown to have a greater screening power than bacterial isolation, detecting 94.0% (79/84) compared to 35.7% (30/84), respectively, of all positive samples. The high prevalence of these zoonotic Bartonella species, coupled with the overpopulation of stray cats, and increased numbers of domestic cats in the major urban centers in Israel represent a significant threat for the public health in this country.

  7. 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.

  8. 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.

  9. 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

  10. An empirical method for calculating melt compositions produced beneath mid-ocean ridges: Application for axis and off-axis (seamounts) melting

    NASA Astrophysics Data System (ADS)

    Niu, Yaoling; Batiza, Rodey

    1991-12-01

    We present a new method for calculating the major element compositions of primary melts parental to mid-ocean ridge basalt (MORB). This model is based on the experimental data of Jaques and Green (1980), Falloon et al. (1988), and Falloon and Green (1987, 1988) which are ideal for this purpose. Our method is empirical and employs solid-liquid partition coefficients (Di) from the experiments. We empirically determine Di = ƒ(P,F) and use this to calculate melt compositions produced by decompression-induced melting along an adiabat (column melting). Results indicate that most MORBs can be generated by 10-20% partial melting at initial pressures (P0) of 12-21 kbar. Our primary MORB melts have MgO = 10-12 wt %. We fractionate these at low pressure to an MgO content of 8.0 wt % in order to interpret natural MORB liquids. This model allows us to calculate Po, Pƒ, To, Tƒ, and F for natural MORB melts. We apply the model to interpret MORB compositions and mantle upwelling patterns beneath a fast ridge (East Pacific Rise (EPR)8°N to 14°N), a slow ridge (mid-Atlantic Ridge (MAR) at 26°S), and seamounts near the EPR (Lament seamount chain). We find mantle temperature differences of up to 50°-60°C over distances of 30-50 km both across axis and along axis at the EPR. We propose that these are due to upward mantle flow in a weakly conductive (versus adiabatic) temperature gradient. We suggest that the EPR is fed by a wide (-100 km) zone of upwelling due to plate separation but has a central core of faster buoyant flow. An along-axis thermal dome between the Siqueiros transform and the 11°45' Overlapping Spreading center (OSC) may represent such an upwelling; however, in general there is a poor correlation between mantle temperature, topography, and the segmentation pattern at the EPR. For the Lament seamounts we find regular across-axis changes in Po and F suggesting that the melt zone pinches out off axis. This observation supports the idea that the EPR is fed by a

  11. An empirical method for calculating melt compositions produced beneath mid-ocean ridges: for axis and off-axis (seamounts) melting application

    NASA Astrophysics Data System (ADS)

    Batiza, Rodey

    1991-12-01

    We present a new method for calculating the major element compositions of primary melts parental to mid-ocean ridge basalt (MORB). This model is based on the experimental data of Jaques and Green (1980), Falloon et al. (1988), and Falloon and Green (1987, 1988) which are ideal for this purpose. Our method is empirical and employs solid-liquid partition coefficients (Di) from the experiments. We empirically determine Di=f(P,F) and use this to calculate melt compositions produced by decompression-induced melting along an adiabat (column melting). Results indicate that most MORBs can be generated by 10-20% partial melting at initial pressures (P0) of 12-21 kbar. Our primary MORB melts have MgO=10-12 wt %. We fractionate these at low pressure to an MgO content of 8.0 wt% in order to interpret natural MORB liquids. This model allows us to calculate Po, Pf, To, Tf, and F for natural MORB melts. We apply the model to interpret MORB compositions and mantle upwelling patterns beneath a fast ridge (East Pacific Rise (EPR) 8°N to 14°N), a slow ridge (mid-Atlantic Ridge (MAR) at 26°S), and seamounts near the EPR (Lamont seamount chain). We find mantle temperature differences of up to 50°-60°C over distances of 30-50 km both across axis and along axis at the EPR. We propose that these are due to upward mantle flow in a weakly conductive (versus adiabatic) temperature gradient. We suggest that the EPR is fed by a wide (~100 km) zone of upwelling due to plate separation but has a central core of faster buoyant flow. An along-axis thermal dome between the Siqueiros transform and the 11°45' Overlapping Spreading Center (OSC) may represent such an upwelling; however, in general there is a poor correlation between mantle temperature, topography, and the segmentation pattern at the EPR. For the Lamont seamounts we find regular across-axis changes in Po and F suggesting that the melt zone pinches out off axis. This observation supports the idea that the EPR is fed by a broad

  12. A modified iterative sandwich method for determination of near-solidus partial melt compositions. II. Application to determination of near-solidus melt compositions of carbonated peridotite

    NASA Astrophysics Data System (ADS)

    Dasgupta, Rajdeep; Hirschmann, Marc M.

    2007-12-01

    We performed modified iterative sandwich experiments (MISE) to determine the composition of carbonatitic melt generated near the solidus of natural, fertile peridotite + CO2 at 1,200 1,245°C and 6.6 GPa. Six iterations were performed with natural peridotite (MixKLB-1: Mg# = 89.7) and ˜10 wt% added carbonate to achieve the equilibrium carbonatite composition. Compositions of melts and coexisting minerals converged to a constant composition after the fourth iteration, with the silicate mineral compositions matching those expected at the solidus of carbonated peridotite at 6.6 GPa and 1,230°C, as determined from a sub-solidus experiment with MixKLB-1 peridotite. Partial melts expected from a carbonated lherzolite at a melt fraction of 0.01 0.05% at 6.6 GPa have the composition of sodic iron-bearing dolomitic carbonatite, with molar Ca/(Ca + Mg) of 0.413 ± 0.001, Ca# [100 × molar Ca/(Ca + Mg + Fe*)] of 37.1 ± 0.1, and Mg# of 83.7 ± 0.6. SiO2, TiO2 and Al2O3 concentrations are 4.1 ± 0.1, 1.0 ± 0.1, and 0.30 ± 0.02 wt%, whereas the Na2O concentration is 4.0 ± 0.2 wt%. Comparison of our results with other iterative sandwich experiments at lower pressures indicate that near-solidus carbonatite derived from mantle lherzolite become less calcic with increasing pressure. Thus carbonatitic melt percolating through the deep mantle must dissolve cpx from surrounding peridotite and precipitate opx. Significant FeO* and Na2O concentrations in near solidus carbonatitic partial melt likely account for the ˜150°C lower solidus temperature of natural carbonated peridotite compared to the solidus of synthetic peridotite in the system CMAS + CO2. The experiments demonstrate that the MISE method can determine the composition of partial melts at very low melt fraction after a small number of iterations.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. On the application and extension of Harten's high resolution scheme

    NASA Technical Reports Server (NTRS)

    Yee, H. C.; Warming, R. F.; Harten, A.

    1982-01-01

    Extensions of a second order high resolution explicit method for the numerical computation of weak solutions of one dimensonal hyperbolic conservation laws are discussed. The main objectives were (1) to examine the shock resoluton of Harten's method for a two dimensional shock reflection problem, (2) to study the use of a high resolution scheme as a post-processor to an approximate steady state solution, and (3) to construct an implicit in the delta-form using Harten's scheme for the explicit operator and a simplified iteration matrix for the implicit operator.

  18. Melt-processable hydrophobic acrylonitrile-based copolymer systems with adjustable elastic properties designed for biomedical applications.

    PubMed

    Cui, J; Trescher, K; Kratz, K; Jung, F; Hiebl, B; Lendlein, A

    2010-01-01

    Acrylonitrile-based polymer systems (PAN) are comprehensively explored as versatile biomaterials having various potential biomedical applications, such as membranes for extra corporal devices or matrixes for guided skin reconstruction. The surface properties (e.g. hydrophilicity or charges) of such materials can be tailored over a wide range by variation of molecular parameters such as different co-monomers or their sequence structure. Some of these materials show interesting biofunctionalities such as capability for selective cell cultivation. So far, the majority of AN-based copolymers, which were investigated in physiological environments, were processed from the solution (e.g. membranes), as these materials are thermo-sensitive and might degrade when heated. In this work we aimed at the synthesis of hydrophobic, melt-processable AN-based copolymers with adjustable elastic properties for preparation of model scaffolds with controlled pore geometry and size. For this purpose a series of copolymers from acrylonitrile and n-butyl acrylate (nBA) was synthesized via free radical copolymerisation technique. The content of nBA in the copolymer varied from 45 wt% to 70 wt%, which was confirmed by 1H-NMR spectroscopy. The glass transition temperatures (Tg) of the P(AN-co-nBA) copolymers determined by differential scanning calorimetry (DSC) decreased from 58 degrees C to 20 degrees C with increasing nBA-content, which was in excellent agreement with the prediction of the Gordon-Taylor equation based on the Tgs of the homopolymers. The Young's modulus obtained in tensile tests was found to decrease significantly with rising nBA-content from 1062 MPa to 1.2 MPa. All copolymers could be successfully processed from the melt with processing temperatures ranging from 50 degrees C to 170 degrees C, whereby thermally induced decomposition was only observed at temperatures higher than 320 degrees C in thermal gravimetric analysis (TGA). Finally, the melt processed P

  19. 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…

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Ultrahigh resolution spectral/Fourier domain OCT systems for retinal imaging applications

    NASA Astrophysics Data System (ADS)

    Srinivasan, V. J.; Wojtkowski, M.; Witkin, A.; Monson, B.; Duker, J. S.; Schuman, J. S.; Shidlovski, V.; Yakubovich, S.; Fujimoto, J. G.

    2006-02-01

    In this manuscript we describe the design and optimization of ultrahigh resolution spectral/Fourier domain OCT systems for three applications in retinal imaging: imaging of the normal retina, three-dimensional (3D) imaging of retinal pathologies, and 3D imaging of the rodent retina. Seven spectrometer configurations were tested for resolution and sensitivity drop with depth, and CCD pixel crosstalk was characterized. The human retina was imaged in vivo with five different axial resolutions between 2 and 10 microns, and with three different transverse resolutions. Information from these experiments enabled the optimization of OCT systems for the above applications. Results include clinical 3D data of retinal pathologies, high quality cross-sectional images of the normal retina with different axial and transverse resolutions and 3D data from the rat and mouse retinas. Factors affecting the sensitivity fall-off are discussed and theoretical predictions are compared with experimental measurements. Different retinal imaging applications necessitate different system designs, depending on the requirements of speed, axial resolution, axial measurement range, transverse resolution, and field of view. While axial resolution is the dominant factor in image quality, a smaller transverse spot size can reduce speckle size and improve contrast at boundaries such as the boundary between the ganglion cell layer and the inner plexiform layer. The effect of reducing the transverse spot size is most pronounced in images with 5-10 um axial resolution. In addition, we characterize all factors responsible for the sensitivity drop with depth in spectral/Fourier domain OCT.

  5. On the accuracy of analytical models of impurity segregation during directional melt crystallization and their applicability for quantitative calculations

    NASA Astrophysics Data System (ADS)

    Voloshin, A. E.; Prostomolotov, A. I.; Verezub, N. A.

    2016-11-01

    The paper deals with the analysis of the accuracy of some one-dimensional (1D) analytical models of the axial distribution of impurities in the crystal grown from a melt. The models proposed by Burton-Prim-Slichter, Ostrogorsky-Muller and Garandet with co-authors are considered, these models are compared to the results of a two-dimensional (2D) numerical simulation. Stationary solutions as well as solutions for the initial transient regime obtained using these models are considered. The sources of errors are analyzed, a conclusion is made about the applicability of 1D analytical models for quantitative estimates of impurity incorporation into the crystal sample as well as for the solution of the inverse problems.

  6. 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.

  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. 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...

  9. An old model in a new perspective: The dynamic melting column and its application in intracontinental basalt petrogenesis

    NASA Astrophysics Data System (ADS)

    Taracsák, Zoltán; Molnár, Gábor; Harangi, Szabolcs

    2016-04-01

    Basaltic melt generation has been thought to be a simple process, involving distinct and well-defined melt batches generated in the asthenosphere or in the lithospheric mantle. However in the last decade, it became clear that complex processes including magma mixing from several sources may take place during magma generation, therefore single melting models might not be able to describe the melting process properly. We suggest that a trace element based melting column model assuming step by-step, dynamic melting caused by decompression would be a good estimation of how the mantle melts in intracontinental settings. This model makes it possible to assume a heterogeneous mantle source by adding melting cells with different composition and mineralogy, and can handle changes in bulk distribution coefficients caused by phase transitions for example the spinel-garnet transition in the upper mantle. If the uppermost part of the melting column reaches the stability of spinel, partitioning of rare earth elements (REEs) change drastically, as heavy REEs are compatible in the garnet stability field during melting while moderately incompatible in depths where spinel is stable. This way, trace element concentrations in primitive basalts can provide information on melting depth. This depth can be quantified with the step-by-step dynamic melting column model if the geotherm or the potential temperature is known. This way the depth of the spinel-garnet transition will be definable. We assume that melting beneath intracontinental volcanic fields is limited to the asthenosphere, and that the top of the melting column will represent the lithosphere-asthenosphere boundary (LAB). To test our model, we calculated lithospheric thicknesses for four Neogene-Quarternary basaltic volcanic fields from the Pannonian Basin, East Central Europe. Our results indicate slightly different LAB depths compared to previous, major element based calculations (Harangi et al., Int J Earth Sci, 2015).

  10. Spectral Variations Among Crystalline and Glassy Apollo 17 Impact Melt Rocks

    NASA Astrophysics Data System (ADS)

    Tompkins, S.; Pieters, C. M.; Ryder, G.

    1996-03-01

    Remote geochemical mapping of lunar impact melt associated with complex craters is a key to better understanding of impact melt formation and the impact cratering process. Ground-based NIR spectra and Clementine multispectral images comprise a dataset with high-resolution spectral and spatial information, respectively. To interpret these data with respect to impact melt, two suites of lunar samples are being measured in NASA's Reflectance Experiment Laboratory (RELAB) at Brown University. The samples include seven Apollo 17 crystalline impact melts as well as synthesized glass equivalents, and 11 naturally occurring impact glasses from several landing sites. Acquisition and analysis of the laboratory spectra is the first step towards quantitatively modeling remote spectra to learn more about the composition and source of the melt found at complex craters. Furthermore, from the laboratory spectra, basic compositional parameters may be determined for application to Clementine data. Initial measurements of the Apollo 17 melt rocks have been completed and are presented below.

  11. 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.

  12. 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.

  13. Applications of high-resolution solid-state NMR spectroscopy in food science.

    PubMed

    Bertocchi, Fabio; Paci, Maurizio

    2008-10-22

    The principal applications of high-resolution solid-state NMR spectroscopy, in the field of food science, are reviewed, after a short general introduction, mainly focusing on the potential of these investigations, which are, today, routine tools for resolving technological problems. Selected examples of the applications in the field of food science of high-resolution solid-state NMR spectroscopy both in (13)C and in (1)H NMR particularly illustrative of the results obtainable are reported in some detail.

  14. Field-calibrated model of melt, refreezing, and runoff for polar ice caps: Application to Devon Ice Cap

    NASA Astrophysics Data System (ADS)

    Morris, Richard M.; Mair, Douglas W. F.; Nienow, Peter W.; Bell, Christina; Burgess, David O.; Wright, Andrew P.

    2014-09-01

    Understanding the controls on the amount of surface meltwater that refreezes, rather than becoming runoff, over polar ice masses is necessary for modeling their surface mass balance and ultimately for predicting their future contributions to global sea level change. We present a modified version of a physically based model that includes an energy balance routine and explicit calculation of near-surface meltwater refreezing capacity, to simulate the evolution of near-surface density and temperature profiles across Devon Ice Cap in Arctic Canada. Uniquely, our model is initiated and calibrated using high spatial resolution measurements of snow and firn densities across almost the entire elevation range of the ice cap for the summer of 2004 and subsequently validated with the same type of measurements obtained during the very different meteorological conditions of summer 2006. The model captures the spatial variability across the transect in bulk snowpack properties although it slightly underestimates the flow of meltwater into the firn of previous years. The percentage of meltwater that becomes runoff is similar in both years; however, the spatial pattern of this melt-runoff relationship is different in the 2 years. The model is found to be insensitive to variation in the depth of impermeable layers within the firn but is very sensitive to variation in air temperature, since the refreezing capacity of firn decreases with increasing temperature. We highlight that the sensitivity of the ice cap's surface mass balance to air temperature is itself dependent on air temperature.

  15. Melting temperature of graphene

    NASA Astrophysics Data System (ADS)

    Los, J. H.; Zakharchenko, K. V.; Katsnelson, M. I.; Fasolino, Annalisa

    2015-01-01

    We present an approach to the melting of graphene based on nucleation theory for a first order phase transition from the two-dimensional (2D) solid to the 3D liquid via an intermediate quasi-2D liquid. The applicability of nucleation theory, supported by the results of systematic atomistic Monte Carlo simulations, provides an intrinsic definition of the melting temperature of graphene, Tm, and allows us to determine it. We find Tm≃4510 K, about 250 K higher than that of graphite using the same interatomic interaction model. The found melting temperature is shown to be in good agreement with the asymptotic results of melting simulations for finite disks and ribbons of graphene. Our results strongly suggest that graphene is the most refractory of all known materials.

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. A new method for simultaneous detection and discrimination of Bovine herpesvirus types 1 (BoHV-1) and 5 (BoHV-5) using real time PCR with high resolution melting (HRM) analysis.

    PubMed

    Marin, M S; Quintana, S; Leunda, M R; Recavarren, M; Pagnuco, I; Späth, E; Pérez, S; Odeón, A

    2016-01-01

    Bovine herpesvirus types 1 (BoHV-1) and 5 (BoHV-5) are antigenically and genetically similar. The aim of this study was to develop a simple and reliable one-step real time PCR assay with high resolution melting (HRM) analysis for the simultaneous detection and differentiation of BoHV-1 and BoHV-5. Optimization of assay conditions was performed with DNA from reference strains. Then, DNA from field isolates, clinical samples and tissue samples of experimentally infected animals were studied by real time PCR-HRM. An efficient amplification of real time PCR products was obtained, and a clear melting curve and appropriate melting peaks for both viruses were achieved in the HRM curve analysis for BoHV type identification. BoHV was identified in all of the isolates and clinical samples, and BoHV types were properly differentiated. Furthermore, viral DNA was detected in 12/18 and 7/18 samples from BoHV-1- and BoHV-5-infected calves, respectively. Real time PCR-HRM achieved a higher sensitivity compared with virus isolation or conventional PCR. In this study, HRM was used as a novel procedure. This method provides rapid, sensitive, specific and simultaneous detection of bovine alpha-herpesviruses DNA. Thus, this technique is an excellent tool for diagnosis, research and epidemiological studies of these viruses in cattle. PMID:26478539

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  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. 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.

  8. Adaptive optics for resolution/throughput optimization; variable-radius-mirror application for a PGM

    NASA Astrophysics Data System (ADS)

    Morikawa, Eizi; Scott, John D.; Saile, Volker

    1992-08-01

    The utilization of a bendable, variable-radius mirror as a key optical element to control resolution (and throughput) of an XUV monochromator is discussed. A bendable mirror is placed between source and grating; by bending it to either a concave or a convex figure along the dispersion direction, a variation of monochromator resolution is accomplished. As an application example, a plane-grating soft X-ray monochromator equipped with this bendable mirror system was investigated with ray-tracing calculations.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

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

    PubMed

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

    2014-07-14

    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.

  15. 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

  16. Mechanisms, Capabilities, and Applications of High-Resolution Electrohydrodynamic Jet Printing.

    PubMed

    Onses, M Serdar; Sutanto, Erick; Ferreira, Placid M; Alleyne, Andrew G; Rogers, John A

    2015-09-01

    This review gives an overview of techniques used for high-resolution jet printing that rely on electrohydrodynamically induced flows. Such methods enable the direct, additive patterning of materials with a resolution that can extend below 100 nm to provide unique opportunities not only in scientific studies but also in a range of applications that includes printed electronics, tissue engineering, and photonic and plasmonic devices. Following a brief historical perspective, this review presents descriptions of the underlying processes involved in the formation of liquid cones and jets to establish critical factors in the printing process. Different printing systems that share similar principles are then described, along with key advances that have been made in the last decade. Capabilities in terms of printable materials and levels of resolution are reviewed, with a strong emphasis on areas of potential application.

  17. 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

  18. P- T phase relations of silicic, alkaline, aluminous liquids: new results and applications to mantle melting and metasomatism

    NASA Astrophysics Data System (ADS)

    Draper, David S.; Green, Trevor H.

    1999-07-01

    We report new experimental results obtained under nominally anhydrous conditions at 1.0-1.5 GPa on a synthetic melt whose composition is typical of extreme-composition xenolith glasses. These results demonstrate that part of this extreme compositional range is in equilibrium with a lherzolitic assemblage (olivine, orthopyroxene, and clinopyroxene on the liquidus), extending our earlier findings [D.S. Draper, T.H. Green P- T phase relations of silicic, alkaline, aluminous mantle-xenolith glasses under anhydrous and C-O-H fluid-saturated conditions, J. Petrol. 38 (1997) 1187-1224] showing saturation with harzburgite minerals (olivine and orthopyroxene on the liquidus). The new results strengthen the view that such liquids can readily coexist with upper mantle rocks. Our results also bear on the current debate regarding the nature of low-degree mantle melts between proponents of the diamond-aggregate technique [who argue for comparatively silica- and alkali-rich low-degree melts; e.g., M.B. Baker, M.M. Hirschmann, M.S. Ghiorso, E.M. Stolper, Compositions of near-solidus peridotite melts from experiments and thermodynamic calculations, Nature 375 (1995) 308-311; M.B. Baker, M.M. Hirschmann, L.E. Wasylenki, E.M. Stolper, M.S. Ghiorso, Quest for low-degree mantle melts, Nature 381 (1996) 286] and those favoring the sandwich technique [who question the value of the diamond-aggregate work and argue that near-solidus melts must be nepheline- and olivine-normative; T.J. Falloon, D.H. Green, H.St.C. O'Neill, C.G. Ballhaus, Quest for low-degree mantle melts, Nature 381 (1996) 285; T.J. Falloon, D.H. Green, H.St.C. O'Neill, W.O. Hibberson, Experimental tests of low degree peridotite partial melt compositions: implications for the nature of anhydrous near-solidus peridotite melts at 1 GPa, Earth Planet. Sci. Lett. 152 (1997) 149-162]. Our results support aspects of both views. The sandwich-technique view is supported, for example, because all our liquids coexisting with mantle

  19. 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.

  20. 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

    ... permit under section 4(f) of the Federal Power Act proposing to study the feasibility of the Yakutat 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;...

  1. Melting and solidification of Bi nanoparticles in a germanate glass

    NASA Astrophysics Data System (ADS)

    Haro-Poniatowski, E.; Jiménez de Castro, M.; Fernández Navarro, J. M.; Morhange, J. F.; Ricolleau, C.

    2007-08-01

    A very large melting-solidification hysteresis of Bi nanoparticles embedded in a bulk alkali germanate glass is reported. Heating and cooling cycles are reproducible and show reversible transitions. High resolution transmission electron microscopy reveals that the glass contains nanocrystals of elementary Bi which are a few tenths of a nanometre in size. Upon heating above the Bi melting temperature the glass transmission increases up to 10% with respect to the initial value, which is most likely related to Bi melting. Upon cooling this high transmission state remains up to temperatures as low as 436 K. This behaviour is confirmed by Raman spectroscopy measurements. This nanostructured glass with a high refractive index can be used in nonlinear optical applications as well as an optical thermo-sensor.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. Military reconnaissance application of high-resolution optical satellite remote sensing

    NASA Astrophysics Data System (ADS)

    Wang, Zheng-gang; Kang, Qing; Xun, Yi-jia; Shen, Zhi-qiang; Cui, Chang-bin

    2014-11-01

    As the remote sensing technology transformation from military use to civil use becomes deeper and faster, the resolution is better and better, and the relative techniques of the civil optical remote sensing satellite are richer and richer. So, modes such as civil use replacing military use, civil use covering military use, and civil use supporting military use are the real portraiture of high-resolution optical satellite remote sensing development currently. Taking the situations of the Taiwan authorities buying commercial remote sensing image to military reconnaissance, and the so-called military establishments exposed by media using satellite image as an example, the military reconnaissance application of civil high-resolution optical satellite remote sensing is discussed. Then, the actuality and reasons of huge measure engineering and ruled configuring, environment and signs of military area, equipment and exercitation establishments and three-dimension information of engineering and equipment which can be detected easily by remote sensing are analyzed.

  7. 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.).

  8. 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.

  9. 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.

  10. Combined application of extrusion-spheronization and hot-melt coating technologies for improving moisture-proofing of herbal extracts.

    PubMed

    Chen, Hao; Shi, Shuai; Liu, Aina; Tang, Xing

    2010-05-01

    The aim of this research was to investigate the moisture-proofing effect and its mechanism for herbal extracts using extrusion-spheronization combined with hot-melt coating. Guizhi Fuling (GF) compound herbal extract with high hygroscopicity was used as a model drug. In the process of extrusion-spheronization, pellets containing 100% GF were prepared, and then coated with hot-melt coating material using a traditional coating pan. The moisture sorption data for GF were determined by storage at a series of different relative humidities. When the pellets were coated with a 96:4 mixture of stearic acid and polyethylene glycol 6000, the cumulative drug release was over 90% at 45 min while the moisture content was 4.9% at 75% RH within 10 days. These pellets have better moisture-proofing than those coated with Opadry AMB at the same coating level due to a different moisture sorption mechanism. The moisture sorption behavior of the hot-melt coating can be attributed to water vapor diffusion via a porous matrix system, while the Opadry AMB coating system involved a swelling controlled system. The Higuchi model was the best fit for the moisture sorption of the hot-melt coating in all formulations whereas the Opadry AMB coating fitted the Nuttanan model.

  11. 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.

  12. High-resolution melting (HRM) of the cytochrome B gene: a powerful approach to identify blood-meal sources in Chagas disease Vectors.

    PubMed

    Peña, Victor H; Fernández, Geysson J; Gómez-Palacio, Andrés M; Mejía-Jaramillo, Ana M; Cantillo, Omar; Triana-Chávez, Omar

    2012-01-01

    Methods to determine blood-meal sources of hematophagous Triatominae bugs (Chagas disease vectors) are serological or based on PCR employing species-specific primers or heteroduplex analysis, but these are expensive, inaccurate, or problematic when the insect has fed on more than one species. To solve those problems, we developed a technique based on HRM analysis of the mitochondrial gene cytochrome B (Cyt b). This technique recognized 14 species involved in several ecoepidemiological cycles of the transmission of Trypanosoma cruzi and it was suitable with DNA extracted from intestinal content and feces 30 days after feeding, revealing a resolution power that can display mixed feedings. Field samples were analyzed showing blood meal sources corresponding to domestic, peridomiciliary and sylvatic cycles. The technique only requires a single pair of primers that amplify the Cyt b gene in vertebrates and no other standardization, making it quick, easy, relatively inexpensive, and highly accurate.

  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. 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

  15. 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

  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.

  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.

  18. A mitochondrial species identification assay for Australian blacktip sharks (Carcharhinus tilstoni, C. limbatus and C. amblyrhynchoides) using real-time PCR and high-resolution melt analysis.

    PubMed

    Morgan, Jess A T; Welch, David J; Harry, Alistair V; Street, Raewyn; Broderick, Damien; Ovenden, Jennifer R

    2011-09-01

    Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing. PMID:21565127

  19. A transportable high-resolution gamma-ray spectrometer and analysis system applicable to mobile, autonomous or unattended applications

    SciTech Connect

    Buckley, W.M.; Neufeld, K.W.

    1995-07-01

    The Safeguards Technology Program at the Lawrence Livermore National Laboratory is developing systems based on a compact electro-mechanically cooled high-purity germanium (HPGe) detector. This detector system broadens the practicality of performing high- resolution gamma-ray spectrometry in the field. Utilizing portable computers, multi-channel analyzers and software these systems greatly improve the ease of performing mobile high-resolution gamma-ray spectrometry. Using industrial computers, we can construct systems that will run autonomously for extended periods of time without operator input or maintenance. These systems can start or make decisions based on sensor inputs rather than operator interactions. Such systems can provide greater capability for wider domain of safeguards, treaty verification application, and other unattended, autonomous or in-situ applications.

  20. Thermodynamics of Oligonucleotide Duplex Melting

    NASA Astrophysics Data System (ADS)

    Schreiber-Gosche, Sherrie; Edwards, Robert A.

    2009-05-01

    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 rigorous thermodynamic analysis to an important biochemical problem. Because the stacking of base pairs on top of one another is a significant factor in the energetics of oligonucleotide melting, several investigators have applied van't Hoff analysis to melting temperature data using a nearest-neighbor model and have obtained entropies and enthalpies for the stacking of bases. The present article explains how the equilibrium constant for the dissociation of strands from double-stranded oligonucleotides can be expressed in terms of the total strand concentration and thus how the total strand concentration influences the melting temperature. It also presents a simplified analysis based on the entropies and enthalpies of stacking that is manually tractable so that students can work examples to help them understand the thermodynamics of oligonucleotide melting.

  1. 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

  2. Speciation in granitic melts

    SciTech Connect

    Burnham, C.W.; Nekvasil, H.

    1985-01-01

    Refinement of the cryoscopic equations for the major granitic melt components, NaAlSi/sub 3/O/sub 8/(ab), CaAl/sub 2/O/sub 8/(an), KAlSi/sub 3/O/sub 8/(or), and Si/sub 4/O/sub 8/(qz), has led to the recognition of several major speciation reactions in anhydrous and hydrous melts of the system Ab-An-Or-Qz-H/sub 2/O. These reactions involve either dissociation of the feldspar-like components, as in incongruent melting, or interaction between them and qz. In all cases of interaction, one of the speciation products has the stoichiometry of dpy or py (pyrophyllite) (Al/sub 1.455/Si/sub 2.91/O/sub 8/ +/- 0.73H/sub 2/O), in which Al is presumed to be in either fivefold (dpy) or sixfold (py) coordination. The py component also is a major product of speciation by interaction between sil (Al/sub 3.2/Si/sub 1.6/O/sub 8/) and qz in peraluminous melts of the system Ab-Or-Qz-Sil-H/sub 2/O; as a consequence, the quartz liquidus field boundary is shifted to lower temperatures and toward qz. There is no evidence in peraluminous haplogranite melts for the existence of a muscovite-like species. Application of the refined thermodynamic model to the system Ab-Qz-Eu - H/sub 2/O at 2.0 kbar predicts the occurrence of a eu and qz-consuming reaction that produces a petalite-like species and a consequent dramatic shift in liquidus field boundaries. Higher pressures favor conversion of pe to qz + sp. In the spodumene-like species, sp, Al presumably is six-coordinated.

  3. 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

  4. 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

  5. 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

  6. 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.

  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.

  8. Applications of High Resolution Mid-Infrared Spectroscopy for Atmospheric and Environmental Measurements

    NASA Astrophysics Data System (ADS)

    Roscioli, Joseph R.; McManus, J. Barry; Nelson, David; Zahniser, Mark; Herndon, Scott C.; Shorter, Joanne; Yacovitch, Tara I.; Jervis, Dylan; Dyroff, Christoph; Kolb, Charles E.

    2016-06-01

    For the past 20 years, high resolution infrared spectroscopy has served as a valuable tool to measure gas-phase concentrations of ambient gas samples. We review recent advances in atmospheric sampling using direct absorption high resolution mid-infrared spectroscopy from the perspective of light sources, detectors, and optical designs. Developments in diode, quantum cascade and interband cascade laser technology have led to thermoelectrically-cooled single-mode laser sources capable of operation between 800 wn and 3100 wn, with <10 MHz resolution and >10 mW power. Advances in detector and preamplifier technology have yielded thermoelectriocally-cooled sensors capable of room-temperature operation with extremely high detectivities. Finally, novel spectrometer optical designs have led to robust multipass absorption cells capable of >400 m effective pathlength in a compact package. In combination with accurate spectroscopic databases, these developments have afforded dramatic improvements in measurement sensitivity, accuracy, precision, and selectivity. We will present several examples of the applications of high resolution mid-IR spectrometers in real-world field measurements at sampling towers and aboard mobile platforms such as vehicles and airplanes.

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

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

    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).

  10. Application of Spatially Resolved High Resolution Crystal Spectrometry to ICF Plasmas

    SciTech Connect

    Kenneth W. Hill, et. al.

    2012-09-15

    High resolution (λ/Δ λ ~ 10 000) 1D imaging x-ray spectroscopy using a spherically bent crystal and a 2D hybrid pixel array detector is used world wide for Doppler measurements of ion-temperature and plasma flow-velocity profiles in magnetic confinement fusion plasmas. Meter sized plasmas are diagnosed with cm spatial resolution and 10 ms time resolution. This concept can also be used as a diagnostic of small sources, such as inertial confinement fusion plasmas and targets on x-ray light source beam lines, with spatial resolution of micrometers, as demonstrated by laboratory experiments using a 250-μm 55 Fe source, and by ray-tracing calculations. Throughput calculations agree with measurements, and predict detector counts in the range 10-8 -10-6 times source x-rays, depending on crystal reflectivity and spectrometer geometry. Results of the lab demonstrations, application of the technique to the National Ignition Facility (NIF), and predictions of performance on NIF will be presented.

  11. Application of spatially resolved high resolution crystal spectrometry to inertial confinement fusion plasmas

    SciTech Connect

    Hill, K. W.; Bitter, M.; Delgado-Aparacio, L.; Pablant, N. A.; Beiersdorfer, P.; Schneider, M.; Widmann, K.; Sanchez del Rio, M.; Zhang, L.

    2012-10-15

    High resolution ({lambda}/{Delta}{lambda}{approx} 10 000) 1D imaging x-ray spectroscopy using a spherically bent crystal and a 2D hybrid pixel array detector is used world wide for Doppler measurements of ion-temperature and plasma flow-velocity profiles in magnetic confinement fusion plasmas. Meter sized plasmas are diagnosed with cm spatial resolution and 10 ms time resolution. This concept can also be used as a diagnostic of small sources, such as inertial confinement fusion plasmas and targets on x-ray light source beam lines, with spatial resolution of micrometers, as demonstrated by laboratory experiments using a 250-{mu}m {sup 55}Fe source, and by ray-tracing calculations. Throughput calculations agree with measurements, and predict detector counts in the range 10{sup -8}-10{sup -6} times source x-rays, depending on crystal reflectivity and spectrometer geometry. Results of the lab demonstrations, application of the technique to the National Ignition Facility (NIF), and predictions of performance on NIF will be presented.

  12. 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

  13. 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.

  14. A Compact "Water Window" Microscope with 60 nm Spatial Resolution for Applications in Biology and Nanotechnology.

    PubMed

    Wachulak, Przemyslaw; Torrisi, Alfio; Nawaz, Muhammad F; Bartnik, Andrzej; Adjei, Daniel; Vondrová, Šárka; Turňová, Jana; Jančarek, Alexandr; Limpouch, Jiří; Vrbová, Miroslava; Fiedorowicz, Henryk

    2015-10-01

    Short illumination wavelength allows an extension of the diffraction limit toward nanometer scale; thus, improving spatial resolution in optical systems. Soft X-ray (SXR) radiation, from "water window" spectral range, λ=2.3-4.4 nm wavelength, which is particularly suitable for biological imaging due to natural optical contrast provides better spatial resolution than one obtained with visible light microscopes. The high contrast in the "water window" is obtained because of selective radiation absorption by carbon and water, which are constituents of the biological samples. The development of SXR microscopes permits the visualization of features on the nanometer scale, but often with a tradeoff, which can be seen between the exposure time and the size and complexity of the microscopes. Thus, herein, we present a desk-top system, which overcomes the already mentioned limitations and is capable of resolving 60 nm features with very short exposure time. Even though the system is in its initial stage of development, we present different applications of the system for biology and nanotechnology. Construction of the microscope with recently acquired images of various samples will be presented and discussed. Such a high resolution imaging system represents an interesting solution for biomedical, material science, and nanotechnology applications.

  15. 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

  16. 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.

  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. 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.

  19. 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.

  20. 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

  1. 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

  2. A comparison of Direct sequencing, Pyrosequencing, High resolution melting analysis, TheraScreen DxS, and the K-ras StripAssay for detecting KRAS mutations in non small cell lung carcinomas

    PubMed Central

    2012-01-01

    Background It is mandatory to confirm the absence of mutations in the KRAS gene before treating metastatic colorectal cancers with epidermal growth factor receptor inhibitors, and similar regulations are being considered for non-small cell lung carcinomas (NSCLC) and other tumor types. Routine diagnosis of KRAS mutations in NSCLC is challenging because of compromised quantity and quality of biological material. Although there are several methods available for detecting mutations in KRAS, there is little comparative data regarding their analytical performance, economic merits, and workflow parameters. Methods We compared the specificity, sensitivity, cost, and working time of five methods using 131 frozen NSCLC tissue samples. We extracted genomic DNA from the samples and compared the performance of Sanger cycle sequencing, Pyrosequencing, High-resolution melting analysis (HRM), and the Conformité Européenne (CE)-marked TheraScreen DxS and K-ras StripAssay kits. Results and conclusions Our results demonstrate that TheraScreen DxS and the StripAssay, in that order, were most effective at diagnosing mutations in KRAS. However, there were still unsatisfactory disagreements between them for 6.1% of all samples tested. Despite this, our findings are likely to assist molecular biologists in making rational decisions when selecting a reliable, efficient, and cost-effective method for detecting KRAS mutations in heterogeneous clinical tumor samples. PMID:22995035

  3. 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.

  4. 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

    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.

  5. Comparative analysis of two broad-range PCR assays for pathogen detection in positive-blood-culture bottles: PCR-high-resolution melting analysis versus PCR-mass spectrometry.

    PubMed

    Jeng, Kevin; Gaydos, Charlotte A; Blyn, Lawrence B; Yang, Samuel; Won, Helen; Matthews, Heather; Toleno, Donna; Hsieh, Yu-Hsiang; Carroll, Karen C; Hardick, Justin; Masek, Billy; Kecojevic, Alexander; Sampath, Rangarajan; Peterson, Stephen; Rothman, Richard E

    2012-10-01

    Detection of pathogens in bloodstream infections is important for directing antimicrobial treatment, but current culture-based approaches can be problematic. Broad-range PCR assays which target conserved genomic motifs for postamplification amplicon analysis permit detection of sepsis-causing pathogens. Comparison of different broad-range assays is important for informing future implementation strategies. In this study, we compared positive-blood-culture bottles processed by PCR coupled to high-resolution melting curve analysis (PCR/HRMA) and PCR coupled to electrospray ionization-mass spectrometry (PCR/ESI-MS) to microbiology culture results. Genus-level concordance was 90% (confidence interval [CI], 80 to 96%) for PCR/HRMA and 94% (CI, 85 to 98%) for PCR/ESI-MS. Species-level concordance was 90% (CI, 80 to 96%) for PCR/HRMA and 86% (CI, 75 to 93%) for PCR/ESI-MS. Unlike PCR/HRMA, PCR/ESI-MS was able to resolve polymicrobial samples. Our results demonstrated that the two assays have similar overall concordance rates but may have different roles as potential adjunctive tests with standard blood culture, since each method has different capabilities, advantages, and disadvantages.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. Widely tunable mode-hop free external cavity quantum cascade laser for high resolution spectroscopic applications

    NASA Astrophysics Data System (ADS)

    Wysocki, G.; Curl, R. F.; Tittel, F. K.; Maulini, R.; Bulliard, J. M.; Faist, J.

    2005-10-01

    An external cavity (EC) quantum cascade laser (QCL) configuration with the thermoelectrically cooled gain medium fabricated using a bound-to-continuum design and operating in continuous wave at ˜5.2 μm is reported. The EC architecture employs a piezo-activated cavity mode tracking system for mode-hop free operation suitable for high resolution spectroscopic applications and multiple species trace-gas detection. The performance of the EC-QCL exhibits coarse single mode tuning over 35 cm-1 and a continuous mode-hop free fine tuning range of ˜1.2 cm-1.

  16. The resolution capability of an irregularly sampled dataset: With application to Geosat altimeter data

    NASA Technical Reports Server (NTRS)

    Chelton, Dudley B.; Schlax, Michael G.

    1994-01-01

    A formalism is presented for determining the wavenumber-frequency transfer function associated with an irregularly sampled multidimensional dataset. This transfer function reveals the filtering characteristics and aliasing patterns inherent in the sample design. In combination with information about the spectral characteristics of the signal, the transfer function can be used to quantify the spatial and temporal resolution capability of the dataset. Application of the method to idealized Geosat altimeter data (i.e., neglecting measurement errors and data dropouts) concludes that the Geosat orbit configuration is capable of resolving scales of about 3 deg in latitude and longitude by about 30 days.

  17. An ultra-high-resolution FBG static-strain sensor for geophysics applications

    NASA Astrophysics Data System (ADS)

    Liu, Qingwen; He, Zuyuan; Tokunaga, Tomochika; Hotate, Kazuo

    2010-09-01

    We report an ultra-high-resolution static-strain measurement with a pair of fiber Bragg gratings (FBGs), one for strain sensing and the other for compensating the error due to temperature disturbance and source drift. The difference between the two FBGs' Bragg wavelengths is evaluated by utilizing a cross-correlation algorithm. The mechanism of noise suppression by the cross-correlation algorithm is quantitatively analyzed and the factor that determines the ability of noise suppression of this algorithm is revealed. The temperature dependence is further subtracted by using a vector operation. When no strain is applied, an ultra-high wavelength resolution corresponding to 2.6 nɛ was obtained, which gives the ultimate performance of the measurement system. With a variable strain applied with a piezo-stage, a resolution of 17.6 nɛ was demonstrated. This is the first demonstration, to the best of our knowledge, that a real-static strain down to 10 nɛ is measured, providing a powerful technique for the measurement in geophysics application.

  18. 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.

  19. 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.

  20. Ground-based high resolution Fourier transform spectrometer and its application in Beijing

    NASA Astrophysics Data System (ADS)

    Fan, Dongdong

    2013-10-01

    The B3M-FTS instrument, inherited from ACE-FTS and PARIS, is built by Canadian ABB and Beijing Vision Sky Aerospace Co., Ltd. The B3M is a complete stand-alone spectrometer designed to operate from the ground in moderate environment. It can acquire atmospheric spectra with the Sun as back illumination. This instrument is an adapted version of the classical Michelson interferometer using an optimized optical layout, and it is a high-resolution infrared Fourier transform spectrometer operating in the 750 to 4100cm-1 spectral range. In this paper, the instrument concept of a compact, portable, high-resolution Fourier transform spectrometer is introduced. Some test results of the instrument such as ILS and SNR are presented, and the spectral resolution of 0.028cm-1 @ 750cm-1 and SNR over 100:1 are achieved. Sample atmospheric absorption spectra and corresponding retrieval results measured by the FTS are given. The B3M-FTS, with its high performance, provides the capability to monitor the atmospheric composition changes by measuring the atmospheric absorption spectra of solar radiance. Lots of measurements have been acquired at the Olympics atmospheric observation super-station. Up to now, the VMRs of near 10 trace gases have been retrieved. The success of atmospheric composition profile retrieval using the FTS measurements makes the further application of FTS type payload possible in China.

  1. Application of the high-resolution grazing-emission x-ray fluorescence method for impurities control in semiconductor nanotechnology

    SciTech Connect

    Szlachetko, J.; Banas, D.; Kubala-Kukus, A.; Pajek, M.; Cao, W.; Dousse, J.-Cl.; Hoszowska, J.; Kayser, Y.; Szlachetko, M.; Kavcic, M.; Salome, M.; Susini, J.

    2009-04-15

    We report on the application of synchrotron radiation based high-resolution grazing-emission x-ray fluorescence (GEXRF) method to measure low-level impurities on silicon wafers. The presented high-resolution GEXRF technique leads to direct detection limits of about 10{sup 12} atoms/cm{sup 2}. The latter can be presumably further improved down to 10{sup 7} atoms/cm{sup 2} by combining the synchrotron radiation-based GEXRF method with the vapor phase decomposition preconcentration technique. The capability of the high-resolution GEXRF method to perform surface-sensitive elemental mappings with a lateral resolution of several tens of micrometers was probed.

  2. 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

  3. 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.

  4. 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.

  5. Long-term ocean simulations in FESOM: evaluation and application in studying the impact of Greenland Ice Sheet melting

    NASA Astrophysics Data System (ADS)

    Wang, Xuezhu; Wang, Qiang; Sidorenko, Dmitry; Danilov, Sergey; Schröter, Jens; Jung, Thomas

    2012-12-01

    The Finite Element Sea-ice Ocean Model (FESOM) is formulated on unstructured meshes and offers geometrical flexibility which is difficult to achieve on traditional structured grids. In this work, the performance of FESOM in the North Atlantic and Arctic Ocean on large time scales is evaluated in a hindcast experiment. A water-hosing experiment is also conducted to study the model sensitivity to increased freshwater input from Greenland Ice Sheet (GrIS) melting in a 0.1-Sv discharge rate scenario. The variability of the Atlantic Meridional Overturning Circulation (AMOC) in the hindcast experiment can be explained by the variability of the thermohaline forcing over deep convection sites. The model also reproduces realistic freshwater content variability and sea ice extent in the Arctic Ocean. The anomalous freshwater in the water-hosing experiment leads to significant changes in the ocean circulation and local dynamical sea level (DSL). The most pronounced DSL rise is in the northwest North Atlantic as shown in previous studies, and also in the Arctic Ocean. The released GrIS freshwater mainly remains in the North Atlantic, Arctic Ocean and the west South Atlantic after 120 model years. The pattern of ocean freshening is similar to that of the GrIS water distribution, but changes in ocean circulation also contribute to the ocean salinity change. The changes in Arctic and sub-Arctic sea level modify exchanges between the Arctic Ocean and subpolar seas, and hence the role of the Arctic Ocean in the global climate. Not only the strength of the AMOC, but also the strength of its decadal variability is notably reduced by the anomalous freshwater input. A comparison of FESOM with results from previous studies shows that FESOM can simulate past ocean state and the impact of increased GrIS melting well.

  6. 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).

  7. 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.

  8. Planar cone-beam computed tomography for high-resolution industrial application

    NASA Astrophysics Data System (ADS)

    Liu, Tong

    2009-12-01

    Traditional reconstruction algorithm in computed tomography (CT) requires a square reconstruction matrix, regardless of the particular object shape. It becomes inefficient when reconstructing planar objects such as IC chips which have a large area-to-thickness ratio. This article presents a modified cone-beam reconstruction algorithm which is efficient for planar multilayer objects. by detecting the orientation and dimension parameters of the object for the first projection, a reconstruction volume can be defined in a region that would exactly cover the object area and follow the actual orientation of the object. This new technology is demonstrated in both its general form and a targeted application. Compared to conventional cone-beam CT reconstruction, this new method uses much less computation time and storage, can achieve higher reconstruction resolution in the thickness dimension, and makes layer separation much easier for multilayer objects. These advantages will be demonstrated with two high-resolution CT inspection applications of a stacked IC and an advanced packaging device.

  9. Application of multivariate curve resolution alternating least squares (MCR-ALS) to remote sensing hyperspectral imaging.

    PubMed

    Zhang, Xin; Tauler, Romà

    2013-01-31

    The application of the MCR-ALS method is demonstrated on two simulated remote sensing spectroscopic images and on one experimental reference remote sensing spectroscopic image obtained by the Airborn Visible/Infrared Imaging Spectrometer (AVIRIS). By application of MCR-ALS, the spectra signatures of the pure constituents present in the image and their concentration distribution at a pixel level are estimated. Results obtained by MCR-ALS are compared to those obtained by other methods frequently used in the remote sensing spectroscopic imaging field like VCA and MVSA. In the case of the analysis of the experimental data set, the resolved pure spectra signatures were compared to reference spectra from USGS library for their identification. In all cases, results were also evaluated for the presence of rotational ambiguities using the MCR-BANDS method. The obtained results confirmed that the MCR-ALS method can be successfully used for remote sensing hyperspectral image resolution purposes. However, the amount of rotation ambiguity still present in the solutions obtained by this and other resolution methods (like VCA or MVSA) can still be large and it should be evaluated with care, trying to reduce its effects by selecting the more appropriate constraints. Only in this way it is possible to increase the reliability of the solutions provided by these methods and decrease the uncertainties associated to their use.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. The potential application of a Cobalt Chrome Molybdenum femoral stem with functionally graded orthotropic structures manufactured using Laser Melting technologies.

    PubMed

    Hazlehurst, K B; Wang, C J; Stanford, M

    2013-12-01

    The cementless fixation of porous coated femoral stems is a common technique employed for Total Hip Arthroplasty (THA). With the rate of revision surgery appearing to rise and younger more active patients requiring primary surgery it can be thought that alternative methods for increasing implant longevity need to be considered. The stress shielding of periprosthetic bone still remains a contributing factor to implant loosening, caused through a mismatch in stiffness between the implant and the bone. However, the ability to achieve stiffness matching characteristics is being realised through the use of Additive Layer Manufacturing (ALM) technologies and Functionally Graded Materials (FGM). This paper proposes an alternative design methodology for a monoblock Cobalt Chrome Molybdenum (CoCrMo) femoral stem. It hypothesises that a femoral stem suitable for cementless fixation can be manufactured using Laser Melting (LM) technology offering orthotropic functionally graded porous structures with similar mechanical properties to human bone. The structure and mechanical properties of the natural femur have been used as a basis for the design criteria which hypothesises that through a combination of numerical analysis and physical testing, an optimal design can be proposed to provide a lightweight, customised femoral stem that can reduce the risk of implant loosening through stress shielding whilst maintaining bone-implant interface stability.

  19. Multi-seeding melt growth process of bulk Y-Ba-Cu-O superconductors for engineering applications

    NASA Astrophysics Data System (ADS)

    Wongsatanawarid, A.; Seki, H.; Murakami, M.

    2010-06-01

    We have prepared polycrystalline and four-domain Y-Ba-Cu-O superconductors in a molar ratio of Y123: Y211 = 10: 4 with lwt% Ce02 addition by melt-processing in air. Trapped field measurements showed that four sharp peaks were observed in a four-domain bulk sample, showing that four grains were successfully formed without defects by a multi-seeding method. Force measurements showed that a four-domain Y-Ba-Cu-O sample exhibited higher repulsive forces and smaller hysteresis loops than polycrystalline Y-Ba-Cu-O sample during the increasing and decreasing field processes, which implies higher pinning performance of the four-domain sample. With the aim of studying the transferable torque forces, we used a multi-pole magnet circuit with NSNS configuration. We confirmed that with the interaction of the magnet circuit, a four-domain Y-Ba-Cu-O sample showed larger forces than a polycrystalline sample both in the field-cooled and the zero-field-cooled mode. We also measured the torque forces acting between the magnet circuit and bulk Y-Ba-Cu-O samples by twisting the magnet circuit in the levitated state. Again a four-domain Y-Ba-Cu-O sample exhibited much higher torque forces than a polycrystalline sample. These results showed that multi-seeded Y-Ba-Cu-O sample with four-domains can be used for torque transfer apllications.

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. Rate-Gyro-Integral Constraint for Ambiguity Resolution in GNSS Attitude Determination Applications

    PubMed Central

    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

  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. Rate-gyro-integral constraint for ambiguity resolution in GNSS attitude determination applications.

    PubMed

    Zhu, Jiancheng; Li, Tao; Wang, Jinling; Hu, Xiaoping; Wu, Meiping

    2013-06-21

    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.

  10. Multi-resolution correlative focused ion beam scanning electron microscopy: applications to cell biology.

    PubMed

    Narayan, Kedar; Danielson, Cindy M; Lagarec, Ken; Lowekamp, Bradley C; Coffman, Phil; Laquerre, Alexandre; Phaneuf, Michael W; Hope, Thomas J; Subramaniam, Sriram

    2014-03-01

    Efficient correlative imaging of small targets within large fields is a central problem in cell biology. Here, we demonstrate a series of technical advances in focused ion beam scanning electron microscopy (FIB-SEM) to address this issue. We report increases in the speed, robustness and automation of the process, and achieve consistent z slice thickness of ∼3 nm. We introduce "keyframe imaging" as a new approach to simultaneously image large fields of view and obtain high-resolution 3D images of targeted sub-volumes. We demonstrate application of these advances to image post-fusion cytoplasmic intermediates of the HIV core. Using fluorescently labeled cell membranes, proteins and HIV cores, we first produce a "target map" of an HIV infected cell by fluorescence microscopy. We then generate a correlated 3D EM volume of the entire cell as well as high-resolution 3D images of individual HIV cores, achieving correlative imaging across a volume scale of 10(9) in a single automated experimental run.

  11. Sensitivity and resolution enhancement of oriented solid-state NMR: Application to membrane proteins

    PubMed Central

    Gopinath, T.; Mote, Kaustubh R.; Veglia, Gianluigi

    2013-01-01

    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 15N 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 15N and 13C 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

  12. Design of an eight-element refractive lens for high resolution imaging applications

    NASA Astrophysics Data System (ADS)

    Rao, D. V. B.

    1987-06-01

    An 8 element refractive lens of 324.4 mm EFL and f/4.5 was designed for the spectral band 520nm to 590nm. The FOV of the lens was +- 5 degrees. The computed MTF of this lens system was better than 0.7 for spatial frequencies up to 60 1p/mm, as against the diffraction limited MTF of 0.81. A similar lens was designed for the spectral band 770nm to 860nm. These two lenses will be configured alongwith a panchromatic catadioptric lens of 900 mm EFL for high resolution spacecraft remote sensing applications. The design details of these lenses were presented in this paper.

  13. 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

  14. 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

  15. 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

  16. Experiments and Monte Carlo modeling of a higher resolution Cadmium Zinc Telluride detector for safeguards applications

    NASA Astrophysics Data System (ADS)

    Borella, Alessandro

    2016-09-01

    The Belgian Nuclear Research Centre is engaged in R&D activity in the field of Non Destructive Analysis on nuclear materials, with focus on spent fuel characterization. A 500 mm3 Cadmium Zinc Telluride (CZT) with enhanced resolution was recently purchased. With a full width at half maximum of 1.3% at 662 keV, the detector is very promising in view of its use for applications such as determination of uranium enrichment and plutonium isotopic composition, as well as measurement on spent fuel. In this paper, I report about the work done with such a detector in terms of its characterization. The detector energy calibration, peak shape and efficiency were determined from experimental data. The data included measurements with calibrated sources, both in a bare and in a shielded environment. In addition, Monte Carlo calculations with the MCNPX code were carried out and benchmarked with experiments.

  17. 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.

  18. Multiple High Resolution Climate Scenarios over North America for Application to Water Resources (Invited)

    NASA Astrophysics Data System (ADS)

    Mearns, L. O.

    2009-12-01

    The North American Regional Climate Change Assessment Program (NARCCAP) is an international program that is serving the climate scenario needs of the United States, Canada, and northern Mexico. We are systematically investigating the uncertainties in regional scale projections of future climate and producing high resolution climate change scenarios using multiple regional climate models(RCMs)and multiple global model responses to a future emission scenario, by nesting the RCMs within atmosphere ocean general circulation models (AOGCMs) forced with the A2 SRES scenario, over a domain covering the conterminous US, northern Mexico, and most of Canada. The project also includes a validation component through nesting the participating RCMs within NCEP reanalyses. The basic spatial resolution of the RCM simulations is 50 km. This program includes RCMs that participated in the European PRUDENCE program (HadRM3 and RegCM), the Canadian regional climate model (CRCM) as well as the NCEP regional spectral model (RSM), the NCAR/PSU MM5, and NCAR WRF. Candidate AOGCMs include the Hadley Centre HadCM3, NCAR CCSM, the Canadian CGCM3 and the GFDL model. The resulting climate model runs form the basis for multiple high resolution climate scenarios that can be used in climate change impacts assessments over North America. High resolution (50 km) global time-slice experiments based on the GFDL atmospheric model and the NCAR atmospheric model (CAM3) have also been produced and will be compared with the simulations of the regional models. There also will be opportunities for double nesting over key regions through which additional modelers in the regional modeling community will be able to participate in NARCCAP. Additional key science issues are being investigated such as the importance of compatible physics in the nested and nesting models. Measures of uncertainty across the multiple runs are being developed by geophysical statisticians. In this overview talk, results from Phase II

  19. 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

  20. 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.

  1. MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay.

    PubMed

    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.

  2. 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

  3. MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay.

    PubMed

    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

  4. Feeder apparatus for melting furnaces, particularly for plasma melting furnaces

    SciTech Connect

    Primke, K.; Papsdorf, P.; Pohle, G.; Trautmann, K.P.

    1984-08-28

    The invention comprises a charging apparatus for melting furnaces, especially for plasma melting furnaces, for the continuous melting of preferably prepared aluminum scrap material. With the help of the proposed solution a controlled and regulated supply of the scrap material along with the prevention of a direct application of the plasma arc or other energy sources directly to the material to be melted, can be accomplished with the simultaneous pre-warming and cleaning of the material to be melted, wherein the metal loss resulting from burning is minimized, the contents of the contaminants within the metallic smelt is reduced and, in addition, an effective environmental protection can be accomplished. This is attained by the provision of an axially movable shaft arranged vertically or tilted in the opening of the furnace and having on the charging side a charging funnel with an exhaust ring nozzle. The shaft is guided in a guiding bushing provided with sliding strips, which is welded to the outer wall of the furnace. For the supply of the combustion air as well as for the production of the axial oscillations, the upper portion of the shaft and below the charging funnel, a compressed air piping and a mechanical shaker is arranged. The regulation of the charging height is performed by means of a mechanical sensor or a mirror system which is arranged in the shaft or outer of the charging apparatus.

  5. Melting of Transition Metals

    SciTech Connect

    Ross, M; Japel, S; Boehler, R

    2005-04-11

    We review the transition melting studies carried out at Mainz, and describe a recently developed model used to explain that the relatively low melting slopes are due to the partially filled d-bands, and the persistence of the pressure induced s-d transition. The basic tenets of the model have now been reconfirmed by new measurements for Cu and Ni. The measurements show that Cu which has a filled 3d-band, has a melt slope that is about 2.5 greater than its neighbor Ni. In the case of Mo, the apparent discrepancy of DAC melting measurements with shock melting can be explained by accounting for the change in melt slope due to the bcc-cp transition observed in the shock studies. The Fe melt curve is revisited. The possible relevance of the Jahn-Teller effect and recently observed transition metal melts with Icosahedral Short-Range Order (ISRO) is discussed.

  6. 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

  7. 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.

  8. 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).

  9. Application of a high-resolution x-ray fluorescence analyzer.

    SciTech Connect

    Adams, B. W.; Attenkofer, K.; Experimental Facilities Division

    2006-01-01

    We have developed a high resolution x-ray fluorescence analyzer based on the principle of active optics. It combines a resolution of ca. 5 eV with a tunability over several keV and a wide solid-angle coverage (ca. 2 by 5 degrees). To date, this analyzer has been used in near-edge spectroscopy of gallium in GaAs, and for the detection and chemical speciation of trace amounts platinum in soot from an diesel engine. The latter application illustrates the use of the analyzer to enhance the signal-to-background ratio in trace-element x-ray fluorescence analysis. The analyzer is shown schematically in Fig. 1. In it, a strip of silicon is bent by an axial force from two pushers at its ends, and eight correctors act from above to bring the shape of the bent crystal to approximate a logarithmic spiral. A more detailed description of the device, its underlying theory, and adjustment procedures may be found elsewhere. The sample consisted of soot collected from the exhaust of a diesel engine burning a fuel with a platinum-based additive that was tested for the purpose of facilitating clean combustion. The concentration of platinum in the soot was about 100 ppm, and the chemical speciation (oxidation state, dispersed or in the form of nanoparticles, etc.) was unknown. A small speck of this soot containing 10{sup 12} to 10{sup 13} atoms was placed into the x-ray beam of the 11-ID-D station of the APS. The incident photon energy was scanned over the Pt L{sub 3} edge, and the Pt L{sub {alpha}1} fluorescence was detected using two silicon drift detectors (Vortex), one directly and one with the analyzer. The purpose of the analyzer in this application was to enhance the energy resolution by a factor of about 50 (250 eV for the drift detector, 5 eV for the analyzer), and thus reduce the background of elastically or Compton-scattered photons, while keeping the fluorescent line. Whereas the detector with the analyzer recorded a clear signature of platinum in the form of an absorption

  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. 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.

  12. Estimation of melting points of organic compounds-II.

    PubMed

    Jain, Akash; Yalkowsky, Samuel H

    2006-12-01

    A model for calculation of melting points of organic compounds from structure is described. The model utilizes additive, constitutive and nonadditive, constitutive molecular properties to calculate the enthalpy of melting and the entropy of melting, respectively. Application of the model to over 2200 compounds, including a number of drugs with complex structures, gives an average absolute error of 30.1 degrees.

  13. 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.

  14. 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

  15. Adaptive large-scale clutter removal from imagery with application to high-resolution sonar imagery

    NASA Astrophysics Data System (ADS)

    Dobeck, Gerald J.

    2010-04-01

    The ability to reliably detect targets having signatures comprised of bright pixels (highlight) and dark pixels (shadow) is challenging when the background texture of the imagery also possesses bright and dark characteristics. This is especially difficult when the background contains large bright and dark areas that can mask target signatures. Detection and classification algorithms would benefit from an adaptive denoising algorithm that would remove or mitigate such background artifacts. This paper presents a Fourier-based denoising algorithm. The large support of the Fourier basis is used to capture and remove large-scale artifacts while leaving the smaller target-size features nearly unchanged. Datadriven soft thresholds allow the algorithm to automatically adapt to changing backgrounds. Preliminary investigations have demonstrated excellent performance. The algorithm is computationally fast and suitable for real-time application. The denoising algorithm is general in nature and can be applied to many types of high-resolution gray-scale imagery; e.g., side-looking sonar and SAR.

  16. Molecular Chemistry of Organic Aerosols Through the Application of High Resolution Mass Spectrometry

    SciTech Connect

    Nizkorodov, Serguei; Laskin, Julia; Laskin, Alexander

    2011-01-05

    Understanding of molecular composition and fundamental chemical transformations of organic aerosols (OA) during their formation and aging is both a major challenge and the area of greatest uncertainty in atmospheric research. Particularly little is known about fundamental relationship between the chemical composition and physicochemical properties of OA, their atmospheric history, evolution, and impact on the environment. Ambient soft-ionization methods combined with high-resolution mass spectrometry (HR-MS) analysis provide detailed information on the molecular content of OA that is pivotal for improved understanding of their complex composition, multi-phase aging chemistry, direct (light absorption and scattering) and indirect (aerosol-cloud interactions) effects on atmospheric radiation and climate, and health effects. The HR-MS methods can detect thousands of individual OA constituents at once, provide their elemental formulae from accurate mass measurements, and provide structural information based on tandem mass spectrometry. Integration with additional analytical tools, such as chromatography and UV/Vis absorption spectroscopy, makes it possible to further separate OA compounds by their polarity and ability to absorb solar radiation. The goal of this perspective is to describe modern HR-MS methods, review recent applications to field and laboratory studies of OA, and explain how the information obtained from HR-MS methods can be translated into improved understanding of OA chemistry.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. Terrestrial Analogues for Lunar Impact Melt Flows

    NASA Technical Reports Server (NTRS)

    Neish, C. D.; Hamilton, C. W.; Hughes, S. S.; Nawotniak, S. Kobs; Garry, W. B.; Skok, J. R.; Elphic, R. C.; Schaefer, E.; Carter, L. M.; Bandfield, J. L.; Osinski, G. R.; Lim, D.; Heldmann, J. L.

    2016-01-01

    Lunar impact melt deposits have unique physical properties. They have among the highest observed radar returns at S-Band (12.6 cm wavelength), implying that they are rough at the decimeter scale. However, they are also observed in high-resolution optical imagery to be quite smooth at the meter scale. These characteristics distinguish them from well-studied terrestrial analogues, such as Hawaiian pahoehoe and ?a ?a lava flows. The morphology of impact melt deposits can be related to their emplacement conditions, so understanding the origin of these unique surface properties will help to inform us as to the circumstances under which they were formed. In this work, we seek to find a terrestrial analogue for well-preserved lunar impact melt flows by examining fresh lava flows on Earth. We compare the radar return and high-resolution topographic variations of impact melt flows to terrestrial lava flows with a range of surface textures. The lava flows examined in this work range from smooth Hawaiian pahoehoe to transitional basaltic flows at Craters of the Moon (COTM) National Monument and Preserve in Idaho to rubbly and spiny pahoehoe-like flows at the recent eruption at Holuhraun in Iceland. The physical properties of lunar impact melt flows appear to differ from those of all the terrestrial lava flows studied in this work. This may be due to (a) differences in post-emplacement modification processes or (b) fundamental differences in the surface texture of the melt flows due to the melts' unique emplacement and/or cooling environment. Information about the surface properties of lunar impact melt deposits will be critical for future landed missions that wish to sample these materials.

  10. 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.

  11. 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.

  12. Application of melt extrusion in the development of a physically and chemically stable high-energy amorphous solid dispersion of a poorly water-soluble drug.

    PubMed

    Lakshman, Jay P; Cao, Yu; Kowalski, James; Serajuddin, Abu T M

    2008-01-01

    Formulation of active pharmaceutical ingredients (API) in high-energy amorphous forms is a common strategy to enhance solubility, dissolution rate and, consequently, oral bioavailability of poorly water-soluble drugs. Amorphous APIs are, however, susceptible to recrystallization and, therefore, there is a need to physically stabilize them as solid dispersions in polymeric carriers. Hot melt extrusion has in recent years gained wide acceptance as a method of choice for the preparation of solid dispersions. There is a potential that the API, the polymer or both may degrade if excessively high temperature is needed in the melt extrusion process, especially when the melting point of the API is high. This report details a novel method where the API was first converted to an amorphous form by solvent evaporation and then melt-extruded with a suitable polymer at a drug load of at least 20% w/w. By this means, melt extrusion could be performed much below the melting temperature of the drug substance. Since the glass transition temperature of the amorphous drug was lower than that of the polymer used, the drug substance itself served as the plasticizer for the polymer. The addition of surfactants in the matrix enhanced dispersion and subsequent dissolution of the drug in aqueous media. The amorphous melt extrusion formulations showed higher bioavailability than formulations containing the crystalline API. There was no conversion of amorphous solid to its crystalline form during accelerated stability testing of dosage forms.

  13. Heterozygote PCR product melting curve prediction.

    PubMed

    Dwight, Zachary L; Palais, Robert; Kent, Jana; Wittwer, Carl T

    2014-03-01

    Melting curve prediction of PCR products is limited to perfectly complementary strands. Multiple domains are calculated by recursive nearest neighbor thermodynamics. However, the melting curve of an amplicon containing a heterozygous single-nucleotide variant (SNV) after PCR is the composite of four duplexes: two matched homoduplexes and two mismatched heteroduplexes. To better predict the shape of composite heterozygote melting curves, 52 experimental curves were compared with brute force in silico predictions varying two parameters simultaneously: the relative contribution of heteroduplex products and an ionic scaling factor for mismatched tetrads. Heteroduplex products contributed 25.7 ± 6.7% to the composite melting curve, varying from 23%-28% for different SNV classes. The effect of ions on mismatch tetrads scaled to 76%-96% of normal (depending on SNV class) and averaged 88 ± 16.4%. Based on uMelt (www.dna.utah.edu/umelt/umelt.html) with an expanded nearest neighbor thermodynamic set that includes mismatched base pairs, uMelt HETS calculates helicity as a function of temperature for homoduplex and heteroduplex products, as well as the composite curve expected from heterozygotes. It is an interactive Web tool for efficient genotyping design, heterozygote melting curve prediction, and quality control of melting curve experiments. The application was developed in Actionscript and can be found online at http://www.dna.utah.edu/hets/.

  14. Stability of foams in silicate melts

    NASA Astrophysics Data System (ADS)

    Proussevitch, Alexander A.; Sahagian, Dork L.; Kutolin, Vladislav A.

    1993-12-01

    Bubble coalescence and the spontaneous disruption of high-porosity foams in silicate melts are the result of physical expulsion of interpore melt (syneresis) leading to bubble coalescence, and diffusive gas exchange between bubbles. Melt expulsion can be achieved either along films between pairs of bubbles, or along Plateau borders which represent the contacts between 3 or more bubbles. Theoretical evaluation of these mechanisms is confirmed by experimental results, enabling us to quantify the relevant parameters and determine stable bubble size and critical film thickness in a foam as a function of melt viscosity, surface tension, and time. Foam stability is controlled primarily by melt viscosity and time. Melt transport leading to coalescence of bubbles proceeds along inter-bubble films for smaller bubbles, and along Plateau borders for larger bubbles. Thus the average bubble size accelerates with time. In silicate melts, the diffusive gas expulsion out of a region of foam is effective only for water (and even then, only at small length scales), as the diffusion of CO 2 is negligible. The results of our analyses are applicable to studies of vesicularity of lavas, melt degassing, and eruption mechanisms.

  15. Application of model output statistics to the GEM-AQ high resolution air quality forecast

    NASA Astrophysics Data System (ADS)

    Struzewska, J.; Kaminski, J. W.; Jefimow, M.

    2016-11-01

    The aim of the presented work was to analyse the impact of data stratification on the efficiency of the Model Output Statistics (MOS) methodology as applied to a high-resolution deterministic air quality forecast carried out with the GEM-AQ model. The following parameters forecasted by the GEM-AQ model were selected as predictors for the MOS equation: pollutant concentration, air temperature in the lowest model layer, wind speed in the lowest model layer, temperature inversion and the precipitation rate. A representative 2-year series were used to construct regression functions. Data series were divided into two subsets. Approximately 75% of the data (first 3 weeks of each month) were used to estimate the regression function parameters. Remaining 25% (last week of each month) were used to test the method (control period). The subsequent 12 months were used for method verification (verification period). A linear model fitted the function based on forecasted parameters to the observations. We have assumed four different temperature-based data stratification methods (for each method, separate equations were constructed). For PM10 and PM2.5, SO2 and NO2 the best correction results were obtained with the application of temperature thresholds in the cold season and seasonal distribution combined with temperature thresholds in the warm season. For the PM10, PM2.5 and SO2 the best results were obtained using a combination of two stratification methods separately for cold and warm seasons. For CO, the systematic bias of the forecasted concentrations was partly corrected. For ozone more sophisticated methods of data stratification did not bring a significant improvement.

  16. 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.

  17. Analyzing Protein Clusters on the Plasma Membrane: Application of Spatial Statistical Analysis Methods on Super-Resolution Microscopy Images.

    PubMed

    Paparelli, Laura; Corthout, Nikky; Pavie, Benjamin; Annaert, Wim; Munck, Sebastian

    2016-01-01

    The spatial distribution of proteins within the cell affects their capability to interact with other molecules and directly influences cellular processes and signaling. At the plasma membrane, multiple factors drive protein compartmentalization into specialized functional domains, leading to the formation of clusters in which intermolecule interactions are facilitated. Therefore, quantifying protein distributions is a necessity for understanding their regulation and function. The recent advent of super-resolution microscopy has opened up the possibility of imaging protein distributions at the nanometer scale. In parallel, new spatial analysis methods have been developed to quantify distribution patterns in super-resolution images. In this chapter, we provide an overview of super-resolution microscopy and summarize the factors influencing protein arrangements on the plasma membrane. Finally, we highlight methods for analyzing clusterization of plasma membrane proteins, including examples of their applications. PMID:27207364

  18. Analyzing Protein Clusters on the Plasma Membrane: Application of Spatial Statistical Analysis Methods on Super-Resolution Microscopy Images.

    PubMed

    Paparelli, Laura; Corthout, Nikky; Pavie, Benjamin; Annaert, Wim; Munck, Sebastian

    2016-01-01

    The spatial distribution of proteins within the cell affects their capability to interact with other molecules and directly influences cellular processes and signaling. At the plasma membrane, multiple factors drive protein compartmentalization into specialized functional domains, leading to the formation of clusters in which intermolecule interactions are facilitated. Therefore, quantifying protein distributions is a necessity for understanding their regulation and function. The recent advent of super-resolution microscopy has opened up the possibility of imaging protein distributions at the nanometer scale. In parallel, new spatial analysis methods have been developed to quantify distribution patterns in super-resolution images. In this chapter, we provide an overview of super-resolution microscopy and summarize the factors influencing protein arrangements on the plasma membrane. Finally, we highlight methods for analyzing clusterization of plasma membrane proteins, including examples of their applications.

  19. 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.

  20. The pulsed all fiber laser application in the high-resolution 3D imaging LIDAR system

    NASA Astrophysics Data System (ADS)

    Gao, Cunxiao; Zhu, Shaolan; Niu, Linquan; Feng, Li; He, Haodong; Cao, Zongying

    2014-05-01

    An all fiber laser with master-oscillator-power-amplifier (MOPA) configuration at 1064nm/1550nm for the high-resolution three-dimensional (3D) imaging light detection and ranging (LIDAR) system was reported. The pulsewidth and the repetition frequency could be arbitrarily tuned 1ns~10ns and 10KHz~1MHz, and the peak power exceeded 100kW could be obtained with the laser. Using this all fiber laser in the high-resolution 3D imaging LIDAR system, the image resolution of 1024x1024 and the distance precision of +/-1.5 cm was obtained at the imaging distance of 1km.

  1. 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.

  2. 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.

  3. Melt inclusions: Chapter 6

    USGS Publications Warehouse

    ,; 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.

  4. 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.

  5. [Study on the configuration and applications of high spectral resolution Raman spectrometer].

    PubMed

    Liu, Zhao-Jun; Zhao, Cun-Hua; Han, Li-Gang; Mo, Yu-Jun

    2010-02-01

    In the present paper the authors studied theoretically and experimentally the relationship between spectral resolution and grating density, the limitations to improve the spectral resolution by using high density grating, the use of longer focal length grating to increase spectral resolution without compromising instrument throughput and the effect of slit width on spectral resolution and sensitivity. Finally, two experiment results were provided to show why higher spectral resolution is important to ensure that critical information is not lost during a Raman measurement. Stressed silicon was produced by growing a thin crystalline layer of Si on an Si(x)Ge(1-x) substrate. It is possible to use Raman spectroscopy to probe the stress in the Si(x)Ge(1-x) and Si layers at the same time. The parameter to monitor the stress is the position of the Si-Si vibrational mode in Si(x)Ge(1-x) and Si. Such a measurement requires high spectral resolution because the peaks exhibit very subtle shifts. The authors' results clearly demonstrate that the resolution offered by a high density grating is necessary to properly monitor the very small frequency shift of this cap-layer Si-Si mode in order to properly characterize the strain structure. The Raman band around 180 cm(-1) is assigned to the radial breath mode of single wall carbon nanotube (SWCN). By measuring the frequencies excited with different laser, the diameters of the sample can be obtained. Practically, sample is always composed of SWCN with different but very close diameters and their Raman bands might overlap together and are difficult to determine the frequencies. The authors' results showed that only higher resolution with the long focal length spectrometer can give accurate number and frequencies of Raman bands, which leads to a correct analysis of the diameter distribution.

  6. Significant melting point depression of two-dimensional folded-chain crystals of isotactic poly(methyl methacrylate)s observed by high-resolution in situ atomic force microscopy.

    PubMed

    Takanashi, Yuma; Kumaki, Jiro

    2013-05-01

    The properties of polymer ultrathin films are a subject of intense study from both practical and academic viewpoints. Previously, we found that upon compression, an isotactic poly(methyl methacrylate) (it-PMMA) Langmuir monolayer crystallized to form a two-dimensional (2D) folded-chain crystal, and the molecular image of the crystal with chain folding and tie chains was clearly visualized by atomic force microscopy (AFM). In the present study, the melting behaviors of the it-PMMA 2D crystals were successfully observed in situ by high-temperature AFM at the molecular lever for the first time. The chain-chain distances (~1.2 nm) of the crystals were clearly resolved even at temperatures close to the melting temperatures (Tm) of the 2D crystals. We found that the Tm of the 2D crystals was at most 90 °C lower than the bulk crystals. The Tm depression strongly depended on the molecular weight, while the molecular weight dependence of the bulk Tm was negligible in the molecular weight regime studied. The Tm depression also depended on the substrates, a slightly larger depression being observed on a sapphire substrate compared to that on a mica. The large Tm depressions of the 2D crystals could not be explained by a simple Thomson-Gibbs argument, theoretical developments are necessary to understand the melting of the 2D crystals.

  7. 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.

  8. 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.

  9. Determination of melt influence on divalent element partitioning between anorthite and CMAS melts

    NASA Astrophysics Data System (ADS)

    Miller, Sarah A.; Asimow, P. D.; Burnett, D. S.

    2006-08-01

    We propose a theory for crystal-melt trace element partitioning that considers the energetic consequences of crystal-lattice strain, of multi-component major-element silicate liquid mixing, and of trace-element activity coefficients in melts. We demonstrate application of the theory using newly determined partition coefficients for Ca, Mg, Sr, and Ba between pure anorthite and seven CMAS liquid compositions at 1330 °C and 1 atm. By selecting a range of melt compositions in equilibrium with a common crystal composition at equal liquidus temperature and pressure, we have isolated the contribution of melt composition to divalent trace element partitioning in this simple system. The partitioning data are fit to Onuma curves with parameterizations that can be thermodynamically rationalized in terms of the melt major element activity product (aO)(a)2 and lattice strain theory modeling. Residuals between observed partition coefficients and the lattice strain plus major oxide melt activity model are then attributed to non-ideality of trace constituents in the liquids. The activity coefficients of the trace species in the melt are found to vary systematically with composition. Accounting for the major and trace element thermodynamics in the melt allows a good fit in which the parameters of the crystal-lattice strain model are independent of melt composition.

  10. Experimental evidence for melt partitioning between olivine and orthopyroxene in partially molten harzburgite

    NASA Astrophysics Data System (ADS)

    Miller, Kevin J.; Zhu, Wen-lu; Montési, Laurent G. J.; Gaetani, Glenn A.; Le Roux, Véronique; Xiao, Xianghui

    2016-08-01

    Observations of dunite channels in ophiolites and uranium series disequilibria in mid-ocean ridge basalt suggest that melt transport in the upper mantle beneath mid-ocean ridges is strongly channelized. We present experimental evidence that spatial variations in mineralogy can also focus melt on the grain scale. This lithologic melt partitioning, which results from differences in the interfacial energies associated with olivine-melt and orthopyroxene-melt boundaries, may complement other melt focusing mechanisms in the upper mantle such as mechanical shear and pyroxene dissolution. We document here lithologic melt partitioning in olivine-/orthopyroxene-basaltic melt samples containing nominal olivine to orthopyroxene ratio of 3 to 2 and melt fractions of 0.02 to 0.20. Experimental samples were imaged using synchrotron-based X-ray microcomputed tomography at a resolution of 700 nm per voxel. By analyzing the local melt fraction distributions associated with olivine and orthopyroxene grains in each sample, we found that the melt partitioning coefficient, i.e., the ratio of melt fraction around olivine to that around orthopyroxene grains, varies between 1.1 and 1.6. The permeability and electrical conductivity of our digital samples were estimated using numerical models and compared to those of samples containing only olivine and basaltic melt. Our results suggest that lithologic melt partitioning and preferential localization of melt around olivine grains might play a role in melt focusing, potentially enhancing average melt ascent velocities.

  11. 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.

  12. Determining Mechanics of Segregating Small Crystals from Melt Using Modeling and SHRIMP-RG Trace Element Analysis of Zircons: Application to the Spirit Mountain Batholith, Nevada

    NASA Astrophysics Data System (ADS)

    Claiborne, L. L.; Furbish, D. J.; Miller, C. F.

    2006-12-01

    Melt segregation from crystal mush is commonly cited as generating the highly differentiated melts that form leucogranites and high-silica rhyolites (i.e. Bachmann and Bergantz, 2004). The Spirit Mountain batholith in southern Nevada appears to be a prime example of an intrusion that records this process. It is composed primarily of a thick (more than 7 km) sequence of cumulate granite overlain by 2 km of high-silica leucogranite, interpreted to have been extracted from the cumulate below (Walker et al., in press). Using SHRIMP geochronology, Ti-in-zircon thermometry (Watson et al., 2006), and trace element analysis of the strongly zoned zircons, we have suggested that the batholith accumulated and evolved through repeated episodes of recharge, reheating, and fractionation via melt expulsion from mush (Walker et al., in press; Lowery Claiborne et al., in press). In the leucogranites, interiors of zircons commonly are similar to much of the zircon in cumulate granites, exhibiting the trace element signature of hotter, less fractionated melt; rims of leucogranite zircons generally reflect low T and fractionated melt compositions, consistent with the highly felsic melt represented by their host rocks. These interiors likely represent zircon crystals that were entrained in the upward moving differentiated melt during segregation from the crystal mush. However, the low bulk rock Zr and Zr/Hf of the leucogranite and the high whole rock Zr concentration of the cumulate indicate that most zircon was retained in the cumulate (Lowery Claiborne et al., in press). So, what determines whether zircon (and other small) crystals are entrained in the upward migrating differentiated melt, or whether they are captured in the cumulate mush and segregated from the high-silica melt? What can this tell us about the mechanics of cumulate-melt segregation? Following Bachmann and Bergantz (2004), we have modeled the critical size of crystals and the critical size to mush porosity ratio

  13. 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.

  14. 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.

  15. 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.

  16. A versatile medium-resolution x-ray emission spectrometer for diamond anvil cell applications.

    PubMed

    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

    2013-08-01

    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.

  17. 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.

  18. 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

  19. 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

  20. Multiple imaging axis microscopy improves resolution for thick-sample applications

    NASA Astrophysics Data System (ADS)

    Swoger, Jim; Huisken, Jan; Stelzer, Ernst H. K.

    2003-09-01

    The multiple imaging axis microscope (MIAM) is a wide-field optical microscope that observes a sample simultaneously from multiple directions without requiring the sample to be rotated or tilted. The prototype is capable of high-resolution imaging of the interior of a 300-μm-diameter sample consisting of fluorescent microbeads suspended in an agarose gel. Compared with a single-axis system, the MIAM can achieve a reduction of the axial point-spread function elongation by a factor of 5.8 and a 3.5-fold improvement in volume resolution by simple linear image combination techniques.

  1. 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.

  2. 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.

  3. Spectral characteristics of lunar impact melts - Implications for remote sensing

    NASA Astrophysics Data System (ADS)

    Tompkins, S.; Pieters, C. M.; Ryder, G.

    1997-03-01

    Remote geochemical mapping of lunar impact melt associated with complex craters may provide a key to a better understanding of impact melt formation and the impact cratering process. Ground-based NIR spectra and Clementine multispectral images provide high-resolution spectral and spatial information, respectively, about lunar impact melts. As part of an effort towards improving our ability to interpret these data, two suites of lunar samples have been measured in NASA's Reflectance Experiment Laboratory (RELAB) at Brown University. The samples include seven Apollo 17 crystalline impact melts as well as synthesized glass equivalents and 15 naturally occurring impact melts from four landing sites. The naturally occurring melts have a range of textures and compositions related to glass abundance.

  4. 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.

  5. Application of high-resolution, remotely sensed data for transient storage modeling parameter estimation

    NASA Astrophysics Data System (ADS)

    Bingham, Q. G.; Neilson, B. T.; Neale, C. M. U.; Cardenas, M. B.

    2012-08-01

    This paper presents a method that uses high-resolution multispectral and thermal infrared imagery from airborne remote sensing for estimating two model parameters within the two-zone in-stream temperature and solute (TZTS) model. Previous TZTS modeling efforts have provided accurate in-stream temperature predictions; however, model parameter ranges resulting from the multiobjective calibrations were quite large. In addition to the data types previously required to populate and calibrate the TZTS model, high-resolution, remotely sensed thermal infrared (TIR) and near-infrared, red, and green (multispectral) band imagery were collected to help estimate two previously calibrated parameters: (1) average total channel width (BTOT) and (2) the fraction of the channel comprising surface transient storage zones (β). Multispectral imagery in combination with the TIR imagery provided high-resolution estimates ofBTOT. In-stream temperature distributions provided by the TIR imagery enabled the calculation of temperature thresholds at which main channel temperatures could be delineated from surface transient storage, permitting the estimation ofβ. It was found that an increase in the resolution and frequency at which BTOT and β were physically estimated resulted in similar objective functions in the main channel and transient storage zones, but the uncertainty associated with the estimated parameters decreased.

  6. 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...

  7. 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.

  8. 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...

  9. 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

  10. 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

  11. 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

  12. 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.

  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. Fe-15Ni-13Cr austenitic stainless steels for fission and fusion reactor applications - Part 1: Effects of minor alloying elements on precipitate phases in melt products and implication in alloy fabrication

    NASA Astrophysics Data System (ADS)

    Lee, E. H.; Mansur, L. K.

    2000-01-01

    In an effort to develop alloys for fission and fusion reactor applications, 28Fe-15Ni-13Cr base alloys were fabricated by adding various combinations of the minor alloying elements, Mo, Ti, C, Si, P, Nb, and B. The results showed that a significant fraction of undesirable residual oxygen was removed as oxides when Ti, C, and Si were added. Accordingly, the concentrations of the latter three essential alloying elements were reduced also. Among these elements, Ti was the strongest oxide former, but the largest oxygen removal (over 80%) was observed when carbon was added alone without Ti, since gaseous CO boiled off during melting. This paper recommends an alloy melting procedure to mitigate solute losses while reducing the undesirable residual oxygen. In this work, 14 different types of precipitate phases were identified. Compositions of precipitate phases and their crystallographic data are documented. Finally, stability of precipitate phases was examined in view of Gibbs free energy of formation.

  15. 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

  16. 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.

  17. Current processes for the cold-wall melting of Titanium

    NASA Astrophysics Data System (ADS)

    Sears, James W.

    1990-03-01

    Conventional vacuum arc consumable electrode melting continues to play a large role in the production of titanium alloy ingots. Titanium melting will be performed by electron-beam and plasma cold-hearth melting in some applications, for the production of titanium rotor-grade ingots. The current reports indicate that hard-alpha defects and high-density inclusions can be eliminated through hearth melting. Automatic controls for electron-beam melting and plasma-arc melting will play an important part in their development for producing high quality titanium ingots. Processes such as cold-wall induction may be integrated into atomization, spray deposition and casting systems. Other combinations of melting techniques can be used for new titanium products in the future.

  18. 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.

  19. 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.

  20. 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.

  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. The application of high spectral and spatial resolution imaging spectrometers for locating downed aircraft

    NASA Technical Reports Server (NTRS)

    Gatlin, James A.; Middleton, Elizabeth M.; Irons, James R.; Robinson, Jon W.

    1991-01-01

    The utility of high-resolution imaging spectrometer data is examined as an aid in locating downed aircraft by using a unique spectral signature while not requiring the extremely high spatial resolution needed to identify an aircraft by shape. Ground spectral measurements of several airplane wings, overflight spectral measurements of aircraft scenes, and the rationale for the chosen spectral signature are presented. It is concluded that imaging spectrometers which can detect and spatially locate a narrow-band spectral signature filling only a few pixels appear to have a utility for search and rescue aircraft or satellite systems as a aid in locating small downed aircraft. This spectral feature would have to be added to the surface coatings applied to aircraft. Proposed for use as such a spectral signature is a significant negative reflectance slope, in the 520 to 580 nm interval.

  3. Neural network application for thermal image recognition of low-resolution objects

    NASA Astrophysics Data System (ADS)

    Fang, Yi-Chin; Wu, Bo-Wen

    2007-02-01

    In the ever-changing situation on a battle field, accurate recognition of a distant object is critical to a commander's decision-making and the general public's safety. Efficiently distinguishing between an enemy's armoured vehicles and ordinary civilian houses under all weather conditions has become an important research topic. This study presents a system for recognizing an armoured vehicle by distinguishing marks and contours. The characteristics of 12 different shapes and 12 characters are used to explore thermal image recognition under the circumstance of long distance and low resolution. Although the recognition capability of human eyes is superior to that of artificial intelligence under normal conditions, it tends to deteriorate substantially under long-distance and low-resolution scenarios. This study presents an effective method for choosing features and processing images. The artificial neural network technique is applied to further improve the probability of accurate recognition well beyond the limit of the recognition capability of human eyes.

  4. 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.

  5. The Palladium-Catalyzed Aerobic Kinetic Resolution of Secondary Alcohols: Reaction Development, Scope, and Applications

    PubMed Central

    Ebner, David C.; Bagdanoff, Jeffrey T.; Ferreira, Eric M.; McFadden, Ryan M.; Caspi, Daniel D.; Trend, Raissa M.

    2010-01-01

    The first palladium-catalyzed enantioselective oxidation of secondary alcohols has been developed, utilizing the readily available diamine (−)-sparteine as chiral ligand and molecular oxygen as the stoichiometric oxidant. Mechanistic insights regarding the role of base and hydrogen bond donors have resulted in several improvements to the original system. Namely, addition of cesium carbonate and tert-butyl alcohol greatly enhances reaction rates, promoting rapid resolutions. The use of chloroform as solvent allows the use of ambient air as the terminal oxidant at 23 °C, resulting in enhanced catalyst selectivity. These improved reaction conditions have permitted the successful kinetic resolution of benzylic, allylic, and cyclopropyl secondary alcohols to high enantiomeric excess with good to excellent selectivity factors. This catalyst system has also been applied to the desymmetrization of meso-diols, providing high yields of enantioenriched hydroxyketones. PMID:19904777

  6. 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.

  7. [Application of high resolution remote sensing technology in research of schistosomiasis surveillance].

    PubMed

    Xue, Jing-bo; Zhang, Li-juan; Wang, Qiang; Lu, Yan-xin; Li, Shi-zhu

    2015-10-01

    Schistosomiasis is closely related to environmental factors, the changes of environmental factors, such as vegetation, temperature, hydrology and soil, could impact the transmission of the disease. The environmental factors associated with schistosomiasis could be extracted by remote sensing technology quickly and precisely, and be applied to monitor the schistosomiasis transmission. The studies on high resolution remote sensing technology applied in the research of schistosomiasis are reviewed in this paper.

  8. 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.

  9. Ultra-high resolution mass separator--application to detection of nuclear weapons tests.

    PubMed

    Peräjärvi, K; Eronen, T; Elomaa, V-V; Hakala, J; Jokinen, A; Kettunen, H; Kolhinen, V S; Laitinen, M; Moore, I D; Penttilä, H; Rissanen, J; Saastamoinen, A; Toivonen, H; Turunen, J; Aystö, J

    2010-03-01

    A Penning trap-based purification process having a resolution of about 1 ppm is reported. In this context, we present for the first time a production method for the most complicated and crucially important nuclear weapons test signature, (133m)Xe. These pure xenon samples are required by the Comprehensive Nuclear-Test-Ban Treaty Organization to standardize and calibrate the worldwide network of xenon detectors.

  10. Application of an ultrahigh-resolution scanning electron microscope (UHS-T1) to biological specimens.

    PubMed

    Tanaka, K; Mitsushima, A; Kashima, Y; Nakadera, T; Osatake, H

    1989-06-01

    In 1985 we developed an ultrahigh-resolution scanning electron microscope with a resolution of 0.5 nm. It is equipped with a field emission gun and an objective lens with a very short focal length. In this study we report a survey of some different preparation techniques and biological specimens using the new scanning electron microscope. Intracellular structures such as cell organelles were observed surprisingly sharper than those observed by ordinary scanning electron microscopes. However, at magnifications over 250,000 x, platinum particles could be discerned as scattered pebbles on the surface of all structures in coated materials. Using an uncoated but conductively stained specimen, we successfully observed ribosomes on a rough endoplasmic reticulum at a direct magnification of 1 million. In these images some protrusions were recognized on the ribosomes. Ferritin and immunoglobulin G were used as samples of biological macromolecules. These samples were observed without metal coating and conductive staining. The ferritin particles appeared as rounded bodies without any substructure on the surface and immunoglobulin G as complexes of three-unit bodies. In the latter the central body might correspond to the Fc fragment and two side ones to Fab fragments. We assume that ultrahigh-resolution scanning electron microscopy is an effective means for observation of the cell fine structures and biological macromolecules. It will open a new research field in biomedicine.

  11. 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.

  12. A compact high resolution flat panel PET detector based on the new 4-side buttable MPPC for biomedical applications

    PubMed Central

    Wang, Qiang; Wen, Jie; Ravindranath, Bosky; O’Sullivan, Andrew W.; Catherall, David; Li, Ke; Wei, Shouyi; Komarov, Sergey; Tai, Yuan-Chuan

    2015-01-01

    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 Ge-68 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. PMID:26085702

  13. 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.

  14. DETERMINATION OF HLW GLASS MELT RATE USING X-RAY COMPUTED TOMOGRAPHY

    SciTech Connect

    Choi, A.; Miller, D.; Immel, D.

    2011-10-06

    significant amount of glassy material interspersed among the gas bubbles will be excluded, thus underestimating the melt rate. Likewise, if they are drawn too high, many large voids will be counted as glass, thus overestimating the melt rate. As will be shown later in this report, there is also no guarantee that a given distribution of glass and gas bubbles along a particular sectioned plane will always be representative of the entire sample volume. Poor reproducibility seen in some LMR data may be related to these difficulties of the visual method. In addition, further improvement of the existing melt rate model requires that the overall impact of feed chemistry on melt rate be reflected on measured data at a greater quantitative resolution on a more consistent basis than the visual method can provide. An alternate method being pursued is X-ray computed tomography (CT). It involves X-ray scanning of glass samples, performing CT on the 2-D X-ray images to build 3-D volumetric data, and adaptive segmentation analysis of CT results to not only identify but quantify the distinct regions within each sample based on material density and morphologies. The main advantage of this new method is that it can determine the relative local density of the material remaining in the beaker after the heat treatment regardless of its morphological conditions by selectively excluding all the voids greater than a given volumetric pixel (voxel) size, thus eliminating much of the subjectivity involved in the visual method. As a result, the melt rate data obtained from CT scan will give quantitative descriptions not only on the fully-melted glass, but partially-melted and unmelted feed materials. Therefore, the CT data are presumed to be more reflective of the actual melt rate trends in continuously-fed melters than the visual data. In order to test the applicability of X-ray CT scan to the HLW glass melt rate study, several new series of HLW simulant/frit mixtures were melted in the Melt Rate

  15. 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.

  16. 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.

  17. 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.

  18. Exploration application of high resolution aeromagnetic surveys in the Gulf of Mexico, USA

    SciTech Connect

    Berger, Z.; Reudavey, G.

    1996-08-01

    High resolution magnetic surveys provide an excellent tool for mapping geological structures in a wide range of tectonic settings and geographical areas. The improved mapping capabilities of these surveys are achieved by: (1) Advanced high resolution data acquisition techniques including lower altitudes, tighter line spacing, and broad-band frequency retention, and (2) advanced data processing and display techniques such as depth slicing, micro-leveling and image processing. Newly acquired high resolution aeromagnetic surveys of Cameron and Vermilion areas have been recently interpreted. The results of this study can be summarized as follows: (1) The magnetic images of high frequency domain can be used to map near surface salt fastuws and growth faults. These images can also be used to define the shape of the salt diapers and assess their interaction with different fault systems. (2) Interpretation and modeling of different depth-slice images can be used to determine the thickness of different salt bodies and establish their progressive changes with depth. This technique can also be used to outline potential sedimentary basins at different depths. (3) Magnetic images of mid to low frequency domains can be used to establish the structural fabric of sub-salt terrain. The result of this study is presented with a series of posters that illustrate the inventory of salt and fault features identified on different magnetic images and their correlation with subsurface structures which are recognized with well and seismic data. Magnetic profiles and models are also being used to illustrate how the magnetic data was calibrate to the recorded travel-time of seismic data and related isochron and time structure maps.

  19. Quantitative analysis with the CAMECA SXFIVE FE at high lateral resolution. Applications to Geochronology and Mineralogy.

    NASA Astrophysics Data System (ADS)

    Ehrke, Hans-Ulrich; Hombourger, Chrystel; Outrequin, Michel

    2013-04-01

    The development of the Schottky emitter and its implementation as electron source in Electron Microprobe has significantly improved the characterization of materials in earth sciences and in metallurgy. The strength of an Electron Probe Microanalysis (EPMA) is the ability to accurately measure and quantify element in traces at few 10's ppm level. The Field Emission (FE) Source allows trace element analysis with high beam currents thanks to the high brightness of the source and the excellent stability of the beam current, trading off spatial resolution. Of course, accuracy of major element quantification is maintained with a FE source. As X-rays are generated from a much larger diameter than the diameter of the incident electron beam, it is advised to work at low voltage and low beam current in order to take full advantage of the small spot sizes achievable with a Field Emission Source. Thus, the analytical resolution is not limited anymore by the beam diameter but only by the diameter of the X-ray emission volume. One of the advantages of the FE Source is to obtain fine focused electron beam at low beam voltage (≤10 keV) while maintaining high and stable beam current. In these experimental conditions, the penetration depth of the primary electrons and thus the interaction volume- in which electrons are scattered and generate X-rays- decreases to sub-µm scale (compared to micron scale of the traditional Electron Microprobe at 15 or 20 keV). Thanks to WDS spectrometers with sub 10eV energy resolution, accurate quantitative analysis can be achieved even on sub micron phases at low beam energy and high lateral resolution using L- and M-Lines for heavy elements. This will be illustrated, in a first example, by measuring different areas in a Monazite grain. U, Pb and Th are quantitatively analyzed with high precision in order to characterize age domains. In a second example, quantification of small refractory phases (hibonite, grossite, perovskite, …) formed by gas

  20. 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.

  1. 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.

  2. 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

  3. Metric-Resolution 2D River Modeling at the Macroscale: Computational Methods and Applications i