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Sample records for melting curve analysis

  1. High-Resolution Melt Curve Analysis in Cancer Mutation Screen.

    PubMed

    Mehrotra, Meenakshi; Patel, Keyur P

    2016-01-01

    High-resolution melt (HRM) curve analysis is a PCR-based assay that identifies sequence alterations based on subtle variations in the melting curves of mutated versus wild-type DNA sequences. HRM analysis is a high-throughput, sensitive, and efficient alternative to Sanger sequencing and is used to assess for mutations in clinically important genes involved in cancer diagnosis. The technique involves PCR amplification of a target sequence in the presence of a fluorescent double-stranded DNA (dsDNA) binding dye, melting of the fluorescent amplicons, and subsequent interpretation of melt curve profiles.

  2. Molecular identification of antelope horn by melting curve analysis.

    PubMed

    Tong, Yuru; Jiang, Chao; Yuan, Yuan; Jin, Yan; Cui, Zhan-Hu; Huang, Luqi

    2016-11-01

    Antelope horn is a valuable Chinese traditional medicine and widely used in clinic. However, with the deterioration of antelope's living environment and a lot of killing, the saiga population begins falling and in some places plummet. Since the increasing demand of this expensive and good bioactive medicine, the horn of artiodactyla animals is often used as the antelope horn. The adulterated or impostor not only cause damage to clinical medicine but also affect the antelope resources protection and sustainable development. Here, in order to establish a melting curve analysis (MCA) method to distinguish the antelope horn from other animal horns and identify the decoction pieces and Chinese patent medicine in a fast and easy way, animal horns and its decoction pieces, Chinese patent medicines were collected from the market and the DNA of all the collected samples were extracted. The melting curve of two universal fragments (COI and Cyt b) was scanned and Cyt b was selected as feasibility fragment for identifying authentic antelope horn from eight adulterant animal horns. After optimizing the condition for MCA, inspecting the precision and the replication of the method, a reference melting curve modern was established and we performed MCA on the antelope horns, fakes, and adulterants on a 1:1 mix, decoction pieces, and Chinese patent medicine. Thus, this study provides fast and easy methods so that MCA can detect the truth, fakes, and adulterations of antelope horns.

  3. Sex determination in beef by melting curve analysis of PCR amplicons from the amelogenin locus.

    PubMed

    Ballin, Nicolai Z; Madsen, Knud G

    2007-11-01

    Sex determination of beef is important to meet the rules of the Commission Regulation (EC) 765/2002 that qualify for export refunds. A SYBR Green sex identification assay based on melting curve analysis of PCR amplicons from the amelogenin locus (AMELX and AMELY) was developed. The PCR amplicons of 130/130 and 130/67 base pairs produced from female and male beef, respectively, are easily distinguished by both melting curve analysis and gel electrophoresis. Results from the melting curve analysis of amplicons are ready in less than three minutes, and requires no additional work in addition to the PCR setup. Applicability of the sex determination assay was studied by analysis of 12 unknown beef samples and the results were compared to an accredited method based on gel electrophoresis. In addition, six different cattle breeds were examined. All test results were correct in respect to sex.

  4. Evaluation of PCR and high resolution melt curve analysis for differentiation of Salmonella isolates.

    PubMed

    Saeidabadi, Mohammad Sadegh; Nili, Hassan; Dadras, Habibollah; Sharifiyazdi, Hassan; Connolly, Joanne; Valcanis, Mary; Raidal, Shane; Ghorashi, Seyed Ali

    2016-12-21

    Consumption of poultry products contaminated with Salmonella is one of the major causes of foodborne diseases worldwide and therefore detection and differentiation of Salmonella spp. in poultry is important. In this study, oligonucleotide primers were designed from hem-D gene and a PCR followed by high-resolution melt (HRM) curve analysis was developed for rapid differentiation of Salmonella isolates. Amplicons of 228 bp were generated from 16 different Salmonella reference strains and from 65 clinical field isolates mainly from poultry farms. High resolution melt (HRM) curve analysis of the amplicons differentiated Salmonella isolates and analysis of the nucleotide sequence of the amplicons from selected isolates revealed that each melting curve profile was related to a unique DNA sequence. The relationship between reference strains and tested specimens was also evaluated using a mathematical model without visual interpretation of HRM curves. In addition, the potential of the PCR-HRM curve analysis was evaluated for genotyping of additional Salmonella isolates from different avian species. The findings indicate that PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping of Salmonella isolates to determine the serovar/serotype.

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

    PubMed

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

    2015-05-01

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

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

    PubMed

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

    2014-11-01

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

  7. STR melting curve analysis as a genetic screening tool for crime scene samples.

    PubMed

    Nguyen, Quang; McKinney, Jason; Johnson, Donald J; Roberts, Katherine A; Hardy, Winters R

    2012-07-01

    In this proof-of-concept study, high-resolution melt curve (HRMC) analysis was investigated as a postquantification screening tool to discriminate human CSF1PO and THO1 genotypes amplified with mini-STR primers in the presence of SYBR Green or LCGreen Plus dyes. A total of 12 CSF1PO and 11 HUMTHO1 genotypes were analyzed on the LightScanner HR96 and LS-32 systems and were correctly differentiated based upon their respective melt profiles. Short STR amplicon melt curves were affected by repeat number, and single-source and mixed DNA samples were additionally differentiated by the formation of heteroduplexes. Melting curves were shown to be unique and reproducible from DNA quantities ranging from 20 to 0.4 ng and distinguished identical from nonidentical genotypes from DNA derived from different biological fluids and compromised samples. Thus, a method is described which can assess both the quantity and the possible probative value of samples without full genotyping.

  8. Methylation-Sensitive Melt Curve Analysis of the Reprimo Gene Methylation in Gastric Cancer

    PubMed Central

    Lai, Junzhong; Luo, Qianping; Ke, Huican; Chen, Qi

    2016-01-01

    Reprimo (RPRM) is a p53-induced tumor suppressor gene. Its aberrant DNA methylation is correlated with carcinogenesis and may be used as a surrogate marker for the early detection of gastric cancer. However, the detail information regarding its DNA methylation has not been revealed. Here, we investigated the RPRM gene methylation in gastric cancer tumor and plasma samples by methylation-sensitive melt curve analysis (MS-MCA) and bisulfite sequencing in depth. We developed a semi-quantitative method based on MS-MCA for detecting DNA methylation and unraveled the RPRM gene methylation pattern in gastric cancer. This study provides a solid foundation for the future application of detecting RPRM gene methylation in human plasma or serum samples to help diagnose gastric cancer or for prognosis evaluation. PMID:27992600

  9. Improved capacitive melting curve measurements

    NASA Astrophysics Data System (ADS)

    Sebedash, Alexander; Tuoriniemi, Juha; Pentti, Elias; Salmela, Anssi

    2009-02-01

    Sensitivity of the capacitive method for determining the melting pressure of helium can be enhanced by loading the empty side of the capacitor with helium at a pressure nearly equal to that desired to be measured and by using a relatively thin and flexible membrane in between. This way one can achieve a nanobar resolution at the level of 30 bar, which is two orders of magnitude better than that of the best gauges with vacuum reference. This extends the applicability of melting curve thermometry to lower temperatures and would allow detecting tiny anomalies in the melting pressure, which must be associated with any phenomena contributing to the entropy of the liquid or solid phases. We demonstrated this principle in measurements of the crystallization pressure of isotopic helium mixtures at millikelvin temperatures by using partly solid pure 4He as the reference substance providing the best possible universal reference pressure. The achieved sensitivity was good enough for melting curve thermometry on mixtures down to 100 μK. Similar system can be used on pure isotopes by virtue of a blocked capillary giving a stable reference condition with liquid slightly below the melting pressure in the reference volume. This was tested with pure 4He at temperatures 0.08-0.3 K. To avoid spurious heating effects, one must carefully choose and arrange any dielectric materials close to the active capacitor. We observed some 100 pW loading at moderate excitation voltages.

  10. High-throughput sex identification by melting curve analysis in blue-breasted quail and chicken.

    PubMed

    Chen, C-C; Liu, Y-S; Cheng, C-C; Wang, C-L; Liao, M-H; Tseng, C-N; Chang, H-W

    2012-06-01

    The objective was to develop a high-throughput method of identifying sex in both Coturnix chinensis and Gallus gallus, which would be useful for biomedical research and hatcheries. Because chromo-helicase-DNA binding protein (CHD)-based Griffiths P2/P8 primers do not produce polymerase chain reaction (PCR) products with distinguishable sex-specific curves in melting curve analysis (MCA), these primers are unsuitable for high throughput application in either species. Conserved regions were identified by basic local alignment search tool (BLAST) analyses of cloned CHD-Z and CHD-W genes of C. chinensis. Based on sequence alignment, a female-specific CHD-W primer (W-cot-F1) and a female/male (or CHD-W/CHD-Z)-common primer (ZW-cot-F1) were redesigned for use in combination with the Griffiths P2 primer for MCA-based PCR reaction. In C. chinensis and G. gallus, W-cot-F1/P2 and ZW-cot-F1/P2 had amplicon lengths of 315/318 and 114 base pairs and melting temperatures (Tm) of approximately 79.5 °C to 80 °C and approximately 78.5 °C to 79°C, respectively. Thus, MCA distinguished sex based on two distinct Tm peaks in females versus only one Tm peak in males. The MCA-based real-time PCR combined with the proposed primer redesign provided a high-throughput method of identifying sex in C. chinensis and G. gallus.

  11. High-throughput gender identification of penguin species using melting curve analysis.

    PubMed

    Tseng, Chao-Neng; Chang, Yung-Ting; Chiu, Hui-Tzu; Chou, Yii-Cheng; Huang, Hurng-Wern; Cheng, Chien-Chung; Liao, Ming-Hui; Chang, Hsueh-Wei

    2014-04-03

    Most species of penguins are sexual monomorphic and therefore it is difficult to visually identify their genders for monitoring population stability in terms of sex ratio analysis. In this study, we evaluated the suitability using melting curve analysis (MCA) for high-throughput gender identification of penguins. Preliminary test indicated that the Griffiths's P2/P8 primers were not suitable for MCA analysis. Based on sequence alignment of Chromo-Helicase-DNA binding protein (CHD)-W and CHD-Z genes from four species of penguins (Pygoscelis papua, Aptenodytes patagonicus, Spheniscus magellanicus, and Eudyptes chrysocome), we redesigned forward primers for the CHD-W/CHD-Z-common region (PGU-ZW2) and the CHD-W-specific region (PGU-W2) to be used in combination with the reverse Griffiths's P2 primer. When tested with P. papua samples, PCR using P2/PGU-ZW2 and P2/PGU-W2 primer sets generated two amplicons of 148- and 356-bp, respectively, which were easily resolved in 1.5% agarose gels. MCA analysis indicated the melting temperature (Tm) values for P2/PGU-ZW2 and P2/PGU-W2 amplicons of P. papua samples were 79.75°C-80.5°C and 81.0°C-81.5°C, respectively. Females displayed both ZW-common and W-specific Tm peaks, whereas male was positive only for ZW-common peak. Taken together, our redesigned primers coupled with MCA analysis allows precise high throughput gender identification for P. papua, and potentially for other penguin species such as A. patagonicus, S. magellanicus, and E. chrysocome as well.

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

    PubMed

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

    2011-01-01

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

  13. The Melting Point of Palladium Using Miniature Fixed Points of Different Ceramic Materials: Part II—Analysis of Melting Curves and Long-Term Investigation

    NASA Astrophysics Data System (ADS)

    Edler, F.; Huang, K.

    2016-12-01

    Fifteen miniature fixed-point cells made of three different ceramic crucible materials (Al2O3, ZrO2, and Al2O3(86 %)+ZrO2(14 %)) were filled with pure palladium and used to calibrate type B thermocouples (Pt30 %Rh/Pt6 %Rh). A critical point by using miniature fixed points with small amounts of fixed-point material is the analysis of the melting curves, which are characterized by significant slopes during the melting process compared to flat melting plateaus obtainable using conventional fixed-point cells. The method of the extrapolated starting point temperature using straight line approximation of the melting plateau was applied to analyze the melting curves. This method allowed an unambiguous determination of an electromotive force (emf) assignable as melting temperature. The strict consideration of two constraints resulted in a unique, repeatable and objective method to determine the emf at the melting temperature within an uncertainty of about 0.1 μ V. The lifetime and long-term stability of the miniature fixed points was investigated by performing more than 100 melt/freeze cycles for each crucible of the different ceramic materials. No failure of the crucibles occurred indicating an excellent mechanical stability of the investigated miniature cells. The consequent limitation of heating rates to values below {± }3.5 K min^{-1} above 1100° C and the carefully and completely filled crucibles (the liquid palladium occupies the whole volume of the crucible) are the reasons for successfully preventing the crucibles from breaking. The thermal stability of the melting temperature of palladium was excellent when using the crucibles made of Al2O3(86 %)+ZrO2(14 %) and ZrO2. Emf drifts over the total duration of the long-term investigation were below a temperature equivalent of about 0.1 K-0.2 K.

  14. Rapid and Reliable Detection of Nonsyndromic Hearing Loss Mutations by Multicolor Melting Curve Analysis

    PubMed Central

    Wang, Xudong; Hong, Yongjun; Cai, Peihong; Tang, Ning; Chen, Ying; Yan, Tizhen; Liu, Yinghua; Huang, Qiuying; Li, Qingge

    2017-01-01

    Hearing loss is a common birth defect worldwide. The GJB2, SLC26A4, MT-RNR1 and MT-TS1 genes have been reported as major pathogenic genes in nonsyndromic hearing loss. Early genetic screening is recommended to minimize the incidence of hearing loss. We hereby described a multicolor melting curve analysis (MMCA)-based assay for simultaneous detection of 12 prevalent nonsyndromic hearing loss-related mutations. The three-reaction assay could process 30 samples within 2.5 h in a single run on a 96-well thermocycler. Allelic types of each mutation could be reproducibly obtained from 10 pg ~100 ng genomic DNA per reaction. For the mitochondrial mutations, 10% ~ 20% heteroplasmic mutations could be detected. A comparison study using 501 clinical samples showed that the MMCA assay had 100% concordance with both SNaPshot minisequencing and Sanger sequencing. We concluded that the MMCA assay is a rapid, convenient and cost-effective method for detecting the common mutations, and can be expectedly a reliable tool in preliminary screening of nonsyndromic hearing loss in the Chinese Han population. PMID:28225033

  15. High resolution melt curve analysis based on methylation status for human semen identification.

    PubMed

    Fachet, Caitlyn; Quarino, Lawrence; Karnas, K Joy

    2017-03-01

    A high resolution melt curve assay to differentiate semen from blood, saliva, urine, and vaginal fluid based on methylation status at the Dapper Isoform 1 (DACT1) gene was developed. Stains made from blood, saliva, urine, semen, and vaginal fluid were obtained from volunteers and DNA was isolated using either organic extraction (saliva, urine, and vaginal fluid) or Chelex(®) 100 extraction (blood and semen). Extracts were then subjected to bisulfite modification in order to convert unmethylated cytosines to uracil, consequently creating sequences whose amplicons have melt curves that vary depending on their initial methylation status. When primers designed to amplify the promoter region of the DACT1 gene were used, DNA from semen samples was distinguishable from other fluids by a having a statistically significant lower melting temperature. The assay was found to be sperm-significant since semen from a vasectomized man produced a melting temperature similar to the non-semen body fluids. Blood and semen stains stored up to 5 months and tested at various intervals showed little variation in melt temperature indicating the methylation status was stable during the course of the study. The assay is a more viable method for forensic science practice than most molecular-based methods for body fluid stain identification since it is time efficient and utilizes instrumentation common to forensic biology laboratories. In addition, the assay is advantageous over traditional presumptive chemical methods for body fluid identification since results are confirmatory and the assay offers the possibility of multiplexing which may test for multiple body fluids simultaneously.

  16. On-chip magnetic bead-based DNA melting curve analysis using a magnetoresistive sensor

    NASA Astrophysics Data System (ADS)

    Rizzi, Giovanni; Østerberg, Frederik W.; Henriksen, Anders D.; Dufva, Martin; Hansen, Mikkel F.

    2015-04-01

    We present real-time measurements of DNA melting curves in a chip-based system that detects the amount of surface-bound magnetic beads using magnetoresistive magnetic field sensors. The sensors detect the difference between the amount of beads bound to the top and bottom sensor branches of the differential sensor geometry. The sensor surfaces are functionalized with wild type (WT) and mutant type (MT) capture probes, differing by a single base insertion (a single nucleotide polymorphism, SNP). Complementary biotinylated targets in suspension couple streptavidin magnetic beads to the sensor surface. The beads are magnetized by the field arising from the bias current passed through the sensors. We demonstrate the first on-chip measurements of the melting of DNA hybrids upon a ramping of the temperature. This overcomes the limitation of using a single washing condition at constant temperature. Moreover, we demonstrate that a single sensor bridge can be used to genotype a SNP.

  17. 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.

  18. High-Throughput Genome Editing and Phenotyping Facilitated by High Resolution Melting Curve Analysis

    PubMed Central

    Thomas, Holly R.; Percival, Stefanie M.; Yoder, Bradley K.; Parant, John M.

    2014-01-01

    With the goal to generate and characterize the phenotypes of null alleles in all genes within an organism and the recent advances in custom nucleases, genome editing limitations have moved from mutation generation to mutation detection. We previously demonstrated that High Resolution Melting (HRM) analysis is a rapid and efficient means of genotyping known zebrafish mutants. Here we establish optimized conditions for HRM based detection of novel mutant alleles. Using these conditions, we demonstrate that HRM is highly efficient at mutation detection across multiple genome editing platforms (ZFNs, TALENs, and CRISPRs); we observed nuclease generated HRM positive targeting in 1 of 6 (16%) open pool derived ZFNs, 14 of 23 (60%) TALENs, and 58 of 77 (75%) CRISPR nucleases. Successful targeting, based on HRM of G0 embryos correlates well with successful germline transmission (46 of 47 nucleases); yet, surprisingly mutations in the somatic tail DNA weakly correlate with mutations in the germline F1 progeny DNA. This suggests that analysis of G0 tail DNA is a good indicator of the efficiency of the nuclease, but not necessarily a good indicator of germline alleles that will be present in the F1s. However, we demonstrate that small amplicon HRM curve profiles of F1 progeny DNA can be used to differentiate between specific mutant alleles, facilitating rare allele identification and isolation; and that HRM is a powerful technique for screening possible off-target mutations that may be generated by the nucleases. Our data suggest that micro-homology based alternative NHEJ repair is primarily utilized in the generation of CRISPR mutant alleles and allows us to predict likelihood of generating a null allele. Lastly, we demonstrate that HRM can be used to quickly distinguish genotype-phenotype correlations within F1 embryos derived from G0 intercrosses. Together these data indicate that custom nucleases, in conjunction with the ease and speed of HRM, will facilitate future high

  19. Barcoding melting curve analysis for rapid, sensitive, and discriminating authentication of saffron (Crocus sativus L.) from its adulterants.

    PubMed

    Jiang, Chao; Cao, Liang; Yuan, Yuan; Chen, Min; Jin, Yan; Huang, Luqi

    2014-01-01

    Saffron (Crocus sativus L.) is one of the most important and expensive medicinal spice products in the world. Because of its high market value and premium price, saffron is often adulterated through the incorporation of other materials, such as Carthamus tinctorius L. and Calendula officinalis L. flowers, Hemerocallis L. petals, Daucus carota L. fleshy root, Curcuma longa L. rhizomes, Zea may L., and Nelumbo nucifera Gaertn. stigmas. To develop a straightforward, nonsequencing method for rapid, sensitive, and discriminating detection of these adulterants in traded saffron, we report here the application of a barcoding melting curve analysis method (Bar-MCA) that uses the universal chloroplast plant DNA barcoding region trnH-psbA to identify adulterants. When amplified at DNA concentrations and annealing temperatures optimized for the curve analysis, peaks were formed at specific locations for saffron (81.92°C) and the adulterants: D. carota (81.60°C), C. tinctorius (80.10°C), C. officinalis (79.92°C), Dendranthema morifolium (Ramat.) Tzvel. (79.62°C), N. nucifera (80.58°C), Hemerocallis fulva (L.) L. (84.78°C), and Z. mays (84.33°C). The constructed melting curves for saffron and its adulterants have significantly different peak locations or shapes. In conclusion, Bar-MCA could be a faster and more cost-effective method to authenticate saffron and detect its adulterants.

  20. 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.

  1. Lineage-specific detection of influenza B virus using real-time polymerase chain reaction with melting curve analysis.

    PubMed

    Tewawong, Nipaporn; Chansaenroj, Jira; Klinfueng, Sirapa; Vichiwattana, Preeyaporn; Korkong, Sumeth; Thongmee, Thanunrat; Theamboonlers, Apiradee; Payungporn, Sunchai; Vongpunsawad, Sompong; Poovorawan, Yong

    2016-06-01

    Influenza B viruses comprise two lineages, Victoria (B/Vic) and Yamagata (B/Yam), which co-circulate globally. The surveillance data on influenza B virus lineages in many countries often underestimate the true prevalence due to the lack of a rapid, accurate, and cost-effective method for virus detection. We have developed a real-time PCR with melting curve analysis for lineage-specific differential detection of influenza B virus. By amplifying a region of the hemagglutinin gene using real-time PCR with SYBR Green I dye, B/Vic and B/Yam could be differentiated based on their melting temperature peaks. This method was efficient (B/Vic = 93.2 %; B/Yam 97.7 %), sensitive (B/Vic, 94.6 %; B/Yam, 96.3 %), and specific (B/Vic, 97.7 %; B/Yam, 97.1 %). The lower detection limit was 10(2) copies per microliter. The assay was evaluated using 756 respiratory specimens that were positive for influenza B virus, obtained between 2010 and 2015. The incidence of influenza B virus was approximately 18.9 % of all influenza cases, and the percentage was highest among children aged 6-17 years (7.57 %). The overall percentage of mismatched influenza B vaccine was 21.1 %. Our findings suggest that real-time PCR with melting curve analysis can provide a rapid, simple, and sensitive lineage-specific influenza B virus screening method to facilitate influenza surveillance.

  2. Assessing contamination of microalgal astaxanthin producer Haematococcus cultures with high-resolution melting curve analysis.

    PubMed

    Dawidziuk, Adam; Popiel, Delfina; Luboinska, Magda; Grzebyk, Michal; Wisniewski, Maciej; Koczyk, Grzegorz

    2016-11-26

    Due to its superior antioxidant capabilities and higher activity than other carotenoids, astaxanthin is used widely in the nutraceutical and medicine industries. The most prolific natural producer of astaxanthin is the unicellular green microalga Haematococcus pluvialis. The correct identification of any contaminants in H. pluvialis cultures is both essential and nontrivial for several reasons. Firstly, while it is possible to distinguish the main microalgal contaminant Coelastrella sp. (in H. pluvialis cultures), in practice, it is frequently a daunting and error-prone task for personnel without extensive experience in the microscopic identification of algal species. Secondly, the undetected contaminants may decrease or stop production of astaxanthin. Lastly, the presence of other contaminants such as fungi can eventually infect and destroy the whole algae collection. In this study, high-resolution melting (HRM) analysis was developed to detect microalgal and fungal contamination. The developed diagnostic procedure allowed to distinguish pure H. pluvialis samples from cultures contaminated with low amounts (1.25 ng/ml) of microalgal DNA and fungal DNA (2.5 ng/ml). Such discrimination is not possible with the use of microscopy observations and allows fast and efficient collection testing.

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

    PubMed

    Schmiderer, Corinna; Ruzicka, Joana; Novak, Johannes

    2015-12-01

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

  4. Detection and Differentiation of In Vitro-Spiked Bacteria by Real-Time PCR and Melting-Curve Analysis

    PubMed Central

    Klaschik, S.; Lehmann, L. E.; Raadts, A.; Book, M.; Gebel, J.; Hoeft, A.; Stuber, F.

    2004-01-01

    We introduce a consensus real-time PCR protocol for the detection of bacterial DNA from laboratory-prepared specimens such as water, urine, and plasma. This prototype detection system enables an exact Gram stain classification and, in particular, screening for specific species of 17 intensive care unit-relevant bacteria by means of fluorescence hybridization probes and melting-curve analysis in a one-run experiment. One strain of every species was tested at a final density of 106 CFU/ml. All bacteria examined except Staphylococcus aureus and Staphylococcus epidermidis could be differentiated successfully; S. aureus and S. epidermidis could only be classified as “Staphylococcus species.” The hands-on time for preparation of the DNA, performance of the PCR, and evaluation of the PCR results was less than 4 h. Nevertheless, this prototype detection system requires more clinical validation. PMID:14766809

  5. Direct detection of Rifampicin and Isoniazid resistance in sputum samples from tuberculosis patients by High Resolution Melt curve analysis.

    PubMed

    Anthwal, Divya; Gupta, Rakesh Kumar; Bhalla, Manpreet; Bhatnagar, Shinjini; Tyagi, Jaya Sivaswami; Haldar, Sagarika

    2017-03-22

    Drug-resistant tuberculosis (TB) is a major threat for TB control worldwide. Globally, only 40% of the 340,000 notified TB patients estimated to have multidrug resistant-TB (MDR-TB) were detected in 2015. This study was carried out to evaluate the utility of High Resolution Melt curve analysis (HRM) for the rapid and direct detection of MDR-TB in Mycobacterium tuberculosis (M. tb) in sputum samples. A reference plasmid library was first generated of the most frequently observed mutations in the resistance determining regions of rpoB, katG and inhA promoter and used as positive controls in HRM. The assay was first validated in 25 MDR-M. tb clinical isolates. The assay was evaluated on DNA isolated from 99 M. tb culture-positive sputum samples that included 84 smear-negative sputum, using DNA sequencing as gold standard. Mutants were discriminated from wild-type by comparing melting-curve patterns with those of control plasmids using HRM software. Rifampicin (RIF) and isoniazid (INH) mono-resistance were detected in 11 and 21 specimens, respectively by HRM. Six samples were classified as MDR-TB by sequencing, one of which was missed by HRM. HRM-RIF, INH-katG and INH-inhA assay had 89% (52;100), 85% (62;97) and 100% (74;100) sensitivity, respectively in smear-negative samples; while all assays had 100% sensitivity in smear-positive samples. All assays had 100% specificity. Concordance of 97%-100% (κ value;0.9-1) was noted between sequencing and HRM. Hetero-resistance was observed in 5 of 99 samples by sequencing. In conclusion, the HRM assay was a cost-effective (INR400/US$6), rapid and closed-tube method for direct detection of MDR-TB in sputum, especially for direct smear negative cases.

  6. Rapid and simultaneous detection of common aneuploidies by quadruplex real-time polymerase chain reaction combined with melting curve analysis

    PubMed Central

    Lou, Jiwu; Sun, Manna; Zhao, Ying; Ji, Zhisong; Liu, Fenghua; Li, Dongzhi; Xu, Wanfang; Lin, Yangyang; Liu, Yanhui

    2017-01-01

    Background During the prenatal period, the number variation of chromosomes 13, 18, 21, X and Y accounts for more than 80% of the clinically significant chromosomal abnormalities diagnosed. Rapid tests for prenatal diagnosis of these abnormalities can improve pregnancy management and alleviate parental anxiety. Here, we present a molecular alternative method for detecting common aneuploidies. Methods This method is based on co-amplification of segmental duplications located on two different chromosomes using a single pair of primers. Segmental duplications have a high degree of sequence identity, but have single-nucleotide differences in some regions. These sequence differences can be quantified using melting curve analysis of dual-labeled probes to estimate the relative dosages of different chromosomes. We designed two quadruplex real-time PCR assays to detect aneuploidies of chromosomes 13, 18, 21, X and Y. Results We examined 75 aneuploid DNA samples and 56 unaffected DNA control samples using these two assays and correctly identified all samples. Four cases of unbalanced translocation were also accurately detected. The observed averaged ratio for each chromosomal disorder was similar to the theoretically expected value. Conclusions Our real-time assay is a robust, rapid, and easy to conduct technique for prenatal diagnosis of common aneuploidies, representing a competitive alternative for use in diagnostic laboratories. PMID:28241016

  7. Ab-inition melting curve of titanium

    NASA Astrophysics Data System (ADS)

    Stutzmann, Vincent; Bouchet, Johann; Bottin, Francois

    2014-03-01

    Thermodynamical properties of titanium are of great interest for aerospace and aviation industries and many studies are done in order to understand its behaviour under pressure (P) and temperature (T) : phase transitions at low T, melting curve at high T and P. In this work we compute the first ab-initio melting curve of titanium. This one is obtained with the Abinit package using DFT, in the GGA approximation, and in the framework of the projector augmented wave method (PAW). At first, we perform ground state calculations and study the five allotropic phases of titanium. Two PAW atomic data are generated with two different cutoff radius. The larger one gives results near previews ab-initio calculations, whereas the smaller one gives results near all electron calculation. Using the second PAW atomic data and performing ab-initio molecular dynamic simulations, we then compute the melting curve of titanium with three different methods. Results show relevance of our calculations, but also discrepencies with experimental data.

  8. 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.

  9. A new method for ABO genotyping using fluorescence melting curve analysis based on peptide nucleic acid probes.

    PubMed

    Lee, Kyungmyung; Park, Hyun-Chul; An, Sanghyun; Ahn, Eu-Ree; Lee, Yang-Han; Kim, Mi-Jung; Lee, Eun-Jung; Park, Jae Sin; Jung, Jin Wook; Lim, Sikeun

    2015-09-01

    ABO genotyping has been routinely used to identify suspects or unknown remains in crime investigations. Probe-based fluorescence melting curve analysis (FMCA) is a powerful tool for mutation detection and is based on melting temperature shifts due to thermal denaturation. In the present study, we developed a new method for ABO genotyping using peptide nucleic acid (PNA) probe-based FMCA. This method allowed for the simultaneous detection of three single nucleotide polymorphism (SNP) sites in the ABO gene (nucleotide positions 261, 526, and 803) and the determination of 14 ABO genotypes (A/A, A/O01 or A/O02, A/O03, B/B, B/O01 or B/O02, B/O03, O01/O01 or O01/O02 or O02/O02, O01/O03 or O02/O03, O03/O03, A/B, cis-AB01/A, cis-AB01/B, cis-AB01/O01 or cis-AB01/O02, and cis-AB01/cis-AB01). Using this method, we analyzed 80 samples and successfully identified ABO genotypes (A/A [n=5], A/O01 or A/O02 [n=23], B/B [n=3], B/O01 or B/O02 [n=18], A/B [n=9], O01/O01 or O01/O02 or O02/O02 [n=20], cis-AB01/A [n=1], and cis-AB01/O01 or cis-AB01/O02 [n=1]). In addition, all steps in the method, including polymerase chain reaction, PNA probe hybridization, and FMCA, could be performed in one single closed tube in less than 3h. Since no processing or separation steps were required during analysis, this method was more convenient and rapid than traditional methods and reduced the risk of contamination. Thus, this method may be an effective and helpful tool in forensic investigations.

  10. Rapid detection of the Clostridium difficile ribotype 027 tcdC gene frame shift mutation at position 117 by real-time PCR and melt curve analysis.

    PubMed

    Wolff, D; Brüning, T; Gerritzen, A

    2009-08-01

    The emergence of the hypervirulent strain Clostridium difficile PCR ribotype 027 has increased the necessity for rapid C. difficile typing tests for clinical and epidemiological purposes. We developed a rapid real-time polymerase chain reaction (PCR) test for the detection of C. difficile. As the target, we chose the tcdC gene, which encodes for a negative regulator in toxin production. A deletion at position 117 of the tcdC gene, which is associated with severe tcdC truncation, is well conserved in all PCR ribotype 027 isolates. Probe sequences of the real-time PCR test were designed to result in distinct melt profiles for sequence variations at positions 117 to 120 of the tcdC gene. The tcdC gene deletion at position 117 was easily detected with real-time PCR and melt curve analysis in all C. difficile ribotype 027 isolates. In five non-027 strains and 46 hospitalised patient samples, melt curve analysis detected no deletion. PCR results were confirmed by DNA sequencing. The combination of real-time PCR and melt curve analysis is a rapid and accurate method for the detection of C. difficile DNA and simultaneous screening for the tcdC gene deletion at position 117, which is closely related to the C. difficile PCR ribotype 027 strain.

  11. High-resolution DNA melt-curve analysis for cost-effective mass screening of pairwise species interactions.

    PubMed

    McCarthy, James K; Didham, Raphael K; Brockerhoff, Eckehard G; van Bysterveldt, Katherine A; Varsani, Arvind

    2013-09-01

    Ecological studies of pairwise interactions are constrained by the methods available for rapid species identification of the interacting organisms. The resolution of data required to characterize species interaction networks at multiple spatio-temporal scales can be intensive, and therefore laborious and costly to collect. We explore the utility of high-resolution DNA melt-curve analysis (HRM) as a rapid species identification method. An approach was developed to identify organisms at the pairwise interaction level, with particular application to cryptic species interactions that are traditionally difficult to study. Here, we selected a challenging application; to identify the presence/absence of pathogenic fungi (Sporothrix inflata, Ophiostoma nigrocarpum and Ophiostoma galeiforme) transported by bark beetle vectors (Hylastes ater and Hylurgus ligniperda). The technique was able to distinguish between different species of DNA within a single, pooled sample. In test applications, HRM was effective in the mass screening and identification of pathogenic fungal species carried by many individual bark beetle vectors (n = 455 beetles screened) across large geographic scales. For two of the fungal species, there was no difference in the frequency of association with either of their vectors, but for the third fungal species there was a shift in vector-pathogen associations across locations. This technique allows rapid, mass screening and characterization of species interactions at a fraction of the time and cost of traditional methods. It is anticipated that this method can be readily applied to explore other cryptic species interactions, or other studies requiring rapid generation of large data sets and/or high-throughput efficiency.

  12. The development and validation of a rapid genetic method for species identification and genotyping of medically important fungal pathogens using high-resolution melting curve analysis.

    PubMed

    Alnuaimi, A D; Wiesenfeld, D; O'Brien-Simpson, N M; Reynolds, E C; Peng, B; McCullough, M J

    2014-06-01

    Accurate, rapid and economical fungal species identification has been a major aim in mycology. In this study, our goal was to examine the feasibility of a high-resolution melting curve analysis (HRMA) of internal transcribed regions ITS1 and ITS2 in ribosomal DNA (rDNA) for a rapid, simple and inexpensive differentiation of eight clinically relevant Candida species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida krusei, Candida tropicalis, Candida guilliermondii, Candida dubliniensis and Candida lusitaniae). In addition, for the first time, we tested the applicability of HRMA to classify C. albicans strains into four previously described genotypes (A, B, C and D) using a primer set that spans the transposable intron region of 25S of rDNA. Type and unknown clinical oral isolates were used in this study and the melting curve analysis was compared with both amplicons' sequencing and agarose gel electrophoresis analysis. Real-time PCR and subsequent HRMA of the two described rDNA regions generated distinct melting curve profiles that were in accord with sequencing and gel electrophoresis analysis, highly reproducible, and characteristic of each of the eight Candida species and C. albicans genotypes. Moreover, results were obtained in 4 h and without the need for any post-amplification handling, so reducing time and cost. Owing to its simplicity and speed, this technique is a good fit for genotypic analysis of hundreds of clinical strains in large epidemiological settings.

  13. 5'-MGB probes allow rapid identification of methanogens and sulfate reducers in cold marine sediments by real-time PCR and melting curve analysis.

    PubMed

    Afonina, Irina; Savvichev, Alexander; Ankoudinova, Irina; Mahoney, Walt

    2009-09-01

    The analysis of microorganism communities in uncultured environmental samples requires laborious and cumbersome techniques such as denaturing gradient gel electrophoresis of amplicons generated with 16S rRNA generic primers with subsequent fragment sequencing. We have developed a simple method for genus identification of methanogen archaea and sulfate-reducing bacteria based on a real-time PCR hybridization probe melting curve analysis. The method takes advantage of a recent explosion of microorganism sequencing data conveniently packaged in the Ribosomal Database Project. Specificity of detection is based on a genus-specific real-time PCR fluorescent 5'-MGB-probe melt. As the probes are designed to have destabilizing mismatches with undesired genera, only samples with a proper melting temperature are called positive.

  14. Evaluation of a new rapid molecular diagnostic system for Plasmodium falciparum combined with DNA filter paper, loop-mediated isothermal amplification, and melting curve analysis.

    PubMed

    Yamamura, Mariko; Makimura, Koichi; Ota, Yasuo

    2009-01-01

    Falciparum malaria is a fatal infection without immediate diagnosability or treatment. There are shortages of clinicians and examiners skilled in the treatment of malaria in non-endemic countries, including Japan. This study was performed to evaluate a novel rapid molecular diagnostic system consisting of loop-mediated isothermal amplification (LAMP) combined with DNA filter paper (FTA card) and melting curve analysis. Combining LAMP with melting curve analysis enabled diagnosis of Plasmodium falciparum more accurately with relative ease. FTA cards could be used to clarify problems regarding storage, infectivity, and transportation. The LAMP assay was carried out at a constant temperature of 63 degrees C for 90 min. The diagnostic system (malaria-LAMP) accurately diagnosed malaria (47 samples from Thailand and 50 from Zimbabwe) with 97.8% sensitivity and 85.7% specificity as compared with microscopic methods, indicating the usefulness of this combined system.

  15. Melting curve of materials: theory versus experiments

    NASA Astrophysics Data System (ADS)

    Alfè, D.; Vocadlo, L.; Price, G. D.; Gillan, M. J.

    2004-04-01

    A number of melting curves of various materials have recently been measured experimentally and calculated theoretically, but the agreement between different groups is not always good. We discuss here some of the problems which may arise in both experiments and theory. We also report the melting curves of Fe and Al calculated recently using quantum mechanics techniques, based on density functional theory with generalized gradient approximations. For Al our results are in very good agreement with both low pressure diamond-anvil-cell experiments (Boehler and Ross 1997 Earth Planet. Sci. Lett. 153 223, Hänström and Lazor 2000 J. Alloys Compounds 305 209) and high pressure shock wave experiments (Shaner et al 1984 High Pressure in Science and Technology ed Homan et al (Amsterdam: North-Holland) p 137). For Fe our results agree with the shock wave experiments of Brown and McQueen (1986 J. Geophys. Res. 91 7485) and Nguyen and Holmes (2000 AIP Shock Compression of Condensed Matter 505 81) and the recent diamond-anvil-cell experiments of Shen et al (1998 Geophys. Res. Lett. 25 373). Our results are at variance with the recent calculations of Laio et al (2000 Science 287 1027) and, to a lesser extent, with the calculations of Belonoshko et al (2000 Phys. Rev. Lett. 84 3638). The reasons for these disagreements are discussed.

  16. Detection of Ehrlichia canis in canine blood samples by real-time fluorescence resonance energy transfer (FRET) PCR and melting curve analysis.

    PubMed

    Kongklieng, Amornmas; Thanchomnang, Tongjit; Intapan, Pewpan M; Boonmars, Thidarut; Janwan, Penchom; Sanpool, Oranuch; Lulitanond, Viraphong; Taweethavonsawat, Piyanan; Chungpivat, Sudchit; Morakote, Nimit; Maleewong, Wanchai

    2014-09-01

    Ehrlichia canis is a small pleomorphic gram-negative, coccoid, obligatory intracellular bacterium and the cause of canine monocytic ehrlichiosis. A real-time fluorescence resonance energy transfer polymerase chain reaction (real-time FRET PCR) coupled with melting curve analysis was established for detection of E. canis infection in canine blood samples. The VirB9 gene was amplified using one pair of primers and the melting curve analysis was generated by heating the hybridizing probes and amplified products. Eight E. canis-infected dog blood samples were initially identified using the Giemsa staining/microscopic method followed by conventional PCR (cPCR)/Sanger sequencing for confirmation. The sensitivity and specificity of the real-time FRET PCR detection were 87.5% and 100%, respectively and the limit of detection was 6.6 x 10(3) copies of positive E. canis control plasmids. The real-time FRET PCR with melting curve analysis reported here is better than microscopic visualization or cPCR because the method is not affected by the false bias inherent in the microscopic method. Furthermore, many samples can be processed rapidly at the same time. This convenient tool is beneficial as an alternative assay for the epidemiologic study of canine ehrlichiosis as well as for eradication of these organisms in prevention and control programs in endemic areas.

  17. Simultaneous Detection and Genotype Determination of HSV 1 and 2 by Real-time PCR Using Melting Curve Analysis and a Unique Pair of Primers.

    PubMed

    Paryan, Mahdi; Mohammadi-Yeganeh, Samira; Rezvan, Houri; Kia, Vahid; Mansouri, Ardalan; Mirab Samiee, Siamak

    2017-02-01

    Herpes simplex virus (HSV) is a human pathogen that causes different pathologic manifestations. Rapid and feasible detection and discrimination methods for HSV genotyping is a challenge in clinical laboratories, especially in children suffering from herpetic encephalitis. A quantitative real-time polymerase chain reaction (PCR)-based genotyping assay using SYBR Green I was established. We designed only 1 pair of primer for HSV 1 and 2, targeting thymidine kinase gene conserved region. HSV genotypes were determined by PCR using melting curve analysis with LightCycler. Different HSV genotypes were successfully detected in all clinical samples. The melting temperature for HSV 1 and 2 was 85.5±0.78°C and 89±0.53°C, respectively. These 2 genotypes were completely distinguished by means of the accurate melting assay. Importantly, detection was reliably performed within only 1 hour. The assay had no cross-reactivity across species, an excellent dynamic range from 10 to 10 copies per reaction, a good intra-assay and interassay reproducibility, and a detection limit of a single copy per reaction. Our homebrew designed and validated quantitative real-time PCR followed by a melting curve analysis provided a rapid and convenient screening test for differential identification of HSV genotypes 1 and 2. We recommend the large-scale application of this method for HSV 1 and 2 detection.

  18. Detection of a Knockdown Resistance Mutation Associated with Permethrin Resistance in the Body Louse Pediculus humanus corporis by Use of Melting Curve Analysis Genotyping

    PubMed Central

    Drali, Rezak; Benkouiten, Samir; Badiaga, Sékéné; Bitam, Idir

    2012-01-01

    Louse-borne diseases are prevalent in the homeless, and body louse eradication has thus far been unsuccessful in this population. We aim to develop a rapid and robust genotyping method usable in large field-based clinical studies to monitor permethrin resistance in the human body louse Pediculus humanus corporis. We assessed a melting curve analysis genotyping method based on real-time PCR using hybridization probes to detect the M815I-T917I-L920F knockdown resistance (kdr) mutation in the paraorthologous voltage-sensitive sodium channel (VSSC) α subunit gene, which is associated with permethrin resistance. The 908-bp DNA fragment of the VSSC gene, encoding the α subunit of the sodium channel and encompassing the three mutation sites, was PCR sequenced from 65 lice collected from a homeless population. We noted a high prevalence of the 3 indicated mutations in the body lice collected from homeless people (100% for the M815I and L920F mutations and 56.73% for the T917I mutation). These results were confirmed by melting curve analysis genotyping, which had a calculated sensitivity of 100% for the M815I and T917I mutations and of 98% for the L920F mutation. The specificity was 100% for M815I and L920F and 96% for T917I. Melting curve analysis genotyping is a fast, sensitive, and specific tool that is fully compatible with the analysis of a large number of samples in epidemiological surveys, allowing the simultaneous genotyping of 96 samples in just over an hour (75 min). Thus, it is perfectly suited for the epidemiological monitoring of permethrin resistance in human body lice in large-scale clinical studies. PMID:22573588

  19. Quantitative detection and differentiation of free-living amoeba species using SYBR green-based real-time PCR melting curve analysis.

    PubMed

    Behets, Jonas; Declerck, Priscilla; Delaedt, Yasmine; Verelst, Lieve; Ollevier, Frans

    2006-12-01

    Real-time polymerase chain reaction melting curve analysis (MCA) allows differentiation of several free-living amoebae species. Distinctive characteristics were found for Naegleria fowleri, N. lovaniensis, N. australiensis, N. gruberi, Hartmanella vermiformis, and Willaertia magna. Species specificity of the amplicons was confirmed using agarose gel electrophoresis and sequence-based approaches. Amplification efficiency ranged from 91% to 98%, indicating the quantitative potential of the assay. This MCA approach can be used for quantitative detection of free-living amoebae after cultivation but also as a culture-independent detection method.

  20. High-resolution melt curve analysis to confirm the presence of co-circulating isolates of avian nephritis virus in commercial chicken flocks.

    PubMed

    Chamings, A; Hewson, K A; O'Rourke, D; Ignjatovic, J; Noormohammadi, A H

    2015-01-01

    Avian Nephritis Virus (ANV) has been implicated in poor growth and renal disease of young chickens. This paper describes the development of a reverse-transcriptase polymerase chain reaction for the detection of ANV in commercial meat chickens and the use of high-resolution melt curves to detect the presence of genetically different ANVs. Pooled cloacal swabs from both healthy and ill commercial chicken broiler flocks were tested for the presence of ANV using a combination of polymerase chain reaction, molecular cloning, high-resolution melt curve analysis and sequencing. Except for one, all specimens were found to contain two genetically different ANVs. Phylogenetic analysis of the capsid amino acid sequences revealed the presence of four of six groups of ANV identified previously in other countries as well as in two novel groups of ANV. Phylogenetic analysis of nucleotide sequences of partial polymerase, capsid and 3' untranslated regions reveal that the genes of individual ANV virus isolates have different ancestors. This was shown to be due to a template-switching event in the capsid gene that resulted in the 3' end of the capsid gene and the 3' untranslated region of one ANV isolate being transferred to another ANV. These results reveal that infection of chicken flocks with multiple ANV isolates is common and this needs to be taken into consideration in diagnosis of ANV using molecular techniques and in future epidemiological investigations.

  1. Interferon λ 3 and 4 Genotyping Using High-Resolution Melt Curve Analysis Suitable for Multiple Clinical Sample Types.

    PubMed

    Lamoury, François M J; Bartlett, Sofia; Jacka, Brendan; Hajarizadeh, Behzad; Grebely, Jason; Matthews, Gail V; Dore, Gregory J; Applegate, Tanya L

    2015-09-01

    Many people living with hepatitis C virus (HCV) infection will continue to rely on interferon-based regimens until effective strategies to minimize the cost of directly acting antivirals (DAAs) and to improve treatment access are implemented. Host single-nucleotide polymorphisms related to IFNL3 and IFNL4 are associated with spontaneous clearance of HCV, and pegylated interferon- and DAA-based treatment outcomes. We describe a simple and rapid genotyping method for IFNL rs12979860, rs8099917, and rs368234815 using high-resolution melting analysis for DNA extracted from whole blood, buffy coat, plasma, serum, and dried blood spots. This assay successfully detected all three polymorphisms on DNA extracted by the automated platform easyMAG from all samples when compared to sequenced amplicons. Analysis of 126 participants with recent HCV infection from the Australian Trial in Acute Hepatitis C study demonstrated the prevalence of favorable single-nucleotide polymorphisms were 62%, 51%, and 45% for rs8099917 TT, rs12979860 CC, and rs368234815 TT/TT, respectively. The genotyping assay described here provides a rapid and affordable IFNL3 and IFNL4 genotyping method for a range of clinical sample types. Until global access to DAAs is achieved, IFNL3 and IFNL4 genotyping could identify those likely to clear naturally and in whom treatment could be delayed, or help prioritize DAA treatment to those less likely to respond to interferon-containing regimens.

  2. A comparison of PCR assays for beak and feather disease virus and high resolution melt (HRM) curve analysis of replicase associated protein and capsid genes.

    PubMed

    Das, Shubhagata; Sarker, Subir; Ghorashi, Seyed Ali; Forwood, Jade K; Raidal, Shane R

    2016-11-01

    Beak and feather disease virus (BFDV) threatens a wide range of endangered psittacine birds worldwide. In this study, we assessed a novel PCR assay and genetic screening method using high-resolution melt (HRM) curve analysis for BFDV targeting the capsid (Cap) gene (HRM-Cap) alongside conventional PCR detection as well as a PCR method that targets a much smaller fragment of the virus genome in the replicase initiator protein (Rep) gene (HRM-Rep). Limits of detection, sensitivity, specificity and discriminatory power for differentiating BFDV sequences were compared. HRM-Cap had a high positive predictive value and could readily differentiate between a reference genotype and 17 other diverse BFDV genomes with more discriminatory power (genotype confidence percentage) than HRM-Rep. Melt curve profiles generated by HRM-Cap correlated with unique DNA sequence profiles for each individual test genome. The limit of detection of HRM-Cap was lower (2×10(-5)ng/reaction or 48 viral copies) than that for both HRM-Rep and conventional BFDV PCR which had similar sensitivity (2×10(-6)ng or 13 viral copies/reaction). However, when used in a diagnostic setting with 348 clinical samples there was strong agreement between HRM-Cap and conventional PCR (kappa=0.87, P<0.01, 98% specificity) and HRM-Cap demonstrated higher specificity (99.9%) than HRM-Rep (80.3%).

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

    PubMed

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

    2015-01-01

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

  4. Explicit analytic equations for multimolecular thermal melting curves.

    PubMed

    Böttcher, Albrecht; Kowerko, Danny; Sigel, Roland K O

    2015-07-01

    The analysis of thermal melting curves requires the knowledge of equations for the temperature dependence of the relative fraction of folded and unfolded components. To implement these equations as standard tools for curve fitting, they should be as explicit as possible. From the van't Hoff formalism it is known that the equilibrium constant and hence the folded fraction is a function of the absolute temperature, the van't Hoff transition enthalpy, and the melting temperature. The work presented here is devoted to the mathematically self-contained derivation and the listing of explicit equations for the folded fraction as a function of the thermodynamic parameters in the case of arbitrary molecularities. Part of the results are known, others are new. It is in particular shown for the first time that the folded fraction is the composition of a universal function which depends solely on the molecularity and a dimensionless function which is governed by the concrete thermodynamic regime but is independent of the molecularity. The results will prove useful for extracting the thermodynamic parameters from experimental data on the basis of regression analysis. As supporting information, open-source Matlab scripts for the computer implementation of the equations are provided.

  5. Application of a qPCR assay with melting curve analysis for detection and differentiation of protozoan oocysts in human fecal samples from Dominican Republic.

    PubMed

    Lalonde, Laura F; Reyes, Julissa; Gajadhar, Alvin A

    2013-11-01

    A quantitative polymerase chain reaction assay with melt curve analysis (qPCR-MCA) was applied for the detection of protozoan oocysts in 501 human fecal samples collected in Dominican Republic. Samples were subjected to qPCR using universal coccidia primers targeting 18S rDNA to detect oocysts followed by MCA to identify oocyst species based on amplicon melting temperature. Putative positive samples were also tested by conventional PCR and microscopy. Cystoisospora belli (×3), Cryptosporidium parvum (×3), Cryptosporidium hominis (×5), Cryptosporidium meleagridis (×1), Cryptosporidium canis (×1), and Cyclospora cayetanensis (×9) were detected by qPCR-MCA and confirmed by sequencing. This assay consistently detected 10 copies of the cloned target fragment and can be considered more efficient and sensitive than microscopy flotation methods for detecting multiple species of oocysts in human feces. The qPCR-MCA is a reliable protozoan oocyst screening assay for use on clinical and environmental samples in public health, food safety and veterinary programs.

  6. Application of a qPCR Assay with Melting Curve Analysis for Detection and Differentiation of Protozoan Oocysts in Human Fecal Samples from Dominican Republic

    PubMed Central

    Lalonde, Laura F.; Reyes, Julissa; Gajadhar, Alvin A.

    2013-01-01

    A quantitative polymerase chain reaction assay with melt curve analysis (qPCR-MCA) was applied for the detection of protozoan oocysts in 501 human fecal samples collected in Dominican Republic. Samples were subjected to qPCR using universal coccidia primers targeting 18S rDNA to detect oocysts followed by MCA to identify oocyst species based on amplicon melting temperature. Putative positive samples were also tested by conventional PCR and microscopy. Cystoisospora belli (×3), Cryptosporidium parvum (×3), Cryptosporidium hominis (×5), Cryptosporidium meleagridis (×1), Cryptosporidium canis (×1), and Cyclospora cayetanensis (×9) were detected by qPCR-MCA and confirmed by sequencing. This assay consistently detected 10 copies of the cloned target fragment and can be considered more efficient and sensitive than microscopy flotation methods for detecting multiple species of oocysts in human feces. The qPCR-MCA is a reliable protozoan oocyst screening assay for use on clinical and environmental samples in public health, food safety and veterinary programs. PMID:24019437

  7. A simple and rapid genotyping assay for simultaneous detection of two ADRB2 allelic variants using fluorescence resonance energy transfer probes and melting curve analysis.

    PubMed

    Sábato, M Fernanda; Irani, Anne-Marie; Bukaveckas, Bonny L; Schwartz, Lawrence B; Wilkinson, David S; Ferreira-Gonzalez, Andrea

    2008-05-01

    Allelic variants at codons 16 and 27 of the beta(2)-adrenergic receptor gene (ADRB2) have shown clinical and pharmacological implications in asthma, hypertension, ischemic heart failure, diabetes, obesity, and cystic fibrosis. We have developed a simultaneous genotyping assay for the c.46A>G and c.79C>G allelic variants using hybridization probes and melting curve analysis. The assay was optimized on a panel of 30 DNA samples of known ADRB2 genotype as determined by sequencing with 100% concordance between the two techniques. Melting temperature (Tm) ranges for the different genotypes were obtained using data from three independent experiments. Single peaks for p.Arg16Arg (Tm = 57.76 degrees C +/- 0.10 degrees C) and p.Gly16Gly (Tm = 66.73 degrees C +/- 0.18 degrees C) and two melting peaks for p.Arg16Gly were obtained. Similarly, single peaks for p.Gln27Gln (Tm = 53.98 degrees C +/- 0.19 degrees C) and p.Glu27Glu (Tm = 64.93 degrees C +/- 0.16 degrees C) and two peaks for p.Gln27Glu were detected. Independent operators easily assigned genotypes in a sample set of 385 asthmatic patients. Haplotype and allele frequencies were in concordance with previously published data: Arg allele frequencies in children/adults were 0.34/0.30 in Caucasians and 0.45/0.52 in African Americans, and Gln allele frequencies were 0.58/0.52 in Caucasians and 0.82/0.84 in African Americans. Thus, the ADRB2 genotyping assay represents a highly reliable and rapid technique for routine clinical use in the simultaneous detection of ADRB2 variants.

  8. Shock melting method to determine melting curve by molecular dynamics: Cu, Pd, and Al

    SciTech Connect

    Liu, Zhong-Li; Zhang, Xiu-Lu; Cai, Ling-Cang

    2015-09-21

    A melting simulation method, the shock melting (SM) method, is proposed and proved to be able to determine the melting curves of materials accurately and efficiently. The SM method, which is based on the multi-scale shock technique, determines melting curves by preheating and/or prepressurizing materials before shock. This strategy was extensively verified using both classical and ab initio molecular dynamics (MD). First, the SM method yielded the same satisfactory melting curve of Cu with only 360 atoms using classical MD, compared to the results from the Z-method and the two-phase coexistence method. Then, it also produced a satisfactory melting curve of Pd with only 756 atoms. Finally, the SM method combined with ab initio MD cheaply achieved a good melting curve of Al with only 180 atoms, which agrees well with the experimental data and the calculated results from other methods. It turned out that the SM method is an alternative efficient method for calculating the melting curves of materials.

  9. Melting curve analysis of a groEL PCR fragment for the rapid genotyping of strains belonging to the Lactobacillus casei group of species.

    PubMed

    Koirala, Ranjan; Taverniti, Valentina; Balzaretti, Silvia; Ricci, Giovanni; Fortina, Maria Grazia; Guglielmetti, Simone

    2015-04-01

    Lactobacillus casei group (Lcs) consists of three phylogenetically closely related species (L. casei, L. paracasei, and L. rhamnosus), which are widely used in the dairy and probiotic industrial sectors. Strategies to easily and rapidly characterize Lcs are therefore of interest. To this aim, we developed a method according to a technique known as high resolution melting analysis (HRMa), which was applied to a 150 bp groEL gene fragment. The analysis was performed on 53 Lcs strains and 29 strains representatives of species that are commonly present in dairy and probiotic products and can be most probably co-isolated with Lcs strains. DNA amplification was obtained only from Lcs strains, demonstrating the specificity of the groEL primers designed in this study. The HRMa clustered Lcs strains in three groups that exactly corresponded to the species of the L. casei group. A following HRMa separated the 39 L. paracasei strains in two well distinct intraspecific groups, indicating the possible existence of at least two distinct genotypes inside the species. Nonetheless, the phenotypic characterization demonstrated that the genotypes do not correspond to the two L. paracasei subspecies, namely paracasei and tolerans. In conclusion, the melting curve analysis developed in this study is demonstrably a simple, labor-saving, and rapid strategy obtain the genotyping of a bacterial isolate and simultaneously potentially confirm its affiliation to the L. casei group of species. The application of this method to a larger collection of strains may validate the possibility to use the proposed HRMa protocol for the taxonomic discrimination of L. casei group of species. In general, this study suggests that HRMa can be a suitable technique for the genetic typization of Lactobacillus strains.

  10. Melting curves of metals by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel

    2015-06-01

    In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).

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

    PubMed

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

    2015-10-01

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

  12. Simple calculation of ab initio melting curves: Application to aluminum

    NASA Astrophysics Data System (ADS)

    Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

    2015-03-01

    We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003), 10.1063/1.1624057] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013), 10.1103/PhysRevE.88.062145]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.

  13. Melting curve of metals Cu, Ag and Au under pressure

    NASA Astrophysics Data System (ADS)

    Tam, Pham Dinh; Hoc, Nguyen Quang; Tinh, Bui Duc; Tan, Pham Duy

    2016-01-01

    In this paper, the dependence of the melting temperature of metals Cu, Ag and Au under pressure in the interval from 0 kbar to 40 kbar is studied by the statistical moment method (SMM). This dependence has the form of near linearity and the calculated slopes of melting curve are 3.9 for Cu, 5.7 for Ag and 6 for Au. These results are in good agreement with the experimental data.

  14. Differential detection of Trichinella papuae, T. spiralis and T. pseudospiralis by real-time fluorescence resonance energy transfer PCR and melting curve analysis.

    PubMed

    Tantrawatpan, Chairat; Intapan, Pewpan M; Thanchomnang, Tongjit; Lulitanond, Viraphong; Boonmars, Thidarut; Wu, Zhiliang; Morakote, Nimit; Maleewong, Wanchai

    2012-04-30

    Trichinellosis caused by nematodes of Trichinella spp. is a zoonotic foodborne disease. Three Trichinella species of the parasite including Trichinella spiralis, Trichinella papuae and Trichinella pseudospiralis, have been etiologic agents of human trichinellosis in Thailand. Definite diagnosis of this helminthiasis is based on a finding of the Trichinella larva (e) in a muscle biopsy. The parasite species or genotype can be determined using molecular methods, e.g., polymerase chain reaction (PCR). This study has utilized real-time fluorescence resonance energy transfer PCR (real-time FRET PCR) and a melting curve analysis for the differential diagnosis of trichinellosis. Three common Trichinella species in Thailand were studied using one set of primers and fluorophore-labeled hybridization probes specific for the small subunit of the mitochondrial ribosomal RNA gene. Using fewer than 35 cycles as the cut-off for positivity and using different melting temperatures (T(m)), this assay detected T. spiralis, T. papuae and T. pseudospiralis in muscle tissue and found the mean T(m) ± SD values to be 51.79 ± 0.06, 66.09 ± 0.46 and 51.46 ± 0.09, respectively. The analytical sensitivity of the technique enabled the detection of a single Trichinella larva of each species, and the detection limit for the target DNA sequence was 16 copies of positive control plasmid. A test of the technique's analytical specificity showed no fluorescence signal for a panel of 19 non-Trichinella parasites or for human and mouse genomic DNA. Due to the sensitivity and specificity of the detection of these Trichinella species, as well as the fast and high-throughput nature of these tools, this method has application potential in differentiating non-encapsulated larvae of T. papuae from T. spiralis and T. pseudospiralis in tissues of infected humans and animals.

  15. Comparative Study on Two Melting Simulation Methods: Melting Curve of Gold

    NASA Astrophysics Data System (ADS)

    Liu, Zhong-Li; Sun, Jun-Sheng; Li, Rui; Zhang, Xiu-Lu; Cai, Ling-Cang

    2016-05-01

    Melting simulation methods are of crucial importance to determining melting temperature of materials efficiently. A high-efficiency melting simulation method saves much simulation time and computational resources. To compare the efficiency of our newly developed shock melting (SM) method with that of the well-established two-phase (TP) method, we calculate the high-pressure melting curve of Au using the two methods based on the optimally selected interatomic potentials. Although we only use 640 atoms to determine the melting temperature of Au in the SM method, the resulting melting curve accords very well with the results from the TP method using much more atoms. Thus, this shows that a much smaller system size in SM method can still achieve a fully converged melting curve compared with the TP method, implying the robustness and efficiency of the SM method. Supported by the National Natural Science Foundation of China under Grant No. 41574076 and the NSAF of China under Grant No. U1230201/A06, and the Young Core Teacher Scheme of Henan Province under Grant No. 2014GGJS-108

  16. Development of a SYBR Green real-time PCR assay with melting curve analysis for simultaneous detection and differentiation of canine adenovirus type 1 and type 2.

    PubMed

    Balboni, Andrea; Dondi, Francesco; Prosperi, Santino; Battilani, Mara

    2015-09-15

    Canine adenovirus type 1 (CAdV-1) and canine adenovirus type 2 (CAdV-2) cause infectious canine hepatitis (ICH) and infectious tracheobronchitis (ITB) in dogs, respectively. Cases of ICH have been documented in recent years and recent surveys have demonstrated a wide percentage of asymptomatic CAdV-1 infection in the canine population. Since both CAdV types are detectable in the same biological matrices, and viral coinfection with CAdV-1 and CAdV-2 are reported with high frequency, it is urgent to have available a rapid, highly sensitive and specific assay for the diagnosis of CAdV infection and distinction between CAdV-1 and CAdV-2. In order to detect canine adenovirus in biological samples and to rapidly distinguish the two viral types, a SYBR Green real-time PCR assay was optimized to discriminate CAdV-1 and CAdV-2 via a melting curve analysis. The developed assay showed high sensitivity and reproducibility and was highly efficient and specific in discriminating the two CAdV types. This reliable and rapid technique may represent a simple, useful and economic option for simultaneous CAdV types detection, which would be feasible and attractive for all diagnostic laboratories, both for clinical purposes and for epidemiological investigations.

  17. Duplex Real-time PCR assay and SYBR green I melting curve analysis for molecular identification of HPV genotypes 16, 18, 31, 35, 51 and 66.

    PubMed

    Tsakogiannis, D; Papacharalampous, M; Toska, E; Kyriakopoulou, Z; Dimitriou, T G; Ruether, I G A; Komiotis, D; Markoulatos, P

    2015-02-01

    Long-term infection with high-risk HPV genotypes is the leading cause of cervical cancer. In the present study a Duplex Real-time PCR assay was developed in order to identify HPV types 16, 18, 31, 35, 51 and 66 in three reactions, through SYBR green I melting curve analysis. The method utilizes type-specific primer sets that allowed the amplification of highly conserved regions of L1 gene. Reconstitution experiments were conducted by using HPV DNA plasmids in order to determine the sensitivity of the assay. The newly designed assay has a limit of detection of 10 copies per reaction. The most prevalent HPV genotype in single and in multiple HPV infections was HPV16 followed by HPV18, HPV51, HPV31, HPV35 and HPV66. The proposed method is a simple, specific, sensitive and cost-effective assay that can be easily incorporated in small and medium size laboratories for the rapid identification of the most clinically important HPV genotypes.

  18. Enhancing melting curve analysis for the discrimination of loop-mediated isothermal amplification products from four pathogenic molds: Use of inorganic pyrophosphatase and its effect in reducing the variance in melting temperature values.

    PubMed

    Tone, Kazuya; Fujisaki, Ryuichi; Yamazaki, Takashi; Makimura, Koichi

    2017-01-01

    Loop-mediated isothermal amplification (LAMP) is widely used for differentiating causative agents in infectious diseases. Melting curve analysis (MCA) in conjunction with the LAMP method reduces both the labor required to conduct an assay and contamination of the products. However, two factors influence the melting temperature (Tm) of LAMP products: an inconsistent concentration of Mg(2+) ion due to the precipitation of Mg2P2O7, and the guanine-cytosine (GC) content of the starting dumbbell-like structure. In this study, we investigated the influence of inorganic pyrophosphatase (PPase), an enzyme that inhibits the production of Mg2P2O7, on the Tm of LAMP products, and examined the correlation between the above factors and the Tm value using MCA. A set of LAMP primers that amplify the ribosomal DNA of the large subunit of Aspergillus fumigatus, Penicillium expansum, Penicillium marneffei, and Histoplasma capsulatum was designed, and the LAMP reaction was performed using serial concentrations of these fungal genomic DNAs as templates in the presence and absence of PPase. We compared the Tm values obtained from the PPase-free group and the PPase-containing group, and the relationship between the GC content of the theoretical starting dumbbell-like structure and the Tm values of the LAMP product from each fungus was analyzed. The range of Tm values obtained for several fungi overlapped in the PPase-free group. In contrast, in the PPase-containing group, the variance in Tm values was smaller and there was no overlap in the Tm values obtained for all fungi tested: the LAMP product of each fungus had a specific Tm value, and the average Tm value increased as the GC% of the starting dumbbell-like structure increased. The use of PPase therefore reduced the variance in the Tm value and allowed the differentiation of these pathogenic fungi using the MCA method.

  19. The melting curve of Ni to 1 Mbar

    NASA Astrophysics Data System (ADS)

    Lord, Oliver T.; Wood, Ian G.; Dobson, David P.; Vočadlo, Lidunka; Wang, Weiwei; Thomson, Andrew R.; Wann, Elizabeth T. H.; Morard, Guillaume; Mezouar, Mohamed; Walter, Michael J.

    2014-12-01

    The melting curve of Ni has been determined to 125 GPa using laser-heated diamond anvil cell (LH-DAC) experiments in which two melting criteria were used: firstly, the appearance of liquid diffuse scattering (LDS) during in situ X-ray diffraction (XRD) and secondly, plateaux in temperature vs. laser power functions in both in situ and off-line experiments. Our new melting curve, defined by a Simon-Glatzel fit to the data where TM (K) =[ (PM/18.78±10.20 + 1) ] 1 / 2.42 ± 0.66 × 1726, is in good agreement with the majority of the theoretical studies on Ni melting and matches closely the available shock wave melting data. It is however dramatically steeper than the previous off-line LH-DAC studies in which determination of melting was based on the visual observation of motion aided by the laser speckle method. We estimate the melting point (TM) of Ni at the inner-core boundary (ICB) pressure of 330 GPa to be TM = 5800 ± 700 K (2 σ), within error of the value for Fe of TM = 6230 ± 500 K determined in a recent in situ LH-DAC study by similar methods to those employed here. This similarity suggests that the alloying of 5-10 wt.% Ni with the Fe-rich core alloy is unlikely to have any significant effect on the temperature of the ICB, though this is dependent on the details of the topology of the Fe-Ni binary phase diagram at core pressures. Our melting temperature for Ni at 330 GPa is ∼2500 K higher than that found in previous experimental studies employing the laser speckle method. We find that those earlier melting curves coincide with the onset of rapid sub-solidus recrystallization, suggesting that visual observations of motion may have misinterpreted dynamic recrystallization as convective motion of a melt. This finding has significant implications for our understanding of the high-pressure melting behaviour of a number of other transition metals.

  20. Automated Forensic Animal Family Identification by Nested PCR and Melt Curve Analysis on an Off-the-Shelf Thermocycler Augmented with a Centrifugal Microfluidic Disk Segment

    PubMed Central

    Zengerle, Roland; von Stetten, Felix; Schmidt, Ulrike

    2015-01-01

    Nested PCR remains a labor-intensive and error-prone biomolecular analysis. Laboratory workflow automation by precise control of minute liquid volumes in centrifugal microfluidic Lab-on-a-Chip systems holds great potential for such applications. However, the majority of these systems require costly custom-made processing devices. Our idea is to augment a standard laboratory device, here a centrifugal real-time PCR thermocycler, with inbuilt liquid handling capabilities for automation. We have developed a microfluidic disk segment enabling an automated nested real-time PCR assay for identification of common European animal groups adapted to forensic standards. For the first time we utilize a novel combination of fluidic elements, including pre-storage of reagents, to automate the assay at constant rotational frequency of an off-the-shelf thermocycler. It provides a universal duplex pre-amplification of short fragments of the mitochondrial 12S rRNA and cytochrome b genes, animal-group-specific main-amplifications, and melting curve analysis for differentiation. The system was characterized with respect to assay sensitivity, specificity, risk of cross-contamination, and detection of minor components in mixtures. 92.2% of the performed tests were recognized as fluidically failure-free sample handling and used for evaluation. Altogether, augmentation of the standard real-time thermocycler with a self-contained centrifugal microfluidic disk segment resulted in an accelerated and automated analysis reducing hands-on time, and circumventing the risk of contamination associated with regular nested PCR protocols. PMID:26147196

  1. Allele specific-PCR and melting curve analysis showed relatively high frequency of β-casein gene A1 allele in Iranian Holstein, Simmental and native cows.

    PubMed

    Gholami, M; Hafezian, S H; Rahimi, G; Farhadi, A; Rahimi, Z; Kahrizi, D; Kiani, S; Karim, H; Vaziri, S; Muhammadi, S; Veisi, F; Ghadiri, K; Shetabi, H; Zargooshi, J

    2016-10-31

    There are two allelic forms of A1 and A2 of β-casein gene in dairy cattle. Proteolytic digestion of bovine β-casein A1 type produces bioactive peptide of β-casomorphin-7 known as milk devil. β-casomorphin-7 causes many diseases, including type 1 diabetes, cardiovascular disease syndrome, sudden death and madness. The aim of the present study was to determine the different allelic forms of β-casein gene in Iranian Holstein, Simmental and native cattle in order to identify A1 and A2 variants. The blood samples were collected randomly and DNA was extracted using modified salting out method. An 854 bp fragment including part of exon 7 and part of intron 6 of β-casein gene was amplified by allele specific polymerase chain reaction (AS-PCR). Also, the accuracy of AS-PCR genotyping has been confirmed by melting temperature curve analysis using Real-time PCR machinery. The comparison of observed allele and genotype frequency among the studied breeds was performed using the Fisher exact and Chi-squared test, respectively by SAS program. Obtained results showed the A1 allele frequencies of 50, 51.57, 54.5, 49.4 and 46.6% in Holstein, Simmental, Sistani, Taleshi and Mazandarani cattle populations, respectively. The chi-square test was shown that no any populations were in Hardy-Weinberg equilibrium for studied marker locus. Comparison and analysis of the test results for allelic frequency showed no any significant differences between breeds (P>0.05). The frequency of observed genotypes only differs significantly between Holstein and Taleshi breeds but no any statistically significant differences were found for other breeds (P>0.05). A relatively high frequency of β-casein A1 allele was observed in Iranian native cattle. Therefore, determine the genotypes and preference alleles A2 in these native and commercial cattle is recommended.

  2. Rapid detection and grouping of porcine bocaviruses by an EvaGreen(®) based multiplex real-time PCR assay using melting curve analysis.

    PubMed

    Zheng, Xiaowen; Liu, Gaopeng; Opriessnig, Tanja; Wang, Zining; Yang, Zongqi; Jiang, Yonghou

    2016-08-01

    Several novel porcine bocaviruses (PBoVs) have been identified in pigs in recent years and association of these viruses with respiratory signs or diarrhea has been suggested. In this study, an EvaGreen(®)-based multiplex real-time PCR (EG-mPCR) with melting curve analysis was developed for simultaneous detection and grouping of novel PBoVs into the same genogroups G1, G2 and G3. Each target produced a specific amplicon with a melting peak of 81.3 ± 0.34 °C for PBoV G1, 78.2 ± 0.37 °C for PBoV G2, and 85.0 ± 0.29 °C for PBoV G3. Non-specific reactions were not observed when other pig viruses were used to assess the EG-mPCR assay. The sensitivity of the EG-mPCR assay using purified plasmid constructs containing the specific viral target fragments was 100 copies for PBoV G1, 50 for PBoV G2 and 100 for PBoV G3. The assay is able to detect and distinguish three PBoV groups with intra-assay and inter-assay variations ranging from 0.13 to 1.59%. The newly established EG-mPCR assay was validated with 227 field samples from pigs. PBoV G1, G2 and G3 was detected in 15.0%, 25.1% and 41.9% of the investigated samples and coinfections of two or three PBoV groups were also detected in 25.1% of the cases, indicating that all PBoV groups are prevalent in Chinese pigs. The agreement of the EG-mPCR assay with an EvaGreen-based singleplex real-time PCR (EG-sPCR) assay was 99.1%. This EG-mPCR will serve as a rapid, sensitive, reliable and cost effective alternative for routine surveillance testing of multiple PBoVs in pigs and will enhance our understanding of the epidemiological features and possible also pathogenetic changes associated with these viruses in pigs.

  3. Simultaneous detection and genotyping of porcine reproductive and respiratory syndrome virus (PRRSV) by real-time RT-PCR and amplicon melting curve analysis using SYBR Green.

    PubMed

    Martínez, E; Riera, P; Sitjà, M; Fang, Y; Oliveira, S; Maldonado, J

    2008-08-01

    The feasibility of using a SYBR Green-based real-time RT-PCR assay (SYBR Green ReTi RT-PCR) followed by melting curve analysis (MCA) for detecting and genotyping porcine reproductive and respiratory syndrome virus (PRRSV) was assessed. The SYBR Green ReTi RT-PCR and a previously reported two-step, non-nested RT-PCR assays were simultaneously tested on selected European (EU) and North American (US) PRRSV strains and isolates collected from diverse clinical, temporal, and geographical origins. The validation experiments showed that the optimised SYBR Green ReTi RT-PCR can sensitively and specifically detect PRRSV, consistently detecting as little as 0.03TCID(50)/sample of each virus genotype, with no type-bias and no amplification signal for other swine pathogens. After MCA, two well-differentiated melting temperature (T(m)) profiles for each virus genotype were obtained, as sequencing confirmed it. High repeatability was obtained for the T(m) values, with intra-run coefficients of variation (CoVs) of 0.25 and 0.32 and inter-run CoVs of 0.42 and 0.52 for EU and US genotypes, respectively. The sensitivity of the SYBR Green ReTi RT-PCR (100%) was higher than that of the RT-PCR (95.7%) when testing field isolates. This greater sensitivity of the SYBR Green ReTi RT-PCR was further confirmed by the detection of a higher proportion of PRRSV-positive diagnostic specimens (29.7%) than by the RT-PCR (28.5%). The SYBR Green ReTi RT-PCR test detected infection as early as 2 dpi in the sera of experimentally infected pigs regardless of virus genotype, and discriminated negative (non-inoculated), EU- and US-infected pigs. In conclusion, the reported SYBR Green ReTi RT-PCR assay coupled with MCA can detect and type PRRSV and may be useful as an alternative diagnostic assay in diverse PRRSV epidemiological circumstances.

  4. Entropy and transport properties of liquid metals along the melting curve

    NASA Astrophysics Data System (ADS)

    Cao, Qi-Long; Wang, Pan-Pan; Shao, Ju-Xiang; Wang, Fan-Hou

    2017-02-01

    Molecular dynamics simulations are performed for several monatomic metals and Fe0.9Ni0.1 metallic alloy to study the transport properties and entropy of liquids along melting curve. Our results show that the self-diffusion coefficients and viscosity of liquids increase with increasing pressure along the melting curves. Analysis suggests that, at high pressure conditions, the pair correlation entropy S2 of liquids along melting curve is bout -3.71kB, independent of the pressure and variety of liquids, which indicates that there is no obvious change in liquid structure along the melting curve. The Rosenfeld entropy-scaling laws with S2 = -3.71kB and the special values of scaling parameters can give reasonable estimates for the self-diffusion coefficients and viscosity of liquid metals along melting curves. The effect of pressure on transport coefficients can be quantified through its corresponding effect on the melting temperature and number density, and this result is in consistent with the Andrade's model. In addition, the variation of S2 provides a useful, experimentally accessible, structure-based criterion for freezing of liquid metals.

  5. Quantitative PCR coupled with melt curve analysis for detection of selected pseudo-nitzschia spp. (Bacillariophyceae) from the Northwestern Mediterranean sea.

    PubMed

    Andree, Karl B; Fernández-Tejedor, Margarita; Elandaloussi, Laurence M; Quijano-Scheggia, Sonia; Sampedro, Nagore; Garcés, Esther; Camp, Jordi; Diogène, Jorge

    2011-03-01

    The frequency and intensity of Pseudo-nitzschia spp. blooms along the coast of Catalonia have been increasing over the past 20 years. As species from this genus that are documented as toxigenic have been found in local waters, with both toxic and nontoxic species cooccurring in the same bloom, there is a need to develop management tools for discriminating the difference. Currently, differentiation of toxic and nontoxic species requires time-consuming electron microscopy to distinguish taxonomic features that would allow identification as to species, and cryptic species can still remain misidentified. In this study, cells of Pseudo-nitzschia from clonal cultures isolated from seawater were characterized to their species identity using scanning electron microscopy, and subsamples of each culture were used to create an internal transcribed spacer 1 (ITS-1), 5.8S, and ITS-2 ribosomal DNA database for development of species-specific quantitative PCR (qPCR) assays. Once developed, these qPCR assays were applied to field samples collected over a 2-year period in Alfaques Bay in the northwestern Mediterranean Sea to evaluate the possibility of a comprehensive surveillance for all Pseudo-nitzschia spp. using molecular methods to supplement optical microscopy, which can discern taxonomy only to the genus level within this taxon. Total Pseudo-nitzschia cell density was determined by optical microscopy from water samples collected weekly and compared to results obtained from the sum of eight Pseudo-nitzschia species-specific qPCR assays using duplicate samples. Species-specific qPCR followed by melt curve analysis allowed differentiation of amplicons and identification of false positives, and results correlated well with the total Pseudo-nitzschia cell counts from optical microscopy.

  6. Quantitative PCR Coupled with Melt Curve Analysis for Detection of Selected Pseudo-nitzschia spp. (Bacillariophyceae) from the Northwestern Mediterranean Sea▿

    PubMed Central

    Andree, Karl B.; Fernández-Tejedor, Margarita; Elandaloussi, Laurence M.; Quijano-Scheggia, Sonia; Sampedro, Nagore; Garcés, Esther; Camp, Jordi; Diogène, Jorge

    2011-01-01

    The frequency and intensity of Pseudo-nitzschia spp. blooms along the coast of Catalonia have been increasing over the past 20 years. As species from this genus that are documented as toxigenic have been found in local waters, with both toxic and nontoxic species cooccurring in the same bloom, there is a need to develop management tools for discriminating the difference. Currently, differentiation of toxic and nontoxic species requires time-consuming electron microscopy to distinguish taxonomic features that would allow identification as to species, and cryptic species can still remain misidentified. In this study, cells of Pseudo-nitzschia from clonal cultures isolated from seawater were characterized to their species identity using scanning electron microscopy, and subsamples of each culture were used to create an internal transcribed spacer 1 (ITS-1), 5.8S, and ITS-2 ribosomal DNA database for development of species-specific quantitative PCR (qPCR) assays. Once developed, these qPCR assays were applied to field samples collected over a 2-year period in Alfaques Bay in the northwestern Mediterranean Sea to evaluate the possibility of a comprehensive surveillance for all Pseudo-nitzschia spp. using molecular methods to supplement optical microscopy, which can discern taxonomy only to the genus level within this taxon. Total Pseudo-nitzschia cell density was determined by optical microscopy from water samples collected weekly and compared to results obtained from the sum of eight Pseudo-nitzschia species-specific qPCR assays using duplicate samples. Species-specific qPCR followed by melt curve analysis allowed differentiation of amplicons and identification of false positives, and results correlated well with the total Pseudo-nitzschia cell counts from optical microscopy. PMID:21193668

  7. Comparison of pyrosequencing, Sanger sequencing, and melting curve analysis for detection of low-frequency macrolide-resistant mycoplasma pneumoniae quasispecies in respiratory specimens.

    PubMed

    Chan, Kwok-Hung; To, Kelvin K W; Chan, Betsy W K; Li, Clara P Y; Chiu, Susan S; Yuen, Kwok-Yung; Ho, Pak-Leung

    2013-08-01

    Macrolide-resistant Mycoplasma pneumoniae (MRMP) is emerging worldwide and has been associated with treatment failure. In this study, we used pyrosequencing to detect low-frequency MRMP quasispecies in respiratory specimens, and we compared the findings with those obtained by Sanger sequencing and SimpleProbe PCR coupled with a melting curve analysis (SimpleProbe PCR). Sanger sequencing, SimpleProbe PCR, and pyrosequencing were successfully performed for 96.7% (88/91), 96.7% (88/91), and 93.4% (85/91) of the M. pneumoniae-positive specimens, respectively. The A-to-G transition at position 2063 was the only mutation identified. Pyrosequencing identified A2063G MRMP quasispecies populations in 78.8% (67/88) of the specimens. Only 38.8% (26/67) of these specimens with the A2063G quasispecies detected by pyrosequencing were found to be A2063G quasispecies by Sanger sequencing or SimpleProbe PCR. The specimens that could be detected by SimpleProbe PCR and Sanger sequencing had higher frequencies of MRMP quasispecies (51% to 100%) than those that could not be detected by those two methods (1% to 44%). SimpleProbe PCR correctly categorized all specimens that were identified as wild type or mutant by Sanger sequencing. The clinical characteristics of the patients were not significantly different when they were grouped by the presence or absence of MRMP quasispecies, while patients with MRMP identified by Sanger sequencing more often required a switch from macrolides to an alternative M. pneumoniae-targeted therapy. The clinical significance of mutant quasispecies should be investigated further with larger patient populations and with specimens obtained before and after macrolide therapy.

  8. Asymmetric real-time PCR and multiplex melting curve analysis with TaqMan probes for detecting PIK3CA mutations.

    PubMed

    Botezatu, Irina V; Nechaeva, Irina O; Stroganova, Аnna М; Senderovich, Anastasia I; Kondratova, Valentina N; Shelepov, Valery P; Lichtenstein, Anatoly V

    2015-12-01

    The data in this article are related to the research article entitled "Optimization of melting analysis with TaqMan probes for detection of KRAS, NRAS, and BRAF mutations" Botezatu et al. [1]. Somatic mutations in the PIK3CA gene ("hot spots" in exons 9 and 20) are found in many human cancers, and their presence can determine prognosis and a treatment strategy. An effective method of mutation scanning PIK3CA in clinical laboratories is DNA Melting Analysis (DMA) (Vorkas et al., 2010; Simi et al., 2008) [2], [3]. It was demonstrated recently that the TaqMan probes which have been long used in Real Time PCR may also be utilized in DMA (Huang et al., 2011) [4]. After optimization of this method Botezatu et al. [1], it was used for multiplex scanning PIK3CA hotspot mutations in formalin-fixed paraffin-embedded (FFPE) samples from patients with colorectal and lung cancer.

  9. Detection of Babesia canis vogeli and Hepatozoon canis in canine blood by a single-tube real-time fluorescence resonance energy transfer polymerase chain reaction assay and melting curve analysis.

    PubMed

    Kongklieng, Amornmas; Intapan, Pewpan M; Boonmars, Thidarut; Thanchomnang, Tongjit; Janwan, Penchom; Sanpool, Oranuch; Lulitanond, Viraphong; Taweethavonsawat, Piyanan; Chungpivat, Sudchit; Maleewong, Wanchai

    2015-03-01

    A real-time fluorescence resonance energy transfer polymerase chain reaction (qFRET PCR) coupled with melting curve analysis was developed for detection of Babesia canis vogeli and Hepatozoon canis infections in canine blood samples in a single tube assay. The target of the assay was a region within the 18S ribosomal RNA gene amplified in either species by a single pair of primers. Following amplification from the DNA of infected dog blood, a fluorescence melting curve analysis was done. The 2 species, B. canis vogeli and H. canis, could be detected and differentiated in infected dog blood samples (n = 37) with high sensitivity (100%). The detection limit for B. canis vogeli was 15 copies of a positive control plasmid, and for H. canis, it was 150 copies of a positive control plasmid. The assay could simultaneously distinguish the DNA of both parasites from the DNA of controls. Blood samples from 5 noninfected dogs were negative, indicating high specificity. Several samples can be run at the same time. The assay can reduce misdiagnosis and the time associated with microscopic examination, and is not prone to the carryover contamination associated with the agarose gel electrophoresis step of conventional PCR. In addition, this qFRET PCR method would be useful to accurately determine the range of endemic areas or to discover those areas where the 2 parasites co-circulate.

  10. Ultrafast real-time PCR with integrated melting curve analysis and duplex capacities using a low-cost polymer lab-on-a-chip system

    NASA Astrophysics Data System (ADS)

    Gransee, Rainer; Schneider, Tristan; Elyorgun, Deniz; Strobach, Xenia; Schunck, Tobias; Gatscha, Theresia; Winkler, Christian; Höth, Julian

    2015-05-01

    Nucleic amplification using quantitative polymeric chain reaction (qPCR) has become the gold standard of molecular testing. These systems offer both amplification and simultaneous fluorescence detection. An ultrafast microfluidic module (allowing 30 PCR cycles in 6 minutes) based on the oscillating fluid plug concept was previously developed [1,2] allowing the amplification of native genomic deoxyribonucleic acid (DNA) molecules. This abstract presents the actual status of the advanced system. The upgraded system generates high quality qPCR amplification plots and additional sensitive melting point analysis comparable to data obtained from commercial real-time cyclers. These features provide the user with all information needed to analyze PCR products. The system uses light emitting diodes (LED) for illumination and a low cost Charge-coupled Device (CCD) camera for optical detection. Image data processing allows the automated process control of the overall system components. The system enables the performance of rapid and robust nucleic acid amplifications together with the integration of real time measurement technology. This allows the amplification and simultaneous quantification of the targeted pathogens. The integration of duplex amplification performance allows the incorporation of the necessary controls into the device to validate the PCR performance. This demonstrator can be run either as fully autonomously working device or as OEM part of a sample-to-answer platform.

  11. Rapid detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini eggs in human fecal samples using a duplex real-time fluorescence resonance energy transfer PCR and melting curve analysis.

    PubMed

    Sanpool, Oranuch; Intapan, Pewpan M; Thanchomnang, Tongjit; Janwan, Penchom; Lulitanond, Viraphong; Doanh, Pham Ngoc; Van Hien, Hoang; Dung, Do Trung; Maleewong, Wanchai; Nawa, Yukifumi

    2012-07-01

    We developed a single step duplex real-time fluorescence resonance energy transfer (FRET) PCR merged with melting curve analysis for the fast detection and differentiation of Clonorchis sinensis and Opisthorchis viverrini eggs in human fecal samples. Two species of mitochondrial NADH dehydrogenase subunit 2 (nad2) DNA elements, the 165-bp nad2 product of C. sinensis and the 209-bp nad2 product of O. viverrini, were amplified by species-specific primers, and the fluorescence melting curve analyses were generated from hybrid of amplicons and two pairs of species-specific fluorophore-labeled probes. By their different fluorescence channels and melting temperatures, both C. sinensis and O. viverrini eggs in infected human fecal samples were detected and differentiated with high (100%) sensitivity and specificity. Detection limit was as little as a single C. sinensis egg and two O. viverrini eggs in 100 mg of fecal sample. The assay could distinguish the DNA of both parasites from the DNA of negative fecal samples and fecal samples with other parasitosis, as well as from the well-defined genomic DNA of human leukocytes and other parasites. It can reduce labor time of microscopic examination and is not prone to carry over contamination of agarose electrophoresis. Our duplex real-time FRET PCR method would be useful to determine the accurate range of endemic areas and/or to discover the co-endemic areas of two liver flukes, C. sinensis and O. viverrini, in Asia. This method also would be helpful for the differential diagnosis of the suspected cases of liver fluke infections among travelers who had visited the endemic countries of those parasites.

  12. 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.

  13. Two alternative multiplex PCRs for the identification of the seven species of anglerfish (Lophius spp.) using an end-point or a melting curve analysis real-time protocol.

    PubMed

    Castigliego, Lorenzo; Armani, Andrea; Tinacci, Lara; Gianfaldoni, Daniela; Guidi, Alessandra

    2015-01-01

    Anglerfish (Lophius spp.) is consumed worldwide and is an important economic resource though its seven species are often fraudulently interchanged due to their different commercial value, especially when sold in the form of fillets or pieces. Molecular analysis is the only possible mean to verify traceability and counteract fraud. We developed two multiplex PCRs, one end-point and one real-time with melting curve post-amplification analysis, which can even be run with the simplest two-channel thermocyclers. The two methods were tested on seventy-five reference samples. Their specificity was checked in twenty more species of those most commonly available on the market and in other species of the Lophiidae family. Both methods, the choice of which depends on the equipment and budget of the lab, provide a rapid and easy-to-read response, improving both the simplicity and cost-effectiveness of existing methods for identifying Lophius species.

  14. Application of a real-time fluorescence resonance energy transfer polymerase chain reaction assay with melting curve analysis for the detection of Paragonimus heterotremus eggs in the feces of experimentally infected cats.

    PubMed

    Tantrawatpan, Chairat; Intapan, Pewpan M; Thanchomnang, Tongjit; Sanpool, Oranuch; Janwan, Penchom; Lulitanond, Viraphong; Anamnart, Witthaya; Maleewong, Wanchai

    2013-09-01

    Paragonimus heterotremus is a medically important lung fluke that causes human and animal paragonimiasis in Southeast Asia, including Thailand. In the current study, a real-time fluorescence resonance energy transfer polymerase chain reaction (real-time FRET PCR) with melting curve analysis was developed and evaluated to detect P. heterotremus eggs in the feces of experimentally infected cats. The detection limit of this method for the P. heterotremus DNA sequence was 3 × 10(2) copies of the positive control plasmid and 10(-3) ng of P. heterotremus genomic DNA. The assay system could detect 10 eggs of P. heterotremus per gram of cat feces. No fluorescence signal was observed when DNA purified from 16 other organisms or genomic DNA from cats and human beings were tested. Real-time FRET PCR yielded positive results for all fecal samples from 17 P. heterotremus-infected cats and showed a negative relationship (r = -0.852, P < 0.001) between the number of parasite eggs in feces and the number of PCR cycles. The assay could detect genomic DNA from P. heterotremus, P. westermani, P. macrorchis, P. siamensis, P. harinasutai, and P. bangkokensis and can differentiate P. heterotremus from the other 5 species. The 6 Paragonimus species examined were divided into 4 groups by melting peak analysis. This assay can be useful for the detection of, and epidemiological studies on, P. heterotremus infection in endemic areas.

  15. Molecular dynamics simulations of the melting curve of NiAl alloy under pressure

    SciTech Connect

    Zhang, Wenjin; Peng, Yufeng; Liu, Zhongli

    2014-05-15

    The melting curve of B2-NiAl alloy under pressure has been investigated using molecular dynamics technique and the embedded atom method (EAM) potential. The melting temperatures were determined with two approaches, the one-phase and the two-phase methods. The first one simulates a homogeneous melting, while the second one involves a heterogeneous melting of materials. Both approaches reduce the superheating effectively and their results are close to each other at the applied pressures. By fitting the well-known Simon equation to our melting data, we yielded the melting curves for NiAl: 1783(1 + P/9.801){sup 0.298} (one-phase approach), 1850(1 + P/12.806){sup 0.357} (two-phase approach). The good agreement of the resulting equation of states and the zero-pressure melting point (calc., 1850 ± 25 K, exp., 1911 K) with experiment proved the correctness of these results. These melting data complemented the absence of experimental high-pressure melting of NiAl. To check the transferability of this EAM potential, we have also predicted the melting curves of pure nickel and pure aluminum. Results show the calculated melting point of Nickel agrees well with experiment at zero pressure, while the melting point of aluminum is slightly higher than experiment.

  16. Classification of Mycoplasma synoviae strains using single-strand conformation polymorphism and high-resolution melting-curve analysis of the vlhA gene single-copy region.

    PubMed

    Jeffery, Nathan; Gasser, Robin B; Steer, Penelope A; Noormohammadi, Amir H

    2007-08-01

    Mycoplasma synoviae is an economically important pathogen of poultry worldwide, causing respiratory infection and synovitis in chickens and turkeys. Identification of M. synoviae isolates is of critical importance, particularly in countries in which poultry flocks are vaccinated with the live attenuated M. synoviae strain MS-H. Using oligonucleotide primers complementary to the single-copy conserved 5' end of the variable lipoprotein and haemagglutinin gene (vlhA), amplicons of approximately 400 bp were generated from 35 different M. synoviae strains/isolates from chickens and subjected to mutation scanning analysis. Analysis of the amplicons by single-strand conformation polymorphism (SSCP) revealed 10 distinct profiles (A-J). Sequencing of the amplicons representing these profiles revealed that each profile related to a unique sequence, some differing from each other by only one base-pair substitution. Comparative high-resolution melting (HRM) curve analysis of the amplicons using SYTO 9 green fluorescent dye also displayed profiles which were concordant with the same 10 SSCP profiles (A-J) and their sequences. For both mutation detection methods, the Australian M. synoviae strains represented one of the A, B, C or D profiles, while the USA strains represented one of the E, F, G, H, I or J profiles. The results presented in this study show that the PCR-based SSCP or HRM curve analyses of vlhA provide high-resolution mutation detection tools for the detection and identification of M. synoviae strains. In particular, the HRM curve analysis is a rapid and effective technique which can be performed in a single test tube in less than 2 h.

  17. Fluid-fluid-solid triple point on melting curves at high temperatures

    NASA Astrophysics Data System (ADS)

    Norman, G. E.; Saitov, I. M.

    2016-11-01

    An analysis is presented of experimental data where fluid-fluid phase transitions are observed for different substances at high temperatures with triple points on melting curves. Viscosity drops point to the structural character of the transition, whereas conductivity jumps remind of both semiconductor-to-metal and plasma nature. The slope of the phase equilibrium dependencies of pressure on temperature and the consequent change of the specific volume, which follows from the Clapeyron-Clausius equation, are discussed. P(V, T) surfaces are presented and discussed for the phase transitions considered in the vicinity of the triple points. The cases of abnormal P(T) dependencies on curves of phase equilibrium are in the focus of discussion. In particular, a P(V, T) surface is presented when both fluid-fluid and melting P(T) curves are abnormal. Particular attention is paid to warm dense hydrogen and deuterium, where remarkable contradictions exist between data of different authors. The possible connection of the P(V, T) surface peculiarities with the experimental data uncertainties is outlined.

  18. The high-pressure melting curve of iron - A technical discussion

    NASA Technical Reports Server (NTRS)

    Williams, Quentin; Knittle, Elise; Jeanloz, Raymond

    1991-01-01

    The melting curve of iron is reliably determined to 105 GPa using the laser-heated diamond cell, in close agreement with independent measurements using piston-cylinder and large-volume presses or shock-wave experiments. In order to obtain reliable melting data from the internally heated diamond cell, whether by laser or Joule heating, temperature gradients across the sample must be quantitatively measured; otherwise, such 'wire heating' experiments can lead to significant underestimates of the melting temperature and its pressure dependence. The best estimate of the high-pressure melting curve of iron, as derived from the laser-heated diamond cell and Hugoniot temperature measurements, yields melting temperatures of 4800 + or - 200 K and 6700 + or - 400 K at 133 GPa and 243 GPa, respectively.

  19. Differentiation of entC1 from entC2/entC3 with a single primer pair using simple and rapid SYBR Green-based RT-PCR melt curve analysis.

    PubMed

    Nagaraj, Sowmya; Ramlal, Shylaja; Venkataswamachari, Bhavani Peddayelachagiri; Paul, Soumya; Kingston, Joseph; Batra, Harsh Vardhan

    2016-10-01

    In spite of their involvement in foodborne illness, the epidemiological relevance of staphylococcal enterotoxin C (SEC) subtypes is poorly documented may be due to high sequence similarity. Among subtypes, SEC1, SEC2, and SEC3 exhibit more than 97 % homology because of which specific detection tools are seldom available to identify and differentiate them. In this study, a SYBR Green-based RT-PCR followed by melt curve analysis was developed for differentiation of entC1 from entC2/entC3 using a single primer pair. Nucleotide sequences of all three subtypes were analyzed using Clustal Omega program and the region with significant sequence variation/heterogeneity (where utmost SNPs were closely located and accessible for RT-PCR) was selected for amplification by designing a single primer pair that could amplify all three subtypes. In spite of same amplicon size, entC1 showed distinct melt peak at 76 °C. However, due to high similarity between entC2 and entC3, the developed format was deficient to discriminate between them and both showed melt peak at 82 °C. Reliability of developed RT-PCR was evaluated using various naturally contaminated samples and 91 food and clinical Staphylococcus aureus isolates where satisfactory results were obtained in comparison with commercial immunoassay kit and conventional PCRs using validated primers. To the best of our knowledge, this is the first method being reported to differentiate entC1 from entC2/entC3 using single primer pair which is unachievable by conventional PCR due to same amplicon size. As benefits, the method is sensitive, rapid, and inexpensive with no requirement of fluorescent probes, multiple primers, and post-PCR procedures. Thus, the assay might find its utility as a detection tool in epidemiological survey of foodborne outbreaks for simultaneous identification and differentiation of entC1 from entC2/entC3.

  20. Rapid detection of the factor XIII Val34Leu (163 G-->T) polymorphism by real-time PCR using fluorescence resonance energy transfer detection and melting curve analysis.

    PubMed

    Shemirani, Amir H; Muszbek, László

    2004-01-01

    The Val34Leu polymorphism in the A subunit of blood coagulation factor XIII (FXIII-A) is located in the activation peptide, just three amino acids upstream of the thrombin cleavage site. The Val-->Leu replacement accelerates the rate of the proteolytic activation of FXIII and it seems to provide protection against myocardial infarction. Methods available for the assessment of the FXIII-A Val34Leu polymorphism are rather time-consuming, laborious and not easily applicable for large-scale studies. In this study a new method based on real-time PCR with fluorescence resonance energy transfer (FRET) detection and melting curve analysis was developed. The rapid, simple method was adapted to the widely used real-time PCR instrument, LightCycler (Roche Diagnostics). The results showed 100% coincidence with those obtained by the traditional PCR-restriction fragment length polymorphism (RFLP) assay and fluorescent DNA sequencing. Using this method, an allele frequency of 24.2% was obtained (n=113), which well agrees with the allele frequency obtained by PCR-RFLP on a different group of the same ethnic Hungarian population (25.9%).

  1. 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.

  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. Molecular dynamics study of the melting curve of NiTi alloy under pressure

    NASA Astrophysics Data System (ADS)

    Zeng, Zhao-Yi; Hu, Cui-E.; Cai, Ling-Cang; Chen, Xiang-Rong; Jing, Fu-Qian

    2011-02-01

    The melting curve of NiTi alloy was predicted by using molecular dynamics simulations combining with the embedded atom model potential. The calculated thermal equation of state consists well with our previous results obtained from quasiharmonic Debye approximation. Fitting the well-known Simon form to our Tm data yields the melting curves for NiTi: 1850(1 + P/21.938)0.328 (for one-phase method) and 1575(1 + P/7.476)0.305 (for two-phase method). The two-phase simulations can effectively eliminate the superheating in one-phase simulations. At 1 bar, the melting temperature of NiTi is 1575 ± 25 K and the corresponding melting slope is 64 K/GPa.

  4. Prediction of solubility curves and melting properties of organic and pharmaceutical compounds.

    PubMed

    Nordström, Fredrik L; Rasmuson, Ake C

    2009-02-15

    The relationships between solubility, temperature dependence of solubility, melting temperature and melting enthalpy are investigated for the purpose of finding relations that can significantly reduce the need for experimental work in the selection of the solvent for processing of organic fine chemicals and pharmaceuticals. The relationships are investigated theoretically and by evaluation of experimental data for 41 organic and pharmaceutical compounds comprising a total of 115 solubility curves in organic and aqueous solvents. The work considers (i) selection of the equation for correlation of solubility data based on thermodynamic considerations and ability to predict melting properties of the solute from solubility data, (ii) prediction of the temperature dependence of solubility, and (iii) prediction of solubility curves in new solvents. While it is a simple task to find an equation to obtain a decent fit of experimental solubility data, it is more challenging to find relations that are sufficiently sound thermodynamically to allow for extrapolation to the melting temperature. However, with a proper choice of equation it is shown that the melting temperature of the solute can readily be predicted from solubility data in organic solvents (average accuracy of -5K, standard deviation of 26K). Relationships are identified by which the entire solubility curve can be predicted of the compound in a new solvent using only the melting properties and a single solubility data point in that solvent.

  5. The melting curve of Ni to 125 GPa: implications for Earth's Fe rich core alloy

    NASA Astrophysics Data System (ADS)

    Lord, O. T.; Wood, I. G.; Dobson, D. P.; Vocadlo, L.; Thomson, A. R.; Wann, E.; Wang, W.; Edgington, A.; Morard, G.; Mezouar, N.; Walter, M. J.

    2014-12-01

    The melting curve of Ni has been determined to 125 GPa using laser-heated diamond anvil cell (LH-DAC) experiments and two melting criteria: the appearance of liquid diffuse scattering (LDS) during in situ X-ray diffraction (XRD) and simultaneous plateaux in temperature vs. laser power functions [1]. Our melting curve (Fig. 1) is in good agreement with most theoretical studies [e.g. 2] and the available shock wave data (Fig. 2). It is, however, dramatically steeper than the previous off-line LH-DAC studies in which the determination of melting was based on the visual observation of motion aided by the laser speckle method [e.g. 3]. We estimate the melting point of Ni at the inner-core boundary (ICB; 330 GPa) to be 5800±700 K (2σ), ~2500 K higher than the estimate based on the laser speckle method [3] and within error of Fe (6230±500 K) as determined in a similar in situ LH-DAC study [4]. We find that laser speckle based melting curves coincide with the onset of rapid sub-solidus recrystallization, suggesting that visual observations of motion may have misinterpreted dynamic recrystallization as melt convection. Our new melting curve suggests that the reduction in ICB temperature due to the alloying of Ni with Fe is likely to be significantly smaller than would be expected had the earlier experimental Ni melting studies been correct. We have applied our methodology to a range of other transition metals (Mo, Ti, V, Cu). In the case of Mo, Ti and V the melting curves are in good agreement with the shock compression and theoretical melting studies but hotter and steeper than those based on the laser speckle method, as with Ni. Cu is an exception in which all studies agree, including those employing the laser speckle method. These results go a long way toward resolving the the long-standing controversy over the phase diagrams of the transition metals as determined from static LH-DAC studies on the one hand, and theoretical and dynamic compression studies on the other

  6. Development of an EvaGreen-based multiplex real-time PCR assay with melting curve analysis for simultaneous detection and differentiation of six viral pathogens of porcine reproductive and respiratory disorder.

    PubMed

    Rao, Pinbin; Wu, Haigang; Jiang, Yonghou; Opriessnig, Tanja; Zheng, Xiaowen; Mo, Yecheng; Yang, Zongqi

    2014-11-01

    Concurrent infection of pigs with two or more pathogens is common in pigs under intensive rearing conditions. Porcine circovirus type 2 (PCV2), porcine parvovirus (PPV), porcine reproductive and respiratory syndrome virus (PRRSV), classical swine fever virus (CSFV), Japanese encephalitis virus (JEV) and pseudorabies virus (PRV) are all associated with reproductive or respiratory disorders or both and can cause significant economic losses in pig production worldwide. An EvaGreen-based multiplex real-time PCR (EG-mPCR) with melting curve analysis was developed in this study for simultaneous detection and differentiation of these six viruses in pigs. This method is able to detect and distinguish PCV2, PPV, PRRSV, CSFV, JEV and PRV with the limits of detection ranging from 100 to 500 copies/μL, high reproducibility, and intra-assay and inter-assay variation ranging from 0.11 to 3.20%. After validation, a total of 118 field samples were tested by the newly developed EG-mPCR. PCV2 was identified in 23%, PPV in 15%, PRRSV in 17% and PRV in 5% of the samples. Concurrent PCV2 and PRRSV infection was detected in 6.7%, PCV2 and PPV in 5% and PPV2 and PRRSV infection was detected in 5% of the cases. The agreement of the EG-mPCR and conventional PCR tests was 99.2%. This EG-mPCR will be a useful, rapid, reliable and cost-effective alternative for routine surveillance testing of viral infections in pigs.

  7. Analysis of Exoplanet Light Curves

    NASA Astrophysics Data System (ADS)

    Erdem, A.; Budding, E.; Rhodes, M. D.; Püsküllü, Ç.; Soydugan, F.; Soydugan, E.; Tüysüz, M.; Demircan, O.

    2015-07-01

    We have applied the close binary system analysis package WINFITTER to a variety of exoplanet transiting light curves taken both from the NASA Exoplanet Archive and our own ground-based observations. WINFitter has parameter options for a realistic physical model, including gravity brightening and structural parameters derived from Kopal's applications of the relevant Radau equation, and it includes appropriate tests for determinacy and adequacy of its best fitting parameter sets. We discuss a number of issues related to empirical checking of models for stellar limb darkening, surface maculation, Doppler beaming, microvariability, and transit time variation (TTV) effects. The Radau coefficients used in the light curve modeling, in principle, allow structural models of the component stars to be tested.

  8. A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses

    PubMed Central

    Wan, Zhenzhou; Zhang, Ya’nan; He, Zhixiang; Liu, Jia; Lan, Ke; Hu, Yihong; Zhang, Chiyu

    2016-01-01

    Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 102 copies for HCoV-OC43, and 3 × 101 copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 μL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples. PMID:27886052

  9. A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses.

    PubMed

    Wan, Zhenzhou; Zhang, Ya'nan; He, Zhixiang; Liu, Jia; Lan, Ke; Hu, Yihong; Zhang, Chiyu

    2016-11-23

    Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 10² copies for HCoV-OC43, and 3 × 10¹ copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 μL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples.

  10. Theoretical calculation of the melting curve of Cu-Zr binary alloys

    DOE PAGES

    Gunawardana, K. G.S.H.; Wilson, S. R.; Mendelev, M. I.; ...

    2014-11-14

    Helmholtz free energies of the dominant binary crystalline solids found in the Cu-Zr system at high temperatures close to the melting curve are calculated. This theoretical approach combines fundamental measure density functional theory (applied to the hard-sphere reference system) and a perturbative approach to include the attractive interactions. The studied crystalline solids are Cu(fcc), Cu51Zr14(β), CuZr(B2), CuZr2(C11b), Zr(hcp), and Zr(bcc). The calculated Helmholtz free energies of crystalline solids are in good agreement with results from molecular-dynamics (MD) simulations. Using the same perturbation approach, the liquid phase free energies are calculated as a function of composition and temperature, from which themore » melting curve of the entire composition range of this system can be obtained. Phase diagrams are determined in this way for two leading embedded atom method potentials, and the results are compared with experimental data. Furthermore, theoretical melting temperatures are compared both with experimental values and with values obtained directly from MD simulations at several compositions.« less

  11. Theoretical calculation of the melting curve of Cu-Zr binary alloys

    SciTech Connect

    Gunawardana, K. G.S.H.; Wilson, S. R.; Mendelev, M. I.; Song, Xueyu

    2014-11-14

    Helmholtz free energies of the dominant binary crystalline solids found in the Cu-Zr system at high temperatures close to the melting curve are calculated. This theoretical approach combines fundamental measure density functional theory (applied to the hard-sphere reference system) and a perturbative approach to include the attractive interactions. The studied crystalline solids are Cu(fcc), Cu51Zr14(β), CuZr(B2), CuZr2(C11b), Zr(hcp), and Zr(bcc). The calculated Helmholtz free energies of crystalline solids are in good agreement with results from molecular-dynamics (MD) simulations. Using the same perturbation approach, the liquid phase free energies are calculated as a function of composition and temperature, from which the melting curve of the entire composition range of this system can be obtained. Phase diagrams are determined in this way for two leading embedded atom method potentials, and the results are compared with experimental data. Furthermore, theoretical melting temperatures are compared both with experimental values and with values obtained directly from MD simulations at several compositions.

  12. Trainable high resolution melt curve machine learning classifier for large-scale reliable genotyping of sequence variants.

    PubMed

    Athamanolap, Pornpat; Parekh, Vishwa; Fraley, Stephanie I; Agarwal, Vatsal; Shin, Dong J; Jacobs, Michael A; Wang, Tza-Huei; Yang, Samuel

    2014-01-01

    High resolution melt (HRM) is gaining considerable popularity as a simple and robust method for genotyping sequence variants. However, accurate genotyping of an unknown sample for which a large number of possible variants may exist will require an automated HRM curve identification method capable of comparing unknowns against a large cohort of known sequence variants. Herein, we describe a new method for automated HRM curve classification based on machine learning methods and learned tolerance for reaction condition deviations. We tested this method in silico through multiple cross-validations using curves generated from 9 different simulated experimental conditions to classify 92 known serotypes of Streptococcus pneumoniae and demonstrated over 99% accuracy with 8 training curves per serotype. In vitro verification of the algorithm was tested using sequence variants of a cancer-related gene and demonstrated 100% accuracy with 3 training curves per sequence variant. The machine learning algorithm enabled reliable, scalable, and automated HRM genotyping analysis with broad potential clinical and epidemiological applications.

  13. Melting curves and structural properties of tantalum from the modified-Z method

    SciTech Connect

    Liu, C. M. E-mail: ycheng@scu.edu.cn; Xu, C.; Cheng, Y. E-mail: ycheng@scu.edu.cn; Chen, X. R.; Cai, L. C.

    2015-12-21

    The melting curves and structural properties of tantalum (Ta) are investigated by molecular dynamics simulations combining with potential model developed by Ravelo et al. [Phys. Rev. B 88, 134101 (2013)]. Before calculations, five potentials are systematically compared with their abilities of producing reasonable compressional and equilibrium mechanical properties of Ta. We have improved the modified-Z method introduced by Wang et al. [J. Appl. Phys. 114, 163514 (2013)] by increasing the sizes in L{sub x} and L{sub y} of the rectangular parallelepiped box (L{sub x} = L{sub y} ≪ L{sub z}). The influences of size and aspect ratio of the simulation box to melting curves are also fully tested. The structural differences between solid and liquid are detected by number density and local-order parameters Q{sub 6}. Moreover, the atoms' diffusion with simulation time, defects, and vacancies formations in the sample are all studied by comparing situations in solid, solid-liquid coexistence, and liquid state.

  14. Fast and Efficient Screening for Wheat Loss-of-Gene Mutants Using Multiplexed Melt Curve Analyses.

    PubMed

    Mieog, Jos C; Ral, Jean-Philippe F

    2016-01-01

    This study describes a new approach in the screening for loss-of-gene mutants in Heavy Ion Bombardment (HIB) mutant populations of genetically complex organisms such as hexaploid bread wheat using multiplexed single-color (SYBR Green) melt curve analyses. The assay was set up for three target genes to test its validity and applicability. For each gene, three genome-specific primer pairs (one for each genome) with distinct melt curves were developed and multiplexed. This allowed screening for "single null mutants" (plants with the target gene deleted in one of the three genomes) for all three genomes in a single reaction. The first two genes (α-Amylase 3 and Epsilon Cyclase) were used to test the approach as HIB null lines for all three genomes were already available for these. The third assay was successfully applied to identify new single null lines of the target gene α-Amylase 2 in an in-house HIB wheat collection. The use of SYBR Green greatly reduced the time and/or cost investment compared to other techniques and the approach proved highly suitable for high-throughput applications.

  15. Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification

    PubMed Central

    Phatak, Sayali S.; Li, Dongmei; Luka, Janos; Calderone, Richard A.

    2017-01-01

    Fungal infections are a global problem imposing considerable disease burden. One of the unmet needs in addressing these infections is rapid, sensitive diagnostics. A promising molecular diagnostic approach is high-resolution melt analysis (HRM). However, there has been little effort in leveraging HRM data for automated, objective identification of fungal species. The purpose of these studies was to assess the utility of distance methods developed for comparison of time series data to classify HRM curves as a means of fungal species identification. Dynamic time warping (DTW), first introduced in the context of speech recognition to identify temporal distortion of similar sounds, is an elastic distance measure that has been successfully applied to a wide range of time series data. Comparison of HRM curves of the rDNA internal transcribed spacer (ITS) region from 51 strains of 18 fungal species using DTW distances allowed accurate classification and clustering of all 51 strains. The utility of DTW distances for species identification was demonstrated by matching HRM curves from 243 previously identified clinical isolates against a database of curves from standard reference strains. The results revealed a number of prior misclassifications, discriminated species that are not resolved by routine phenotypic tests, and accurately identified all 243 test strains. In addition to DTW, several other distance functions, Edit Distance on Real sequence (EDR) and Shape-based Distance (SBD), showed promise. It is concluded that DTW-based distances provide a useful metric for the automated identification of fungi based on HRM curves of the ITS region and that this provides the foundation for a robust and automatable method applicable to the clinical setting. PMID:28264030

  16. Dynamic time warping assessment of high-resolution melt curves provides a robust metric for fungal identification.

    PubMed

    Lu, Sha; Mirchevska, Gordana; Phatak, Sayali S; Li, Dongmei; Luka, Janos; Calderone, Richard A; Fonzi, William A

    2017-01-01

    Fungal infections are a global problem imposing considerable disease burden. One of the unmet needs in addressing these infections is rapid, sensitive diagnostics. A promising molecular diagnostic approach is high-resolution melt analysis (HRM). However, there has been little effort in leveraging HRM data for automated, objective identification of fungal species. The purpose of these studies was to assess the utility of distance methods developed for comparison of time series data to classify HRM curves as a means of fungal species identification. Dynamic time warping (DTW), first introduced in the context of speech recognition to identify temporal distortion of similar sounds, is an elastic distance measure that has been successfully applied to a wide range of time series data. Comparison of HRM curves of the rDNA internal transcribed spacer (ITS) region from 51 strains of 18 fungal species using DTW distances allowed accurate classification and clustering of all 51 strains. The utility of DTW distances for species identification was demonstrated by matching HRM curves from 243 previously identified clinical isolates against a database of curves from standard reference strains. The results revealed a number of prior misclassifications, discriminated species that are not resolved by routine phenotypic tests, and accurately identified all 243 test strains. In addition to DTW, several other distance functions, Edit Distance on Real sequence (EDR) and Shape-based Distance (SBD), showed promise. It is concluded that DTW-based distances provide a useful metric for the automated identification of fungi based on HRM curves of the ITS region and that this provides the foundation for a robust and automatable method applicable to the clinical setting.

  17. Melting curve of SiO2 at multimegabar pressures: implications for gas giants and super-Earths.

    PubMed

    González-Cataldo, Felipe; Davis, Sergio; Gutiérrez, Gonzalo

    2016-05-23

    Ultrahigh-pressure phase boundary between solid and liquid SiO2 is still quite unclear. Here we present predictions of silica melting curve for the multimegabar pressure regime, as obtained from first principles molecular dynamics simulations. We calculate the melting temperatures from three high pressure phases of silica (pyrite-, cotunnite-, and Fe2P-type SiO2) at different pressures using the Z method. The computed melting curve is found to rise abruptly around 330 GPa, an increase not previously reported by any melting simulations. This is in close agreement with recent experiments reporting the α-PbO2-pyrite transition around this pressure. The predicted phase diagram indicates that silica could be one of the dominant components of the rocky cores of gas giants, as it remains solid at the core of our Solar System's gas giants. These results are also relevant to model the interior structure and evolution of massive super-Earths.

  18. 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 .

  19. Determination of the Melting Curve of the Modified Lennard-Jones System Using the Nonequilibrium Relaxation Method

    NASA Astrophysics Data System (ADS)

    Asano, Yuta; Fuchizaki, Kazuhiro

    2017-02-01

    The melting curve of the modified Lennard-Jones system, which has been obtained by equating the free energies between the solid and liquid phases, was reinvestigated using the nonequilibrium relaxation method. The latter method satisfactorily reproduced the previous result with much simplified procedures.

  20. Analysis of HIV Using a High Resolution Melting (HRM) Diversity Assay: Automation of HRM Data Analysis Enhances the Utility of the Assay for Analysis of HIV Incidence

    PubMed Central

    Cousins, Matthew M.; Swan, David; Magaret, Craig A.; Hoover, Donald R.; Eshleman, Susan H.

    2012-01-01

    Background HIV diversity may be a useful biomarker for discriminating between recent and non-recent HIV infection. The high resolution melting (HRM) diversity assay was developed to quantify HIV diversity in viral populations without sequencing. In this assay, HIV diversity is expressed as a single numeric HRM score that represents the width of a melting peak. HRM scores are highly associated with diversity measures obtained with next generation sequencing. In this report, a software package, the HRM Diversity Assay Analysis Tool (DivMelt), was developed to automate calculation of HRM scores from melting curve data. Methods DivMelt uses computational algorithms to calculate HRM scores by identifying the start (T1) and end (T2) melting temperatures for a DNA sample and subtracting them (T2–T1 = HRM score). DivMelt contains many user-supplied analysis parameters to allow analyses to be tailored to different contexts. DivMelt analysis options were optimized to discriminate between recent and non-recent HIV infection and to maximize HRM score reproducibility. HRM scores calculated using DivMelt were compared to HRM scores obtained using a manual method that is based on visual inspection of DNA melting curves. Results HRM scores generated with DivMelt agreed with manually generated HRM scores obtained from the same DNA melting data. Optimal parameters for discriminating between recent and non-recent HIV infection were identified. DivMelt provided greater discrimination between recent and non-recent HIV infection than the manual method. Conclusion DivMelt provides a rapid, accurate method of determining HRM scores from melting curve data, facilitating use of the HRM diversity assay for large-scale studies. PMID:23240016

  1. Melting curve of the deep mantle applied to properties of early magma ocean and actual core-mantle boundary

    NASA Astrophysics Data System (ADS)

    Andrault, Denis; Lo Nigro, Giacomo; Bolfan-Casanova, Nathalie; Bouhifd, Mohamed A.; Garbarino, Gaston; Mezouar, Mohamed

    2010-05-01

    Our planet experienced partial melting early in its history as a consequence of energy release due to accretion. Partial mantle melting could still happen today in the lowermost mantle. Occurrence of melting is primordial for the chemical segregation between the different Earth's reservoirs and for the dynamics of the whole planet. Melting of iron-alloys is relatively easy to achieve, but the silicated mantle happens to be more refractory. We investigated experimentally melting properties of two starting material, forsterite and chondritic-mantle, at pressures ranging from 25 to 140 GPa, using laser-heated diamond anvil cell coupled with synchrotron radiation. We show that partial melting in the lowermost mantle, as suggested by seismology on the basis of the ultra-low velocity zones (ULVZ), requires temperatures above 4200 K at the core-mantle boundary. At low pressures, our curve plots significantly lower than previous reports. Compared to recent estimates of mantle geotherm, while this temperature remains possible if the Earth's core is very hot, it is more likely that ULVZs correspond to high concentration of incompatible elements driven down to the D"-layer by subducting slabs or extracted out from the outer core. When our chondritic melting curve is coupled with recent isentropic temperature profiles for a magma ocean, we obtain a correlation between magma ocean depth and the potential temperature (Tp) at its surface; an ocean depth of 1000 km (equivalent to ~40 GPa) corresponds to Tp=2000 K, which happens to be significantly hotter than the estimated surface temperature of a sustained magma ocean. It emphasizes the importance of a lid at the magma ocean surface at an epoch as early as that of core-mantle segregation.

  2. 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

  3. The Melting Curve and High-Pressure Chemistry of Formic Acid to 8 GPa and 600 K

    SciTech Connect

    Montgomery, W; Zaug, J M; Howard, W M; Goncharov, A F; Crowhurst, J C; Jeanloz, R

    2005-04-13

    We have determined the melting temperature of formic acid (HCOOH) to 8.5 GPa using infrared absorption spectroscopy, Raman spectroscopy and visual observation of samples in a resistively heated diamond-anvil cell. The experimentally determined melting curve compares favorably with a two-phase thermodynamic model. Decomposition reactions were observed above the melting temperature up to a pressure of 6.5 GPa, where principal products were CO{sub 2}, H{sub 2}O and CO. At pressures above 6.5 GPa, decomposition led to solid-like reaction products. Infrared and Raman spectra of these recovered products indicate that pressure affects the nature of carbon-carbon bonding.

  4. Calculating the melting curves by the thermodynamic data matching method: Platinum-group refractory metals (Ru, Os, and Ir)

    NASA Astrophysics Data System (ADS)

    Kulyamina, E. Yu.; Zitserman, V. Yu.; Fokin, L. R.

    2017-01-01

    A technique for reconstructing thermal properties, including the melting curve, of refractory metals based on the use of experimental data on caloric properties available up to the melting point and some regularities of the Debye-Grüneisen theory has been proposed. The calculation result is the consistent system of high-temperature thermal data, including the thermal expansion coefficient, solid-phase density, and volume jump upon melting. This technique was tried-out on refractory platinum-group metals based on experimental data on the enthalpy of the metals and confirmed by consistency with a thermodynamic calculation using shock-wave experiments and results obtained by the quantum molecular dynamics method.

  5. Melting curve of SiO2 at multimegabar pressures: implications for gas giants and super-Earths

    PubMed Central

    González-Cataldo, Felipe; Davis, Sergio; Gutiérrez, Gonzalo

    2016-01-01

    Ultrahigh-pressure phase boundary between solid and liquid SiO2 is still quite unclear. Here we present predictions of silica melting curve for the multimegabar pressure regime, as obtained from first principles molecular dynamics simulations. We calculate the melting temperatures from three high pressure phases of silica (pyrite-, cotunnite-, and Fe2P-type SiO2) at different pressures using the Z method. The computed melting curve is found to rise abruptly around 330 GPa, an increase not previously reported by any melting simulations. This is in close agreement with recent experiments reporting the α-PbO2–pyrite transition around this pressure. The predicted phase diagram indicates that silica could be one of the dominant components of the rocky cores of gas giants, as it remains solid at the core of our Solar System’s gas giants. These results are also relevant to model the interior structure and evolution of massive super-Earths. PMID:27210813

  6. Analysis of light curve of LP Camelopardalis

    NASA Astrophysics Data System (ADS)

    Prudil, Z.; Skarka, M.; Zejda, M.

    2016-05-01

    We present photometric analysis of the RRab type pulsating star LP Cam. The star was observed at Brno Observatory and Planetarium during nine nights. Measurements were calibrated to the Johnson photometric system. Four captured and thirteen previously published maxima timings allowed us to refine the pulsation period and the zero epoch. The light curve was Fourier decomposed to estimate physical parameters using empirical relations. Our results suggest that LP Cam is a common RR Lyrae star with high, almost solar metallicity.

  7. Incorporating Experience Curves in Appliance Standards Analysis

    SciTech Connect

    Garbesi, Karina; Chan, Peter; Greenblatt, Jeffery; Kantner, Colleen; Lekov, Alex; Meyers, Stephen; Rosenquist, Gregory; Buskirk, Robert Van; Yang, Hung-Chia; Desroches, Louis-Benoit

    2011-10-31

    The technical analyses in support of U.S. energy conservation standards for residential appliances and commercial equipment have typically assumed that manufacturing costs and retail prices remain constant during the projected 30-year analysis period. There is, however, considerable evidence that this assumption does not reflect real market prices. Costs and prices generally fall in relation to cumulative production, a phenomenon known as experience and modeled by a fairly robust empirical experience curve. Using price data from the Bureau of Labor Statistics, and shipment data obtained as part of the standards analysis process, we present U.S. experience curves for room air conditioners, clothes dryers, central air conditioners, furnaces, and refrigerators and freezers. These allow us to develop more representative appliance price projections than the assumption-based approach of constant prices. These experience curves were incorporated into recent energy conservation standards for these products. The impact on the national modeling can be significant, often increasing the net present value of potential standard levels in the analysis. In some cases a previously cost-negative potential standard level demonstrates a benefit when incorporating experience. These results imply that past energy conservation standards analyses may have undervalued the economic benefits of potential standard levels.

  8. Electrochemistry of cations in diopsidic melt - Determining diffusion rates and redox potentials from voltammetric curves

    NASA Technical Reports Server (NTRS)

    Colson, Russell O.; Haskin, Larry A.; Crane, Daniel

    1990-01-01

    Results are presented on determinations of reduction potentials and their temperature dependence of selected ions in diopsidic melt, by using linear sweep voltammetry. Diffusion coefficients were measured for cations of Eu, Mn, Cr, and In. Enthalpies and entropies of reduction were determined for the cations V(V), Cr(3+), Mn(2+), Mn(3+), Fe(2+), Cu(2+), Mo(VI), Sn(IV), and Eu(3+). Reduction potentials were used to study the structural state of cations in the melt.

  9. Use of the melting curve assay as a means for high-throughput quantification of Illumina sequencing libraries.

    PubMed

    Shinozuka, Hiroshi; Forster, John W

    2016-01-01

    Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to issues of cost and/or processing time. Methods. An inexpensive and high-throughput library quantification method has been developed, based on an adaptation of the melting curve assay. Sequencing libraries were subjected to the assay using the Bio-Rad Laboratories CFX Connect(TM) Real-Time PCR Detection System. The library quantity was calculated through summation of reduction of relative fluorescence units between 86 and 95 °C. Results.PCR-enriched sequencing libraries are suitable for this quantification without pre-purification of DNA. Short DNA molecules, which ideally should be eliminated from the library for subsequent processing, were differentiated from the target DNA in a mixture on the basis of differences in melting temperature. Quantification results for long sequences targeted using the melting curve assay were correlated with those from existing methods (R (2) > 0.77), and that observed from MiSeq sequencing (R (2) = 0.82). Discussion.The results of multiplexed sequencing suggested that the normalisation performance of the described method is equivalent to that of another recently reported high-throughput bead-based method, BeNUS. However, costs for the melting curve assay are considerably lower and processing times shorter than those of other existing methods, suggesting greater suitability for highly multiplexed sequencing applications.

  10. NEXT Performance Curve Analysis and Validation

    NASA Technical Reports Server (NTRS)

    Saripalli, Pratik; Cardiff, Eric; Englander, Jacob

    2016-01-01

    Performance curves of the NEXT thruster are highly important in determining the thruster's ability in performing towards mission-specific goals. New performance curves are proposed and examined here. The Evolutionary Mission Trajectory Generator (EMTG) is used to verify variations in mission solutions based on both available thruster curves and the new curves generated. Furthermore, variations in BOL and EOL curves are also examined. Mission design results shown here validate the use of EMTG and the new performance curves.

  11. 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.

  12. Mathematics analysis of polymerase chain reaction kinetic curves.

    PubMed

    Sochivko, D G; Fedorov, A A; Varlamov, D A; Kurochkin, V E; Petrov, R V

    2016-01-01

    The paper reviews different approaches to the mathematical analysis of polymerase chain reaction (PCR) kinetic curves. The basic principles of PCR mathematical analysis are presented. Approximation of PCR kinetic curves and PCR efficiency curves by various functions is described. Several PCR models based on chemical kinetics equations are suggested. Decision criteria for an optimal function to describe PCR efficiency are proposed.

  13. Detection and differentiation of classical swine fever virus strains C and Shimen by high-resolution melt analysis.

    PubMed

    Ning, Pengbo; Li, Helin; Liang, Wulong; Guo, Kangkang; Tan, Xuechao; Cao, Weiwei; Cheng, Liang; Zhang, Yanming

    2013-12-01

    Differentiation of classical swine fever virus (CSFV) strains is crucial for the development of effective vaccination programs and in epidemiological investigations. Most of current detection methods do not discriminate between wild-type CSFV strains and those used in vaccines. In this study, method involving high-resolution melt (HRM) curve analysis for the simultaneous detection and differentiation of the C and Shimen strains of CSFV was developed. A specific fragment of the NS2 gene was amplified from various CSFV strains and subjected to HRM curve analysis. Analysis of the melt curve profile for the amplicons of each strain allowed the differentiation of CSFV strains in blood samples taken from the field, or from vaccinated commercial flocks. These findings indicate that HRM curve analysis is a rapid and practical technique for discriminating CSFV isolates/strains; it can contribute to epidemiological studies of CSFV and effective control of classical swine fever.

  14. SCALE ANALYSIS OF CONVECTIVE MELTING WITH INTERNAL HEAT GENERATION

    SciTech Connect

    John Crepeau

    2011-03-01

    Using a scale analysis approach, we model phase change (melting) for pure materials which generate internal heat for small Stefan numbers (approximately one). The analysis considers conduction in the solid phase and natural convection, driven by internal heat generation, in the liquid regime. The model is applied for a constant surface temperature boundary condition where the melting temperature is greater than the surface temperature in a cylindrical geometry. We show the time scales in which conduction and convection heat transfer dominate.

  15. Recession curve analysis for groundwater levels: case study in Latvia

    NASA Astrophysics Data System (ADS)

    Gailuma, A.; VÄ«tola, I.; Abramenko, K.; Lauva, D.; Vircavs, V.; Veinbergs, A.; Dimanta, Z.

    2012-04-01

    Recession curve analysis is powerful and effective analysis technique in many research areas related with hydrogeology where observations have to be made, such as water filtration and absorption of moisture, irrigation and drainage, planning of hydroelectric power production and chemical leaching (elution of chemical substances) as well as in other areas. The analysis of the surface runoff hydrograph`s recession curves, which is performed to conceive the after-effects of interaction of precipitation and surface runoff, has approved in practice. The same method for analysis of hydrograph`s recession curves can be applied for the observations of the groundwater levels. There are manually prepared hydrograph for analysis of recession curves for observation wells (MG2, BG2 and AG1) in agricultural monitoring sites in Latvia. Within this study from the available monitoring data of groundwater levels were extracted data of declining periods, splitted by month. The drop-down curves were manually (by changing the date) moved together, until to find the best match, thereby obtaining monthly drop-down curves, representing each month separately. Monthly curves were combined and manually joined, for obtaining characterizing drop-down curves of the year for each well. Within the process of decreased recession curve analysis, from the initial curve was cut out upward areas, leaving only the drops of the curve, consequently, the curve is transformed more closely to the groundwater flow, trying to take out the impact of rain or drought periods from the curve. Respectively, the drop-down curve is part of the data, collected with hydrograph, where data with the discharge dominates, without considering impact of precipitation. Using the recession curve analysis theory, ready tool "A Visual Basic Spreadsheet Macro for Recession Curve Analysis" was used for selection of data and logarithmic functions matching (K. Posavec et.al., GROUND WATER 44, no. 5: 764-767, 2006), as well as

  16. SS433 Trek 2: light curve analysis.

    NASA Astrophysics Data System (ADS)

    Fukue, J.; Obana, Y.; Okugami, M.

    The authors have calculated theoretical light curves of SS433 during eclipse and precession, using a model in which SS433 consists of a geometrically thick torus around a compact star and a companion star filling the Roche lobe. The favorite combination is that the mass ratio is about 2 (a compact star is a black hole) and the surface temperature of the companion is around 17000K.

  17. Delamination Analysis Of Composite Curved Bars

    NASA Technical Reports Server (NTRS)

    Ko, William L.; Jackson, Raymond H.

    1990-01-01

    Classical anisotropic elasticity theory used to construct "multilayer" composite semicircular curved bar subjected to end forces and end moments. Radial location and intensity of open-mode delamination stress calculated and compared with results obtained from anisotropic continuum theory and from finite element method. Multilayer theory gave more accurate predictions of location and intensity of open-mode delamination stress. Currently being applied to predict open-mode delamination stress concentrations in horse-shoe-shaped composite test coupons.

  18. PSD analysis of optical QSO light curves

    NASA Astrophysics Data System (ADS)

    Simm, Torben; Salvato, M.; Saglia, R.; Ponti, G.; Lanzuisi, G.; Trakhtenbrot, B.; Nandra, K.; Bender, R.

    2016-08-01

    One of the elementary properties of quasar activity is continuous variability in the UV/optical bands. The power spectral density (PSD) potentially contains information about the underlying processes connected to variability. We applied a novel method based on continuous-time autoregressive moving average (CARMA) models (Kelly et al. 2014) to derive the PSD even for irregularly sampled light curves. Using a sample of ~100 X-ray selected non-local QSOs from the XMM-COSMOS catalog and optical light curves provided by the Pan-STARRS1 MDF survey we find that the PSD resembles a broken power-law with a high-frequency slope significantly steeper than observed in X-ray studies. The PSD normalization is observed to scale inversely with bolometric luminosity and Eddington ratio, whereas there is no correlation between the characteristic bend timescale and black hole mass. We find a weak tendency for QSOs with higher black hole mass to have steeper high-frequency PSD slopes. In an ongoing work we extend these studies employing a sample of ~700 variable broad-line QSOs with high-quality black hole mass estimates and well-sampled light curves from the SDSS-RM project.

  19. Rapid identification and classification of bacteria by 16S rDNA restriction fragment melting curve analyses (RFMCA).

    PubMed

    Rudi, Knut; Kleiberg, Gro H; Heiberg, Ragnhild; Rosnes, Jan T

    2007-08-01

    The aim of this work was to evaluate restriction fragment melting curve analyses (RFMCA) as a novel approach for rapid classification of bacteria during food production. RFMCA was evaluated for bacteria isolated from sous vide food products, and raw materials used for sous vide production. We identified four major bacterial groups in the material analysed (cluster I-Streptococcus, cluster II-Carnobacterium/Bacillus, cluster III-Staphylococcus and cluster IV-Actinomycetales). The accuracy of RFMCA was evaluated by comparison with 16S rDNA sequencing. The strains satisfying the RFMCA quality filtering criteria (73%, n=57), with both 16S rDNA sequence information and RFMCA data (n=45) gave identical group assignments with the two methods. RFMCA enabled rapid and accurate classification of bacteria that is database compatible. Potential application of RFMCA in the food or pharmaceutical industry will include development of classification models for the bacteria expected in a given product, and then to build an RFMCA database as a part of the product quality control.

  20. 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.

  1. DETECTION OF DNA DAMAGE USING MELTING ANALYSIS TECHNIQUES

    EPA Science Inventory

    A rapid and simple fluorescence screening assay for UV radiation-, chemical-, and enzyme-induced DNA damage is reported. This assay is based on a melting/annealing analysis technique and has been used with both calf thymus DNA and plasmid DNA (puc 19 plasmid from E. coli). DN...

  2. Instantaneous normal mode analysis of melting of finite dust clusters.

    PubMed

    Melzer, André; Schella, André; Schablinski, Jan; Block, Dietmar; Piel, Alexander

    2012-06-01

    The experimental melting transition of finite two-dimensional dust clusters in a dusty plasma is analyzed using the method of instantaneous normal modes. In the experiment, dust clusters are heated in a thermodynamic equilibrium from a solid to a liquid state using a four-axis laser manipulation system. The fluid properties of the dust cluster, such as the diffusion constant, are measured from the instantaneous normal mode analysis. Thereby, the phase transition of these finite clusters is approached from the liquid phase. From the diffusion constants, unique melting temperatures have been assigned to dust clusters of various sizes that very well reflect their dynamical stability properties.

  3. Melting analysis on microbeads in rapid temperature-gradient inside microchannels for single nucleotide polymorphisms detectiona)

    PubMed Central

    Li, Kan-Chien; Ding, Shih-Torng; Lin, En-Chung; Wang, Lon (Alex); Lu, Yen-Wen

    2014-01-01

    A continuous-flow microchip with a temperature gradient in microchannels was utilized to demonstrate spatial melting analysis on microbeads for clinical Single Nucleotide Polymorphisms (SNPs) genotyping on animal genomic DNA. The chip had embedded heaters and thermometers, which created a rapid and yet stable temperature gradient between 60 °C and 85 °C in a short distance as the detection region. The microbeads, which served as mobile supports carrying the target DNA and fluorescent dye, were transported across the temperature gradient. As the surrounding temperature increased, the fluorescence signals of the microbeads decayed with this relationship being acquired as the melting curve. Fast DNA denaturation, as a result of the improved heat transfer and thermal stability due to scaling, was also confirmed. Further, each individual microbead could potentially bear different sequences and pass through the detection region, one by one, for a series of melting analysis, with multiplex, high-throughput capability being possible. A prototype was tested with target DNA samples in different genotypes (i.e., wild and mutant types) with a SNP location from Landrace sows. The melting temperatures were obtained and compared to the ones using a traditional tube-based approach. The results showed similar levels of SNP discrimination, validating our proposed technique for scanning homozygotes and heterozygotes to distinguish single base changes for disease research, drug development, medical diagnostics, agriculture, and animal production. PMID:25553186

  4. Melting analysis on microbeads in rapid temperature-gradient inside microchannels for single nucleotide polymorphisms detection.

    PubMed

    Li, Kan-Chien; Ding, Shih-Torng; Lin, En-Chung; Wang, Lon Alex; Lu, Yen-Wen

    2014-11-01

    A continuous-flow microchip with a temperature gradient in microchannels was utilized to demonstrate spatial melting analysis on microbeads for clinical Single Nucleotide Polymorphisms (SNPs) genotyping on animal genomic DNA. The chip had embedded heaters and thermometers, which created a rapid and yet stable temperature gradient between 60 °C and 85 °C in a short distance as the detection region. The microbeads, which served as mobile supports carrying the target DNA and fluorescent dye, were transported across the temperature gradient. As the surrounding temperature increased, the fluorescence signals of the microbeads decayed with this relationship being acquired as the melting curve. Fast DNA denaturation, as a result of the improved heat transfer and thermal stability due to scaling, was also confirmed. Further, each individual microbead could potentially bear different sequences and pass through the detection region, one by one, for a series of melting analysis, with multiplex, high-throughput capability being possible. A prototype was tested with target DNA samples in different genotypes (i.e., wild and mutant types) with a SNP location from Landrace sows. The melting temperatures were obtained and compared to the ones using a traditional tube-based approach. The results showed similar levels of SNP discrimination, validating our proposed technique for scanning homozygotes and heterozygotes to distinguish single base changes for disease research, drug development, medical diagnostics, agriculture, and animal production.

  5. Determination of calcium carbonate and sodium carbonate melting curves up to Earth's transition zone pressures with implications for the deep carbon cycle

    NASA Astrophysics Data System (ADS)

    Li, Zeyu; Li, Jie; Lange, Rebecca; Liu, Jiachao; Militzer, Burkhard

    2017-01-01

    Melting of carbonated eclogite or peridotite in the mantle influences the Earth's deep volatile cycles and bears on the long-term evolution of the atmosphere. Existing data on the melting curves of calcium carbonate (CaCO3) and sodium carbonate (Na2CO3) are limited to 7 GPa and therefore do not allow a full understanding of carbon storage and cycling in deep Earth. We determined the melting curves of CaCO3 and Na2CO3 to the pressures of Earth's transition zone using a multi-anvil apparatus. Melting was detected in situ by monitoring a steep and large increase in ionic conductivity, or inferred from sunken platinum markers in recovered samples. The melting point of CaCO3 rises from 1870 K at 3 GPa to ∼2000 K at 6 GPa and then stays within 50 K of 2000 K between 6 and 21 GPa. In contrast, the melting point of Na2CO3 increases continuously from ∼1123 K at 3 GPa to ∼1950 K at 17 GPa. A pre-melting peak in the alternating current through solid CaCO3 is attributed to the transition from aragonite to calcite V. Accordingly the calcite V-aragonite-liquid invariant point is placed at 13 ± 1 GPa and 1970 ± 40 K, with the Clapeyron slope of the calcite V to aragonite transition constrained at ∼70 K/GPa. The experiments on CaCO3 suggest a slight decrease in the melting temperature from 8 to 13 GPa, followed by a slight increase from 14 to 21 GPa. The negative melting slope is consistent with the prediction from our ab initio simulations that the liquid may be more compressible and become denser than calcite V at sufficiently high pressure. The positive melting slope at higher pressures is supported by the ab initio prediction that aragonite is denser than the liquid at pressures up to 30 GPa. At transition zone pressures the melting points of CaCO3 are comparable to that of Na2CO3 but nearly 400 K and 500 K lower than that of MgCO3. The fusible nature of compressed CaCO3 may be partially responsible for the majority of carbonatitic melts found on Earth's surface

  6. Light curve demography via Bayesian functional data analysis

    NASA Astrophysics Data System (ADS)

    Loredo, Thomas; Budavari, Tamas; Hendry, Martin A.; Kowal, Daniel; Ruppert, David

    2015-08-01

    Synoptic time-domain surveys provide astronomers, not simply more data, but a different kind of data: large ensembles of multivariate, irregularly and asynchronously sampled light curves. We describe a statistical framework for light curve demography—optimal accumulation and extraction of information, not only along individual light curves as conventional methods do, but also across large ensembles of related light curves. We build the framework using tools from functional data analysis (FDA), a rapidly growing area of statistics that addresses inference from datasets that sample ensembles of related functions. Our Bayesian FDA framework builds hierarchical models that describe light curve ensembles using multiple levels of randomness: upper levels describe the source population, and lower levels describe the observation process, including measurement errors and selection effects. Schematically, a particular object's light curve is modeled as the sum of a parameterized template component (modeling population-averaged behavior) and a peculiar component (modeling variability across the population), subsequently subjected to an observation model. A functional shrinkage adjustment to individual light curves emerges—an adaptive, functional generalization of the kind of adjustments made for Eddington or Malmquist bias in single-epoch photometric surveys. We are applying the framework to a variety of problems in synoptic time-domain survey astronomy, including optimal detection of weak sources in multi-epoch data, and improved estimation of Cepheid variable star luminosities from detailed demographic modeling of ensembles of Cepheid light curves.

  7. Identification of Chlamydial species in crocodiles and chickens by PCR-HRM curve analysis.

    PubMed

    Robertson, T; Bibby, S; O'Rourke, D; Belfiore, T; Agnew-Crumpton, R; Noormohammadi, A H

    2010-10-26

    Recently, a PCR protocol (16SG), targeting 16S rRNA gene coupled with high resolution melt (HRM) curve analysis was developed in our laboratory and shown to reliably detect and identify the seven different Chlamydiaceae spp. In this study, the potential of this method was assessed for detection and differentiation of Chlamydiosis in clinical specimens. Of the total number of 733 specimens from a range of animal species, 219 (30%) were found positive by 16SG PCR. When a sufficient amount of DNA was available (64 submissions), amplicons generated by the 16SG PCR were subjected to HRM curve analysis and results were compared to that of nucleotide sequencing. In all instances, the infecting Chlamydiaceae spp. was genotyped according to the identity of its nucleotide sequence to a reference species. Analysis of the HRM curves and nucleotide sequences from 16SG PCR amplicons also revealed the occurrence of a Chlamydophila-like, a Parachlamydia-like and a variant of Chlamydophila psittaci in chickens. These results reveal the potential of 16SG PCR-HRM curve analysis for rapid and simultaneous detection and identification of Chlamydiaceae spp. in animals and demonstrate the capacity of this system for rapid identification of new Chlamydiaceae spp. in animals during routine diagnostic testings.

  8. Hydrogen-bond breaking by O/sub 2/ and N/sub 2/. II. Melting curves of DNA

    SciTech Connect

    Mathers, T.L.; Schoeffler, G.; McGlynn, S.P.

    1982-01-01

    Evidence for hydrogen bond breaking (HBB) by O/sub 2/ and N/sub 2/ in the denaturation or melting of DNA is presented. It was found that air and oxygen significantly reduce the temperature of the DNA melting process. The possible relationship of this HBB ability of oxygen and nitrogen to phenomena observed in vivo are discussed. (ACR)

  9. Decision curve analysis revisited: overall net benefit, relationships to ROC curve analysis, and application to case-control studies

    PubMed Central

    2011-01-01

    Background Decision curve analysis has been introduced as a method to evaluate prediction models in terms of their clinical consequences if used for a binary classification of subjects into a group who should and into a group who should not be treated. The key concept for this type of evaluation is the "net benefit", a concept borrowed from utility theory. Methods We recall the foundations of decision curve analysis and discuss some new aspects. First, we stress the formal distinction between the net benefit for the treated and for the untreated and define the concept of the "overall net benefit". Next, we revisit the important distinction between the concept of accuracy, as typically assessed using the Youden index and a receiver operating characteristic (ROC) analysis, and the concept of utility of a prediction model, as assessed using decision curve analysis. Finally, we provide an explicit implementation of decision curve analysis to be applied in the context of case-control studies. Results We show that the overall net benefit, which combines the net benefit for the treated and the untreated, is a natural alternative to the benefit achieved by a model, being invariant with respect to the coding of the outcome, and conveying a more comprehensive picture of the situation. Further, within the framework of decision curve analysis, we illustrate the important difference between the accuracy and the utility of a model, demonstrating how poor an accurate model may be in terms of its net benefit. Eventually, we expose that the application of decision curve analysis to case-control studies, where an accurate estimate of the true prevalence of a disease cannot be obtained from the data, is achieved with a few modifications to the original calculation procedure. Conclusions We present several interrelated extensions to decision curve analysis that will both facilitate its interpretation and broaden its potential area of application. PMID:21696604

  10. Cepheid light curve demography via Bayesian functional data analysis

    NASA Astrophysics Data System (ADS)

    Loredo, Thomas J.; Hendry, Martin; Kowal, Daniel; Ruppert, David

    2016-01-01

    Synoptic time-domain surveys provide astronomers, not simply more data, but a different kind of data: large ensembles of multivariate, irregularly and asynchronously sampled light curves. We describe a statistical framework for light curve demography—optimal accumulation and extraction of information, not only along individual light curves as conventional methods do, but also across large ensembles of related light curves. We build the framework using tools from functional data analysis (FDA), a rapidly growing area of statistics that addresses inference from datasets that sample ensembles of related functions. Our Bayesian FDA framework builds hierarchical models that describe light curve ensembles using multiple levels of randomness: upper levels describe the source population, and lower levels describe the observation process, including measurement errors and selection effects. Roughly speaking, a particular object's light curve is modeled as the sum of a parameterized template component (modeling population-averaged behavior) and a peculiar component (modeling variability across the population), subsequently subjected to an observation model. A functional shrinkage adjustment to individual light curves emerges—an adaptive, functional generalization of the kind of adjustments made for Eddington or Malmquist bias in single-epoch photometric surveys. We describe ongoing work applying the framework to improved estimation of Cepheid variable star luminosities via FDA-based refinement and generalization of the Cepheid period-luminosity relation.

  11. Assessment of high resolution melting analysis as a potential SNP genotyping technique in forensic casework.

    PubMed

    Venables, Samantha J; Mehta, Bhavik; Daniel, Runa; Walsh, Simon J; van Oorschot, Roland A H; McNevin, Dennis

    2014-11-01

    High resolution melting (HRM) analysis is a simple, cost effective, closed tube SNP genotyping technique with high throughput potential. The effectiveness of HRM for forensic SNP genotyping was assessed with five commercially available HRM kits evaluated on the ViiA™ 7 Real Time PCR instrument. Four kits performed satisfactorily against forensically relevant criteria. One was further assessed to determine the sensitivity, reproducibility, and accuracy of HRM SNP genotyping. The manufacturer's protocol using 0.5 ng input DNA and 45 PCR cycles produced accurate and reproducible results for 17 of the 19 SNPs examined. Problematic SNPs had GC rich flanking regions which introduced additional melting domains into the melting curve (rs1800407) or included homozygotes that were difficult to distinguish reliably (rs16891982; a G to C SNP). A proof of concept multiplexing experiment revealed that multiplexing a small number of SNPs may be possible after further investigation. HRM enables genotyping of a number of SNPs in a large number of samples without extensive optimization. However, it requires more genomic DNA as template in comparison to SNaPshot®. Furthermore, suitably modifying pre-existing forensic intelligence SNP panels for HRM analysis may pose difficulties due to the properties of some SNPs.

  12. Droplet Array Platform for High-Resolution Melt Analysis of DNA Methylation Density.

    PubMed

    Athamanolap, Pornpat; Shin, Dong Jin; Wang, Tza-Huei

    2014-06-01

    High-resolution melting (HRM) has garnered significant interest as an analytical technique for a number of applications, including DNA methylation detection, due to its inherent sensitivity and robustness. In this study, we describe a miniaturized assay platform for quantitative methylation density analysis using a microfluidic droplet array cartridge. We demonstrate that the DNA methylation level of the RASSF1A promoter can be directly analyzed using HRM. PCR products were generated by amplifying bisulfite-treated DNA with varying CpG densities using CpG island-flanking primer sets. Subsequent HRM analysis on the miniaturized droplet platform shows distinct melting curve profiles associated with methylation levels, which was verified using a conventional benchtop PCR-HRM system. The characteristic melting temperature (Tm) of the PCR products was used to directly quantify the respective levels of DNA methylation density. Our approach provides a key advantage over current gold standard methods such as methylation-specific PCR (MSP), which are incapable of providing specific information regarding the overall methylation density of the target genes. The miniaturized platform establishes a practical approach to methylation density profiling from multiple DNA samples with a potential application in point-of-care diagnostics.

  13. Monitoring temperature with fluorescence during real-time PCR and melting analysis.

    PubMed

    Sanford, Lindsay N; Wittwer, Carl T

    2013-03-01

    Accurate control of the sample temperature during thermal cycling is critical for successful polymerase chain reaction (PCR). Direct sensor contact with the reaction is problematic, forcing measurements external to the sample and compromising accuracy during rapid temperature transitions. The widespread use of fluorescence in real-time PCR and melting analysis suggests another measure of temperature, the intrinsic fluorescence of temperature-sensitive passive dyes. Calibration curves correlating sulforhodamine B fluorescence to temperature on nine real-time PCR instruments were obtained by heating at 0.018-0.1 °C/s between 50 and 95 °C, with a twofold change in fluorescence. After instrument stabilization for 20 min, no dye photobleaching was observed and thermal degradation was 2.2%/h at 80 °C. During cycling, solution temperatures derived from fluorescence were well matched to thermocouples placed within samples, but not to temperatures recorded by the instrument. Solution temperatures lagged instrument temperatures by up to 8 °C during cycling, often requiring 5-10 s at target temperatures for equilibration. Melting curves were displaced by 0.2-1.1 °C. Temperature inaccuracies were dependent on the instrument, the ramp rate, and the sample volume. The fluorescence of passive dyes can be used to accurately assess solution temperatures during PCR and should be particularly useful at fast cycling speeds.

  14. Testing Main Effects and Interactions in Latent Curve Analysis

    ERIC Educational Resources Information Center

    Curran, Patrick J.; Bauer, Daniel J.; Willoughby, Michael T.

    2004-01-01

    A key strength of latent curve analysis (LCA) is the ability to model individual variability in rates of change as a function of 1 or more explanatory variables. The measurement of time plays a critical role because the explanatory variables multiplicatively interact with time in the prediction of the repeated measures. However, this interaction…

  15. Analysis of Magnetization Curves and Magnetocrystalline Anisotropy of Uniaxial Ferromagnets

    NASA Astrophysics Data System (ADS)

    Lyakhova, M. B.; Zhdanova, O. V.

    2017-01-01

    Theoretical analysis of the processes of magnetization of uniaxial ferromagnetic materials is performed within the Neel theory of magnetic phases. Relations are obtained for the constants of magnetic crystal anisotropy K 1, K 2, the form factor N, and the saturation magnetization I s , at which the magnetization curves exhibit jumps (FOMP). Formulas for computing the saturation fields H s and the jump fields H FOMP are derived for crystals with different types of magnetocrystalline anisotropy MCA. It is shown that the Sucksmith-Thompson method is applicable for computing the first too MCAconstants of uniaxial ferromagnets with any type of MCA. Constants K 1 and K 2 are computed with allowance for the form factor of the specimen. Model magnetization curves are plotted for uniaxial ferromagnets with different types of MCA along and perpendicularly to crystallographic axis c. The analytical results match the model curves well.

  16. 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.

  17. Determination of zircon/melt trace element partition coefficients from SIMS analysis of melt inclusions in zircon

    NASA Astrophysics Data System (ADS)

    Thomas, J. B.; Bodnar, R. J.; Shimizu, N.; Sinha, A. K.

    2002-09-01

    Partition coefficients ( zircon/meltD M) for rare earth elements (REE) (La, Ce, Nd, Sm, Dy, Er and Yb) and other trace elements (Ba, Rb, B, Sr, Ti, Y and Nb) between zircon and melt have been calculated from secondary ion mass spectrometric (SIMS) analyses of zircon/melt inclusion pairs. The melt inclusion-mineral (MIM) technique shows that D REE increase in compatibility with increasing atomic number, similar to results of previous studies. However, D REE determined using the MIM technique are, in general, lower than previously reported values. Calculated D REE indicate that light REE with atomic numbers less than Sm are incompatible in zircon and become more incompatible with decreasing atomic number. This behavior is in contrast to most previously published results which indicate D > 1 and define a flat partitioning pattern for elements from La through Sm. The partition coefficients for the heavy REE determined using the MIM technique are lower than previously published results by factors of ≈15 to 20 but follow a similar trend. These differences are thought to reflect the effects of mineral and/or glass contaminants in samples from earlier studies which employed bulk analysis techniques. D REE determined using the MIM technique agree well with values predicted using the equations of Brice (1975), which are based on the size and elasticity of crystallographic sites. The presence of Ce 4+ in the melt results in elevated D Ce compared to neighboring REE due to the similar valence and size of Ce 4+ and Zr 4+. Predicted zircon/meltD values for Ce 4+ and Ce 3+ indicate that the Ce 4+/Ce 3+ ratios of the melt ranged from about 10 -3 to 10 -2. Partition coefficients for other trace elements determined in this study increase in compatibility in the order Ba < Rb < B < Sr < Ti < Y < Nb, with Ba, Rb, B and Sr showing incompatible behavior (D M < 1.0), and Ti, Y and Nb showing compatible behavior (D M > 1.0). The effect of partition coefficients on melt evolution during

  18. 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.

  19. Tiling analysis of melting in strongly-coupled dusty plasma*

    NASA Astrophysics Data System (ADS)

    Suranga Ruhunusiri, W. D.; Feng, Yan; Liu, Bin; Goree, John

    2010-11-01

    A dusty plasma is an ionized gas containing micron-size particles of solid matter, which collect electrons and ions and become negatively charged. Due to large Coulomb interparticle potential energies, the microparticles represent a strongly-coupled plasma. In the absence of an external disturbance, the microparticles self-organize, arranging themselves in a crystalline lattice, due to their Coulomb interaction. If kinetic energy is added, the arrangement of microparticles becomes disordered, like atoms in a liquid. This melting process can be characterized by a proliferation of defects, which previous experimenters measured using Voronoi analysis. Here we use another method, tiling [1] to quantify defects. We demonstrate this method, which until now has been used only in simulations, in a dusty plasma experiment. A single layer of 4.83 μm polymer microparticles was electrically levitated in a glow discharge argon plasma. The lattice was melted by applying random kicks to the micoparticles from rastered laser beams. We imaged the particle positions and computed the corresponding tiling for both the crystalline lattice and liquid states. [1] Matthew A. Glaser, Phys. Rev A 41, 4585 (1990) ^*Work supported by NSF and NASA.

  20. Developmental trajectories of adolescent popularity: a growth curve modelling analysis.

    PubMed

    Cillessen, Antonius H N; Borch, Casey

    2006-12-01

    Growth curve modelling was used to examine developmental trajectories of sociometric and perceived popularity across eight years in adolescence, and the effects of gender, overt aggression, and relational aggression on these trajectories. Participants were 303 initially popular students (167 girls, 136 boys) for whom sociometric data were available in Grades 5-12. The popularity and aggression constructs were stable but non-overlapping developmental dimensions. Growth curve models were run with SAS MIXED in the framework of the multilevel model for change [Singer, J. D., & Willett, J. B. (2003). Applied longitudinal data analysis. Oxford, UK: Oxford University Press]. Sociometric popularity showed a linear change trajectory; perceived popularity showed nonlinear change. Overt aggression predicted low sociometric popularity but an increase in perceived popularity in the second half of the study. Relational aggression predicted a decrease in sociometric popularity, especially for girls, and continued high-perceived popularity for both genders. The effect of relational aggression on perceived popularity was the strongest around the transition from middle to high school. The importance of growth curve models for understanding adolescent social development was discussed, as well as specific issues and challenges of growth curve analyses with sociometric data.

  1. High resolution melting analysis for identification of commercially-important Mytilus species.

    PubMed

    Jilberto, Felipe; Araneda, Cristián; Larraín, María Angélica

    2017-08-15

    Mytilus are edible mussels, including commercially-significant species such as M. chilensis, M. galloprovincialis and M. edulis. The scientific name of the species must be indicated on commercial products to satisfy labelling and traceability requirements. Species identification using morphological criteria is difficult due the plasticity of these characteristics and the absence of shells in processed products, and conventional PCR-based methods are laborious and time-intensive. As alternative, we propose high resolution melting (HRM) analysis as a simple tool to detect and identify SNP (single nucleotide polymorphisms) and length polymorphisms in Mytilus spp. We designed HRM-specific primers for the Mytilus genus to identify M. chilensis, M. galloprovincialis, M. edulis and their hybrids through clearly-distinguishable melting curves. HRM analysis showed high sensitivity (0.9639), specificity (1.0000) and precision (1.0000) compared to a conventional PCR-RFLP test. HRM is a fast and low cost method, being a reliable tool for species identification within the Mytilus genus.

  2. Determining the melting curves of NiSi using the laser-heated diamond anvil cell and the multi-anvil press

    NASA Astrophysics Data System (ADS)

    Wann, E.; Lord, O. T.; Dobson, D. P.; Hunt, S. A.; Wood, I. G.; Vocadlo, L.; Ahmed, J.; Walker, A. M.; Santangeli, J. R.; Walter, M. J.

    2012-12-01

    It is believed that the cores of terrestrial planets consist primarily of an iron-nickel alloy with a small fraction of light elements1. In the case of the Earth, the possible candidates for the light elements are constrained by cosmochemical arguments2. However, although the exact nature of the light element is in dispute, it is widely believed that Si is a significant light element in the core3. Research into the iron-nickel-silicon ternary system is therefore invaluable for our understanding of the composition of the Earth's core and of planetary cores in general. We have initially focused on the FeSi and NiSi end-members as a first step in understanding the ternary system. Recent work on NiSi4,5 has revealed a more complicated phase diagram than that of FeSi, with a range of stable phases found at high pressure and temperature. In order to constrain the liquidus of NiSi, we have carried out experiments in the laser-heated diamond anvil cell (LHDAC) using perturbations in the power versus temperature function as the melting criterion6. Thus far we have determined the melting curve of the room-pressure MnP structured phase to ~20 GPa, which agrees closely with an in situ multi-anvil press experiment in which the melting criteria were 1) the appearance of diffuse scattering during X-ray diffraction and 2) the appearance of convection during X-ray videography. We have also detected the break-in-slope of the melting curve associated with the MnP+ɛ-FeSi+liquid triple point, and extended the melting curve of the ɛ-FeSi structure of NiSi to 50 GPa. We are currently undertaking further experimental work to extend the melting curve above 100 GPa, beyond the pressure at which the CsCl structure becomes the liquid phase. Previous studies indicate that the CsCl structure is likely stable to inner core conditions4,5 making the results of relevance to planetary cores including that of the Earth. (1) Birch, F. Journal of Geophysical Research 1952, 57, 227. (2) Poirier, J. P

  3. 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.

  4. 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.

  5. 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.

  6. High-resolution melt PCR analysis for genotyping of Ureaplasma parvum isolates directly from clinical samples.

    PubMed

    Payne, Matthew S; Tabone, Tania; Kemp, Matthew W; Keelan, Jeffrey A; Spiller, O Brad; Newnham, John P

    2014-02-01

    Ureaplasma sp. infection in neonates and adults underlies a variety of disease pathologies. Of the two human Ureaplasma spp., Ureaplasma parvum is clinically the most common. We have developed a high-resolution melt (HRM) PCR assay for the differentiation of the four serovars of U. parvum in a single step. Currently U. parvum strains are separated into four serovars by sequencing the promoter and coding region of the multiple-banded antigen (MBA) gene. We designed primers to conserved sequences within this region for PCR amplification and HRM analysis to generate reproducible and distinct melt profiles that distinguish clonal representatives of serovars 1, 3, 6, and 14. Furthermore, our HRM PCR assay could classify DNA extracted from 74 known (MBA-sequenced) test strains with 100% accuracy. Importantly, HRM PCR was also able to identify U. parvum serovars directly from 16 clinical swabs. HRM PCR performed with DNA consisting of mixtures of combined known serovars yielded profiles that were easily distinguished from those for single-serovar controls. These profiles mirrored clinical samples that contained mixed serovars. Unfortunately, melt curve analysis software is not yet robust enough to identify the composition of mixed serovar samples, only that more than one serovar is present. HRM PCR provides a single-step, rapid, cost-effective means to differentiate the four serovars of U. parvum that did not amplify any of the known 10 serovars of Ureaplasma urealyticum tested in parallel. Choice of reaction reagents was found to be crucial to allow sufficient sensitivity to differentiate U. parvum serovars directly from clinical swabs rather than requiring cell enrichment using microbial culture techniques.

  7. Stress analysis in curved composites due to thermal loading

    NASA Astrophysics Data System (ADS)

    Polk, Jared Cornelius

    Many structures in aircraft, cars, trucks, ships, machines, tools, bridges, and buildings, consist of curved sections. These sections vary from straight line segments that have curvature at either one or both ends, segments with compound curvatures, segments with two mutually perpendicular curvatures or Gaussian curvatures, and segments with a simple curvature. With the advancements made in multi-purpose composites over the past 60 years, composites slowly but steadily have been appearing in these various vehicles, compound structures, and buildings. These composite sections provide added benefits over isotropic, polymeric, and ceramic materials by generally having a higher specific strength, higher specific stiffnesses, longer fatigue life, lower density, possibilities in reduction of life cycle and/or acquisition cost, and greater adaptability to intended function of structure via material composition and geometry. To be able to design and manufacture a safe composite laminate or structure, it is imperative that the stress distributions, their causes, and effects are thoroughly understood in order to successfully accomplish mission objectives and manufacture a safe and reliable composite. The objective of the thesis work is to expand upon the knowledge of simply curved composite structures by exploring and ascertaining all pertinent parameters, phenomenon, and trends in stress variations in curved laminates due to thermal loading. The simply curved composites consist of composites with one radius of curvature throughout the span of the specimen about only one axis. Analytical beam theory, classical lamination theory, and finite element analysis were used to ascertain stress variations in a flat, isotropic beam. An analytical method was developed to ascertain the stress variations in an isotropic, simply curved beam under thermal loading that is under both free-free and fixed-fixed constraint conditions. This is the first such solution to Author's best knowledge

  8. Multi-wavelength analysis of Ellerman Bomb Light Curves

    NASA Astrophysics Data System (ADS)

    Herlender, M.; Berlicki, A.

    We present the results of a multi-wavelength photometric analysis of Ellerman Bomb (EB) observations obtained from the Dutch Open Telescope. In our data we have found 6 EBs located in the super-penumbra of the main spot in the active region NOAA 10781. We present light curves of EB observed in the Hα line centre and wing +0.7 Å, in the Ca II H line centre and wing~+2.35 Å, in the G-band and in the TRACE 1600 Å filter. We have shown that EBs were visible in the G-band and moreover, there was a good correlation between the light curves in the G-band and in the Hα line wings. We also found quasi-periodic oscillations of EBs brightness in the G-band, CaII H line and TRACE 1600 Å filter.

  9. High-throughput identification and quantification of Candida species using high resolution derivative melt analysis of panfungal amplicons.

    PubMed

    Mandviwala, Tasneem; Shinde, Rupali; Kalra, Apoorv; Sobel, Jack D; Akins, Robert A

    2010-01-01

    Fungal infections pose unique challenges to molecular diagnostics; fungal molecular diagnostics consequently lags behind bacterial and viral counterparts. Nevertheless, fungal infections are often life-threatening, and early detection and identification of species is crucial to successful intervention. A high throughput PCR-based method is needed that is independent of culture, is sensitive to the level of one fungal cell per milliliter of blood or other tissue types, and is capable of detecting species and resistance mutations. We introduce the use of high resolution melt analysis, in combination with more sensitive, inclusive, and appropriately positioned panfungal primers, to address these needs. PCR-based amplification of the variable internal transcribed regions of the rDNA genes generates an amplicon whose sequence melts with a shape that is characteristic and therefore diagnostic of the species. Simple analysis of the differences between test and reference melt curves generates a single number that calls the species. Early indications suggest that high resolution melt analysis can distinguish all eight major species of Candida of clinical significance without interference from excess human DNA. Candida species, including mixed and novel species, can be identified directly in vaginal samples. This tool can potentially detect, count, and identify fungi in hundreds of samples per day without further manipulation, costs, or delays, offering a major step forward in fungal molecular diagnostics.

  10. Magnetostatic interaction in soft magnetic bilayer ribbons unambiguously identified by first-order reversal curve analysis

    NASA Astrophysics Data System (ADS)

    Rivas, M.; Martínez-García, J. C.; Škorvánek, I.; Marcin, J.; Švec, P.; Gorria, P.

    2015-09-01

    Monolithic amorphous Fe73.5Nb3Si13.5B9Cu1/Fe74.5Nb3Si13.5B9 bilayer ribbons were obtained by double-nozzle melt-spinning and subsequently annealed to produce a composite with a tailored nano/micro-crystalline structure. The overall magnetic behavior is characterized by butterfly-shaped high field hysteresis loops and positively biased low field ones. The main questions we wish to address here are whether the global magnetic behavior of the bilayer can be separated into the individual contributions of each layer and the magneto-coupling between them can be well understood. For that purpose, we performed first-order reversal curve analysis, which enabled us to distinctly identify two phases, of ultra-soft and semi-soft magnetic natures, whose mutual predominant interaction is the magnetostatic coupling.

  11. 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.

  12. 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.

  13. High-resolution melt analysis without DNA extraction affords rapid genotype resolution and species identification.

    PubMed

    Rugman-Jones, Paul F; Stouthamer, Richard

    2016-09-22

    Extracting and sequencing DNA from specimens can impose major time and monetary costs to studies requiring genotyping, or identification to species, of large numbers of individuals. As such, so-called direct PCR methods have been developed enabling significant savings at the DNA extraction step. Similarly, real-time quantitative PCR techniques (qPCR) offer very cost-effective alternatives to sequencing. High-resolution melt analysis (HRM) is a qPCR method that incorporates an intercalating dye into a double-stranded PCR amplicon. The dye fluoresces brightly, but only when it is bound. Thus, after PCR, raising the temperature of the amplicon while measuring the fluorescence of the reaction results in the generation of a sequence-specific melt curve, allowing discrimination of genotypes. Methods combining HRM (or other qPCR methods) and direct PCR have not previously been reported, most likely due to concerns that any tissue in the reaction tube would interfere with detection of the fluorescent signal. Here, we couple direct PCR with HRM and, by way of three examples, demonstrate a very quick and cost-effective method for genotyping large numbers of specimens, using Rotor-Gene HRM instruments (QIAGEN). In contrast to the heated-block design of most qPCR/HRM instruments, the Rotor-Gene's centrifugal rotor and air-based temperature-regulation system facilitate our method by depositing tissues away from the pathway of the machine's fluorescence detection optics.

  14. Rapid detection and identification of four major Schistosoma species by high-resolution melt (HRM) analysis.

    PubMed

    Li, Juan; Zhao, Guang-Hui; Lin, RuiQing; Blair, David; Sugiyama, Hiromu; Zhu, Xing-Quan

    2015-11-01

    Schistosomiasis, caused by blood flukes belonging to several species of the genus Schistosoma, is a serious and widespread parasitic disease. Accurate and rapid differentiation of these etiological agents of animal and human schistosomiasis to species level can be difficult. We report a real-time PCR assay coupled with a high-resolution melt (HRM) assay targeting a portion of the nuclear 18S rDNA to detect, identify, and distinguish between four major blood fluke species (Schistosoma japonicum, Schistosoma mansoni, Schistosoma haematobium, and Schistosoma mekongi). Using this system, the Schistosoma spp. was accurately identified and could also be distinguished from all other trematode species with which they were compared. As little as 10(-5) ng genomic DNA from a Schistosoma sp. could be detected. This process is inexpensive, easy, and can be completed within 3 h. Examination of 21 representative Schistosoma samples from 15 geographical localities in seven endemic countries validated the value of the HRM detection assay and proved its reliability. The melting curves were characterized by peaks of 83.65 °C for S. japonicum and S. mekongi, 85.65 °C for S. mansoni, and 85.85 °C for S. haematobium. The present study developed a real-time PCR coupled with HRM analysis assay for detection and differential identification of S. mansoni, S. haematobium, S. japonicum, and S. mekongi. This method is rapid, sensitive, and inexpensive. It has important implications for epidemiological studies of Schistosoma.

  15. 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

  16. Dissection of the hormetic curve: analysis of components and mechanisms.

    PubMed

    Lushchak, Volodymyr I

    2014-07-01

    The relationship between the dose of an effector and the biological response frequently is not described by a linear function and, moreover, in some cases the dose-response relationship may change from positive/adverse to adverse/positive with increasing dose. This complicated relationship is called "hormesis". This paper provides a short analysis of the concept along with a description of used approaches to characterize hormetic relationships. The whole hormetic curve can be divided into three zones: I - a lag-zone where no changes are observed with increasing dose; II - a zone where beneficial/adverse effects are observed, and III - a zone where the effects are opposite to those seen in zone II. Some approaches are proposed to analyze the molecular components involved in the development of the hormetic character of dose-response relationships with the use of specific genetic lines or inhibitors of regulatory pathways. The discussion is then extended to suggest a new parameter (half-width of the hormetic curve at zone II) for quantitative characterization of the hormetic curve. The problems limiting progress in the development of the hormesis concept such as low reproducibility and predictability may be solved, at least partly, by deciphering the molecular mechanisms underlying the hormetic dose-effect relationship.

  17. Dissection of the Hormetic Curve: Analysis of Components and Mechanisms

    PubMed Central

    Lushchak, Volodymyr I.

    2014-01-01

    The relationship between the dose of an effector and the biological response frequently is not described by a linear function and, moreover, in some cases the dose-response relationship may change from positive/adverse to adverse/positive with increasing dose. This complicated relationship is called “hormesis”. This paper provides a short analysis of the concept along with a description of used approaches to characterize hormetic relationships. The whole hormetic curve can be divided into three zones: I – a lag-zone where no changes are observed with increasing dose; II – a zone where beneficial/adverse effects are observed, and III – a zone where the effects are opposite to those seen in zone II. Some approaches are proposed to analyze the molecular components involved in the development of the hormetic character of dose-response relationships with the use of specific genetic lines or inhibitors of regulatory pathways. The discussion is then extended to suggest a new parameter (half-width of the hormetic curve at zone II) for quantitative characterization of the hormetic curve. The problems limiting progress in the development of the hormesis concept such as low reproducibility and predictability may be solved, at least partly, by deciphering the molecular mechanisms underlying the hormetic dose-effect relationship. PMID:25249836

  18. Analysis of rotation curves in the framework of Rn gravity

    NASA Astrophysics Data System (ADS)

    Frigerio Martins, C.; Salucci, P.

    2007-11-01

    We present an analysis of a devised sample of rotation curves (RCs), with the aim of checking the consequences of a modified f(R) gravity on galactic scales. Originally motivated by the mystery of dark energy, this theory may explain the observed non-Keplerian profiles of galactic RCs in terms of a breakdown of Einstein general relativity. We show that, in general, the power-law f(R) version could fit the observations well, with reasonable values for the mass model parameters. This could encourage further investigation into Rn gravity from both observational and theoretical points of view.

  19. A new approach to the analysis of Mira light curves

    NASA Technical Reports Server (NTRS)

    Mennessier, M. O.; Barthes, D.; Mattei, J. A.

    1990-01-01

    Two different but complementary methods for predicting Mira luminosities are presented. One method is derived from a Fourier analysis, it requires performing deconvolution, and its results are not certain due to the inherent instability of deconvolution problems. The other method is a learning method utilizing artificial intelligence techniques where a light curve is presented as an ordered sequence of pseudocycles, and rules are learned by linking the characteristics of several consecutive pseudocycles to one characteristic of the future cycle. It is observed that agreement between these methods is obtainable when it is possible to eliminate similar false frequencies from the preliminary power spectrum and to improve the degree of confidence in the rules.

  20. A visual basic spreadsheet macro for recession curve analysis.

    PubMed

    Posavec, Kristijan; Bacani, Andrea; Nakić, Zoran

    2006-01-01

    A Visual Basic program for an Excel spreadsheet was written to construct a master recession curve (MRC), using the adapted matching strip method, for recession analysis of ground water level time series. The program uses five different linear/nonlinear regression models to adjust individual recession segments to their proper positions in the MRC. The program can also be used to analyze the recession segments of other time series, such as daily stream discharge or stage. Some examples of field data from Croatia are used to illustrate the usefulness of its application.

  1. Cusum analysis for learning curve of videothoracoscopic lobectomy

    PubMed Central

    Avcı, Alper; Türktan, Mediha

    2016-01-01

    Abstract Background Video assisted thoracoscopic (VATS) lobectomy has a demanding learning curve due to its technical complexity and risk of uncontrollable bleeding. We investigated the case number required for gaining technical proficiency by applying cumulative sum analysis on initial VATS lobectomy operations of a single surgeon. Methods CALGB definition was used for the definition of VATS lobectomy. The data of the initial cases evaluated and cumulative sum (CUSUM) analysis was applied to duration of the operations and length of hospital stay. Results Fifty-eight patients underwent VATS lobectomy. Of those 51 were malignant and 7 were benign. Fifty-five of the procedures were lobectomy, 2 were inferior bi-lobectomy and 1 was left upper lobectomy with chest wall resection. CUSUM analysis reached to proficiency at 27 cases for duration of the operations. Conclusions The length of learning curve depends on previous experience of the surgeon on open lobectomy and simpler VATS operations, potential number of VATS lobectomy cases and VATS capability of the surgeon. Depending on these factors, it is possible to obtain technical proficiency with an inferior number of procedures compared with existing literature (50-200). PMID:28352848

  2. First-order-reversal-curve analysis of Pr-Fe-B-based nanocomposites

    NASA Astrophysics Data System (ADS)

    Cornejo, D. R.; Peixoto, T. R. F.; Reboh, S.; Fichtner, P. F. P.; de Franco, V. C.; Villas-Boas, V.; Missell, F. P.

    2010-04-01

    Ribbons of nominal composition (Pr9.5Fe84.5B6)0.96Cr0.01(TiC)0.03 were produced by arc-melting and melt-spinning the alloys on a Cu wheel. X-ray diffraction reveals two main phases, one based upon α-Fe and the other upon Pr2Fe14B. The ribbons show exchange spring behavior with Hc=12.5 kOe and (BH)max=13.6 MGOe when these two phases are well coupled. Transmission electron microscopy revealed that the coupled behavior is observed when the microstructure consists predominantly of α-Fe grains (diameter ˜100 nm.) surrounded by hard material containing Pr2Fe14B. A first-order-reversal-curve (FORC) analysis was performed for both a well-coupled sample and a partially-coupled sample. The FORC diagrams show two strong peaks for both the partially-coupled sample and for the well-coupled material. In both cases, the localization of the FORC probability suggests demagnetizing interactions between particles. Switching field distributions were calculated and are consistent with the sample microstructure.

  3. Analysis of melt ejection during long pulsed laser drilling

    NASA Astrophysics Data System (ADS)

    Ting-Zhong, Zhang; Zhi-Chao, Jia; Hai-Chao, Cui; De-Hua, Zhu; Xiao-Wu, Ni; Jian, Lu

    2016-05-01

    In pulsed laser drilling, melt ejection greatly influences the keyhole shape and its quality as well, but its mechanism has not been well understood. In this paper, numerical simulation and experimental investigations based on 304 stainless steel and aluminum targets are performed to study the effects of material parameters on melt ejection. The numerical method is employed to predict the temperatures, velocity fields in the solid, liquid, and vapour front, and melt pool dynamics of targets as well. The experimental methods include the shadow-graphic technique, weight method, and optical microscope imaging, which are applied to real-time observations of melt ejection phenomena, measurements of collected melt and changes of target mass, observations of surface morphology and the cross-section of the keyhole, respectively. Numerical and experimental results show that the metallic material with high thermal diffusivity like aluminum is prone to have a thick liquid zone and a large quantity of melt ejection. Additionally, to the best of our knowledge, the liquid zone is used to illustrate the relations between melt ejection and material thermal diffusivity for the first time. The research result in this paper is useful for manufacturing optimization and quality control in laser-material interaction. Project supported by the Natural Science Foundation of Jiangsu Province, China (Grant No. KYLX_0341) and the National Natural Science Foundation of China (Grant No. 61405147).

  4. Thermodynamic temperature assignment to the point of inflection of the melting curve of high-temperature fixed points.

    PubMed

    Woolliams, E R; Anhalt, K; Ballico, M; Bloembergen, P; Bourson, F; Briaudeau, S; Campos, J; Cox, M G; del Campo, D; Dong, W; Dury, M R; Gavrilov, V; Grigoryeva, I; Hernanz, M L; Jahan, F; Khlevnoy, B; Khromchenko, V; Lowe, D H; Lu, X; Machin, G; Mantilla, J M; Martin, M J; McEvoy, H C; Rougié, B; Sadli, M; Salim, S G R; Sasajima, N; Taubert, D R; Todd, A D W; Van den Bossche, R; van der Ham, E; Wang, T; Whittam, A; Wilthan, B; Woods, D J; Woodward, J T; Yamada, Y; Yamaguchi, Y; Yoon, H W; Yuan, Z

    2016-03-28

    The thermodynamic temperature of the point of inflection of the melting transition of Re-C, Pt-C and Co-C eutectics has been determined to be 2747.84 ± 0.35 K, 2011.43 ± 0.18 K and 1597.39 ± 0.13 K, respectively, and the thermodynamic temperature of the freezing transition of Cu has been determined to be 1357.80 ± 0.08 K, where the ± symbol represents 95% coverage. These results are the best consensus estimates obtained from measurements made using various spectroradiometric primary thermometry techniques by nine different national metrology institutes. The good agreement between the institutes suggests that spectroradiometric thermometry techniques are sufficiently mature (at least in those institutes) to allow the direct realization of thermodynamic temperature above 1234 K (rather than the use of a temperature scale) and that metal-carbon eutectics can be used as high-temperature fixed points for thermodynamic temperature dissemination. The results directly support the developing mise en pratique for the definition of the kelvin to include direct measurement of thermodynamic temperature.

  5. Thermal expansivity, bulk modulus, and melting curve of H2O-ice VII to 20 GPa

    NASA Technical Reports Server (NTRS)

    Fei, Yingwei; Mao, Ho-Kwang; Hemley, Russell J.

    1993-01-01

    Equation of state properties of ice VII and fluid H2O at high pressures and temperatures have been studied experimentally from 6 to 20 GPa and 300-700 K. The techniques involve direct measurements of the unit-cell volume of the solid using synchrotron X-ray diffraction with an externally heated diamond-anvil cell. The pressure dependencies of the volume and bulk modulus of ice VII at room temperature are in good agreement with previous synchrotron X-ray studies. The thermal expansivity was determined as a function of pressure and the results fit to a newly proposed phenomenological relation and to a Mie-Gruneisen equation of state formalism. The onset of melting of ice VII was determined directly by X-ray diffraction at a series of pressures and found to be in accord with previous volumetric determinations. Thermodynamic calculations based on the new data are performed to evaluate the range of validity of previously proposed equations of state for fluid water derived from static and shock-wave compression experiments and from simulations.

  6. 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

  7. Rapid discrimination between Anopheles gambiae s.s. and Anopheles arabiensis by High-Resolution Melt (HRM) analysis.

    PubMed

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

    2013-04-01

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

  8. Light Curve and Orbital Period Analysis of VX Lac

    NASA Astrophysics Data System (ADS)

    Yılmaz, M.; Nelson, R. H.; Şenavcı, H. V.; İzci, D.; Özavcı, İ.; Gümüş, D.

    2017-04-01

    In this study, we performed simultaneously light curve and radial velocity, and also period analyses of the eclipsing binary system VX Lac. Four color (BVRI) light curves of the system were analysed using the W-D code. The results imply that VX Lac is a classic Algol-type binary with a mass ratio of q=0.27, of which the less massive secondary component fills its Roche lobe. The orbital period behaviour of the system was analysed by assuming the light time effect (LITE) from a third body. The O-C analysis yielded a mass transfer rate of dM/dt=1.86×10-8Mȯyr-1 and the minimal mass of the third body to be M3=0.31Mȯ. The residuals from mass transfer and the third body were also analysed because another cyclic variation is seen in O-C diagram. This periodic variation was examined under the hypotheses of stellar magnetic activity and fourth body.

  9. WASP-14 b: transit timing analysis of 19 light curves

    NASA Astrophysics Data System (ADS)

    Raetz, St.; Maciejewski, G.; Seeliger, M.; Marka, C.; Fernández, M.; Güver, T.; Göğüş, E.; Nowak, G.; Vaňko, M.; Berndt, A.; Eisenbeiss, T.; Mugrauer, M.; Trepl, L.; Gelszinnis, J.

    2015-08-01

    Although WASP-14 b is one of the most massive and densest exoplanets on a tight and eccentric orbit, it has never been a target of photometric follow-up monitoring or dedicated observing campaigns. We report on new photometric transit observations of WASP-14 b obtained within the framework of Transit Timing Variations @ Young Exoplanet Transit Initiative (TTV@YETI). We collected 19 light curves of 13 individual transit events using six telescopes located in five observatories distributed in Europe and Asia. From light-curve modelling, we determined the planetary, stellar, and geometrical properties of the system and found them in agreement with the values from the discovery paper. A test of the robustness of the transit times revealed that in case of a non-reproducible transit shape the uncertainties may be underestimated even with a wavelet-based error estimation methods. For the timing analysis, we included two publicly available transit times from 2007 and 2009. The long observation period of seven years (2007-2013) allowed us to refine the transit ephemeris. We derived an orbital period 1.2 s longer and 10 times more precise than the one given in the discovery paper. We found no significant periodic signal in the timing-residuals and, hence, no evidence for TTV in the system.

  10. 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

  11. High resolution melting analysis is a more sensitive and effective alternative to gel-based platforms in analysis of SSR--an example in citrus.

    PubMed

    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

  12. 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

  13. 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.

  14. Concentrated photovoltaics system costs and learning curve analysis

    NASA Astrophysics Data System (ADS)

    Haysom, Joan E.; Jafarieh, Omid; Anis, Hanan; Hinzer, Karin

    2013-09-01

    An extensive set of costs in /W for the installed costs of CPV systems has been amassed from a range of public sources, including both individual company prices and market reports. Cost reductions over time are very evident, with current prices for 2012 in the range of 3.0 ± 0.7 /W and a predicted cost of 1.5 /W for 2020. Cost data is combined with deployment volumes in a learning curve analysis, providing a fitted learning rate of either 18.5% or 22.3% depending on the methodology. This learning rate is compared to that of PV modules and PV installed systems, and the influence of soft costs is discussed. Finally, if an annual growth rate of 39% is assumed for deployed volumes, then, using the learning rate of 20%, this would predict the achievement of a cost point of 1.5 /W by 2016.

  15. Influence of spatial location on the timing of the snow accumulation and melt in the Sierra Nevada: An analysis with FANOVA.

    NASA Astrophysics Data System (ADS)

    Montoya, E.; Meiring, W.; Dozier, J.

    2015-12-01

    In California, snow represents one of the primary water resources. California precipitation occurs predominately in the winter and spring months, whereas the summer and fall generally are dry. Variation in the timing of snowpack accumulation and melt in the Sierra Nevada can be quantified through statistical curve registration summaries of seasonal cycle variation in daily snow pillow records. This procedure provides a set of functional sample observations that may be used to study the characteristics that influence the timing of snowpack events. Using functional analysis of variance, we investigate differences in the timing of snowpack accumulation and melt associated with spatial location attributes.

  16. Analysis of melting of pyrope compound at high pressures

    NASA Astrophysics Data System (ADS)

    Singh, B. P.; Singh, K. S.

    2012-02-01

    The pressure-volume-temperature relationships have been studied for the pyrope mineral. Values of volumes at simultaneously elevated temperatures and pressures have been evaluated using the Rydberg-Vinet equation of state for isothermal compression and the Singh-Suzuki equation for isobaric thermal expansion. It has been found that the results obtained from these two conventional equations can be reproduced very well by a single equation of state which covers both temperature and pressure changes in solids namely the Hartmann equation of state. Values of volumes at melting temperatures corresponding to elevated pressures have been obtained and found to compare well with the experimental values. It is also found that there exists a simple linear relationship between relative change in melting volume and melting temperature in case of pyrope at different pressures. This is supported by the earlier findings of Anderson in case of forsterite mineral.

  17. Rapid identification of Borrelia by high resolution melting analysis of the groEL gene.

    PubMed

    Koś, Władysław; Wodecka, Beata; Anklewicz, Marek; Skotarczak, Bogumiła

    2013-01-01

    This study examined the possibility of applying a new diagnostic method, high resolution analysis of DNA denaturation curve (high resolution melting - HRM), for identification of Borrelia species. DNA samples were obtained from Ixodes ricinus ticks collected from vegetation and removed from hunted roe deer. For differentiation of Borrelia species, the HRM protocol based on the analysis of the groEL gene was applied. A product characteristic for Borrelia was obtained in 19/123 samples (15.4%). The studied isolates were classified as four species: B. garinii, B. valaisiana, B. afzelii and B. miyamotoi. Two separate groups of isolates within the B. afzelii species were also found. The results show that the groEL gene is useful for rapid differentiation of B. burgdorferi sensu lato with the HRM method from different extracts of DNA and it also allows precise differentiation of Borrelia species and strains. The HRM method shortened and simplified detection and differentiation of Borrelia species from different biological sources.

  18. Light curve analysis of southern eclipsing binary EM Car

    NASA Astrophysics Data System (ADS)

    Ćiçek, C.; Bulut, I.; Bulut, A.

    2017-02-01

    In this study, ASAS light curve of the eclipsing binary EM Car (Sp = O8V, P = 3.4 days) has been analyzed using the Wilson-Devinney method. The light curve analyses have found that EM Car is a detached eclipsing binary system with small eccentric orbit

  19. Three-Dimensional Postbuckling Analysis of Curved Beams

    NASA Technical Reports Server (NTRS)

    Pai, P. Frank; Lee, Seung-Yoon

    2002-01-01

    Presented here is a method of solving highly flexible curved beam undergoing huge static or quasi-static deformations. A geometrically exact beam theory based on the use of Jaumann stresses and strains and exact coordinate transformation is presented in terms of 17 first-order ordinary differential equations, and a multiple shooting method is used to solve the corresponding nonlinear two-point boundary value problems. The geometrically exact beam theory accounts far large rotations, large displacements, initial curvatures, extensionality, and transverse shear strains. Four examples are used to demonstrate this method, including a rotating clamped-free beam under the influence of gravity and centrifugal forces, an L-frame subjected to an in-plane tip load, a circular arch subjected to a concentrated load, and a clamped-hinged helical spring subjected to an axial displacement. Results show that the combination of the multiple shooting method and the geometrically exact beam theory works very well. Moreover, the obtained numerically exact solutions can be used to verify the accuracy of nonlinear finite element codes for nonlinear analysis of complex structures.

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

    PubMed Central

    Thong, Kwai Lin

    2014-01-01

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

  1. Magneto-electro-elastic buckling analysis of nonlocal curved nanobeams

    NASA Astrophysics Data System (ADS)

    Ebrahimi, Farzad; Reza Barati, Mohammad

    2016-09-01

    In this work, a size-dependent curved beam model is developed to take into account the effects of nonlocal stresses on the buckling behavior of curved magneto-electro-elastic FG nanobeams for the first time. The governing differential equations are derived based on the principle of virtual work and Euler-Bernoulli beam theory. The power-law function is employed to describe the spatially graded magneto-electro-elastic properties. By extending the radius of the curved nanobeam to infinity, the results of straight nonlocal FG beams can be rendered. The effects of magnetic potential, electric voltage, opening angle, nonlocal parameter, power-law index and slenderness ratio on buckling loads of curved MEE-FG nanobeams are studied.

  2. High-resolution melting analysis for bird sexing: a successful approach to molecular sex identification using different biological samples.

    PubMed

    Morinha, Francisco; Travassos, Paulo; Seixas, Fernanda; Santos, Nuno; Sargo, Roberto; Sousa, Luís; Magalhães, Paula; Cabral, João A; Bastos, Estela

    2013-05-01

    High-resolution melting (HRM) analysis is a very attractive and flexible advanced post-PCR method with high sensitivity/specificity for simple, fast and cost-effective genotyping based on the detection of specific melting profiles of PCR products. Next generation real-time PCR systems, along with improved saturating DNA-binding dyes, enable the direct acquisition of HRM data after quantitative PCR. Melting behaviour is particularly influenced by the length, nucleotide sequence and GC content of the amplicons. This method is expanding rapidly in several research areas such as human genetics, reproductive biology, microbiology and ecology/conservation of wild populations. Here we have developed a successful HRM protocol for avian sex identification based on the amplification of sex-specific CHD1 fragments. The melting curve patterns allowed efficient sexual differentiation of 111 samples analysed (plucked feathers, muscle tissues, blood and oral cavity epithelial cells) of 14 bird species. In addition, we sequenced the amplified regions of the CHD1 gene and demonstrated the usefulness of this strategy for the genotype discrimination of various amplicons (CHD1Z and CHD1W), which have small size differences, ranging from 2 bp to 44 bp. The established methodology clearly revealed the advantages (e.g. closed-tube system, high sensitivity and rapidity) of a simple HRM assay for accurate sex differentiation of the species under study. The requirements, strengths and limitations of the method are addressed to provide a simple guide for its application in the field of molecular sexing of birds. The high sensitivity and resolution relative to previous real-time PCR methods makes HRM analysis an excellent approach for improving advanced molecular methods for bird sexing.

  3. Analysis of Thermoluminescence Glow Curves Using Derivatives of Different Orders.

    PubMed

    Karmakar, Mahua; Bhattacharyya, S; Sarkar, A; Mazumdar, P S; Singh, S D

    2017-01-16

    The suitability of the second derivative method for locating component peaks in complex thermoluminescence (TL) glow curves has been investigated in this work by considering both numerically simulated and experimental TL peaks. This technique is useful to acquire knowledge of the number of component peaks in a complex TL curve which in turn serves as a basic information before applying the deconvolution technique to the glow curve. To check the consistency of the results so obtained, we have also applied the first derivative technique to TL glow curves. It is well-known that kinetic order formalism fails for saturated TL peaks with heavy retrapping. Such peaks are usually broad and, to the best of our knowledge, have not yet been observed experimentally. The present derivative technique has been used to detect whether such broad peaks are truly single or not by considering a number of numerically simulated saturated glow curves with heavy retrapping where the conventional peak shape method fails. In all the cases considered here, the second derivative technique proves to be a potential candidate for estimating the number of peaks and their respective locations in a complex TL glow curve.

  4. Empirical Bayes Analysis of Families of Survival Curves: Applications to the Analysis of Degree Attainment.

    ERIC Educational Resources Information Center

    Braun, Henry I.; Zwick, Rebecca

    1993-01-01

    An approach to empirical Bayes analysis of aggregated survival data from different groups of subjects is presented based on a contingency table representation of data using transformations to permit the use of normal priors. Analysis of families of survival curves leads to improvements over classical estimates. (SLD)

  5. 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.

  6. Voronoi analysis of the short–range atomic structure in iron and iron–carbon melts

    SciTech Connect

    Sobolev, Andrey; Mirzoev, Alexander

    2015-08-17

    In this work, we simulated the atomic structure of liquid iron and iron–carbon alloys by means of ab initio molecular dynamics. Voronoi analysis was used to highlight changes in the close environments of Fe atoms as carbon concentration in the melt increases. We have found, that even high concentrations of carbon do not affect short–range atomic order of iron atoms — it remains effectively the same as in pure iron melts.

  7. Melt analysis of mismatch amplification mutation assays (Melt-MAMA): a functional study of a cost-effective SNP genotyping assay in bacterial models.

    PubMed

    Birdsell, Dawn N; Pearson, Talima; Price, Erin P; Hornstra, Heidie M; Nera, Roxanne D; Stone, Nathan; Gruendike, Jeffrey; Kaufman, Emily L; Pettus, Amanda H; Hurbon, Audriana N; Buchhagen, Jordan L; Harms, N Jane; Chanturia, Gvantsa; Gyuranecz, Miklos; Wagner, David M; Keim, Paul S

    2012-01-01

    Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and biologically informative markers extensively used across broad scientific disciplines. Newly identified SNP markers are publicly available at an ever-increasing rate due to advancements in sequencing technologies. Efficient, cost-effective SNP genotyping methods to screen sample populations are in great demand in well-equipped laboratories, but also in developing world situations. Dual Probe TaqMan assays are robust but can be cost-prohibitive and require specialized equipment. The Mismatch Amplification Mutation Assay, coupled with melt analysis (Melt-MAMA), is flexible, efficient and cost-effective. However, Melt-MAMA traditionally suffers from high rates of assay design failures and knowledge gaps on assay robustness and sensitivity. In this study, we identified strategies that improved the success of Melt-MAMA. We examined the performance of 185 Melt-MAMAs across eight different pathogens using various optimization parameters. We evaluated the effects of genome size and %GC content on assay development. When used collectively, specific strategies markedly improved the rate of successful assays at the first design attempt from ~50% to ~80%. We observed that Melt-MAMA accurately genotypes across a broad DNA range (~100 ng to ~0.1 pg). Genomic size and %GC content influence the rate of successful assay design in an independent manner. Finally, we demonstrated the versatility of these assays by the creation of a duplex Melt-MAMA real-time PCR (two SNPs) and conversion to a size-based genotyping system, which uses agarose gel electrophoresis. Melt-MAMA is comparable to Dual Probe TaqMan assays in terms of design success rate and accuracy. Although sensitivity is less robust than Dual Probe TaqMan assays, Melt-MAMA is superior in terms of cost-effectiveness, speed of development and versatility. We detail the parameters most important for the successful application of Melt-MAMA, which

  8. Optical analysis of miniature lenses with curved imaging surfaces.

    PubMed

    Reshidko, Dmitry; Sasian, Jose

    2015-10-01

    Miniature cameras for consumer electronics and mobile phones have been, and continue to be, in fast development. The system level requirements, such as manufacturing cost, packaging, and sensor characteristics, impose unique challenges for optical designers. In this paper, we discuss the potential optical benefits of having a curved image surface rather than a flat one. We show that curved sensor technology allows for optically faster lens solutions. We discuss trade-offs of several relevant characteristics, such as packaging, chief ray angle, image quality, and tolerance sensitivity. A comparison of a benchmark flat field lens, and an evaluation design imaging on a curved surface and working at f/1.6, provides useful specific insights. For a given image quality, departing from a flat imaging surface does not allow significantly reducing the total length of a lens.

  9. Automatic generation and analysis of solar cell IV curves

    DOEpatents

    Kraft, Steven M.; Jones, Jason C.

    2014-06-03

    A photovoltaic system includes multiple strings of solar panels and a device presenting a DC load to the strings of solar panels. Output currents of the strings of solar panels may be sensed and provided to a computer that generates current-voltage (IV) curves of the strings of solar panels. Output voltages of the string of solar panels may be sensed at the string or at the device presenting the DC load. The DC load may be varied. Output currents of the strings of solar panels responsive to the variation of the DC load are sensed to generate IV curves of the strings of solar panels. IV curves may be compared and analyzed to evaluate performance of and detect problems with a string of solar panels.

  10. Experimental study of the structural characteristics of Al melts on the basis of Fourier analysis of acoustic emission signals

    NASA Astrophysics Data System (ADS)

    Vorontsov, Vadim; Zhuravlev, Danil; Cherepanov, Alexander

    2014-09-01

    This scientific work is devoted to the study of the genetic connection structures of solid and liquid phases. Fourier analysis of signals of acoustic emission (AE) accompanying the melting of high purity aluminum from the melting point up to t=860°C was performed. The experimental data allowed for following the dynamics of the range order of the disorder zones in the melt with increasing melt temperature until their complete destruction.

  11. rpoB gene: a target for identification of LAB cocci by PCR-DGGE and melting curves analyses in real time PCR.

    PubMed

    Renouf, Vincent; Claisse, Olivier; Lonvaud-Funel, Aline

    2006-10-01

    Lactic acid bacteria (LAB) are essential in the quality of many fermented beverages like beer, cider and wine. In the two later cases, they convert malic acid into lactic acid during the malolactic fermentation. After fermentation, microbial stabilization is needed to prevent the development of spoilage bacteria species. Among them, cocci lead to different alterations: Pediococcus sp., and some strains of Leuconostoc mesenteroides and Oenococcus oeni can produce exopolysaccharides which modify wine viscosity and lead to ropiness. They also can produce acetic acid, biogenic amine, ethyl carbamate and volatile phenols. Therefore detection and identification are crucial. Results of phenotypic tests and DNA-DNA probes are not accurate enough. 16S RNA gene which is currently used for bacterial species identification presents intraspecies heterogeneity. The rpoB gene is an alternative to this limitation. However previous PCR targeting partial sequence of rpoB gene could not delimit cocci species. Therefore we compared the rpoB gene sequence of the six main cocci species found in fermented beverages: P. damnosus, P. dextrinicus, P. parvulus, P. pentosaceus, L. mesenteroides and O. oeni. The most discriminating partial sequence of the rpoB gene was chosen for designing primers. By PCR-DGGE the reliability of these primers was verified. It was controlled in a mixture of several cocci and other lactic acid bacteria (Lactobacillus sp.). Then we adapted the primers and the PCR conditions in order to achieve the identification of cocci species by real time PCR program including the fluorescent dye SYBR Green I, which gives faster results. PCR melt curves were established and a specific T(m) was attributed to each species.

  12. Mediation Analysis in a Latent Growth Curve Modeling Framework

    ERIC Educational Resources Information Center

    von Soest, Tilmann; Hagtvet, Knut A.

    2011-01-01

    This article presents several longitudinal mediation models in the framework of latent growth curve modeling and provides a detailed account of how such models can be constructed. Logical and statistical challenges that might arise when such analyses are conducted are also discussed. Specifically, we discuss how the initial status (intercept) and…

  13. Developmental Trajectories of Adolescent Popularity: A Growth Curve Modelling Analysis

    ERIC Educational Resources Information Center

    Cillessen, Antonius H. N.; Borch, Casey

    2006-01-01

    Growth curve modelling was used to examine developmental trajectories of sociometric and perceived popularity across eight years in adolescence, and the effects of gender, overt aggression, and relational aggression on these trajectories. Participants were 303 initially popular students (167 girls, 136 boys) for whom sociometric data were…

  14. Multiresolution Analysis of UTAT B-spline Curves

    NASA Astrophysics Data System (ADS)

    Lamnii, A.; Mraoui, H.; Sbibih, D.; Zidna, A.

    2011-09-01

    In this paper, we describe a multiresolution curve representation based on periodic uniform tension algebraic trigonometric (UTAT) spline wavelets of class ??? and order four. Then we determine the decomposition and the reconstruction vectors corresponding to UTAT-spline spaces. Finally, we give some applications in order to illustrate the efficiency of the proposed approach.

  15. Use of the Zoom in the Analysis of a Curve.

    ERIC Educational Resources Information Center

    Montaner, F. Rubio

    1987-01-01

    How the computer can aid the teacher in discussing plane curves is shown. Use of the zoom enables the teacher to illustrate aspects of graphs that would be difficult and time-consuming to show in other ways. Many illustrative graphs are included, and four programs are listed. (MNS)

  16. Analysis of Water Recovery Rate from the Heat Melt Compactor

    NASA Technical Reports Server (NTRS)

    Balasubramaniam, R.; Hegde, U.; Gokoglu, S.

    2013-01-01

    Human space missions generate trash with a substantial amount of plastic (20% or greater by mass). The trash also contains water trapped in food residue and paper products and other trash items. The Heat Melt Compactor (HMC) under development by NASA Ames Research Center (ARC) compresses the waste, dries it to recover water and melts the plastic to encapsulate the compressed trash. The resulting waste disk or puck represents an approximately ten-fold reduction in the volume of the initial trash loaded into the HMC. In the current design concept being pursued, the trash is compressed by a piston after it is loaded into the trash chamber. The piston face, the side walls of the waste processing chamber and the end surface in contact with the waste can be heated to evaporate the water and to melt the plastic. Water is recovered by the HMC in two phases. The first is a pre-process compaction without heat or with the heaters initially turned on but before the waste heats up. Tests have shown that during this step some liquid water may be expelled from the chamber. This water is believed to be free water (i.e., not bound with or absorbed in other waste constituents) that is present in the trash. This phase is herein termed Phase A of the water recovery process. During HMC operations, it is desired that liquid water recovery in Phase A be eliminated or minimized so that water-vapor processing equipment (e.g., condensers) downstream of the HMC are not fouled by liquid water and its constituents (i.e., suspended or dissolved matter) exiting the HMC. The primary water recovery process takes place next where the trash is further compacted while the heated surfaces reach their set temperatures for this step. This step will be referred to herein as Phase B of the water recovery process. During this step the waste chamber may be exposed to different selected pressures such as ambient, low pressure (e.g., 0.2 atm), or vacuum. The objective for this step is to remove both bound and

  17. Analysis of a DNA simulation model through hairpin melting experiments

    PubMed Central

    Linak, Margaret C.; Dorfman, Kevin D.

    2010-01-01

    We compare the predictions of a two-bead Brownian dynamics simulation model to melting experiments of DNA hairpins with complementary AT or GC stems and noninteracting loops in buffer A. This system emphasizes the role of stacking and hydrogen bonding energies, which are characteristics of DNA, rather than backbone bending, stiffness, and excluded volume interactions, which are generic characteristics of semiflexible polymers. By comparing high throughput data on the open-close transition of various DNA hairpins to the corresponding simulation data, we (1) establish a suitable metric to compare the simulations to experiments, (2) find a conversion between the simulation and experimental temperatures, and (3) point out several limitations of the model, including the lack of G-quartets and cross stacking effects. Our approach and experimental data can be used to validate similar coarse-grained simulation models. PMID:20886965

  18. UNSUPERVISED TRANSIENT LIGHT CURVE ANALYSIS VIA HIERARCHICAL BAYESIAN INFERENCE

    SciTech Connect

    Sanders, N. E.; Soderberg, A. M.; Betancourt, M.

    2015-02-10

    Historically, light curve studies of supernovae (SNe) and other transient classes have focused on individual objects with copious and high signal-to-noise observations. In the nascent era of wide field transient searches, objects with detailed observations are decreasing as a fraction of the overall known SN population, and this strategy sacrifices the majority of the information contained in the data about the underlying population of transients. A population level modeling approach, simultaneously fitting all available observations of objects in a transient sub-class of interest, fully mines the data to infer the properties of the population and avoids certain systematic biases. We present a novel hierarchical Bayesian statistical model for population level modeling of transient light curves, and discuss its implementation using an efficient Hamiltonian Monte Carlo technique. As a test case, we apply this model to the Type IIP SN sample from the Pan-STARRS1 Medium Deep Survey, consisting of 18,837 photometric observations of 76 SNe, corresponding to a joint posterior distribution with 9176 parameters under our model. Our hierarchical model fits provide improved constraints on light curve parameters relevant to the physical properties of their progenitor stars relative to modeling individual light curves alone. Moreover, we directly evaluate the probability for occurrence rates of unseen light curve characteristics from the model hyperparameters, addressing observational biases in survey methodology. We view this modeling framework as an unsupervised machine learning technique with the ability to maximize scientific returns from data to be collected by future wide field transient searches like LSST.

  19. Thermoluminescence glow curve analysis of natural onyx from Turkey.

    PubMed

    Dogan, Tamer; Toktamış, Hüseyin; Yüksel, Mehmet; Topaksu, Mustafa; Yazici, A Necmeddin

    2015-02-01

    In this study, the thermoluminesce (TL) properties of natural onyx were determined after β-irradiation ((90)Sr/(90)Y) at room temperature. The effect of the additive dose and variable heating rate for TL glow peaks of the sample were investigated. Computerized glow curve deconvolution (CGCD) methods were used to determine the number of peaks and kinetic parameters related to the TL glow peaks in natural onyx from Turkey. It was also determined kinetic parameters of onyx by means of the variable heating rate (VHR) method. The sample was exposed to β-irradiation between 2.4 Gy and 2.457 kGy. The CGCD methods showed that the glow curve of sample is the superposition of at least six first order components which were ascribed as P1-P6. The dose responses of some peaks have similar patterns and they follow linearity. The effect of heating rates on the response of dosimetric glow peaks of sample was studied. The maximum TL peak intensities of glow curve are decreasing with increasing heating rate and maximum TL peak intensities at 1 °C/s drops to 20% of the initial value when the sample is read at 6 °C/s.

  20. Thermoluminescence glow curve analysis and CGCD method for erbium doped CaZrO3 phosphor

    NASA Astrophysics Data System (ADS)

    Tiwari, Ratnesh; Chopra, Seema

    2016-05-01

    The manuscript report the synthesis, thermoluminescence study at fixed concentration of Er3+ (1 mol%) doped CaZrO3 phosphor. The phosphors were prepared by modified solid state reaction method. The powder sample was characterized by thermoluminescence (TL) glow curve analysis. In TL glow curve the optimized concentration in 1mol% for UV irradiated sample. The kinetic parameters were calculated by computerized glow curve deconvolution (CGCD) techniaue. Trapping parameters gives the information of dosimetry loss in prepared phosphor and its usability in environmental monitoring and for personal monitoring. CGCD is the advance tool for analysis of complicated TL glow curves.

  1. 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.

  2. Reconstructing CO2 concentrations in basaltic melt inclusions using Raman analysis of vapor bubbles

    NASA Astrophysics Data System (ADS)

    Aster, Ellen M.; Wallace, Paul J.; Moore, Lowell R.; Watkins, James; Gazel, Esteban; Bodnar, Robert J.

    2016-09-01

    Melt inclusions record valuable information about pre-eruptive volatile concentrations of melts. However, a vapor bubble commonly forms in inclusions after trapping, and this decreases the dissolved CO2 concentration in the melt (glass) phase in the inclusion. To quantify CO2 loss to vapor bubbles, Raman spectroscopic analysis was used to determine the density of CO2 in bubbles in melt inclusions from two Cascade cinder cones near Mt. Lassen and two Mexican cinder cones (Jorullo, Parícutin). Using analyses of dissolved CO2 and H2O in the glass in the inclusions, the measured CO2 vapor densities were used to reconstruct the original dissolved CO2 contents of the melt inclusions at the time of trapping. Our results show that 30-90% of the CO2 in a melt inclusion is contained in the vapor bubble, values similar to those found in other recent studies. We developed a model for vapor bubble growth to show how post-entrapment bubbles form in melt inclusions as a result of cooling, crystallization, and eruptive quenching. The model allows us to predict the bubble volume fraction as a function of ΔT (the difference between the trapping temperature and eruptive temperature) and the amount of CO2 lost to a bubble. Comparison of the Raman and modeling methods shows highly variable agreement. For 10 of 17 inclusions, the two methods are within ± 550 ppm CO2 (avg. difference 290 ppm), equivalent to ±~300 bars uncertainty in estimated trapping pressure for restored inclusions. Discrepancies between the two methods occur for inclusions that have been strongly affected by post-entrapment diffusive H+ loss, because this process enhances bubble formation. For our dataset, restoring the CO2 lost to vapor bubbles increases inferred trapping pressures of the inclusions by 600 to as much as 4000 bars, highlighting the importance of accounting for vapor bubble formation in melt inclusion studies.

  3. Paleomagnetic analysis of curved thrust belts reproduced by physical models

    NASA Astrophysics Data System (ADS)

    Costa, Elisabetta; Speranza, Fabio

    2003-12-01

    This paper presents a new methodology for studying the evolution of curved mountain belts by means of paleomagnetic analyses performed on analogue models. Eleven models were designed aimed at reproducing various tectonic settings in thin-skinned tectonics. Our models analyze in particular those features reported in the literature as possible causes for peculiar rotational patterns in the outermost as well as in the more internal fronts. In all the models the sedimentary cover was reproduced by frictional low-cohesion materials (sand and glass micro-beads), which detached either on frictional or on viscous layers. These latter were reproduced in the models by silicone. The sand forming the models has been previously mixed with magnetite-dominated powder. Before deformation, the models were magnetized by means of two permanent magnets generating within each model a quasi-linear magnetic field of intensity variable between 20 and 100 mT. After deformation, the models were cut into closely spaced vertical sections and sampled by means of 1×1-cm Plexiglas cylinders at several locations along curved fronts. Care was taken to collect paleomagnetic samples only within virtually undeformed thrust sheets, avoiding zones affected by pervasive shear. Afterwards, the natural remanent magnetization of these samples was measured, and alternating field demagnetization was used to isolate the principal components. The characteristic components of magnetization isolated were used to estimate the vertical-axis rotations occurring during model deformation. We find that indenters pushing into deforming belts from behind form non-rotational curved outer fronts. The more internal fronts show oroclinal-type rotations of a smaller magnitude than that expected for a perfect orocline. Lateral symmetrical obstacles in the foreland colliding with forward propagating belts produce non-rotational outer curved fronts as well, whereas in between and inside the obstacles a perfect orocline forms

  4. Rouse Mode Analysis of Chain Relaxation in Homopolymer Melts

    PubMed Central

    2015-01-01

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inversely with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. These facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion. PMID:25328247

  5. Rouse mode analysis of chain relaxation in homopolymer melts

    DOE PAGES

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; ...

    2014-09-15

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inverselymore » with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.« less

  6. Rouse mode analysis of chain relaxation in homopolymer melts

    SciTech Connect

    Kalathi, Jagannathan T.; Kumar, Sanat K.; Rubinstein, Michael; Grest, Gary S.

    2014-09-15

    We use molecular dynamics simulations of the Kremer–Grest (KG) bead–spring model of polymer chains of length between 10 and 500, and a closely related analogue that allows for chain crossing, to clearly delineate the effects of entanglements on the length-scale-dependent chain relaxation in polymer melts. We analyze the resulting trajectories using the Rouse modes of the chains and find that entanglements strongly affect these modes. The relaxation rates of the chains show two limiting effective monomeric frictions, with the local modes experiencing much lower effective friction than the longer modes. The monomeric relaxation rates of longer modes vary approximately inversely with chain length due to kinetic confinement effects. The time-dependent relaxation of Rouse modes has a stretched exponential character with a minimum of stretching exponent in the vicinity of the entanglement chain length. None of these trends are found in models that allow for chain crossing. As a result, these facts, in combination, argue for the confined motion of chains for time scales between the entanglement time and their ultimate free diffusion.

  7. Transit light curves with finite integration time: Fisher information analysis

    SciTech Connect

    Price, Ellen M.; Rogers, Leslie A.

    2014-10-10

    Kepler has revolutionized the study of transiting planets with its unprecedented photometric precision on more than 150,000 target stars. Most of the transiting planet candidates detected by Kepler have been observed as long-cadence targets with 30 minute integration times, and the upcoming Transiting Exoplanet Survey Satellite will record full frame images with a similar integration time. Integrations of 30 minutes affect the transit shape, particularly for small planets and in cases of low signal to noise. Using the Fisher information matrix technique, we derive analytic approximations for the variances and covariances on the transit parameters obtained from fitting light curve photometry collected with a finite integration time. We find that binning the light curve can significantly increase the uncertainties and covariances on the inferred parameters when comparing scenarios with constant total signal to noise (constant total integration time in the absence of read noise). Uncertainties on the transit ingress/egress time increase by a factor of 34 for Earth-size planets and 3.4 for Jupiter-size planets around Sun-like stars for integration times of 30 minutes compared to instantaneously sampled light curves. Similarly, uncertainties on the mid-transit time for Earth and Jupiter-size planets increase by factors of 3.9 and 1.4. Uncertainties on the transit depth are largely unaffected by finite integration times. While correlations among the transit depth, ingress duration, and transit duration all increase in magnitude with longer integration times, the mid-transit time remains uncorrelated with the other parameters. We provide code in Python and Mathematica for predicting the variances and covariances at www.its.caltech.edu/∼eprice.

  8. Modeling and analysis of doubly curved aerobrake truss structures

    NASA Technical Reports Server (NTRS)

    Washington, Gregory; Klang, Eric

    1992-01-01

    An aerobrake structural concept featuring a double curved tetrahedral truss support system and hexagonal heat shield panels was modeled and analyzed. Modeling equations for a sphere, cone, and paraboloid were developed for the purpose. Design equation and computer codes were also evolved and employed to determine the total mass of the aerobrake as well as any parameters that had an adverse effect on the total aerobrake mass. These data were used in a point design for a Mars mission aerobrake. A 131-ft diameter aerobrake was found to be viable using the present structural concept (i.e., the total aerobrake mass is not greater than 450,000 lb, which is the attached spacecraft mass). It is also shown that curvature, load point placement, number of load points, number of strut designs, and number of rings all have an effect on the mass of the aerobrake.

  9. High-resolution melting analysis for detection of a single-nucleotide polymorphism and the genotype of the myostatin gene in warmblood horses.

    PubMed

    Serpa, Priscila B S; Garbade, Petra; Natalini, Cláudio C; Pires, Ananda R; Tisotti, Tainor M

    2017-01-01

    OBJECTIVE To develop a high-resolution melting (HRM) assay to detect the g.66493737C>T polymorphism in the myostatin gene (MSTN) and determine the frequency of 3 previously defined g.66493737 genotypes (T/T, T/C, and C/C) in warmblood horses. SAMPLES Blood samples from 23 horses. PROCEDURES From each blood sample, DNA was extracted and analyzed by standard PCR methods and an HRM assay to determine the MSTN genotype. Three protocols (standard protocol, protocol in which a high-salt solution was added to the reaction mixture before the first melting cycle, and protocol in which an unlabeled probe was added to the reaction mixture before analysis) for the HRM assay were designed and compared. Genotype results determined by the HRM protocol that generated the most consistent melting curves were compared with those determined by sequencing. RESULTS The HRM protocol in which an unlabeled probe was added to the reaction mixture generated the most consistent melting curves. The genotypes of the g.66493737C>T polymorphism were determined for 22 horses (16 by HRM analysis and 20 by sequencing); 14, 7, and 1 had the T/T, T/C, and C/C genotypes, respectively. The genotype determined by HRM analysis agreed with that determined by sequencing for 14 of 16 horses. The frequency of alleles T and C was 79.5% and 20.5%, respectively. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that HRM analysis may be a faster and more economical alternative than PCR methods for genotyping. Genotyping results might be useful as predictors of athletic performance for horses.

  10. Melt Analysis of Mismatch Amplification Mutation Assays (Melt-MAMA): A Functional Study of a Cost-Effective SNP Genotyping Assay in Bacterial Models

    PubMed Central

    Birdsell, Dawn N.; Pearson, Talima; Price, Erin P.; Hornstra, Heidie M.; Nera, Roxanne D.; Stone, Nathan; Gruendike, Jeffrey; Kaufman, Emily L.; Pettus, Amanda H.; Hurbon, Audriana N.; Buchhagen, Jordan L.; Harms, N. Jane; Chanturia, Gvantsa; Gyuranecz, Miklos; Wagner, David M.; Keim, Paul S.

    2012-01-01

    Single nucleotide polymorphisms (SNPs) are abundant in genomes of all species and biologically informative markers extensively used across broad scientific disciplines. Newly identified SNP markers are publicly available at an ever-increasing rate due to advancements in sequencing technologies. Efficient, cost-effective SNP genotyping methods to screen sample populations are in great demand in well-equipped laboratories, but also in developing world situations. Dual Probe TaqMan assays are robust but can be cost-prohibitive and require specialized equipment. The Mismatch Amplification Mutation Assay, coupled with melt analysis (Melt-MAMA), is flexible, efficient and cost-effective. However, Melt-MAMA traditionally suffers from high rates of assay design failures and knowledge gaps on assay robustness and sensitivity. In this study, we identified strategies that improved the success of Melt-MAMA. We examined the performance of 185 Melt-MAMAs across eight different pathogens using various optimization parameters. We evaluated the effects of genome size and %GC content on assay development. When used collectively, specific strategies markedly improved the rate of successful assays at the first design attempt from ∼50% to ∼80%. We observed that Melt-MAMA accurately genotypes across a broad DNA range (∼100 ng to ∼0.1 pg). Genomic size and %GC content influence the rate of successful assay design in an independent manner. Finally, we demonstrated the versatility of these assays by the creation of a duplex Melt-MAMA real-time PCR (two SNPs) and conversion to a size-based genotyping system, which uses agarose gel electrophoresis. Melt-MAMA is comparable to Dual Probe TaqMan assays in terms of design success rate and accuracy. Although sensitivity is less robust than Dual Probe TaqMan assays, Melt-MAMA is superior in terms of cost-effectiveness, speed of development and versatility. We detail the parameters most important for the successful application of Melt

  11. Analysis of driver's characteristics on a curved road in a lattice model

    NASA Astrophysics Data System (ADS)

    Kaur, Ramanpreet; Sharma, Sapna

    2017-04-01

    The present paper investigates the effect of driver's behavior on the curved road via lattice hydrodynamic approach. The basic model for straight road is extended for the curved road and the characteristics of driver's behavior is incorporated in the lattice model. The extended model is investigated theoretically by the means of linear stability analysis and the effect of curved road and intensity of influence of driver's behavior on the traffic flow stability is examined. Through nonlinear stability analysis, the modified Korteweg-de Vries (MKdV) equation near the critical point is derived to describe the evolution properties of traffic density waves by applying the reductive perturbation method. Furthermore, the numerical simulation is carried out to validate the theoretical results which indicates that the curved road has a negative influence on the stability of the traffic flow. It is also seen that the traffic jam on a curved road can be suppressed efficiently via taking into account aggressive drivers.

  12. Parent involvement and science achievement: A latent growth curve analysis

    NASA Astrophysics Data System (ADS)

    Johnson, Ursula Yvette

    This study examined science achievement growth across elementary and middle school and parent school involvement using the Early Childhood Longitudinal Study - Kindergarten Class of 1998--1999 (ECLS-K). The ECLS-K is a nationally representative kindergarten cohort of students from public and private schools who attended full-day or half-day kindergarten class in 1998--1999. The present study's sample (N = 8,070) was based on students that had a sampling weight available from the public-use data file. Students were assessed in science achievement at third, fifth, and eighth grades and parents of the students were surveyed at the same time points. Analyses using latent growth curve modeling with time invariant and varying covariates in an SEM framework revealed a positive relationship between science achievement and parent involvement at eighth grade. Furthermore, there were gender and racial/ethnic differences in parents' school involvement as a predictor of science achievement. Findings indicated that students with lower initial science achievement scores had a faster rate of growth across time. The achievement gap between low and high achievers in earth, space and life sciences lessened from elementary to middle school. Parents' involvement with school usually tapers off after elementary school, but due to parent school involvement being a significant predictor of eighth grade science achievement, later school involvement may need to be supported and better implemented in secondary schooling.

  13. GLOBAL ANALYSIS OF KOI-977: SPECTROSCOPY, ASTEROSEISMOLOGY, AND PHASE-CURVE ANALYSIS

    SciTech Connect

    Hirano, Teruyuki; Sato, Bun'ei; Kobayashi, Atsushi; Masuda, Kento; Benomar, Othman; Takeda, Yoichi; Omiya, Masashi; Harakawa, Hiroki

    2015-01-20

    We present a global analysis of KOI-977, one of the planet host candidates detected by Kepler. The Kepler Input Catalog (KIC) reports that KOI-977 is a red giant, for which few close-in planets have been discovered. Our global analysis involves spectroscopic and asteroseismic determinations of stellar parameters (e.g., mass and radius) and radial velocity (RV) measurements. Our analyses reveal that KOI-977 is indeed a red giant, possibly in the red clump, but its estimated radius (≳ 20 R {sub ☉} = 0.093 AU) is much larger than KOI-977.01's orbital distance (∼0.027 AU) estimated from its period (P {sub orb} ∼ 1.35 days) and host star's mass. RV measurements show a small variation, which also contradicts the amplitude of ellipsoidal variations seen in the light curve folded with KOI-977.01's period. Therefore, we conclude that KOI-977.01 is a false positive, meaning that the red giant, for which we measured the radius and RVs, is different from the object that produces the transit-like signal (i.e., an eclipsing binary). On the basis of this assumption, we also perform a light curve analysis including the modeling of transits/eclipses and phase-curve variations, adopting various values for the dilution factor D, which is defined as the flux ratio between the red giant and eclipsing binary. Fitting the whole folded light curve as well as individual transits in the short cadence data simultaneously, we find that the estimated mass and radius ratios of the eclipsing binary are consistent with those of a solar-type star and a late-type star (e.g., an M dwarf) for D ≳ 20.

  14. High-resolution DNA melting analysis in plant research

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 developed...

  15. A Brief Review: The Z-curve Theory and its Application in Genome Analysis

    PubMed Central

    Zhang, Ren; Zhang, Chun-Ting

    2014-01-01

    In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis. PMID:24822026

  16. Detection and identification of vegetative insecticidal proteins vip3 genes of Bacillus thuringiensis strains using polymerase chain reaction-high resolution melt analysis.

    PubMed

    Li, Haitao; Shu, Changlong; He, Xiaoming; Gao, JiGuo; Liu, Rongmei; Huang, Dafang

    2012-05-01

    In this study, vegetative insecticidal proteins vip3 genes from Bacillus thuringiensis strains were detected based on polymerase chain reaction-high resolution melt (PCR-HRM) analysis. A pair of primers was designed according to the conservative sequences in 150 bp region of the known vip3 subfamily. The 150 bp regions of difference vip3 genes have only a few nucleotide difference vip3 genes were detected in 8 of 11 standard B. thuringiensis strains, and vip3Aa genes, vip3Af genes and vip3Ba gene can be distinguished as different melting curves by this method. The results demonstrate the utility of the HRM assay for mutant screening using vip3 gene. The PCR-HRM method may be a valuable and reliable tool for specific detection and identification of vip3 genes.

  17. Genotyping of the protozoan pathogen Toxoplasma gondii using high-resolution melting analysis of the repeated B1 gene.

    PubMed

    Costa, Jean-Marc; Cabaret, Odile; Moukoury, Sandrine; Bretagne, Stéphane

    2011-09-01

    Genetic studies of the protozoan parasite Toxoplasma gondii have identified three main distinct types according to virulence in some hosts. Several methods have been developed to differentiate genotypes currently dominated by microsatellite markers targeting single-copy loci. We analyzed the possibility of using the 35-fold repetitive B1 gene via high-resolution melting (HRM) curve analysis. Sequencing of the B1 gene of 14 reference strains (four Type I, six Type II, and four Type III strains) identified 18 single nucleotide polymorphisms (SNP). Primers were designed to amplify eight of them for HRM analysis and for relative quantification of each nucleotide variation using SNaPshot mini-sequencing. Genotyping with five microsatellite markers was performed for comparison. Two to four HRM profiles were obtained depending on the SNP tested. The differences observed relied on the different ratios of nucleotides at the SNP locus as evidenced via SNaPshot mini-sequencing. The three main lineages could be distinguished by using several HRM profiles. Some HRM profiles proved more informative than the analysis based on five microsatellite markers, showing additional differences in Type I and Type II strains. Using HRM analysis, we obtained at least an equally good discrimination of the main lineages than that based on five microsatellite markers.

  18. Decline Curve Analysis for Production Forecast and Optimization of Liquid-Dominated Geothermal Reservoir

    NASA Astrophysics Data System (ADS)

    Hidayat, I.

    2016-09-01

    Power projects in the geothermal field has a long span of about 30 years. The power supply should be maintained at a certain value across a range of time. A geothermal field, however, has the characteristics of natural production decline with time. In a geothermal field, development of decline curve model of steam production is important for forecasting production decline in the future. This study was developed using decline curve by production data along 3 years liquid-dominated geothermal reservoir in Ulubelu field. Decline curve in geothermal field based on decline curve in petroleum industry. The decline curve was correlated by reservoir management in geothermal. The purposes of this study to get best match model decline curve and forecasting production in the future. Based on decline curve analysis by production data in Ulubelu field, the result model decline curve is exponential model. From the model, we can get the value of decline rate in the field is 9.4 %/year. Then, the formula of forecasting steam flow used exponent decline to forecast in the future. By using separated system cycle in Ulubelu field, the minimal steam flowrate towards turbine was 502018.4 ton/month. Based on formula of forecasting production and minimal steam flowrate, we can get the time make up wells to maintain steam supply for stability in generator power capacity.

  19. Constraints on the Parental Melts of Enriched Shergottites from Image Analysis and High Pressure Experiments

    NASA Technical Reports Server (NTRS)

    Collinet, M.; Medard, E.; Devouard, B.; Peslier, A.

    2012-01-01

    Martian basalts can be classified in at least two geochemically different families: enriched and depleted shergottites. Enriched shergottites are characterized by higher incompatible element concentrations and initial Sr-87/Sr-86 and lower initial Nd-143/Nd-144 and Hf-176/Hf-177 than depleted shergottites [e.g. 1, 2]. It is now generally admitted that shergottites result from the melting of at least two distinct mantle reservoirs [e.g. 2, 3]. Some of the olivine-phyric shergottites (either depleted or enriched), the most magnesian Martian basalts, could represent primitive melts, which are of considerable interest to constrain mantle sources. Two depleted olivine-phyric shergottites, Yamato (Y) 980459 and Northwest Africa (NWA) 5789, are in equilibrium with their most magnesian olivine (Fig. 1) and their bulk rock compositions are inferred to represent primitive melts [4, 5]. Larkman Nunatak (LAR) 06319 [3, 6, 7] and NWA 1068 [8], the most magnesian enriched basalts, have bulk Mg# that are too high to be in equilibrium with their olivine megacryst cores. Parental melt compositions have been estimated by subtracting the most magnesian olivine from the bulk rock composition, assuming that olivine megacrysts have partially accumulated [3, 9]. However, because this technique does not account for the actual petrography of these meteorites, we used image analysis to study these rocks history, reconstruct their parent magma and understand the nature of olivine megacrysts.

  20. A light-curve distortion-wave analysis of eight RS Canum Venaticorum systems

    NASA Astrophysics Data System (ADS)

    Caton, D. B.

    1986-01-01

    A program of differential U,B,V photometry of 14 RS CVn systems carried out at Rosemary Hill Observatory in 1978 - 1981 is described, and an analysis of the light curves for the characteristic distortion wave for eight of the systems is presented. The V light curves of the systems are shown. Significant waves were observed in RS CVn, RZ Eri, and RW UMa. No significant waves were found in UX Com, GK Hya, AR Lac, LX Per, or TY Pyx. Unusual light curve distortions were observed in UX Com and AR Lac.

  1. Constraining the equation of state of fluid H2O to 60 GPa using the melting curve of Ice VII and the formation of Mg(OH)2 in the MgO-H2O system.

    NASA Astrophysics Data System (ADS)

    Frank, M. R.; Fei, Y.

    2002-12-01

    The physical properties of fluid H2O are important geologically over a large range of pressure and temperature. Shock-wave data have served as the main resource for the derivations of many equations of state for fluid H2O. Direct measurements of the specific volume of water are required to test the validity of these models; however, direct measurements at elevated pressures and temperatures are difficult and, as a result, rare. The study presented here sought to determine the PVT properties of Ice VII along the melting curve at pressures > 20 GPa using the a Mao-Bell type diamond anvil cell with an external Mo-wire resistance heater. Small grains of MgO, gold and a relatively large volume of H2O were loaded in a sample chamber drilled in a pre-indented Re-gasket. The temperature of the experiment was determined by placing a thermocouple between the diamond anvil and Re-gasket, directly against the surface of the diamond. The experiments were conducted on beam line X17C at the Brookhaven National Synchrotron Light Source using the Energy Dispersive X-ray Diffraction (EDXD) technique. The unit cells of Ice VII, MgO, and gold were monitored during the experiment with gold being used as an internal pressure calibrant. The methodology was to use the disappearance of the diffraction pattern of Ice VII with the production of brucite following the reaction of fluid H2O with MgO. Generally, experiments would follow the following sequence as temperature was increased: 1.) slight drop in pressure, 2.) the appearance of diffraction lines indicative of brucite, and 3.) total disappearance of Ice VII diffraction lines and noticeable drop in pressure (up to ~2 GPa at the highest pressures). The appearance of brucite would always proceed the disappearance of Ice VII diffraction lines. The data suggest that brucite formed as soon as fluid H2O became available whereas Ice VII melted over a small range over temperature (<50 K). The melting curve for Ice VII from 3-60 GPa can be

  2. Type Ia Supernova Light-Curve Inference: Hierarchical Bayesian Analysis in the Near-Infrared

    NASA Astrophysics Data System (ADS)

    Mandel, Kaisey S.; Wood-Vasey, W. Michael; Friedman, Andrew S.; Kirshner, Robert P.

    2009-10-01

    We present a comprehensive statistical analysis of the properties of Type Ia supernova (SN Ia) light curves in the near-infrared using recent data from Peters Automated InfraRed Imaging TELescope and the literature. We construct a hierarchical Bayesian framework, incorporating several uncertainties including photometric error, peculiar velocities, dust extinction, and intrinsic variations, for principled and coherent statistical inference. SN Ia light-curve inferences are drawn from the global posterior probability of parameters describing both individual supernovae and the population conditioned on the entire SN Ia NIR data set. The logical structure of the hierarchical model is represented by a directed acyclic graph. Fully Bayesian analysis of the model and data is enabled by an efficient Markov Chain Monte Carlo algorithm exploiting the conditional probabilistic structure using Gibbs sampling. We apply this framework to the JHKs SN Ia light-curve data. A new light-curve model captures the observed J-band light-curve shape variations. The marginal intrinsic variances in peak absolute magnitudes are σ(MJ ) = 0.17 ± 0.03, σ(MH ) = 0.11 ± 0.03, and σ(MKs ) = 0.19 ± 0.04. We describe the first quantitative evidence for correlations between the NIR absolute magnitudes and J-band light-curve shapes, and demonstrate their utility for distance estimation. The average residual in the Hubble diagram for the training set SNe at cz > 2000kms-1 is 0.10 mag. The new application of bootstrap cross-validation to SN Ia light-curve inference tests the sensitivity of the statistical model fit to the finite sample and estimates the prediction error at 0.15 mag. These results demonstrate that SN Ia NIR light curves are as effective as corrected optical light curves, and, because they are less vulnerable to dust absorption, they have great potential as precise and accurate cosmological distance indicators.

  3. Late-phase melt progression experiment: MP-2. Results and analysis

    SciTech Connect

    Gasser, R.D.; Gauntt, R.O.; Bourcier, S.C.

    1997-05-01

    In-pile experiments addressing late-phase processes in Light Water Reactors (LWRs) were performed in the Annular Core Research Reactor (ACRR) at Sandia National Laboratories. Melt Progression (MP) experiments were designed to provide information to develop and verify computer models for analysis of LWR core damage in severe accidents. Experiments examine the formation and motion of ceramic molten pools in disrupted reactor core regions. The MP-2 experiment assembly consisted of: (1) a rubble bed of enriched UO{sub 2} and ZrO{sub 2} simulating severely disrupted reactor core regions, (2) a ceramic/metallic crust representing blockage formed by early phase melting, relocation, and refreezing of core components, and (3) an intact rod stub region that remained in place below the blockage region. The test assembly was fission heated in the central cavity of the ACRR at an average rate of about 0.2 KA, reaching a peak molten pool temperature around 3400 K. Melting of the debris bed ceramic components was initiated near the center of the bed. The molten material relocated downward, refreezing to form a ceramic crust near the bottom of the rubble bed. As power levels were increased, the crust gradually remelted and reformed at progressively lower positions in the bed until late in the experiment when it penetrated into and attacked the ceramic/metallic blockage. The metallic components of the blockage region melted and relocated to the bottom of the intact rod stub region before the ceramic melt penetrated the blockage region from above. The ceramic pool penetrated halfway into the blockage region by the end of the experiment. Measurements of thermal response and material relocation are compared to the results of the computer simulations. Postexperiment examination of the assembly with the associated material interactions and metallurgy are also discussed in detail with the analyses and interpretation of results. 16 refs., 206 figs., 24 tabs.

  4. Development of synthetic flood damage curve by explicit costs analysis

    NASA Astrophysics Data System (ADS)

    Martina, Mario; Molinari, Daniela; Dottori, Francesco; Scorzini, Annarita

    2015-04-01

    characteristics. Such functions were developed using a what-if analysis using data collected after the 2012 flood in the Umbria Region in Central Italy, as well as authors' experience, as reference to understand damage mechanisms. Observed damage data were also used to calibrate the functions.

  5. Peristaltic Flow of Rabinowitsch Fluid in a Curved Channel: Mathematical Analysis Revisited

    NASA Astrophysics Data System (ADS)

    Ali, Nasir; Sajid, Muhammad; Javid, Khurram; Ahmed, Raheel

    2017-03-01

    Recently, Maraj and Nadeem (E. N. Maraj, S. Nadeem, Z. Naturforsch. A 70, 513 (2015)) discussed the application of Rabinowitsch fluid model for the mathematical analysis of peristaltic flow in a curved channel. The mathematical analysis presented by these authors is scrutinised in detail and certain subtle details are pointed out which affect the final results.

  6. High-resolution melt analysis for rapid comparison of bacterial community compositions.

    PubMed

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Baelum, Jacob; Feld, Louise; Holben, William E; Jacobsen, Carsten Suhr

    2014-06-01

    In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized that HRM analysis of amplified 16S rRNA genes from a soil ecosystem could be used as a screening tool to identify changes in bacterial community structure. This hypothesis was tested using a soil microcosm setup exposed to a total of six treatments representing different combinations of pesticide and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon sequencing. HRM analysis was shown to be a fast, high-throughput technique that can serve as an effective alternative to gel-based screening methods to monitor microbial community composition.

  7. A new methodology for free wake analysis using curved vortex elements

    NASA Technical Reports Server (NTRS)

    Bliss, Donald B.; Teske, Milton E.; Quackenbush, Todd R.

    1987-01-01

    A method using curved vortex elements was developed for helicopter rotor free wake calculations. The Basic Curve Vortex Element (BCVE) is derived from the approximate Biot-Savart integration for a parabolic arc filament. When used in conjunction with a scheme to fit the elements along a vortex filament contour, this method has a significant advantage in overall accuracy and efficiency when compared to the traditional straight-line element approach. A theoretical and numerical analysis shows that free wake flows involving close interactions between filaments should utilize curved vortex elements in order to guarantee a consistent level of accuracy. The curved element method was implemented into a forward flight free wake analysis, featuring an adaptive far wake model that utilizes free wake information to extend the vortex filaments beyond the free wake regions. The curved vortex element free wake, coupled with this far wake model, exhibited rapid convergence, even in regions where the free wake and far wake turns are interlaced. Sample calculations are presented for tip vortex motion at various advance ratios for single and multiple blade rotors. Cross-flow plots reveal that the overall downstream wake flow resembles a trailing vortex pair. A preliminary assessment shows that the rotor downwash field is insensitive to element size, even for relatively large curved elements.

  8. Numerical analysis of curved frequency selective surface by finite-difference time-domain

    NASA Astrophysics Data System (ADS)

    Chen, Xin-yi; Wang, Jian-bo; Chen, Gui-bo; Sun, Guan-cheng; Lu, Jun

    2011-08-01

    Frequency selective surface is a monolayer or multilayer 2D periodic structure which is composed of multiple resonance units scattering by a two-dimensional periodic array on dielectric layer. FSS can't absorb radio frequency energy, but can filter the frequency which is therefore applied in microwave technique or stealth technology. The relative research on curved FSS is relatively scarce since the curved FSS structure can be obtained only when FSS is attached on the materials surfaces of curved structures in engineering application. However, curved FSS is widely applied in practical engineering; therefore, the research on curved FSS structure has important significance. In this paper, a curved FSS structure model of Y-pore unit is established and numerical simulated by means of FDTD. The influence of curvature on FSS transmission characteristics is studied according to the analysis on the changing of radar cross section (RCS). The results show: the center frequency point of the plane band pass FSS structure drifts after the curve surface deformation of the structure; the center frequency point of the curved band pass FSS structure drifts with the changing of the curvature radius, i. e. with the decreasing of curvature radius, the frequency point drifts towards high points and the transmittance decreases. The design of FSS radome demands of accurate and stable center resonance frequency; therefore, the actual situation of curved surface should be considered in practical engineering application when band pass FSS is made into frequency selection filtering radome. The curvature radius should be long enough to avoid center frequency drifting and transmittance deceasing.

  9. The random walk function in the analysis of time-activity curves from dynamic radionuclide studies.

    PubMed

    Hart, G C; Bunday, B; Kiri, V

    1987-04-01

    The random walk function is a mathematical function derived from studies of the mass transport and flow of diffusible materials through tubes. Approximations to the function were first used some time ago in the field of cardiac tracer dilution curves, but in the absence of rapid and reproducible curve fitting the method never became commonplace. The current study uses the latest curve-fitting techniques and shows how the method may be used with precision in the analysis of time-activity curves from dynamic oesophageal and blood flow studies. The physiological basis of the method is given and parameters obtained which relate to both the rate of flow and the local dispersion of the bolus.

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

    PubMed

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

    2015-07-16

    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.

  11. First report of Tasmanian sheep strain (G2) genotype isolated from Iranian goat using the high resolution melting (HRM) analysis

    PubMed Central

    Hosseini-Safa, Ahmad; Mohag, hegh, Mohammad Ali; Pestechian, Nader; Ganji, Maryam; Mohammadi, Rasoul; Mahmoudi Lamouki, Reza; Rostami-Nejad, Mohammad

    2016-01-01

    Aim: The present study was aimed to evaluate E. granulosus genotypes isolated from goats using HRM analysis in Isfahan province. Background: Cystic echincoccosis, so-called hydatidosis, is widespread infection caused by the larval stage of Echinococcus granulosus. This is an important zoonotic disease worldwide, especially in the developing countries such as Iran. To date, molecular studies mainly based on the mitochondrial DNA sequences have identified distinct genotypes termed G1-G10 which can differ in some characteristics such as the growth and infectivity to different intermediate hosts or the survival rate in the definitive hosts that are important for the development of control strategies. Methods: From August to December 2014, 1341 goats were investigated and hydatid cysts were collected from the liver and lungs of 43 infected goats in Isfahan province abattoirs, Isfahan, Iran. Total genomic DNA was extracted from each sample, amplified for the presence of polymorphism of mitochondrial gene coding for cytochrome c oxidase subunit 1 (CO1), using high resolution melting curve (HRM) method. Results: the results of HRM analysis using the sequence of CO1 gene for 43 Echinococcus granulosus isolates from goats showed 31, 2 and 10 isolates were identified as G1, G2, and G3 genotypes, respectively. Conclusion: G1 is the predominant genotype in the isolated goat samples in Isfahan province, and the presence of G2 strain was reported for the first time in goat in Iran. PMID:28224031

  12. Analysis of Pu Isotopes in Melted Fuel by Neutron Resonance Transmission: Examination by Linear Absorption Model

    NASA Astrophysics Data System (ADS)

    Kitatani, F.; Harada, H.; Takamine, J.; Kureta, M.; Seya, M.

    2014-04-01

    We have been studying the feasibility of neutron resonance transmission analysis (NRTA) for quantifying nuclear materials (Pu/U isotopes) in particle-like debris of melted fuel for nuclear material accountability and safeguards. The achievable measurement accuracy of NRTA was examined using a linear absorption model for the sample which contain substances other than nuclear fuel materials, such as boron and iron. The impurities (boron and iron etc.) in melted fuel are from the support structure and criticality control materials of the reactor core, and should be included to study the feasibility of NRTA for actual application. Neutron transmission spectra were calculated using the total neutron cross-sections in JENDL-4.0. The transmission spectra together with their uncertainties were evaluated. The study showed quantitatively that the statistical uncertainty in the determination of atomic number density of each isotope depends on the impurity density in the sample. The optimal thickness of the sample was determined for various impurity densities.

  13. Sensitive quantitative analysis of murine LINE1 DNA methylation using high resolution melt analysis.

    PubMed

    Newman, Michelle; Blyth, Benjamin J; Hussey, Damian J; Jardine, Daniel; Sykes, Pamela J; Ormsby, Rebecca J

    2012-01-01

    We present here the first high resolution melt (HRM) assay to quantitatively analyze differences in murine DNA methylation levels utilizing CpG methylation of Long Interspersed Elements-1 (LINE1 or L1). By calculating the integral difference in melt temperature between samples and a methylated control, and biasing PCR primers for unmethylated CpGs, the assay demonstrates enhanced sensitivity to detect changes in methylation in a cell line treated with low doses of 5-aza-2'-deoxycytidine (5-aza). The L1 assay was confirmed to be a good marker of changes in DNA methylation of L1 elements at multiple regions across the genome when compared with total 5-methyl-cytosine content, measured by Liquid Chromatography-Mass Spectrometry (LC-MS). The assay design was also used to detect changes in methylation at other murine repeat elements (B1 and Intracisternal-A-particle Long-terminal Repeat elements). Pyrosequencing analysis revealed that L1 methylation changes were non-uniform across the CpGs within the L1-HRM target region, demonstrating that the L1 assay can detect small changes in CpG methylation among a large pool of heterogeneously methylated DNA templates. Application of the assay to various tissues from Balb/c and CBA mice, including previously unreported peripheral blood (PB), revealed a tissue hierarchy (from hypermethylated to hypomethylated) of PB > kidney > liver > prostate > spleen. CBA mice demonstrated overall greater methylation than Balb/c mice, and male mice demonstrated higher tissue methylation compared with female mice in both strains. Changes in DNA methylation have been reported to be an early and fundamental event in the pathogenesis of many human diseases, including cancer. Mouse studies designed to identify modulators of DNA methylation, the critical doses, relevant time points and the tissues affected are limited by the low throughput nature and exorbitant cost of many DNA methylation assays. The L1 assay provides a high throughput, inexpensive

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

    PubMed Central

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

    2016-01-01

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

  15. AtomicJ: An open source software for analysis of force curves

    NASA Astrophysics Data System (ADS)

    Hermanowicz, Paweł; Sarna, Michał; Burda, Kvetoslava; Gabryś, Halina

    2014-06-01

    We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

  16. AtomicJ: An open source software for analysis of force curves

    SciTech Connect

    Hermanowicz, Paweł Gabryś, Halina; Sarna, Michał; Burda, Kvetoslava

    2014-06-15

    We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

  17. Retrospective North American CFL Experience Curve Analysis and Correlation to Deployment Programs

    SciTech Connect

    Smith, Sarah J.; Wei, Max; Sohn, Michael D.

    2015-07-01

    Retrospective experience curves are a useful tool for understanding historic technology development, and can contribute to investment program analysis and future cost estimation efforts. This work documents our development of an analysis approach for deriving retrospective experience curves with a variable learning rate, and its application to develop an experience curve for compact fluorescent lamps for the global and North American markets over the years 1990-2007. Uncertainties and assumptions involved in interpreting data for our experience curve development are discussed, including the processing and transformation of empirical data, the selection of system boundaries, and the identification of historical changes in the learning rate over the course of 15 years. In the results that follow, we find that that the learning rate has changed at least once from 1990-2007. We also explore if, and to what degree, public deployment programs may have contributed to an increased technology learning rate in North America. We observe correlations between the changes in the learning rate and the initiation of new policies, abrupt technological advances, including improvements to ballast technology, and economic and political events such as trade tariffs and electricity prices. Finally, we discuss how the findings of this work (1) support the use of segmented experience curves for retrospective and prospective analysis and (2) may imply that investments in technological research and development have contributed to a change in market adoption and penetration.

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

    PubMed

    Housden, Benjamin E; Perrimon, Norbert

    2016-09-01

    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.

  19. A novel snapback primer probe assay for the detection and discrimination of sympatric Haemonchus species using DNA melting analysis.

    PubMed

    Pichler, Rudolf; Silbermayr, Katja; Periasamy, Kathiravan

    2017-02-20

    Different sympatric species of Haemonchus parasites infecting ruminants and camels can be distinguished morphologically, but involves tedious microscopic examinations, measurements and several other limitations. Information on internal transcribed spacer-2 (ITS-2) sequence provides confirmatory differentiation of sympatric Haemonchus species. The present study introduces a novel, snapback primer probe based, real time PCR assay for the differentiation of three sympatric Haemonchus species, H. contortus (Hco), H. placei (Hpl) and H. longistipes (Hlo). The assay was designed to amplify a region of 130bp within the ITS-2 gene that included three diagnostic mutational sites capable of discriminating Hco, Hpl and Hlo. Following melt curve analysis, species-specific diagnostic melt peaks were obtained for Hco, Hpl and Hlo with a mean melting temperature of 56.6±0.3°C, 64.4±0.1°C and 54.4±0.1°C respectively. The test for analytical sensitivity revealed the ability of the assay to detect up to 5 copies per reaction. To evaluate the discriminating power of the assay, 174 samples from adult worms and 3rd stage larvae belonging to different Haemonchus species and various other nematode species including Cooperia curticei, Trichostrongylus axei, Trichostrongylus colubriformis, and Teladorsagia circumcincta were tested. Additionally, DNA extracted from 25 fecal egg samples was also tested and the specificity of the assay was verified by sequencing the ITS-2 gene of all the Haemonchus positive and non-Haemonchus samples. The assay worked accurately with 100% specificity in at least three real time PCR platforms. The assay is an effective alternative to the sequencing approach and is expected to be helpful for the screening of individual adult and larval Haemonchus parasites. However, caution needs to be applied while interpreting the results from fecal egg samples due to varying levels of sympatric co-infections from different Haemonchus species. The present study is the

  20. Testing and analysis of flat and curved panels with multiple cracks

    NASA Technical Reports Server (NTRS)

    Broek, David; Jeong, David Y.; Thomson, Douglas

    1994-01-01

    An experimental and analytical investigation of multiple cracking in various types of test specimens is described in this paper. The testing phase is comprised of a flat unstiffened panel series and curved stiffened and unstiffened panel series. The test specimens contained various configurations for initial damage. Static loading was applied to these specimens until ultimate failure, while loads and crack propagation were recorded. This data provides the basis for developing and validating methodologies for predicting linkup of multiple cracks, progression to failure, and overall residual strength. The results from twelve flat coupon and ten full scale curved panel tests are presented. In addition, an engineering analysis procedure was developed to predict multiple crack linkup. Reasonable agreement was found between predictions and actual test results for linkup and residual strength for both flat and curved panels. The results indicate that an engineering analysis approach has the potential to quantitatively assess the effect of multiple cracks in the arrest capability of an aircraft fuselage structure.

  1. Microstructures define melting of molybdenum at high pressures

    PubMed Central

    Hrubiak, Rostislav; Meng, Yue; Shen, Guoyin

    2017-01-01

    High-pressure melting anchors the phase diagram of a material, revealing the effect of pressure on the breakdown of the ordering of atoms in the solid. An important case is molybdenum, which has long been speculated to undergo an exceptionally steep increase in melting temperature when compressed. On the other hand, previous experiments showed nearly constant melting temperature as a function of pressure, in large discrepancy with theoretical expectations. Here we report a high-slope melting curve in molybdenum by synchrotron X-ray diffraction analysis of crystalline microstructures, generated by heating and subsequently rapidly quenching samples in a laser-heated diamond anvil cell. Distinct microstructural changes, observed at pressures up to 130 gigapascals, appear exclusively after melting, thus offering a reliable melting criterion. In addition, our study reveals a previously unsuspected transition in molybdenum at high pressure and high temperature, which yields highly textured body-centred cubic nanograins above a transition temperature. PMID:28248309

  2. Microstructures define melting of molybdenum at high pressures

    NASA Astrophysics Data System (ADS)

    Hrubiak, Rostislav; Meng, Yue; Shen, Guoyin

    2017-03-01

    High-pressure melting anchors the phase diagram of a material, revealing the effect of pressure on the breakdown of the ordering of atoms in the solid. An important case is molybdenum, which has long been speculated to undergo an exceptionally steep increase in melting temperature when compressed. On the other hand, previous experiments showed nearly constant melting temperature as a function of pressure, in large discrepancy with theoretical expectations. Here we report a high-slope melting curve in molybdenum by synchrotron X-ray diffraction analysis of crystalline microstructures, generated by heating and subsequently rapidly quenching samples in a laser-heated diamond anvil cell. Distinct microstructural changes, observed at pressures up to 130 gigapascals, appear exclusively after melting, thus offering a reliable melting criterion. In addition, our study reveals a previously unsuspected transition in molybdenum at high pressure and high temperature, which yields highly textured body-centred cubic nanograins above a transition temperature.

  3. Visualization and Analysis of Structural and Dynamical Properties of Hydrous Silicate Melt

    NASA Astrophysics Data System (ADS)

    Karki, B. B.; Bhattarai, D.; Stixrude, L. P.

    2008-12-01

    We have carried out a detailed visualization-based analysis of position-time data produced by first principles molecular dynamics simulations of hydrous MgSiO3 liquid to gain insight into its structural and dynamical behavior. A wide range of pressure (0 to ~100 GPa) and temperature (2000 to 6000 K) is covered and the water content is also varied (5 and 10 wt percent water in the melt). By exploring a number of structural parameters associated with short- and mid-range orders, we have shown that the melt structure changes substantially on compression. The speciation of the water component at low pressures is dominated by the isolated structures (with over 90 percent hydrogen participated) consisting of hydroxyls, water molecules, O- H-O bridging, and four-atom (O-H-O-H and H-O-H-O) groups, where every oxygen atom may be a part of polyhedron or free (i.e., bound to only magnesium atom). Hydroxyls slightly favor polyhedral sites over magnesium sites whereas molecular water is almost entirely bound to magnesium sites, and also interpolyhedral bridging (Si-O-H-O-Si) dominates other bridging. As compression increases, these isolated structures increasingly combine with each other to form extended structures involving a total of five or more O and H atoms and/or containing three-fold coordination species, which together consume over 60 percent hydrogen at the highest compression studied. Protons in the melt can be considered on equal footing with other cations (or more precisely as network modifier cations), and they are shown to increase and decrease, respectively, the contents of non-bridging and bridging oxygen. Relatively long runs are used to calculate the self-diffusion coefficients of all atomic species, which are enhanced in the presence of water compared to those of anhydrous melt. This is consistent with the prediction that water depolymerizes the melt structure at all pressures. Our analysis suggests that proton diffusion involves two processes - the transfer

  4. Melted Paraffin Wax as an Innovative Liquid and Solid Extractant for Elemental Analysis by Laser-Induced Breakdown Spectroscopy.

    PubMed

    Papai, Rodrigo; Sato, Roseli Hiromi; Nunes, Lidiane Cristina; Krug, Francisco José; Gaubeur, Ivanise

    2017-03-07

    This work proposes a new development in the use of melted paraffin wax as a new extractant in a procedure designed to aggregate the advantages of liquid phase extraction (extract homogeneity, fast, and efficient transfer, low cost and simplicity) to solid phase extraction. As proof of concept, copper(II) in aqueous samples was converted into a hydrophobic complex of copper(II) diethyldithiocarbamate and subsequently extracted into paraffin wax. Parameters which affect the complexation and extraction (pH, DDTC, and Triton X-100 concentration, vortex agitation time and complexation time) were optimized in a univariate way. The combination of the extraction proposed procedure with laser-induced breakdown spectroscopy allowed the precise copper determination (coefficient of variation = 3.1%, n = 10) and enhanced detectability because of the concentration factor of 18 times. A calibration curve was obtained with a linear range of 0.50-10.00 mg L(-1) (R(2) = 0.9990, n = 7), LOD = 0.12 mg L(-1), and LOQ = 0.38 mg L(-1) under optimized conditions. An extraction procedure efficiency of 94% was obtained. The accuracy of the method was confirmed through the analysis of a reference material of human blood serum, by the spike and recovery trials with seawater, tap water, mineral water, and alcoholic beverages and by comparing with those results obtained by graphite furnace atomic absorption spectrometry.

  5. Aptitude-Treatment Interaction Effects on Explicit Rule Learning: A Latent Growth Curve Analysis

    ERIC Educational Resources Information Center

    Hwu, Fenfang; Pan, Wei; Sun, Shuyan

    2014-01-01

    Finding the match between individuals and educational treatments is the aim of both educators and the aptitude-treatment interaction research paradigm. Using the latent growth curve analysis, the present study investigates the interaction between the type of explicit instructional approaches (deductive vs. explicit-inductive) and the level of…

  6. Taxometrics, Polytomous Constructs, and the Comparison Curve Fit Index: A Monte Carlo Analysis

    ERIC Educational Resources Information Center

    Walters, Glenn D.; McGrath, Robert E.; Knight, Raymond A.

    2010-01-01

    The taxometric method effectively distinguishes between dimensional (1-class) and taxonic (2-class) latent structure, but there is virtually no information on how it responds to polytomous (3-class) latent structure. A Monte Carlo analysis showed that the mean comparison curve fit index (CCFI; Ruscio, Haslam, & Ruscio, 2006) obtained with 3…

  7. Computational Tools for Probing Interactions in Multiple Linear Regression, Multilevel Modeling, and Latent Curve Analysis

    ERIC Educational Resources Information Center

    Preacher, Kristopher J.; Curran, Patrick J.; Bauer, Daniel J.

    2006-01-01

    Simple slopes, regions of significance, and confidence bands are commonly used to evaluate interactions in multiple linear regression (MLR) models, and the use of these techniques has recently been extended to multilevel or hierarchical linear modeling (HLM) and latent curve analysis (LCA). However, conducting these tests and plotting the…

  8. Practical Prediction of Ten Common Streptococcus pneumoniae Serotypes/Serogroups in One PCR Reaction by Multiplex Ligation-Dependent Probe Amplification and Melting Curve (MLPA-MC) Assay in Shenzhen, China

    PubMed Central

    Zheng, Lei; Zou, Jianhua; Jin, Ping; Hu, Yanwei; Kudinha, Timothy; Kong, Fanrong; Chen, Xu; Wang, Qian

    2015-01-01

    Background Streptococcus pneumoniae has more than 95 distinct serotypes described to date. However, only certain serotypes are more likely to cause pneumococcal diseases. Thus serotype surveillance is important for vaccine formula design as well as in post-vaccine serotype shift monitor. The goal of this study was to develop a practical screening assay for ten Shenzhen China common pneumococcal serotypes/serogroups in one molecular reaction. Methods A molecular assay, based on multiplex ligation-dependent probe amplification (MLPA) and melting curve (MC) analysis, was developed in an integrated approach (MLPA-MC) for the detection of ten capsular serotypes/serogroups 4, 6 (6A/6B/6C/6D), 9V/9A, 14, 15F/15A, 15B/15C, 18 (18F/18A/18B/18C), 19F, 19A and 23F. We designed serotype/serogroup-specific MLPA probes and fluorescent detection probes to discriminate the different serotypes/serogroups in one molecular reaction. The three steps of MLPA-MC assay are continuous reactions in one well detected by LightCycler 480. A total of 210 S. pneumoniae isolates from our local Maternity and Child Health Hospital were randomly chosen to evaluate the assay against published multiplex PCR assays. Results Our results showed that 198 (94.3%) of S. pneumoniae isolates were type-able by our assays and the results were in complete concordance with the published multiplex PCRs. Using the MLPA-MC assay, 96 S. pneumoniae isolates could be typed within 3 hours with limited hands-on time. This serotype/serogroup-screening assay can be easily modified or extended by modification of the serotype/serogroup-specific MLPA probes combinations according to the needs of different laboratories. Conclusions We recommend use of this assay as a starting point for screening serotype/serogroup frequencies. There is a need for this assay to be combined with other molecular typing assays, like published serotype specific PCRs, or even the Quellung reaction for serotype confirmation. PMID:26151828

  9. IMAGE-PLANE ANALYSIS OF n-POINT-MASS LENS CRITICAL CURVES AND CAUSTICS

    SciTech Connect

    Danek, Kamil; Heyrovský, David E-mail: heyrovsky@utf.mff.cuni.cz

    2015-06-10

    The interpretation of gravitational microlensing events caused by planetary systems or multiple stars is based on the n-point-mass lens model. The first planets detected by microlensing were well described by the two-point-mass model of a star with one planet. By the end of 2014, four events involving three-point-mass lenses had been announced. Two of the lenses were stars with two planetary companions each; two were binary stars with a planet orbiting one component. While the two-point-mass model is well understood, the same cannot be said for lenses with three or more components. Even the range of possible critical-curve topologies and caustic geometries of the three-point-mass lens remains unknown. In this paper we provide new tools for mapping the critical-curve topology and caustic cusp number in the parameter space of n-point-mass lenses. We perform our analysis in the image plane of the lens. We show that all contours of the Jacobian are critical curves of re-scaled versions of the lens configuration. Utilizing this property further, we introduce the cusp curve to identify cusp-image positions on all contours simultaneously. In order to track cusp-number changes in caustic metamorphoses, we define the morph curve, which pinpoints the positions of metamorphosis-point images along the cusp curve. We demonstrate the usage of both curves on simple two- and three-point-mass lens examples. For the three simplest caustic metamorphoses we illustrate the local structure of the image and source planes.

  10. Rapid and efficient zebrafish genotyping using PCR with high-resolution melt analysis.

    PubMed

    Xing, Lingyan; Quist, Tyler S; Stevenson, Tamara J; Dahlem, Timothy J; Bonkowsky, Joshua L

    2014-02-05

    Zebrafish is a powerful vertebrate model system for studying development, modeling disease, and performing drug screening. Recently a variety of genetic tools have been introduced, including multiple strategies for inducing mutations and generating transgenic lines. However, large-scale screening is limited by traditional genotyping methods, which are time-consuming and labor-intensive. Here we describe a technique to analyze zebrafish genotypes by PCR combined with high-resolution melting analysis (HRMA). This approach is rapid, sensitive, and inexpensive, with lower risk of contamination artifacts. Genotyping by PCR with HRMA can be used for embryos or adult fish, including in high-throughput screening protocols.

  11. Asymptotic analysis of a cohesive crack. 2: Influence of the softening curve

    NASA Astrophysics Data System (ADS)

    Planas, J.; Elices, M.

    1993-12-01

    This paper presents a numerical method well suited to solve the integral equation governing the asymptotic behavior of a cohesive crack, and uses it to analyze the influence of the softening curve on the cracking response of large specimens. The analysis is performed with two main objectives in mind: (1) providing criteria to determine when a simplified linear elastic fracture mechanics (LEFM) approach can be applied, and (2) providing possible procedures of extracting information on the softening behavior from experimental data. The main conclusion is that the effective crack extension prior to peak is nearly determined by the length of the softening curve (the critical crack opening) and so is the deviation from LEFM. Furthermore, a simplified R-curve approach is proposed as an approximate alternative to solving the governing integral equation.

  12. Learning Curve Analysis of Different Stages of Robotic-Assisted Laparoscopic Hysterectomy

    PubMed Central

    Tang, Feng-Hsiang

    2017-01-01

    Objective. To analyze the learning curves of the different stages of robotic-assisted laparoscopic hysterectomy. Design. Retrospective analysis. Design Classification. Canadian Task Force classification II-2. Setting. Kaohsiung Medical University Hospital, Kaohsiung, Taiwan. Patient Intervention. Women receiving robotic-assisted total and subtotal laparoscopic hysterectomies for benign conditions from May 1, 2013, to August 31, 2015. Measurements and Main Results. The mean age, body mass index (BMI), and uterine weight were 46.44 ± 5.31 years, 23.97 ± 4.75 kg/m2, and 435.48 ± 250.62 g, respectively. The most rapid learning curve was obtained for the main surgery console stage; eight experiences were required to achieve duration stability, and the time spent in this stage did not violate the control rules. The docking stage required 14 experiences to achieve duration stability, and the suture stage was the most difficult to master, requiring 26 experiences. BMI did not considerably affect the duration of the three stages. The uterine weight and the presence of adhesion did not substantially affect the main surgery console time. Conclusion. Different stages of robotic-assisted laparoscopic hysterectomy have different learning curves. The main surgery console stage has the most rapid learning curve, whereas the suture stage has the slowest learning curve. PMID:28373977

  13. The analysis of dose-response curve from bioassays with quantal response: Deterministic or statistical approaches?

    PubMed

    Mougabure-Cueto, G; Sfara, V

    2016-04-25

    Dose-response relations can be obtained from systems at any structural level of biological matter, from the molecular to the organismic level. There are two types of approaches for analyzing dose-response curves: a deterministic approach, based on the law of mass action, and a statistical approach, based on the assumed probabilities distribution of phenotypic characters. Models based on the law of mass action have been proposed to analyze dose-response relations across the entire range of biological systems. The purpose of this paper is to discuss the principles that determine the dose-response relations. Dose-response curves of simple systems are the result of chemical interactions between reacting molecules, and therefore are supported by the law of mass action. In consequence, the shape of these curves is perfectly sustained by physicochemical features. However, dose-response curves of bioassays with quantal response are not explained by the simple collision of molecules but by phenotypic variations among individuals and can be interpreted as individual tolerances. The expression of tolerance is the result of many genetic and environmental factors and thus can be considered a random variable. In consequence, the shape of its associated dose-response curve has no physicochemical bearings; instead, they are originated from random biological variations. Due to the randomness of tolerance there is no reason to use deterministic equations for its analysis; on the contrary, statistical models are the appropriate tools for analyzing these dose-response relations.

  14. A computational model-based validation of Guyton's analysis of cardiac output and venous return curves

    NASA Technical Reports Server (NTRS)

    Mukkamala, R.; Cohen, R. J.; Mark, R. G.

    2002-01-01

    Guyton developed a popular approach for understanding the factors responsible for cardiac output (CO) regulation in which 1) the heart-lung unit and systemic circulation are independently characterized via CO and venous return (VR) curves, and 2) average CO and right atrial pressure (RAP) of the intact circulation are predicted by graphically intersecting the curves. However, this approach is virtually impossible to verify experimentally. We theoretically evaluated the approach with respect to a nonlinear, computational model of the pulsatile heart and circulation. We developed two sets of open circulation models to generate CO and VR curves, differing by the manner in which average RAP was varied. One set applied constant RAPs, while the other set applied pulsatile RAPs. Accurate prediction of intact, average CO and RAP was achieved only by intersecting the CO and VR curves generated with pulsatile RAPs because of the pulsatility and nonlinearity (e.g., systemic venous collapse) of the intact model. The CO and VR curves generated with pulsatile RAPs were also practically independent. This theoretical study therefore supports the validity of Guyton's graphical analysis.

  15. 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.

  16. 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.

  17. Rapid detection of functional gene polymorphisms of TLRs and IL-17 using high resolution melting analysis

    PubMed Central

    Teräsjärvi, Johanna; Hakanen, Antti; Korppi, Matti; Nuolivirta, Kirsi; Gröndahl-Yli-Hannuksela, Kirsi; Mertsola, Jussi; Peltola, Ville; He, Qiushui

    2017-01-01

    Genetic variations in toll-like receptors (TLRs) and IL-17A have been widely connected to different diseases. Associations between susceptibility and resistance to different infections and single nucleotide polymorphisms (SNPs) in TLR1 to TLR4 and IL17A have been found. In this study, we aimed to develop a rapid and high throughput method to detect functional SNPs of above mentioned proteins. The following most studied and clinically important SNPs: TLR1 (rs5743618), TLR2 (rs5743708), TLR3 (rs3775291), TLR4 (rs4986790) and IL17 (rs2275913) were tested. High resolution melting analysis (HRMA) based on real-time PCR combined with melting analysis of a saturating double stranded-DNA binding dye was developed and used. The obtained results were compared to the “standard” sequencing method. A total of 113 DNA samples with known genotypes were included. The HRMA method correctly identified all genotypes of these five SNPs. Co-efficient values of variation of intra- and inter-run precision repeatability ranged from 0.04 to 0.23%. The determined limit of qualification for testing samples was from 0.5 to 8.0 ng/μl. The identical genotyping result was obtained from the same sample with these concentrations. Compared to “standard” sequencing methods HRMA is cost-effective, rapid and simple. All the five SNPs can be analyzed separately or in combination. PMID:28148965

  18. Better P-curves: Making P-curve analysis more robust to errors, fraud, and ambitious P-hacking, a Reply to Ulrich and Miller (2015).

    PubMed

    Simonsohn, Uri; Simmons, Joseph P; Nelson, Leif D

    2015-12-01

    When studies examine true effects, they generate right-skewed p-curves, distributions of statistically significant results with more low (.01 s) than high (.04 s) p values. What else can cause a right-skewed p-curve? First, we consider the possibility that researchers report only the smallest significant p value (as conjectured by Ulrich & Miller, 2015), concluding that it is a very uncommon problem. We then consider more common problems, including (a) p-curvers selecting the wrong p values, (b) fake data, (c) honest errors, and (d) ambitiously p-hacked (beyond p < .05) results. We evaluate the impact of these common problems on the validity of p-curve analysis, and provide practical solutions that substantially increase its robustness.

  19. Diagnosis of genetic predisposition for lactose intolerance by high resolution melting analysis.

    PubMed

    Delacour, Hervé; Leduc, Amandine; Louçano-Perdriat, Andréa; Plantamura, Julie; Ceppa, Franck

    2017-02-01

    Lactose, the principle sugar in milk, is a disaccharide hydrolyzed by intestinal lactase into glucose and galactose, which are absorbed directly by diffusion in the intestine. The decline of lactase expression (or hypolactasia) in intestinal microvilli after weaning is a normal phenomenon in mammals known as lactase deficiency. It is observed in nearly 75% of the world population and is an inherited autosomal recessive trait with incomplete penetrance. It is caused by SNPs in a regulatory element for lactase gene. In Indo-European, lactase deficiency is associated with rs4982235 SNP (or -13910C>T). The aim of this study is to describe a method based on high resolution melting for rapidly detecting genetic predisposition to lactose intolerance. Analytical performance of the assay was assessed by evaluating within and betwwen-run precision and by comparing the results (n = 50 patients) obtained with the HRM assay to those obtained with the gold standard (Sanger sequencing of the region of interest). In silico prediction of HRM curves was performed to evaluate the potential impact of the other SNPs described within the PCR product on the HRM analytical performances. The assay has good performance (CV <0.2% during the between-run study). A perfect agreement with the gold standard method was observed. The presence of other polymorphisms within the amplified sequence is detected, the misclassification risk is low. This assay can be used for rapidly diagnosing genetic predisposition to lactose intolerance.

  20. Light curve analysis of beta Lyrae type binary star EM TrA

    NASA Astrophysics Data System (ADS)

    Özkardeş, B.

    2017-02-01

    An analysis of photometric observations of the eclipsing binary system EM TrA (TYC 9258-211-1=CD-67 1660) is presented in this study. The V light curve of the system from All Sky Automated Survey (ASAS) was solved using the Wilson-Devinney code. The final solution describes EM TrA as a detached system. The absolute parameters of the components of the system were estimated.

  1. Synergistic Effects of Phase Folding and Wavelet Denoising with Applications in Light Curve Analysis

    DTIC Science & Technology

    2016-09-15

    FOLDING AND WAVELET DENOISING WITH APPLICATIONS IN LIGHT CURVE ANALYSIS I. Introduction Moore’s law, and other exponential growth patterns in technology...that the universe underwent a period of exponential growth shortly after the big bang. The exponential growth of the universe can be accounted for in the...The second section discusses the exponential growth of the solution space which accompanies the linear growth of components. Inherent Error. In

  2. Effect of silicate structure on thermodynamic properties of calcium silicate melts: Quantitative analysis of Raman spectra

    NASA Astrophysics Data System (ADS)

    Park, Joo Hyun

    2013-05-01

    The distribution of silicate anionic species (Qn units, n=0, 1, 2, 3) and the chemical speciation of oxygen in CaO-SiO2-MO (M=Mn and Mg) slags were investigated by micro-Raman spectroscopic analysis. Furthermore, the thermochemical properties were evaluated using a concentration of free oxygen and a degree of polymerization. A good linear relationship was obtained between sulfide capacity and concentration of free oxygen in the CaO-SiO2 (-MnO) melts at 1500 to 1600 °C. However, even though there was more abundant free oxygen in the CaO-SiO2-MgO system than in the CaO-SiO2 system, the sulfide capacity of the former was lower than the latter, indicating that the sulfur dissolution behavior in the silicate melts cannot be simply explained by the content of free oxygen, because the composition dependency of the stability ratio of oxygen and sulfide ions should be taken into account. The excess free energy of CaO, MgO and MnO linearly decreased as the ln (Q3/Q2) increased. The effect of the degree of polymerization on the excess free energy of mixing of MgO-containing slag was larger than that of MnO-containing slag, which was explained by the difference of the ionization potential between Mn2+ and Mg2+ ions.

  3. Efficient curve-skeleton computation for the analysis of biomedical 3d images - biomed 2010.

    PubMed

    Brun, Francesco; Dreossi, Diego

    2010-01-01

    Advances in three dimensional (3D) biomedical imaging techniques, such as magnetic resonance (MR) and computed tomography (CT), make it easy to reconstruct high quality 3D models of portions of human body and other biological specimens. A major challenge lies in the quantitative analysis of the resulting models thus allowing a more comprehensive characterization of the object under investigation. An interesting approach is based on curve-skeleton (or medial axis) extraction, which gives basic information concerning the topology and the geometry. Curve-skeletons have been applied in the analysis of vascular networks and the diagnosis of tracheal stenoses as well as a 3D flight path in virtual endoscopy. However curve-skeleton computation is a crucial task. An effective skeletonization algorithm was introduced by N. Cornea in [1] but it lacks in computational performances. Thanks to the advances in imaging techniques the resolution of 3D images is increasing more and more, therefore there is the need for efficient algorithms in order to analyze significant Volumes of Interest (VOIs). In the present paper an improved skeletonization algorithm based on the idea proposed in [1] is presented. A computational comparison between the original and the proposed method is also reported. The obtained results show that the proposed method allows a significant computational improvement making more appealing the adoption of the skeleton representation in biomedical image analysis applications.

  4. Improving Accuracy and Temporal Resolution of Learning Curve Estimation for within- and across-Session Analysis

    PubMed Central

    Tabelow, Karsten; König, Reinhard; Polzehl, Jörg

    2016-01-01

    Estimation of learning curves is ubiquitously based on proportions of correct responses within moving trial windows. Thereby, it is tacitly assumed that learning performance is constant within the moving windows, which, however, is often not the case. In the present study we demonstrate that violations of this assumption lead to systematic errors in the analysis of learning curves, and we explored the dependency of these errors on window size, different statistical models, and learning phase. To reduce these errors in the analysis of single-subject data as well as on the population level, we propose adequate statistical methods for the estimation of learning curves and the construction of confidence intervals, trial by trial. Applied to data from an avoidance learning experiment with rodents, these methods revealed performance changes occurring at multiple time scales within and across training sessions which were otherwise obscured in the conventional analysis. Our work shows that the proper assessment of the behavioral dynamics of learning at high temporal resolution can shed new light on specific learning processes, and, thus, allows to refine existing learning concepts. It further disambiguates the interpretation of neurophysiological signal changes recorded during training in relation to learning. PMID:27303809

  5. Identification and discrimination of Toxoplasma gondii, Sarcocystis spp., Neospora spp., and Cryptosporidium spp. by righ-resolution melting analysis

    PubMed Central

    2017-01-01

    The objective of this study was to standardize the high-resolution melting method for identification and discrimination of Toxoplasma gondii, Sarcocystis spp., Neospora spp., and Cryptosporidium spp. by amplification of 18S ribosomal DNA (rDNA) using a single primer pair. The analyses were performed on individual reactions (containing DNA from a single species of a protozoan), on duplex reactions (containing DNA from two species of protozoa in each reaction), and on a multiplex reaction (containing DNA of four parasites in a single reaction). The proposed method allowed us to identify and discriminate the four species by analyzing the derivative, normalized, and difference melting curves, with high reproducibility among and within the experiments, as demonstrated by low coefficients of variation (less than 2.2% and 2.0%, respectively). This is the first study where this method is used for discrimination of these four species of protozoa in a single reaction. PMID:28346485

  6. 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.

  7. 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

  8. Hierarchical band-target entropy minimization curve resolution and Pearson VII curve-fitting analysis of cellular protein infrared imaging spectra.

    PubMed

    Xu, Weiyin; Chen, Kejia; Liang, Dayang; Chew, Wee

    2009-04-01

    A soft-modeling multivariate numerical approach that combines self-modeling curve resolution (SMCR) and mixed Lorentzian-Gaussian curve fitting was successfully implemented for the first time to elucidate spatially and spectroscopically resolved spectral information from infrared imaging data of oral mucosa cells. A novel variant form of the robust band-target entropy minimization (BTEM) SMCR technique, coined as hierarchical BTEM (hBTEM), was introduced to first cluster similar cellular infrared spectra using the unsupervised hierarchical leader-follower cluster analysis (LFCA) and subsequently apply BTEM to clustered subsets of data to reconstruct three protein secondary structure (PSS) pure component spectra-alpha-helix, beta-sheet, and ambiguous structures-that associate with spatially differentiated regions of the cell infrared image. The Pearson VII curve-fitting procedure, which approximates a mixed Lorentzian-Gaussian model for spectral band shape, was used to optimally curve fit the resolved amide I and II bands of various hBTEM reconstructed PSS pure component spectra. The optimized Pearson VII band-shape parameters and peak center positions serve as means to characterize amide bands of PSS spectra found in various cell locations and for approximating their actual amide I/II intensity ratios. The new hBTEM methodology can also be potentially applied to vibrational spectroscopic datasets with dynamic or spatial variations arising from chemical reactions, physical perturbations, pathological states, and the like.

  9. An analysis of the massless planet approximation in transit light curve models

    NASA Astrophysics Data System (ADS)

    Millholland, Sarah; Ruch, Gerry

    2015-08-01

    Many extrasolar planet transit light curve models use the approximation of a massless planet. They approximate the planet as orbiting elliptically with the host star at the orbit’s focus instead of depicting the planet and star as both orbiting around a common center of mass. This approximation should generally be very good because the transit is a small fraction of the full-phase curve and the planet to stellar mass ratio is typically very small. However, to fully examine the legitimacy of this approximation, it is useful to perform a robust, all-parameter space-encompassing statistical comparison between the massless planet model and the more accurate model.Towards this goal, we establish two questions: (1) In what parameter domain is the approximation invalid? (2) If characterizing an exoplanetary system in this domain, what is the error of the parameter estimates when using the simplified model? We first address question (1). Given each parameter vector in a finite space, we can generate the simplified and more complete model curves. Associated with these model curves is a measure of the deviation between them, such as the root mean square (RMS). We use Gibbs sampling to generate a sample that is distributed according to the RMS surface. The high-density regions in the sample correspond to a large deviation between the models. To determine the domains of these high-density areas, we first employ the Ordering Points to Identify the Clustering Structure (OPTICS) algorithm. We then characterize the subclusters by performing the Patient Rule Induction Method (PRIM) on the transformed Principal Component spaces of each cluster. This process yields descriptors of the parameter domains with large discrepancies between the models.To consider question (2), we start by generating synthetic transit curve observations in the domains specified by the above analysis. We then derive the best-fit parameters of these synthetic light curves according to each model and examine

  10. Rapid screening for sickle cell disease by polymerase chain reaction-high resolution melting analysis.

    PubMed

    Yue, Liang; Lin, Min; Chen, Jiang-Tao; Zhan, Xiao-Fen; Zhong, De-Shang; Monte-Nguba, Santiago-M; Liu, Pei-Fen; Pan, Xue-Fen; Huang, Jiang-Hua; Wang, Xi; Ehapo, Juan Carlos Salas; Eyi, Urbano Monsuy; Yang, Hui-Tian; Yang, Li-Ye

    2014-06-01

    Each year, ~300,000 individuals with sickle cell disease (SCD), a hemoglobinopathy caused by β-globin gene mutation, are born, and >75% of those are in Africa. The present study examined 511 individuals on the island of Bioko (Equatorial Guinea) and attempted to establish a method for rapid sickle cell disease screening. Following DNA extraction and polymerase chain reaction (PCR) amplification, high resolution melting (HRM) analysis was used to assess the specificity of fluorescence signals of the PCR products and to differentiate various genotypes of these products. The analytical results of HRM were validated using DNA sequencing. By HRM analysis, 80 out of 511 samples were classified as hemoglobin S (Hb S) heterozygotes, while 431 out of 511 samples were classified as wild-type. No mutant homozygote was identified. DNA sequencing indicated that within the 431 wild-type samples as indicated by HRM analysis, one case was actually a Hb S heterozygote and another case was a rare hemoglobin S-C genotype (sickle-hemoglobin C disease). One out of 80 suspected Hb S heterozygotes as indicated by HRM was confirmed as wild-type by DNA sequencing and the results of residual 508 cases were consistent for HRM analysis and sequencing. In conclusion, HRM analysis is a simple, high-efficiency approach for Hb S screening and is useful for early diagnosis of SCD and particularly suitable for application in the African area.

  11. Analysis of Characteristics of Light Curve Profiles of the Flares Erupted from Sun-like Stars

    NASA Astrophysics Data System (ADS)

    Duo, Yun; Hua-ning, Wang; Han, He

    2017-01-01

    Solar flares belong to a kind of eruptive phenomena caused by the sudden release of magnetic energy nearby sunspots. It is found that similar flares occurred as well in many Sun-like stars (called as Sun-like star flares). From the data acquired by the Kepler space telescope the SC (Short Cadence) data are mainly selected to make analysis, in order to find the characteristic parameters of light curve profiles of the flares erupted from Sun-like stars for a statistical study, and to summarize the activity features of these stellar flares. The analyzed results show that the light curve profiles and characteristic timescales of the flares of Sun-like stars are quite similar to those of solar flares, which may indicate the same physical mechanism for these two kinds of flares.

  12. Consequence analysis to determine the damage to humans from vapour cloud explosions using characteristic curves.

    PubMed

    Alonso, Fernando Díaz; Ferradás, Enrique González; Sánchez, Teresa de Jesús Jiménez; Aznar, Agustín Miñana; Gimeno, José Ruiz; Alonso, Jesús Martínez

    2008-01-15

    The aim of this paper is to provide a methodology to facilitate consequence analysis for vapour cloud explosions (VCE). Firstly, the main PROBIT equations to evaluate direct damage on humans from those accidents (eardrum rupture, death due to skull fracture, death due to whole body impact and lung damage) are discussed and the most suitable ones are selected. Secondly, a new methodology is developed to relate characteristic overpressure-impulse-distance curves for VCE, obtained in a previous paper (F. Diaz Alonso et al., Characteristic overpressure-impulse-distance curves for vapour cloud explosions using the TNO Multi-Energy model, J. Hazard. Mater. A137 (2006) 734-741) with the selected PROBIT equations. This methodology allows the determination of damage as a function of distance to the accident's origin in only one step, using explosion energy and VCE Multi-Energy charge strength as input parameters.

  13. Ice shelf structure derived from dispersion curve analysis of ambient seismic noise, Ross Ice Shelf, Antarctica

    NASA Astrophysics Data System (ADS)

    Diez, A.; Bromirski, P. D.; Gerstoft, P.; Stephen, R. A.; Anthony, R. E.; Aster, R. C.; Cai, C.; Nyblade, A.; Wiens, D. A.

    2016-05-01

    An L-configured, three-component short period seismic array was deployed on the Ross Ice Shelf, Antarctica during November 2014. Polarization analysis of ambient noise data from these stations shows linearly polarized waves for frequency bands between 0.2 and 2 Hz. A spectral peak at about 1.6 Hz is interpreted as the resonance frequency of the water column and is used to estimate the water layer thickness below the ice shelf. The frequency band from 4 to 18 Hz is dominated by Rayleigh and Love waves propagating from the north that, based on daily temporal variations, we conclude were generated by field camp activity. Frequency-slowness plots were calculated using beamforming. Resulting Love and Rayleigh wave dispersion curves were inverted for the shear wave velocity profile within the firn and ice to ˜150 m depth. The derived density profile allows estimation of the pore close-off depth and the firn-air content thickness. Separate inversions of Rayleigh and Love wave dispersion curves give different shear wave velocity profiles within the firn. We attribute this difference to an effective anisotropy due to fine layering. The layered structure of firn, ice, water and the seafloor results in a characteristic dispersion curve below 7 Hz. Forward modelling the observed Rayleigh wave dispersion curves using representative firn, ice, water and sediment structures indicates that Rayleigh waves are observed when wavelengths are long enough to span the distance from the ice shelf surface to the seafloor. The forward modelling shows that analysis of seismic data from an ice shelf provides the possibility of resolving ice shelf thickness, water column thickness and the physical properties of the ice shelf and underlying seafloor using passive-source seismic data.

  14. Selection of excipients for melt extrusion with two poorly water-soluble drugs by solubility parameter calculation and thermal analysis.

    PubMed

    Forster, A; Hempenstall, J; Tucker, I; Rades, T

    2001-09-11

    The aim of this study was to determine the miscibility of drug and excipient to predict if glass solutions are likely to form when drug and excipient are melt extruded. Two poorly water-soluble drugs, indomethacin and lacidipine, were selected along with 11 excipients (polymeric and non-polymeric). Estimation of drug/excipient miscibility was performed using a combination of the Hoy and Hoftzyer/Van Krevelen methods for Hansen solubility parameter calculation. Miscibility was experimentally investigated with differential scanning calorimetry (DSC) and hot stage microscopy (HSM). Studies were performed at drug/excipient ratios, 1:4, 1:1 and 4:1. Analysis of the glass transition temperature (T(g)) was performed by quench cooling drug/excipient melts in the DSC. Differences in the drug/excipient solubility parameters of <7.0 MPa(1/2) were predicted to indicate significant miscibility and, therefore, glass solution formation on melt extrusion. In comparison, differences of >10 MPa(1/2) were expected to indicate a lack of miscibility and not form glass solutions when melt extruded. Experimentally, miscibility was shown by changes in drug/excipient melting endotherms and confirmed by HSM investigations. Experimental results were in agreement with solubility parameter predictions. In addition, drug/excipient combinations predicted to be largely immiscible often exhibited more than one T(g) upon reheating in the DSC. Melt extrusion of miscible components resulted in amorphous solid solution formation, whereas extrusion of an "immiscible" component led to amorphous drug dispersed in crystalline excipient. In conclusion, combining calculation of Hansen solubility parameters with thermal analysis of drug/excipient miscibility can be successfully applied to predict formation of glass solutions with melt extrusion.

  15. Segregation during directional melting and its implications on seeded crystal growth: A theoretical analysis

    NASA Technical Reports Server (NTRS)

    Bourret, E. D.; Favier, J. J.; Witt, A. F.

    1982-01-01

    Directional melting of binary systems, as encountered during seeding in melt growth, is analyzed for concurrent compositional changes at the crystal-melt interface. It is shown that steady state conditions cannot normally be reached during seeding and that the growth interface temperature at the initial stages of seeded growth is a function of backmelt conditions. The theoretical treatment is numerically applied to Hg1-xCdXTe and Ga-doped Ge.

  16. Thermal analysis and FTIR spectral curve-fitting investigation of formation mechanism and stability of indomethacin-saccharin cocrystals via solid-state grinding process.

    PubMed

    Zhang, Gang-Chun; Lin, Hong-Liang; Lin, Shan-Yang

    2012-07-01

    The cocrystal formation of indomethacin (IMC) and saccharin (SAC) by mechanical cogrinding or thermal treatment was investigated. The formation mechanism and stability of IMC-SAC cocrystal prepared by cogrinding process were explored. Typical IMC-SAC cocrystal was also prepared by solvent evaporation method. All the samples were identified and characterized by using differential scanning calorimetry (DSC) and Fourier transform infrared (FTIR) microspectroscopy with curve-fitting analysis. The physical stability of different IMC-SAC ground mixtures before and after storage for 7 months was examined. The results demonstrate that the stepwise measurements were carried out at specific intervals over a continuous cogrinding process showing a continuous growth in the cocrystal formation between IMC and SAC. The main IR spectral shifts from 3371 to 3,347 cm(-1) and 1693 to 1682 cm(-1) for IMC, as well as from 3094 to 3136 cm(-1) and 1718 to 1735 cm(-1) for SAC suggested that the OH and NH groups in both chemical structures were taken part in a hydrogen bonding, leading to the formation of IMC-SAC cocrystal. A melting at 184 °C for the 30-min IMC-SAC ground mixture was almost the same as the melting at 184 °C for the solvent-evaporated IMC-SAC cocrystal. The 30-min IMC-SAC ground mixture was also confirmed to have similar components and contents to that of the solvent-evaporated IMC-SAC cocrystal by using a curve-fitting analysis from IR spectra. The thermal-induced IMC-SAC cocrystal formation was also found to be dependent on the temperature treated. Different IMC-SAC ground mixtures after storage at 25 °C/40% RH condition for 7 months had an improved tendency of IMC-SAC cocrystallization.

  17. An elastic-plastic finite-element analysis of the J-resistance curve using a CTOD criterion

    NASA Technical Reports Server (NTRS)

    Newman, J. C., Jr.; Booth, B. C.; Shivakumar, K. N.

    1988-01-01

    The fracture process in compact and bend specimens was simulated using a two-dimensional finite-element analysis of the J-resistance (J-R) curve and a CTOD criterion. The J-R curves were calculated from the numerical results for each specimen type using several different methods. In general, the J-R curves obtained for the bend specimens were found to be higher than those for the compact specimens, especially beyond maximum load. However, below the maximum load, the modified deformation theory of plasticity and the contour-integral J(r) method resulted in very similar J-R curves for both specimen types.

  18. 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.

  19. Design curves for non-linear analysis of simply-supported, uniformly-loaded rectangular plates

    NASA Technical Reports Server (NTRS)

    Moore, D.

    1979-01-01

    Design curves for the non-linear analysis of simply-supported rectangular plates subjected to uniform normal pressure loads have been developed. These curves yield the center deflection, center stress and corner stress in non-dimensionalized form plotted against a dimensionless parameter describing the load intensity. The results presented are based on extensive non-linear finite element analysis employing the ARGUS structural analysis program. Plates with length to width ratios of 1, 1.5, 2, 3 and 4 are included. The load range considered extends to 1000 times the load at which the behavior of the plate becomes significantly non-linear. Over the load range considered, the analysis shows that the ratio of center deflection to plate thickness for a square plate is less than 16 to 1, whereas linear theory would predict a center deflection 400 times the plate thickness. Likewise, the stress is markedly lower than would be predicted by linear theory. The present results are shown to be in excellent agreement with the classical linear theory up to a central deflection to plate thickness ratio of about one-half. In the non-linear regime the present results for deflection and stress are in very good agreement with the analytical and experimental work of other investigators.

  20. Assessing the Classification Accuracy of Early Numeracy Curriculum-Based Measures Using Receiver Operating Characteristic Curve Analysis

    ERIC Educational Resources Information Center

    Laracy, Seth D.; Hojnoski, Robin L.; Dever, Bridget V.

    2016-01-01

    Receiver operating characteristic curve (ROC) analysis was used to investigate the ability of early numeracy curriculum-based measures (EN-CBM) administered in preschool to predict performance below the 25th and 40th percentiles on a quantity discrimination measure in kindergarten. Areas under the curve derived from a sample of 279 students ranged…

  1. Direct determination of enzyme kinetic parameters from single reactions using a new progress curve analysis tool.

    PubMed

    Bäuerle, Felix; Zotter, Agnes; Schreiber, Gideon

    2016-10-15

    With computer-based data-fitting methods becoming a standard tool in biochemistry, progress curve analysis of enzyme kinetics is a feasible, yet seldom used tool. Here we present a versatile Matlab-based tool (PCAT) to analyze catalysis progress curves with three complementary model approaches. The first two models are based on the known closed-form solution for this problem: the first describes the required Lambert W function with an analytical approximation and the second provides a numerical solution of the Lambert W function. The third model is a direct simulation of the enzyme kinetics. Depending on the chosen model, the tools excel in speed, accuracy or initial value requirements. Using simulated and experimental data, we show the strengths and pitfalls of the different fitting models. Direct simulation proves to have the highest level of accuracy, but it also requires reasonable initial values to converge. Finally, we propose a standard procedure to obtain optimized enzyme kinetic parameters from single progress curves.

  2. Pg 1115+080: New Analysis of the Light Curves Confirms Old Time Delay Results

    NASA Astrophysics Data System (ADS)

    Artamonov, B.; Koptelova, E.; Oknyanskij, V.; Shimanovskaya, E.

    We analyze all publicly available long-term optical observations of the gravitationally lensed quasar PG1115+080 with the aim of measuring time delays between its four components. In particular, we present analysis of the Maidanak light curves of the PG1115+080 components obtained between 2001 and 2006 (Tsvetkova et al. 2010). We find that the light curves of the 2006 observational season show almost linear trend with some fast variations seen only in the A1 and C components. This can be as due to microlensing or observational errors. These fast variations can decrease statistical significance of the time delay estimates or even produce misleading results. Application of the MCCF technique (Oknyanskij 1993) to photometric data collected in the 2004-2005 seasons gives time delay values tBC = 22±3, tAC = 12±3, and tBA = 10±3 days, which are in agreement with previous results of Schechter et al. (1997) and Barkana (1997) reported for the 1995-1996 light curves analyzed using two different statistical methods. The ratio tAC/tBA between our intermediate delays is about 1.2 that is close to the value reported by Barkana ( ∼1.13) and predicted by lens models (∼1.4) unlike the Schechter's and Vakulik's (2009) values (∼ 0.7 and ∼2.7).

  3. Bayesian analysis of stage-fall-discharge rating curves and their uncertainties

    NASA Astrophysics Data System (ADS)

    Mansanarez, V.; Le Coz, J.; Renard, B.; Lang, M.; Pierrefeu, G.; Vauchel, P.

    2016-09-01

    Stage-fall-discharge (SFD) rating curves are traditionally used to compute streamflow records at sites where the energy slope of the flow is variable due to variable backwater effects. We introduce a model with hydraulically interpretable parameters for estimating SFD rating curves and their uncertainties. Conventional power functions for channel and section controls are used. The transition to a backwater-affected channel control is computed based on a continuity condition, solved either analytically or numerically. The practical use of the method is demonstrated with two real twin-gauge stations, the Rhône River at Valence, France, and the Guthusbekken stream at station 0003ṡ0033, Norway. Those stations are typical of a channel control and a section control, respectively, when backwater-unaffected conditions apply. The performance of the method is investigated through sensitivity analysis to prior information on controls and to observations (i.e., available gaugings) for the station of Valence. These analyses suggest that precisely identifying SFD rating curves requires adapted gauging strategy and/or informative priors. The Madeira River, one of the largest tributaries of the Amazon, provides a challenging case typical of large, flat, tropical river networks where bed roughness can also be variable in addition to slope. In this case, the difference in staff gauge reference levels must be estimated as another uncertain parameter of the SFD model. The proposed Bayesian method is a valuable alternative solution to the graphical and empirical techniques still proposed in hydrometry guidance and standards.

  4. Analysis of microstrip antennas on a curved surface using the conformal grids FD-TD method

    NASA Astrophysics Data System (ADS)

    Fukai, Ichiro; Onishi, Teruo; Kashiwa, Tatsuya

    1994-03-01

    The need for small, potable antennas for mobile communications has recently spurred the study of microstrip antennas (MSA). MSA are quite flexible and have been used as conformal antennas on arbitrary curved surfaces. The characteristics of conformal MSA can be expected to differ from those of planar models. Dependable numerical analyses will obviate many of the costs and other inconveniences associated with experiments, but as antennas may be mounted on the surfaces of arbitrary topological complexity, analysis methods must have as general applicability as possible. The curvilinear finite difference time-domain (FD-TD) method has shown excellent versatility. In this paper, the curvilinear FD-TD method is applied to analyze microstrip antennas mounted on curved surfaces. The numerical predictions are compared with the experimental values. The results confirm the predictions within acceptable limits and appear to confirm the validity of the method. As a result, it was confirmed that the input impedance and directivity of MSA on curved surfaces are different from the flat MSA.

  5. A fast and accurate method for controlling the correct labeling of products containing buffalo meat using High Resolution Melting (HRM) analysis.

    PubMed

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

    2013-05-01

    The substitution of high priced meat with low cost ones and the fraudulent labeling of meat products make the identification and traceability of meat species and their processed products in the food chain important. A polymerase chain reaction followed by a High Resolution Melting (HRM) analysis was developed for species specific detection of buffalo; it was applied in six commercial meat products. A pair of specific 12S and universal 18S rRNA primers were employed and yielded DNA fragments of 220bp and 77bp, respectively. All tested products were found to contain buffalo meat and presented melting curves with at least two visible inflection points derived from the amplicons of the 12S specific and 18S universal primers. The presence of buffalo meat in meat products and the adulteration of buffalo products with unknown species were established down to a level of 0.1%. HRM was proven to be a fast and accurate technique for authentication testing of meat products.

  6. A novel high-resolution melting analysis-based method for Yersinia pseudotuberculosis genotyping.

    PubMed

    Souza, Roberto A; Falcão, Juliana P

    2012-12-01

    Yersinia pseudotuberculosis is an enteric pathogen that is environmentally widespread and is known to cause human and animal infections. The development of a fast and inexpensive typing system is necessary to facilitate epidemiological studies of Y. pseudotuberculosis infections. In this study, we aimed to develop a method of Y. pseudotuberculosis genotyping based on determining differences in single-nucleotide polymorphisms (SNPs) using a high-resolution melting analysis (HRMA). Using a set of nine primer pairs, ten SNPs were screened from sequences in the 16S rRNA, glnA, gyrB and recA sequences of 12 Y. pseudotuberculosis strains that were deposited in the GenBank database. The genetic diversity of a collection of 40 clinical Y. pseudotuberculosis strains was determined using the HRMA method and the multilocus sequence typing (MLST) technique was used for comparison. Different melting profiles were found in five out of a total of nine analyzed fragments. A phylogenetic tree was constructed from the nucleotides that were identified in the nine analyzed fragments, and the tree demonstrated that Y. pseudotuberculosis strains were separated into two groups. The first cluster was composed of strains from the 1/O:1a serogroup and the second of strains from the 2/O:3 serogroup. The separation into two clusters based on distinct bio-serogroups of Y. pseudotuberculosis was consistent with the results in the MLST database. The simple and highly reproducible HRMA assay developed by us may be used as a rapid and cost-effective method to genotype Y. pseudotuberculosis strains of O:1 and O:3 serogroups and it can complement sequence-based methods facilitating epidemiological studies of this Yersinia species.

  7. Analysis of saturated and aromatic hydrocarbons migrating from a polyolefin-based hot-melt adhesive into food.

    PubMed

    Lommatzsch, Martin; Biedermann, Maurus; Grob, Koni; Simat, Thomas J

    2016-01-01

    Hot-melt adhesives are widely utilised to glue cardboard boxes used as food packaging material. They have to comply with the requirements of Article 3 of the European Framework Regulation for food contact materials (1935/2004). The hot melt raw materials analysed mainly consisted of paraffinic waxes, hydrocarbon resins and polyolefins. The hydrocarbon resins, functioning as tackifiers, were the predominant source of hydrocarbons of sufficient volatility to migrate into dry foods: the 18 hydrocarbon resins analysed contained 8.2-118 g kg(-1) saturated and up to 59 g kg(-1) aromatic hydrocarbons eluted from GC between n-C16 and n-C24, substantially more than the paraffinic waxes and the polyolefins. These tackfier resins, especially the oligomers ≤ C24, have been characterised structurally by GC×GC-MS and (1)H-NMR spectroscopy. Migration into food was estimated using a simulating system with polenta as food simulant, which was verified by the analysis of a commercial risotto rice sample packed in a virgin fibre folding box sealed with a hot melt. About 0.5-1.5% of the potentially migrating substances (between n-C16 and n-C24) of a hot melt were found to be transferred into food under storage conditions, which can result in a food contamination in the order of 1 mg kg(-1) food (depending on the amount of potentially migrating substances from the hot melt, the hot melt surface, amount of food, contact time etc.). Migrates from hot melts are easily mistaken for mineral oil hydrocarbons from recycled cardboard.

  8. Analysis of strain relatedness using High Resolution Melting in a case of recurrent candiduria

    PubMed Central

    2013-01-01

    Background Several genotyping protocols have been described to study Candida albicans strains with different sensitivity values. In this study we have analyzed the genetic relatedness and the antifungal susceptibility of several Candida albicans strains isolated from a patient who from suffered recurrent candiduria for a period of five years. Strains were genotyped using Microsatellite Length Polymorphism (MLP) with three microsatellite markers (HIS 3, EF 3 and CDC 3), and a new method based on high resolution melting (HRM) was developed to analyze the microsatellite region. This method was compared with the conventional technique that uses capillary electrophoresis. Results MICs of the isolates showed the existence of fluconazole susceptible and resistant strains. An inter-colony test using single concentration (8 and 16 mg/l) of fluconazole revealed the coexistence of both fluconazole susceptible and resistant strains. Both genotyping analysis methods showed that all the patient’s isolates had a clonal origin. HRM analysis method developed was able to accurately establish strain relatedness and presented a discriminatory power of 0.77. Conclusions Although HRM analysis method presented a lower discriminatory power compared to methods based on capillary electrophoresis, it provided a more cost-effective and suitable alternative for genotyping C. albicans in a clinical laboratory. PMID:23343107

  9. High resolution melt analysis (HRMA); a viable alternative to agarose gel electrophoresis for mouse genotyping.

    PubMed

    Thomsen, Nicole; Ali, Radiya G; Ahmed, Jehangir N; Arkell, Ruth M

    2012-01-01

    Most mouse genetics laboratories maintain mouse strains that require genotyping in order to identify the genetically modified animals. The plethora of mutagenesis strategies and publicly available mouse alleles means that any one laboratory may maintain alleles with random or targeted insertions of orthologous or unrelated sequences as well as random or targeted deletions and point mutants. Many experiments require that different strains be cross bred conferring the need to genotype progeny at more than one locus. In contrast to the range of new technologies for mouse mutagenesis, genotyping methods have remained relatively static with alleles typically discriminated by agarose gel electrophoresis of PCR products. This requires a large amount of researcher time. Additionally it is susceptible to contamination of future genotyping experiments because it requires that tubes containing PCR products be opened for analysis. Progress has been made with the genotyping of mouse point mutants because a range of new high-throughput techniques have been developed for the detection of Single Nucleotide Polymorphisms. Some of these techniques are suitable for genotyping point mutants but do not detect insertion or deletion alleles. Ideally, mouse genetics laboratories would use a single, high-throughput platform that enables closed-tube analysis to genotype the entire range of possible insertion and deletion alleles and point mutants. Here we show that High Resolution Melt Analysis meets these criteria, it is suitable for closed-tube genotyping of all allele types and current genotyping assays can be converted to this technology with little or no effort.

  10. On the Analysis and Construction of the Butterfly Curve Using "Mathematica"[R

    ERIC Educational Resources Information Center

    Geum, Y. H.; Kim, Y. I.

    2008-01-01

    The butterfly curve was introduced by Temple H. Fay in 1989 and defined by the polar curve r = e[superscript cos theta] minus 2 cos 4 theta plus sin[superscript 5] (theta divided by 12). In this article, we develop the mathematical model of the butterfly curve and analyse its geometric properties. In addition, we draw the butterfly curve and…

  11. Development of a Rapid High-Throughput Method for High-Resolution Melting Analysis for Routine Detection and Genotyping of Noroviruses▿

    PubMed Central

    Tajiri-Utagawa, Etsuko; Hara, Masayuki; Takahashi, Kuniaki; Watanabe, Mayumi; Wakita, Takaji

    2009-01-01

    We developed a simple, rapid, high-throughput detection and genotyping method for noroviruses using real-time reverse transcription-PCR (RT-PCR) and high-resolution melting (HRM) analysis to create a difference plot. The capsid gene was amplified by real-time RT-PCR in the presence of ResoLight HRM dye, a saturating DNA dye. Following optimization of the HRM assay conditions, the major norovirus genotypes were selected. Because we had only small quantities of the patient stool samples used in this study, we constructed plasmids for each genotype and used these to optimize the HRM assay. We selected six stool samples, each positive for one of the six dominant subtypes of noroviruses that have been circulating in Japan, namely, genotypes 4, 8, and 9 from genogroup 1 and genotypes 3, 4, and 10 from genogroup 2. The specific high-resolution derivate plot of the HRM assay for each plasmid was constructed by subtracting the melting-curve shape of the plasmid from the reference or base curve. The RNAs extracted from 14 clinical samples positive for small round structured viruses were then directly analyzed using the HRM assay. The HRM data from the clinical RNA samples corresponded with the genotype results obtained by RT-PCR and sequencing of the clinical samples. In addition, the HRM data from the clinical RNA samples corresponded with the HRM data from the six reference plasmid DNAs, indicating that this assay is useful for the direct detection and genotyping of noroviruses in clinical samples. This assay requires no multiplexing or hybridization probes and provides a new approach to the genetic screening of noroviruses in clinical virology laboratories. PMID:19073870

  12. Analysis of gravity and conduction-driven melting in a sphere

    NASA Technical Reports Server (NTRS)

    Bahrami, P. A.; Wang, T. G.

    1987-01-01

    An approach similar to those employed in the theories of lubrication and film condensation is applied to the problem of melting within a sphere. An approximate closed-form solution is obtained which yields relationships between the solid speed, position, and time. The results are compared with those obtained by Bareiss and Beer (1984) for the case of melting in a horizontal cylinder.

  13. LA-ICPMS analyses of silicate melt inclusions in co-precipitated minerals: Quantification, data analysis and mineral/melt partitioning

    NASA Astrophysics Data System (ADS)

    Zajacz, Zoltán; Halter, Werner

    2007-02-01

    We present a new approach to determine the composition of silicate melt inclusions (SMI) using LA-ICPMS. In this study, we take advantage of the occurrence of SMI in co-precipitated mineral phases to quantify their composition without depending on additional sources of information. Quantitative SMI analyses are obtained by assuming that the ratio of selected elements in SMI trapped in different phases are identical. In addition Fe/Mg exchange equilibrium between olivine and melt was successfully used to quantify LA-ICPMS analyses of SMI in olivine. Results show that compositions of SMI from the different host minerals are identical within their uncertainty. Thus (1) the quantification approach is valid; (2) analyses are not affected by the composition of the host phase; (3) the derived melt compositions are representative of the original melt, excluding significant syn- or postentrapment modification such as boundary layer effects or diffusive reequilibration with the host mineral. With this data we established a large dataset of mineral/melt partition coefficients for the investigated mineral phases in hydrous calc-alkaline basaltic-andesitic melts. The clinopyroxene/melt and plagioclase/melt partition coefficients are consistent with the lattice strain model of Blundy and Wood [Blundy, J., Wood B., 1994. Prediction of crystal-melt partition-coefficients from elastic-moduli. Nature372, 452-454].

  14. Evaluation of the formation of a junctional DNA nanostructure through annealing curve analysis.

    PubMed

    Shin, Seung Won; Park, Kyung Soo; Um, Soong Ho

    2015-02-20

    During the self-assembly of different numbers of oligonucleotides comprising junctional DNA nanostructures, a change in environmental variables (e.g., temperature or salt concentration) has a substantial influence on the final products. Further, distinctive annealing temperatures of oligonucleotides are observed depending on the state of hybridization. Here, we present an evaluation of the annealing characteristics of oligonucleotides for the formation of a simple junctional DNA nanostructure using an annealing curve analysis. This method may be useful for analyzing the formation of complex junctional DNA nanostructures.

  15. 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

  16. Rapid determination of lymphogranuloma venereum serovars of Chlamydia trachomatis by quantitative high-resolution melt analysis (HRMA).

    PubMed

    Twin, Jimmy; Stevens, Matthew P; Garland, Suzanne M; Zaia, Angelo M; Tabrizi, Sepehr N

    2012-11-01

    A quantitative high-resolution melt analysis assay was developed to differentiate lymphogranuloma venereum-causing serovars of Chlamydia trachomatis (L1 to L3) from other C. trachomatis serovars (D to K). The detection limit of this assay is approximately 10 copies per reaction, comparable to the limits of other quantitative-PCR-based methods.

  17. Asymptotic analysis of a newtonian fluid in a curved pipe with moving walls

    NASA Astrophysics Data System (ADS)

    Castiñeira, Gonzalo; Rodríguez, José M.

    2016-06-01

    This communication is devoted to the presentation of our recent results regarding the asymptotic analysis of a viscous flow in a tube with elastic walls. This study can be applied, for example, to the blood flow in an artery. With this aim, we consider the dynamic problem of the incompressible flow of a viscous fluid through a curved pipe with a smooth central curve. Our analysis leads to the obtention of an one dimensional model via singular perturbation of the Navier-Stokes system as ɛ, a non dimensional parameter related to the radius of cross-section of the tube, tends to zero. We allow the radius depend on tangential direction and time, so a coupling with an elastic or viscoelastic law on the wall of the pipe is possible. To perform the asymptotic analysis, we do a change of variable to a reference domain where we assume the existence of asymptotic expansions on ɛ for both velocity and pressure which, upon substitution on Navier-Stokes equations, leads to the characterization of various terms of the expansion. This allows us to obtain an approximation of the solution of the Navier-Stokes equations.

  18. Improved factor analysis of dynamic PET images to estimate arterial input function and tissue curves

    NASA Astrophysics Data System (ADS)

    Boutchko, Rostyslav; Mitra, Debasis; Pan, Hui; Jagust, William; Gullberg, Grant T.

    2015-03-01

    Factor analysis of dynamic structures (FADS) is a methodology of extracting time-activity curves (TACs) for corresponding different tissue types from noisy dynamic images. The challenges of FADS include long computation time and sensitivity to the initial guess, resulting in convergence to local minima far from the true solution. We propose a method of accelerating and stabilizing FADS application to sequences of dynamic PET images by adding preliminary cluster analysis of the time activity curves for individual voxels. We treat the temporal variation of individual voxel concentrations as a set of time-series and use a partial clustering analysis to identify the types of voxel TACs that are most functionally distinct from each other. These TACs provide a good initial guess for the temporal factors for subsequent FADS processing. Applying this approach to a set of single slices of dynamic 11C-PIB images of the brain allows identification of the arterial input function and two different tissue TACs that are likely to correspond to the specific and non-specific tracer binding-tissue types. These results enable us to perform direct classification of tissues based on their pharmacokinetic properties in dynamic PET without relying on a compartment-based kinetic model, without identification of the reference region, or without using any external methods of estimating the arterial input function, as needed in some techniques.

  19. Analysis of the effect of symmetric/asymmetric CUSP magnetic fields on melt/crystal interface during Czochralski silicon growth

    NASA Astrophysics Data System (ADS)

    Daggolu, Parthiv; Ryu, Jae Woo; Galyukov, Alex; Kondratyev, Alexey

    2016-10-01

    With the use of 300 mm silicon wafers for industrial semiconductor device manufacturing, the Czochralski (Cz) crystal growth process has to be optimized to achieve higher quality and productivity. Numerical studies based on 2D global thermal models combined with 3D simulation of melt convection are widely used today to save time and money in the process development. Melt convection in large scale Cz Si growth is controlled by a CUSP or transversal magnetic field (MF) to suppress the melt turbulence. MF can be optimized to meet necessary characteristics of the growing crystal, in terms of point defects, as MF affects the melt/crystal interface geometry and allows adjustment of the pulling rate. Among the different knobs associated with the CUSP magnetic field, the nature of its configuration, going from symmetric to asymmetric, is also reported to be an important tool for the control of crystallization front. Using a 3D unsteady model of the CGSim software, we have studied these effects and compared with several experimental results. In addition, physical mechanisms behind these observations are explored through a detailed modeling analysis of the effect of an asymmetric CUSP MF on convection features governing the heat transport in the silicon melt.

  20. Ammonia-water mixtures at high pressures - Melting curves of ammonia dihydrate and ammonia monohydrate and a revised high-pressure phase diagram for the water-rich region. [in primordial solar system ices

    NASA Technical Reports Server (NTRS)

    Boone, S.; Nicol, M. F.

    1991-01-01

    The phase relations of some mixtures of ammonia and water are investigated to create a phase diagram in pressure-temperature-composition space relevant to the geophysical study of bodies in the outer solar system. The mixtures of NH3(x)H2O(1-x), where x is greater than 0.30 but less than 0.51, are examined at pressures and temperatures ranging from 0-6.5 GPa and 125-400 K, respectively. The ruby luminescence technique monitors the pressure and a diamond-anvil cell compresses the samples, and the phases are identified by means of normal- and polarized-light optical microscopy. The melting curve for NH3H2O(2) is described by the equation T = 176 + 60P - 8.5P squared for the ranges of 0.06-1.4 GPa and 179-243 K. The equation for NH3H2O is T = 194 + 37P - P squared, which represents a minor correction of a previous description by Johnson et al. (1985). Observed phase transitions are consistent with the high-pressure stability limit of NH3H2O(2), and the transition boundary is found to be linear.

  1. Differentiation of Variola major and Variola minor Variants by MGB-Eclipse Probe Melt Curves and Genotyping Analysis

    DTIC Science & Technology

    2009-01-01

    In addition real - time PCR assays specific for variola virus have been developed that distinguish it from other orthopoxviruses. However, a positive...less severe form of the disease. This study reports the development of a real - time PCR minor groove binder (MGB) -Eclipse probe assay utilizing a unique

  2. Pseudoperonospora cubensis and P. humuli detection using species-specific probes and high definition melt curve analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Three assays were developed for molecular differentiation of Pseudoperonospora cubensis and P. humuli, causal agents of cucurbit and hop downy mildew, respectively, for detection of airborne sporangia and diagnosis of symptomatic leaf tissue. The assays were based on previously identified single nuc...

  3. Spoligotyping of Mycobacterium tuberculosis Complex Isolates by Use of Ligation-Based Amplification and Melting Curve Analysis

    PubMed Central

    Zeng, Xiaohong; Li, Hui; Zheng, Rongrong; Kurepina, Natalia; Kreiswirth, Barry N.; Zhao, Xilin

    2016-01-01

    We report here a ligation-based spoligotyping that can identify unamplified spacers in membrane-based spoligotyping due to asymmetric insertion of IS6110 in the direct repeat locus. Our typing yielded 84.4% (411/487) concordance with traditional typing and 100% (487/487) accuracy when confirmed by DNA sequencing. PMID:27335152

  4. High resolution melt-curve analysis to fine map a locus controlling the paternal sorting of mitochondria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mitochondria are required for normal growth and development and play an important role in programmed cell death and aging. The mitochondrial DNA is maternally transmitted in the vast majority of eukaryotes. One exception is cucumber (Cucumis sativus), whose mitochondrial DNA is paternally transmit...

  5. [Analysis of the polarization properties of snow in a different melting state].

    PubMed

    Zhang, Li-Li; Zhao, Yun-Sheng; Zhang, Xia; Sun, Tian-Lin; Liang, Ren-Feng; Liu, Jie

    2013-01-01

    Nowdays, under the circumstance of global warming, the traditional study of solid-state snow can not meet the current needs. The present paper involves qualitative analysis of the polarization reflectance spectrum of snow in a different melting state. Special attention is paid to the investigation of the relationship among polarization angles, azimuth angles, the light incidence zenith angles, the detection zenith angles and the different types of snowmelt. It turns out that all these factors have certain influences on the polarization reflectance spectrum of different types of snowmelt. At the waveband of the visible light, the polarization reflectance of snowmelt is the largest at 90 degrees, and the smallest at 0 degrees. The wider the detection angles and the incidence angles, the larger the polarization reflectance. Anomalies (unusual phenomena), different from other spectra, occur when the polarization reflectance spectrum of snowmelt is observed at different azimuth angles. The characteristics of polarization spectra at some certain wavebands play an important role in determining the water content of snowmelt, and meanwhile with the increase of which, the polarization reflectance will go down obviously. These rules have laid a solid foundation for the quantitative analysis of snowmelt properties by using polarization spectrum in the future and are also of great importance in fresh water management as well as monitoring natural disasters such as the spring flood.

  6. 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.

  7. Pyrazinamide susceptibility testing of Mycobacterium tuberculosis by high resolution melt analysis.

    PubMed

    Pholwat, Suporn; Stroup, Suzanne; Gratz, Jean; Trangan, Varittha; Foongladda, Suporn; Kumburu, Happiness; Juma, Saumu Pazia; Kibiki, Gibson; Houpt, Eric

    2014-01-01

    Pyrazinamide (PZA) plays the important role in shortening the tuberculosis treatment period and in treating MDR-TB. Phenotypic PZA susceptibility methods are limited because they require specialized acidified media, which increases costs and complexity. In this study we developed a genotypic high resolution melt (HRM) analysis technique to detect pncA mutations associated with PZA resistant Mycobacterium tuberculosis. Seven overlapping primer pairs were designed to cover the entire pncA gene and upstream regions. Each gene segment was individually amplified by real-time PCR followed by HRM analysis. The assay was evaluated on 98 clinical M. tuberculosis isolates (41 PZA susceptible by MGIT method, 55 PZA resistant, 2 undetermined). HRM was 94% concordant to full-length sequencing results, with most discrepancies attributable to mixed populations per HRM or transversions. Sequencing and HRM yielded 82% and 84% concordance, respectively, to phenotypic PZA susceptibilities by MGIT, with most discrepancies attributable to isolates with wild-type pncA but phenotypic PZA resistance. This HRM technique is a simple and high-throughput method for screening clinical M. tuberculosis samples for PZA resistance.

  8. Analysis of the molten/solidified zone in selective laser melted parts

    NASA Astrophysics Data System (ADS)

    Campanelli, Sabina Luisa; Casalino, Giuseppe; Contuzzi, Nicola; Angelastro, Andrea; Ludovico, Antonio D.

    2014-02-01

    The process of Selective Laser Melting (SLM) is an innovative technology for rapid prototyping that can be included among the SFF (Solid Freeform Fabrication) techniques, which are characterized by "free-form" manufacturing of solid parts. SLM is an additive technology that operates starting from the data encoded in the three-dimensional computer aided design (CAD) file of the component to be built. After the slicing operation made on the 3D model of the component, the consequent data file is sent to a computer-controlled laser device that fuses successive layers of metal powder to create the three-dimensional product. The SLM is a technological process which involves optical, thermal and solidification phenomena; thus the analysis of the process is rather complex. This work aims to study the molten/solidified zone in SLM samples through the experimental analysis of the shape and the size of laser tracks. The functional relationships between dimensional parameter of the molten/solidified track and the main parameters used to control the process was identified.

  9. School-based extracurricular activity involvement and adolescent self-esteem: a growth-curve analysis.

    PubMed

    Kort-Butler, Lisa A; Hagewen, Kellie J

    2011-05-01

    Research on adolescent self-esteem indicates that adolescence is a time in which individuals experience important changes in their physical, cognitive, and social identities. Prior research suggests that there is a positive relationship between an adolescent's participation in structured extracurricular activities and well-being in a variety of domains, and some research indicates that these relationships may be dependent on the type of activities in which adolescents participate. Building on previous research, a growth-curve analysis was utilized to examine self-esteem trajectories from adolescence (age 14) to young adulthood (age 26). Using 3 waves of data from National Longitudinal Study of Adolescent Health (n = 5,399; 47.8% male), the analysis estimated a hierarchical growth-curve model emphasizing the effects of age and type of school-based extracurricular activity portfolio, including sports and school clubs, on self-esteem. The results indicated that age had a linear relationship with self-esteem over time. Changes in both the initial level of self-esteem and the growth of self-esteem over time were significantly influenced by the type of extracurricular activity portfolio. The findings were consistent across race and sex. The results support the utility of examining the longitudinal impact of portfolio type on well-being outcomes.

  10. Analysis of Rail Vehicle Suspension Spring with Special Emphasis on Curving, Tracking and Tractive Efforts

    NASA Astrophysics Data System (ADS)

    Kumbhalkar, M. A.; Bhope, D. V.; Vanalkar, A. V.

    2016-09-01

    The dynamics of the rail vehicle represents a balance between the forces acting between wheel and rail, the inertia forces and the forces exerted by suspension and articulation. Axial loading on helical spring causes vertical deflection at straight track but failures calls to investigate for lateral and longitudinal loading at horizontal and vertical curves respectively. Goods carrying vehicle has the frequent failures of middle axle inner suspension spring calls for investigation. The springs are analyzed for effect of stress concentration due to centripetal force and due to tractive and breaking effort. This paper also discusses shear failure analysis of spring at curvature and at uphill at various speeds for different loading condition analytically and by finite element analysis. Two mass rail vehicle suspension systems have been analyzed for vibration responses analytically using mathematical tool Matlab Simulink and the same will be evaluated using FFT vibration analyzer to find peak resonance in vertical, lateral and longitudinal direction. The results prove that the suspension acquires high repeated load in vertical and lateral direction due to tracking and curving causes maximum stress concentration on middle axle suspension spring as height of this spring is larger than end axle spring in primary suspension system and responsible for failure of middle axle suspension spring due to high stress acquisition.

  11. Antigen-antibody biorecognition events as discriminated by noise analysis of force spectroscopy curves

    NASA Astrophysics Data System (ADS)

    Bizzarri, Anna Rita; Cannistraro, Salvatore

    2014-08-01

    Atomic force spectroscopy is able to extract kinetic and thermodynamic parameters of biomolecular complexes provided that the registered unbinding force curves could be reliably attributed to the rupture of the specific complex interactions. To this aim, a commonly used strategy is based on the analysis of the stretching features of polymeric linkers which are suitably introduced in the biomolecule-substrate immobilization procedure. Alternatively, we present a method to select force curves corresponding to specific biorecognition events, which relies on a careful analysis of the force fluctuations of the biomolecule-functionalized cantilever tip during its approach to the partner molecules immobilized on a substrate. In the low frequency region, a characteristic 1/f α noise with α equal to one (flickering noise) is found to replace white noise in the cantilever fluctuation power spectrum when, and only when, a specific biorecognition process between the partners occurs. The method, which has been validated on a well-characterized antigen-antibody complex, represents a fast, yet reliable alternative to the use of linkers which may involve additional surface chemistry and reproducibility concerns.

  12. An explicit solution for progress curve analysis in systems characterized by endogenous substrate production.

    PubMed

    Goudar, Chetan T

    2012-05-01

    The Lambert W function was used to explicitly relate substrate concentration S, to time t, and the kinetic parameters V (m), K (m), and R in the modified Michaelis-Menten equation that accounts for endogenous substrate production. The applicability of this explicit formulation for kinetic parameter estimation by progress curve analysis was demonstrated using a combination of synthetic and experimental substrate depletion data. Synthetic substrate depletion data were generated using S (0) values of 1, 2, and 3 μM and V (m), K (m), and R values of 1.0 μM h(-1), 1.0 μM, and 0.1 μM h(-1), respectively, and contained 5% normally distributed error. Experimental data were obtained from two previously published studies on hydrogen depletion in four experimental systems. In all instances, experimental data were well described by the explicit solution presented in this study. Differential equation solution and iterative S estimation are eliminated with the explicit solution approach, thereby simplifying progress curve analysis in systems characterized by endogenous substrate production.

  13. Antigen-antibody biorecognition events as discriminated by noise analysis of force spectroscopy curves.

    PubMed

    Bizzarri, Anna Rita; Cannistraro, Salvatore

    2014-08-22

    Atomic force spectroscopy is able to extract kinetic and thermodynamic parameters of biomolecular complexes provided that the registered unbinding force curves could be reliably attributed to the rupture of the specific complex interactions. To this aim, a commonly used strategy is based on the analysis of the stretching features of polymeric linkers which are suitably introduced in the biomolecule-substrate immobilization procedure. Alternatively, we present a method to select force curves corresponding to specific biorecognition events, which relies on a careful analysis of the force fluctuations of the biomolecule-functionalized cantilever tip during its approach to the partner molecules immobilized on a substrate. In the low frequency region, a characteristic 1/f (α) noise with α equal to one (flickering noise) is found to replace white noise in the cantilever fluctuation power spectrum when, and only when, a specific biorecognition process between the partners occurs. The method, which has been validated on a well-characterized antigen-antibody complex, represents a fast, yet reliable alternative to the use of linkers which may involve additional surface chemistry and reproducibility concerns.

  14. Nonlinear Analysis and Post-Test Correlation for a Curved PRSEUS Panel

    NASA Technical Reports Server (NTRS)

    Gould, Kevin; Lovejoy, Andrew E.; Jegley, Dawn; Neal, Albert L.; Linton, Kim, A.; Bergan, Andrew C.; Bakuckas, John G., Jr.

    2013-01-01

    The Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) concept, developed by The Boeing Company, has been extensively studied as part of the National Aeronautics and Space Administration's (NASA s) Environmentally Responsible Aviation (ERA) Program. The PRSEUS concept provides a light-weight alternative to aluminum or traditional composite design concepts and is applicable to traditional-shaped fuselage barrels and wings, as well as advanced configurations such as a hybrid wing body or truss braced wings. Therefore, NASA, the Federal Aviation Administration (FAA) and The Boeing Company partnered in an effort to assess the performance and damage arrestments capabilities of a PRSEUS concept panel using a full-scale curved panel in the FAA Full-Scale Aircraft Structural Test Evaluation and Research (FASTER) facility. Testing was conducted in the FASTER facility by subjecting the panel to axial tension loads applied to the ends of the panel, internal pressure, and combined axial tension and internal pressure loadings. Additionally, reactive hoop loads were applied to the skin and frames of the panel along its edges. The panel successfully supported the required design loads in the pristine condition and with a severed stiffener. The panel also demonstrated that the PRSEUS concept could arrest the progression of damage including crack arrestment and crack turning. This paper presents the nonlinear post-test analysis and correlation with test results for the curved PRSEUS panel. It is shown that nonlinear analysis can accurately calculate the behavior of a PRSEUS panel under tension, pressure and combined loading conditions.

  15. Statistical Analysis of Quasar Light Curves from Pan-STARRS1

    NASA Astrophysics Data System (ADS)

    Hernandez, Betsy; Liu, Tingting; Gezari, Suvi

    2017-01-01

    We present a statistical analysis of variable quasars in the Pan-STARRS1 Medium Deep Survey (PS1 MDS). PS1 MDS obtained multi-epoch images of 10 fields, each 8 square degrees in size, over 4 years, starting in May 2010. The MDS fields were observed in 5 filters (gp1, rp1, ip1, zp1, and yp1) during their season of visibility, with a typical cadence per filter of 3 days. We extracted the light curves of 670 color-selected quasars in the PS1 MDS using Point Spread Function photometry from the Image Processing Pipeline data products. From the quasar sample, we selected 104 quasars whose variability was at least 2 standard deviations higher than the non-variable reference star sample. We performed a statistical analysis of the light curves of the selected quasars in the g,r,i and z bands using a maximum likelihood method to find the best-fit Damped Random Walk parameters (sigma and tau - also incorporating the Zoghbi et al. 2013 method for uneven sampling). The resulting distributions for sigma and tau were similar to those found in previous studies of quasars.

  16. A Scientific Analysis of Galaxy Tangential Speed of Revolution Curves III

    NASA Astrophysics Data System (ADS)

    Taff, Laurence

    2015-04-01

    I last reported on my preliminary analysis of 350 + spiral, lenticular, irregular, polar ring, ring, and dwarf elliptical galaxies' tangential speed of revolution curves [TSRCs; and not rotation (sic) curves]. I now know that the consensus opinion in the literature--for which I can find no geometrical, numerical, statistical, nor scientific testing in 2,500 + publications--that the TSRC, vB(r), in the central bulges of these galaxies, is a linear function of the radial distance from the minor axis of symmetry r--is false. For the majority (>98%) vB(r) is rarely well represented by vB(r) = ωB r (for which the unique material model is an homogeneous, oblate, spheroid). Discovered via a scientific analysis of the gravitational potential energy computed directly from the observational data, vB(r) is almost exactly given by vB2(r) = (ωB r)2(1 + η r2) with | η | < 10-2 and frequently orders of magnitude less. The corresponding mass model is the simplest generalization: a two component homoeoid. The set of possible periodic orbits, based on circular trigonometric functions, becomes a set of periodic orbits based on the Jacobian elliptic functions. Once again it is possible to prove that the mass-to-light ratio can neither be a constant nor follow the de Vaucouleurs R1/4 rule.

  17. Thermal and x-ray analysis on the origin of double melting phenomena of poly(L-lactic acid) films

    NASA Astrophysics Data System (ADS)

    Ling, Xiaoyun

    Thermal analysis is one of the most commonly used techniques to characterize the structure and properties of semicrystalline polymers. However, the complexity involved is often overlooked, leading to erroneous or, at least, questionable results and interpretations. In the present study we carry out an extensive investigation of the complex thermal behavior of poly(L-lactic acid), PLLA, films prepared under a wide range of crystallization conditions, including isothermal and non-isothermal crystallization from both the glassy state and the melt. The primary techniques used were differential scanning calorimetry (DSC), temperature modulated DSC (TMDSC), wide-angle x-ray diffraction (WAXD), and small angle x-ray scattering (SAXS). A major goal of the research was to sort out the various phenomena and to understand the mechanisms that produced them. Depending on the sample preparation conditions up to three crystallization peaks and two melting peaks could be observed during heating in the DSC. The occurrence of double melting is a function of crystallization temperature, crystallization time, heating rate, and molecular weight. It occurs under many experimental conditions, and it depends largely on the size and perfection of initial crystals, not the overall initial crystallinity, nor the completion of crystallization. It was found that the first endotherm was often obscured by the recrystallization exotherm. It was concluded that PLLA double melting originates mainly from the melt-recrystallization of metastable crystals. For samples cold-crystallized above 140°C, it is due to a dual lamellar population present in the samples. For crystallization below 120°C, a proposal in the literature that PLLA double melting is caused by the formation and subsequent transformation of beta-phase could not be ruled out. A unique double "cold-crystallization" peak was observed when amorphous PLLA was heated at 10°C/min. It was concluded to result from the sum of conventional cold

  18. Z curve theory-based analysis of the dynamic nature of nucleosome positioning in Saccharomyces cerevisiae.

    PubMed

    Wu, Xueting; Liu, Hui; Liu, Hongbo; Su, Jianzhong; Lv, Jie; Cui, Ying; Wang, Fang; Zhang, Yan

    2013-11-01

    Nucleosome is the elementary structural unit of eukaryotic chromatin. Instability of nucleosome positioning plays critical roles in chromatin remodeling in differentiation and disease. In this study, we investigated nucleosome dynamics in the Saccharomyces cerevisiae genome using a geometric model based on Z curve theory. We identified 52,941 stable nucleosomes and 7607 dynamic nucleosomes, compiling them into a genome-wide nucleosome dynamic positioning map and constructing a user-friendly visualization platform (http://bioinfo.hrbmu.edu.cn/nucleosome). Our approach achieved a sensitivity of 90.31% and a specificity of 87.76% for S. cerevisiae. Analysis revealed transcription factor binding sites (TFBSs) were enriched in linkers. And among the sparse nucleosomes around TFBSs, dynamic nucleosomes were slightly preferred. Gene Ontology (GO) enrichment analysis indicated that stable and dynamic nucleosomes were enriched on genes involved in different biological processes and functions. This study provides an approach for comprehending chromatin remodeling and transcriptional regulation of genes.

  19. The composition-explicit distillation curve technique: Relating chemical analysis and physical properties of complex fluids.

    PubMed

    Bruno, Thomas J; Ott, Lisa S; Lovestead, Tara M; Huber, Marcia L

    2010-04-16

    The analysis of complex fluids such as crude oils, fuels, vegetable oils and mixed waste streams poses significant challenges arising primarily from the multiplicity of components, the different properties of the components (polarity, polarizability, etc.) and matrix properties. We have recently introduced an analytical strategy that simplifies many of these analyses, and provides the added potential of linking compositional information with physical property information. This aspect can be used to facilitate equation of state development for the complex fluids. In addition to chemical characterization, the approach provides the ability to calculate thermodynamic properties for such complex heterogeneous streams. The technique is based on the advanced distillation curve (ADC) metrology, which separates a complex fluid by distillation into fractions that are sampled, and for which thermodynamically consistent temperatures are measured at atmospheric pressure. The collected sample fractions can be analyzed by any method that is appropriate. The analytical methods we have applied include gas chromatography (with flame ionization, mass spectrometric and sulfur chemiluminescence detection), thin layer chromatography, FTIR, corrosivity analysis, neutron activation analysis and cold neutron prompt gamma activation analysis. By far, the most widely used analytical technique we have used with the ADC is gas chromatography. This has enabled us to study finished fuels (gasoline, diesel fuels, aviation fuels, rocket propellants), crude oils (including a crude oil made from swine manure) and waste oils streams (used automotive and transformer oils). In this special issue of the Journal of Chromatography, specifically dedicated to extraction technologies, we describe the essential features of the advanced distillation curve metrology as an analytical strategy for complex fluids.

  20. A multi-scale analysis of the impact of pressure on melting of crystalline phase change material germanium telluride

    SciTech Connect

    Liu, Jie

    2014-10-27

    The impact of the moderate pressure (about 10{sup 0 }GPa) on the melting of crystalline (c-) phase change material (PCM) germanium telluride (GeTe) is analyzed, by combining the heat transfer equation in the PCM device scale (10{sup 1}–10{sup 2 }nm and beyond), and the ab initio molecular dynamics and the nudged elastic band simulations in the atomistic scale (10{sup −1}–10{sup 0 }nm). The multi-scale analysis unravels that a pressure P = 1.0 GPa can increase the melting temperature of c-GeTe and the PCM device “reset” operation energy consumption by 6%–7%. It is shown that the melting temperature increase originates from the pressure-induced raise of the energy barrier of the umbrella-flip transition of the Ge atom from the octahedral symmetry site to the tetrahedral symmetry site. It is revealed that when P > 1.0 GPa, which is normal in PCM devices, the “reset” energy will be increased even by more. Based on the analysis, suggestions to alleviate pressure-induced raise of melting temperature and “reset” energy are provided.

  1. Detection of sdhB Gene Mutations in SDHI-Resistant Isolates of Botrytis cinerea Using High Resolution Melting (HRM) Analysis

    PubMed Central

    Samaras, Anastasios; Madesis, Panagiotis; Karaoglanidis, George S.

    2016-01-01

    Botrytis cinerea, is a high risk pathogen for fungicide resistance development. Pathogen’ resistance to SDHIs is associated with several mutations in sdh gene. The diversity of mutations and their differential effect on cross-resistance patterns among SDHIs and the fitness of resistant strains necessitate the availability of a tool for their rapid identification. This study was initiated to develop and validate a high-resolution melting (HRM) analysis for the identification of P225H/F/L//T, N230I, and H272L/R/Y mutations. Based on the sequence of sdhB subunit of resistant and sensitive isolates, a universal primer pair was designed. The specificity of the HRM analysis primers was verified to ensure against the cross-reaction with other fungal species and its sensitivity was evaluated using concentrations of known amounts of mutant’s DNA. The melting curve analysis generated nine distinct curve profiles, enabling the discrimination of all the four mutations located at codon 225, the N230I mutation, the three mutations located in codon 272, and the non-mutated isolates (isolates of wild-type sensitivity). Similar results were obtained when DNA was extracted directly from artificially inoculated strawberry fruit. The method was validated by monitoring the presence of sdhB mutations in samples of naturally infected strawberry fruits and stone fruit rootstock seedling plants showing damping-off symptoms. HRM analysis data were compared with a standard PIRA–PCR technique and an absolute agreement was observed suggesting that in both populations the H272R mutation was the predominant one, while H272Y, N230I, and P225H were detected in lower frequencies. The results of the study suggest that HRM analysis can be a useful tool for sensate, accurate, and rapid identification of several sdhB mutations in B. cinerea and it is expected to contribute in routine fungicide resistance monitoring or assessments of the effectiveness of anti-resistance strategies implemented in

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

    DOE PAGES

    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

  3. 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.

  4. Numerical analysis of radiation propagation in innovative volumetric receivers based on selective laser melting techniques

    NASA Astrophysics Data System (ADS)

    Alberti, Fabrizio; Santiago, Sergio; Roccabruna, Mattia; Luque, Salvador; Gonzalez-Aguilar, Jose; Crema, Luigi; Romero, Manuel

    2016-05-01

    Volumetric absorbers constitute one of the key elements in order to achieve high thermal conversion efficiencies in concentrating solar power plants. Regardless of the working fluid or thermodynamic cycle employed, design trends towards higher absorber output temperatures are widespread, which lead to the general need of components of high solar absorptance, high conduction within the receiver material, high internal convection, low radiative and convective heat losses and high mechanical durability. In this context, the use of advanced manufacturing techniques, such as selective laser melting, has allowed for the fabrication of intricate geometries that are capable of fulfilling the previous requirements. This paper presents a parametric design and analysis of the optical performance of volumetric absorbers of variable porosity conducted by means of detailed numerical ray tracing simulations. Sections of variable macroscopic porosity along the absorber depth were constructed by the fractal growth of single-cell structures. Measures of performance analyzed include optical reflection losses from the absorber front and rear faces, penetration of radiation inside the absorber volume, and radiation absorption as a function of absorber depth. The effects of engineering design parameters such as absorber length and wall thickness, material reflectance and porosity distribution on the optical performance of absorbers are discussed, and general design guidelines are given.

  5. Study of the Melting Behavior of YAG Single Crystal by Optical Differential Thermal Analysis

    DTIC Science & Technology

    1979-11-01

    melting point of AI2O3 as determined by the DOSMTOP agreed well with the 2055 ± 1. VIECHNICKI, D. J., and SCHMID, F. Crystal Growth Using the Heat...Exchanger Method (HEM). L Crystal Growth , v. 26, 1974, p. 162-164. 2. VIECHNICKI, D. J., and CASLAVSKY, J. L. Solid State Formation O/AW.-FJ^/JO...temperature was near the 1937 C thermoarrest temperature observed during the melting of large boules of sintered YAG material in the crystal growth

  6. Determination of secondary flow morphologies by wavelet analysis in a curved artery model with physiological inflow

    NASA Astrophysics Data System (ADS)

    Bulusu, Kartik V.; Hussain, Shadman; Plesniak, Michael W.

    2014-11-01

    Secondary flow vortical patterns in arterial curvatures have the potential to affect several cardiovascular phenomena, e.g., progression of atherosclerosis by altering wall shear stresses, carotid atheromatous disease, thoracic aortic aneurysms and Marfan's syndrome. Temporal characteristics of secondary flow structures vis-à-vis physiological (pulsatile) inflow waveform were explored by continuous wavelet transform (CWT) analysis of phase-locked, two-component, two-dimensional particle image velocimeter data. Measurements were made in a 180° curved artery test section upstream of the curvature and at the 90° cross-sectional plane. Streamwise, upstream flow rate measurements were analyzed using a one-dimensional antisymmetric wavelet. Cross-stream measurements at the 90° location of the curved artery revealed interesting multi-scale, multi-strength coherent secondary flow structures. An automated process for coherent structure detection and vortical feature quantification was applied to large ensembles of PIV data. Metrics such as the number of secondary flow structures, their sizes and strengths were generated at every discrete time instance of the physiological inflow waveform. An autonomous data post-processing method incorporating two-dimensional CWT for coherent structure detection was implemented. Loss of coherence in secondary flow structures during the systolic deceleration phase is observed in accordance with previous research. The algorithmic approach presented herein further elucidated the sensitivity and dependence of morphological changes in secondary flow structures on quasiperiodicity and magnitude of temporal gradients in physiological inflow conditions.

  7. Regionalization of subsurface stormflow parameters of hydrologic models: Derivation from regional analysis of streamflow recession curves

    SciTech Connect

    Ye, Sheng; Li, Hongyi; Huang, Maoyi; Ali, Melkamu; Leng, Guoyong; Leung, Lai-Yung R.; Wang, Shaowen; Sivapalan, Murugesu

    2014-07-21

    Subsurface stormflow is an important component of the rainfall–runoff response, especially in steep terrain. Its contribution to total runoff is, however, poorly represented in the current generation of land surface models. The lack of physical basis of these common parameterizations precludes a priori estimation of the stormflow (i.e. without calibration), which is a major drawback for prediction in ungauged basins, or for use in global land surface models. This paper is aimed at deriving regionalized parameterizations of the storage–discharge relationship relating to subsurface stormflow from a top–down empirical data analysis of streamflow recession curves extracted from 50 eastern United States catchments. Detailed regression analyses were performed between parameters of the empirical storage–discharge relationships and the controlling climate, soil and topographic characteristics. The regression analyses performed on empirical recession curves at catchment scale indicated that the coefficient of the power-law form storage–discharge relationship is closely related to the catchment hydrologic characteristics, which is consistent with the hydraulic theory derived mainly at the hillslope scale. As for the exponent, besides the role of field scale soil hydraulic properties as suggested by hydraulic theory, it is found to be more strongly affected by climate (aridity) at the catchment scale. At a fundamental level these results point to the need for more detailed exploration of the co-dependence of soil, vegetation and topography with climate.

  8. VizieR Online Data Catalog: GRB X-ray afterglows light curves analysis (Racusin+, 2016)

    NASA Astrophysics Data System (ADS)

    Racusin, J. L.; Oates, S. R.; de Pasquale, M.; Kocevski, D.

    2016-09-01

    All GRBs discovered with Swift-BAT, with X-ray afterglows detected by Swift-XRT and measured redshifts, between 2004 December and 2014 March are included in the analysis. We include only those X-ray afterglows with at least three light-curve bins (>~60 counts) and T90 measurements are available in the BAT catalogs (Sakamoto+ 2008, J/ApJS/175/179; 2011, J/ApJS/195/2 and Lien+ 2016, arXiv:1606.01956). The final sample includes 237 long-duration GRBs (9 short), 47 of which also appear in the Oates et al. (2012MNRAS.426L..86O; 2015MNRAS.453.4121O) sample for the UVOT correlation (sample only extends through 2010). The redshift measurements come from a convolution of databases and the literature and are listed in Table 1. All light curves were retrieved from the University of Leicester Swift XRT Team GRB repository (Evans et al. 2007A&A...469..379E; 2009, J/MNRAS/397/1177). See section 2.2 for further explanations. (2 data files).

  9. Finite element analysis of the effect of loading curve shape on brain injury predictors.

    PubMed

    Post, Andrew; Hoshizaki, Blaine; Gilchrist, Michael D

    2012-02-23

    Prediction of traumatic and mild traumatic brain injury is an important factor in managing their prevention. Currently, the prediction of these injuries is limited to peak linear and angular acceleration loading curves derived from laboratory reconstructions. However it remains unclear as to what aspect of these loading curves contributes to brain tissue damage. This research uses the University College Dublin Brain Trauma Model (UCDBTM) to analyse three distinct loading curve shapes meant to represent different helmet loading scenarios. The loading curves were applied independently in each axis of linear and angular acceleration and their effect on currently used predictors of TBI and mTBI was examined. Loading curve shape A had a late time to peak, B an early time to peak and C had a consistent plateau. The areas under the curve for all three loading curve shapes were identical. The results indicate that loading curve A produced consistently higher maximum principal strains and Von Mises stress than the other two loading curve types. Loading curve C consistently produced the lowest values of maximum principal strain and Von Mises stress, with loading curve B being lowest in only 2 cases. The areas of peak Von Mises stress and Principal strain also varied depending on loading curve shape and acceleration input.

  10. Melting of Ice under Pressure

    SciTech Connect

    Schwegler, E; Sharma, M; Gygi, F; Galli, G

    2008-07-31

    The melting of ice under pressure is investigated with a series of first principles molecular dynamics simulations. In particular, a two-phase approach is used to determine the melting temperature of the ice-VII phase in the range of 10 to 50 GPa. Our computed melting temperatures are consistent with existing diamond anvil cell experiments. We find that for pressures between 10 to 40 GPa, ice melts as a molecular solid. For pressures above {approx}45 GPa there is a sharp increase in the slope of the melting curve due to the presence of molecular dissociation and proton diffusion in the solid, prior to melting. The onset of significant proton diffusion in ice-VII as a function of increasing temperature is found to be gradual and bears many similarities to that of a type-II superionic solid.

  11. Melting of ice under pressure.

    PubMed

    Schwegler, Eric; Sharma, Manu; Gygi, François; Galli, Giulia

    2008-09-30

    The melting of ice under pressure is investigated with a series of first-principles molecular dynamics simulations. In particular, a two-phase approach is used to determine the melting temperature of the ice-VII phase in the range of 10-50 GPa. Our computed melting temperatures are consistent with existing diamond anvil cell experiments. We find that for pressures between 10 and 40 GPa, ice melts as a molecular solid. For pressures above approximately 45 Gpa, there is a sharp increase in the slope of the melting curve because of the presence of molecular dissociation and proton diffusion in the solid before melting. The onset of significant proton diffusion in ice-VII as a function of increasing temperature is found to be gradual and bears many similarities to that of a type-II superionic solid.

  12. High-Resolution Melting Analysis of the TPMT Gene: A Study in the Polish Population

    PubMed Central

    Borun, Pawel; Milanowska, Katarzyna; Jakubowska-Burek, Ludwika; Zakerska, Oliwia; Dobrowolska-Zachwieja, Agnieszka; Plawski, Andrzej; Froster, Ursula G.; Szalata, Marlena; Slomski, Ryszard

    2013-01-01

    The thiopurine S-methyltransferase (TPMT) gene encoding thiopurine methyltransferase is a crucial enzyme in metabolism of thiopurine drugs: azathioprine and 6-mercoptopurine, which are used in the treatment of leukemia or inflammatory bowel diseases. Genetic polymorphism of the TPMT gene correlates with activity of this enzyme, individual reaction, and dosing of thiopurines. Thirty-one variants of the TPMT gene with low enzymatic activity have been described with three major alleles: TPMT*2 (c.238G>C), *3A (c.460 G>A, c.719A>G), and *3C (c.719A>G), accounting for 80% to 95% of inherited TPMT deficiency in different populations in the world. The aim of the study was to establish a rapid and highly sensitive method of analysis for the complete coding sequence of the TPMT gene and to determine the spectrum and prevalence of the TPMT gene sequence variations in the Polish population. Recently, high-resolution melting analysis (HRMA) has become a highly sensitive, automated, and economical technique for mutation screening or genotyping. We applied HRMA for the first time to TPMT gene scanning. In total, we analyzed 548 alleles of the Polish population. We found 11 different sequence variations, where two are novel changes: c.200T>C (p.P67S, TPMT*30) and c.595G>A (p.V199I, TPMT*31). Detection of these new rare alleles TPMT*30 and *31 in the Polish population suggests the need to analyze the whole TPMT gene and maybe also the extension of routinely used tests containing three major alleles, TPMT*2, *3A, and *3C. Identification of sequence variants using HRMA is highly sensitive and less time consuming compared to standard sequencing. We conclude that HRMA can be easy integrated into genetic testing of the TPMT gene in patients treated with thiopurines. PMID:23252704

  13. High-resolution melting analysis of the TPMT gene: a study in the Polish population.

    PubMed

    Skrzypczak-Zielinska, Marzena; Borun, Pawel; Milanowska, Katarzyna; Jakubowska-Burek, Ludwika; Zakerska, Oliwia; Dobrowolska-Zachwieja, Agnieszka; Plawski, Andrzej; Froster, Ursula G; Szalata, Marlena; Slomski, Ryszard

    2013-02-01

    The thiopurine S-methyltransferase (TPMT) gene encoding thiopurine methyltransferase is a crucial enzyme in metabolism of thiopurine drugs: azathioprine and 6-mercoptopurine, which are used in the treatment of leukemia or inflammatory bowel diseases. Genetic polymorphism of the TPMT gene correlates with activity of this enzyme, individual reaction, and dosing of thiopurines. Thirty-one variants of the TPMT gene with low enzymatic activity have been described with three major alleles: TPMT*2 (c.238G>C), *3A (c.460 G>A, c.719A>G), and *3C (c.719A>G), accounting for 80% to 95% of inherited TPMT deficiency in different populations in the world. The aim of the study was to establish a rapid and highly sensitive method of analysis for the complete coding sequence of the TPMT gene and to determine the spectrum and prevalence of the TPMT gene sequence variations in the Polish population. Recently, high-resolution melting analysis (HRMA) has become a highly sensitive, automated, and economical technique for mutation screening or genotyping. We applied HRMA for the first time to TPMT gene scanning. In total, we analyzed 548 alleles of the Polish population. We found 11 different sequence variations, where two are novel changes: c.200T>C (p.P67S, TPMT*30) and c.595G>A (p.V199I, TPMT*31). Detection of these new rare alleles TPMT*30 and *31 in the Polish population suggests the need to analyze the whole TPMT gene and maybe also the extension of routinely used tests containing three major alleles, TPMT*2, *3A, and *3C. Identification of sequence variants using HRMA is highly sensitive and less time consuming compared to standard sequencing. We conclude that HRMA can be easy integrated into genetic testing of the TPMT gene in patients treated with thiopurines.

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

    SciTech Connect

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

    2016-01-01

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

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

    DOE PAGES

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

    2016-01-01

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

  16. Correlation Analysis of Optical and Radio Light Curves for a Large Sample of Active Galactic Nuclei

    NASA Astrophysics Data System (ADS)

    Clements, S. D.; Smith, A. G.; Aller, H. D.; Aller, M. F.

    1995-08-01

    The Rosemary Hill Observatory has accumulated internally consistent light curves extending over as much as 26 years for a large sample of active galactic nuclei. Forty-six of these optical records have been compared with similar radio records from the University of Michigan Radio Astronomy Observatory and the Algonquin Radio Observatory. For 18 objects, pairs of records were sufficiently long and unconfused to allow reliable application of the Discrete Correlation Function analysis; this group included 8 BL Lacertids, 8 quasars, and 2 Seyfert galaxies. Nine of the 18 sources showed positive radio-optical correlations, with the radio events lagging the optical by intervals ranging from 0 to 14 months. Consistent with the relativistic beaming model of the BL Lacertids, the group displaying correlations was dominated by this type of object.

  17. Recurrence plot analysis of nonstationary data: The understanding of curved patterns

    NASA Astrophysics Data System (ADS)

    Facchini, A.; Kantz, H.; Tiezzi, E.

    2005-08-01

    Recurrence plots of the calls of the Nomascus concolor (Western black crested gibbon) and Hylobates lar (White-handed gibbon) show characteristic circular, curved, and hyperbolic patterns superimposed to the main temporal scale of the signal. It is shown that these patterns are related to particular nonstationarities in the signal. Some of them can be reproduced by artificial signals like frequency modulated sinusoids and sinusoids with time divergent frequency. These modulations are too faint to be resolved by conventional time-frequency analysis with similar precision. Therefore, recurrence plots act as a magnifying glass for the detection of multiple temporal scales in slightly modulated signals. The detected phenomena in these acoustic signals can be explained in the biomechanical context by taking in account the role of the muscles controlling the vocal folds.

  18. Microwave melt and offgas analysis results from a Ferro Corporation{reg_sign} glass frit

    SciTech Connect

    Phillips, J.A.; Hoffman, C.R.; Knutson, P.T.

    1995-03-01

    In support of the Residue Treatment Technology (RTT) Microwave Solidification project, Waste Projects and Surface Water personnel conducted a series of experiments to determine the feasibility of encapsulating a surrogate sludge waste using the microwave melter. The surrogate waste was prepared by RTT and melted with five varying compositions of low melting glass frit supplied by the Ferro Corporation. Samples were melted using a 50% waste/50% glass frit and a 47.5% waste/47.5% glass frit/5% carbon powder. This was done to evaluate the effectiveness of carbon at reducing a sulfate-based surface scale which has been observed in previous experiments and in full-scale testing. These vitrified samples were subsequently submitted to Environmental Technology for toxicity characteristic leaching procedure (TCLP) testing. Two of the five frits tested in this experiment merit further evaluation as raw materials for the microwave melter. Ferro frit 3110 with and without carbon powder produced a crystalline product which passed TCLP testing. The quality of the melt product could be improved by increasing the melting temperature from 900{degrees}C to approximately 1150-1200{degrees}C. Ferro frit 3249 produced the optimal quality of glass based on visual observations, but failed TCLP testing for silver when melted without carbon powder. This frit requires a slightly higher melting temperature ({ge} 1200{degrees}C) compared to frit 3110 and produces a superior product. In conjunction with this work, Surface Water personnel conducted offgas analyses using a Thermal Desorption Mass Spectrometer (TDMS) on selected formulations. The offgas analyses identified and quantified water vapor (H{sub 2}O), oxygen (O{sub 2}) and carbon oxides (CO and CO{sub 2}), sulfur (S) and sulfur oxides (SO and SO{sub 2}), and nitrogen (N{sub 2}) and nitrogen oxides (NO and NO{sub 2}) that volatilized during glass formation.

  19. Multivariate Curve Resolution Applied to Hyperspectral Imaging Analysis of Chocolate Samples.

    PubMed

    Zhang, Xin; de Juan, Anna; Tauler, Romà

    2015-08-01

    This paper shows the application of Raman and infrared hyperspectral imaging combined with multivariate curve resolution (MCR) to the analysis of the constituents of commercial chocolate samples. The combination of different spectral data pretreatment methods allowed decreasing the high fluorescent Raman signal contribution of whey in the investigated chocolate samples. Using equality constraints during MCR analysis, estimations of the pure spectra of the chocolate sample constituents were improved, as well as their relative contributions and their spatial distribution on the analyzed samples. In addition, unknown constituents could be also resolved. White chocolate constituents resolved from Raman hyperspectral image indicate that, at macro scale, sucrose, lactose, fat, and whey constituents were intermixed in particles. Infrared hyperspectral imaging did not suffer from fluorescence and could be applied for white and milk chocolate. As a conclusion of this study, micro-hyperspectral imaging coupled to the MCR method is confirmed to be an appropriate tool for the direct analysis of the constituents of chocolate samples, and by extension, it is proposed for the analysis of other mixture constituents in commercial food samples.

  20. Rapid identification of biothreat and other clinically relevant bacterial species by use of universal PCR coupled with high-resolution melting analysis.

    PubMed

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

    2009-07-01

    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.

  1. Light curve analysis of GSC 2750-0054 and GSC 03208-02644

    NASA Astrophysics Data System (ADS)

    Elkhateeb, M. M.; Nouh, M. I.

    2016-11-01

    We present the first photometric analysis for the newly discovered eclipsing binary systems of Algole-type GSC 2750-0054 and GSC 03208-02644. Our analysis was carried out by means of the most recent version of Wilson Devinney (WD) code, which applies the model atmosphere by (Kurucz, R., 1993. In: Milon, E. (Ed.), Light Curve Modeling of Eclipsing Binary Stars. Springer-Verlag, New York, p. 93) with a prescription in passband for the radiative treatment. The accepted light curve solutions reveal absolute physical parameters and the spectral classifications for the components are adopted. We derived the spectral types of the system GSC 2750-0054 as K3 and K7. The physical parameters of the system are M1 = 0.72 ± 0.03 M⊙, M2 = 0.47 ± 0.02 M⊙, R1 = 0.81 ± 0.03 R⊙, R2 = 0.62 ± 0.03 R⊙, L1 = 0.27 ± 0.01 L⊙ and L2 = 0.1 ± 0.004 L⊙. For the system, GSC 03208 02644 the spectral types of the components are A5 and A8. The physical parameters are M1 = 1.86 ± 0.076 M⊙, M2 = 1.21 ± 0.049 M⊙, R1 = 1.84 ± 0.075 R⊙, R2 = 1.75 ± 0.072 R⊙, L1 = 13.58 ± 0.55 L⊙ and L2 = 9.94 ± 0.41 L⊙. Comparison with the evolutionary models as well as the empirical databases is presented.

  2. 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.

  3. TaqMan probes as blocking agents for enriched PCR amplification and DNA melting analysis of mutant genes.

    PubMed

    Botezatu, Irina V; Panchuk, Irina O; Stroganova, Anna M; Senderovich, Anastasia I; Kondratova, Valentina N; Shelepov, Valery P; Lichtenstein, Anatoly V

    2017-02-01

    Asymmetric PCR and DNA melting analysis with TaqMan probes applied for mutation detection is effectively used in clinical diagnostics. The method is simple, cost-effective, and carried out in a closed-tube format, minimizing time, labor, and risk of sample cross-contamination. Although DNA melting analysis is more sensitive than Sanger sequencing (mutation detection thresholds are ~5% and 15%-20%, respectively), it is less sensitive than more labor-intensive and expensive techniques such as pyrosequencing and droplet digital PCR. Here, we demonstrate that, under specially selected conditions of asymmetric PCR, TaqMan probes can play the role of blocking agents. Preferential blocking of the wild-type allele brings about enriched amplification of mutant alleles. As a result, an ~10-fold increase in the detection sensitivity for mutant BRAF and NRAS genes was achieved.

  4. Analysis of Surface Plasmon Resonance Curves with a Novel Sigmoid-Asymmetric Fitting Algorithm.

    PubMed

    Jang, Daeho; Chae, Geunhyoung; Shin, Sehyun

    2015-09-30

    The present study introduces a novel curve-fitting algorithm for surface plasmon resonance (SPR) curves using a self-constructed, wedge-shaped beam type angular interrogation SPR spectroscopy technique. Previous fitting approaches such as asymmetric and polynomial equations are still unsatisfactory for analyzing full SPR curves and their use is limited to determining the resonance angle. In the present study, we developed a sigmoid-asymmetric equation that provides excellent curve-fitting for the whole SPR curve over a range of incident angles, including regions of the critical angle and resonance angle. Regardless of the bulk fluid type (i.e., water and air), the present sigmoid-asymmetric fitting exhibited nearly perfect matching with a full SPR curve, whereas the asymmetric and polynomial curve fitting methods did not. Because the present curve-fitting sigmoid-asymmetric equation can determine the critical angle as well as the resonance angle, the undesired effect caused by the bulk fluid refractive index was excluded by subtracting the critical angle from the resonance angle in real time. In conclusion, the proposed sigmoid-asymmetric curve-fitting algorithm for SPR curves is widely applicable to various SPR measurements, while excluding the effect of bulk fluids on the sensing layer.

  5. Kepler light-curve analysis of the blazar W2R 1926+42

    NASA Astrophysics Data System (ADS)

    Mohan, P.; Gupta, Alok C.; Bachev, Rumen; Strigachev, Anton

    2016-02-01

    We study the long term Kepler light curve of the blazar W2R 1926+42 (˜1.6 yr) which indicates a variety of variability properties during different intervals of observation. The normalized excess variance, Fvar ranges from 1.8 per cent in the quiescent phase and 43.3 per cent in the outburst phase. We find no significant deviation from linearity in the Fvar-flux relation. Time series analysis is conducted using the Fourier power spectrum and the wavelet analysis methods to study the power spectral density (PSD) shape, infer characteristic time-scales and statistically significant quasi-periodic oscillations (QPOs). A bending power law with an associated time-scale of T_B = 6.2^{+6.4}_{-3.1} hours is inferred in the PSD analysis. We obtain a black hole mass of M• = (1.5-5.9) × 107 M⊙ for the first time using Fvar and the bend time-scale for this source. From a mean outburst lifetime of days, we infer a distance from the jet base r ≤ 1.75 pc indicating that the outburst originates due to a shock. A possible QPO peaked at 9.1 d and lasting 3.4 cycles is inferred from the wavelet analysis. Assuming that the QPO is a true feature, r = (152-378)GM•/c2 and supported by the other timing analysis products such as a weighted mean PSD slope of -1.5 ± 0.2 from the PSD analysis, we argue that the observed variability and the weak and short duration QPO could be due to jet based processes including orbital features in a relativistic helical jet and others such as shocks and turbulence.

  6. Molecular Identification of Broomrape Species from a Single Seed by High Resolution Melting Analysis.

    PubMed

    Rolland, Mathieu; Dupuy, Aurélie; Pelleray, Aude; Delavault, Philippe

    2016-01-01

    Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species (Phelipanche aegyptiaca, Orobanche cernua, O. crenata, O. cumana, O. foetida, O. hederae, O. minor, and P. ramosa) from a single seed. Based on trnL and rbcL plastidial genes amplification, the designed assay successfully identifies O. cumana, O. cernua, O. crenata, O. minor, O. hederae, and O. foetida; P. ramosa, and P. aegyptiaca can be differentiated from other species but not from each other. Tested on 50 seed lots, obtained results perfectly matched identifications performed by sequencing. Through the analysis of common seed lots by different analysts, the reproducibility of the assay was evaluated at 90%. Despite an original sample preparation process it was not possible to extract enough DNA from some seeds (10% of the samples). The described assay fulfills its objectives and allows an accurate identification of the targeted broomrape species. It can be used to identify contaminants in commercial seed lots or for any other purpose. The assay might be extended to vegetative material.

  7. Molecular Identification of Broomrape Species from a Single Seed by High Resolution Melting Analysis

    PubMed Central

    Rolland, Mathieu; Dupuy, Aurélie; Pelleray, Aude; Delavault, Philippe

    2016-01-01

    Broomrapes are holoparasitic plants spreading through seeds. Each plant produces hundreds of thousands of seeds which remain viable in the soils for decades. To limit their spread, drastic measures are being taken and the contamination of a commercial seed lot by a single broomrape seed can lead to its rejection. Considering that broomrapes species identification from a single seed is extremely difficult even for trained botanists and that among all the described species, only a few are really noxious for the crops, numerous seed lots are rejected because of the contamination by seeds of non-noxious broomrape species. The aim of this study was to develop and evaluate a High Resolution Melting assay identifying the eight most noxious and common broomrape species (Phelipanche aegyptiaca, Orobanche cernua, O. crenata, O. cumana, O. foetida, O. hederae, O. minor, and P. ramosa) from a single seed. Based on trnL and rbcL plastidial genes amplification, the designed assay successfully identifies O. cumana, O. cernua, O. crenata, O. minor, O. hederae, and O. foetida; P. ramosa, and P. aegyptiaca can be differentiated from other species but not from each other. Tested on 50 seed lots, obtained results perfectly matched identifications performed by sequencing. Through the analysis of common seed lots by different analysts, the reproducibility of the assay was evaluated at 90%. Despite an original sample preparation process it was not possible to extract enough DNA from some seeds (10% of the samples). The described assay fulfills its objectives and allows an accurate identification of the targeted broomrape species. It can be used to identify contaminants in commercial seed lots or for any other purpose. The assay might be extended to vegetative material. PMID:28018378

  8. Evaluation of drug-polymer solubility curves through formal statistical analysis: comparison of preparation techniques.

    PubMed

    Knopp, Matthias Manne; Olesen, Niels Erik; Holm, Per; Löbmann, Korbinian; Holm, René; Langguth, Peter; Rades, Thomas

    2015-01-01

    In this study, the influence of the preparation technique (ball milling, spray drying, and film casting) of a supersaturated amorphous dispersion on the quality of solubility determinations of indomethacin in polyvinylpyrrolidone was investigated by means of statistical analysis. After annealing of the amorphous dispersions above the crystallization temperature for 2 h, the solubility curve was derived from the glass transition temperature of the demixed material using the Gordon-Taylor relationship and fitting with the Flory-Huggins model. The study showed that the predicted solubility from the ball-milled mixtures was not consistent with those from spray drying and film casting, indicating fundamental differences between the preparation techniques. Through formal statistical analysis, the best combination of fit to the Flory-Huggins model and reproducibility of the measurements was analyzed. Ball milling provided the best reproducibility of the three preparation techniques; however, an analysis of residuals revealed a systematic error. In contrast, film casting demonstrated a good fit to the model but poor reproducibility of the measurements. Therefore, this study recommends that techniques such as spray drying or potentially film casting (if experimental reproducibility can be improved) should be used to prepare the amorphous dispersions when performing solubility measurements of this kind.

  9. Reconstructing CO2 concentrations in basaltic melt inclusions from Cascade cinder cones using Raman analysis of vapor bubbles

    NASA Astrophysics Data System (ADS)

    Aster, E. M.; Wallace, P. J.; Moore, L.; Gazel, E.; Bodnar, R. J.

    2014-12-01

    Because melt inclusions (MIs) trap melt prior to eruptive degassing, they are useful probes of melt volatile concentrations. However, during post-entrapment cooling and crystallization, the melt in the inclusion contracts more than the mineral host, causing depressurization and nucleation of a vapor bubble. This causes pressure-soluble volatiles, particularly CO2, to exsolve from the melt into the bubble. To explore the extent of CO2 loss, CO2 densities in bubbles were estimated using data from Raman analysis of olivine-hosted melt inclusions from two cinder cones in the southern Cascade Arc (Basalt of Round Valley Butte [BRVB]; Basalt of Old Railroad Grade [BORG]). In BRVB, bubble vol. % (bubble vol./MI vol.) and measured CO2 densities ranged from 0.9 - 6.7 vol. % and 0.05- 0.24 g/cm3, respectively. In BORG, bubble vol. % and CO2 densities ranged from 1.4 - 9.2 vol. % and 0.07 - 0.29 g/cm3, respectively. To eliminate MI containing bubbles that were co-entrapped with the melt, we used a model from Riker (2005) to predict bubble vol. % as a function of the difference between eruption and formation temperatures. This suggested that bubbles larger than ~3.3 vol. % should be eliminated from CO2 reconstructions. Using average values of MI H2O and CO2 measured by FTIR, we added CO2 from the bubbles back into the MIs to obtain estimates of dissolved CO2 at the time of trapping. Analyzed concentrations were 933 ppm CO2 and 2.8 wt. % H2O for BORG (2.7 kbar, or ~9 km depth), with a reconstructed CO2 concentration of 1860 ± 612 (2s) ppm. Analyzed concentrations for BRVB were 426 ppm CO2 and 1.6 wt. % H2O (1.1 kbar, or ~3.7 km depth), with a reconstructed CO2 concentration of 2320 ± 1688 (2s) ppm. Using the reconstructed CO2 concentrations, VolatileCalc estimates place both BORG and BRVB MI entrapment at 4.3 kbar, or ~14 km depth. Thus, adding the CO2 in bubbles back to the CO2 in the glass of MIs is essential for determining accurate depths of magma crystallization.

  10. Testing and Analysis of the First Plastic Melt Waste Compactor Prototype

    NASA Technical Reports Server (NTRS)

    Pace, Gregory S.; Fisher, John W.

    2005-01-01

    A half scale Plastic Melt Waste Compactor prototype has been developed at NASA Ames Research Center. The half scale prototype unit will lead to the development of a full scale Plastic Melt Waste Compactor prototype that is representative of flight hardware that would be used on near and far term space missions. This report details the testing being done on the prototype Plastic Melt Waste Compactor by the Solid Waste Management group at NASA Ames Research Center. The tests are designed to determine the prototype's functionality, simplicity of operation, ability to contain and control noxious off-gassing, biological stability of the processed waste, and water recovery potential using a waste composite that is representative of the types of wastes produced on the International Space Station, Space Shuttle, MIR and Skylab missions.

  11. A parametric model for analysis of melt progression in U-A1 assemblies

    SciTech Connect

    Paik, I.K. ); Kim, S.H.; Leonard, M.T.; Amos, C.N. )

    1990-06-15

    A computational model has been developed that calculates the thermal degradation of the reactor core of the production reactors at the Savannah River Site (SRS) under postulated severe accident conditions. This model addresses heatup and degradation of the U-Al fuel and Li-Al or U-metal target assemblies and neighboring structures. Models included are those for assembly heatup due to decay heat generation, material melting and relocation, volume expansion of fuel due to foaming and melt/debris accumulation in assembly bottom end-fittings. Sample results are presented that illustrate the effect of alternative assumptions regarding the temperature at which U-Al alloy melts and relocates and the extent to which fuel foaming thermally couples adjacent fuel and target tubes. 5 refs., 6 figs., 1 tab.

  12. Optimization of melting analysis with TaqMan probes for detection of KRAS, NRAS, and BRAF mutations.

    PubMed

    Botezatu, Irina V; Nechaeva, Irina O; Stroganova, Аnna М; Senderovich, Anastasia I; Kondratova, Valentina N; Shelepov, Valery P; Lichtenstein, Anatoly V

    2015-12-15

    The TaqMan probes that have been long and effectively used in real-time polymerase chain reaction (PCR) may also be used in DNA melting analysis. We studied some factors affecting efficiency of the approach such as (i) number of asymmetric PCR cycles preceding DNA melting analysis, (ii) choice of fluorophores for the multiplex DNA melting analysis, and (iii) choice of sense or antisense TaqMan probes for optimal resolution of wild-type and mutant alleles. We also determined ΔTm (i.e., the temperature shift of a heteroduplex relative to the corresponding homoduplex) as a means of preliminary identification of mutation type. In experiments with serial dilution of mutant KRAS DNA with wild-type DNA, the limit of detection of mutant alleles was 1.5-3.0%. Using DNA from both tumor and formalin-fixed paraffin-embedded tissues, we demonstrated a high efficiency of TaqMan probes in mono- and multiplex mutation scanning of KRAS, NRAS (codons 12, 13, and 61), and BRAF (codon 600) genes. This cost-effective method, which can be applied to practically any mutation hot spot in the human genome, combines simplicity, ease of execution, and high sensitivity-all of the qualities required for clinical genotyping.

  13. Fully non-parametric receiver operating characteristic curve estimation for random-effects meta-analysis.

    PubMed

    Martínez-Camblor, Pablo

    2017-02-01

    Meta-analyses, broadly defined as the quantitative review and synthesis of the results of related but independent comparable studies, allow to know the state of the art of one considered topic. Since the amount of available bibliography has enhanced in almost all fields and, specifically, in biomedical research, its popularity has drastically increased during the last decades. In particular, different methodologies have been developed in order to perform meta-analytic studies of diagnostic tests for both fixed- and random-effects models. From a parametric point of view, these techniques often compute a bivariate estimation for the sensitivity and the specificity by using only one threshold per included study. Frequently, an overall receiver operating characteristic curve based on a bivariate normal distribution is also provided. In this work, the author deals with the problem of estimating an overall receiver operating characteristic curve from a fully non-parametric approach when the data come from a meta-analysis study i.e. only certain information about the diagnostic capacity is available. Both fixed- and random-effects models are considered. In addition, the proposed methodology lets to use the information of all cut-off points available (not only one of them) in the selected original studies. The performance of the method is explored through Monte Carlo simulations. The observed results suggest that the proposed estimator is better than the reference one when the reported information is related to a threshold based on the Youden index and when information for two or more points are provided. Real data illustrations are included.

  14. Impact Analysis of Embedded Delamination Location in Hybrid Curved Laminated Composite Stiffened Panel

    NASA Astrophysics Data System (ADS)

    Naini, Jeevan Kumar; P, Ramesh Babu

    2016-08-01

    Modern, aero structures are predominantly of curved construction characterized by a skin and stiffeners. The latest generation of large passenger aircraft also uses mostly composite material in their primary structure and there is trend towards the utilization of bonding of subcomponents. The presence of delamination is a major problem in composite laminated panels and so, it is of great concern to both the academic and aeronautical industrial worlds Indeed delamination can strongly affect the material strength and, sometimes, can cause their breaking up in service. A Pre-damaged configuration is loaded to study the delamination location and mode for delamination initiation and propagation. A parametric study is conducted to investigate the effect of the location of the delamination propagation when delamination is embedded inbetween plies of the skin-stiffener interface, with the cases i) delamination located at front and inbetween plies of the skin-stiffener interface ii) delamination located in middle and inbetween plies of the skin-stiffener interface iii) delamination located at the end and inbetween plies of the skin- stiffener interface. Further the influence of the location of the delamination on load carrying capacity of the panel is investigated. The effect of location of debonds on crack growth and collapse behavior is analyzed using analysis tool. An analysis tool is applied that includes an approach for predicting interlaminar damage initiation and interlaminar damage growth as well as in-plane damage mechanisms to predict the design of defect free panel.

  15. THE XMM-NEWTON/EPIC X-RAY LIGHT CURVE ANALYSIS OF WR 6

    SciTech Connect

    Ignace, R.; Gayley, K. G.; Hamann, W.-R.; Oskinova, L. M.; Huenemoerder, D. P.; Pollock, A. M. T.; McFall, M.

    2013-09-20

    We obtained four pointings of over 100 ks each of the well-studied Wolf-Rayet star WR 6 with the XMM-Newton satellite. With a first paper emphasizing the results of spectral analysis, this follow-up highlights the X-ray variability clearly detected in all four pointings. However, phased light curves fail to confirm obvious cyclic behavior on the well-established 3.766 day period widely found at longer wavelengths. The data are of such quality that we were able to conduct a search for event clustering in the arrival times of X-ray photons. However, we fail to detect any such clustering. One possibility is that X-rays are generated in a stationary shock structure. In this context we favor a corotating interaction region (CIR) and present a phenomenological model for X-rays from a CIR structure. We show that a CIR has the potential to account simultaneously for the X-ray variability and constraints provided by the spectral analysis. Ultimately, the viability of the CIR model will require both intermittent long-term X-ray monitoring of WR 6 and better physical models of CIR X-ray production at large radii in stellar winds.

  16. An interactive computer program for randomization analysis of response curves with facilities for multiple comparisons.

    PubMed

    Tan, E S; Roos, J M; Volovics, A; Van Baak, M A; Does, R J

    1992-04-01

    An interactive Fortran program, MUCRA, is presented. The program can perform randomization analysis of a completely randomized or randomized-blocks design extended to growth and response curves. A single-step Scheffé-type procedure as well as the Peritz's closed step-down procedure have been implemented which control the familywise type I error-rate. In general, MUCRA is suitable as a computer tool for a distribution-free analysis of variance with repeated measures. The use of MUCRA is demonstrated by analyzing the effects oxprenolol and atenolol have on exercise heart rate. Oxprenolol is a non-selective beta-blocker with moderate intrinsic sympathomimetic activity (ISA), given by the Oros delivery system. Atenolol is a beta 1-selective blocker without ISA. A randomized placebo-controlled crossover design was used to compare the effects of the beta 1-blockers on heart rate during a progressive maximal exercise test on a bicycle ergometer. Application of the Scheffé-type procedure showed that the two drugs significantly (alpha = .05) reduce the heart rate during the exercise test at the three prechosen times (2, 5, and 24 hr) after intake. The reduction from atenolol is more pronounced than from oxprenolol Oros at 2 and 5 hr.

  17. High-resolution melting analysis for identification of the Cryptococcus neoformans-Cryptococcus gattii complex.

    PubMed

    Gago, Sara; Zaragoza, Óscar; Cuesta, Isabel; Rodríguez-Tudela, Juan L; Cuenca-Estrella, Manuel; Buitrago, María J

    2011-10-01

    We have developed a two-step method based on high-resolution melting (HRM) that reliably identifies species from the Cryptococcus species complex (Cryptococcus neoformans var. grubii, Cryptococcus neoformans var. neoformans, and Cryptococcus gattii). Our results indicate that HRM can provide a fast protocol to identify and distinguish among the main Cryptococcus species.

  18. Accounting for wind-induced spatial heterogeneities in snow accumulation and melt using terrain analysis

    NASA Astrophysics Data System (ADS)

    Winstral, A.; Marks, D.

    2001-12-01

    In mountainous headwater basins, local topography and canopy cover strongly affect snow distribution, snowpack energy fluxes, and resultant melt rates. Wind has often been cited as the dominant control on snow accumulation in these alpine regions. Snow accumulation in the Reynolds Mountain East research area, a 0.36 km2 headwater basin in southwestern Idaho, is typical of such regions; a wind-exposed ridgeline accumulates very little snow throughout the winter while hydrologically significant drifts develop on lee slopes persisting well into the spring. In this study we established an efficient means of accounting for the spatially variable wind effects upon snow accumulation and melt in this basin. Wind speeds and effective precipitation rates were distributed based on upwind topography adjusted for vegetative cover and applied as input to ISNOBAL, a spatially distributed energy balance snowmelt model. Simulations of the accumulation and melt of the snowcover were performed for three winter seasons. In all three seasons, modeled snow distribution closely matched a time-series of snow-cover-classified aerial photographs taken during each melt season. The timing and magnitude of modeled surface water inputs also exhibited a strong correspondence to the basin hydrograph.

  19. Analysis and Preliminary Design of a Suppressive Structure for a Melt Loading Operation

    DTIC Science & Technology

    1976-05-01

    PRELIMINARY DESIGN OF A SUPPRESSIVE STRUCTURE FOR A MELT LOADING OPERATION by W. E. Baker P. S. Westine P. A. Cox E. D. Espa rza TECHNICAL...overlap is OL = (3.5 + 0.5)(.707) — 2.41 5 OL = 0.413 in. *As noted earlier, this value should be multiplied by 1.630 to be correct. All succeeding

  20. XCT analysis of the influence of melt strategies on defect population in Ti–6Al–4V components manufactured by Selective Electron Beam Melting

    SciTech Connect

    Tammas-Williams, S.; Zhao, H.; Léonard, F.; Derguti, F.; Todd, I.; Prangnell, P.B.

    2015-04-15

    Selective Electron Beam Melting (SEBM) is a promising powder bed Additive Manufacturing technique for near-net-shape manufacture of high-value titanium components. However without post-manufacture HIPing the fatigue life of SEBM parts is currently dominated by the presence of porosity. In this study, the size, volume fraction, and spatial distribution of the pores in model samples have been characterised in 3D, using X-ray Computed Tomography, and correlated to the process variables. The average volume fraction of the pores (< 0.2%) was measured to be lower than that usually observed in competing processes, such as selective laser melting, but a strong relationship was found with the different beam strategies used to contour, and infill by hatching, a part section. The majority of pores were found to be small spherical gas pores, concentrated in the infill hatched region; this was attributed to the lower energy density and less focused beam used in the infill strategy allowing less opportunity for gas bubbles to escape the melt pool. Overall, increasing the energy density or focus of the beam was found to correlate strongly to a reduction in the level of gas porosity. Rarer irregular shaped pores were mostly located in the contour region and have been attributed to a lack of fusion between powder particles. - Graphical abstract: Display Omitted - Highlights: • Vast majority of defects detected were small spherical gas pores. • Gas bubbles trapped in the powder granules expand and coalesce in the melt pool. • Pores have been shown not to be randomly distributed. • Larger and deeper melt pools give more opportunity for gas to escape. • Minor changes to melt strategy result in significant reductions in pore population.

  1. Study of iron nanoparticle melting

    NASA Astrophysics Data System (ADS)

    Fedorov, A. V.; Shulgin, A. V.; Lavruk, S. A.

    2016-10-01

    In paper melting process of iron nanoparticles was investigated with molecular dynamics method. Melting temperatures was found for particles with radius from 1.5 to 4 nm. Results match with data of other authors. Heat capacity was calculated based on investigation of caloric curves. Dependence between heat capacity and temperature for different size of nanoparticles was approximated. Heat conductivity of iron nanoparticles was calculated.

  2. SAXS Study and Thermal Analysis of Two-Stage Melt Crystallization of PEEK

    NASA Astrophysics Data System (ADS)

    Georgiev, Georgi; Dai, Patrick; Oyebode, Elizabeth; Cebe, Peggy; Capel, Malcolm

    1998-03-01

    We have been studying dual stage melt crystalization of PEEK using a treatment scheme involving annealing/crystallization at Ta1 followed by annealing/crystallization at Ta2, where either Ta1Ta2. We compare single and double stages of melt crystallization using differential scanning calorimetry (DSC) and small angle X-ray scattering (SAXS). Double stage crystallization was used to study the relative perfection of the crystals formed from the melt. The samples were heated to 375 C in a Mettler hot stage and were held there for three minutes so as to erase the crystals from previous treatments before cooling to 280 C. Crystallization occurred rapidly during cooling below 300 C. The samples were held for ten minutes at Ta1=280 C before being heated to the annealing temperature, Ta2=295 C, where they were held at for a period of time, t( t = 0, 1, 3.5, or 10 min. ),and then immediately heated to 360 C. We observe a double peak in SAXS intensity. During the isothermal periods, the intensity of the major peak at lower scattering vector, s, stays constant. A shoulder grows up on the high side of the major peak, and increases in intensity with the holding time at 280 C. During heating from below to above of the minor melting endotherm, the intensity in the high s shoulder decreases. After the sample is annealed at 295 C, the shoulder intensity is restored once again. The population scattering at higher s remains longer before it disappears in the sample treated to the second stage of melt crystallization, compare to the sample crystallized with a single stage. Research was supported by the National Aeronautics and Space Administration, Grant NAG8

  3. Modeling and regression analysis of semiochemical dose-response curves of insect antennal reception and behavior

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Dose-response curves with semiochemicals are reported in many articles in insect chemical ecology regarding neurophysiology and behavioral bioassays. Most such curves are shown in figures where the x-axis has order of magnitude increases in dosages versus responses on the y-axis represented by point...

  4. Nonlinearities and adaptation of color vision from sequential principal curves analysis.

    PubMed

    Laparra, Valero; Jiménez, Sandra; Camps-Valls, Gustavo; Malo, Jesús

    2012-10-01

    Mechanisms of human color vision are characterized by two phenomenological aspects: the system is nonlinear and adaptive to changing environments. Conventional attempts to derive these features from statistics use separate arguments for each aspect. The few statistical explanations that do consider both phenomena simultaneously follow parametric formulations based on empirical models. Therefore, it may be argued that the behavior does not come directly from the color statistics but from the convenient functional form adopted. In addition, many times the whole statistical analysis is based on simplified databases that disregard relevant physical effects in the input signal, as, for instance, by assuming flat Lambertian surfaces. In this work, we address the simultaneous statistical explanation of the nonlinear behavior of achromatic and chromatic mechanisms in a fixed adaptation state and the change of such behavior (i.e., adaptation) under the change of observation conditions. Both phenomena emerge directly from the samples through a single data-driven method: the sequential principal curves analysis (SPCA) with local metric. SPCA is a new manifold learning technique to derive a set of sensors adapted to the manifold using different optimality criteria. Here sequential refers to the fact that sensors (curvilinear dimensions) are designed one after the other, and not to the particular (eventually iterative) method to draw a single principal curve. Moreover, in order to reproduce the empirical adaptation reported under D65 and A illuminations, a new database of colorimetrically calibrated images of natural objects under these illuminants was gathered, thus overcoming the limitations of available databases. The results obtained by applying SPCA show that the psychophysical behavior on color discrimination thresholds, discount of the illuminant, and corresponding pairs in asymmetric color matching emerge directly from realistic data regularities, assuming no a priori

  5. An analysis of watershed hydrological double mass curve based on elasticity index

    NASA Astrophysics Data System (ADS)

    Liu, Wenzhao; Ning, Tingting; Lin, Wen; Cheng, Liping; Han, Xiaoyang

    2016-04-01

    The method of double mass curve (DMC) is often used in the analysis of the consistency of hydro-meteorological factors and their inter-annual variations. The trend and slope of DMC are the focus of general concern. By taking the DMC of annual precipitation-runoff in a watershed as an example, this paper analyzed the characteristics of DMC variations by means of the elasticity index obtained by the curve slope divided by the ratio of accumulated runoff to accumulated precipitation at corresponding location. Using a year as a time step, the index was further simplified to be the ratio of annual runoff coefficient to the runoff coefficient averaged over the period from starting year to computing year. An elasticity index greater than, less than, or equal to one indicated rising, decline, or stability of average annual runoff coefficient, respectively. Variation trend of elasticity index was analyzed to extract the information on the years with significant change and then, dominant factors and their impacts could be enquired further. The Jinghe River is located in the middle reaches of the Yellow River, being the largest tributary of the Weihe River. The elasticity index was used to analyze the DMC of annual precipitation-runoff on the scale of water year for the Jinghe River watershed from 1961 to 2012 and the two years of 1971 and 1997 were first chosen as the years showing abrupt changes. The elasticity indices in three periods separated by the two years in the past 50 years averaged 1.08, 0.89 and 0.64 and annual runoff coefficients, 0.08, 0.07 and 0.05, respectively. The human activities disturbing underlying surface were found to be the important factor responsible for the remarkable decline of runoff coefficient. The large-scale comprehensive control of soil erosion and the adjustment of landuse structure had made some achievements in the recent twenty years. However, their disturbing effects on underlying surface interacted with the impacts of climate change

  6. BEER ANALYSIS OF KEPLER AND CoRoT LIGHT CURVES. II. EVIDENCE FOR SUPERROTATION IN THE PHASE CURVES OF THREE KEPLER HOT JUPITERS

    SciTech Connect

    Faigler, S.; Mazeh, T.

    2015-02-10

    We analyzed the Kepler light curves of four transiting hot Jupiter systems—KOI-13, HAT-P-7, TrES-2, and Kepler-76, which show BEaming, Ellipsoidal, and Reflection (BEER) phase modulations. The mass of the four planets can be estimated from either the beaming or the ellipsoidal amplitude, given the mass and radius of their parent stars. For KOI-13, HAT-P-7, and Kepler-76 we find that the beaming-based planetary mass estimate is larger than the mass estimated from the ellipsoidal amplitude, consistent with previous studies. This apparent discrepancy may be explained by equatorial superrotation of the planet atmosphere, which induces an angle shift of the planet reflection/emission phase modulation, as was suggested for Kepler-76 in the first paper of this series. We propose a modified BEER model that supports superrotation, assuming either a Lambertian or geometric reflection/emission phase function, and provides a photometry-consistent estimate of the planetary mass. Our analysis shows that for Kepler-76 and HAT-P-7, the Lambertian superrotation BEER model is highly preferable over an unshifted null model, while for KOI-13 it is preferable only at a 1.4σ level. For TrES-2 we do not find such preference. For all four systems the Lambertian superrotation model mass estimates are in excellent agreement with the planetary masses derived from, or constrained by, radial velocity measurements. This makes the Lambertian superrotation BEER model a viable tool for estimating the masses of hot Jupiters from photometry alone. We conclude that hot Jupiter superrotation may be a common phenomenon that can be detected in the visual light curves of Kepler.

  7. BEER Analysis of Kepler and CoRoT Light Curves. II. Evidence for Superrotation in the Phase Curves of Three Kepler Hot Jupiters

    NASA Astrophysics Data System (ADS)

    Faigler, S.; Mazeh, T.

    2015-02-01

    We analyzed the Kepler light curves of four transiting hot Jupiter systems—KOI-13, HAT-P-7, TrES-2, and Kepler-76, which show BEaming, Ellipsoidal, and Reflection (BEER) phase modulations. The mass of the four planets can be estimated from either the beaming or the ellipsoidal amplitude, given the mass and radius of their parent stars. For KOI-13, HAT-P-7, and Kepler-76 we find that the beaming-based planetary mass estimate is larger than the mass estimated from the ellipsoidal amplitude, consistent with previous studies. This apparent discrepancy may be explained by equatorial superrotation of the planet atmosphere, which induces an angle shift of the planet reflection/emission phase modulation, as was suggested for Kepler-76 in the first paper of this series. We propose a modified BEER model that supports superrotation, assuming either a Lambertian or geometric reflection/emission phase function, and provides a photometry-consistent estimate of the planetary mass. Our analysis shows that for Kepler-76 and HAT-P-7, the Lambertian superrotation BEER model is highly preferable over an unshifted null model, while for KOI-13 it is preferable only at a 1.4σ level. For TrES-2 we do not find such preference. For all four systems the Lambertian superrotation model mass estimates are in excellent agreement with the planetary masses derived from, or constrained by, radial velocity measurements. This makes the Lambertian superrotation BEER model a viable tool for estimating the masses of hot Jupiters from photometry alone. We conclude that hot Jupiter superrotation may be a common phenomenon that can be detected in the visual light curves of Kepler.

  8. Periodicity Analysis of X-ray Light Curves of SS 433

    NASA Astrophysics Data System (ADS)

    Jun-yi, Wang; Xiang-long, Lu; Qiu-wen, Zhao; Dian-qiao, Dong; Bao-qiang, Lao; Yang, Lu; Yan-heng, Wei; Xiao-cong, Wu; Tao, An

    2017-01-01

    SS 433 is sofar the unique X-ray binary that has the simultaneously detected orbital period, super-orbital period, and nutation period, as well as a bidirectional spiral jet. The study on its X-ray light variability is helpful for understanding the dynamic process of the system, and the correlations between the different wavebands. In this paper, two time-series analysis techniques, i.e., the Lomb-Scargle periodogram and weighted wavelet Z-transform, are employed to search for the periods in the Swift/BAT (Burst Alert Telescope) (15-50 keV) and RXTE/ASM (Rose X-ray Timing Explorer/All Sky Monitor) (1.5-3, 3- 4, and 5-12 keV) light curves of SS 433, and the Monte Carlo simulation is performed for the obtained periodical components. For the 15-50 keV energy band, five significant periodical components are detected, which are P1(∼6.29 d), P2 (∼6.54 d), P3 (∼13.08 d), P4 (∼81.50 d), and P5 (∼162.30 d). For the 3-5 and 5-12 keV energy bands, the periodical components P3 (∼13 d) and P5 (∼162 d) are detected in both energy bands. However, for the 1.5-3 keV energy band, no significant periodic signal is detected. P5 is the strongest periodic signal in the power spectrum for all the energy bands of 3-5, 5-12, and 15-50 keV, and it is consistent with the previous result obtained from the study of optical light curves. Furthermore, in combination with the radio spiral jet of SS 433, it is suggested that the X-ray and optical variability of P5 (∼162 d) is probably related to the precession of its relativistic jet. The high correlation between the X-ray and optical light curves may also imply that the X-ray and optical radiations are of the same physical origin. P3 shows a good agreement with the orbital period (∼13.07 d) obtained by the previous study, and P2 and P4 are respectively the high-frequency harmonics of P3 and P5. P1 is detected only in the power spectrum of the 15-50 keV energy band, and it is consistent with the nutation period of the system. As

  9. The role of Soil Water Retention Curve in slope stability analysis in unsaturated and heterogeneous soils.

    NASA Astrophysics Data System (ADS)

    Antinoro, Chiara; Arnone, Elisa; Noto, Leonardo V.

    2015-04-01

    The mechanisms of rainwater infiltration causing slope instability had been analyzed and reviewed in many scientific works. Rainwater infiltration into unsaturated soil increases the degree of saturation, hence affecting the shear strength properties and thus the probability of slope failure. It has been widely proved that the shear strength properties change with the soil water suction in unsaturated soils; therefore, the accuracy to predict the relationship between soil water content and soil water suction, parameterized by the soil-water characteristic curve, has significant effects on the slope stability analysis. The aim of this study is to investigate how the characterization of SWRC of differently structured unsaturated soils affects the slope stability on a simple infinite slope. In particular, the unimodal and bimodal distributions of the soil pore size were compared. Samples of 40 soils, highly different in terms of structure and texture, were collected and used to calibrate two bimodal SWRCs, i.e. Ross and Smettem (1993) and Dexter et al., (2008). The traditional unimodal van Genuchten (1980) model was also applied for comparison. Slope stability analysis was conducted in terms of Factor of Safety (FS) by applying the infinite slope model for unsaturated soils. In the used formulation, the contribution of the suction effect is tuned by a parameter 'chi' in a rate proportional to the saturation conditions. Different parameterizations of this term were also compared and analyzed. Results indicated that all three SWRC models showed good overall performance in fitting the sperimental SWRCs. Both the RS and DE models described adequately the water retention data for soils with a bimodal behavior confirmed from the analysis of pore size distribution, but the best performance was obtained by DE model confirmed. In terms of FS, the tree models showed very similar results as soil moisture approached to the saturated condition; however, within the residual zone

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

    PubMed

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

    2015-04-01

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

  11. Selecting a linear mixed model for longitudinal data: repeated measures analysis of variance, covariance pattern model, and growth curve approaches.

    PubMed

    Liu, Siwei; Rovine, Michael J; Molenaar, Peter C M

    2012-03-01

    With increasing popularity, growth curve modeling is more and more often considered as the 1st choice for analyzing longitudinal data. Although the growth curve approach is often a good choice, other modeling strategies may more directly answer questions of interest. It is common to see researchers fit growth curve models without considering alterative modeling strategies. In this article we compare 3 approaches for analyzing longitudinal data: repeated measures analysis of variance, covariance pattern models, and growth curve models. As all are members of the general linear mixed model family, they represent somewhat different assumptions about the way individuals change. These assumptions result in different patterns of covariation among the residuals around the fixed effects. In this article, we first indicate the kinds of data that are appropriately modeled by each and use real data examples to demonstrate possible problems associated with the blanket selection of the growth curve model. We then present a simulation that indicates the utility of Akaike information criterion and Bayesian information criterion in the selection of a proper residual covariance structure. The results cast doubt on the popular practice of automatically using growth curve modeling for longitudinal data without comparing the fit of different models. Finally, we provide some practical advice for assessing mean changes in the presence of correlated data.

  12. BEER analysis of Kepler and CoRoT light curves. III. Spectroscopic confirmation of seventy new beaming binaries discovered in CoRoT light curves

    NASA Astrophysics Data System (ADS)

    Tal-Or, L.; Faigler, S.; Mazeh, T.

    2015-08-01

    Context. The BEER algorithm searches stellar light curves for the BEaming, Ellipsoidal, and Reflection photometric modulations that are caused by a short-period companion. These three effects are typically of very low amplitude and can mainly be detected in light curves from space-based photometers. Unlike eclipsing binaries, these effects are not limited to edge-on inclinations. Aims: Applying the algorithm to wide-field photometric surveys such as CoRoT and Kepler offers an opportunity to better understand the statistical properties of short-period binaries. It also widens the window for detecting intrinsically rare systems, such as short-period brown-dwarf and massive-planetary companions to main-sequence stars. Methods: Applying the search to the first five long-run center CoRoT fields, we identified 481 non-eclipsing candidates with periodic flux amplitudes of 0.5-87 mmag. Optimizing the Anglo-Australian-Telescope pointing coordinates and the AAOmega fiber-allocations with dedicated softwares, we acquired six spectra for 231 candidates and seven spectra for another 50 candidates in a seven-night campaign. Analysis of the red-arm AAOmega spectra, which covered the range of 8342-8842 Å, yielded a radial-velocity precision of ~1 km s-1. Spectra containing lines of more than one star were analyzed with the two-dimensional correlation algorithm TODCOR. Results: The measured radial velocities confirmed the binarity of seventy of the BEER candidates - 45 single-line binaries, 18 double-line binaries, and 7 diluted binaries. We show that red giants introduce a major source of false candidates and demonstrate a way to improve BEER's performance in extracting higher fidelity samples from future searches of CoRoT light curves. The periods of the confirmed binaries span a range of 0.3-10 days and show a rise in the number of binaries per ΔlogP toward longer periods. The estimated mass ratios of the double-line binaries and the mass ratios assigned to the single

  13. Comparison of five digital scintigraphic display modes. An ROC curve analysis of detection performance.

    PubMed

    Goin, J E; Preston, D F; Gallagher, J H; Wegst, A V

    1983-01-01

    In the last decade diagnostic imaging departments, even those of moderate size, have experienced unprecedented growth. Much of this expansion can be attributed directly to technological developments, including systems for the acquisition of diagnostic images in digital format. In modern imaging departments, digital-based systems are quite common and are found across the specialities of nuclear medicine, ultrasound, transmission and emission computed tomography, and angiography. Nuclear magnetic resonance is the newest digital-based modality, and it appears destined to achieve its place in the diagnostic arsenal. These systems all have one trait in common, which is the topic of this paper. They offer the potential of increasing diagnostic accuracy by varying the methods used to process and display the acquired imaged data. We present the results of a nuclear medicine study designed to compare observer performance among five digital scintigraphic display modes. The observer's task was to detect artificially created lesions in brain scintigrams. Each mode is defined by a combination of an image processing function and a method of display. Using 40 trained observers, a receiver operating characteristic curve analysis was performed. The results support the use of color displays in nuclear medicine.

  14. Quantitative analysis by laser-induced breakdown spectroscopy based on generalized curves of growth

    NASA Astrophysics Data System (ADS)

    Aragón, C.; Aguilera, J. A.

    2015-08-01

    A method for quantitative elemental analysis by laser-induced breakdown spectroscopy (LIBS) is proposed. The method (Cσ-LIBS) is based on Cσ graphs, generalized curves of growth which allow including several lines of various elements at different concentrations. A so-called homogeneous double (HD) model of the laser-induced plasma is used, defined by an integration over a single-region of the radiative transfer equation, combined with a separated treatment for neutral atoms (z = 0) and singly-charged ions (z = 1) in Cσ graphs and characteristic parameters. The procedure includes a criterion, based on a model limit, for eliminating data which, due to a high line intensity or concentration, are not well described by the HD model. An initial procedure provides a set of parameters (βA)z, (ηNl)z, Tz and Nez (z = 0, 1) which characterize the plasma and the LIBS system. After characterization, two different analytical procedures, resulting in relative and absolute concentrations, may be applied. To test the method, fused glass samples prepared from certified slags and pure compounds are analyzed. We determine concentrations of Ca, Mn, Mg, V, Ti, Si and Al relative to Fe in three samples prepared from slags, and absolute concentrations of Fe, Ca and Mn in three samples prepared from Fe2O3, CaCO3 and Mn2O3. The accuracy obtained is 3.2% on the average for relative concentrations and 9.2% for absolute concentrations.

  15. An explicit expression for determining cometabolism kinetics using progress curve analysis.

    PubMed

    Goudar, Chetan T

    2012-05-31

    We present an explicit expression for describing the kinetics of cometabolic biotransformation of environmental pollutants. This expression is based on the Lambert W function and explicitly relates the substrate concentration, S, to time, t, the two experimentally measured variables. This explicit relationship simplifies kinetic parameter estimation as differential equation solution and iterative estimation of the substrate concentration are eliminated. The applicability of this new expression for nonlinear kinetic parameter estimation was first demonstrated using noise containing synthetic data where final estimates of the kinetic parameters were very close to their actual values. Subsequently 1.1.1-trichloroethane degradation data at initial concentrations of 750 and 375 μM were described using the explicit expression resulting in r and K(s) estimates of 0.26 μM/mg d and 28.08 μM and 0.30 μM/mg d and 28.70 μM, respectively, very similar to 0.276 μM/mg d and 31.2 μM, respectively, that were reported in the original study. The new explicit expression presented in this study simplifies estimation of cometabolic kinetic parameters and can be easily used across all computational platforms thereby providing an attractive alternative for progress curve analysis.

  16. The application of latent curve analysis to testing developmental theories in intervention research.

    PubMed

    Curran, P J; Muthén, B O

    1999-08-01

    The effectiveness of a prevention or intervention program has traditionally been assessed using time-specific comparisons of mean levels between the treatment and the control groups. However, many times the behavior targeted by the intervention is naturally developing over time, and the goal of the treatment is to alter this natural or normative developmental trajectory. Examining time-specific mean levels can be both limiting and potentially misleading when the behavior of interest is developing systematically over time. It is argued here that there are both theoretical and statistical advantages associated with recasting intervention treatment effects in terms of normative and altered developmental trajectories. The recently developed technique of latent curve (LC) analysis is reviewed and extended to a true experimental design setting in which subjects are randomly assigned to a treatment intervention or a control condition. LC models are applied to both artificially generated and real intervention data sets to evaluate the efficacy of an intervention program. Not only do the LC models provide a more comprehensive understanding of the treatment and control group developmental processes compared to more traditional fixed-effects models, but LC models have greater statistical power to detect a given treatment effect. Finally, the LC models are modified to allow for the computation of specific power estimates under a variety of conditions and assumptions that can provide much needed information for the planning and design of more powerful but cost-efficient intervention programs for the future.

  17. Effect of intrinsic motivation on affective responses during and after exercise: latent curve model analysis.

    PubMed

    Shin, Myoungjin; Kim, Inwoo; Kwon, Sungho

    2014-12-01

    Understanding the relationship between affect and exercise is helpful in predicting human behavior with respect to exercise participation. The goals of the present study were to investigate individual differences in affective response during and after exercise and to identify the role of intrinsic motivation in affective changes. 30 active male college students (M age = 21.4 yr.) who regularly participated in sports activities volunteered to answer a questionnaire measuring intrinsic motivation toward running activities and performed a 20-min. straight running protocol at heavy intensity (about 70% of VO2max). Participants' affective responses were measured every 5 min. from the beginning of the run to 10 min. after completing the run. Latent curve model analysis indicated that individuals experienced different changes in affective state during exercise, moderated by intrinsic motivation. Higher intrinsic motivation was associated with more positive affect during exercise. There were no significant individual differences in the positive tendency of the participants' affective responses after exercise over time. Intrinsic motivation seems to facilitate positive feelings during exercise and encourages participation in exercise.

  18. Ecological inference on bacterial succession using curve-based community fingerprint data analysis, demonstrated with rhizoremediation experiment.

    PubMed

    Mikkonen, Anu; Lappi, Kaisa; Wallenius, Kaisa; Lindström, Kristina; Suominen, Leena

    2011-12-01

    Nucleic acid-based community fingerprinting methods are valuable tools in microbial ecology, as they offer rapid and robust means to compare large series of replicates and references. To avoid the time-consuming and potentially subjective procedures of peak-based examination, we assessed the possibility to apply direct curve-based data analysis on community fingerprints produced with bacterial length heterogeneity PCR (LH-PCR). The dataset comprised 180 profiles from a 21-week rhizoremediation greenhouse experiment with three treatments and 10 sampling times. Curve-based analysis quantified the progressive effect of the plant (Galega orientalis) and the reversible effect of the contaminant (fuel oil) on bacterial succession. The major observed community shifts were assigned to changes in plant biomass and contamination level by canonical correlation analysis. A novel method to extract relative abundance data from the fingerprint curves for Shannon diversity index revealed contamination to reversibly decrease community complexity. By cloning and sequencing the fragment lengths, recognized to change in time in the averaged LH-PCR profiles, we identified Aquabacterium (Betaproteobacteria) as the putative r-strategic fuel oil degrader, and K-strategic Alphaproteobacteria growing in abundance later in succession. Curve-based community fingerprint analysis can be used for rapid data prescreening or as a robust alternative for the more heavily parameterized peak-based analysis.

  19. High-resolution melting analysis: a new molecular approach for the early detection of Diplodia pinea in Austrian pine.

    PubMed

    Luchi, Nicola; Pratesi, Nicola; Simi, Lisa; Pazzagli, Mario; Capretti, Paolo; Scala, Aniello; Slippers, Bernard; Pinzani, Pamela

    2011-08-01

    The differentiation of Diplodia pinea from closely related species, such as Diplodia scrobiculata and Diplodia seriata, and its detection in plant tissue, represented a critical issue for a long time. Molecular screening tools have recently been developed to address this topic. In this study we applied one of the most sensitive and rapid diagnostic screening method so far developed, called High-Resolution Melting Analysis (HRMA), to detect D. pinea in Austrian pine (Pinus nigra). HRMA exploits differences in the melting behaviour of PCR products to rapidly identify DNA sequence variants without the need for cumbersome post-PCR methods. We developed a HRMA method to detect specific fungal sequences in the mitochondrial small subunit ribosome gene (mt SSU rDNA). The reliability of this technique was firstly assessed on DNA extracted from pure cultures of D. pinea and closely related species. Amplicon differences were screened by HRMA and the results confirmed by direct DNA sequencing. Subsequently, HRMA was tested on DNA from symptomatic and symptomless pine shoots, and the presence of the fungus was also confirmed by both conventional and molecular quantitative approaches. The HRMA allowed the distinction of D. pinea from closely related species, showing specific melting profiles for the each pathogen. This new molecular technique, here tested in a plant-fungus pathosystem for the first time, was very reliable in both symptomatic and symptomless shoots. HRMA is therefore a highly effective and accurate technique that permits the rapid screening of pathogens in the host.

  20. Rapid Detection and Identification of Nontuberculous Mycobacterial Pathogens in Fish by Using High-Resolution Melting Analysis

    PubMed Central

    Phung, Thu Nguyet; Caruso, Domenico; Godreuil, Sylvain; Keck, Nicolas; Vallaeys, Tatiana

    2013-01-01

    Mycobacterial infections in fish are commonly referred to as piscine mycobacteriosis, irrespectively of the specific identity of the causal organism. They usually cause a chronic disease and sometimes may result in high mortalities and severe economic losses. Nearly 20 species of Mycobacterium have been reported to infect fish. Among them, Mycobacterium marinum, M. fortuitum, and M. chelonae are generally considered the major agents responsible for fish mycobacteriosis. As no quick and inexpensive diagnostic test exists, we tested the potential of high-resolution melting analysis (HRMA) to rapidly identify and differentiate several Mycobacterium species involved in fish infections. By analyzing both the melting temperature and melting profile of the 16S-23S rRNA internal transcribed spacer (ITS), we were able to discriminate 12 different species simultaneously. Sensitivity tests conducted on purified M. marinum and M. fortuitum DNA revealed a limit of detection of 10 genome equivalents per reaction. The primers used in this procedure did not lead to any amplification signal with 16 control non-Mycobacterium species, thereby demonstrating their specificity for the genus Mycobacterium. PMID:24123734

  1. Performance curves of medical researchers during their career: analysis of scientific production from a retrospective cohort

    PubMed Central

    Duclos, Antoine; Herquelot, Eléonore; Polazzi, Stéphanie; Malbezin, Muriel; Claris, Olivier

    2017-01-01

    Objectives To establish the pattern of change in individual scientific production over the career of medical researchers. Design Retrospective cohort based on prospectively collected data in a hospital information system. Setting Multicentre university hospital in France. Participants Two distinct populations of 1835 researchers (full professors vs non-academic physicians) having produced 44 723 publications between 1995 and 2014. Main outcome measures Annual number of publications referenced in Medline/PubMed with a sensitivity analysis based on publications as first/last author and in high impact journals. The individual volume of publications was modelled by age using generalised estimating equations adjusted for birth cohort, biomedical discipline and academic position of researchers. Results Averaged over the whole career, the annual number of publications was 5.28 (95% CI 4.90 to 5.69) among professors compared to 0.82 (95% CI 0.76 to 0.89) among non-academic physicians (p<0.0001). The performance curve of professors evolved in three successive phases, including an initiation phase with a sharp increase in scientific production between 25 and 35 years (adjusted incidence rate ratio 102.20, 95% CI 60.99 to 171.30), a maturation phase with a slower increase from 35 to 50 years (2.10, 95% CI 1.75 to 2.51) until a stabilisation phase with constant production followed by a potential decline at the end of career (0.90, 95% CI 0.77 to 1.06). The non-academic physicians experienced a slower pace of learning curve at the beginning of their careers (42.38, 95% CI 25.37 to 70.81) followed by a smaller increase in the annual number of publications (1.29, 95% CI 1.11 to 1.51). Conclusions Compared to full professors, non-academic physicians had a poor capacity to publish, indicating a low productivity when medical doctors have limited time or little interest in undertaking research. This finding highlights the potential for rethinking the missions of medical doctors

  2. Phase-Change Characteristic Analysis of Partially Melted Sodium Acetate Trihydrate Using DSC

    NASA Astrophysics Data System (ADS)

    Jin, Xing; Medina, Mario A.; Zhang, Xiaosong; Zhang, Shuanglong

    2014-01-01

    Sodium acetate trihydrate (SAT), which is a kind of phase-change material, offers high potential for application in thermal energy storage. However, SAT has a natural tendency to supercool during its solidification process. Adding nucleating agents has been suggested as a possible solution. In this paper, the phase-change characteristics of the partially melted SAT were analyzed using a differential scanning calorimeter (DSC). A phenomenon related to SAT undergoing phase change was discovered and analyzed. The results showed that if SAT were cooled when it was partially melted, it would release heat and quickly solidify without adding any nucleating agents. Therefore, if the temperature range of SAT was controlled properly, supercooling could be significantly prevented.

  3. 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.

  4. Phase-Specific Raman Analysis of n-Alkane Melting by Moving-Window Two-Dimensional Correlation Spectroscopy.

    PubMed

    Jin, Ying; Kotula, Anthony P; Hight Walker, Angela R; Migler, Kalman B; Lee, Young Jong

    2016-11-01

    We use moving-window two-dimensional correlation spectroscopy (MW-2DCOS) for phase-specific Raman analysis of the n-alkane (C21H44) during melting from the crystalline solid phase to the intermediate rotator phase and to the amorphous molten phase. In MW-2DCOS, individual peak-to-peak correlation analysis within a small subset of spectra provides both temperature-resolved and spectrally disentangled Raman assignments conducive to understanding phase-specific molecular interactions and chain configurations. We demonstrate that autocorrelation MW-2DCOS can determine the phase transition temperatures with a higher resolving power than commonly-used analysis methods including individual peak intensity analysis or principal component analysis. Besides the enhanced temperature resolving power, we demonstrate that asynchronous 2DCOS near the orthorhombic-to-rotator transition temperature can spectrally resolve the two overlapping peaks embedded in the Raman CH2 twisting band in the orthorhombic phase, which had been only predicted but not observed due to thermal broadening near the melting temperature.

  5. Specimen analysis of Skylab, M553 experiment, flight specimens, phase C.. [on metals melting containerless solidification

    NASA Technical Reports Server (NTRS)

    Larson, D. J., Jr.

    1974-01-01

    Skylab 2 flight samples were analyzed to study containerless solidification and the effects of weightlessness on the process. A record of solute redistribution processes and of solidification terracing is reported. The solute redistribution process was highly localized, and low index, crystallographic system were suggested. Samples demonstrated that under reduced pressure and gravity conditions the anticipated solid/liquid solidification process was perturbed and superseded by solid/liquid/gas reactions during melting and solidification.

  6. Re-Analysis of the Solar Phase Curves of the Icy Galilean Satellites

    NASA Technical Reports Server (NTRS)

    Domingue, Deborah; Verbiscer, Anne

    1997-01-01

    Re-analysis of the solar phase curves of the icy Galilean satellites demonstrates that the quantitative results are dependent on the single particle scattering function incorporated into the photometric model; however, the qualitative properties are independent. The results presented here show that the general physical characteristics predicted by a Hapke model (B. Hapke, 1986, Icarus 67, 264-280) incorporating a two parameter double Henyey-Greenstein scattering function are similar to the predictions given by the same model incorporating a three parameter double Henyey-Greenstein scattering function as long as the data set being modeled has adequate coverage in phase angle. Conflicting results occur when the large phase angle coverage is inadequate. Analysis of the role of isotropic versus anisotropic multiple scattering shows that for surfaces as bright as Europa the two models predict very similar results over phase angles covered by the data. Differences arise only at those phase angles for which there are no data. The single particle scattering behavior between the leading and trailing hemispheres of Europa and Ganymede is commensurate with magnetospheric alterations of their surfaces. Ion bombardment will produce more forward scattering single scattering functions due to annealing of potential scattering centers within regolith particles (N. J. Sack et al., 1992, Icarus 100, 534-540). Both leading and trailing hemispheres of Europa are consistent with a high porosity model and commensurate with a frost surface. There are no strong differences in predicted porosity between the two hemispheres of Callisto, both are consistent with model porosities midway between that deduced for Europa and the Moon. Surface roughness model estimates predict that surface roughness increases with satellite distance from Jupiter, with lunar surface roughness values falling midway between those measured for Ganymede and Callisto. There is no obvious variation in predicted surface

  7. Development of synthetic velocity - depth damage curves using a Weighted Monte Carlo method and Logistic Regression analysis

    NASA Astrophysics Data System (ADS)

    Vozinaki, Anthi Eirini K.; Karatzas, George P.; Sibetheros, Ioannis A.; Varouchakis, Emmanouil A.

    2014-05-01

    Damage curves are the most significant component of the flood loss estimation models. Their development is quite complex. Two types of damage curves exist, historical and synthetic curves. Historical curves are developed from historical loss data from actual flood events. However, due to the scarcity of historical data, synthetic damage curves can be alternatively developed. Synthetic curves rely on the analysis of expected damage under certain hypothetical flooding conditions. A synthetic approach was developed and presented in this work for the development of damage curves, which are subsequently used as the basic input to a flood loss estimation model. A questionnaire-based survey took place among practicing and research agronomists, in order to generate rural loss data based on the responders' loss estimates, for several flood condition scenarios. In addition, a similar questionnaire-based survey took place among building experts, i.e. civil engineers and architects, in order to generate loss data for the urban sector. By answering the questionnaire, the experts were in essence expressing their opinion on how damage to various crop types or building types is related to a range of values of flood inundation parameters, such as floodwater depth and velocity. However, the loss data compiled from the completed questionnaires were not sufficient for the construction of workable damage curves; to overcome this problem, a Weighted Monte Carlo method was implemented, in order to generate extra synthetic datasets with statistical properties identical to those of the questionnaire-based data. The data generated by the Weighted Monte Carlo method were processed via Logistic Regression techniques in order to develop accurate logistic damage curves for the rural and the urban sectors. A Python-based code was developed, which combines the Weighted Monte Carlo method and the Logistic Regression analysis into a single code (WMCLR Python code). Each WMCLR code execution

  8. The analysis of the withdrawal force curve of the wetting curve using 63Sn-37Pb and 96.5Sn-3.5Ag eutectic solders

    NASA Astrophysics Data System (ADS)

    Park, Jae Yong; Kang, Choon Sik; Jung, Jae Pil

    1999-11-01

    To analyze the withdrawal force curve in the wetting balance curve, wetting balance tests using the 63Sn-37Pb and 96.5Sn-3.6Ag eutectic solders were conducted by varying the immersion speed, sample perimeter, and solder temperature. The mechanism of the withdrawal force curve was reviewed and a new method for calculating the surface tension of solders using the withdrawal force curve was introduced. The results showed that the maximum point of the withdrawal force curve is generated when the sliding solder meets the bottom corners of a sample and the contact angle is reduced to zero. The maximum withdrawal force subtracted by end force can be expressed using force balance equation as F=pγ. Therefore, the surface tension of the solder can be calculated by dividing the maximum withdrawal force by the sample parameter.

  9. Video meteor light curve analysis of Orionids and Geminids and developing a method for obtaining the absolute light curves of shower meteors from the single station data

    NASA Astrophysics Data System (ADS)

    Grašić, L.; Milanović, N.; Pavlović, D.

    2016-01-01

    We developed a method for obtaining the absolute light curves of the shower meteors from single station video data. We found that even though the height of a meteor atmospheric trajectory obtained by using this method may have a large error, the absolute light curve shape is preserved. We used our method to calculate the F parameters of the Orionid and Geminid light curves. The light curves were obtained from the single station video data by the instrument with a limiting sensitivity of 3.5m. We found that for our sample of the light curves the zenith distance of meteor radiant does not affect the F parameter for either of the two showers. The value of F parameter of the Orionids obtained in this paper matches the values obtained by other authors, whilst for the Geminids it is significantly different.

  10. Mixed Waste Treatment Cost Analysis for a Range of GeoMelt Vitrification Process Configurations

    SciTech Connect

    Thompson, L. E.

    2002-02-27

    GeoMelt is a batch vitrification process used for contaminated site remediation and waste treatment. GeoMelt can be applied in several different configurations ranging from deep subsurface in situ treatment to aboveground batch plants. The process has been successfully used to treat a wide range of contaminated wastes and debris including: mixed low-level radioactive wastes; mixed transuranic wastes; polychlorinated biphenyls; pesticides; dioxins; and a range of heavy metals. Hypothetical cost estimates for the treatment of mixed low-level radioactive waste were prepared for the GeoMelt subsurface planar and in-container vitrification methods. The subsurface planar method involves in situ treatment and the in-container vitrification method involves treatment in an aboveground batch plant. The projected costs for the subsurface planar method range from $355-$461 per ton. These costs equate to 18-20 cents per pound. The projected cost for the in-container method is $1585 per ton. This cost equates to 80 cents per pound. These treatment costs are ten or more times lower than the treatment costs for alternative mixed waste treatment technologies according to a 1996 study by the US Department of Energy.

  11. Melt Inclusion Analysis of RBT 04262 with Relationship to Shergottites and Mars Surface Compositions

    NASA Technical Reports Server (NTRS)

    Potter, S. A.; Brandon, A. D.; Peslier, A. H.

    2015-01-01

    Martian meteorite RBT 04262 is in the shergottite class. It displays the two lithologies typically found in "lherzolitic shergottites": one with a poikilitic texture of large pyroxene enclosing olivine and another with non-poikilitic texture. In the case of RBT 04262, the latter strongly ressembles an olivine- phyric shergottite which led the initial classification of this meteorite in that class. RBT 04262 has been studied with regards to its petrology, geochemistry and cosmic ray exposure and belongs to the enriched oxidized end-member of the shergottites. Studies on RBT 04262 have primarily focused on the bulk rock composition or each of the lithologies independently. To further elucidate RBT 04262's petrology and use it to better understand Martian geologic history, an in-depth study of its melt inclusions (MI) is being conducted. The MI chosen for this study are found within olivine grains. MI are thought to be trapped melts of the crystallizing magma preserved by the encapsulating olivine and offer snapshots of the composition of the magma as it evolves. Some MI, in the most Mg-rich part of the olivine of olivine-pyric shergottites, may even be representative of the meteorite parent melt.

  12. [A mathematical analysis of strain-gauge curves in the diagnosis of deep venous thrombosis].

    PubMed

    Vega Gómez, M E; Ley Pozo, J; Aldama Figueroa, A; Alvarez Sánchez, J A; Charles-Edouard Otrante, D; Fernández Boloña, A; Gutierrez Jiménez, O

    1991-01-01

    The plethysmographic strain gauge venous outflow curves were studied by means of an exponential function. The parameters analyzed made possible the establishment of differences between patients with and without DVT.

  13. Enhancing the Psychological Well-Being of Elderly Individuals through Tai Chi Exercise: A Latent Growth Curve Analysis.

    ERIC Educational Resources Information Center

    Li, Fuzhong; Duncan, Terry E.; Duncan, Susan C.; McAuley, Edward; Chaumeton, Nigel R.; Harmer, Peter

    2001-01-01

    Examined whether a Tai Chi exercise program enhanced the psychological well-being of 98 elderly individuals. Analyzed repeated measures data about participants using latent growth curve analysis. Results indicate the beneficial effects of participation in the Tai Chi program. Discusses implications related to the exercise-psychological health…

  14. Development of a viability standard curve for microencapsulated probiotic bacteria using confocal microscopy and image analysis software.

    PubMed

    Moore, Sarah; Kailasapathy, Kasipathy; Phillips, Michael; Jones, Mark R

    2015-07-01

    Microencapsulation is proposed to protect probiotic strains from food processing procedures and to maintain probiotic viability. Little research has described the in situ viability of microencapsulated probiotics. This study successfully developed a real-time viability standard curve for microencapsulated bacteria using confocal microscopy, fluorescent dyes and image analysis software.

  15. Self-Esteem Trajectories among Ethnic Minority Adolescents: A Growth Curve Analysis of the Patterns and Predictors of Change

    ERIC Educational Resources Information Center

    Greene, Melissa L.; Way, Niobe

    2005-01-01

    The current study presents a growth curve analysis of self-esteem among Black, Latino, and Asian American high school students. A series of hierarchical linear models were used to examine patterns and predictors of change in self-esteem over time. Results revealed an average increase in self-esteem with age. Although boys and girls experienced…

  16. Rapid identification of dairy mesophilic and thermophilic sporeforming bacteria using DNA high resolution melt analysis of variable 16S rDNA regions.

    PubMed

    Chauhan, Kanika; Dhakal, Rajat; Seale, R Brent; Deeth, Hilton C; Pillidge, Christopher J; Powell, Ian B; Craven, Heather; Turner, Mark S

    2013-07-15

    Due to their ubiquity in the environment and ability to survive heating processes, sporeforming bacteria are commonly found in foods. This can lead to product spoilage if spores are present in sufficient numbers and where storage conditions favour spore germination and growth. A rapid method to identify the major aerobic sporeforming groups in dairy products, including Bacillus licheniformis group, Bacillus subtilis group, Bacillus pumilus group, Bacillus megaterium, Bacillus cereus group, Geobacillus species and Anoxybacillus flavithermus was devised. This method involves real-time PCR and high resolution melt analysis (HRMA) of V3 (~70 bp) and V6 (~100 bp) variable regions in the 16S rDNA. Comparisons of HRMA curves from 194 isolates of the above listed sporeforming bacteria obtained from dairy products which were identified using partial 16S rDNA sequencing, allowed the establishment of criteria for differentiating them from each other and several non-sporeforming bacteria found in samples. A blinded validation trial on 28 bacterial isolates demonstrated complete accuracy in unambiguous identification of the 7 different aerobic sporeformers. The reliability of HRMA method was also verified using boiled extractions of crude DNA, thereby shortening the time needed for identification. The HRMA method described in this study provides a new and rapid approach to identify the dominant mesophilic and thermophilic aerobic sporeforming bacteria found in a wide variety of dairy products.

  17. A Bayesian analysis of the effect of selection for growth rate on growth curves in rabbits

    PubMed Central

    Blasco, Agustín; Piles, Miriam; Varona, Luis

    2003-01-01

    Gompertz growth curves were fitted to the data of 137 rabbits from control (C) and selected (S) lines. The animals came from a synthetic rabbit line selected for an increased growth rate. The embryos from generations 3 and 4 were frozen and thawed to be contemporary of rabbits born in generation 10. Group C was the offspring of generations 3 and 4, and group S was the contemporary offspring of generation 10. The animals were weighed individually twice a week during the first four weeks of life, and once a week thereafter, until 20 weeks of age. Subsequently, the males were weighed weekly until 40 weeks of age. The random samples of the posterior distributions of the growth curve parameters were drawn by using Markov Chain Monte Carlo (MCMC) methods. As a consequence of selection, the selected animals were heavier than the C animals throughout the entire growth curve. Adult body weight, estimated as a parameter of the Gompertz curve, was 7% higher in the selected line. The other parameters of the Gompertz curve were scarcely affected by selection. When selected and control growth curves are represented in a metabolic scale, all differences disappear. PMID:12605849

  18. Periodicity Analysis of X-ray Light Curves of SS 433

    NASA Astrophysics Data System (ADS)

    Wang, J. Y.; Lu, X. L.; Zhao, Q. W.; Dong, D. Q.; Lao, B. Q.; Lu, Y.; Wei, Y. H.; Wu, X. C.; An, T.

    2016-03-01

    SS 433 is the only X-ray binary to date that was detected to have a pair of well-collimated jets, and its orbital period, super orbital period, and nutation period were all detected at the same time. The study on the periodic X-ray variabilities is helpful for understanding its dynamic process of the central engine and the correlation with other bands. In the present paper, two time series analysis techniques, Lomb-Scargle periodogram and weighted wavelet Z-transform, are employed to search for the periodicities from the Swift/BAT (Burst Alert Telescope)(15--50 keV) and RXTE/ASM (Rossi X-Ray Timing Explorer/All-Sky Monitor)(1.5--3, 3--5 and 5--12 keV) light curves of SS 433, and the Monte Carlo simulation is performed. For the 15--50 keV energy band, five significant periodic signals are detected, which are P_1(˜6.29 d), P_2 (˜6.54 d), P_3 (˜13.08 d), P_4 (˜81.50 d), and P_5 (˜162.30 d). For the 3--5 and 5--12 keV energy bands, periodic signals P_3 (˜13 d) and P_5 (˜162 d) are detected in both energy bands. However, for the 1.5--3 keV energy band, no significant periodic signal is detected. P_5 has the strongest periodic signal in the power spectrum for all the energy bands of 3--5, 5--12, and 15--50 keV, and it is consistent with that obtained by previous study in optical band. Further, due to the existence of relativistic radio jets, the X-ray and optical band variability of P_5 (˜162 d) is probably related to the precession of the relativistic jets. High coherence between X-ray and optical light curves may also imply that the X-ray and optical emissions are of the same physical origin. P_3 shows a good agreement with the orbital period (˜13.07 d) first obtained by previous study, and P_2 and P_4 are the high frequency harmonic components of P_3 and P_5, respectively. P_1 is detected from the power spectrum of 15--50 keV energy band only, and it is consistent with the systematic nutation period. As the power of energy band decreases (from hard X-ray to

  19. Evaluation of qPCR curve analysis methods for reliable biomarker discovery: bias, resolution, precision, and implications.

    PubMed

    Ruijter, Jan M; Pfaffl, Michael W; Zhao, Sheng; Spiess, Andrej N; Boggy, Gregory; Blom, Jochen; Rutledge, Robert G; Sisti, Davide; Lievens, Antoon; De Preter, Katleen; Derveaux, Stefaan; Hellemans, Jan; Vandesompele, Jo

    2013-01-01

    RNA transcripts such as mRNA or microRNA are frequently used as biomarkers to determine disease state or response to therapy. Reverse transcription (RT) in combination with quantitative PCR (qPCR) has become the method of choice to quantify small amounts of such RNA molecules. In parallel with the democratization of RT-qPCR and its increasing use in biomedical research or biomarker discovery, we witnessed a growth in the number of gene expression data analysis methods. Most of these methods are based on the principle that the position of the amplification curve with respect to the cycle-axis is a measure for the initial target quantity: the later the curve, the lower the target quantity. However, most methods differ in the mathematical algorithms used to determine this position, as well as in the way the efficiency of the PCR reaction (the fold increase of product per cycle) is determined and applied in the calculations. Moreover, there is dispute about whether the PCR efficiency is constant or continuously decreasing. Together this has lead to the development of different methods to analyze amplification curves. In published comparisons of these methods, available algorithms were typically applied in a restricted or outdated way, which does not do them justice. Therefore, we aimed at development of a framework for robust and unbiased assessment of curve analysis performance whereby various publicly available curve analysis methods were thoroughly compared using a previously published large clinical data set (Vermeulen et al., 2009) [11]. The original developers of these methods applied their algorithms and are co-author on this study. We assessed the curve analysis methods' impact on transcriptional biomarker identification in terms of expression level, statistical significance, and patient-classification accuracy. The concentration series per gene, together with data sets from unpublished technical performance experiments, were analyzed in order to assess the

  20. High-throughput quantitative analysis with cell growth kinetic curves for low copy number mutant cells.

    PubMed

    Xing, James Z; Gabos, Stephan; Huang, Biao; Pan, Tianhong; Huang, Min; Chen, Jie

    2012-10-01

    The mutation rate in cells induced by environmental genotoxic hazards is very low and difficult to detect using traditional cell counting assays. The established genetic toxicity tests currently recognized by regulatory authorities, such as conventional Ames and hypoxanthine guanine phosphoribosyl-transferase (HPRT) assays, are not well suited for higher-throughput screening as they require large amounts of test compounds and are very time consuming. In this study, we developed a novel cell-based assay for quantitative analysis of low numbers of cell copies with HPRT mutation induced by an environmental mutagen. The HPRT gene mutant cells induced by the mutagen were selected by 6-thioguanine (6-TG) and the cell's kinetic growth curve monitored by a real-time cell electronic sensor (RT-CES) system. When a threshold is set at a certain cell index (CI) level, samples with different initial mutant cell copies take different amounts of time in order for their growth (or CI accumulation) to cross this threshold. The more cells that are initially seeded in the test well, the faster the cell accumulation and therefore the shorter the time required to cross this threshold. Therefore, the culture time period required to cross the threshold of each sample corresponds to the original number of cells in the sample. A mutant cell growth time threshold (MT) value of each sample can be calculated to predict the number of original mutant cells. For mutagenesis determination, the RT-CES assay displayed an equal sensitivity (p > 0.05) and coefficients of variation values with good correlation to conventional HPRT mutagenic assays. Most importantly, the RT-CES mutation assay has a higher throughput than conventional cellular assays.

  1. First order reversal curves (FORC) analysis of individual magnetic nanostructures using micro-Hall magnetometry

    NASA Astrophysics Data System (ADS)

    Pohlit, Merlin; Eibisch, Paul; Akbari, Maryam; Porrati, Fabrizio; Huth, Michael; Müller, Jens

    2016-11-01

    Alongside the development of artificially created magnetic nanostructures, micro-Hall magnetometry has proven to be a versatile tool to obtain high-resolution hysteresis loop data and access dynamical properties. Here we explore the application of First Order Reversal Curves (FORC)—a technique well-established in the field of paleomagnetism for studying grain-size and interaction effects in magnetic rocks—to individual and dipolar-coupled arrays of magnetic nanostructures using micro-Hall sensors. A proof-of-principle experiment performed on a macroscopic piece of a floppy disk as a reference sample well known in the literature demonstrates that the FORC diagrams obtained by magnetic stray field measurements using home-built magnetometers are in good agreement with magnetization data obtained by a commercial vibrating sample magnetometer. We discuss in detail the FORC diagrams and their interpretation of three different representative magnetic systems, prepared by the direct-write Focused Electron Beam Induced Deposition (FEBID) technique: (1) an isolated Co-nanoisland showing a simple square-shaped hysteresis loop, (2) a more complex CoFe-alloy nanoisland exhibiting a wasp-waist-type hysteresis, and (3) a cluster of interacting Co-nanoislands. Our findings reveal that the combination of FORC and micro-Hall magnetometry is a promising tool to investigate complex magnetization reversal processes within individual or small ensembles of nanomagnets grown by FEBID or other fabrication methods. The method provides sub-μm spatial resolution and bridges the gap of FORC analysis, commonly used for studying macroscopic samples and rather large arrays, to studies of small ensembles of interacting nanoparticles with the high moment sensitivity inherent to micro-Hall magnetometry.

  2. First order reversal curves (FORC) analysis of individual magnetic nanostructures using micro-Hall magnetometry.

    PubMed

    Pohlit, Merlin; Eibisch, Paul; Akbari, Maryam; Porrati, Fabrizio; Huth, Michael; Müller, Jens

    2016-11-01

    Alongside the development of artificially created magnetic nanostructures, micro-Hall magnetometry has proven to be a versatile tool to obtain high-resolution hysteresis loop data and access dynamical properties. Here we explore the application of First Order Reversal Curves (FORC)-a technique well-established in the field of paleomagnetism for studying grain-size and interaction effects in magnetic rocks-to individual and dipolar-coupled arrays of magnetic nanostructures using micro-Hall sensors. A proof-of-principle experiment performed on a macroscopic piece of a floppy disk as a reference sample well known in the literature demonstrates that the FORC diagrams obtained by magnetic stray field measurements using home-built magnetometers are in good agreement with magnetization data obtained by a commercial vibrating sample magnetometer. We discuss in detail the FORC diagrams and their interpretation of three different representative magnetic systems, prepared by the direct-write Focused Electron Beam Induced Deposition (FEBID) technique: (1) an isolated Co-nanoisland showing a simple square-shaped hysteresis loop, (2) a more complex CoFe-alloy nanoisland exhibiting a wasp-waist-type hysteresis, and (3) a cluster of interacting Co-nanoislands. Our findings reveal that the combination of FORC and micro-Hall magnetometry is a promising tool to investigate complex magnetization reversal processes within individual or small ensembles of nanomagnets grown by FEBID or other fabrication methods. The method provides sub-μm spatial resolution and bridges the gap of FORC analysis, commonly used for studying macroscopic samples and rather large arrays, to studies of small ensembles of interacting nanoparticles with the high moment sensitivity inherent to micro-Hall magnetometry.

  3. Magnetic unmixing of first-order reversal curve diagrams using principal component analysis

    NASA Astrophysics Data System (ADS)

    Lascu, Ioan; Harrison, Richard J.; Li, Yuting; Muraszko, Joy R.; Channell, James E. T.; Piotrowski, Alexander M.; Hodell, David A.

    2015-09-01

    We describe a quantitative magnetic unmixing method based on principal component analysis (PCA) of first-order reversal curve (FORC) diagrams. For PCA, we resample FORC distributions on grids that capture diagnostic signatures of single-domain (SD), pseudosingle-domain (PSD), and multidomain (MD) magnetite, as well as of minerals such as hematite. Individual FORC diagrams are recast as linear combinations of end-member (EM) FORC diagrams, located at user-defined positions in PCA space. The EM selection is guided by constraints derived from physical modeling and imposed by data scatter. We investigate temporal variations of two EMs in bulk North Atlantic sediment cores collected from the Rockall Trough and the Iberian Continental Margin. Sediments from each site contain a mixture of magnetosomes and granulometrically distinct detrital magnetite. We also quantify the spatial variation of three EM components (a coarse silt-sized MD component, a fine silt-sized PSD component, and a mixed clay-sized component containing both SD magnetite and hematite) in surficial sediments along the flow path of the North Atlantic Deep Water (NADW). These samples were separated into granulometric fractions, which helped constrain EM definition. PCA-based unmixing reveals systematic variations in EM relative abundance as a function of distance along NADW flow. Finally, we apply PCA to the combined data set of Rockall Trough and NADW sediments, which can be recast as a four-EM mixture, providing enhanced discrimination between components. Our method forms the foundation of a general solution to the problem of unmixing multicomponent magnetic mixtures, a fundamental task of rock magnetic studies.

  4. More basic approach to the analysis of multiple specimen R-curves for determination of J/sub c/

    SciTech Connect

    Carlson, K.W.; Williams, J.A.

    1980-02-01

    Multiple specimen J-R curves were developed for groups of 1T compact specimens with different a/W values and depth of side grooving. The purpose of this investigation was to determine J/sub c/ (J at onset of crack extension) for each group. Judicious selection of points on the load versus load-line deflection record at which to unload and heat tint specimens permitted direct observation of approximate onset of crack extension. It was found that the present recommended procedure for determining J/sub c/ from multiple specimen R-curves, which is being considered for standardization, consistently yielded nonconservative J/sub c/ values. A more basic approach to analyzing multiple specimen R-curves is presented, applied, and discussed. This analysis determined J/sub c/ values that closely corresponded to actual observed onset of crack extension.

  5. Analysis of late-time light curves of Type IIb, Ib and Ic supernovae

    NASA Astrophysics Data System (ADS)

    Wheeler, J. Craig; Johnson, V.; Clocchiatti, A.

    2015-06-01

    The shape of the light-curve peak of radioactive-powered core-collapse `stripped-envelope' supernovae constrains the ejecta mass, nickel mass and kinetic energy by the brightness and diffusion time for a given opacity and observed expansion velocity. Late-time light curves give constraints on the ejecta mass and energy, given the gamma-ray opacity. Previous work has shown that the principal light-curve peaks for SN IIb with small amounts of hydrogen and for hydrogen/helium-deficient SN Ib/c are often rather similar near maximum light, suggesting similar ejecta masses and kinetic energies, but that late-time light curves show a wide dispersion, suggesting a dispersion in ejecta masses and kinetic energies. It was also shown that SN IIb and SN Ib/c can have very similar late-time light curves, but different ejecta velocities demanding significantly different ejecta masses and kinetic energies. We revisit these topics by collecting and analysing well-sampled single-band and quasi-bolometric light curves from the literature. We find that the late-time light curves of stripped-envelope core-collapse supernovae are heterogeneous. We also show that the observed properties, the photospheric velocity at peak, the rise time and the late decay time, can be used to determine the mean opacity appropriate to the peak. The opacity determined in this way is considerably smaller than common estimates. We discuss how the small effective opacity may result from recombination and asymmetries in the ejecta.

  6. Vibrational spectroscopic and ultrasound analysis for in-process characterization of high-density polyethylene/polypropylene blends during melt extrusion.

    PubMed

    Barnes, S E; Brown, E C; Sibley, M G; Edwards, H G M; Scowen, I J; Coates, P D

    2005-05-01

    Spectroscopic techniques such as Raman, mid-infrared (MIR), and near-infrared (NIR) have become indispensable analytical tools for rapid chemical quality control and process monitoring. This paper presents the application of in-line Fourier transform near-infrared (FT-NIR) spectroscopy, Raman spectroscopy, and ultrasound transit time measurements for in-line monitoring of the composition of a series of high-density polyethylene (HDPE)/polypropylene (PP) blends during single-screw extrusion. Melt composition was determined by employing univariate analysis of the ultrasound transit time data and partial least squares (PLS) multivariate analysis of the data from both spectroscopic techniques. Each analytical technique was determined to be highly sensitive to changes in melt composition, allowing accurate prediction of blend content to within +/- 1% w/w (1sigma) during monitoring under fixed extrusion conditions. FT-NIR was determined to be the most sensitive of the three techniques to changes in melt composition. A four-factor PLS model of the NIR blend spectra allowed determination of melt content with a standard prediction error of +/- 0.30% w/w (1sigma). However, the NIR transmission probes employed for analysis were invasive into the melt stream, whereas the single probes adopted for Raman and ultrasound analysis were noninvasive, making these two techniques more versatile. All three measurement techniques were robust to the high temperatures and pressures experienced during melt extrusion, demonstrating each system's suitability for process monitoring and control.

  7. Combined statistical analysis of vasodilation and flow curves in brachial ultrasonography: technique and its connection to cardiovascular risk factors

    NASA Astrophysics Data System (ADS)

    Boisrobert, Loic; Laclaustra, Martin; Bossa, Matias; Frangi, Andres G.; Frangi, Alejandro F.

    2005-04-01

    Clinical studies report that impaired endothelial function is associated with Cardio-Vascular Diseases (CVD) and their risk factors. One commonly used mean for assessing endothelial function is Flow-Mediated Dilation (FMD). Classically, FMD is quantified using local indexes e.g. maximum peak dilation. Although such parameters have been successfully linked to CVD risk factors and other clinical variables, this description does not consider all the information contained in the complete vasodilation curve. Moreover, the relation between flow impulse and the vessel vasodilation response to this stimulus, although not clearly known, seems to be important and is not taken into account in the majority of studies. In this paper we propose a novel global parameterization for the vasodilation and the flow curves of a FMD test. This parameterization uses Principal Component Analysis (PCA) to describe independently and jointly the variability of flow and FMD curves. These curves are obtained using computerized techniques (based on edge detection and image registration, respectively) to analyze the ultrasound image sequences. The global description obtained through PCA yields a detailed characterization of the morphology of such curves allowing the extraction of intuitive quantitative information of the vasodilation process and its interplay with flow changes. This parameterization is consistent with traditional measurements and, in a database of 177 subjects, seems to correlate more strongly (and with more clinical parameters) than classical measures to CVD risk factors and clinical parameters such as LDL- and HDL-Cholesterol.

  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. Does the Budyko curve reflect a maximum power state of hydrological systems? A backward analysis

    NASA Astrophysics Data System (ADS)

    Westhoff, Martijn; Zehe, Erwin; Archambeau, Pierre; Dewals, Benjamin

    2016-04-01

    Almost all catchments plot within a small envelope around the Budyko curve. This apparent behaviour suggests that organizing principles may play a role in the evolution of catchments. In this paper we applied the thermodynamic principle of maximum power as the organizing principle. In a top-down approach we derived mathematical formulations of the relation between relative wetness and gradients driving runoff and evaporation for a simple one-box model. We did this in an inverse manner such that when the conductances are optimized with the maximum power principle, the steady state behaviour of the model leads exactly to a point on the asymptotes of the Budyko curve. Subsequently, we added dynamics in forcing and actual evaporations, causing the Budyko curve to deviate from the asymptotes. Despite the simplicity of the model, catchment observations compare reasonably well with the Budyko curves subject to observed dynamics in rainfall and actual evaporation. Thus by constraining the - with the maximum power principle optimized - model with the asymptotes of the Budyko curve we were able to derive more realistic values of the aridity and evaporation index without any parameter calibration. Future work should focus on better representing the boundary conditions of real catchments and eventually adding more complexity to the model.

  10. Comparative Analysis of Biologically Relevant Response Curves in Gene Expression Experiments: Heteromorphy, Heterochrony, and Heterometry.

    PubMed

    Baker, Stuart G

    2014-02-14

    To gain biological insights, investigators sometimes compare sequences of gene expression measurements under two scenarios (such as two drugs or species). For this situation, we developed an algorithm to fit, identify, and compare biologically relevant response curves in terms of heteromorphy (different curves), heterochrony (different transition times), and heterometry (different magnitudes). The curves are flat, linear, sigmoid, hockey-stick (sigmoid missing a steady state), transient (sigmoid missing two steady states), impulse (with peak or trough), step (with intermediate-level plateau), impulse+ (impulse with an extra parameter), step+ (step with an extra parameter), further characterized by upward or downward trend. To reduce overfitting, we fit the curves to every other response, evaluated the fit in the remaining responses, and identified the most parsimonious curves that yielded a good fit. We measured goodness of fit using a statistic comparable over different genes, namely the square root of the mean squared prediction error as a percentage of the range of responses, which we call the relative prediction error (RPE). We illustrated the algorithm using data on gene expression at 14 times in the embryonic development in two species of frogs. Software written in Mathematica is freely available.

  11. Statistical signal processing methods for intraoral pressure curve analysis in orthodontics.

    PubMed

    Jung, Klaus; Engelke, Wilfried; Knösel, Michael

    2012-08-01

    A thorough understanding of the intraoral pressure conditions of patients with different forms of malocclusion may help to characterize their aetiology in more detail and improve orthodontic treatment approaches by adding strategies to achieve a normalization of intraoral pressure levels. These pressure curve analyses should not only provide information on intraoral activity or during rest but also detail characterization of swallowing features and pressure plateau stages. For this purpose, algorithms for extracting swallowing peaks and plateau stages were developed and evaluated. Established curve characteristics such as the average or maximum pressure as well as the number of swallowing peaks or resting phases were compared between each other. Their usefulness and correlation (Kendall's τ) were evaluated in a data example of different occlusal groups (Angle Class I: n = 30; Angle Class II division 1: n = 12; and Angle Class II division 2: n = 13). Curve characteristics were compared among these groups using the Kruskal-Wallis test. Some of the derived curve characteristics were found to be uncorrelated, thus providing different information concerning the intraoral pressure condition of subjects. Based on these findings, it is recommended to employ the curve characteristics described in this study to obtain a holistic image of factors that may affect the formation of the dentition.

  12. Nonlinear stability analysis of double-curved shallow fgm panels on elastic foundations in thermal environments

    NASA Astrophysics Data System (ADS)

    Duc, Nguyen Dinh; Quan, Tran Quoc

    2012-09-01

    An analytical investigation into the nonlinear response of thick functionally graded double-curved shallow panels resting on elastic foundations and subjected to thermal and thermomechanical loads is presented. Young's modulus and Poisson's ratio are both graded in the thickness direction according to a simple power-law distribution in terms of volume fractions of constituents. All formulations are based on the classical shell theory with account of geometrical nonlinearity and initial geometrical imperfection in the cases of Pasternak-type elastic foundations. By applying the Galerkin method, explicit relations for the thermal load-deflection curves of simply supported curved panels are found. The effects of material and geometrical properties and foundation stiffness on the buckling and postbuckling load-carrying capacity of the panels in thermal environments are analyzed and discussed.

  13. Hierarchical Bayesian modeling and Markov chain Monte Carlo sampling for tuning-curve analysis.

    PubMed

    Cronin, Beau; Stevenson, Ian H; Sur, Mriganka; Körding, Konrad P

    2010-01-01

    A central theme of systems neuroscience is to characterize the tuning of neural responses to sensory stimuli or the production of movement. Statistically, we often want to estimate the parameters of the tuning curve, such as preferred direction, as well as the associated degree of uncertainty, characterized by error bars. Here we present a new sampling-based, Bayesian method that allows the estimation of tuning-curve parameters, the estimation of error bars, and hypothesis testing. This method also provides a useful way of visualizing which tuning curves are compatible with the recorded data. We demonstrate the utility of this approach using recordings of orientation and direction tuning in primary visual cortex, direction of motion tuning in primary motor cortex, and simulated data.

  14. A linear analysis of the transition curve for the baroclinic annulus

    NASA Technical Reports Server (NTRS)

    Miller, T. L.; Gall, R. L.

    1983-01-01

    A primitive equation linear model is shown to be capable of quantitatively predicting the neutral curve for a baroclinic annulus. Flows unstable to small nonaxisymmetric perturbations are assumed to lie on the nonaxisymmetric side of a transition curve, while the stable flows are on the axisymmetric side. The stability in the presence of perturbations is tested with linearized hydrostatic primitive equations. Attention is given to the fastest growing eigenmodes, demonstrating that the linear and nonlinear wave have similar structures at a particular point in the nonaxisymmetric regime. All the waves are similar to the Eddy wave except at the extreme to the transition curve, where the waves maintain little structure with height. The eddy kinetic energy is baroclinic with a potential energy suppresed by the large static stability of the basic state. Eddy dissipation is noted to be significant near all boundaries.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  17. Harmonisation of coupled calibration curves to reduce correlated effects in the analysis of natural gas by gas chromatography.

    PubMed

    Vargha, Gergely; Milton, Martin; Cox, Maurice; Kamvissis, Sarantis

    2005-01-14

    Quantitative analysis of natural gas depends on the calibration of a gas chromatograph with certified gas mixtures and the determination of a response relationship for each species by regression analysis. The uncertainty in this calibration is dominated by variations in the amount of the sample used for each analysis that are strongly correlated for all species measured in the same run. The "harmonisation" method described here minimises the influence of these correlations on the calculated calibration curves and leads to a reduction in the root-mean-square residual deviations from the fitted curve of a factor between 2 and 5. Consequently, it removes the requirement for each run in the calibration procedure to be carried out under the same external conditions, and opens the possibility that new data, measured under different environmental or instrumental conditions, can be appended to an existing calibration database.

  18. The mathematical analysis for peristaltic flow of nano fluid in a curved channel with compliant walls

    NASA Astrophysics Data System (ADS)

    Nadeem, S.; Maraj, E. N.

    2014-01-01

    In the present paper, we have investigated the peristaltic flow of nano fluid in a curved channel with compliant walls. The governing equations of nano fluid model for curved channel are derived including the effects of curvature. The highly nonlinear partial differential equations are simplified using the long wave length and low Reynolds number assumptions. The reduced nonlinear partial differential equation is solved analytically with the help of homotopy perturbation method. The physical features of pertinent parameters have been discussed by plotting the graphs of pressure rise, velocity, temperature, nano particle volume fraction and stream functions.

  19. New Spectroscopic Analysis and Light Curve Model of the Eclipsing Binary V356 Sgr

    NASA Astrophysics Data System (ADS)

    Cabezas, M.; Mennickent, R.; Djurasević, G.

    2017-02-01

    We present a new orbital solution for the V356 Sgr binary system based on new and accurate radial velocities. It consists of a B3 V star accreting matter from a Roche-Lobe filling A2 II star. The spectra were disentangled using KOREL. The UBV light curves by Popper (1957) and Wilson & Woodward (1995) as well as the ASAS V-band light curve were modeled with a multicomponent synthesis code including an accretion disk. The system parameters, such as the effective temperature and surface gravity for both stars as well as the disk temperature and radius, were determined.

  20. 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.

  1. Rapid High-Resolution Melt Analysis of Cytauxzoon felis Cytochrome b To Aid in the Prognosis of Cytauxzoonosis.

    PubMed

    Schreeg, Megan E; Marr, Henry S; Tarigo, Jaime L; Cohn, Leah A; Levy, Michael G; Birkenheuer, Adam J

    2015-08-01

    Cytauxzoon felis is a virulent, tick-transmitted, protozoan parasite that infects felines. Cytauxzoonosis was previously thought to be uniformly fatal in domestic cats. Treatment combining atovaquone and azithromycin (A&A) has been associated with survival rates of over 60%. Atovaquone, a ubiquinone analogue, targets C. felis cytochrome b (cytb), of which 30 unique genotypes have been identified. The C. felis cytb genotype cytb1 is associated with increased survival rates in cats treated with A&A. The purpose of this study was to design a PCR panel that could distinguish C. felis cytb1 from other cytochrome b genotypes. Primer pairs were designed to span five different nucleotide positions at which single-nucleotide polymorphisms in the C. felis cytb gene had been identified. Through the use of high-resolution melt analysis, this panel was predicted to distinguish cytb1 from other cytb genotypes. Assays were validated using samples from 69 cats with cytauxzoonosis for which the C. felis cytb genotypes had been characterized previously. The PCR panel identified C. felis cytb1 with 100% sensitivity and 98.2% specificity. High-resolution melt analysis can rapidly provide prognostic information for clients considering A&A treatment in cats with cytauxzoonosis.

  2. Melting of Bridgmanite to 135 Gpa: Toward a Coherent Model for the Melting Behavior in the Lower Mantle

    NASA Astrophysics Data System (ADS)

    Andrault, D.; Pesce, G.; Mezouar, N.

    2015-12-01

    Our knowledge on the melting behavior in the deep mantle remains based on a limited number of experimental and theoretical works. Today, thanks to (i) availability of very brilliant X-ray synchrotron sources and (ii) improved control of the P-T conditions in the laser-heated diamond anvil cell (LH-DAC), the experimental results should reach some agreement about the melting diagrams. However, it is not the case and major controversies remain. For example, liquidi of peridotitic (1) and chondritic-type (2) mantles are reported with a temperature difference of ~1000 K at a pressure of ~90 GPa (corresponding to ~2000 km depth), which cannot be explained by the relatively small compositional difference between these two materials. To bring new insights about the melting properties of the deep mantle, our strategy has been to study the melting curve of the end-member liquidus phase, the (Mg,Fe)(Al,Si)O3 bridgmanite (Bg), before applying a basic thermodynamical approach to the mineralogical system made of Bg, CaSiO3-perovskite and (Mg,Fe)O ferropericlase. Our approach cannot be as formal as currently done for melting in the shallow mantle, due to lack of major thermodynamical parameters. Still, our analysis yields original information, such as the degree of partial melting as a function of P, T and fraction of Bg in the geological material. The Mg/Si ratio in melts can also be addressed. Concerning the controversy between LH-DAC experiments, it can be solved taking into account migration in the temperature gradient of the pseudo-eutectic melt, when the sample starts to melt. This effect is expected to occur more extensively in absence of an insulating material between the sample and the diamond anvils. It yields an overestimation of the liquidus temperature for a given chemical composition, due to loss of the most fusing elements. References:1. Fiquet et al. (2010) Melting of Peridotite to 140 Gigapascals. Science 329, 1516-1518. 2. Andrault et al. (2011) Melting curve of

  3. Evaluation of the influences of various force magnitudes and configurations on scoliotic curve correction using finite element analysis.

    PubMed

    Karimi, Mohammad Taghi; Ebrahimi, Mohammad Hossein; Mohammadi, Ali; McGarry, Anthony

    2017-03-01

    Scoliosis is a lateral curvature in the normally straight vertical line of the spine, and the curvature can be moderate to severe. Different treatment can be used based on severity and age of subjects, but most common treatment for this disease is using orthosis. To design orthosis types of force arrangement can be varied, from transverse loads to vertical loads or combination of them. But it is not well introduced how orthoses control scoliotic curve and how to achieve the maximum correction based on force configurations and magnitude. Therefore, it was aimed to determine the effect of various loads configurations and magnitudes on curve correction of a degenerative scoliotic subject. A scoliotic subject participated in this study. The CT-Scan of the subject was used to produce 3D model of spine. The 3D model of spine was produced by Mimics software and the finite element analysis and deformation of scoliotic curve of the spine under seven different forces and in three different conditions was determined by ABAQUS software. The Cobb angle in scoliosis curve decreased significantly by applying forces. In each condition depends on different forces, different corrections have been achieved. It can be concluded that the configurations of the force application mentioned in this study is effective to decrease the scoliosis curve. Although it is a case study, it can be used for a vast number of subjects to predict the correction of scoliosis curve before orthotic treatment. Moreover, it is recommended that this method and the outputs can be compared with clinical findings.

  4. Development of Oral Reading Fluency in Children with Speech or Language Impairments: A Growth Curve Analysis

    ERIC Educational Resources Information Center

    Puranik, Cynthia S.; Petscher, Yaacov; Al Otaiba, Stephanie; Catts, Hugh W.; Lonigan, Christopher J.

    2008-01-01

    This longitudinal study used piece-wise growth curve analyses to examine growth patterns in oral reading fluency for 1,991 students with speech impairments (SI) or language impairments (LI) from first through third grade. The main finding of this study was that a diagnosis of SI or LI can have a detrimental and persistent effect on early reading…

  5. Parent Involvement and Science Achievement: A Cross-Classified Multilevel Latent Growth Curve Analysis

    ERIC Educational Resources Information Center

    Johnson, Ursula Y.; Hull, Darrell M.

    2014-01-01

    The authors examined science achievement growth at Grades 3, 5, and 8 and parent school involvement at the same time points using the Early Childhood Longitudinal Study-Kindergarten Class of 1998-1999. Data were analyzed using cross-classified multilevel latent growth curve modeling with time invariant and varying covariates. School-based…

  6. Analysis of the Curved Junction Edge between a Flat Plate and a Prolate Spheroid.

    DTIC Science & Technology

    1981-05-01

    report. Our approach to this problem is first to find the intersection point between a line (i.e., one edge of the plate) and the prolate spheroid. Then...one can follow the same idea to find the curved junction edge between a flat plate and the prolate spheroid. (Author)

  7. Analysis of equi-intensity curves and NU distribution of EAS

    NASA Astrophysics Data System (ADS)

    Tanahashi, G.

    1985-08-01

    The distribution of the number of muons in extensive air showers (EAS) and the equi-intensity curves of EAS are analyzed on the basis of Monte Carlo simulation of various cosmic ray composition and the interaction models. Problems in the two best combined models are discussed.

  8. On the analysis of Canadian Holstein dairy cow lactation curves using standard growth functions.

    PubMed

    López, S; France, J; Odongo, N E; McBride, R A; Kebreab, E; AlZahal, O; McBride, B W; Dijkstra, J

    2015-04-01

    Six classical growth functions (monomolecular, Schumacher, Gompertz, logistic, Richards, and Morgan) were fitted to individual and average (by parity) cumulative milk production curves of Canadian Holstein dairy cows. The data analyzed consisted of approximately 91,000 daily milk yield records corresponding to 122 first, 99 second, and 92 third parity individual lactation curves. The functions were fitted using nonlinear regression procedures, and their performance was assessed using goodness-of-fit statistics (coefficient of determination, residual mean squares, Akaike information criterion, and the correlation and concordance coefficients between observed and adjusted milk yields at several days in milk). Overall, all the growth functions evaluated showed an acceptable fit to the cumulative milk production curves, with the Richards equation ranking first (smallest Akaike information criterion) followed by the Morgan equation. Differences among the functions in their goodness-of-fit were enlarged when fitted to average curves by parity, where the sigmoidal functions with a variable point of inflection (Richards and Morgan) outperformed the other 4 equations. All the functions provided satisfactory predictions of milk yield (calculated from the first derivative of the functions) at different lactation stages, from early to late lactation. The Richards and Morgan equations provided the most accurate estimates of peak yield and total milk production per 305-d lactation, whereas the least accurate estimates were obtained with the logistic equation. In conclusion, classical growth functions (especially sigmoidal functions with a variable point of inflection) proved to be feasible alternatives to fit cumulative milk production curves of dairy cows, resulting in suitable statistical performance and accurate estimates of lactation traits.

  9. A LIGHT CURVE ANALYSIS OF CLASSICAL NOVAE: FREE-FREE EMISSION VERSUS PHOTOSPHERIC EMISSION

    SciTech Connect

    Hachisu, Izumi; Kato, Mariko E-mail: mariko@educ.cc.keio.ac.jp

    2015-01-10

    We analyzed light curves of seven relatively slower novae, PW Vul, V705 Cas, GQ Mus, RR Pic, V5558 Sgr, HR Del, and V723 Cas, based on an optically thick wind theory of nova outbursts. For fast novae, free-free emission dominates the spectrum in optical bands rather than photospheric emission, and nova optical light curves follow the universal decline law. Faster novae blow stronger winds with larger mass-loss rates. Because the brightness of free-free emission depends directly on the wind mass-loss rate, faster novae show brighter optical maxima. In slower novae, however, we must take into account photospheric emission because of their lower wind mass-loss rates. We calculated three model light curves of free-free emission, photospheric emission, and their sum for various white dwarf (WD) masses with various chemical compositions of their envelopes and fitted reasonably with observational data of optical, near-IR (NIR), and UV bands. From light curve fittings of the seven novae, we estimated their absolute magnitudes, distances, and WD masses. In PW Vul and V705 Cas, free-free emission still dominates the spectrum in the optical and NIR bands. In the very slow novae, RR Pic, V5558 Sgr, HR Del, and V723 Cas, photospheric emission dominates the spectrum rather than free-free emission, which makes a deviation from the universal decline law. We have confirmed that the absolute brightnesses of our model light curves are consistent with the distance moduli of four classical novae with known distances (GK Per, V603 Aql, RR Pic, and DQ Her). We also discussed the reason why the very slow novae are about ∼1 mag brighter than the proposed maximum magnitude versus rate of decline relation.

  10. Stepwise melting of a model glass former under confinement

    NASA Astrophysics Data System (ADS)

    Calvo, F.; Wales, D. J.

    2009-10-01

    The equilibrium thermodynamics of a binary Lennard-Jones model glass former are investigated using exchange Monte Carlo simulations, covering the crystalline and amorphous regions of configuration space in appropriate temperature ranges. We investigate both bulk and film mixtures, the latter being confined between noninteracting flat walls. Both the bulk and film systems exhibit a principal heat capacity peak at the melting point, but confinement leads to a significant depression in the melting temperature by about 25%. Microcanonical caloric curves, as well as analysis of the probability distributions of a bond-orientational order parameter, show that this transition has first-order character. However, the film system shows additional features at lower temperatures, which are interpreted in terms of localized partial melting, perpendicular to the confining walls and near the walls, with some increase in layering. This premelting is associated with local minima on the underlying potential energy surface that are not supported by the bulk system.

  11. Electron Backscatter Diffraction Analysis of Inconel 718 Parts Fabricated by Selective Laser Melting Additive Manufacturing

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoqing; Chou, Kevin

    2016-11-01

    In this study, the crystallographic texture of an Inconel 718 part fabricated by selective laser melting was investigated. The front surface (X-Z plane) microstructure is characterized by the columnar grains growing along the build direction, and the width of columnar grains is in the range of about 75-150 µm, with the bottom layers having narrower grains as a result of a higher cooling rate. In addition to equiaxed grains, the top surface (X-Y plane) has a feature of patch patterns resulting from the laser scanning strategy. Based on the electron backscatter diffraction results, there appears only weak crystallographic texture in both the X-Z plane and the X-Y plane of the part. From the grain boundary map, the microstructures are composed of high-angle boundaries with a larger fraction of subgrain boundaries.

  12. Electron Backscatter Diffraction Analysis of Inconel 718 Parts Fabricated by Selective Laser Melting Additive Manufacturing

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoqing; Chou, Kevin

    2017-02-01

    In this study, the crystallographic texture of an Inconel 718 part fabricated by selective laser melting was investigated. The front surface (X-Z plane) microstructure is characterized by the columnar grains growing along the build direction, and the width of columnar grains is in the range of about 75-150 µm, with the bottom layers having narrower grains as a result of a higher cooling rate. In addition to equiaxed grains, the top surface (X-Y plane) has a feature of patch patterns resulting from the laser scanning strategy. Based on the electron backscatter diffraction results, there appears only weak crystallographic texture in both the X-Z plane and the X-Y plane of the part. From the grain boundary map, the microstructures are composed of high-angle boundaries with a larger fraction of subgrain boundaries.

  13. Numerical analysis on thermal characteristics and ice melting efficiency for microwave deicing vehicle

    NASA Astrophysics Data System (ADS)

    Wang, Can; Yang, Bo; Tan, Gangfeng; Guo, Xuexun; Zhou, Li; Xiong, Shengguang

    2016-05-01

    In the high latitudes, the icy patches on the road are frequently generated and have a wide distribution, which are difficult to remove and obviously affect the normal usage of the highways, bridges and airport runways. Physical deicing, such as microwave (MW) deicing, help the ice melt completely through heating mode and then the ice layer can be swept away. Though it is no pollution and no damage to the ground, the low efficiency hinders the development of MW deicing vehicle equipped without sufficient speed. In this work, the standard evaluation of deicing is put forward firstly. The intensive MW deicing is simplified to ice melting process characterized by one-dimensional slab with uniform volumetric energy generation, which results in phase transformation and interface motion between ice and water. The heating process is split into the superposition of three parts — non-heterogeneous heating for ground without phase change, heat transfer with phase change and the heat convection between top surface of ice layer and flow air. Based on the transient heat conduction theory, a mathematical model, combining electromagnetic and two-phase thermal conduction, is proposed in this work, which is able to reveal the relationship between the deicing efficiency and ambient conditions, as well as energy generation and material parameters. Using finite difference time-domain, this comprehensive model is developed to solve the moving boundary heat transfer problem in a one-dimensional structured gird. As a result, the stimulation shows the longitudinal temperature distributions in all circumstances and quantitative validation is obtained by comparing simulated temperature distributions under different conditions. In view of the best economy and fast deicing, these analytic solutions referring to the complex influence factors of deicing efficiency demonstrate the optimal matching for the new deicing design.

  14. The early melting of closed duplex DNA: analysis by banding in buoyant neutral rubidium trichloroacetate.

    PubMed Central

    Burke, R L; Bauer, W R

    1980-01-01

    Aqueous RbTCA permits the buoyant banding of both native and denatured DNA at room temperature and neutral pH. A unique property of this solvent is the bouyant resolution of closed circular, underwound DNA (I) from the corresponding nicked (II) species. Conditions are reported here in which PM-2 DNA I is physically resolved from native PM-2 DNA II, the buoyant separation being 1.27 mq/ml in 3.3 M RbTCA at 25 degrees C. The separation between nicked and closed DNAs increases with temperature up to 35.5 degrees C, at which PM-2 DNA II cooperatively melts and subsequently pellets. The isothermal buoyant density of a cloed DNA increases linearly as the linking number (Lk) of the closed DNA decreases. The early melting of closed DNA may be monitored with high precision by buoyant banding in RbTCA, it being possible to detect the disruption of as few as 40 base pairs in PM-2 DNA (10,000 base pairs). The constraint that the linking number be conserved in closed DNA requires that a change in duplex winding be accompanied by a compensating change in supercoiling. We estimate the linking number deficiency of PM-2 DNA I to be 0.094 turns per decibase pair. This result permits the estimation of the EtdBr unwinding angle, phi, by comparison with alternative determinations of the linking number deficiency which depend upom the value of phi. The result obtained here is that phi = 27.7 degrees +/- 0.5 degrees and is approximately independent of temperature over the range 15 degrees-35 degrees. PMID:7443544

  15. Spectral analysis of sealevel during the altimetry era, and evidence for GIA and glacial melting fingerprints

    NASA Astrophysics Data System (ADS)

    Spada, Giorgio; Galassi, Gaia

    2016-04-01

    We study the spatial patterns of the mass and steric components of sea-level change during the "altimetry era" (1992-today), and we characterize them at different scales by the orthonormal functions method. The spectrum of the altimetry-derived rate of sea-level rise is red and decays with increasing wavenumber nearly following a power law with exponent ≈ 10. By analyzing the degree correlation and the admittance function, we find that the altimetric rate of sea-level change is coherent with the total steric field in the whole range of wavelengths considered (down to 1000 km), but particularly for wavelengths exceeding 2000 km. Thermosteric and halosteric components are moderately anti-correlated within the range of wavelengths 1000-4000 km. Their power spectrum varies significantly with the wavelength and, for 2000 km, it is equally partitioned between the two components. The power of regional sea-level variations driven by Glacial Isostatic Adjustment (GIA) and the melting of continental ice sheets is small compared to that held by the steric component, which explains most of the regional variability shown by the altimetry record. This causes the elusiveness of the "static" sea-level fingerprints, which at present are hidden in the pattern of the residual sea-level (i.e., the altimetry-derived sea-level minus the steric component). However, we find that at harmonic degree 2, mainly associated with rotational variations, the power of glacial melting is significant and it will progressively increase during next century in response to global warming. We also estimate that at the end of the Mid-Holocene the strength of the GIA fingerprints was ≈ 10 times larger than today, well above the long-wavelength component of residual sea-level.

  16. Evaluation of dose-response curve analysis in delineating shared or different molecular sites of action for osteolathyrogens.

    PubMed

    Dawson, Douglas A; Scott, Brenda D; Ellenberger, M Jason; Pöch, Gerald; Rinaldi, Andrea C

    2004-03-01

    Single-chemical and mixture concentration-response curves generated using a frog embryo model were examined for value in assessing whether chemicals exert toxic effects at the same or at different molecular sites of action. Toxicity tests were conducted on a series of osteolathyrogens, i.e. chemicals that inhibit cross-linking of developing connective tissue fibers. Induction of osteolathyrism, which manifests as lesions in the notochord of exposed tadpoles, has several possible molecular sites of action, including agent-cofactor reactivity during the enzyme-mediated cross-linking process. UV-VIS spectrophotometry of osteolathyrogen-cofactor reactivity (i.e. in vitro analysis) was coupled with the 96-h frog embryo mixture toxicity assay (i.e. in vivo toxicity) to compare molecular sites of action for several osteolathyrogens with the combined osteolathyritic effects of the agents. Single-chemical concentration-response curves were used to calculate theoretical curves for the dose-addition model of combined effect. Slope and EC(50) values for both theoretical and experimental mixture curves were then generated to statistically examine the hypothesis that agents with shared sites of action have dose-response curve (DRC) slopes that are similar when given alone and in combination, and slope and EC(50) values that, when administered together, are consistent with those calculated for dose-addition. For combinations of cofactor-binding agents (semicarbazide, thiosemicarbazide, aminoacetonitrile), slope values were generally similar with additivity quotients near 1.0 (1.0=dose-additive) and combined osteolathyritic effects that were consistent with dose-addition. None of these were true for combinations that included agents that did not show rapid cofactor binding (β-aminopropionitrile, methyleneaminoacetonitrile). The results suggest that DRC analysis could be a useful tool for delineating common or different molecular sites of toxic action and that the approaches used

  17. Generalized semi-analytical finite difference method for dispersion curves calculation and numerical dispersion analysis for Lamb waves.

    PubMed

    Packo, Pawel; Uhl, Tadeusz; Staszewski, Wieslaw J

    2014-09-01

    The paper presents an efficient and accurate method for dispersion curve calculation and analysis of numerical models for guided waves. The method can be used for any arbitrarily selected anisotropic material. The proposed approach utilizes the wave equation and through-thickness-only discretization of anisotropic, layered plates to obtain the Lamb wave characteristics. Thus, layered structures, such as composites, can be analyzed in a straightforward manner. A general framework for the proposed analysis is given, along with application examples. Although these examples are based on the local interaction simulation approach for elastic waves propagation, the proposed methodology can be easily adopted for other methods (e.g., finite elements). The method can be also used to study the influence of discretization parameters on dispersion curves estimates.

  18. 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.

  19. Open-Mode Debonding Analysis of Curved Sandwich Panels Subjected to Heating and Cryogenic Cooling on Opposite Faces

    NASA Technical Reports Server (NTRS)

    Ko, William L.

    1999-01-01

    Increasing use of curved sandwich panels as aerospace structure components makes it vital to fully understand their thermostructural behavior and identify key factors affecting the open-mode debonding failure. Open-mode debonding analysis is performed on a family of curved honeycomb-core sandwich panels with different radii of curvature. The curved sandwich panels are either simply supported or clamped, and are subjected to uniform heating on the convex side and uniform cryogenic cooling on the concave side. The finite-element method was used to study the effects of panel curvature and boundary condition on the open-mode stress (radial tensile stress) and displacement fields in the curved sandwich panels. The critical stress point, where potential debonding failure could initiate, was found to be at the midspan (or outer span) of the inner bonding interface between the sandwich core and face sheet on the concave side, depending on the boundary condition and panel curvature. Open-mode stress increases with increasing panel curvature, reaching a maximum value at certain high curvature, and then decreases slightly as the panel curvature continues to increase and approach that of quarter circle. Changing the boundary condition from simply supported to clamped reduces the magnitudes of open-mode stresses and the associated sandwich core depth stretching.

  20. NEW REACTOR DESIGN AND ANALYSIS OF NON LINEAR VIBRATIONS OF DOUBLY CURVED SHALLOW SHELL UNDER A THERMAL GRADIENT

    SciTech Connect

    Chanda, S.

    2004-10-06

    The present study concerns with the effects of material orthotropy,curvature, shear ratio and circumferential modulus under the influence of a temperature distribution throughout the shell structure. Here analysis is restricted to the study of nonlinear vibration of a doubly curved shell structure considering the periodic response of a simple bending mode due to curtailment of pages. Solutions of the problems with suitable illustrations are also presented.

  1. Molecular differentiation of Opisthorchis viverrini and Clonorchis sinensis eggs by multiplex real-time PCR with high resolution melting analysis.

    PubMed

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

    2013-12-01

    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.

  2. Differential diagnosis of Goatpox virus in Taiwan by multiplex polymerase chain reaction assay and high-resolution melt analysis.

    PubMed

    Chan, Kun-Wei; Lee, Ming-Liang; Yang, Wei-Cheng; Wong, Min-Liang; Hsu, Wei-Li; Ho, Chia-Fang; Hsieh, Yao-Ching; Wang, Chi-Young

    2014-03-01

    The A32L gene from a Goatpox virus (GTPV) strain isolated from a goat in Yunlin County (Taiwan) displays several substitutions compared with the sequence of the Kenyan GTPV vaccine strain SGP0240 and the Pellor GTPV strain. Samples from the skin lesions on 6 goats with GTPV infection or from goats with Orf virus (ORFV) infection were tested in a multiplex polymerase chain reaction (PCR) system that used primers GPF, GPR1, and GPR2 as well as previously published primers specific for ORFV. These primers were able to amplify either GTPV or ORFV without cross-reactivity. A high-resolution melt analysis (HRMA) was carried out on amplified DNA from the skin lesions of 6 goats with GTPV infection and with the GTPV SGP0240 strain. The results indicated that the melting temperature profiles amplified from samples with Yunlin GTPV infection can be differentiated from the GTPV SGP0240 strain. The findings showed that a successful differential assay for these GTPVs had been developed. Accordingly, both methods can be used to detect and differentiate GTPV isolated from animals that may have either been vaccinated or been infected with a wild strain. The multiplex PCR and HRMA could be used on skin samples of suspected cases to serve as the front-line and confirmative assays, respectively, which will be beneficial to the eradication of GTPV.

  3. [Scanning for KRAS, NRAS, BRAF, and PIK3CA mutations by DNA melting analysis with TaqMan probes].

    PubMed

    Botezatu, I V; Panchuk, I O; Stroganova, A M; Senderovich, A I; Kondratova, V N; Shelepov, V P; Lichtenstein, A V

    2017-01-01

    Scanning for mutations by DNA melting analysis (DMA) is based on asymmetric PCR followed by the melting of duplexes formed by single-stranded amplicons with TaqMan probes. The method is optimally suited for clinical genetic testing; it is easy to perform, high-throughput, and sensitive. The detection limit of mutant alleles by the DMA method is about 3%, which is much higher than the sensitivity of Sanger sequencing. In addition, the DMA method is realized in a closed-tube format, while 2-h assay is carried out in a single tube without any intermediate or additional procedures thereby minimizing the risk of cross contamination of the samples. The validation of the DMA method was performed by scanning for mutations of clinically significant genes KRAS, NRAS, BRAF, and   PIK3CA in 324 DNA samples from tumors of patients with melanoma, colorectal and lung cancer. DNA was isolated either directly from tumor tissues, or from formalin-fixed paraffin-embedded tumor tissues. The detected mutations were verified by Sanger sequencing. The spectra of mutations identified in each tumor type correspond to the literature data and, thus, validate the use of DMA.

  4. Fitting sediment rating curves using regression analysis: a case study of Russian Arctic rivers

    NASA Astrophysics Data System (ADS)

    Tananaev, N. I.

    2015-03-01

    Published suspended sediment data for Arctic rivers is scarce. Suspended sediment rating curves for three medium to large rivers of the Russian Arctic were obtained using various curve-fitting techniques. Due to the biased sampling strategy, the raw datasets do not exhibit log-normal distribution, which restricts the applicability of a log-transformed linear fit. Non-linear (power) model coefficients were estimated using the Levenberg-Marquardt, Nelder-Mead and Hooke-Jeeves algorithms, all of which generally showed close agreement. A non-linear power model employing the Levenberg-Marquardt parameter evaluation algorithm was identified as an optimal statistical solution of the problem. Long-term annual suspended sediment loads estimated using the non-linear power model are, in general, consistent with previously published results.

  5. Eigen analysis of tree-ring records: Part 1, a limited representativeness of regional curve

    NASA Astrophysics Data System (ADS)

    Yang, Bao; Sonechkin, Dmitry M.; Datsenko, Nina M.; Ivashchenko, Nadezda N.; Liu, Jingjing; Qin, Chun

    2011-12-01

    Based on a set of very long-living (2,000 years) Qilian junipers ( Sabina przewalskii Kom.) from the north-eastern part of the Tibetan Plateau (the region of Dulan), we carefully consider the regional curve standardization (RCS) technique. For this goal, we correlate deviations of individual tree-ring width records from their regional mean age-dependent curve (RC). It turns out that these correlations keep their positivity for almost all shifts between ages compared (up to 500 years and even more) evidencing each Dulan juniper to be a unique "thermometer". Just the unification of these "thermometers" in the form RC creates a spurious positive trend in the Dulan chronology. We modify the RCS technique to closer attach RC to these "thermometers" in order to construct a new chronology in which the trend is absent.

  6. Fracture toughness master-curve analysis of the tempered martensitic steel Eurofer97

    NASA Astrophysics Data System (ADS)

    Mueller, Pablo; Spätig, P.; Bonadé, R.; Odette, G. R.; Gragg, D.

    2009-04-01

    We report fracture toughness data for the reduced activation tempered martensitic steel Eurofer97 in the lower to middle transition region. The fracture toughness was measured from tests carried out on 0.35 T and 0.87 T pre-cracked compact tension specimens. The data were first analyzed using the ASTM E1921 standard. The toughness-temperature behavior and scatter were shown to deviate from the ASTM E1921 standard predictions near the lower shelf. Using the method of maximum likelihood, the athermal component of the master-curve was calculated to better fit the data from the lower to the middle transition region. We showed that these master-curve adjustments are necessary to make the To values obtained near the lower shelf with 0.35 TC( T) specimens consistent with those obtained in the middle transition region with 0.87 TC( T) specimens.

  7. Effects of experimental design on calibration curve precision in routine analysis

    PubMed Central

    Pimentel, Maria Fernanda; Neto, Benício de Barros; Saldanha, Teresa Cristina B.

    1998-01-01

    A computational program which compares the effciencies of different experimental designs with those of maximum precision (D-optimized designs) is described. The program produces confidence interval plots for a calibration curve and provides information about the number of standard solutions, concentration levels and suitable concentration ranges to achieve an optimum calibration. Some examples of the application of this novel computational program are given, using both simulated and real data. PMID:18924816

  8. Analysis of spatial variability of extreme rainfall at radar subpixel scale using IDF curves

    NASA Astrophysics Data System (ADS)

    Peleg, Nadav; Marra, Francesco; Fatichi, Simone; Paschalis, Athanasios; Molnar, Peter; Burlando, Paolo

    2016-04-01

    Extreme rainfall is quantified in engineering practice using Intensity-Duration-Frequency curves (IDFs) that are traditionally derived from rain-gauges and, more recently, also from weather radars. These instruments measure rainfall at different spatial scales: rain-gauge samples rainfall at the point scale while weather radar averages precipitation over a relatively large area, generally around 1 km2. As such, a radar derived IDF curve is representative of the mean areal rainfall over a given radar pixel and neglects the within-pixel rainfall variability. In this study, we quantify subpixel variability of extreme rainfall by using a novel space-time rainfall generator (STREAP model) that downscales in space the rainfall within a given radar pixel. The study was conducted using a long radar data record (23 years) and a very dense rain-gauge network in the Eastern Mediterranean area. Radar-IDF curves, together with an ensemble of point-based IDF curves representing the radar subpixel extreme rainfall variability, were developed fitting GEV distributions to annual rainfall maxima. It was found that the mean areal extreme rainfall derived from the radar underestimate most of the extreme values computed for point locations within the radar pixel. The subpixel variability of extreme rainfall was found to increase with longer return periods and shorter durations. For the longer return periods, a considerable enhancement of extreme rainfall variability was found when stochastic (natural) climate variability was taken into account. Bounding the range of the subpixel extreme rainfall derived from radar-IDF can be of major importance for applications that require very local estimates of rainfall extremes.

  9. Analysis of diffusion in curved surfaces and its application to tubular membranes

    PubMed Central

    Klaus, Colin James Stockdale; Raghunathan, Krishnan; DiBenedetto, Emmanuele; Kenworthy, Anne K.

    2016-01-01

    Diffusion of particles in curved surfaces is inherently complex compared with diffusion in a flat membrane, owing to the nonplanarity of the surface. The consequence of such nonplanar geometry on diffusion is poorly understood but is highly relevant in the case of cell membranes, which often adopt complex geometries. To address this question, we developed a new finite element approach to model diffusion on curved membrane surfaces based on solutions to Fick’s law of diffusion and used this to study the effects of geometry on the entry of surface-bound particles into tubules by diffusion. We show that variations in tubule radius and length can distinctly alter diffusion gradients in tubules over biologically relevant timescales. In addition, we show that tubular structures tend to retain concentration gradients for a longer time compared with a comparable flat surface. These findings indicate that sorting of particles along the surfaces of tubules can arise simply as a geometric consequence of the curvature without any specific contribution from the membrane environment. Our studies provide a framework for modeling diffusion in curved surfaces and suggest that biological regulation can emerge purely from membrane geometry. PMID:27733625

  10. CONFIRMATION OF HOT JUPITER KEPLER-41b VIA PHASE CURVE ANALYSIS

    SciTech Connect

    Quintana, Elisa V.; Rowe, Jason F.; Caldwell, Douglas A.; Christiansen, Jessie L.; Jenkins, Jon M.; Morris, Robert L.; Smith, Jeffrey C.; Thompson, Susan E.; Barclay, Thomas; Ciardi, David R.; Klaus, Todd C.

    2013-04-20

    We present high precision photometry of Kepler-41, a giant planet in a 1.86 day orbit around a G6V star that was recently confirmed through radial velocity measurements. We have developed a new method to confirm giant planets solely from the photometric light curve, and we apply this method herein to Kepler-41 to establish the validity of this technique. We generate a full phase photometric model by including the primary and secondary transits, ellipsoidal variations, Doppler beaming, and reflected/emitted light from the planet. Third light contamination scenarios that can mimic a planetary transit signal are simulated by injecting a full range of dilution values into the model, and we re-fit each diluted light curve model to the light curve. The resulting constraints on the maximum occultation depth and stellar density combined with stellar evolution models rules out stellar blends and provides a measurement of the planet's mass, size, and temperature. We expect about two dozen Kepler giant planets can be confirmed via this method.

  11. A light curve and its analysis of Type Ia SN 1604

    NASA Astrophysics Data System (ADS)

    Lee, Eun Hee; Lee, Dae-Young; Mihn, Byeong-Hee

    2015-08-01

    SN 1604, known as Kepler’s supernova, was first detected by European observers, but a full light curve including its peak brightness and initial decline part can only be completed by extra data from Korean royal astronomers of four centuries ago. Nowadays, it is considered one of the Type Ia galactic supernovae, which show the empirical correlation between decline rate and peak luminosity - so called Phillips relation or width-luminosity (W-L) relation. Here, we reconstruct a new light curve based on both the Korean and European records of SN 1604. Using this light curve and W-L relation, we present an observed rise time and decline rates after peak, and derive its absolute peak magnitude and distance. In this study, observed rise time (≈ 19±1 days) shows a good agreement with typical mean time of Type Ia SNe, while the initial decline rates such as Δm15(V) and Δm20(V) represent steeper and faster values than the extra-galactic SNe Ia. Moreover, its absolute peak magnitude and distance derived from the W-L relation show much fainter and nearer values, respectively than the estimated results by different methods

  12. Statistically generated weighted curve fit of residual functions for modal analysis of structures

    NASA Technical Reports Server (NTRS)

    Bookout, P. S.

    1995-01-01

    A statistically generated weighting function for a second-order polynomial curve fit of residual functions has been developed. The residual flexibility test method, from which a residual function is generated, is a procedure for modal testing large structures in an external constraint-free environment to measure the effects of higher order modes and interface stiffness. This test method is applicable to structures with distinct degree-of-freedom interfaces to other system components. A theoretical residual function in the displacement/force domain has the characteristics of a relatively flat line in the lower frequencies and a slight upward curvature in the higher frequency range. In the test residual function, the above-mentioned characteristics can be seen in the data, but due to the present limitations in the modal parameter evaluation (natural frequencies and mode shapes) of test data, the residual function has regions of ragged data. A second order polynomial curve fit is required to obtain the residual flexibility term. A weighting function of the data is generated by examining the variances between neighboring data points. From a weighted second-order polynomial curve fit, an accurate residual flexibility value can be obtained. The residual flexibility value and free-free modes from testing are used to improve a mathematical model of the structure. The residual flexibility modal test method is applied to a straight beam with a trunnion appendage and a space shuttle payload pallet simulator.

  13. Breakthrough curve analysis of pressure swing adsorption for hydrogen isotope separation

    SciTech Connect

    Kotoh, K.; Tanaka, M.; Sakamoto, T.; Nakamura, Y.; Asakura, Y.; Uda, T.; Sugiyama, T.

    2008-07-15

    For the purpose of developing an effective system for hydrogen isotope separation, we have been studying the adsorption-desorption dynamic behavior of hydrogen and deuterium in a packed-bed column with synthetic zeolites, aimed at applying the pressure swing adsorption process. The adsorption behavior of molecules in the packed-bed is reflected in the breakthrough curves. To understand the characteristic behaviors of hydrogen isotopes in the packed-bed, we carried out breakthrough experiments in a conventional adsorption process and in a practical process following sequential processes alternating between adsorption and desorption. From the former experiments, the results were obtained that the overall mass transfer was influenced by longitudinal dispersion relating to the superficial velocity and that the process governing the mass transfer within adsorbents was diffusion in the macro-pores of pellets. In the latter experiments, unique profile breakthrough curves were observed. These curves can be described with the numerical simulation assuming the initial distributions in a packed-bed. (authors)

  14. 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

  15. AN ANALYSIS OF THE SHAPES OF INTERSTELLAR EXTINCTION CURVES. VI. THE NEAR-IR EXTINCTION LAW

    SciTech Connect

    Fitzpatrick, E. L.; Massa, D. E-mail: massa@derckmassa.net

    2009-07-10

    We combine new observations from the Hubble Space Telescope's Advanced Camera of Survey with existing data to investigate the wavelength dependence of near-IR (NIR) extinction. Previous studies suggest a power law form for NIR extinction, with a 'universal' value of the exponent, although some recent observations indicate that significant sight line-to-sight line variability may exist. We show that a power-law model for the NIR extinction provides an excellent fit to most extinction curves, but that the value of the power, {beta}, varies significantly from sight line to sight line. Therefore, it seems that a 'universal NIR extinction law' is not possible. Instead, we find that as {beta} decreases, R(V) {identical_to} A(V)/E(B - V) tends to increase, suggesting that NIR extinction curves which have been considered 'peculiar' may, in fact, be typical for different R(V) values. We show that the power-law parameters can depend on the wavelength interval used to derive them, with the {beta} increasing as longer wavelengths are included. This result implies that extrapolating power-law fits to determine R(V) is unreliable. To avoid this problem, we adopt a different functional form for NIR extinction. This new form mimics a power law whose exponent increases with wavelength, has only two free parameters, can fit all of our curves over a longer wavelength baseline and to higher precision, and produces R(V) values which are consistent with independent estimates and commonly used methods for estimating R(V). Furthermore, unlike the power-law model, it gives R(V)s that are independent of the wavelength interval used to derive them. It also suggests that the relation R(V) = -1.36 E(K-V)/(E(B-V)) - 0.79 can estimate R(V) to {+-}0.12. Finally, we use model extinction curves to show that our extinction curves are in accord with theoretical expectations, and demonstrate how large samples of observational quantities can provide useful constraints on the grain properties.

  16. Magnetic unmixing of first-order reversal curve diagrams using principal component analysis

    NASA Astrophysics Data System (ADS)

    Lascu, Ioan; Harrison, Richard; Li, Yuting; Piotrowski, Alexander; Channell, James; Muraszko, Joy; Hodell, David

    2015-04-01

    We have developed a magnetic unmixing method based on principal component analysis (PCA) of entire first-order reversal curve (FORC) diagrams. FORC diagrams are an advanced hysteresis technique that allows the quantitative characterisation of magnetic grain size, domain state, coercivity and spatial distribution of ensembles of particles within a sample. PCA has been previously applied on extracted central ridges from FORC diagrams of sediment samples containing single domain (SD) magnetite produced by magnetotactic bacteria (Heslop et al., 2014). We extend this methodology to the entire FORC space, which incorporates additional SD signatures, pseudo-single domain (PSD) and multi domain (MD) magnetite signatures, as well as fingerprints of other minerals, such as hematite (HEM). We apply the PCA by resampling the FORC distribution on a regular grid designed to encompass all significant features. Typically 80-90% of the variability within the FORC dataset is described by one or two principal components. Individual FORCs are recast as linear combinations of physically distinct end-member FORCs defined using the principal components and constraints derived from physical modelling. In a first case study we quantify the spatial variation of end-member components in surficial sediments along the North Atlantic Deep Water (NADW) from Iceland to Newfoundland. The samples have been physically separated into granulometric fractions, which added a further constraint in determining three end members used to model the magnetic ensemble, namely a coarse silt-sized MD component, a fine silt-sized PSD component, and a mixed clay-sized component containing both SD magnetite and hematite (SD+HEM). Sediments from core tops proximal to Iceland are dominated by the SD+HEM component, whereas those closer to Greenland and Canada are increasingly dominated by MD grains. Iceland sediments follow a PSD to SD+HEM trend with increasing grain-size fraction, whereas the Greenland and North

  17. Petrogenesis and volatile stratigraphy of the Bishop Tuff - evidence from melt inclusion analysis

    SciTech Connect

    Dunbar, N.W.; Hervig, R.L. Arizona State Univ., Tempe )

    1992-10-01

    The preeruptive volatile gradient of the Bishop Tuff (BT) is determined on the basis of detailed analyses of the H2O, F, and Cl contents of melt inclusions in phenocrysts from different stratigraphic levels of the deposit. The magma which produced BT was found to be strongly zoned with respect to H2O, and slightly zoned with respect to F and B. The bulk of the volatile zonation within the BT magma was in the 120 cu km of magma which produced the Plinian tephra, where the H2O content decreases from a mean of 6 wt pct to a mean of 3.3 wt pct to between 2 and 3 wt pct for the magma which formed the ignimbrite. The strong H2O gradient suggests that only the magma from the very upper portion of the magma chamber could have been saturated with respect to an H2O-dominated vapor phase, because of the decrease in H2O contents with decreasing pressure. The volatile enrichment in the magma which formed the BT Plinian tephra appears to have occurred independently of strong trace element enrichment and may have been generated by rapid diffusion from a sidewall crystallization zone. 60 refs.

  18. 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

  19. Finite element analysis of laser irradiated metal heating and melting processes

    NASA Astrophysics Data System (ADS)

    Sowdari, Dharani; Majumdar, Pradip

    2010-09-01

    Laser technology has shown fast growth due to its demands in material processing and manufacturing. Laser material processing includes various applications like cutting, welding, drilling, cladding and surface treatment. In laser surface treatment, the material properties at the surface are altered through surface alloying and transformation hardening. In this study, an enthalpy-based computational model is developed for analyzing laser heating and melting of metals. The solution to the problem is obtained by using a finite element method and validated by comparing the results with that given by an analytical solution to a limiting case problem. A solution algorithm and a computational code are developed to estimate the temperature distribution, solid-liquid interface location and shape and size of the molten pool. The computational model is validated by comparing results with a limiting case analytical model. The study is conducted to analyze the heating rate, the heat affected zone, and the shape and size of the molten pool using a Gaussian laser beam.

  20. The Vanderbilt EB Factory: Development of Light Curve Analysis Tools for Precision Stellar Astrophysics with Kepler Eclipsing Binaries

    NASA Astrophysics Data System (ADS)

    Stassun, Keivan; Paegert, M.; De Lee, N. M.; Cargile, P.

    2013-01-01

    The goal of the Vanderbilt EB Factory is to develop an end-to-end computational pipeline that allows automatic processing of massive amounts of light curve data -- from period finding, to object classification, to determination of the stellar physical properties -- in order to find the most scientifically interesting eclipsing binaries (EBs) and to permit accurate modeling of these EBs for detailed tests and benchmarking of theoretical stellar evolution models. We are integrating the most successful algorithms into a single, cohesive workflow environment, and are applying this 'EB Factory' to the full public Kepler dataset to find and characterize new "benchmark grade" EBs, and will disseminate both the enhanced data products from this pipeline and the pipeline itself to the broader NASA science community, especially other Kepler mission researchers. More generally, we are developing the EB Factory as a flexible, open source, modular framework in order to permit simple modifications by other users for a wide array of other types of variable stars of interest, such as RR Lyraes. Finally, we will present our developing suite of light-curve analysis tools available to the community from the Vanderbilt Initiative in Data-intensive Astrophysics (VIDA), including the Filtergraph instant data portal service, and the web-based LCchopper and LCanimator light-curve analysis services.

  1. How to detect melting in laser heating diamond anvil cell

    NASA Astrophysics Data System (ADS)

    Liuxiang, Yang

    2016-07-01

    Research on the melting phenomenon is the most challenging work in the high pressure/temperature field. Until now, large discrepancies still exist in the melting curve of iron, the most interesting and extensively studied element in geoscience research. Here we present a summary about techniques detecting melting in the laser heating diamond anvil cell.

  2. On the Limitations of Breakthrough Curve Analysis in Fixed-Bed Adsorption

    NASA Technical Reports Server (NTRS)

    Knox, James C.; Ebner, Armin D.; LeVan, M. Douglas; Coker, Robert F.; Ritter, James A.

    2016-01-01

    This work examined in detail the a priori prediction of the axial dispersion coefficient from available correlations versus obtaining it and also mass transfer information from experimental breakthrough data and the consequences that may arise when doing so based on using a 1-D axially dispersed plug flow model and its associated Danckwerts outlet boundary condition. These consequences mainly included determining the potential for erroneous extraction of the axial dispersion coefficient and/or the LDF mass transfer coefficient from experimental data, especially when non-plug flow conditions prevailed in the bed. Two adsorbent/adsorbate cases were considered, i.e., carbon dioxide and water vapor in zeolite 5A, because they both experimentally exhibited significant non-plug flow behavior, and the water-zeolite 5A system exhibited unusual concentration front sharpening that destroyed the expected constant pattern behavior (CPB) when modeled with the 1-D axially dispersed plug flow model. Overall, this work showed that it was possible to extract accurate mass transfer and dispersion information from experimental breakthrough curves using a 1-D axial dispersed plug flow model when they were measured both inside and outside the bed. To ensure the extracted information was accurate, the inside the bed breakthrough curves and their derivatives from the model were plotted to confirm whether or not the adsorbate/adsorbent system was exhibiting CPB or any concentration front sharpening near the bed exit. Even when concentration front sharpening was occurring with the water-zeolite 5A system, it was still possible to use the experimental inside and outside the bed breakthrough curves to extract fundamental mass transfer and dispersion information from the 1-D axial dispersed plug flow model based on the systematic methodology developed in this work.

  3. An analysis of the light curve of the post common envelope binary MT Serpentis

    NASA Astrophysics Data System (ADS)

    Bruch, A.; Vaz, L. P. R.; Diaz, M. P.

    2001-10-01

    Photometric observations of MT Ser, the central star of the planetary nebula Abell 41 are presented. The periodic modulations detected by Grauer & Bond (\\cite{Gra83}) are confirmed, thus firmly establishing the binary nature of MT Ser. The significantly enlarged time base permits us to derive more accurate ephemeris. The orbital period is either P1 = 0.113226533 days or twice that value, P2 = 0.226453066 days. We analyze the light curve (after a careful subtraction of the nebular contribution) with the Wilson-Devinney light curve synthesis routine. Since it is not a priori clear which is the true orbital period of MT Ser, two radically different models, one based on P1 the other on P2 are considered: (1) A low temperature component orbiting around a hot sub-dwarf. The variability is then due to a reflection effect together with ellipsoidal variations of one or both components. (2) Two hot sub-dwarfs of similar temperature and luminosity, partially eclipsing each other and exhibiting ellipsoidal variations. In both models, the primary as well as the secondary component are required to almost fill their respective Roche lobes. A contact configuration is possible. Pros and cons can be found for either of the two models. A final decision between them has to await the observations of a radial velocity curve. The orbital period is currently decreasing at a rate of dot {P}/P = -1.15 x 10-9 d-1. Interpreting this as due to mass loss via a stellar winds permits us to estimate mass loss rates depending on the different model assumptions. Based on observations obtained at the Observatório do Pico dos Dias, LNA/MCT, Itajubá, Brazil.

  4. Regional frequency analysis of extreme precipitation with consideration of uncertainties to update IDF curves for the city of Trondheim

    NASA Astrophysics Data System (ADS)

    Hailegeorgis, Teklu T.; Thorolfsson, Sveinn T.; Alfredsen, Knut

    2013-08-01

    Regional frequency analysis based on the method of L-moments is performed from annual maximum series of extreme precipitation intensity to update Intensity-Duration-Frequency (IDF) curves for the city of Trondheim. The main problems addressed are (1) reduction of uncertainties of different sources for reliable estimation of quantiles: (i) testing of trend patterns and stationarity of the data series from the target site and demonstrating the dependency of results on the data used; (ii) testing regional homogeneity of extreme precipitation events for the climate regime in the study area and “pooling” of regional data for data augmentation and reduction of uncertainty due to short length of data series; and (iii) selection of distributions for extreme precipitation events of different durations to reduce the uncertainty due to choice of distributions; and (2) assessment and quantification of sampling uncertainty in terms of interval estimates (confidence bounds) of quantiles. Trend patterns and check for stationarity were demonstrated for a data from a target site based on both non-parametric Mann-Kendall and parametric regression tests. Selection of distributions was performed based on Z-statistics and L-moment ratio diagrams. Non-parametric balanced bootstrap resampling was used to quantify the sampling uncertainty. For extreme precipitation events of shorter durations (5-30 min) there are statistically significant increasing trend patterns for the data series with start years of 1992-1998 while there are no significant trend patterns for recent extremes and there are no statistically significant trend patterns for longer durations (45-180 min). The results of the analyses indicate that: (1) significance tests for trend patterns and stationarity are dependent on the data series used but the stationarity assumption is valid for the data series used from the target site. (2) the extreme precipitation events from four sites in Trondheim are homogeneous and can be

  5. Buckling Analysis of Anisotropic Curved Panels and Shells with Variable Curvature

    NASA Technical Reports Server (NTRS)

    Jaunky, Navin; Knight, Norman F., Jr.; Ambur, Damodar R.

    1998-01-01

    A buckling formulation for anisotropic curved panels with variable curvature is presented in this paper. The variable curvature panel is assumed to consists of two or more panels of constant but different curvatures. Bezier functions are used as Ritz functions Displacement (C(sup 0)), and slope (C(sup 1)) continuities between segments are imposed by manipulation of the Bezier control points. A first-order shear-deformation theory is used in the buckling formulation. Results obtained from the present formulation are compared with those from finite element simulations and are found to be in good agreement.

  6. Dose-response curve slope is a missing dimension in the analysis of HIV-1 drug resistance.

    PubMed

    Sampah, Maame Efua S; Shen, Lin; Jilek, Benjamin L; Siliciano, Robert F

    2011-05-03

    HIV-1 drug resistance is a major clinical problem. Resistance is evaluated using in vitro assays measuring the fold change in IC(50) caused by resistance mutations. Antiretroviral drugs are used at concentrations above IC(50), however, and inhibition at clinical concentrations can only be predicted from IC(50) if the shape of the dose-response curve is also known. Curve shape is influenced by cooperative interactions and is described mathematically by the slope parameter or Hill coefficient (m). Implicit in current analysis of resistance is the assumption that mutations shift dose-response curves to the right without affecting the slope. We show here that m is altered by resistance mutations. For reverse transcriptase and fusion inhibitors, single resistance mutations affect both slope and IC(50). For protease inhibitors, single mutations primarily affect slope. For integrase inhibitors, only IC(50) is affected. Thus, there are fundamental pharmacodynamic differences in resistance to different drug classes. Instantaneous inhibitory potential (IIP), the log inhibition of single-round infectivity at clinical concentrations, takes into account both slope and IC(50), and thus provides a direct measure of the reduction in susceptibility produced by mutations and the residual activity of drugs against resistant viruses. The standard measure, fold change in IC(50), does not correlate well with changes in IIP when mutations alter slope. These results challenge a fundamental assumption underlying current analysis of HIV-1 drug resistance and suggest that a more complete understanding of how resistance mutations reduce antiviral activity requires consideration of a previously ignored parameter, the dose-response curve slope.

  7. Common Variants in 6 Lipid-Related Genes Discovered by High-Resolution DNA Melting Analysis and Their Association with Plasma Lipids.

    PubMed

    Carlquist, John F; McKinney, Jason T; Horne, Benjamin D; Camp, Nicola J; Cannon-Albright, Lisa; Muhlestein, Joseph B; Hopkins, Paul; Clarke, Jessica L; Mower, Chrissa P; Park, James J; Nicholas, Zachary P; Huntinghouse, John A; Anderson, Jeffrey L

    2011-07-10

    BACKGROUND: Total cholesterol was among the earliest identified risk factors for coronary heart disease (CHD). We sought to identify genetic variants in six genes associated with lipid metabolism and estimate their respective contribution to risk for CHD. METHODS: For 6 lipid-associated genes (LCAT, CETP, LIPC, LPL, SCARB1, and ApoF) we scanned exons, 5' and 3' untranslated regions, and donor and acceptor splice sites for variants using Hi-Res Melting® curve analysis (HRMCA) with confirmation by cycle sequencing. Healthy subjects were used for SNP discovery (n=64), haplotype determination/tagging SNP discovery (n=339), and lipid association testing (n=786). RESULTS: In 17,840 bases of interrogated sequence, 90 variant SNPs were identified; 19 (21.1%) previously unreported. Thirty-four variants (37.8%) were exonic(16 non-synonymous), 28 (31.1%) in intron-exon boundaries, and 28 (31.1%) in the 5' and 3' untranslated regions. Compared to cycle sequencing, HRMCA had sensitivity of 99.4% and specificity of 97.7%. Tagging SNPs (n=38) explained >90% of the variation in the 6 genes and identified linkage disequilibrium (LD) groups. Significant beneficial lipid profiles were observed for CETP LD group 2, LIPC LD groups 1 and 7, and SCARB1 LD groups 1, 3 and 4. Risk profiles worsened for CETP LD group 3, LPL LD group 4. CONCLUSIONS: These findings demonstrate the feasibility, sensitivity, and specificity of HRMCA for SNP discovery. Variants identified in these genes may be used to predict lipid-associated risk and reclassification of clinical CHD risk.

  8. 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

  9. Rapid and inexpensive body fluid identification by RNA profiling-based multiplex High Resolution Melt (HRM) analysis.

    PubMed

    Hanson, Erin K; Ballantyne, Jack

    2013-01-01

    Positive identification of the nature of biological material present on evidentiary items can be crucial for understanding the circumstances surrounding a crime. However, traditional protein-based methods do not permit the identification of all body fluids and tissues, and thus molecular based strategies for the conclusive identification of all forensically relevant biological fluids and tissues need to be developed. Messenger RNA (mRNA) profiling is an example of such a molecular-based approach. Current mRNA body fluid identification assays involve capillary electrophoresis (CE) or quantitative RT-PCR (qRT-PCR) platforms, each with its own limitations. Both platforms require the use of expensive fluorescently labeled primers or probes. CE-based assays require separate amplification and detection steps thus increasing the analysis time. For qRT-PCR assays, only 3-4 markers can be included in a single reaction since each requires a different fluorescent dye. To simplify mRNA profiling assays, and reduce the time and cost of analysis, we have developed single- and multiplex body fluid High Resolution Melt (HRM) assays for the identification of common forensically relevant biological fluids and tissues. The incorporated biomarkers include IL19 (vaginal secretions), IL1F7 (skin), ALAS2 (blood), MMP10 (menstrual blood), HTN3 (saliva) and TGM4 (semen).  The HRM assays require only unlabeled PCR primers and a single saturating intercalating fluorescent dye (Eva Green). Each body-fluid-specific marker can easily be identified by the presence of a distinct melt peak. Usually, HRM assays are used to detect variants or isoforms for a single gene target. However, we have uniquely developed duplex and triplex HRM assays to permit the simultaneous detection of multiple targets per reaction. Here we describe the development and initial performance evaluation of the developed HRM assays. The results demonstrate the potential use of HRM assays for rapid, and relatively inexpensive

  10. Distinguishing Mantle Components by Sr and Nd Isotope Analysis of Single Melt Inclusions: Case Study on Italian Potassium-rich Lavas

    NASA Astrophysics Data System (ADS)

    Koornneef, J.; Nikogosian, I.; van Bergen, M.; Smeets, R.; Bouman, C.; Schwieters, J. B.; Davies, G. R.

    2014-12-01

    Melt inclusions record more extreme isotopic variability than their bulk host lavas and offer the potential to better constrain mantle components that contribute to magmatism. Isotopic analyses of melt inclusions are, however, challenging because of their limited size. To date, Sr and Pb isotope data have been obtained for oceanic islands by application of in situ analysis techniques, either by SIMS or LA-(MC)-ICPMS. Comprehensive studies of inclusions from other settings have yet to be performed. Here, we report the first combined Sr and Nd isotope data on individual melt inclusions from Pliocene-Quaternary K-rich lavas from mainland Italy, obtained using wet chemistry techniques and TIMS analysis. We use newly developed 1013 Ohm resistors mounted in the feedback loop of Faraday cup amplifiers. Compared to default 1011 Ohm resistors, use of 1013 Ohm resistors results in a 10-fold improvement of the signal-to-noise ratio and more precise data when analysing small ion beams (< 20 mV). Twenty-one olivine hosted (85 - 92 mol % Fo) melt inclusions from seven volcanic centres along the Italian peninsula were analysed. Inclusions were homogenised and analysed for trace elements prior to isotopic analysis. 87Sr/86Sr ratios in the melt inclusions range from 0.70508 to 0.71543; 143Nd/144Nd ratios from 0.51175 to 0.51268. Significant differences in 87Sr/86Sr and 143Nd/144Nd were found between melt inclusions and host lavas indicating distinct evolution paths for the lava groundmasses and the primitive melts that were trapped in the phenocrysts. The isotopic variability is interpreted to be the result of (1) mixing of melts derived from a heterogeneous mantle modified by subduction-related metasomatism, (2) mingling of distinct batches of olivine-bearing magma within a plumbing system, and (3) local assimilation of crustal material. These preliminary data suggest that combined analysis of individual melt inclusions for trace elements and Sr-Nd isotope ratios is a promising

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

    PubMed

    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

  12. 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

  13. The Application of the Principal Curve Analysis Technique to Smooth Beam Lines

    SciTech Connect

    Friedsam, H.; Oren, W.; /SLAC

    2005-08-12

    The smoothness of a beam line refers to the quality of the relative positioning of a number of adjacent beam guiding components. The fact that smoothness is of highest priority when positioning magnets can be seen in the local tolerances imposed by the beam optics. In the past, smoothing has been done by separating horizontal and vertical misalignments and then applying some sort of analytical or manual ''feathering'' technique. The Stanford Linear Collider (SLC) did not easily lend itself to this sort of smoothing because of the highly coupled nature of its pitched and rolled beam line. This paper will discuss an attempt to develop a repeatable method which is independent of the inconsistencies of human judgment and can simultaneously smooth in two or more dimensions. Four major goals were defined for the smoothing algorithm used on the SLC alignment. The first, was to simultaneously model errors for both horizontal and vertical directions. Secondly, a smooth curve whose shape was suggested by the data and not by a predetermined model was implied by the fact that unknown systematic errors were being eliminated. Thirdly, this curve must be a reproducibly fit, independent of the inconsistent nature of human judgment. Fourth, the result of the procedure was to minimize the number and size of magnet movements to reach the final alignment criteria.

  14. Thermodynamic analysis of chain-melting transition temperatures for monounsaturated phospholipid membranes: dependence on cis-monoenoic double bond position.

    PubMed Central

    Marsh, D

    1999-01-01

    Unsaturated phospholipid is the membrane component that is essential to the dynamic environment needed for biomembrane function. The dependence of the chain-melting transition temperature, T(t), of phospholipid bilayer membranes on the position, n(u), of the cis double bond in the glycerophospholipid sn-2 chain can be described by an expression of the form T(t) = T(t)(c)(1 + h'(c)|n(u) - n(c)|)/(1 + s'(c)|n(u) - n(c)|), where n(c) is the chain position of the double bond corresponding to the minimum transition temperature, T(t)(c), for constant diacyl lipid chain lengths. This implies that the incremental transition enthalpy (and entropy) contributed by the sn-2 chain is greater for whichever of the chain segments, above or below the double-bond position, is the longer. The critical position, n(c), of the double bond is offset from the center of the sn-2 chain by an approximately constant amount, deltan(c) approximately 1. 5 C-atom units. The dependence of the parameters T(t)(c), h'(c), and s'(c) on sn-1 and sn-2 chain lengths can be interpreted consistently when allowance is made for the chain packing mismatch between the sn-1 and sn-2 chains. The length of the sn-2 chain is reduced by approximately 0.8 C-atom units by the cis double bond, in addition to a shortening by approximately 1.3 C-atom units by the bent configuration at the C-2 position. Based on this analysis, a general thermodynamic expression is proposed for the dependence of the chain-melting transition temperature on the position of the cis double bond and on the sn-1 and sn-2 chain lengths. The above treatment is restricted mostly to double-bond positions close to the center of the sn-2 chain. For double bonds positioned closer to the carboxyl or terminal methyl ends of the sn-2 chain, the effects on transition enthalpy can be considerably larger. They may be interpreted by the same formalism, but with different characteristic parameters, h'(c) and s'(c), such that the shorter of the chain segments

  15. Classification of breast mass lesions using model-based analysis of the characteristic kinetic curve derived from fuzzy c-means clustering.

    PubMed

    Chang, Yeun-Chung; Huang, Yan-Hao; Huang, Chiun-Sheng; Chang, Pei-Kang; Chen, Jeon-Hor; Chang, Ruey-Feng

    2012-04-01

    The purpose of this study is to evaluate the diagnostic efficacy of the representative characteristic kinetic curve of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) extracted by fuzzy c-means (FCM) clustering for the discrimination of benign and malignant breast tumors using a novel computer-aided diagnosis (CAD) system. About the research data set, DCE-MRIs of 132 solid breast masses with definite histopathologic diagnosis (63 benign and 69 malignant) were used in this study. At first, the tumor region was automatically segmented using the region growing method based on the integrated color map formed by the combination of kinetic and area under curve color map. Then, the FCM clustering was used to identify the time-signal curve with the larger initial enhancement inside the segmented region as the representative kinetic curve, and then the parameters of the Tofts pharmacokinetic model for the representative kinetic curve were compared with conventional curve analysis (maximal enhancement, time to peak, uptake rate and washout rate) for each mass. The results were analyzed with a receiver operating characteristic curve and Student's t test to evaluate the classification performance. Accuracy, sensitivity, specificity, positive predictive value and negative predictive value of the combined model-based parameters of the extracted kinetic curve from FCM clustering were 86.36% (114/132), 85.51% (59/69), 87.30% (55/63), 88.06% (59/67) and 84.62% (55/65), better than those from a conventional curve analysis. The A(Z) value was 0.9154 for Tofts model-based parametric features, better than that for conventional curve analysis (0.8673), for discriminating malignant and benign lesions. In conclusion, model-based analysis of the characteristic kinetic curve of breast mass derived from FCM clustering provides effective lesion classification. This approach has potential in the development of a CAD system for DCE breast MRI.

  16. Mixed convection analysis in lid-driven cavity with sinusoidally curved bottom wall using CNT-water nanofluid

    NASA Astrophysics Data System (ADS)

    Khan, Mohieminul Islam; Rabbi, Khan Md.; Khan, Saadbin; Mamun, M. A. H.

    2016-07-01

    Mixed convection in a lid-driven enclosure with a curved bottom wall has been investigated using CNT (Carbon Nanotube)-water nanofluid in this paper. The curvature of the bottom wall follows the sine function. Studies have been made with different amplitudes (λ = 0.05, 0.1, 0.15) of the sine function hence wall curvature. The curved wall at the bottom is heated and the top wall is kept at a relatively low temperature. Left vertical and right vertical surface are assumed to be adiabatic. Top wall has been moving at a constant lid velocity U0 at right direction. Galerkin method of FEA (Finite Element Analysis) has been used to solve the governing equations. Different parameters like Richardson number (Ri = 0.1 ˜ 10) at a fixed Reynolds number (Re = 100), solid volume fraction of CNT particle (φ = 0 ˜ 0.09) are used to observe better heat transfer rate. Streamlines, isothermal lines and average Nusselt number plots are included to discuss the result of the investigation. A 2D plot between average Nusselt number and solid volume fraction of CNT-water nanofluid is also given to analyse heat transfer rate. It is observed that higher value of Richardson number shows better heat transfer rate. Finally, the paper concludes that better heat transfer is achieved at higher amplitude (λ = 0.15) of curved surface at higher solid volume fraction (φ = 0.09).

  17. Progress curve analysis for enzyme and microbial kinetic reactions using explicit solutions based on the Lambert W function.

    PubMed

    Goudar, Chetan T; Harris, Steve K; McInerney, Michael J; Suflita, Joseph M

    2004-12-01

    We present a simple method for estimating kinetic parameters from progress curve analysis of biologically catalyzed reactions that reduce to forms analogous to the Michaelis-Menten equation. Specifically, the Lambert W function is used to obtain explicit, closed-form solutions to differential rate expressions that describe the dynamics of substrate depletion. The explicit nature of the new solutions greatly simplifies nonlinear estimation of the kinetic parameters since numerical techniques such as the Runge-Kutta and Newton-Raphson methods used to solve the differential and integral forms of the kinetic equations, respectively, are replaced with a simple algebraic expression. The applicability of this approach for estimating Vmax and Km in the Michaelis-Menten equation was verified using a combination of simulated and experimental progress curve data. For simulated data, final es