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.

Detection and discrimination of members of the family Luteoviridae by real-time PCR and SYBR® GreenER™ melting curve analysis.

PubMed

Chomic, Anastasija; Winder, Louise; Armstrong, Karen F; Pearson, Michael N; Hampton, John G

2011-01-01

This study investigated the suitability of a two step real-time RT-PCR melting curve analysis as a tool for the detection and discrimination of nine species in the plant virus family Luteoviridae, being Soybean dwarf virus [SbDV], Bean leafroll virus [BLRV], Beet chlorosis virus [BChV], Beet mild yellowing virus [BMYV], Beet western yellows virus [BWYV], Cereal yellow dwarf virus-RPV [CYDV-RPV], Cucurbit aphid-borne yellows virus [CABYV], Potato leafroll virus [PLRV] and Turnip yellows virus [TuYV]. Melting temperature and shape of the melting peak were analysed for 68 bp and 148 bp coat protein gene amplicons using SYBR® GreenER™ fluorescent dye. Specific melting peaks with unique melting temperature were observed for the various species of the family Luteoviridae using the 68 bp amplicon, but not with the 148 bp amplicon. Due to the high variability of sequences for some members of this family, different melting temperatures were also observed between different isolates of the species CYDV-RPV and TuYV. Nevertheless, discrimination between species was achieved for SbDV, BLRV, BChV, BMYV, CABYV and either PLRV or BWYV. Melting curve analysis, in this study, is a faster and more discriminatory alternative to gel electrophoresis of end-point PCR products for the detection of Luteoviridae infection. Copyright © 2010 Elsevier B.V. All rights reserved.

A novel method of multiple nucleic acid detection: Real-time RT-PCR coupled with probe-melting curve analysis.

PubMed

Han, Yang; Hou, Shao-Yang; Ji, Shang-Zhi; Cheng, Juan; Zhang, Meng-Yue; He, Li-Juan; Ye, Xiang-Zhong; Li, Yi-Min; Zhang, Yi-Xuan

2017-11-15

A novel method, real-time reverse transcription PCR (real-time RT-PCR) coupled with probe-melting curve analysis, has been established to detect two kinds of samples within one fluorescence channel. Besides a conventional TaqMan probe, this method employs another specially designed melting-probe with a 5' terminus modification which meets the same label with the same fluorescent group. By using an asymmetric PCR method, the melting-probe is able to detect an extra sample in the melting stage effectively while it almost has little influence on the amplification detection. Thus, this method allows the availability of united employment of both amplification stage and melting stage for detecting samples in one reaction. The further demonstration by simultaneous detection of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) in one channel as a model system is presented in this essay. The sensitivity of detection by real-time RT-PCR coupled with probe-melting analysis was proved to be equal to that detected by conventional real-time RT-PCR. Because real-time RT-PCR coupled with probe-melting analysis can double the detection throughputs within one fluorescence channel, it is expected to be a good solution for the problem of low-throughput in current real-time PCR. Copyright © 2017 Elsevier Inc. All rights reserved.

Differentiation of five enterohepatic Helicobacter species by nested PCR with high-resolution melting curve analysis.

PubMed

Wu, Miaoli; Rao, Dan; Zhu, Yujun; Wang, Jing; Yuan, Wen; Zhang, Yu; Huang, Ren; Guo, Pengju

2017-04-01

Enterohepatic Helicobacter species (EHS) are widespread in rodent species around the world. Several studies have demonstrated that infection with EHS can interfere with the outcomes of animal experiments in cancer research and significantly influence the study results. Therefore, it is essential to establish a rapid detection and identification of EHS for biomedical research using laboratory rodents. Our study aimed to develop a rapid and sensitive method to detect and distinguish five enterohepatic Helicobacter species. Nested PCR followed by high-resolution melting curve analysis (HRM) was developed for identification of H. bilis, H. rodentium, H. muridarum, H. typhlonius, as well as H. hepaticus. To validate the accuracy of nested PCR-HRM analysis, quantitative real-time PCR methods for five different enterohepatic Helicobacter species were developed. A total of 50 cecal samples were tested using both nested PCR-HRM analysis and qPCR method. The nested PCR-HRM method could distinguish five enterohepatic Helicobacter species by different melting temperatures. The melting curve were characterized by peaks of 78.7 ± 0.12°C for H. rodentium, 80.51 ± 0.09°C for H. bilis, 81.6 ± 0.1°C for H. typhlonius, 82.11 ± 0.18°C for H. muridarum, and 82.95 ± 0.09°C for H. hepaticus. The nested PCR-HRM assay is a simple, rapid, and cost-effective assay. This assay could be a useful tool for molecular epidemiology study of enterohepatic Helicobacter infection and an attractive alternative for genotyping of enterohepatic Helicobacter species. © 2016 John Wiley & Sons Ltd.

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.

On a possible melting curve of C60 fullerite

NASA Astrophysics Data System (ADS)

Zubov, V. I.; Rodrigues, C. G.; Zubov, I. V.

2003-07-01

We study the thermodynamic properties of the high-temperature modification of fullerites on the basis of the Girifalco intermolecular potential. In the present work, using Lindemann's melting criterion, we estimate a possible melting curve Tm(P) of C60 fullerite. To take into account the lattice anharmonicity, which has a strong effect at T > 700 K, we use the correlative method of unsymmetrized self-consistent field. To check this approach, first we have applied it to solid Ar. In the range between its triple point Tt = 83.807 K and 260 K we obtained the mean square relative deviation from experimental data of about 0.7%. The melting curve for C60 fullerite has been calculated from the melting point at normal pressure estimated at 1500 K up to 15 kbar, which corresponds to Tm = 4000 K, i.e. to the temperature estimated by Kim and Tománek [Phys. Rev. Lett. 72, 2418 (1994)] as that of the decomposition of the C60 molecule itself. The temperature dependence of the melting pressure is approximated very well by the Simon equation (Pm(T)/bar - 1)/b = (T/T0)c with T0 = 1500 K, b = 6643.8, and c = 1.209. The temperature dependence of the molar volume along the melting curve is described by Vs(T) = Vs(T0) - 29.20 ln (T/T0.

Evaluation of methods for characterizing the melting curves of a high temperature cobalt-carbon fixed point to define and determine its melting temperature

NASA Astrophysics Data System (ADS)

Lowe, David; Machin, Graham

2012-06-01

The future mise en pratique for the realization of the kelvin will be founded on the melting temperatures of particular metal-carbon eutectic alloys as thermodynamic temperature references. However, at the moment there is no consensus on what should be taken as the melting temperature. An ideal melting or freezing curve should be a completely flat plateau at a specific temperature. Any departure from the ideal is due to shortcomings in the realization and should be accommodated within the uncertainty budget. However, for the proposed alloy-based fixed points, melting takes place over typically some hundreds of millikelvins. Including the entire melting range within the uncertainties would lead to an unnecessarily pessimistic view of the utility of these as reference standards. Therefore, detailed analysis of the shape of the melting curve is needed to give a value associated with some identifiable aspect of the phase transition. A range of approaches are or could be used; some purely practical, determining the point of inflection (POI) of the melting curve, some attempting to extrapolate to the liquidus temperature just at the end of melting, and a method that claims to give the liquidus temperature and an impurity correction based on the analytical Scheil model of solidification that has not previously been applied to eutectic melting. The different methods have been applied to cobalt-carbon melting curves that were obtained under conditions for which the Scheil model might be valid. In the light of the findings of this study it is recommended that the POI continue to be used as a pragmatic measure of temperature but where required a specified limits approach should be used to define and determine the melting temperature.

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.

Silver ion-mediated killing of a food pathogen: Melting curve analysis data of silver resistance genes and growth curve data.

PubMed

Gokulan, Kuppan; Williams, Katherine; Khare, Sangeeta

2017-04-01

Limited antibacterial activity of silver ions leached from silver-impregnated food contact materials could be due to: 1) the presence of silver resistance genes in tested bacteria ; or 2) lack of susceptibility to silver ion-mediated killing in the bacterial strain (K. Williams, L. Valencia, K. Gokulan, R. Trbojevich, S. Khare, 2016 [1]). This study contains data to address the specificity of silver resistance genes in Salmonella Typhimurium during the real time PCR using melting curve analysis and an assessment of the minimum inhibitory concentration of silver ions for Salmonella .

Differentiation of minute virus of mice and mouse parvovirus by high resolution melting curve analysis.

PubMed

Rao, Dan; Wu, Miaoli; Wang, Jing; Yuan, Wen; Zhu, Yujun; Cong, Feng; Xu, Fengjiao; Lian, Yuexiao; Huang, Bihong; Wu, Qiwen; Chen, Meili; Zhang, Yu; Huang, Ren; Guo, Pengju

2017-12-01

Murine parvovirus is one of the most prevalent infectious pathogens in mouse colonies. A specific primer pair targeting the VP2 gene of minute virus of mice (MVM) and mouse parvovirus (MPV) was utilized for high resolution melting (HRM) analysis. The resulting melting curves could distinguish these two virus strains and there was no detectable amplification of the other mouse pathogens which included rat parvovirus (KRV), ectromelia virus (ECT), mouse adenovirus (MAD), mouse cytomegalovirus (MCMV), polyoma virus (Poly), Helicobactor hepaticus (H. hepaticus) and Salmonella typhimurium (S. typhimurium). The detection limit of the standard was 10 copies/μL. This study showed that the PCR-HRM assay could be an alternative useful method with high specificity and sensitivity for differentiating murine parvovirus strains MVM and MPV. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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)] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013)]. 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.

Shock-induced superheating and melting curves of geophysically important minerals

NASA Astrophysics Data System (ADS)

Luo, Sheng-Nian; Ahrens, Thomas J.

2004-06-01

Shock-state temperature and sound-speed measurements on crystalline materials, demonstrate superheating-melting behavior distinct from equilibrium melting. Shocked solid can be superheated to the maximum temperature, Tc'. At slightly higher pressure, Pc, shock melting occurs, and induces a lower shock temperature, Tc. The Hugoniot state, ( Pc, Tc), is inferred to lie along the equilibrium melting curve. The amount of superheating achieved on Hugoniot is, ΘH+= Tc'/ Tc-1. Shock-induced superheating for a number of silicates, alkali halides and metals agrees closely with the predictions of a systematic framework describing superheating at various heating rates [Appl. Phys. Lett. 82 (12) (2003) 1836]. High-pressure melting curves are constructed by integration from ( Pc, Tc) based on the Lindemann law. We calculate the volume and entropy changes upon melting at ( Pc, Tc) assuming the R ln 2 rule ( R is the gas constant) for the disordering entropy of melting [J. Chem. Phys. 19 (1951) 93; Sov. Phys. Usp. 117 (1975) 625; Poirier, J.P., 1991. Introduction to the Physics of the Earth's Interior. Cambridge University Press, Cambridge, 102 pp.]. ( Pc, Tc) and the Lindemann melting curves are in excellent accord with diamond-anvil cell (DAC) results for NaCl, KBr and stishovite. But significant discrepancies exist for transition metals. If we extrapolate the DAC melting data [Phys. Rev. B 63 (2001) 132104] for transition metals (Fe, V, Mo, W and Ta) to 200-400 GPa where shock melting occurs, shock temperature measurement and calculation would indicate ΘH+˜0.7-2.0. These large values of superheating are not consistent with the superheating systematics. The discrepancies could be reconciled by possible solid-solid phase transitions at high pressures. In particular, this work suggests that Fe undergoes a possible solid-solid phase transition at ˜200 GPa and melts at ˜270 GPa upon shock wave loading, and the melting temperature is ˜6300 K at 330 GPa.

Simultaneous detection of Fusarium culmorum and F. graminearum in plant material by duplex PCR with melting curve analysis.

PubMed

Brandfass, Christoph; Karlovsky, Petr

2006-01-23

Fusarium head blight (FHB) is a disease of cereal crops, which has a severe impact on wheat and barley production worldwide. Apart from reducing the yield and impairing grain quality, FHB leads to contamination of grain with toxic secondary metabolites (mycotoxins), which pose a health risk to humans and livestock. The Fusarium species primarily involved in FHB are F. graminearum and F. culmorum. A key prerequisite for a reduction in the incidence of FHB is an understanding of its epidemiology. We describe a duplex-PCR-based method for the simultaneous detection of F. culmorum and F. graminearum in plant material. Species-specific PCR products are identified by melting curve analysis performed in a real-time thermocycler in the presence of the fluorescent dye SYBR Green I. In contrast to multiplex real-time PCR assays, the method does not use doubly labeled hybridization probes. PCR with product differentiation by melting curve analysis offers a cost-effective means of qualitative analysis for the presence of F. culmorum and F. graminearum in plant material. This method is particularly suitable for epidemiological studies involving a large number of samples.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Wenjin; Peng, Yufeng; Liu, Zhongli, E-mail: zhongliliu@yeah.net

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).more » 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.« less

Barcoding Melting Curve Analysis for Rapid, Sensitive, and Discriminating Authentication of Saffron (Crocus sativus L.) from Its Adulterants

PubMed Central

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. PMID:25548775

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.

Application of real-time PCR and melting curve analysis in rapid Diego blood group genotyping.

PubMed

Novaretti, M C Z; Ruiz, A S; Dorlhiac-Llacer, P E; Chamone, D A F

2010-01-01

The paucity of appropriate reagents for serologic typing of the Diego blood group antigens has prompted the development of a real-time PCR and melting curve analysis for Diego blood group genotyping. In this study, we phenotyped 4326 donor blood samples for Di(a) using semiautomated equipment. All 157 Di(a+) samples were then genotyped by PCR using sequence-specific primers (PCR-SSP) for DI*02 because of anti-Di(b) scarcity. Of the 4326 samples, we simultaneously tested 160 samples for Di(a) and Di(b) serology, and DI*01 and DI*02 by PCR-SSP and by real-time PCR. We used the same primers for Diego genotyping by real-time PCR and PCR-SSP. Melting curve profiles obtained using the dissociation software of the real-time PCR apparatus enabled the discrimination of Diego alleles. Of the total samples tested, 4169 blood donors, 96.4 percent (95% confidence interval [CI], 95.8-96.9%), were homozygous for DI*02 and 157, 3.6 percent (95% CI, 3.1%-4.2%), were heterozygous DI*01/02. No blood donor was found to be homozygous for DI*01 in this study. The calculated DI*01 and DI*02 allele frequencies were 0.0181 (95% CI, 0.0173-0.0189) and 0.9819 (95% CI, 0.9791-0.9847), respectively, showing a good fit for the Hardy-Weinberg equilibrium. There was full concordance among Diego phenotype results by PCR-SSP and real-time PCR. DI*01 and DI*02 allele determination with SYBR Green I and thermal cycler technology are useful methods for Diego determination. The real-time PCR with SYBR Green I melting temperature protocol can be used as a rapid screening tool for DI*01 and DI*02 blood group genotyping.

High-resolution melting-curve (HRM) analysis for C. meleagridis identification in stool samples.

PubMed

Chelbi, Hanen; Essid, Rym; Jelassi, Refka; Bouzekri, Nesrine; Zidi, Ines; Ben Salah, Hamza; Mrad, Ilhem; Ben Sghaier, Ines; Abdelmalek, Rym; Aissa, Sameh; Bouratbine, Aida; Aoun, Karim

2018-02-01

Cryptosporidiosis represents a major public health problem. This infection, caused by a protozoan parasite of the genus Cryptosporidium, has been reported worldwide as a frequent cause of diarrhoea. In the immunocompetent host, the typical watery diarrhea can be self-limiting. However, it is severe and chronic, in the immunocompromised host and may cause death. Cryptosporidium spp. are coccidians, which complete their life cycle in both humans and animals. The two species C. hominis and C. parvum are the major cause of human infection. Compared to studies on C. hominis and C. parvum, only a few studies have developed methods to identify C. meleagridis. To develop a new real time PCR-coupled High resolution melting assay allowing the detection for C. meleagridis, in addition of the other dominant species (C. hominis and C. parvum). The polymorphic sequence on the dihydrofolate reductase gene (DHFR) of three species was sequenced to design primers pair and establish a sensitive real-time PCR coupled to a high-resolution melting-curve (HRM) analysis method, allowing the detection of Cryptosporidium sp. and discrimination between three prevalent species in Tunisia. We analyzed a collection of 42 archived human isolates of the three studied species. Real-time PCR coupled to HRM assay allowed detection of Cryptosporidium, using the new designed primers, and basing on melting profile, we can distinguish C. meleagridis species in addition to C. parvum and C. hominis. We developed a qPCR-HRM assay that allows Cryptosporidium genotyping. This method is sensitive and able to distinguish three Cryptosporidium species. Copyright © 2017. Published by Elsevier Ltd.

A Real-Time PCR with Melting Curve Analysis for Molecular Typing of Vibrio parahaemolyticus.

PubMed

He, Peiyan; Wang, Henghui; Luo, Jianyong; Yan, Yong; Chen, Zhongwen

2018-05-23

Foodborne disease caused by Vibrio parahaemolyticus is a serious public health problem in many countries. Molecular typing has a great scientific significance and application value for epidemiological research of V. parahaemolyticus. In this study, a real-time PCR with melting curve analysis was established for molecular typing of V. parahaemolyticus. Eighteen large variably presented gene clusters (LVPCs) of V. parahaemolyticus which have different distributions in the genome of different strains were selected as targets. Primer pairs of 18 LVPCs were distributed into three tubes. To validate this newly developed assay, we tested 53 Vibrio parahaemolyticus strains, which were classified in 13 different types. Furthermore, cluster analysis using NTSYS PC 2.02 software could divide 53 V. parahaemolyticus strains into six clusters at a relative similarity coefficient of 0.85. This method is fast, simple, and conveniently for molecular typing of V. parahaemolyticus.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

Assessment of genetic mutations in the XRCC2 coding region by high resolution melting curve analysis and the risk of differentiated thyroid carcinoma in Iran

PubMed Central

Fayaz, Shima; Fard-Esfahani, Pezhman; Fard-Esfahani, Armaghan; Mostafavi, Ehsan; Meshkani, Reza; Mirmiranpour, Hossein; Khaghani, Shahnaz

2012-01-01

Homologous recombination (HR) is the major pathway for repairing double strand breaks (DSBs) in eukaryotes and XRCC2 is an essential component of the HR repair machinery. To evaluate the potential role of mutations in gene repair by HR in individuals susceptible to differentiated thyroid carcinoma (DTC) we used high resolution melting (HRM) analysis, a recently introduced method for detecting mutations, to examine the entire XRCC2 coding region in an Iranian population. HRM analysis was used to screen for mutations in three XRCC2 coding regions in 50 patients and 50 controls. There was no variation in the HRM curves obtained from the analysis of exons 1 and 2 in the case and control groups. In exon 3, an Arg188His polymorphism (rs3218536) was detected as a new melting curve group (OR: 1.46; 95%CI: 0.432–4.969; p = 0.38) compared with the normal melting curve. We also found a new Ser150Arg polymorphism in exon 3 of the control group. These findings suggest that genetic variations in the XRCC2 coding region have no potential effects on susceptibility to DTC. However, further studies with larger populations are required to confirm this conclusion. PMID:22481871

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.

Development and inter-laboratory validation of unlabeled probe melting curve analysis for detection of JAK2 V617F mutation in polycythemia vera.

PubMed

Wu, Zhiyuan; Yuan, Hong; Zhang, Xinju; Liu, Weiwei; Xu, Jinhua; Zhang, Wei; Guan, Ming

2011-01-01

JAK2 V617F, a somatic point mutation that leads to constitutive JAK2 phosphorylation and kinase activation, has been incorporated into the WHO classification and diagnostic criteria of myeloid neoplasms. Although various approaches such as restriction fragment length polymorphism, amplification refractory mutation system and real-time PCR have been developed for its detection, a generic rapid closed-tube method, which can be utilized on routine genetic testing instruments with stability and cost-efficiency, has not been described. Asymmetric PCR for detection of JAK2 V617F with a 3'-blocked unlabeled probe, saturate dye and subsequent melting curve analysis was performed on a Rotor-Gene® Q real-time cycler to establish the methodology. We compared this method to the existing amplification refractory mutation systems and direct sequencing. Hereafter, the broad applicability of this unlabeled probe melting method was also validated on three diverse real-time systems (Roche LightCycler® 480, Applied Biosystems ABI® 7500 and Eppendorf Mastercycler® ep realplex) in two different laboratories. The unlabeled probe melting analysis could genotype JAK2 V617F mutation explicitly with a 3% mutation load detecting sensitivity. At level of 5% mutation load, the intra- and inter-assay CVs of probe-DNA heteroduplex (mutation/wild type) covered 3.14%/3.55% and 1.72%/1.29% respectively. The method could equally discriminate mutant from wild type samples on the other three real-time instruments. With a high detecting sensitivity, unlabeled probe melting curve analysis is more applicable to disclose JAK2 V617F mutation than conventional methodologies. Verified with the favorable inter- and intra-assay reproducibility, unlabeled probe melting analysis provided a generic mutation detecting alternative for real-time instruments.

Identification of squid species by melting temperature shifts on fluorescence melting curve analysis (FMCA) using single dual-labeled probe

NASA Astrophysics Data System (ADS)

Koh, Eunjung; Song, Ha Jeong; Kwon, Na Young; Kim, Gi Won; Lee, Kwang Ho; Jo, Soyeon; Park, Sujin; Park, Jihyun; Park, Eun Kyeong; Hwang, Seung Yong

2017-06-01

Real time PCR is a standard method for identification of species. One of limitations of the qPCR is that there would be false-positive result due to mismatched hybridization between target sequence and probe depending on the annealing temperature in the PCR condition. As an alternative, fluorescence melting curve analysis (FMCA) could be applied for species identification. FMCA is based on a dual-labeled probe. Even with subtle difference of target sequence, there are visible melting temperature (Tm) shift. One of FMCA applications is distinguishing organisms distributed and consumed globally as popular food ingredients. Their prices are set by species or country of origin. However, counterfeiting or distributing them without any verification procedure are becoming social problems and threatening food safety. Besides distinguishing them in naked eye is very difficult and almost impossible in any processed form. Therefore, it is necessary to identify species in molecular level. In this research three species of squids which have 1-2 base pair differences each are selected as samples since they have the same issue. We designed a probe which perfectly matches with one species and the others mismatches 2 and 1 base pair respectively and labeled with fluorophore and quencher. In an experiment with a single probe, we successfully distinguished them by Tm shift depending on the difference of base pair. By combining FMCA and qPCR chip, smaller-scale assay with higher sensitivity and resolution could be possible, andc furthermore, enabling results analysis with smart phone would realize point-of-care testing (POCT).

T85C polymorphisms of the dihydropyrimidine dehydrogenase gene detected in gastric cancer tissues by high-resolution melting curve analysis.

PubMed

Fang, Weijia; Xu, Nong; Jin, Dazhi; Chen, Yu; Chen, Xiaogang; Zheng, Yi; Shen, Hong; Yuan, Ying; Zheng, Shusen

2012-01-01

Dihydropyrimidine dehydrogenase is a key enzyme acting on the metabolic pathway of medications for gastric cancer. High-resolution melting curve technology, which was developed recently, can distinguish the wild-type dihydropyrimidine dehydrogenase gene from multiple polymorphisms by fluorescent quantitative polymerase chain reaction products in a direct and effective manner. T85C polymorphisms of dihydropyrimidine dehydrogenase in the peripheral blood of 112 Chinese gastric cancer patients were detected by real-time polymerase chain reaction combined with high-resolution melting curve technology. Primer design, along with the reaction system and conditions, was optimized based on the GenBank sequence. Seventy nine cases of wild-type (TT, [70.5%]), 29 cases of heterozygous (TC, [25.9%]), and 4 cases of homozygous mutant (CC, [3.6%]) were observed. The result was completely consistent with the results of the sequencing. Real-time polymerase chain reaction combined with high-resolution melting curve technology is a rapid, simple, reliable, direct-viewing, and convenient method for the detection and screening of polymorphisms.

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.

A novel real time PCR assay using melt curve analysis for ivory identification.

PubMed

Kitpipit, Thitika; Penchart, Kitichaya; Ouithavon, Kanita; Satasook, Chutamas; Linacre, Adrian; Thanakiatkrai, Phuvadol

2016-10-01

Demand for ivory and expansion of human settlements have resulted in a rapid decline in the number of elephants. Enforcement of local and international laws and regulations requires identification of the species from which any ivory, or ivory products, originated. Further geographical assignment of the dead elephant from which the ivory was taken can assist in forensic investigations. In this study, a real-time PCR assay using melt curve analysis was developed and fully validated for forensic use. The presence or absence of three Elephantidae-specific and elephant species-specific melting peaks was used to identify the elephant species. Using 141 blood and ivory samples from the three extant elephant species, the assay demonstrated very high reproducibility and accuracy. The limit of detection was as low as 0.031ng of input DNA for conventional amplification and 0.002ng for nested amplification. Both DNA concentrations are typically encountered in forensic casework, especially for degraded samples. No cross-reactivity was observed for non-target species. Evaluation of direct amplification and nested amplification demonstrated the assay's flexibility and capability of analyzing low-template DNA samples and aged samples. Additionally, blind trial testing showed the assay's suitability application in real casework. In conclusion, wildlife forensic laboratories could use this novel, quick, and low-cost assay to help combat the continuing poaching crises leading to the collapse of elephant numbers in the wild. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Gene Scanning of an Internalin B Gene Fragment Using High-Resolution Melting Curve Analysis as a Tool for Rapid Typing of Listeria monocytogenes

PubMed Central

Pietzka, Ariane T.; Stöger, Anna; Huhulescu, Steliana; Allerberger, Franz; Ruppitsch, Werner

2011-01-01

The ability to accurately track Listeria monocytogenes strains involved in outbreaks is essential for control and prevention of listeriosis. Because current typing techniques are time-consuming, cost-intensive, technically demanding, and difficult to standardize, we developed a rapid and cost-effective method for typing of L. monocytogenes. In all, 172 clinical L. monocytogenes isolates and 20 isolates from culture collections were typed by high-resolution melting (HRM) curve analysis of a specific locus of the internalin B gene (inlB). All obtained HRM curve profiles were verified by sequence analysis. The 192 tested L. monocytogenes isolates yielded 15 specific HRM curve profiles. Sequence analysis revealed that these 15 HRM curve profiles correspond to 18 distinct inlB sequence types. The HRM curve profiles obtained correlated with the five phylogenetic groups I.1, I.2, II.1, II.2, and III. Thus, HRM curve analysis constitutes an inexpensive assay and represents an improvement in typing relative to classical serotyping or multiplex PCR typing protocols. This method provides a rapid and powerful screening tool for simultaneous preliminary typing of up to 384 samples in approximately 2 hours. PMID:21227395

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.

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

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.

Quantification of HER2/neu gene amplification by competitive pcr using fluorescent melting curve analysis.

PubMed

Lyon, E; Millson, A; Lowery, M C; Woods, R; Wittwer, C T

2001-05-01

Molecular detection methods for HER2/neu gene amplification include fluorescence in situ hybridization (FISH) and competitive PCR. We designed a quantitative PCR system utilizing fluorescent hybridization probes and a competitor that differed from the HER2/neu sequence by a single base change. Increasing twofold concentrations of competitor were coamplified with DNA from cell lines with various HER2/neu copy numbers at the HER2/neu locus. Competitor DNA was distinguished from the HER2/neu sequence by a fluorescent hybridization probe and melting curve analysis on a fluorescence-monitoring thermal cycler. The percentages of competitor to target peak areas on derivative fluorescence vs temperature curves were used to calculate copy number. Real-time monitoring of the PCR reaction showed comparable relative areas throughout the log phase and during the PCR plateau, indicating that only end-point detection is necessary. The dynamic range was over two logs (2000-250 000 competitor copies) with CVs < 20%. Three cell lines (MRC-5, T-47D, and SK-BR-3) were determined to have gene doses of 1, 3, and 11, respectively. Gene amplification was detected in 3 of 13 tumor samples and was correlated with conventional real-time PCR and FISH analysis. Use of relative peak areas allows gene copy numbers to be quantified against an internal competitive control in < 1 h.

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

Detection of diarrheagenic Escherichia coli by use of melting-curve analysis and real-time multiplex PCR.

PubMed

Guion, Chase E; Ochoa, Theresa J; Walker, Christopher M; Barletta, Francesca; Cleary, Thomas G

2008-05-01

Diarrheagenic Escherichia coli strains are important causes of diarrhea in children from the developing world and are now being recognized as emerging enteropathogens in the developed world. Current methods of detection are too expensive and labor-intensive for routine detection of these organisms to be practical. We developed a real-time fluorescence-based multiplex PCR for the detection of all six of the currently recognized classes of diarrheagenic E. coli. The primers were designed to specifically amplify eight different virulence genes in the same reaction: aggR for enteroaggregative E. coli, stIa/stIb and lt for enterotoxigenic E. coli, eaeA for enteropathogenic E. coli and Shiga toxin-producing E. coli (STEC), stx(1) and stx(2) for STEC, ipaH for enteroinvasive E. coli, and daaD for diffusely adherent E. coli (DAEC). Eighty-nine of ninety diarrheagenic E. coli and 36/36 nonpathogenic E. coli strains were correctly identified using this approach (specificity, 1.00; sensitivity, 0.99). The single false negative was a DAEC strain. The total time between preparation of DNA from E. coli colonies on agar plates and completion of PCR and melting-curve analysis was less than 90 min. The cost of materials was low. Melting-point analysis of real-time multiplex PCR is a rapid, sensitive, specific, and inexpensive method for detection of diarrheagenic E. coli.

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), Cu 51Zr 14(β), CuZr(B 2), CuZr 2(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 andmore » 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.« less

Using newly developed multiplex polymerase chain reaction and melting curve analysis for detection and discrimination of β-lactamases in Escherichia coli isolates from intensive care patients.

PubMed

Chromá, Magdaléna; Hricová, Kristýna; Kolář, Milan; Sauer, Pavel; Koukalová, Dagmar

2011-11-01

A total of 78 bacterial strains with known β-lactamases were used to optimize a rapid detection system consisting of multiplex polymerase chain reaction and melting curve analysis to amplify and identify blaTEM, blaSHV, and blaCTX-M genes in a single reaction. Additionally, to evaluate the applicability of this method, 32 clinical isolates of Escherichia coli displaying an extended-spectrum β-lactamase phenotype from patients hospitalized at intensive care units were tested. Results were analyzed by the Rotor-Gene operating software and Rotor-Gene ScreenClust HRM Software. The individual melting curves differed by a temperature shift or curve shape, according to the presence of β-lactamase genes. With the use of this method and direct sequencing, blaCTX-M-15-like was identified as the most prevalent β-lactamase gene. In conclusion, this novel detection system seems to be a suitable tool for rapid detection of present β-lactamase genes and their characterization. Copyright © 2011 Elsevier Inc. All rights reserved.

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

PubMed

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

2009-01-01

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

Evaluation of Two Multiplex PCR-High-Resolution Melt Curve Analysis Methods for Differentiation of Campylobacter jejuni and Campylobacter coli Intraspecies.

PubMed

Banowary, Banya; Dang, Van Tuan; Sarker, Subir; Connolly, Joanne H; Chenu, Jeremy; Groves, Peter; Raidal, Shane; Ghorashi, Seyed Ali

2018-03-01

Campylobacter infection is a common cause of bacterial gastroenteritis in humans and remains a significant global public health issue. The capability of two multiplex PCR (mPCR)-high-resolution melt (HRM) curve analysis methods (i.e., mPCR1-HRM and mPCR2-HRM) to detect and differentiate 24 poultry isolates and three reference strains of Campylobacter jejuni and Campylobacter coli was investigated. Campylobacter jejuni and C. coli were successfully differentiated in both assays, but the differentiation power of mPCR2-HRM targeting the cadF gene was found superior to that of mPCR1-HRM targeting the gpsA gene or a hypothetical protein gene. However, higher intraspecies variation within C. coli and C. jejuni isolates was detected in mPCR1-HRM when compared with mPCR2-HRM. Both assays were rapid and required minimum interpretation skills for discrimination between and within Campylobacter species when using HRM curve analysis software.

Rapid identification of the NAT2 genotype in tuberculosis patients by multicolor melting curve analysis.

PubMed

Hu, Yanjie; Chen, Suting; Yu, Xia; Dai, Guangming; Dong, Lingling; Li, Yunxu; Zhao, Liping; Huang, Hairong

2016-07-01

NAT2 genotype is an indicator for isoniazid dosage adjusting for tuberculosis treatment. Multicolor melting curve analysis (MMCA) was evaluated as a potential method for NAT2 genotyping. 352 blood samples were analyzed by MMCA kit (Zeesan Biotech Co., Xiamen, China) targeting NAT2 SNPs at T341C, C481T, G590A and G857A, and direct sequencing was used as control. The sensitivity, specificity and accuracy of the MMCA assay for rapid NAT2 genotype detection were 97.9, 99.6 and 99.1% respectively, whereas for intermediate genotypes the values were 99.5, 98.7 and 99.1%, respectively, and for slow genotypes the values were 100% for the three aspects. The 24 saliva and blood for the control samples were also successfully analyzed using the MMCA assay, both produced uniform outcomes. The MMCA assay described in our study is very promising for the efficient determination of NAT2 genotype, and can facilitate the personalized dosing of isoniazid.

Sound velocity measurement of nuclear-ordered U2D2 solid 3He along the melting curve

NASA Astrophysics Data System (ADS)

Nomura, R.; Suzuki, M.; Yamaguchi, M.; Sasaki, Y.; Mizusaki, T.

2000-05-01

The sound velocity of a single-domain 3He crystal was measured in the nuclear-ordered low-field phase and the paramagnetic phase along the melting curve, using 10.98 MHz longitudinal sound. The temperature dependence of the sound velocity along the melting curve was explained by a nuclear spin contribution and the molar volume change along the melting curve. By comparing the measured velocity with thermodynamic quantities, we extracted the Grüneizen constant for the exchange energy. The anisotropy of the velocity in the ordered phase was investigated for three samples and was found to be smaller than 2×10 -5 in Δ v/ v. The attenuation coefficient of the sound was much smaller than 0.2 cm-1.

Detection of monoclonal immunoglobulin heavy chain gene rearrangement (FR3) in Thai malignant lymphoma by High Resolution Melting curve analysis.

PubMed

Kummalue, Tanawan; Chuphrom, Anchalee; Sukpanichanant, Sanya; Pongpruttipan, Tawatchai; Sukpanichanant, Sathien

2010-05-19

Malignant lymphoma, especially non-Hodgkin lymphoma, is one of the most common hematologic malignancies in Thailand. The diagnosis of malignant lymphoma is often problematic, especially in early stages of the disease. Detection of antigen receptor gene rearrangement including T cell receptor (TCR) and immunoglobulin heavy chain (IgH) by polymerase chain reaction followed by heteroduplex has currently become standard whereas fluorescent fragment analysis (GeneScan) has been used for confirmation test. In this study, three techniques had been compared: thermocycler polymerase chain reaction (PCR) followed by heteroduplex and polyacrylamide gel electrophoresis, GeneScan analysis, and real time PCR with High Resolution Melting curve analysis (HRM). The comparison was carried out with DNA extracted from paraffin embedded tissues diagnosed as B- cell non-Hodgkin lymphoma. Specific PCR primers sequences for IgH gene variable region 3, including fluorescence labeled IgH primers were used and results were compared with HRM. In conclusion, the detection IgH gene rearrangement by HRM in the LightCycler System showed potential for distinguishing monoclonality from polyclonality in B-cell non-Hodgkin lymphoma. Malignant lymphoma, especially non-Hodgkin lymphoma, is one of the most common hematologic malignancies in Thailand. The incidence rate as reported by Ministry of Public Health is 3.1 per 100,000 population in female whereas the rate in male is 4.5 per 100,000 population 1. At Siriraj Hospital, the new cases diagnosed as malignant lymphoma were 214.6 cases/year 2. The diagnosis of malignant lymphoma is often problematic, especially in early stages of the disease. Therefore, detection of antigen receptor gene rearrangement including T cell receptor (TCR) and immunoglobulin heavy chain (IgH) by polymerase chain reaction (PCR) assay has recently become a standard laboratory test for discrimination of reactive from malignant clonal lymphoproliferation 34. Analyzing DNA

Image analysis of speckle patterns as a probe of melting transitions in laser-heated diamond anvil cell experiments.

PubMed

Salem, Ran; Matityahu, Shlomi; Melchior, Aviva; Nikolaevsky, Mark; Noked, Ori; Sterer, Eran

2015-09-01

The precision of melting curve measurements using laser-heated diamond anvil cell (LHDAC) is largely limited by the correct and reliable determination of the onset of melting. We present a novel image analysis of speckle interference patterns in the LHDAC as a way to define quantitative measures which enable an objective determination of the melting transition. Combined with our low-temperature customized IR pyrometer, designed for measurements down to 500 K, our setup allows studying the melting curve of materials with low melting temperatures, with relatively high precision. As an application, the melting curve of Te was measured up to 35 GPa. The results are found to be in good agreement with previous data obtained at pressures up to 10 GPa.

Rapid detection of Opisthorchis viverrini and Strongyloides stercoralis in human fecal samples using a duplex real-time PCR and melting curve analysis.

PubMed

Janwan, Penchom; Intapan, Pewpan M; Thanchomnang, Tongjit; Lulitanond, Viraphong; Anamnart, Witthaya; Maleewong, Wanchai

2011-12-01

Human opisthorchiasis caused by the liver fluke Opisthorchis viverrini is an endemic disease in Southeast Asian countries including the Lao People's Democratic Republic, Cambodia, Vietnam, and Thailand. Infection with the soil-transmitted roundworm Strongyloides stercoralis is an important problem worldwide. In some areas, both parasitic infections are reported as co-infections. A duplex real-time fluorescence resonance energy transfer (FRET) PCR merged with melting curve analysis was developed for the rapid detection of O. viverrini and S. stercoralis in human fecal samples. Duplex real-time FRET PCR is based on fluorescence melting curve analysis of a hybrid of amplicons generated from two genera of DNA elements: the 162 bp pOV-A6 DNA sequence specific to O. viverrini and the 244 bp 18S rRNA sequence specific to S. stercoralis, and two pairs of specific fluorophore-labeled probes. Both O. viverrini and S. stercoralis can be differentially detected in infected human fecal samples by this process through their different fluorescence channels and melting temperatures. Detection limit of the method was as little as two O. viverrini eggs and four S. stercoralis larvae 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 parasite materials, as well as from the DNA of human leukocytes and other control parasites. The technique showed 100% sensitivity and specificity. The introduced duplex real-time FRET PCR can reduce labor time and reagent costs and is not prone to carry over contamination. The method is important for simultaneous detection especially in areas where both parasites overlap incidence and is useful as the screening tool in the returning travelers and immigrants to industrialized countries where number of samples in the diagnostic units will become increasing.

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

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

2012-01-01

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. 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. 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. 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.

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

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

PubMed Central

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

2015-01-01

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

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.

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

Three-Phase Melting Curves in the Binary System of Carbon Dioxide and Water

NASA Astrophysics Data System (ADS)

Abramson, E. H.

2017-10-01

Invariant, three-phase melting curves, of ice VI in equilibrium with solid CO2, of ice VII in equilibrium with solid CO2, and of solid CO2 in simultaneous equilibrium with a majority aqueous and a majority CO2 fluid, were explored in the binary system of carbon dioxide and water. Diamond-anvil cells were used to develop pressures of 5 GPa. Water exhibits a large melting temperature depression (73°C less than its pure melting temperature of 253°C at 5 GPa) indicative of large concentrations of CO2 in the aqueous solution. The melting point of water-saturated CO2 does not show a measureable departure from that of the pure system at temperatures lower than ∼200°C and only 10°C at 5 GPa (from 327°C).

Melting curve of compressed barium carbonate from in situ ionic conductivity measurements: Implications for the melting behavior of alkaline earth carbonates in Earth's deep carbon cycle

NASA Astrophysics Data System (ADS)

Dong, J.; Li, J.; Zhu, F.; Li, Z.; Farawi, R.

2017-12-01

The whereabouts of subducted carbonates place a major constraint on the Earth's deep carbon cycle, but the fraction of carbon retained in the slab and transported into the deep mantle, compared to that released from the slab and recycled to the surface, is still under debate. Knowledge of the stability of carbonated mantle rocks is pivotal for assessing the ability of slabs to carry carbonates into the deep mantle. Determination and systematic comparison of the melting curves of alkali and alkaline earth carbonates at high pressure can help construct thermodynamic models to predict the melting behavior of complex carbonated mantle rocks. Among alkaline earth carbonates, the melting behavior of barium carbonate (BaCO3) has not been adequately understood. The reported melting point of BaCO3at 1 bar differ by nearly 800 °C and constraints on the melting curve of BaCO3 at high pressure are not available. In this study, the melting temperatures of BaCO3 were determined up to 11 GPa from in situ ionic conductivity measurements using the multi-anvil apparatus at the University of Michigan. The solid-liquid boundary at high pressure was detected on the basis of a steep rise in conductivity through the sample upon melting. The melting point of BaCO3 was found to drop from 1797 °C at 3.3 GPa to 1600 °C at 5.5 GPa and then rise with pressure to 2180 °C at 11 GPa. The observed melting depression point at 5.5 GPa corresponds to the phase transition of BaCO3 from the aragonite structure (Pmcn) to post-aragonite structure (Pmmn) at 6.3 GPa, 877 °C and 8.0 GPa, 727 °C, determined from synchrotron X-ray diffraction measurements using laser-heated DAC experiments at the Advanced Photon Source, Argonne National Laboratory. These results are also compared with ex situ falling marker experiments, and the three methods together place tight constraints on the melting curve of BaCO3 and elucidates the effect of structural phase transitions on its melting behavior.

Rapid detection of Wuchereria bancrofti and Brugia malayi in mosquito vectors (Diptera: Culicidae) using a real-time fluorescence resonance energy transfer multiplex PCR and melting curve analysis.

PubMed

Intapan, Pewpan M; Thanchomnang, Tongjit; Lulitanond, Viraphong; Maleewong, Wanchai

2009-01-01

We developed a single-step real-time fluorescence resonance energy transfer (FRET) multiplex polymerase chain reaction (PCR) merged with melting curve analysis for the detection of Wuchereria bancrofti and Brugia malayi DNA in blood-fed mosquitoes. Real-time FRET multiplex PCR is based on fluorescence melting curve analysis of a hybrid of amplicons generated from two families of repeated DNA elements: the 188 bp SspI repeated sequence, specific to W. bancrofti, and the 153-bp HhaI repeated sequence, specific to the genus Brugia and two pairs of specific fluorophore-labeled probes. Both W. bancrofti and B. malayi can be differentially detected in infected vectors by this process through their different fluorescence channel and melting temperatures. The assay could distinguish both human filarial DNAs in infected vectors from the DNAs of Dirofilaria immitis- and Plasmodium falciparum-infected human red blood cells and noninfected mosquitoes and human leukocytes. The technique showed 100% sensitivity and specificity and offers a rapid and reliable procedure for differentially identifying lymphatic filariasis. The introduced real-time FRET multiplex PCR can reduce labor time and reagent costs and is not prone to carry over contamination. The test can be used to screen mosquito vectors in endemic areas and therefore should be a useful diagnostic tool for the evaluation of infection rate of the mosquito populations and for xenomonitoring in the community after eradication programs such as the Global Program to Eliminate Lymphatic Filariasis.

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

PubMed

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

2011-01-01

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

Direct Detection of Rifampin and Isoniazid Resistance in Sputum Samples from Tuberculosis Patients by High-Resolution Melt Curve Analysis

PubMed Central

Anthwal, Divya; Gupta, Rakesh Kumar; Bhalla, Manpreet; Bhatnagar, Shinjini

2017-01-01

ABSTRACT Drug-resistant tuberculosis (TB) is a major threat to 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 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 an inhA promoter and used as positive controls in HRM. The assay was first validated in 25 MDR M. tuberculosis clinical isolates. The assay was evaluated on DNA isolated from 99 M. tuberculosis culture-positive sputum samples that included 84 smear-negative sputum samples, using DNA sequencing as gold standard. Mutants were discriminated from the wild type by comparing melting-curve patterns with those of control plasmids using HRM software. Rifampin (RIF) and isoniazid (INH) monoresistance 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. The HRM-RIF, INH-katG, and INH-inhA assays had 89% (95% confidence interval [CI], 52, 100%), 85% (95% CI, 62, 97%), and 100% (95% CI, 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% to 100% (κ value, 0.9 to 1) was noted between sequencing and HRM. Heteroresistance was observed in 5 of 99 samples by sequencing. In conclusion, the HRM assay was a cost-effective (Indian rupee [INR]400/US$6), rapid, and closed-tube method for the direct detection of MDR-TB in sputum, especially for direct smear-negative cases. PMID:28330890

Rapid screening of rpoB and katG mutations in Mycobacterium tuberculosis isolates by high-resolution melting curve analysis.

PubMed

Haeili, M; Fooladi, A I; Bostanabad, S Z; Sarokhalil, D D; Siavoshi, F; Feizabadi, M M

2014-01-01

Early detection of multidrug-resistant tuberculosis (MDR-TB) is essential to prevent its transmission in the community and initiate effective anti-TB treatment regimen. High-resolution melting curve (HRM) analysis was evaluated for rapid detection of resistance conferring mutations in rpoB and katG genes. We screened 95 Mycobacterium tuberculosis clinical isolates including 20 rifampin resistant (RIF-R), 21 isoniazid resistant (INH-R) and 54 fully susceptible (S) isolates determined by proportion method of drug susceptibility testing. Nineteen M. tuberculosis isolates with known drug susceptibility genotypes were used as references for the assay validation. The nucleotide sequences of the target regions rpoB and katG genes were determined to investigate the frequency and type of mutations and to confirm HRM results. HRM analysis of a 129-bp fragment of rpoB allowed correct identification of 19 of the 20 phenotypically RIF-R and all RIF-S isolates. All INH-S isolates generated wild-type HRM curves and 18 out of 21 INH-R isolates harboured any mutation in 109-bp fragment of katG exhibited mutant type HRM curves. However, 1 RIF-R and 3 INH-R isolates were falsely identified as susceptible which were confirmed for having no mutation in their target regions by sequencing. The main mutations involved in RIF and INH resistance were found at codons rpoB531 (60% of RIF-R isolates) and katG315 (85.7% of INH-R isolates), respectively. HRM was found to be a reliable, rapid and low cost method to characterise drug susceptibility of clinical TB isolates in resource-limited settings.

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

Experimental platform utilising melting curve technology for detection of mutations in Mycobacterium tuberculosis isolates.

PubMed

Broda, Agnieszka; Nikolayevskyy, Vlad; Casali, Nicki; Khan, Huma; Bowker, Richard; Blackwell, Gemma; Patel, Bhakti; Hume, James; Hussain, Waqar; Drobniewski, Francis

2018-04-20

Tuberculosis (TB) remains one of the most deadly infections with approximately a quarter of cases not being identified and/or treated mainly due to a lack of resources. Rapid detection of TB or drug-resistant TB enables timely adequate treatment and is a cornerstone of effective TB management. We evaluated the analytical performance of a single-tube assay for multidrug-resistant TB (MDR-TB) on an experimental platform utilising RT-PCR and melting curve analysis that could potentially be operated as a point-of-care (PoC) test in resource-constrained settings with a high burden of TB. Firstly, we developed and evaluated the prototype MDR-TB assay using specimens extracted from well-characterised TB isolates with a variety of distinct rifampicin and isoniazid resistance conferring mutations and nontuberculous Mycobacteria (NTM) strains. Secondly, we validated the experimental platform using 98 clinical sputum samples from pulmonary TB patients collected in high MDR-TB settings. The sensitivity of the platform for TB detection in clinical specimens was 75% for smear-negative and 92.6% for smear-positive sputum samples. The sensitivity of detection for rifampicin and isoniazid resistance was 88.9 and 96.0% and specificity was 87.5 and 100%, respectively. Observed limitations in sensitivity and specificity could be resolved by adjusting the sample preparation methodology and melting curve recognition algorithm. Overall technology could be considered a promising PoC methodology especially in resource-constrained settings based on its combined accuracy, convenience, simplicity, speed, and cost characteristics.

Theoretical Understanding the Relations of Melting-point Determination Methods from Gibbs Thermodynamic Surface and Applications on Melting Curves of Lower Mantle Minerals

NASA Astrophysics Data System (ADS)

Yin, K.; Belonoshko, A. B.; Zhou, H.; Lu, X.

2016-12-01

The melting temperatures of materials in the interior of the Earth has significant implications in many areas of geophysics. The direct calculations of the melting point by atomic simulations would face substantial hysteresis problem. To overcome the hysteresis encountered in the atomic simulations there are a few different melting-point determination methods available nowadays, which are founded independently, such as the free energy method, the two-phase or coexistence method, and the Z method, etc. In this study, we provide a theoretical understanding the relations of these methods from a geometrical perspective based on a quantitative construction of the volume-entropy-energy thermodynamic surface, a model first proposed by J. Willard Gibbs in 1873. Then combining with an experimental data and/or a previous melting-point determination method, we apply this model to derive the high-pressure melting curves for several lower mantle minerals with less computational efforts relative to using previous methods only. Through this way, some polyatomic minerals at extreme pressures which are almost unsolvable before are calculated fully from first principles now.

Identification and quantification of virulence factors of enterotoxigenic Escherichia coli by high-resolution melting curve quantitative PCR.

PubMed

Wang, Weilan; Zijlstra, Ruurd T; Gänzle, Michael G

2017-05-15

Diagnosis of enterotoxigenic E. coli (ETEC) associated diarrhea is complicated by the diversity of E.coli virulence factors. This study developed a multiplex quantitative PCR assay based on high-resolution melting curves analysis (HRM-qPCR) to identify and quantify genes encoding five ETEC fimbriae related to diarrhea in swine, i.e. K99, F41, F18, F6 and K88. Five fimbriae expressed by ETEC were amplified in multiple HRM-qPCR reactions to allow simultaneous identification and quantification of five target genes. The assay was calibrated to allow quantification of the most abundant target gene, and validated by analysis of 30 samples obtained from piglets with diarrhea and healthy controls, and comparison to standard qPCR detection. The five amplicons with melting temperatures (Tm) ranging from 74.7 ± 0.06 to 80.5 ± 0.15 °C were well-separated by HRM-qPCR. The area of amplicons under the melting peak correlated linearly to the proportion of the template in the calibration mixture if the proportion exceeded 4.8% (K88) or <1% (all other amplicons). The suitability of the method was evaluated using 30 samples from weaned pigs aged 6-7 weeks; 14 of these animals suffered from diarrhea in consequence of poor sanitary conditions. Genes encoding fimbriae and enterotoxins were quantified by HRM-qPCR and/or qPCR. The multiplex HRM-qPCR allowed accurate analysis when the total gene copy number of targets was more than 1 × 10 5 / g wet feces and the HRM curves were able to simultaneously distinguish fimbriae genes in the fecal samples. The relative quantification of the most abundant F18 based on melting peak area was highly correlated (P < 0.001; r 2  = 0.956) with that of individual qPCR result but the correlation for less abundant fimbriae was much lower. The multiplex HRM assay identifies ETEC virulence factors specifically and efficiently. It correctly indicated the predominant fimbriae type and additionally provides information of presence/ absence of

A polymerase chain reaction-coupled high-resolution melting curve analytical approach for the monitoring of monospecificity of avian Eimeria species.

PubMed

Kirkpatrick, Naomi C; Blacker, Hayley P; Woods, Wayne G; Gasser, Robin B; Noormohammadi, Amir H

2009-02-01

Coccidiosis is a significant disease of poultry caused by different species of Eimeria. Differentiation of Eimeria species is important for the quality control of the live attenuated Eimeria vaccines derived from monospecific lines of Eimeria spp. In this study, high-resolution melting (HRM) curve analysis of the amplicons generated from the second internal transcribed spacer of nuclear ribosomal DNA (ITS-2) was used to distinguish between seven pathogenic Eimeria species of chickens, and the results were compared with those obtained from the previously described technique, capillary electrophoresis. Using a series of known monospecific lines of Eimeria species, HRM curve analysis was shown to distinguish between Eimeria acervulina, Eimeria brunetti, Eimeria maxima, Eimeria mitis, Eimeria necatrix, Eimeria praecox and Eimeria tenella. Computerized analysis of the HRM curves and capillary electrophoresis profiles could detect the dominant species in several specimens containing different ratios of E. necatrix and E. maxima and of E. tenella and E. acervulina. The HRM curve analysis identified all of the mixtures as "variation" to the reference species, and also identified the minor species in some mixtures. Computerized HRM curve analysis also detected impurities in 21 possible different combinations of the seven Eimeria species. The PCR-based HRM curve analysis of the ITS-2 provides a powerful tool for the detection and identification of pure Eimeria species. The HRM curve analysis could also be used as a rapid tool in the quality assurance of Eimeria vaccine production to confirm the purity of the monospecific cell lines. The HRM curve analysis is rapid and reliable and can be performed in a single test tube in less than 3 h.

Diagnosis and identification of Leishmania spp. from Giemsa-stained slides, by real-time PCR and melting curve analysis in south-west of Iran.

PubMed

Khademvatan, S; Neisi, N; Maraghi, S; Saki, J

2011-12-01

The aim of present study was describing a real-time PCR assay for the diagnosis and direct identification of Leishmania species on Giemsa-stained slides in south-west of Iran. Altogether, 102 Giemsa-stained slides were collected from different part of south-west of Iran between 2008 and 2011. All the Giemsa-stained slides were examined under light microscope. After DNA extraction, real-time PCR amplification and detection were conducted with fluorescent SYBR Green I. For identification, PCR products were analysed with melting curve analysis. One hundred and two archived slides from suspected lesion examined by microscopy and real-time PCR. The sensitivity of the real-time PCR on Giemsa-stained slid was 98% (96/102). The melting curve analysis (T(m)) were 88·3±0·2°C for L. tropica (MHOM/IR/02/Mash10), 86·5±0·2°C for L. major (MHOM/IR/75/ER) and 89·4±0·3°C for L. infantum (MCAN/IR/97/LON 49), respectively. This study is first report in use of real-time PCR for diagnosis and identification of Leishmania spp. in Iran. Up to now, in Iran, the majority of identification of Leishmania species is restriction fragment length polymorphism (PCR-RFLP) of ITS1 and kinetoplast DNA. Our data showed that Giemsa-stained slides that were stored more than 3 years, can be use for Leishmania DNA extraction and amplification by real-time PCR. Compared to conventional PCR-based methods, the real-time PCR is extremely rapid with results and more samples can be processed at one time.

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

PubMed

Bester, Rachelle; Jooste, Anna E C; Maree, Hans J; Burger, Johan T

2012-09-27

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

Clapeyron slope reversal in the melting curve of AuGa2 at 5.5 GPa.

PubMed

Geballe, Z M; Raju, S V; Godwal, B K; Jeanloz, R

2013-10-16

We use x-ray diffraction in a resistively heated diamond anvil cell to extend the melting curve of AuGa2 beyond its minimum at 5.5 GPa and 720 K, and to constrain the high-temperature phase boundaries between cubic (fluorite structure), orthorhombic (cottunite structure) and monoclinic phases. We document a large change in Clapeyron slope that coincides with the transitions from cubic to lower symmetry phases, showing that a structural transition is the direct cause of the change in slope. In addition, moderate (~30 K) to large (90 K) hysteresis is detected between melting and freezing, from which we infer that at high pressures, AuGa2 crystals can remain in a metastable state at more than 5% above the thermodynamic melting temperature.

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.

High resolution melting analysis to genotype the most common variants in the HFE gene.

PubMed

Marotta, Roberta V; Turri, Olivia; Morandi, Antonella; Murano, Manuela; d'Eril, Gianlodovico Melzi; Biondi, Maria Luisa

2011-09-01

High resolution melting (HRM) analysis of PCR amplicons was recently introduced as a closed-tube, rapid, and inexpensive method of genotyping. This study evaluated this system as an option for detecting the three most common mutations in the HFE gene (C282Y, H63D, S65C), accounting for the main form of hereditary haemochromatosis. Ninety samples, previously screened by direct sequencing, and 27 controls were used. The analysis were performed on the Rotor Gene Q, using the commercial HRM mix containing the Eva Green dye (Qiagen). Specific primers allowed the amplification of the regions of interest in the HFE gene. Following amplification, a HRM analysis was conducted to detect DNA variants. The thermal denaturation profiles of the samples were compared with those of the controls. One hundred percent of heterozygous and homozygous samples were readily identified. Heterozygotes were easily identified because heteroduplexes altered the shape of the melting curves, but significant differences were also present in the melting curves of the homozygous carries compared with those of the wild-type subjects. HRM analysis is an appealing technology for HFE gene screening. It is a robust technique that can be widely adopted in diagnostic laboratories to facilitate gene mutation screening.

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%). Copyright © 2016 Elsevier B.V. All rights reserved.

Melting curves and entropy of fusion of body-centered cubic tungsten under pressure

NASA Astrophysics Data System (ADS)

Liu, Chun-Mei; Chen, Xiang-Rong; Xu, Chao; Cai, Ling-Cang; Jing, Fu-Qian

2012-07-01

The melting curves and entropy of fusion of body-centered cubic (bcc) tungsten (W) under pressure are investigated via molecular dynamics (MD) simulations with extended Finnis-Sinclair (EFS) potential. The zero pressure melting point obtained is better than other theoretical results by MD simulations with the embedded-atom-method (EAM), Finnis-Sinclair (FS) and modified EAM potentials, and by ab initio MD simulations. Our radial distribution function and running coordination number analyses indicate that apart from the expected increase in disorder, the main change on going from solid to liquid is thus a slight decrease in coordination number. Our entropy of fusion of W during melting, ΔS, at zero pressure, 7.619 J/mol.K, is in good agreement with the experimental and other theoretical data. We found that, with the increasing pressure, the entropy of fusion ΔS decreases fast first and then oscillates with pressure; when the pressure is higher than 100 GPa, the entropy of fusion ΔS is about 6.575 ± 0.086 J/mol.K, which shows less pressure effect.

Stability of the bcc phase of 4He close to the melting curve: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Belonoshko, A. B.; Koči, L.; Rosengren, A.

2012-01-01

We have investigated whether the Aziz [J. Chem. Phys.JCPSA60021-960610.1063/1.438007 70, 4330 (1979)] model for 4He renders the body-centered cubic phase more stable than the face-centered cubic phase in the proximity of the melting curve. Using molecular dynamics, we have simulated these solid phases in equilibrium with the liquid at a number of densities. In contrast to previous free energy molecular dynamics calculations, the model stabilizes the body-centered cubic phase. The stability field is just 5∘ wide below the melting curve at pressures around 140 Kbar and about 70∘ wide at pressures around 750 Kbar. Considering that the body-centered cubic phase is dynamically unstable at low temperature, this result bears striking similarities to transition metal phase diagrams.

A new method for detection and discrimination of Pepino mosaic virus isolates using high resolution melting analysis of the triple gene block 3.

PubMed

Hasiów-Jaroszewska, Beata; Komorowska, Beata

2013-10-01

Diagnostic methods distinguished different Pepino mosaic virus (PepMV) genotypes but the methods do not detect sequence variation in particular gene segments. The necrotic and non-necrotic isolates (pathotypes) of PepMV share a 99% sequence similarity. These isolates differ from each other at one nucleotide site in the triple gene block 3. In this study, a combination of real-time reverse transcription polymerase chain reaction and high resolution melting curve analysis of triple gene block 3 was developed for simultaneous detection and differentiation of PepMV pathotypes. The triple gene block 3 region carrying a transition A → G was amplified using two primer pairs from twelve virus isolates, and was subjected to high resolution melting curve analysis. The results showed two distinct melting curve profiles related to each pathotype. The results also indicated that the high resolution melting method could readily differentiate between necrotic and non-necrotic PepMV pathotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

The melting curve of iron to 250 gigapascals - A constraint on the temperature at earth's center

NASA Technical Reports Server (NTRS)

Williams, Quentin; Jeanloz, Raymond; Bass, Jay; Svendsen, Bob; Ahrens, Thomas J.

1987-01-01

The melting curve of iron, the primary constituent of earth's core, has been measured to pressures of 250 gigapascals with a combination of static and dynamic techniques. The melting temperature of iron at the pressure of the core-mantle boundary (136 GPa) is 4800 + or - 200 K, whereas at the inner core-outer core boundary (330 GPa), it is 7600 + or - 500 K. A melting temperature for iron-rich alloy of 6600 K at the inner core-outer core boundary and a maximum temperature of 6900 K at earth's center are inferred. This latter value is the first experimental upper bound on the temperature at earth's center, and these results imply that the temperature of the lower mantle is significantly less than that of the outer core.

On high-pressure melting of tantalum

NASA Astrophysics Data System (ADS)

Luo, Sheng-Nian; Swift, Damian C.

2007-01-01

The issues related to high-pressure melting of Ta are discussed within the context of diamond-anvil cell (DAC) and shock wave experiments, theoretical calculations and common melting models. The discrepancies between the extrapolations of the DAC melting curve and the melting point inferred from shock wave experiments, cannot be reconciled either by superheating or solid-solid phase transition. The failure to reproduce low-pressure DAC melting curve by melting models such as dislocation-mediated melting and the Lindemann law, and molecular dynamics and quantum mechanics-based calculations, undermines their predictions at moderate and high pressures. Despite claims to the contrary, the melting curve of Ta (as well as Mo and W) remains inconclusive at high pressures.

High-Resolution Melting Curve Analysis of the 16S Ribosomal Gene to Detect and Identify Pathogenic and Saprophytic Leptospira species in Colombian Isolates

PubMed Central

Peláez Sánchez, Ronald G.; Quintero, Juan Álvaro López; Pereira, Martha María; Agudelo-Flórez, Piedad

2017-01-01

It is important to identify the circulating Leptospira agent to enhance the performance of serodiagnostic tests by incorporating specific antigens of native species, develop vaccines that take into account the species/serovars circulating in different regions, and optimize prevention and control strategies. The objectives of this study were to develop a polymerase chain reaction (PCR)–high-resolution melting (HRM) assay for differentiating between species of the genus Leptospira and to verify its usefulness in identifying unknown samples to species level. A set of primers from the initial region of the 16S ribosomal gene was designed to detect and differentiate the 22 species of Leptospira. Eleven reference strains were used as controls to establish the reference species and differential melting curves. Twenty-five Colombian Leptospira isolates were studied to evaluate the usefulness of the PCR–HRM assay in identifying unknown samples to species level. This identification was confirmed by sequencing and phylogenetic analysis of the 16S ribosomal gene. Eleven Leptospira species were successfully identified, except for Leptospira meyeri/Leptospira yanagawae because the sequences were 100% identical. The 25 isolates from humans, animals, and environmental water sources were identified as Leptospira santarosai (twelve), Leptospira interrogans (nine), and L. meyeri/L. yanagawae (four). The species verification was 100% concordant between PCR–HRM and phylogenetic analysis of the 16S ribosomal gene. The PCR–HRM assay designed in this study is a useful tool for identifying Leptospira species from isolates. PMID:28500802

Equations of state and melting curve of boron carbide in the high-pressure range of shock compression

DOE Office of Scientific and Technical Information (OSTI.GOV)

Molodets, A. M., E-mail: molodets@icp.ac.ru; Golyshev, A. A.; Shakhrai, D. V.

We have constructed the equations of state for crystalline boron carbide B{sub 11}C (C–B–C) and its melt under high dynamic and static pressures. A kink on the shock adiabat for boron carbide has been revealed in the pressure range near 100 GPa, and the melting curve with negative curvature in the pressure range 0–120 GPa has been calculated. The results have been used for interpreting the kinks on the shock adiabat for boron carbide in the pressure range of 0–400 GPa.

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. © 2015 The Author(s).

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

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

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.

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

Decoding DNA labels by melting curve analysis using real-time PCR.

PubMed

Balog, József A; Fehér, Liliána Z; Puskás, László G

2017-12-01

Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.

High-pressure melting of molybdenum.

PubMed

Belonoshko, A B; Simak, S I; Kochetov, A E; Johansson, B; Burakovsky, L; Preston, D L

2004-05-14

The melting curve of the body-centered cubic (bcc) phase of Mo has been determined for a wide pressure range using both direct ab initio molecular dynamics simulations of melting as well as a phenomenological theory of melting. These two methods show very good agreement. The simulations are based on density functional theory within the generalized gradient approximation. Our calculated equation of state of bcc Mo is in excellent agreement with experimental data. However, our melting curve is substantially higher than the one determined in diamond anvil cell experiments up to a pressure of 100 GPa. An explanation is suggested for this discrepancy.

High-throughput avian molecular sexing by SYBR green-based real-time PCR combined with melting curve analysis.

PubMed

Chang, Hsueh-Wei; Cheng, Chun-An; Gu, De-Leung; Chang, Chia-Che; Su, San-Hua; Wen, Cheng-Hao; Chou, Yii-Cheng; Chou, Ta-Ching; Yao, Cheng-Te; Tsai, Chi-Li; Cheng, Chien-Chung

2008-02-12

Combination of CHD (chromo-helicase-DNA binding protein)-specific polymerase chain reaction (PCR) with electrophoresis (PCR/electrophoresis) is the most common avian molecular sexing technique but it is lab-intensive and gel-required. Gender determination often fails when the difference in length between the PCR products of CHD-Z and CHD-W genes is too short to be resolved. Here, we are the first to introduce a PCR-melting curve analysis (PCR/MCA) to identify the gender of birds by genomic DNA, which is gel-free, quick, and inexpensive. Spilornis cheela hoya (S. c. hoya) and Pycnonotus sinensis (P. sinensis) were used to illustrate this novel molecular sexing technique. The difference in the length of CHD genes in S. c. hoya and P. sinensis is 13-, and 52-bp, respectively. Using Griffiths' P2/P8 primers, molecular sexing failed both in PCR/electrophoresis of S. c. hoya and in PCR/MCA of S. c. hoya and P. sinensis. In contrast, we redesigned sex-specific primers to yield 185- and 112-bp PCR products for the CHD-Z and CHD-W genes of S. c. hoya, respectively, using PCR/MCA. Using this specific primer set, at least 13 samples of S. c. hoya were examined simultaneously and the Tm peaks of CHD-Z and CHD-W PCR products were distinguished. In this study, we introduced a high-throughput avian molecular sexing technique and successfully applied it to two species. This new method holds a great potential for use in high throughput sexing of other avian species, as well.

High-Throughput Genotyping of Single Nucleotide Polymorphisms in the Plasmodium falciparum dhfr Gene by Asymmetric PCR and Melt-Curve Analysis▿

PubMed Central

Cruz, Rochelle E.; Shokoples, Sandra E.; Manage, Dammika P.; Yanow, Stephanie K.

2010-01-01

Mutations within the Plasmodium falciparum dihydrofolate reductase gene (Pfdhfr) contribute to resistance to antimalarials such as sulfadoxine-pyrimethamine (SP). Of particular importance are the single nucleotide polymorphisms (SNPs) within codons 51, 59, 108, and 164 in the Pfdhfr gene that are associated with SP treatment failure. Given that traditional genotyping methods are time-consuming and laborious, we developed an assay that provides the rapid, high-throughput analysis of parasite DNA isolated from clinical samples. This assay is based on asymmetric real-time PCR and melt-curve analysis (MCA) performed on the LightCycler platform. Unlabeled probes specific to each SNP are included in the reaction mixture and hybridize differentially to the mutant and wild-type sequences within the amplicon, generating distinct melting curves. Since the probe is present throughout PCR and MCA, the assay proceeds seamlessly with no further addition of reagents. This assay was validated for analytical sensitivity and specificity using plasmids, purified genomic DNA from reference strains, and parasite cultures. For all four SNPs, correct genotypes were identified with 100 copies of the template. The performance of the assay was evaluated with a blind panel of clinical isolates from travelers with low-level parasitemia. The concordance between our assay and DNA sequencing ranged from 84 to 100% depending on the SNP. We also directly compared our MCA assay to a published TaqMan real-time PCR assay and identified major issues with the specificity of the TaqMan probes. Our assay provides a number of technical improvements that facilitate the high-throughput screening of patient samples to identify SP-resistant malaria. PMID:20631115

Peptide nucleic acid probe-based fluorescence melting curve analysis for rapid screening of common JAK2, MPL, and CALR mutations.

PubMed

Park, Joonhong; Song, Minsik; Jang, Woori; Chae, Hyojin; Lee, Gun Dong; Kim, KyungTak; Park, Heekyung; Kim, Myungshin; Kim, Yonggoo

2017-02-01

We developed and evaluated the feasibility of peptide nucleic acid (PNA)-based fluorescence melting curve analysis (FMCA) to detect common mutations in myeloproliferative neoplasms (MPNs). We have set up two separate reactions of PNA-based FMCA: JAK2 V617F &CALR p.Leu367fs*46 (set A) and MPL W515L/K &CALR p.Lys385fs*47 (set B). Clinical usefulness was validated with allele-specific real-time PCR, fragment analysis, Sanger sequencing in 57 BCR-ABL1-negative MPNs. The limit of detection (LOD) of PNA-based FMCA was approximately 10% for each mutation and interference reactions using mixtures of different mutations were not observed. Non-specific amplification was not observed in normal control. PNA-based FMCA was able to detect all JAK2 V617F (n=20), CALR p.Leu367fs*46 (n=10) and p.Lys385fs*47 (n=8). Three of six MPL mutations were detected except three samples with low mutant concentration in out of LOD. JAK2 exon 12 mutations (n=7) were negative without influencing V617F results. Among six variant CALR exon 9 mutations, two were detected by this method owing to invading of probe binding site. PNA-based FMCA for detecting common JAK2, MPL, and CALR mutations is a rapid, simple, and sensitive technique in BCR-ABL1-negative MPNs with >10% mutant allele at the time of initial diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

Detection of Anti-Hepatitis B Virus Drug Resistance Mutations Based on Multicolor Melting Curve Analysis.

PubMed

Mou, Yi; Athar, Muhammad Ammar; Wu, Yuzhen; Xu, Ye; Wu, Jianhua; Xu, Zhenxing; Hayder, Zulfiqar; Khan, Saeed; Idrees, Muhammad; Nasir, Muhammad Israr; Liao, Yiqun; Li, Qingge

2016-11-01

Detection of anti-hepatitis B virus (HBV) drug resistance mutations is critical for therapeutic decisions for chronic hepatitis B virus infection. We describe a real-time PCR-based assay using multicolor melting curve analysis (MMCA) that could accurately detect 24 HBV nucleotide mutations at 10 amino acid positions in the reverse transcriptase region of the HBV polymerase gene. The two-reaction assay had a limit of detection of 5 copies per reaction and could detect a minor mutant population (5% of the total population) with the reverse transcriptase M204V amino acid mutation in the presence of the major wild-type population when the overall concentration was 10 4 copies/μl. The assay could be finished within 3 h, and the cost of materials for each sample was less than $10. Clinical validation studies using three groups of samples from both nucleos(t)ide analog-treated and -untreated patients showed that the results for 99.3% (840/846) of the samples and 99.9% (8,454/8,460) of the amino acids were concordant with those of Sanger sequencing of the PCR amplicon from the HBV reverse transcriptase region (PCR Sanger sequencing). HBV DNA in six samples with mixed infections consisting of minor mutant subpopulations was undetected by the PCR Sanger sequencing method but was detected by MMCA, and the results were confirmed by coamplification at a lower denaturation temperature-PCR Sanger sequencing. Among the treated patients, 48.6% (103/212) harbored viruses that displayed lamivudine monoresistance, adefovir monoresistance, entecavir resistance, or lamivudine and adefovir resistance. Among the untreated patients, the Chinese group had more mutation-containing samples than did the Pakistani group (3.3% versus 0.56%). Because of its accuracy, rapidness, wide-range coverage, and cost-effectiveness, the real-time PCR assay could be a robust tool for the detection if anti-HBV drug resistance mutations in resource-limited countries. Copyright © 2016, American Society for

Improved detection of genetic markers of antimicrobial resistance by hybridization probe-based melting curve analysis using primers to mask proximal mutations: examples include the influenza H275Y substitution.

PubMed

Whiley, David M; Jacob, Kevin; Nakos, Jennifer; Bletchly, Cheryl; Nimmo, Graeme R; Nissen, Michael D; Sloots, Theo P

2012-06-01

Numerous real-time PCR assays have been described for detection of the influenza A H275Y alteration. However, the performance of these methods can be undermined by sequence variation in the regions flanking the codon of interest. This is a problem encountered more broadly in microbial diagnostics. In this study, we developed a modification of hybridization probe-based melting curve analysis, whereby primers are used to mask proximal mutations in the sequence targets of hybridization probes, so as to limit the potential for sequence variation to interfere with typing. The approach was applied to the H275Y alteration of the influenza A (H1N1) 2009 strain, as well as a Neisseria gonorrhoeae mutation associated with antimicrobial resistance. Assay performances were assessed using influenza A and N. gonorrhoeae strains characterized by DNA sequencing. The modified hybridization probe-based approach proved successful in limiting the effects of proximal mutations, with the results of melting curve analyses being 100% consistent with the results of DNA sequencing for all influenza A and N. gonorrhoeae strains tested. Notably, these included influenza A and N. gonorrhoeae strains exhibiting additional mutations in hybridization probe targets. Of particular interest was that the H275Y assay correctly typed influenza A strains harbouring a T822C nucleotide substitution, previously shown to interfere with H275Y typing methods. Overall our modified hybridization probe-based approach provides a simple means of circumventing problems caused by sequence variation, and offers improved detection of the influenza A H275Y alteration and potentially other resistance mechanisms.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

Detecting differential allelic expression using high-resolution melting curve analysis: application to the breast cancer susceptibility gene CHEK2

PubMed Central

2011-01-01

Background The gene CHEK2 encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though CHEK2 has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk families have been explained by genetic variants located in its coding region. Alteration in gene expression regulation provides a potential mechanism for generating disease susceptibility. The detection of differential allelic expression (DAE) represents a sensitive assay to direct the search for a functional sequence variant within the transcriptional regulatory elements of a candidate gene. We aimed to assess whether CHEK2 was subject to DAE in lymphoblastoid cell lines (LCLs) from high-risk breast cancer patients for whom no mutation in BRCA1 or BRCA2 had been identified. Methods We implemented an assay based on high-resolution melting (HRM) curve analysis and developed an analysis tool for DAE assessment. Results We observed allelic expression imbalance in 4 of the 41 LCLs examined. All four were carriers of the truncating mutation 1100delC. We confirmed previous findings that this mutation induces non-sense mediated mRNA decay. In our series, we ruled out the possibility of a functional sequence variant located in the promoter region or in a regulatory element of CHEK2 that would lead to DAE in the transcriptional regulatory milieu of freely proliferating LCLs. Conclusions Our results support that HRM is a sensitive and accurate method for DAE assessment. This approach would be of great interest for high-throughput mutation screening projects aiming to identify genes carrying functional regulatory polymorphisms. PMID:21569354

Vibrational density of states and Lindemann melting law

NASA Astrophysics Data System (ADS)

Luo, Sheng-Nian; Strachan, Alejandro; Swift, Damian C.

2005-05-01

We examine the Lindemann melting law at different pressures using the vibrational density of states (DOS), equilibrium melting curve, and Lindemann parameter δL (fractional root-mean-squared displacement, rmsd, at equilibrium melting) calculated independently from molecular dynamics simulations of the Lennard-Jones system. The DOS is obtained using spectra analysis of atomic velocities and accounts for anharmonicity. The increase of δL with pressure is non-negligible: δL is about 0.116 and 0.145 at ambient and extreme pressures, respectively. If the component of rmsd normal to a reflecting plane as in the Debye-Waller-factor-type measurements using x rays is adopted for δL, these values are about 0.067(±0.002) and 0.084(±0.003), and are comparable with experimental and calculated values for face-centered-cubic elements. We find that the Lindemann relation holds accurately at ambient and high pressures. The non-negligible pressure dependence of δL suggests that caution should be exerted in applying the Lindemann law to obtaining the high pressure melting curve anchored at ambient pressure.

Thermophoretic melting curves quantify the conformation and stability of RNA and DNA

PubMed Central

Wienken, Christoph J.; Baaske, Philipp; Duhr, Stefan; Braun, Dieter

2011-01-01

Measuring parameters such as stability and conformation of biomolecules, especially of nucleic acids, is important in the field of biology, medical diagnostics and biotechnology. We present a thermophoretic method to analyse the conformation and thermal stability of nucleic acids. It relies on the directed movement of molecules in a temperature gradient that depends on surface characteristics of the molecule, such as size, charge and hydrophobicity. By measuring thermophoresis of nucleic acids over temperature, we find clear melting transitions and resolve intermediate conformational states. These intermediate states are indicated by an additional peak in the thermophoretic signal preceding most melting transitions. We analysed single nucleotide polymorphisms, DNA modifications, conformational states of DNA hairpins and microRNA duplexes. The method is validated successfully against calculated melting temperatures and UV absorbance measurements. Interestingly, the methylation of DNA is detected by the thermophoretic amplitude even if it does not affect the melting temperature. In the described setup, thermophoresis is measured all-optical in a simple setup using a reproducible capillary format with only 250 nl probe consumption. The thermophoretic analysis of nucleic acids shows the technique’s versatility for the investigation of nucleic acids relevant in cellular processes like RNA interference or gene silencing. PMID:21297115

X-ray fluorescence analysis of K, Al and trace elements in chloroaluminate melts

NASA Astrophysics Data System (ADS)

Shibitko, A. O.; Abramov, A. V.; Denisov, E. I.; Lisienko, D. G.; Rebrin, O. I.; Bunkov, G. M.; Rychkov, V. N.

2017-09-01

Energy dispersive x-ray fluorescence spectrometry was applied to quantitative determination of K, Al, Cr, Fe and Ni in chloroaluminate melts. To implement the external standard calibration method, an unconventional way of samples preparation was suggested. A mixture of metal chlorides was melted in a quartz cell at 350-450 °C under a slightly excessive pressure of purified argon (99.999 %). The composition of the calibration samples (CSs) prepared was controlled by means of the inductively coupled plasma atomic emission spectrometry (ICP-AES). The optimal conditions for analytical lines excitation were determined, the analytes calibration curves were obtained. There was some influence of matrix effects in synthesized samples on the analytical signal of some elements. The CSs are to be stored in inert gas atmosphere. The precision, accuracy, and reproducibility factors of the quantitative chemical analysis were computed.

Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs.

PubMed

Mishra, Priyanka; Shukla, Ashutosh K; Sundaresan, Velusamy

2018-01-01

Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes ( rbcL and matK ) and intergenic spacers ( psbA-trnH and ITS ) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S . italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 ( S. alexandrina crude drug sample from Bangalore) and HSA06 ( S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S . italica subsp. micrantha . Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply

Candidate DNA Barcode Tags Combined With High Resolution Melting (Bar-HRM) Curve Analysis for Authentication of Senna alexandrina Mill. With Validation in Crude Drugs

PubMed Central

Mishra, Priyanka; Shukla, Ashutosh K.; Sundaresan, Velusamy

2018-01-01

Senna alexandrina (Fabaceae) is a globally recognized medicinal plant for its laxative properties as well as the only source of sennosides, and is highly exported bulk herb from India. Its major procurement is exclusively from limited cultivation, which leads to risks of deliberate or unintended adulteration. The market raw materials are in powdered or finished product form, which lead to difficulties in authentication. Here, DNA barcode tags based on chloroplast genes (rbcL and matK) and intergenic spacers (psbA-trnH and ITS) were developed for S. alexandrina along with the allied species. The ability and performance of the ITS1 region to discriminate among the Senna species resulted in the present proposal of the ITS1 tags as successful barcode. Further, these tags were coupled with high-resolution melting (HRM) curve analysis in a real-time PCR genotyping method to derive Bar-HRM (Barcoding-HRM) assays. Suitable HRM primer sets were designed through SNP detection and mutation scanning in genomic signatures of Senna species. The melting profiles of S. alexandrina and S. italica subsp. micrantha were almost identical and the remaining five species were clearly separated so that they can be differentiated by HRM method. The sensitivity of the method was utilized to authenticate market samples [Herbal Sample Assays (HSAs)]. HSA01 (S. alexandrina crude drug sample from Bangalore) and HSA06 (S. alexandrina crude drug sample from Tuticorin, Tamil Nadu, India) were found to be highly contaminated with S. italica subsp. micrantha. Species admixture samples mixed in varying percentage was identified sensitively with detection of contamination as low as 1%. The melting profiles of PCR amplicons are clearly distinct, which enables the authentic differentiation of species by the HRM method. This study reveals that DNA barcoding coupled with HRM is an efficient molecular tool to authenticate Senna herbal products in the market for quality control in the drug supply chain

Melting behavior of SnI4 reexamined

NASA Astrophysics Data System (ADS)

Fuchizaki, Kazuhiro

2013-12-01

The low-pressure crystalline phase of a molecular crystal, SnI4, has a rising melting curve that breaks abruptly at around 1.5 GPa, beyond which it becomes almost flat, with a slight maximum at about 3 GPa. Although the overall aspect of this melting curve can be captured by the Kumari-Dass-Kechin equation, the values for the parameters involved in the equation were definitely different from those predicted on the basis of the Clapeyron-Clausius relationship. On the other hand, the accuracy of our experimental data prevented us from judging whether the parameters are derivable from the Lindemann melting law, as shown independently by Kumari and Dass, and by Kechin. The Kraut-Kennedy and Magalinskii-Zubov relationships seem to be valid in the low-pressure region where the melting curve is rising. The breakdown of these relationships suggests a qualitative change in the intermolecular interaction upon compression, thereby making the melting behavior unusual.

MgO melting curve constraints from shock temperature and rarefaction overtake measurements in samples preheated to 2300 K

NASA Astrophysics Data System (ADS)

Fat'yanov, O.; Asimow, P.

2013-06-01

In a continuous effort to determine experimentally the melting curve of MgO at 100-200 GPa, we extended our target preheating capability to 2300 K. The limit was primarily caused by intense sublimation of pure MgO in vacuum above ~2050 K. Completely redesigned Mo capsules holding ~20 mm long MgO crystals with controlled thermal gradients were impacted by thin Ta flyers launched at 6.5 to 7.5 km/s on the Caltech two-stage light-gas gun. Radiative shock temperatures and rarefaction overtake times were measured simultaneously by a 6-channel pyrometer with 3 ns time resolution, over 440-750 nm spectral range. All our experiments showed smooth pressure dependence of MgO sound speed consistent with the solid phase at 204-239 GPa. Observed temperatures are ~1000 K lower than those predicted by the solid phase model, but the plot of measured shock temperature versus pressure exhibits a pattern typical of shock melting at the highest pressure investigated. This may suggest that the Hugoniot of MgO preheated to 2300 K crosses its melting line at 220-240 GPa. Sound speed data indistinguishable from the solid phase model do not exclude the possibility of melting there.

High-Resolution Melting Analysis for Rapid Detection of Sequence Type 131 Escherichia coli.

PubMed

Harrison, Lucas B; Hanson, Nancy D

2017-06-01

Escherichia coli isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high-resolution melting (HRM) analysis to differentiate ST131 from non-ST131 E. coli in large sample populations in the absence of sequence analysis. The method was optimized using DNA from 12 E. coli isolates. Singleplex PCR was performed using 10 ng of DNA, Type-it HRM buffer, and multilocus sequence typing primers and was followed by multiplex PCR. The amplicon sizes ranged from 630 to 737 bp. Melt temperature peaks were determined by performing HRM analysis at 0.1°C resolution from 50 to 95°C on a Rotor-Gene Q 5-plex HRM system. Derivative melt curves were compared between sequence types and analyzed by principal component analysis. A blinded study of 191 E. coli isolates of ST131 and unknown sequence types validated this methodology. This methodology returned 99.2% specificity (124 true negatives and 1 false positive) and 100% sensitivity (66 true positives and 0 false negatives). This HRM methodology distinguishes ST131 from non-ST131 E. coli without sequence analysis. The analysis can be accomplished in about 3 h in any laboratory with an HRM-capable instrument and principal component analysis software. Therefore, this assay is a fast and cost-effective alternative to sequencing-based ST131 identification. Copyright © 2017 Harrison and Hanson.

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.

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

PubMed Central

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

2013-01-01

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

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

Application of high-resolution melting curve analysis for typing of fowl adenoviruses in field cases of inclusion body hepatitis.

PubMed

Steer, P A; O'Rourke, D; Ghorashi, S A; Noormohammadi, A H

2011-05-01

Fowl adenoviruses (FAdVs) cause inclusion body hepatitis (IBH) in chickens. In this study, clinical cases of IBH from Australian broiler flocks were screened for the presence and genotype of FAdVs. Twenty-six IBH cases from commercial poultry farms were screened. Polymerase chain reaction (PCR) coupled with high-resolution melt (HRM) curve analysis (PCR/HRM genotyping) was used to determine the presence and genotype of FAdVs. For comparison, field isolates were also assessed by virus microneutralisation and nucleotide sequence analysis of the hexon loop 1 (Hex L1) gene. PCR detection of chicken anaemia virus (CAV) and infectious bursal disease virus (IBDV) was also employed. FAdV-8b and FAdV-11 were identified in 13 cases each. In one case, FAdV-1 was also identified. Cross-neutralisation was observed between the FAdV-11 field strain and the reference FAdV-2 and 11 antisera, a result also seen with the type 2 and 11 reference FAdVs. Field strains 1 and 8b were neutralised only by their respective type antisera. The FAdV-8b field strain was identical to the Australian FAdV vaccine strain (type 8b) in the Hex L1 region. The Hex L1 sequence of the FAdV-11 field strain had the highest identity to FAdV-11 (93.2%) and FAdV-2 (92.7%) reference strains. In the five cases tested for CAV and IBDV, neither virus was detected. The evidence suggested the presence of sufficient antibodies against CAV and IBD in the parent flocks and there was no indication of immunosuppression caused by these viruses. These results indicate that PCR/HRM genotyping is a reliable diagnostic method for FAdV identification and is more rapid than virus neutralisation and direct sequence analysis. Furthermore, they suggest that IBH in Australian broiler flocks is a primary disease resulting from two alternative FAdV strains from different species. © 2011 The Authors. Australian Veterinary Journal © 2011 Australian Veterinary Association.

Differentiation of BHV-1 isolates from vaccine virus by high-resolution melting analysis.

PubMed

Ostertag-Hill, Claire; Fang, Liang; Izume, Satoko; Lee, Megan; Reed, Aimee; Jin, Ling

2015-02-16

An efficacious bovine herpesvirus type-1 (BHV-1) vaccine has been used for many years. However, in the past few years, abortion and respiratory diseases have occurred after administration of the modified live vaccine. To investigate whether BHV-1 isolates from disease outbreaks are identical to those of the vaccines used, selected regions of the BHV-1 genome were investigated by high-resolution melting (HRM) analysis and PCR-DNA sequencing. When a target region within the thymidine kinase (TK) gene was examined by HRM analysis, 6 out of the 11 isolates from abortion cases and 22 out of the 25 isolates from bovine respiratory disease (BRD) cases had different melting curves compared to the vaccine virus. Surprisingly, when a conserved region within the US6 gene that encodes glycoprotein D (gD) was examined by HRM analysis, 5 out of the 11 abortion isolates and 18 out of the 23 BRD isolates had different melting curves from the vaccine virus. To determine whether SNPs within the coding regions of glycoprotein E (gE) and TK genes can be used to differentiate the isolates from the vaccine virus, PCR-DNA sequencing was used to examine these SNPs in all the isolates. This revealed that only 1 out of 11 of the abortion isolates and 4 out of 24 of the BRD isolates are different in the target region of gE from the vaccine virus, while 5 out of 11 abortion isolates and 4 out of 22 BRD isolates are different in the target region of TK from the vaccine virus. No DNA sequence differences were observed in glycoprotein G (gG) region between disease and vaccine isolates. Our study demonstrated that many disease isolates had genetic differences from the vaccine virus in regions examined by HRM and PCR-DNA sequencing analysis. In addition, many isolates contained more than one type of mutation and were composed of mixed variants. Our study suggests that a mixture of variants were present in isolates collected post-vaccination. HRM is a rapid diagnostic method that can be used for

Rapid detection of α-thalassaemia alleles of --(SEA)/, -α(3.7)/ and -α(4.2)/ using a dual labelling, self-quenching hybridization probe/melting curve analysis.

PubMed

Gao, Lan; Liu, Yanhui; Sun, Manna; Zhao, Ying; Xie, Rungui; He, Yi; Xu, Wanfang; Liu, Jianxin; Lin, Yangyang; Lou, Jiwu

2015-12-01

The aim of the study was to set up an alternative automatic molecular diagnostic method for deletional α-thalassaemia mutations without gel electrophoresis. Based on the sequence variation within the two Z boxes and melting curve analysis of dually labelled probes, a real-time PCR assay was developed and validated for the rapid detection of major α-genotypes (--(SEA)/αα, --(SEA)/-α(3.7), --(SEA)/-α(4.2), --(SEA)/--(SEA), -α(3.7)/-α(3.7) and -α(4.2)/-α(4.2)). Samples with the -α(3.7)/-α(3.7), -α(4.2)/-α(4.2), --(SEA)/αα, --(SEA)/-α(3.7), --(SEA)/-α(4.2), and --(SEA)/--(SEA) genotypes could be clearly distinguished. The accuracy of this technique for these samples was 100% sensitivity and specificity. This technique is rapid and reliable, demonstrating feasibility for use in large-scale population screening and prenatal diagnosis of deletional Hb H disease and Hb Bart's hydrops fetalis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Salt melt synthesis of curved nitrogen-doped carbon nanostructures: ORR kinetics boost

NASA Astrophysics Data System (ADS)

Rybarczyk, Maria K.; Gontarek, Emilia; Lieder, Marek; Titirici, Maria-Magdalena

2018-03-01

Implementing metal-free electrocatalysts for the oxygen reduction reaction (ORR) and revealing crucial chemical or topographical parameters driving their activity are vital for the development of power cells. The carbon-based catalysts are very often synthesized through carbonization of biopolymers, in particular, those one containing nitrogen groups such as chitosan. Unfortunately, the resulting carbonaceous materials usually lack specific porosity and exhibit low catalytic activity. Here, we demonstrate that pyrolysis of chitosan in a ZnCl2 melt assisted by the presence of LiCl results not only in a highly porous activated carbon material with a specific surface area of 1317.97 m2/g and the total nitrogen content of 6.5%, but also induces unexpected curvature in the grown graphitic layers. This is the first work that shows curved graphene layers obtained from a biopolymer precursor by its pyrolytic decomposition in the melted salt media. On the other hand, a carbonaceous material obtained from chitosan but without the salts has very low specific surface area of 7.8 m2/g, possesses no specific structural features, and contains 4.7% of nitrogen. The electrochemical studies show, that the former material is highly active towards four-electron pathway of the ORR in terms of an onset potential (0.89 V vs RHE) and the turnover frequency (TOFmax = 0.095 e site-1 s-1). We attribute this high catalytic performance to the presence of the pyridinic and pyrrolic sites in the structure. The ORR kinetics is probably further promoted by curvature in the graphitic layers.

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.

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

Miltenberger blood group typing by real-time polymerase chain reaction (qPCR) melting curve analysis in Thai population.

PubMed

Vongsakulyanon, A; Kitpoka, P; Kunakorn, M; Srikhirin, T

2015-12-01

To develop reliable and convenient methods for Miltenberger (Mi(a) ) blood group typing. To apply real-time polymerase chain reaction (qPCR) melting curve analysis to Mi(a) blood group typing. The Mi(a) blood group is the collective set of glycophorin hybrids in the MNS blood group system. Mi(a+) blood is common among East Asians and is also found in the Thai population. Incompatible Mi(a) blood transfusions pose the risk of life-threatening haemolysis; therefore, Mi(a) blood group typing is necessary in ethnicities where the Mi(a) blood group is prevalent. One hundred and forty-three blood samples from Thai blood donors were used in the study. The samples included 50 Mi(a+) samples and 93 Mi(a-) samples, which were defined by serology. The samples were typed by Mi(a) typing qPCR, and 50 Mi(a+) samples were sequenced to identify the Mi(a) subtypes. Mi(a) subtyping qPCR was performed to define GP.Mur. Both Mi(a) typing and Mi(a) subtyping were tested on a conventional PCR platform. The results of Mi(a) typing qPCR were all concordant with serology. Sequencing of the 50 Mi(a+) samples revealed 47 GP.Mur samples and 3 GP.Hop or Bun samples. Mi(a) subtyping qPCR was the supplementary test used to further define GP.Mur from other Mi(a) subtypes. Both Mi(a) typing and Mi(a) subtyping performed well using a conventional PCR platform. Mi(a) typing qPCR correctly identified Mi(a) blood groups in a Thai population with the feasibility of Mi(a) subtype discrimination, and Mi(a) subtyping qPCR was able to further define GP.Mur from other Mi(a) subtypes. © 2015 British Blood Transfusion Society.

Methylation-sensitive high-resolution melting-curve analysis of the SNRPN gene as a diagnostic screen for Prader-Willi and Angelman syndromes.

PubMed

White, Helen E; Hall, Victoria J; Cross, Nicholas C P

2007-11-01

Angelman syndrome (AS) and Prader-Willi syndrome (PWS) are 2 distinct neurodevelopmental disorders caused primarily by deficiency of specific parental contributions at an imprinted domain within the chromosomal region 15q11.2-13. Lack of paternal contribution results in PWS either by paternal deletion (approximately 70%) or maternal uniparental disomy (UPD) (approximately 25%). Most cases of AS result from the lack of a maternal contribution from this same region, by maternal deletion (70%) or paternal UPD (approximately 5%). Analysis of allelic methylation differences at the small nuclear ribonucleoprotein polypeptide N (SNRPN) locus differentiates the maternally and paternally inherited chromosome 15 and can be used as a diagnostic test for AS and PWS. Methylation-sensitive high-resolution melting-curve analysis (MS-HRM) using the DNA binding dye EvaGreen was used to analyze methylation differences at the SNRPN locus in anonymized DNA samples from individuals with PWS (n = 39) or AS (n = 31) and from healthy control individuals (n = 95). Results from the MS-HRM assay were compared to those obtained by use of a methylation-specific PCR (MSP) protocol that is used commonly in diagnostic practice. With the MS-HRM assay 97.6% of samples were unambiguously assigned to the 3 diagnostic categories (AS, PWS, normal) by use of automated calling with an 80% confidence percentage threshold, and the failure rate was 0.6%. One PWS sample showed a discordant result for the MS-HRM assay compared to MSP data. MS-HRM is a simple, rapid, and robust method for screening methylation differences at the SNRPN locus and could be used as a diagnostic screen for PWS and AS.

MgO melting curve constraints from shock temperature and rarefaction overtake measurements in samples preheated to 2300 K

NASA Astrophysics Data System (ADS)

Fat'yanov, O. V.; Asimow, P. D.

2014-05-01

Continuing our effort to obtain experimental constraints on the melting curve of MgO at 100-200 GPa, we extended our target preheating capability to 2300 K. Our new Mo capsule design holds a long MgO crystal in a controlled thermal gradient until impact by a Ta flyer launched at up to 7.5 km/s on the Caltech two-stage light-gas gun. Radiative shock temperatures and rarefaction overtake times were measured simultaneously by a 6-channel VIS/NIR pyrometer with 3 ns time resolution. The majority of our experiments showed smooth monotonic increases in MgO sound speed and shock temperature with pressure from 197 to 243 GPa. The measured temperatures as well as the slopes of the pressure dependences for both temperature and sound speed were in good agreement with those calculated numerically for the solid phase at our peak shock compression conditions. Most observed sound speeds, however, were ~800 m/s higher than those predicted by the model. A single unconfirmed data point at 239 GPa showed anomalously low temperature and sound speed, which could both be explained by partial melting in this experiment and could suggest that the Hugoniot of MgO preheated to 2300 K crosses its melting line just slightly above 240 GPa.

Melting in super-earths.

PubMed

Stixrude, Lars

2014-04-28

We examine the possible extent of melting in rock-iron super-earths, focusing on those in the habitable zone. We consider the energetics of accretion and core formation, the timescale of cooling and its dependence on viscosity and partial melting, thermal regulation via the temperature dependence of viscosity, and the melting curves of rock and iron components at the ultra-high pressures characteristic of super-earths. We find that the efficiency of kinetic energy deposition during accretion increases with planetary mass; considering the likely role of giant impacts and core formation, we find that super-earths probably complete their accretionary phase in an entirely molten state. Considerations of thermal regulation lead us to propose model temperature profiles of super-earths that are controlled by silicate melting. We estimate melting curves of iron and rock components up to the extreme pressures characteristic of super-earth interiors based on existing experimental and ab initio results and scaling laws. We construct super-earth thermal models by solving the equations of mass conservation and hydrostatic equilibrium, together with equations of state of rock and iron components. We set the potential temperature at the core-mantle boundary and at the surface to the local silicate melting temperature. We find that ancient (∼4 Gyr) super-earths may be partially molten at the top and bottom of their mantles, and that mantle convection is sufficiently vigorous to sustain dynamo action over the whole range of super-earth masses.

Using the weighted area under the net benefit curve for decision curve analysis.

PubMed

Talluri, Rajesh; Shete, Sanjay

2016-07-18

Risk prediction models have been proposed for various diseases and are being improved as new predictors are identified. A major challenge is to determine whether the newly discovered predictors improve risk prediction. Decision curve analysis has been proposed as an alternative to the area under the curve and net reclassification index to evaluate the performance of prediction models in clinical scenarios. The decision curve computed using the net benefit can evaluate the predictive performance of risk models at a given or range of threshold probabilities. However, when the decision curves for 2 competing models cross in the range of interest, it is difficult to identify the best model as there is no readily available summary measure for evaluating the predictive performance. The key deterrent for using simple measures such as the area under the net benefit curve is the assumption that the threshold probabilities are uniformly distributed among patients. We propose a novel measure for performing decision curve analysis. The approach estimates the distribution of threshold probabilities without the need of additional data. Using the estimated distribution of threshold probabilities, the weighted area under the net benefit curve serves as the summary measure to compare risk prediction models in a range of interest. We compared 3 different approaches, the standard method, the area under the net benefit curve, and the weighted area under the net benefit curve. Type 1 error and power comparisons demonstrate that the weighted area under the net benefit curve has higher power compared to the other methods. Several simulation studies are presented to demonstrate the improvement in model comparison using the weighted area under the net benefit curve compared to the standard method. The proposed measure improves decision curve analysis by using the weighted area under the curve and thereby improves the power of the decision curve analysis to compare risk prediction models in

High-pressure melting of MgSiO3.

PubMed

Belonoshko, A B; Skorodumova, N V; Rosengren, A; Ahuja, R; Johansson, B; Burakovsky, L; Preston, D L

2005-05-20

The melting curve of MgSiO(3) perovskite has been determined by means of ab initio molecular dynamics complemented by effective pair potentials, and a new phenomenological model of melting. Using first principles ground state calculations, we find that the MgSiO(3) perovskite phase transforms into post perovskite at pressures above 100 GPa, in agreement with recent theoretical and experimental studies. We find that the melting curve of MgSiO(3), being very steep at pressures below 60 GPa, rapidly flattens on increasing pressure. The experimental controversy on the melting of the MgSiO(3) perovskite at high pressures is resolved, confirming the data by Zerr and Boehler.

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

PubMed

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

2016-09-01

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

Predicted reentrant melting of dense hydrogen at ultra-high pressures

PubMed Central

Geng, Hua Y.; Wu, Q.

2016-01-01

The phase diagram of hydrogen is one of the most important challenges in high-pressure physics and astrophysics. Especially, the melting of dense hydrogen is complicated by dimer dissociation, metallization and nuclear quantum effect of protons, which together lead to a cold melting of dense hydrogen when above 500 GPa. Nonetheless, the variation of the melting curve at higher pressures is virtually uncharted. Here we report that using ab initio molecular dynamics and path integral simulations based on density functional theory, a new atomic phase is discovered, which gives an uplifting melting curve of dense hydrogen when beyond 2 TPa, and results in a reentrant solid-liquid transition before entering the Wigner crystalline phase of protons. The findings greatly extend the phase diagram of dense hydrogen, and put metallic hydrogen into the group of alkali metals, with its melting curve closely resembling those of lithium and sodium. PMID:27834405

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

Keller, Mark; Naue, Jana; 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.

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

simulation of the DNA force-extension curve

NASA Astrophysics Data System (ADS)

Shinaberry, Gregory; Mikhaylov, Ivan; Balaeff, Alexander

A molecular dynamics simulation study of the force-extension curve of double-stranded DNA is presented. Extended simulations of the DNA at multiple points along the force-extension curve are conducted with DNA end-to-end length constrained at each point. The calculated force-extension curve qualitatively reproduces the experimental one. The DNA conformational ensemble at each extension shows that the famous plateau of the force-extension curve results from B-DNA melting, whereas the formation of the earlier-predicted novel DNA conformation called 'zip-DNA' takes place at extensions past the plateau. An extensive analysis of the DNA conformational ensemble in terms of base configuration, backbone configuration, solvent interaction energy, etc., is conducted in order to elucidate the physical origin of DNA elasticity and the main interactions responsible for the shape of the force-extension curve.

Melting Behavior of a Model Molecular Crystalline GeI4

NASA Astrophysics Data System (ADS)

Fuchizaki, Kazuhiro; Asano, Yuta

2015-06-01

A model molecular crystalline GeI4 was examined using molecular dynamics simulation. The model was constructed in such a way that rigid tetrahedral molecules interact with each other via Lennard-Jones potentials whose centers are located at the vertices of a tetrahedron. Because no other interaction that can "soften" the intermolecular interaction was introduced, the melting curve of the model crystalline material does not exhibit the anomaly that was found for the real substance. However, the current investigation is useful in that it could settle the upper bound of pressure below which the model can predict properties of the molecular liquid. Moreover, singularity-free nature of the melting curve allowed us to analytically treat the melting curve in the light of the Kumari-Dass-Kechin equation. As a result, we could definitely conclude that the well-known Simon equation for the melting curve is merely an approximate expression. The condition for the validity of Simon's equation was identified.

Experimental constraints on melting temperatures in the MgO-SiO2 system at lower mantle pressures

NASA Astrophysics Data System (ADS)

Baron, Marzena A.; Lord, Oliver T.; Myhill, Robert; Thomson, Andrew R.; Wang, Weiwei; Trønnes, Reidar G.; Walter, Michael J.

2017-08-01

Eutectic melting curves in the system MgO-SiO2 have been experimentally determined at lower mantle pressures using laser-heated diamond anvil cell (LH-DAC) techniques. We investigated eutectic melting of bridgmanite plus periclase in the MgO-MgSiO3 binary, and melting of bridgmanite plus stishovite in the MgSiO3-SiO2 binary, as analogues for natural peridotite and basalt, respectively. The melting curve of model basalt occurs at lower temperatures, has a shallower dT / dP slope and slightly less curvature than the model peridotitic melting curve. Overall, melting temperatures detected in this study are in good agreement with previous experiments and ab initio simulations at ∼25 GPa (Liebske and Frost, 2012; de Koker et al., 2013). However, at higher pressures the measured eutectic melting curves are systematically lower in temperature than curves extrapolated on the basis of thermodynamic modelling of low-pressure experimental data, and those calculated from atomistic simulations. We find that our data are inconsistent with previously computed melting temperatures and melt thermodynamic properties of the SiO2 endmember, and indicate a maximum in short-range ordering in MgO-SiO2 melts close to Mg2SiO4 composition. The curvature of the model peridotite eutectic relative to an MgSiO3 melt adiabat indicates that crystallization in a global magma ocean would begin at ∼100 GPa rather than at the bottom of the mantle, allowing for an early basal melt layer. The model peridotite melting curve lies ∼ 500 K above the mantle geotherm at the core-mantle boundary, indicating that it will not be molten unless the addition of other components reduces the solidus sufficiently. The model basalt melting curve intersects the geotherm at the base of the mantle, and partial melting of subducted oceanic crust is expected.

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

High resolution melting analysis (HRM) for the assessment of clonality in feline B-cell lymphomas.

PubMed

Henrich, Manfred; Scheffold, Svenja; Hecht, Werner; Reinacher, Manfred

2018-06-01

Analysis of clonality is gaining importance in diagnosing lymphomas in veterinary medicine. Usually, PCR for the analysis of antigen receptor rearrangement (PARR) is followed by electrophoretic separation of the PCR products. Aim of this study was to test the feasibility of HRM for the assessment of clonality in B-cell lymphomas of cats. High resolution melting analysis differentiates PCR products by their different melting point using the decrease in fluorescence of an intercalating dye during melting of the PCR product. Additionally, the method is easy to use with no post-PCR manipulation of the samples. Forty-seven feline B-cell lymphomas and 31 reactive lymphatic proliferations of cats were investigated by PARR followed either by capillary electrophoresis or an HRM assay. To objectify the interpretation of the HRM results a recently published mathematical approach was applied to the melting curve. To overcome discrepancies between the visual interpretation and the mathematical approach, the latter was modified to include testing of reproducibility and recognition of pseudoclonality. In 11 of 47 lymphoma cases clonal populations were detectable by HRM assay compared to 14 of 47 lymphomas in which clonal populations were detected by capillary electrophoresis assay. Neither of the methods showed a clonal pattern in any of the reactive samples. However, the HRM assay showed a unique pattern in cases of follicular lymphatic hyperplasia that had no corresponding pattern in capillary electrophoresis. The capillary electrophoresis assay could identify 3 lymphomas that were not detected by the HRM assay and is therefore regarded superior to the HRM assay. The comparison however, was hampered by the overall bad performance of the PARR, that might be the consequence of insufficient primer binding due to somatic hypermutation of the binding sites during antigen stimulated proliferation of the B lymphocytes. Copyright © 2018 Elsevier B.V. All rights reserved.

Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array.

PubMed

Rizzi, Giovanni; Lee, Jung-Rok; Dahl, Christina; Guldberg, Per; Dufva, Martin; Wang, Shan X; Hansen, Mikkel F

2017-09-26

Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.

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

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

PubMed

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

2016-01-01

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. 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. 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. 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. 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 determine the A. paniculata species in herbal products tested

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

PubMed

Rousson, Valentin; Zumbrunn, Thomas

2011-06-22

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. 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. 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. We present several interrelated extensions to decision curve analysis that will both facilitate its interpretation and broaden its potential area of application.

Eutectic melting in the MgO-SiO2 system and its implication to Earth's lower mantle evolution

NASA Astrophysics Data System (ADS)

Baron, M. A.; Lord, O. T.; Myhill, R.; Thomson, A.; Wang, W.; Tronnes, R. G.; Walter, M. J.

2017-12-01

Eutectic melting curves in the system MgO-SiO2 have been experimentally studied at lower mantle pressures using laser-heated diamond anvil cell (LH-DAC) techniques. We investigated eutectic melting of bridgmanite plus periclase in the MgO-MgSiO3 binary and bridgmanite plus stishovite in the MgSiO3-SiO2 sub-system as the simplest models of natural peridotite and basalt. The eutectic melting have been detected on the basis of the thermal perturbations (i.e. melting plateau) during the experiment but also post-experimental textural and chemical analyses of the recovered samples. We also performed a suite of sub-solidus experiments in order to compare and bracket the eutectic melting experiments. The melting curve of model basalt occurs at lower temperatures, has a shallower dT/dP slope and slightly less curvature than the model peridotitic melting curve. Overall, melting temperatures detected in this study are in good agreement with previous experiments and ab initio simulations at 25 GPa (Liebske and Frost, 2012; de Koker et al., 2013). However, at higher pressures the measured eutectic melting curves are systematically lower in temperature than curves extrapolated on the basis of thermodynamic modelling of low-pressure experimental data, and those calculated from atomistic simulations. In turn, when comparing with previously published solidus curves obtained for natural basalt and peridotite (e.g. Fiquet et al., 2010; Andrault et al. 2011; Nomura et al. 2014; Hirose et al. 1999; Andrault et al. 2014 and Pradhan et al. 2015) the melting curves from this study are higher. However, the difference in temperature is less significant than previously though. Based on the comparison of the curvature of the model peridotite eutectic relative to an MgSiO3 melt adiabat we infer that crystallization in a global magma ocean would begin at 100 GPa rather than at the bottom of the mantle, allowing for an early basal melt layer. The model peridotite melting curve lies 500 K above

Genotyping of Listeria monocytogenes isolates from poultry carcasses using high resolution melting (HRM) analysis.

PubMed

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

2014-01-02

An outbreak situation of human listeriosis requires a fast and accurate protocol for typing Listeria monocytogenes . Existing techniques are either characterized by low discriminatory power or are laborious and require several days to give a final result. Polymerase chain reaction (PCR) coupled with high resolution melting (HRM) analysis was investigated in this study as an alternative tool for a rapid and precise genotyping of L. monocytogenes isolates. Fifty-five isolates of L. monocytogenes isolated from poultry carcasses and the environment of four slaughterhouses were typed by HRM analysis using two specific markers, internalin B and ssrA genes. The analysis of genotype confidence percentage of L. monocytogenes isolates produced by HRM analysis generated dendrograms with two major groups and several subgroups. Furthermore, the analysis of the HRM curves revealed that all L. monocytogenes isolates could easily be distinguished. In conclusion, HRM was proven to be a fast and powerful tool for genotyping isolates of L. monocytogenes .

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

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

PubMed

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

2016-06-01

We report the development of an automated genetic analyzer for human sample testing based on microfluidic rapid polymerase chain reaction (PCR) with high-resolution melting analysis (HRMA). The integrated DNA microfluidic cartridge was used on a platform designed with a robotic pipettor system that works by sequentially picking up different test solutions from a 384-well plate, mixing them in the tips, and delivering mixed fluids to the DNA cartridge. A novel image feedback flow control system based on a Canon 5D Mark II digital camera was developed for controlling fluid movement through a complex microfluidic branching network without the use of valves. The same camera was used for measuring the high-resolution melt curve of DNA amplicons that were generated in the microfluidic chip. Owing to fast heating and cooling as well as sensitive temperature measurement in the microfluidic channels, the time frame for PCR and HRMA was dramatically reduced from hours to minutes. Preliminary testing results demonstrated that rapid serial PCR and HRMA are possible while still achieving high data quality that is suitable for human sample testing. © 2015 Society for Laboratory Automation and Screening.

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

PubMed Central

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

2012-01-01

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

A singleplex real-time fluorescence resonance energy transfer PCR with melting curve analysis for the differential detection of Paragonimus heterotremus, Echinostoma malayanum and Fasciola gigantica eggs in faeces.

PubMed

Tantrawatpan, Chairat; Saijuntha, Weerachai; Manochantr, Sirikul; Kheolamai, Pakpoom; Thanchomnang, Tongjit; Sadaow, Lakkhana; Intapan, Pewpan M; Maleewong, Wanchai

2016-01-01

Because the eggs of Paragonimus, Echinostoma and Fasciola are very similar in size and shape, it is difficult to distinguish and accurately identify species by the morphology of their eggs, which is a standard diagnostic method. In this study, a novel assay combining a real-time fluorescence resonance energy transfer PCR and melting curve analysis using one set of primers and fluorophore-labelled hybridization probes specific for the 28S rDNA region was developed for the molecular detection of Paragonimus heterotremus, Echinostoma malayanum and Fasciola gigantica eggs. This assay could detect and distinguish P. heterotremus, E. malayanum and F. gigantica DNA with the distinct melting temperature (Tm) values of 57.99±0.08, 62.12±0.15 and 74.10±0.18, respectively. The assay can also be used to detect and distinguish DNA from P. bangkokensis, P. harinasutai, P. machorchis, E. revolutum, Hypodereum conoideum and F. hepatica, which have different Tm values. The sensitivity of this assay enabled the detection of one egg of P. heterotremus, E. malayanum or F. gigantica per 100 mg of faeces. In addition, the specificity testing showed no fluorescence signal for other parasites. Due to the sensitivity and specificity of our assay in detecting P. heterotremus, E. malayanum and F. gigantica, our method could be used to accurately diagnose these three medically important parasitic groups and has potential implications for molecular epidemiological investigations of human and/or animal infections. © The Author 2015. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) for the characterisation of pathogenic leptospires: intra-serovar divergence, inter-serovar convergence, and evidence of attenuation in Leptospira reference collections.

PubMed

Tulsiani, S M; Craig, S B; Graham, G C; Cobbold, R C; Dohnt, M F; Burns, M-A; Jansen, C C; Leung, L K-P; Field, H E; Smythe, L D

2010-07-01

High-resolution melt-curve analysis of random amplified polymorphic DNA (RAPD-HRM) is a novel technology that has emerged as a possible method to characterise leptospires to serovar level. RAPD-HRM has recently been used to measure intra-serovar convergence between strains of the same serovar as well as inter-serovar divergence between strains of different serovars. The results indicate that intra-serovar heterogeneity and inter-serovar homogeneity may limit the application of RAPD-HRM in routine diagnostics. They also indicate that genetic attenuation of aged, high-passage-number isolates could undermine the use of RAPD-HRM or any other molecular technology. Such genetic attenuation may account for a general decrease seen in titres of rabbit hyperimmune antibodies over time. Before RAPD-HRM can be further advanced as a routine diagnostic tool, strains more representative of the wild-type serovars of a given region need to be identified. Further, RAPD-HRM analysis of reference strains indicates that the routine renewal of reference collections, with new isolates, may be needed to maintain the genetic integrity of the collections.

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. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of synthetic nuclear melt glass for forensic analysis.

PubMed

Molgaard, Joshua J; Auxier, John D; Giminaro, Andrew V; Oldham, C J; Cook, Matthew T; Young, Stephen A; Hall, Howard L

A method for producing synthetic debris similar to the melt glass produced by nuclear surface testing is demonstrated. Melt glass from the first nuclear weapon test (commonly referred to as trinitite) is used as the benchmark for this study. These surrogates can be used to simulate a variety of scenarios and will serve as a tool for developing and validating forensic analysis methods.

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.

High-Resolution Melting-Curve Analysis of obg Gene to Differentiate the Temperature-Sensitive Mycoplasma synoviae Vaccine Strain MS-H from Non-Temperature-Sensitive Strains

PubMed Central

Shahid, Muhammad A.; Markham, Philip F.; Marenda, Marc S.; Agnew-Crumpton, Rebecca; Noormohammadi, Amir H.

2014-01-01

Temperature-sensitive (ts +) vaccine strain MS-H is the only live attenuated M. synoviae vaccine commercially available for use in poultry. With increasing use of this vaccine to control M. synoviae infections, differentiation of MS-H from field M. synoviae strains and from rarely occurring non-temperature-sensitive (ts –) MS-H revertants has become important, especially in countries where local strains are indistinguishable from MS-H by sequence analysis of variable lipoprotein haemagglutinin (vlhA) gene. Single nucleotide polymorphisms (SNPs) in the obg of MS-H have been found to associate with ts phenotype. In this study, four PCRs followed by high-resolution melting (HRM)-curve analysis of the regions encompassing these SNPs were developed and evaluated for their potential to differentiate MS-H from 36 M. synoviae strains/isolates. The nested-obg PCR-HRM differentiated ts + MS-H vaccine not only from field M. synoviae strains/isolates but also from ts – MS-H revertants. The mean genotype confidence percentages, 96.9±3.4 and 8.8±11.2 for ts + and ts – strains, respectively, demonstrated high differentiating power of the nested-obg PCR-HRM. Using a combination of nested-obg and obg-F3R3 PCR-HRM, 97% of the isolates/strains were typed according to their ts phenotype with all MS-H isolates typed as MS-H. A set of respiratory swabs from MS-H vaccinated specific pathogen free chickens and M. synoviae infected commercial chicken flocks were tested using obg PCR-HRM system and results were consistent with those of vlhA genotyping. The PCR-HRM system developed in this study, proved to be a rapid and reliable tool using pure M. synoviae cultures as well as direct clinical specimens. PMID:24643035

REVIEWS OF TOPICAL PROBLEMS: Universal viscosity growth in metallic melts at megabar pressures: the vitreous state of the Earth's inner core

NASA Astrophysics Data System (ADS)

Brazhkin, Vadim V.; Lyapin, A. G.

2000-05-01

Experimental data on and theoretical models for the viscosity of various types of liquids and melts under pressure are reviewed. Experimentally, the least studied melts are those of metals, whose viscosity is considered to be virtually constant along the melting curve. The authors' new approach to the viscosity of melts involves the measurement of the grain size in solidified samples. Measurements on liquid metals at pressures up to 10 GPa using this method show, contrary to the empirical approach, that the melt viscosity grows considerably along the melting curves. Based on the experimental data and on the critical analysis of current theories, a hypothesis of a universal viscosity behavior is introduced for liquids under pressure. Extrapolating the liquid iron results to the pressures and temperatures at the Earth's core reveals that the Earth's outer core is a very viscous melt with viscosity values ranging from 102 Pa s to 1011 Pa s depending on the depth. The Earth's inner core is presumably an ultraviscous (>1011 Pa s) glass-like liquid — in disagreement with the current idea of a crystalline inner core. The notion of the highly viscous interior of celestial bodies sheds light on many mysteries of planetary geophysics and astronomy. From the analysis of the pressure variation of the melting and glass-transition temperatures, an entirely new concept of a stable metallic vitreous state arises, calling for further experimental and theoretical study.

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

Development of a two-step high-resolution melting (HRM) analysis for screening sequence variants associated with resistance to the QoIs, benzimidazoles and dicarboximides in airborne inoculum of Botrytis cinerea.

PubMed

Chatzidimopoulos, Michael; Ganopoulos, Ioannis; Vellios, Evangelos; Madesis, Panagiotis; Tsaftaris, Athanasios; Pappas, Athanassios C

2014-11-01

A rapid, high-resolution melting (HRM) analysis protocol was developed to detect sequence variations associated with resistance to the QoIs, benzimidazoles and dicarboximides in Botrytis cinerea airborne inoculum. HRM analysis was applied directly in fungal DNA collected from air samplers with selective medium. Three and five different genotypes were detected and classified according to their melting profiles in BenA and bos1 genes associated with resistance to benzimidazoles and dicarboximides, respectively. The sensitivity of the methodology was evident in the case of the QoIs, where genotypes varying either by a single nucleotide polymorphism or an additional 1205-bp intron were separated accurately with a single pair of primers. The developed two-step protocol was completed in 82 min and showed reduced variation in the melting curves' formation. HRM analysis rapidly detected the major mutations found in greenhouse strains providing accurate data for successfully controlling grey mould. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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.

Application of the zone-melting technique to metal chelate systems-VI A new apparatus for zone-melting chromatography.

PubMed

Maeda, S; Kobayashi, H; Ueno, K

1973-07-01

An improved apparatus has been constructed for zone-melting chromatography. An essential feature of the apparatus is that the length of the molten zone can be kept constant during a zone-melting operation, by employing heating and cooling compartments which are separated from each other by double partition plates. Each compartment is heated or cooled with jets of hot or cold air. The apparatus is suitable for organic materials melting in the range between 40 degrees and 180 degrees . The distribution of metal ion along the column after zone melting of copper acetylacetonate in 2-methoxynaphthalene was a smooth curve. The plot of the position of maximum concentration, x(max), against the number of zone passes, n, gave a relationship in accordance with theoretical prediction.

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

PubMed

Ngoi, Soo Tein; Thong, Kwai Lin

2014-01-01

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

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

Melting of iron determined by X-ray absorption spectroscopy to 100 GPa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aquilanti, Giuliana; Trapananti, Angela; Karandikar, Amol

2015-09-14

There is a long-standing controversy over the melting curve of Fe at high pressure as determined from static laser heated diamond anvil cell and dynamic compression studies. X-ray absorption spectroscopy measurements are used here as a criterion to detect melting under pressure. Confronted with a diversity of obtained melting curves, this technique, used at such pressure and temperature conditions, is eligible to be at the forefront to probe Earth's deep interior. Furthermore, the experiment reported here holds promise for addressing important issues related to the structure and phase diagram of compressed melts, such as the existence of structural complexity (polyamorphism)more » in the liquid phase or the extent of icosahedral ordering whose investigation has been limited until now to ambient conditions.« less

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. © 2013 Blackwell Publishing Ltd.

Molecular dynamics simulation of UO2 nanocrystals melting under isolated and periodic boundary conditions

NASA Astrophysics Data System (ADS)

Boyarchenkov, A. S.; Potashnikov, S. I.; Nekrasov, K. A.; Kupryazhkin, A. Ya.

2012-08-01

Melting of uranium dioxide (UO2) nanocrystals has been studied by molecular dynamics (MD) simulation. Ten recent and widely used sets of pair potentials were assessed in the rigid ion approximation. Both isolated (in vacuum) and periodic boundary conditions (PBC) were explored. Using barostat under PBC the pressure dependences of melting point were obtained. These curves intersected zero near -20 GPa, saturated near 25 GPa and increased nonlinearly in between. Using simulation of surface under isolated boundary conditions (IBC) recommended melting temperature and density jump were successfully reproduced. However, the heat of fusion is still underestimated. These melting characteristics were calculated for nanocrystals of cubic shape in the range of 768-49 152 particles (volume range of 10-1000 nm3). The obtained reciprocal size dependences decreased nonlinearly. Linear and parabolic extrapolations to macroscopic values are considered. The parabolic one is found to be better suited for analysis of the data on temperature and heat of melting.

Dynamic melting of metals in the diamond cell: Clues for melt viscosity?

NASA Astrophysics Data System (ADS)

Boehler, R.; Karandikar, A.; Yang, L.

2011-12-01

From the observed decreasing mobility of liquid iron at high pressure in the laser-heated diamond cell and the gradual decrease in the shear modulus in shock experiments, one may derive high viscosity in the liquid outer core of the Earth. A possible explanation could be the presence of local structures in the liquid as has been observed for several transition metals. In order to bridge the large gap in the timescales between static and dynamic melting experiments, we have developed new experimental techniques to solve the large discrepancies in the melting curves of transition metals (Fe, W, Ta, Mo) measured statically in the laser-heated diamond cell and in shock experiments. The new methods employ "single-shot" laser heating in order to reduce problems associated with mechanical instabilities and chemical reactions of the samples subjected to several thousand degrees at megabar pressures. For melt detection, both synchrotron X-ray diffraction and Scanning Electron Microscopy (SEM) on recovered samples are used. A third approach is the measurement of latent heat effects associated with melting or freezing. This method employs simultaneous CW and pulse laser heating and monitoring the temperature-time history with fast photomultipliers. Using the SEM recovery method, we measured first melting temperatures of rhenium, which at high pressure may be one of the most refractory materials. From the melt textures of Re, we did not observe a significant pressure dependence of viscosity.

Melting and glass transition for Ni clusters.

PubMed

Teng, Yuyong; Zeng, Xianghua; Zhang, Haiyan; Sun, Deyan

2007-03-08

The melting of NiN clusters (N = 29, 50-150) has been investigated by using molecular dynamics (MD) simulations with a quantum corrected Sutton-Chen (Q-SC) many-body potential. Surface melting for Ni147, direct melting for Ni79, and the glass transition for Ni29 have been found, and those melting points are equal to 540, 680, and 940 K, respectively. It shows that the melting temperatures are not only size-dependent but also a symmetrical structure effect; in the neighborhood of the clusters, the cluster with higher symmetry has a higher melting point. From the reciprocal slopes of the caloric curves, the specific heats are obtained as 4.1 kB per atom for the liquid and 3.1 kB per atom for the solid; these values are not influenced by the cluster size apart in the transition region. The calculated results also show that latent heat of fusion is the dominant effect on the melting temperatures (Tm), and the relationship between S and L is given.

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

PubMed

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 sdh B 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 sdh B 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 sdh B 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

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

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.

VOLATILECALC: A silicate melt-H2O-CO2 solution model written in Visual Basic for excel

USGS Publications Warehouse

Newman, S.; Lowenstern, J. B.

2002-01-01

We present solution models for the rhyolite-H2O-CO2 and basalt-H2O-CO2 systems at magmatic temperatures and pressures below ~ 5000 bar. The models are coded as macros written in Visual Basic for Applications, for use within MicrosoftR Excel (Office'98 and 2000). The series of macros, entitled VOLATILECALC, can calculate the following: (1) Saturation pressures for silicate melt of known dissolved H2O and CO2 concentrations and the corresponding equilibrium vapor composition; (2) open- and closed-system degassing paths (melt and vapor composition) for depressurizing rhyolitic and basaltic melts; (3) isobaric solubility curves for rhyolitic and basaltic melts; (4) isoplethic solubility curves (constant vapor composition) for rhyolitic and basaltic melts; (5) polybaric solubility curves for the two end members and (6) end member fugacities of H2O and CO2 vapors at magmatic temperatures. The basalt-H2O-CO2 macros in VOLATILECALC are capable of calculating melt-vapor solubility over a range of silicate-melt compositions by using the relationships provided by Dixon (American Mineralogist 82 (1997) 368). The output agrees well with the published solution models and experimental data for silicate melt-vapor systems for pressures below 5000 bar. ?? 2002 Elsevier Science Ltd. All rights reserved.

Experimental analysis and modeling of melt growth processes

NASA Astrophysics Data System (ADS)

Müller, Georg

2002-04-01

Melt growth processes provide the basic crystalline materials for many applications. The research and development of crystal growth processes is therefore driven by the demands which arise from these specific applications; however, common goals include an increased uniformity of the relevant crystal properties at the micro- and macro-scale, a decrease of deleterious crystal defects, and an increase of crystal dimensions. As melt growth equipment and experimentation becomes more and more expensive, little room remains for improvements by trial and error procedures. A more successful strategy is to optimize the crystal growth process by a combined use of experimental process analysis and computer modeling. This will be demonstrated in this paper by several examples from the bulk growth of silicon, gallium arsenide, indium phosphide, and calcium fluoride. These examples also involve the most important melt growth techniques, crystal pulling (Czochralski methods) and vertical gradient freeze (Bridgman-type methods). The power and success of the above optimization strategy, however, is not limited only to the given examples but can be generalized and applied to many types of bulk crystal growth.

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...

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. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Ab initio molecular dynamics study of high-pressure melting of beryllium oxide

PubMed Central

Li, Dafang; Zhang, Ping; Yan, Jun

2014-01-01

We investigate, through first-principles molecular dynamics simulations, the high-pressure melting of BeO in the range 0 ≤ p ≤ 100 GPa. The wurtzite (WZ), zinc blend (ZB), and rocksalt (RS) phases of BeO are considered. It is shown that below 40 GPa, the melting temperature for the WZ phase is higher than that for the ZB and RS phases. When the pressure is beyond 66 GPa, the melting temperature for the RS phase is the highest one, in consistent with the previously reported phase diagram calculated within the quasiharmonic approximation. We find that in the medium pressure range between 40 to 66 GPa, the ZB melting data are very close to those of RS, which results from the fact that the ZB structure first transforms to RS phase before melting. The ZB-RS-liquid phase transitions have been observed directly during the molecular dynamics runs and confirmed using the pair correlation functions analysis. In addition, we propose the melting curve of BeO in the form Tm = 2696.05 (1 + P/24.67)0.42, the zero-pressure value of 2696.05 K falling into the experimental data range of 2693 ~ 2853 K. PMID:24759594

A novel typing method for Listeria monocytogenes using high-resolution melting analysis (HRMA) of tandem repeat regions.

PubMed

Ohshima, Chihiro; Takahashi, Hajime; Iwakawa, Ai; Kuda, Takashi; Kimura, Bon

2017-07-17

Listeria monocytogenes, which is responsible for causing food poisoning known as listeriosis, infects humans and animals. Widely distributed in the environment, this bacterium is known to contaminate food products after being transmitted to factories via raw materials. To minimize the contamination of products by food pathogens, it is critical to identify and eliminate factory entry routes and pathways for the causative bacteria. High resolution melting analysis (HRMA) is a method that takes advantage of differences in DNA sequences and PCR product lengths that are reflected by the disassociation temperature. Through our research, we have developed a multiple locus variable-number tandem repeat analysis (MLVA) using HRMA as a simple and rapid method to differentiate L. monocytogenes isolates. While evaluating our developed method, the ability of MLVA-HRMA, MLVA using capillary electrophoresis, and multilocus sequence typing (MLST) was compared for their ability to discriminate between strains. The MLVA-HRMA method displayed greater discriminatory ability than MLST and MLVA using capillary electrophoresis, suggesting that the variation in the number of repeat units, along with mutations within the DNA sequence, was accurately reflected by the melting curve of HRMA. Rather than relying on DNA sequence analysis or high-resolution electrophoresis, the MLVA-HRMA method employs the same process as PCR until the analysis step, suggesting a combination of speed and simplicity. The result of MLVA-HRMA method is able to be shared between different laboratories. There are high expectations that this method will be adopted for regular inspections at food processing facilities in the near future. Copyright © 2017. Published by Elsevier B.V.

Melting properties of Pt and its transport coefficients in liquid states under high pressures

NASA Astrophysics Data System (ADS)

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

2016-11-01

Molecular dynamics (MD) simulations of the melting and transport properties in liquid states of platinum for the pressure range (50-200 GPa) are reported. The melting curve of platinum is consistent with previous ab initio MD simulation results and the first-principles melting curve. Calculated results for the pressure dependence of fusion entropy and fusion volume show that the fusion entropy and the fusion volume decrease with increasing pressure, and the ratio of the fusion volume to fusion entropy roughly reproduces the melting slope, which has a moderate decrease along the melting line. The Arrhenius law well describes the temperature dependence of self-diffusion coefficients and viscosity under high pressure, and the diffusion activation energy decreases with increasing pressure, while the viscosity activation energy increases with increasing pressure. In addition, the entropy-scaling law, proposed by Rosenfeld under ambient pressure, still holds well for liquid Pt under high pressure conditions.

Stochastic dynamics of melt ponds and sea ice-albedo climate feedback

NASA Astrophysics Data System (ADS)

Sudakov, Ivan

Evolution of melt ponds on the Arctic sea surface is a complicated stochastic process. We suggest a low-order model with ice-albedo feedback which describes stochastic dynamics of melt ponds geometrical characteristics. The model is a stochastic dynamical system model of energy balance in the climate system. We describe the equilibria in this model. We conclude the transition in fractal dimension of melt ponds affects the shape of the sea ice albedo curve.

Using Melting Ice to Teach Radiometric Dating.

ERIC Educational Resources Information Center

Wise, Donald Underkofler

1990-01-01

Presented is an activity in which a mystery setting is used to motivate students to construct their own decay curves of melting ice used as an analogy to radioactive decay. Procedures, materials, apparatus, discussion topics, presentation, and thermodynamics are discussed. (CW)

Monte Carlo Study of Melting of a Model Bulk Ice.

NASA Astrophysics Data System (ADS)

Han, Kyu-Kwang

analysis and calculation of the P-T curve for ice Ih melting at constant volume and the first NPT study of ice and of ice melting. In the NVT simulation we found for rho = 0.904g/cm^3 T_ {rm m} ~eq 280 K which is much closer to physical T_ {rm m} than any other published NVT simulation of ice. Finally it is shown that RSL2 potentials do a credible job of describing the thermodynamic properties of ice Ih near its melting point.

Interaction Analysis of Longevity Interventions Using Survival Curves.

PubMed

Nowak, Stefan; Neidhart, Johannes; Szendro, Ivan G; Rzezonka, Jonas; Marathe, Rahul; Krug, Joachim

2018-01-06

A long-standing problem in ageing research is to understand how different factors contributing to longevity should be expected to act in combination under the assumption that they are independent. Standard interaction analysis compares the extension of mean lifespan achieved by a combination of interventions to the prediction under an additive or multiplicative null model, but neither model is fundamentally justified. Moreover, the target of longevity interventions is not mean life span but the entire survival curve. Here we formulate a mathematical approach for predicting the survival curve resulting from a combination of two independent interventions based on the survival curves of the individual treatments, and quantify interaction between interventions as the deviation from this prediction. We test the method on a published data set comprising survival curves for all combinations of four different longevity interventions in Caenorhabditis elegans . We find that interactions are generally weak even when the standard analysis indicates otherwise.

Interaction Analysis of Longevity Interventions Using Survival Curves

PubMed Central

Nowak, Stefan; Neidhart, Johannes; Szendro, Ivan G.; Rzezonka, Jonas; Marathe, Rahul; Krug, Joachim

2018-01-01

A long-standing problem in ageing research is to understand how different factors contributing to longevity should be expected to act in combination under the assumption that they are independent. Standard interaction analysis compares the extension of mean lifespan achieved by a combination of interventions to the prediction under an additive or multiplicative null model, but neither model is fundamentally justified. Moreover, the target of longevity interventions is not mean life span but the entire survival curve. Here we formulate a mathematical approach for predicting the survival curve resulting from a combination of two independent interventions based on the survival curves of the individual treatments, and quantify interaction between interventions as the deviation from this prediction. We test the method on a published data set comprising survival curves for all combinations of four different longevity interventions in Caenorhabditis elegans. We find that interactions are generally weak even when the standard analysis indicates otherwise. PMID:29316622

High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single nucleotide polymorphisms.

PubMed

Tong, Steven Y C; Xie, Shirley; Richardson, Leisha J; Ballard, Susan A; Dakh, Farshid; Grabsch, Elizabeth A; Grayson, M Lindsay; Howden, Benjamin P; Johnson, Paul D R; Giffard, Philip M

2011-01-01

We have developed a single nucleotide polymorphism (SNP) nucleated high-resolution melting (HRM) technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST) database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the results with MLST, pulsed-field gel electrophoresis (PFGE) and an allele specific real-time PCR (AS kinetic PCR) SNP typing method. In silico analysis based on predicted HRM curves according to the G+C content of each fragment for all 567 sequence types (STs) in the MLST database together with empiric data from the 85 isolates demonstrated that HRM analysis resolves E. faecium into 231 "melting types" (MelTs) and provides a Simpson's Index of Diversity (D) of 0.991 with respect to MLST. This is a significant improvement on the AS kinetic PCR SNP typing scheme that resolves 61 SNP types with D of 0.95. The MelTs were concordant with the known ST of the isolates. For the 85 isolates, there were 13 PFGE patterns, 17 STs, 14 MelTs and eight SNP types. There was excellent concordance between PFGE, MLST and MelTs with Adjusted Rand Indices of PFGE to MelT 0.936 and ST to MelT 0.973. In conclusion, this HRM based method appears rapid and reproducible. The results are concordant with MLST and the MLST based population structure.

Optimizing high-resolution melting analysis for the detection of mutations of GPR30/GPER-1 in breast cancer.

PubMed

Aihara, Masamune; Yamamoto, Shigeru; Nishioka, Hiroko; Inoue, Yutaro; Hamano, Kimikazu; Oka, Masaaki; Mizukami, Yoichi

2012-06-15

G protein-coupled receptor 30/G protein estrogen receptor-1 (GPR30/GPER-1) is a novel membrane receptor for estrogen whose mRNA is expressed at high levels in estrogen-dependent cells such as breast cancer cell lines. However, mutations in GRP30 related to diseases remain unreported. To detect unknown mutations in the GPR30 open reading frame (ORF) quickly, the experimental conditions for high-resolution melting (HRM) analysis were examined for PCR primers, Taq polymerases, saturation DNA binding dyes, Mg(2+) concentration, and normalized temperatures. Nine known SNPs and 13 artificial point mutations within the GPR30 ORF, as well as single nucleotide variants in DNA extracted from subjects with breast cancers were tested under the optimal experimental conditions. The combination of Expand High Fidelity(PLUS) and SYTO9 in the presence of 2.0 mM MgCl(2) produced the best separation in melting curves of mutations in all regions of the GPR30 ORF. Under these experimental conditions, the mutations were clearly detected in both heterozygotes and homozygotes. HRM analysis of GPR30 using genomic DNA from subjects with breast cancers showed a novel single nucleotide variant, 111C>T in GPR30 and 4 known SNPs. The experimental conditions determined in this study for HRM analysis are useful for high throughput assays to detect unknown mutations within the GPR30 ORF. Copyright © 2012 Elsevier B.V. All rights reserved.

Guest Chain ``Melting'' in Incommensurate Host-Guest Potassium

NASA Astrophysics Data System (ADS)

McBride, Emma; Munro, Keith; McMahon, Malcolm

2013-06-01

Upon increasing pressure the group-I elements transform from close-packed structures (bcc and fcc) to a series of low-symmetry complex structures. Residing in the middle of the group, potassium (K) has numerous structures in common with its neighbours, and, in fact, is remarkably structurally similar to sodium (Na) and rubidium (Rb). For example, the post-fcc transition in K is to a composite incommensurate host-guest structure (tI19), and the host structure of this phase is isostructural with that found in Na and Rb. Previously we have reported that below 16.7GPa, the Bragg peaks from the guest component of tI19-Rb broaden considerably, signalling a loss of the inter-chain correlation, or a ``melting'' of the chains. Furthermore, in tI19-Na above 125 GPa, the Bragg peaks from the guest component are also broadened, suggesting that the guest chains are also nearly ``melted.'' During studies of the melting curve of K, we observed that the guest peaks from tI19-K broaden dramatically on heating. Here we report single-crystal, quasi-single-crystal, and powder synchrotron x-ray diffraction measurements of tI19-K to 50 GPa and 800 K, which allowed a detailed study of this chain ``melting'' transition. The order-disorder transition is clearly visible over a 30 GPa pressure range, and there are significant changes in the gradient of the phase boundary, which may be influenced by the nature of the guest structure. Furthermore, data extending the melting curve will also be presented.

Impact of fixation artifacts and threshold selection on high resolution melting analysis for KRAS mutation screening.

PubMed

Pérez-Báez, Wendy; García-Latorre, Ethel A; Maldonado-Martínez, Héctor Aquiles; Coronado-Martínez, Iris; Flores-García, Leonardo; Taja-Chayeb, Lucía

2017-10-01

Treatment in metastatic colorectal cancer (mCRC) has expanded with monoclonal antibodies targeting epidermal growth factor receptor, but is restricted to patients with a wild-type (WT) KRAS mutational status. The most sensitive assays for KRAS mutation detection in formalin-fixed paraffin embedded (FFPE) tissues are based on real-time PCR. Among them, high resolution melting analysis (HRMA), is a simple, fast, highly sensitive, specific and cost-effective method, proposed as adjunct for KRAS mutation detection. However the method to categorize WT vs mutant sequences in HRMA is not clearly specified in available studies, besides the impact of FFPE artifacts on HRMA performance hasn't been addressed either. Avowedly adequate samples from 104 consecutive mCRC patients were tested for KRAS mutations by Therascreen™ (FDA Validated test), HRMA, and HRMA with UDG pre-treatment to reverse FFPE fixation artifacts. Comparisons of KRAS status allocation among the three methods were done. Focusing on HRMA as screening test, ROC curve analyses were performed for HRMA and HMRA-UDG against Therascreen™, in order to evaluate their discriminative power and to determine the threshold of profile concordance between WT control and sample for KRAS status determination. Comparing HRMA and HRMA-UDG against Therascreen™ as surrogate gold standard, sensitivity was 1 for both HRMA and HRMA-UDG; and specificity and positive predictive values were respectively 0.838 and 0.939; and 0.777 and 0.913. As evaluated by the McNemar test, HRMA-UDG allocated samples to a WT/mutated genotype in a significatively different way from HRMA (p > 0.001). On the other hand HRMA-UDG did not differ from Therascreen™ (p = 0.125). ROC-curve analysis showed a significant discriminative power for both HRMA and HRMA-UDG against Therascreen™ (respectively, AUC of 0.978, p > 0.0001, CI 95% 0.957-0.999; and AUC of 0.98, p > 0.0001, CI 95% 0.000-1.0). For HRMA as a screening tool, the best threshold

V OLATILEC ALC: a silicate melt-H 2O-CO 2 solution model written in Visual Basic for excel

NASA Astrophysics Data System (ADS)

Newman, Sally; Lowenstern, Jacob B.

2002-06-01

We present solution models for the rhyolite-H 2O-CO 2 and basalt-H 2O-CO 2 systems at magmatic temperatures and pressures below ˜5000 bar. The models are coded as macros written in Visual Basic for Applications, for use within Microsoft ® Excel (Office'98 and 2000). The series of macros, entitled V OLATILEC ALC, can calculate the following: (1) Saturation pressures for silicate melt of known dissolved H 2O and CO 2 concentrations and the corresponding equilibrium vapor composition; (2) open- and closed-system degassing paths (melt and vapor composition) for depressurizing rhyolitic and basaltic melts; (3) isobaric solubility curves for rhyolitic and basaltic melts; (4) isoplethic solubility curves (constant vapor composition) for rhyolitic and basaltic melts; (5) polybaric solubility curves for the two end members and (6) end member fugacities of H 2O and CO 2 vapors at magmatic temperatures. The basalt-H 2O-CO 2 macros in V OLATILEC ALC are capable of calculating melt-vapor solubility over a range of silicate-melt compositions by using the relationships provided by Dixon (American Mineralogist 82 (1997) 368). The output agrees well with the published solution models and experimental data for silicate melt-vapor systems for pressures below 5000 bar.

Peptide Nucleic Acid Based Molecular Authentication for Identification of Four Medicinal Paeonia Species Using Melting Array Analysis of the Internal Transcribed Spacer 2 Region.

PubMed

Kim, Wook Jin; Yang, Sungyu; Choi, Goya; Moon, Byeong Cheol

2017-11-07

Accurate taxonomic identification of plant materials in herbal medicines is important for product quality control. The genus Paeonia (Saxifragales) is the source of the herbal preparations Paeoniae Radix (Paeoniae Radix Alba and Paeoniae Radix Rubra) and Moutan Radicis Cotex. However, confusion has arisen regarding their contents due to linguistic and taxonomic ambiguities, similar morphologies and different definitions of Paeoniae Radix in the Korean and Chinese national pharmacopoeias, leading to the distribution of adulterated products. To develop a method for identifying the four Paeonia species used in these medicines, three fluorescently-labeled peptide nucleic acid (PNA) probes were designed against ITS2 sequences containing single nucleotide polymorphisms (SNPs) and used in a real-time PCR melting curve assay. Each of the four Paeonia species was accurately identified using this analysis. The accuracy and analytical stability of the PNA melting curve assay was confirmed using commercially available samples of the four Paeonia species. This assay is a reliable genetic tool to distinguish between different Paeonia -derived herbal medicines and identify the botanical origins of Paeoniae Radix and Moutan Radicis Cortex. This technique may also contribute to quality control and standardization of herbal medicines by providing a reliable authentication tool and preventing the distribution of inauthentic adulterants.

High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science.

PubMed

Dos Santos Rocha, Alípio; de Amorim, Isis Salviano Soares; Simão, Tatiana de Almeida; da Fonseca, Adenilson de Souza; Garrido, Rodrigo Grazinoli; Mencalha, Andre Luiz

2018-03-01

Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics. © 2017 American Academy of Forensic Sciences.

Theory of melting at high pressures: Amending density functional theory with quantum Monte Carlo

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shulenburger, L.; Desjarlais, M. P.; Mattsson, T. R.

We present an improved first-principles description of melting under pressure based on thermodynamic integration comparing Density Functional Theory (DFT) and quantum Monte Carlo (QMC) treatments of the system. The method is applied to address the longstanding discrepancy between density functional theory (DFT) calculations and diamond anvil cell (DAC) experiments on the melting curve of xenon, a noble gas solid where van der Waals binding is challenging for traditional DFT methods. The calculations show excellent agreement with data below 20 GPa and that the high-pressure melt curve is well described by a Lindemann behavior up to at least 80 GPa, amore » finding in stark contrast to DAC data.« less

Theory of melting at high pressures: Amending density functional theory with quantum Monte Carlo

DOE PAGES

Shulenburger, L.; Desjarlais, M. P.; Mattsson, T. R.

2014-10-01

We present an improved first-principles description of melting under pressure based on thermodynamic integration comparing Density Functional Theory (DFT) and quantum Monte Carlo (QMC) treatments of the system. The method is applied to address the longstanding discrepancy between density functional theory (DFT) calculations and diamond anvil cell (DAC) experiments on the melting curve of xenon, a noble gas solid where van der Waals binding is challenging for traditional DFT methods. The calculations show excellent agreement with data below 20 GPa and that the high-pressure melt curve is well described by a Lindemann behavior up to at least 80 GPa, amore » finding in stark contrast to DAC data.« less

Density Measurement for MORB Melts by X-ray Absorption Method

NASA Astrophysics Data System (ADS)

Sakamaki, T.; Urakawa, S.; Suzuki, A.; Ohtani, E.; Katayama, Y.

2006-12-01

Density of silicate melts at high pressure is one of the most important properties to understand magma migration in the planetary interior and the differentiation of the terrestrial planets. The density measurements of silicate melts have been carried out by several methods (shock compression experiments and sink-float method in static experiments, etc.). However, since these methods have difficulties in acquisition of data at a desired pressure and temperature, the density of the silicate melt have been measured under only a few conditions. Recently a new density measurement was developed by the X-ray absorption method. Advantage of this method is to measure density of liquids at a desired pressure and temperature. In the present study we measured the density of MORB melt by X-ray absorption method. Experiments were carried out at the BL22XU beamline at SPring-8. A DIA-type cubic anvil apparatus was used for generation of high pressure and temperature. We used tungsten carbide anvils with the top anvil sizes of 6 mm and 4 mm. The energy of monochromateized X-ray beam was 23 keV. The intensities of incident and transmitted X-ray were measured by ion chambers. The density of the melt was calculated on the basis of Beer-Lambert law. The starting material was a glass with the MORB composition. Experiments were made from 1 atm to 5 GPa, from 300 to 2000 K. We compared the density of MORB melt with the compression curve of the melt in previous works. The density measured by this study is lower than that expected from the compression curve determined at higher pressures by the sink-float method. Structural change of the MORB melt with increasing pressure might be attributed to this discrepancy.

Density Measurement for MORB Melts by X-ray Absorption Method

NASA Astrophysics Data System (ADS)

Sakamaki, T.; Urakawa, S.; Ohtani, E.; Suzuki, A.; Katayama, Y.

2005-12-01

Density of silicate melts at high pressure is one of the most important properties to understand magma migration in the planetary interior and the differentiation of the terrestrial planets. The density measurements of silicate melts have been carried out by several methods (shock compression experiments and sink-float method in static experiments, etc.). However, since these methods have difficulties in acquisition of data at a desired pressure and temperature, the density of the silicate melt have been measured under only a few conditions. Recently a new density measurement was developed by the X-ray absorption method. Advantage of this method is to measure density of liquids at a desired pressure and temperature. In the present study we measured the density of MORB melt by X-ray absorption method. Experiments were carried out at the BL22XU beamline at SPring-8. A DIA-type cubic anvil apparatus was used for generation of high pressure and temperature. We used tungsten carbide anvils with the edge-length of 6 mm. The energy of monochromateized X-ray beam was 23 keV. The intensities of incident and transmitted X-ray were measured by ion chambers. The density of the melt was calculated on the basis of Beer-Lambert law. The starting material was a glass with the MORB composition. Experiments were made from 1 atm to 4 GPa, from 300 to 2200 K. We compared the density of MORB melt with the compression curve of the melt in previous works. The density measured by this study is lower than that expected from the compression curve determined at higher pressures by the sink-float method. Structural change of the MORB melt with increasing pressure might be attributed to this discrepancy.

Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers.

PubMed

Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S; Garcia-Closas, Montserrat; Sherman, Mark E; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P; Khan, Javed; Chanock, Stephen

2011-01-17

Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples.

Detection of Somatic Mutations by High-Resolution DNA Melting (HRM) Analysis in Multiple Cancers

PubMed Central

Gonzalez-Bosquet, Jesus; Calcei, Jacob; Wei, Jun S.; Garcia-Closas, Montserrat; Sherman, Mark E.; Hewitt, Stephen; Vockley, Joseph; Lissowska, Jolanta; Yang, Hannah P.; Khan, Javed; Chanock, Stephen

2011-01-01

Identification of somatic mutations in cancer is a major goal for understanding and monitoring the events related to cancer initiation and progression. High resolution melting (HRM) curve analysis represents a fast, post-PCR high-throughput method for scanning somatic sequence alterations in target genes. The aim of this study was to assess the sensitivity and specificity of HRM analysis for tumor mutation screening in a range of tumor samples, which included 216 frozen pediatric small rounded blue-cell tumors as well as 180 paraffin-embedded tumors from breast, endometrial and ovarian cancers (60 of each). HRM analysis was performed in exons of the following candidate genes known to harbor established commonly observed mutations: PIK3CA, ERBB2, KRAS, TP53, EGFR, BRAF, GATA3, and FGFR3. Bi-directional sequencing analysis was used to determine the accuracy of the HRM analysis. For the 39 mutations observed in frozen samples, the sensitivity and specificity of HRM analysis were 97% and 87%, respectively. There were 67 mutation/variants in the paraffin-embedded samples, and the sensitivity and specificity for the HRM analysis were 88% and 80%, respectively. Paraffin-embedded samples require higher quantity of purified DNA for high performance. In summary, HRM analysis is a promising moderate-throughput screening test for mutations among known candidate genomic regions. Although the overall accuracy appears to be better in frozen specimens, somatic alterations were detected in DNA extracted from paraffin-embedded samples. PMID:21264207

High Resolution Melting (HRM) for High-Throughput Genotyping-Limitations and Caveats in Practical Case Studies.

PubMed

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz; Strapagiel, Dominik

2017-11-03

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup.

High Resolution Melting (HRM) for High-Throughput Genotyping—Limitations and Caveats in Practical Case Studies

PubMed Central

Słomka, Marcin; Sobalska-Kwapis, Marta; Wachulec, Monika; Bartosz, Grzegorz

2017-01-01

High resolution melting (HRM) is a convenient method for gene scanning as well as genotyping of individual and multiple single nucleotide polymorphisms (SNPs). This rapid, simple, closed-tube, homogenous, and cost-efficient approach has the capacity for high specificity and sensitivity, while allowing easy transition to high-throughput scale. In this paper, we provide examples from our laboratory practice of some problematic issues which can affect the performance and data analysis of HRM results, especially with regard to reference curve-based targeted genotyping. We present those examples in order of the typical experimental workflow, and discuss the crucial significance of the respective experimental errors and limitations for the quality and analysis of results. The experimental details which have a decisive impact on correct execution of a HRM genotyping experiment include type and quality of DNA source material, reproducibility of isolation method and template DNA preparation, primer and amplicon design, automation-derived preparation and pipetting inconsistencies, as well as physical limitations in melting curve distinction for alternative variants and careful selection of samples for validation by sequencing. We provide a case-by-case analysis and discussion of actual problems we encountered and solutions that should be taken into account by researchers newly attempting HRM genotyping, especially in a high-throughput setup. PMID:29099791

Incorporating Experience Curves in Appliance Standards Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garbesi, Karina; Chan, Peter; Greenblatt, Jeffery

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,more » 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.« less

Melting temperatures of H2O up to 72 GPa measured in a diamond anvil cell using CO2 laser heating technique.

PubMed

Kimura, T; Kuwayama, Y; Yagi, T

2014-02-21

The melting curve of H2O from 49 to 72 GPa was determined by using a laser-heated diamond anvil cell. Double-sided CO2 laser heating technique was employed in order to heat the sample directly. Discontinuous changes of the heating efficiency attributed to the H2O melting were observed between 49 and 72 GPa. The obtained melting temperatures at 49 and 72 GPa are 1200 and 1410 K, respectively. We found that the slope of the melting curve significantly decreases with increasing pressure, only 5 K/GPa at 72 GPa while 44 K/GPa at 49 GPa. Our results suggest that the melting curve does not intersect with the isentropes of Uranus and Neptune, and hence, H2O should remain in the liquid state even at the pressure and temperature conditions found deep within Uranus and Neptune.

Corrosion resistance of steel materials in LiCl-KCl melts

NASA Astrophysics Data System (ADS)

Wang, Le; Li, Bing; Shen, Miao; Li, Shi-yan; Yu, Jian-guo

2012-10-01

The corrosion behaviors of 304SS, 316LSS, and Q235A in LiCl-KCl melts were investigated at 450°C by Tafel curves and electrochemical impedance spectroscopy (EIS). 316LSS shows the best corrosion resistance behaviors among the three materials, including the most positive corrosion potential and the smallest corrosion current from the Tafel curves and the largest electron transfer resistance from the Nyquist plots. The results are in good agreement with the weight losses in the static corrosion experiments for 45 h. This may be attributed to the better corrosion resistance of Mo and Ni existing as alloy elements in 316LSS, which exhibit the lower corrosion current densities and more positive corrosion potentials than 316LSS in the same melts.

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.

Highly Sensitive Detection of Isoniazid Heteroresistance in Mycobacterium tuberculosis by DeepMelt Assay.

PubMed

Liang, Bin; Tan, Yaoju; Li, Zi; Tian, Xueshan; Du, Chen; Li, Hui; Li, Guoli; Yao, Xiangyang; Wang, Zhongan; Xu, Ye; Li, Qingge

2018-02-01

Detection of heteroresistance of Mycobacterium tuberculosis remains challenging using current genotypic drug susceptibility testing methods. Here, we described a melting curve analysis-based approach, termed DeepMelt, that can detect less-abundant mutants through selective clamping of the wild type in mixed populations. The singleplex DeepMelt assay detected 0.01% katG S315T in 10 5 M. tuberculosis genomes/μl. The multiplex DeepMelt TB/INH detected 1% of mutant species in the four loci associated with isoniazid resistance in 10 4 M. tuberculosis genomes/μl. The DeepMelt TB/INH assay was tested on a panel of DNA extracted from 602 precharacterized clinical isolates. Using the 1% proportion method as the gold standard, the sensitivity was found to be increased from 93.6% (176/188, 95% confidence interval [CI] = 89.2 to 96.3%) to 95.7% (180/188, 95% CI = 91.8 to 97.8%) compared to the MeltPro TB/INH assay. Further evaluation of 109 smear-positive sputum specimens increased the sensitivity from 83.3% (20/24, 95% CI = 64.2 to 93.3%) to 91.7% (22/24, 95% CI = 74.2 to 97.7%). In both cases, the specificity remained nearly unchanged. All heteroresistant samples newly identified by the DeepMelt TB/INH assay were confirmed by DNA sequencing and even partially by digital PCR. The DeepMelt assay may fill the gap between current genotypic and phenotypic drug susceptibility testing for detecting drug-resistant tuberculosis patients. Copyright © 2018 American Society for Microbiology.

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

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

PubMed

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

2013-11-01

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

Greater-than-bulk melting temperatures explained: Gallium melts Gangnam style

NASA Astrophysics Data System (ADS)

Gaston, Nicola; Steenbergen, Krista

2014-03-01

The experimental discovery of superheating in gallium clusters contradicted the clear and well-demonstrated paradigm that the melting temperature of a particle should decrease with its size. However the extremely sensitive dependence of melting temperature on size also goes to the heart of cluster science, and the interplay between the effects of electronic and geometric structure. We have performed extensive first-principles molecular dynamics calculations, incorporating parallel tempering for an efficient exploration of configurational phase space. This is necessary, due to the complicated energy landscape of gallium. In the nanoparticles, melting is preceded by a transitions between phases. A structural feature, referred to here as the Gangnam motif, is found to increase with the latent heat and appears throughout the observed phase changes of this curious metal. We will present our detailed analysis of the solid-state isomers, performed using extensive statistical sampling of the trajectory data for the assignment of cluster structures to known phases of gallium. Finally, we explain the greater-than-bulk melting through analysis of the factors that stabilise the liquid structures.

Models and observations of Arctic melt ponds

NASA Astrophysics Data System (ADS)

Golden, K. M.

2016-12-01

During the Arctic melt season, the sea ice surface undergoes a striking transformation from vast expanses of snow covered ice to complex mosaics of ice and melt ponds. Sea ice albedo, a key parameter in climate modeling, is largely determined by the complex evolution of melt pond configurations. In fact, ice-albedo feedback has played a significant role in the recent declines of the summer Arctic sea ice pack. However, understanding melt pond evolution remains a challenge to improving climate projections. It has been found that as the ponds grow and coalesce, the fractal dimension of their boundaries undergoes a transition from 1 to about 2, around a critical length scale of 100 square meters in area. As the ponds evolve they take complex, self-similar shapes with boundaries resembling space-filling curves. I will outline how mathematical models of composite materials and statistical physics, such as percolation and Ising models, are being used to describe this evolution and predict key geometrical parameters that agree very closely with observations.

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.

Theoretical analysis of heat flow in horizontal ribbon growth from a melt. [silicon metal

NASA Technical Reports Server (NTRS)

Zoutendyk, J. A.

1978-01-01

A theoretical heat flow analysis for horizontalribbon growth is presented. Equations are derived relating pull speed, ribbon thickness, thermal gradient in the melt, and melt temperature for limiting cases of heat removal by radiation only and isothermal heat removal from the solid surface over the melt. Geometrical cross sections of the growth zone are shown to be triangular and nearly parabolic for the two respective cases. Theoretical pull speed for silicon ribbon 0.01 cm thick, where the loss of latent heat of fusion is by radiation to ambient temperature (300 K) only, is shown to be 1 cm/sec for horizontal growth extending 2 cm over the melt and with no heat conduction either to or from the melt. Further enhancement of ribbon growth rate by placing cooling blocks adjacent to the top surface is shown to be theoretically possible.

Ultrasensitive Detection of Drug-Resistant Pandemic 2009 (H1N1) Influenza A Virus by Rare-Variant-Sensitive High-Resolution Melting-Curve Analysis▿‡

PubMed Central

Chen, Neng; Pinsky, Benjamin A.; Lee, Betty P.; Lin, Min; Schrijver, Iris

2011-01-01

Oseltamivir (Tamiflu), an oral neuraminidase inhibitor, has been widely used to treat pandemic 2009 (H1N1) influenza A. Although a majority of 2009 (H1N1) influenza A virus remains oseltamivir susceptible, the threat of resistance due to the His275Tyr mutation is highlighted by the limitations of alternative therapies and the potential for rapid, global fixation of this mutation in the circulating influenza A virus population. In order to better understand the emergence of resistance, we developed a rare-variant-sensitive high-resolution melting-curve analysis method (RVS-HRM) that is able to detect the His275Tyr oseltamivir resistance mutation to 0.5% in a background of susceptible virus. We applied RVS-HRM to clinical specimens from patients who developed oseltamivir resistance and demonstrated the ultrasensitive detection of influenza A virus N1 neuraminidase quasispecies. Interestingly, we were unable to detect the oseltamivir resistance mutation in pretreatment samples, suggesting that resistant virus does not reach even this very low detection threshold until exposed to selective drug pressure. Thus, patients naive to oseltamivir are most likely to be susceptible when this drug is used as a first-line treatment modality. PMID:21543559

Fatigue behavior of porous biomaterials manufactured using selective laser melting.

PubMed

Yavari, S Amin; Wauthle, R; van der Stok, J; Riemslag, A C; Janssen, M; Mulier, M; Kruth, J P; Schrooten, J; Weinans, H; Zadpoor, A A

2013-12-01

Porous titanium alloys are considered promising bone-mimicking biomaterials. Additive manufacturing techniques such as selective laser melting allow for manufacturing of porous titanium structures with a precise design of micro-architecture. The mechanical properties of selective laser melted porous titanium alloys with different designs of micro-architecture have been already studied and are shown to be in the range of mechanical properties of bone. However, the fatigue behavior of this biomaterial is not yet well understood. We studied the fatigue behavior of porous structures made of Ti6Al4V ELI powder using selective laser melting. Four different porous structures were manufactured with porosities between 68 and 84% and the fatigue S-N curves of these four porous structures were determined. The three-stage mechanism of fatigue failure of these porous structures is described and studied in detail. It was found that the absolute S-N curves of these four porous structures are very different. In general, given the same absolute stress level, the fatigue life is much shorter for more porous structures. However, the normalized fatigue S-N curves of these four structures were found to be very similar. A power law was fitted to all data points of the normalized S-N curves. It is shown that the measured data points conform to the fitted power law very well, R(2)=0.94. This power law may therefore help in estimating the fatigue life of porous structures for which no fatigue test data is available. It is also observed that the normalized endurance limit of all tested porous structures (<0.2) is lower than that of corresponding solid material (c.a. 0.4). © 2013.

Melting of KCl and pressure calibration from in situ ionic conductivity measurements in a multi-anvil apparatus

NASA Astrophysics Data System (ADS)

Li, J.; Dong, J.; Zhu, F.

2017-12-01

Melting plays an unparalleled role in planetary differentiation processes including the formation of metallic cores, basaltic crusts, and atmospheres. Knowledge of the melting behavior of Earth materials provides critical constraints for establishing the Earth's thermal structure, interpreting regional seismic anomalies, and understanding the nature of chemical heterogeneity. Measuring the melting points of compressed materials, however, have remained challenging mainly because melts are often mobile and reactive, and temperature and pressure gradients across millimeter or micron-sized samples introduce large uncertainties in melting detection. Here the melting curve of KCl was determined through in situ ionic conductivity measurements, using the multi-anvil apparatus at the University of Michigan. The method improves upon the symmetric configuration that was used recently for studying the melting behaviors of NaCl, Na2CO3, and CaCO3 (Li and Li 2015 American Mineralogist, Li et al. 2017 Earth and Planetary Science Letters). In the new configuration, the thermocouple and electrodes are placed together with the sample at the center of a cylindrical heater where the temperature is the highest along the axis, in order to minimize uncertainties in temperature measurements and increase the stability of the sample and electrodes. With 1% reproducibility in melting point determination at pressures up to 20 GPa, this method allows us to determine the sample pressure to oil load relationship at high temperatures during multiple heating and cooling cycles, on the basis of the well-known melting curves of ionic compounds. This approach enables more reliable pressure measurements than relying on a small number of fixed-point phase transitions. The new data on KCl bridge the gap between the piston-cylinder results up to 4 GPa (Pistorius 1965 J. of Physics and Chemistry of Solids) and several diamond-anvil cell data points above 20 GPa (Boehler et al. 1996 Physical Review). We

Partial melting of metagreywackes, Part II. Compositions of minerals and melts

NASA Astrophysics Data System (ADS)

Montel, Jean-Marc; Vielzeuf, Daniel

A series of experiments on the fluid-absent melting of a quartz-rich aluminous metagreywacke has been carried out. In this paper, we report the chemical composition of the phases present in the experimental charges as determined by electron microprobe. This analytical work includes biotite, plagioclase, orthopyroxene, garnet, cordierite, hercynite, staurolite, gedrite, oxide, and glass, over the range 100-1000MPa, 780-1025°C. Biotites are Na- and Mg-rich, with Ti contents increasing with temperature. The compositions of plagioclase range from An17 to An35, with a significant orthoclase component, and are always different from the starting minerals. At high temperature, plagioclase crystals correspond to ternary feldspars with Or contents in the range 11-20 mol%. Garnets are almandine pyrope grossular spessartine solid solutions, with a regular and significant increase of the grossular content with pressure. All glasses are silicic (SiO2=67.6-74.4 wt%), peraluminous, and leucocratic (FeO+MgO=0.9-2.9 wt%), with a bulk composition close to that of peraluminous leucogranites, even for degrees of melting as high as 60 vol.%. With increasing pressure, SiO2 contents decrease while K2O increases. At any pressure, the melt compositions are more potassic than the water-saturated granitic minima. The H2O contents estimated by mass balance are in the range 2.5-5.6 wt%. These values are higher than those predicted by thermodynamic models. Modal compositions were estimated by mass balance calculations and by image processing of the SEM photographs. The positions of the 20 to 70% isotects (curves of equal proportion of melt) have been located in the pressure-temperature space between 100MPa and 1000MPa. With increasing pressure, the isotects shift toward lower temperature between 100 and 200MPa, then bend back toward higher temperature. The melting interval increases with pressure; the difference in temperature between the 20% and the 70% isotects is 40°C at 100MPa, and 150�

Melt segregation from partially molten source regions - The importance of melt density and source region size

NASA Technical Reports Server (NTRS)

Stolper, E.; Hager, B. H.; Walker, D.; Hays, J. F.

1981-01-01

An investigation is conducted regarding the changes expected in the density contrast between basic melts and peridotites with increasing pressure using the limited data available on the compressibilities of silicate melts and data on the densities of mantle minerals. It is concluded that since compressibilities of silicate melts are about an order of magnitude greater than those of mantle minerals, the density contrast between basic melts and mantle minerals must diminish significantly with increasing pressure. An earlier analysis regarding the migration of liquid in partially molten source regions conducted by Walker et al. (1978) is extended, giving particular attention to the influence of the diminished density contrast between melt and residual crystals with increasing source region depth and to the influence of source region size. This analysis leads to several generalizations concerning the factors influencing the depths at which magmas will segregate from their source regions and the degrees of partial melting that can be achieved in these source regions before melt segregation occurs.

Optically induced melting of colloidal crystals and their recrystallization.

PubMed

Harada, Masashi; Ishii, Masahiko; Nakamura, Hiroshi

2007-04-15

Colloidal crystals melt by applying focused light of optical tweezers and recrystallize after removing it. The disturbed zone by the light grows radially from the focus point and the ordering starts from the interface with the crystal. Although the larger disturbed zone is observed for the higher power optical tweezers, a master curve is extracted by normalization of the disturbed zone. The temporal changes of the normalized disturbed zone are well described with exponential functions, indicating that the melting and recrystallization process is governed by a simple relaxation mechanism.

Automated realization of the gallium melting and triple points

NASA Astrophysics Data System (ADS)

Yan, X.; Duan, Y.; Zhang, J. T.; Wang, W.

2013-09-01

In order to improve the automation and convenience of the process involved in realizing the gallium fixed points, an automated apparatus, based on thermoelectric and heat pipe technologies, was designed and developed. This paper describes the apparatus design and procedures for freezing gallium mantles and realizing gallium melting and triple points. Also, investigations on the melting behavior of a gallium melting point cell and of gallium triple point cells were carried out while controlling the temperature outside the gallium point cells at 30 °C, 30.5 °C, 31 °C, and 31.5 °C. The obtained melting plateau curves show dentate temperature oscillations on the melting plateaus for the gallium point cells when thermal couplings occurred between the outer and inner liquid-solid interfaces. The maximum amplitude of the temperature fluctuations was about 1.5 mK. Therefore, the temperature oscillations can be used to indicate the ending of the equilibrium phase transitions. The duration and amplitude of such temperature oscillations depend on the temperature difference between the setting temperature and the gallium point temperature; the smaller the temperature difference, the longer the duration of both the melting plateaus and the temperature fluctuations.

High resolution DNA melting analysis: an application for prenatal control of alpha-thalassemia.

PubMed

Sirichotiyakul, Supatra; Wanapirak, Chanane; Saetung, Rattika; Sanguansermsri, Torpong

2010-04-01

To report the use of real-time gap-PCR using SYTO9 with high-resolution melting analysis (HRMA) in prenatal diagnosis of alpha-thalassemia 1. Real-time gap-PCR using SYTO9 with HRMA was performed in 33 DNA samples from chorionic villi sampling (8 normal, 16 heterozygous, and 9 homozygous) to determine the alpha-thalassemia 1 gene [normal and Southeast Asia (-SEA) allele]. The dissociation curve analysis in normal and - SEA allele gave a peak of T(m) at 91.80 +/- 0.14 degrees C and 88.67 +/- 0.08 degrees C, respectively. Normal genotype and homozygous alpha-thalassemia 1 showed a single peak of T(m) that corresponded to their alleles. The heterozygotes gave both peaks with higher normal peak and smaller - SEA peak. Thirty one samples showed consistent results with the conventional gap-PCR. Two samples with ambiguous results were confirmed to be maternal DNA contamination on real-time quantitative PCR and microsatellite assay. HRMA from both samples showed similar pattern to that of heterozygotes. However, they showed much smaller normal peak compared with the - SEA peak, which is in contrast to those of heterozygotes and can readily be distinguished. HRMA with SYTO9 is feasible for prenatal diagnosis of alpha-thalassemia. It had potential advantage of prompt detection maternal DNA contamination. Copyright (c) 2010 John Wiley & Sons, Ltd.

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

PubMed

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

2012-06-01

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

High-resolution melting-curve analysis of ligation-mediated real-time PCR for rapid evaluation of an epidemiological outbreak of extended-spectrum-beta-lactamase-producing Escherichia coli.

PubMed

Woksepp, Hanna; Jernberg, Cecilia; Tärnberg, Maria; Ryberg, Anna; Brolund, Alma; Nordvall, Michaela; Olsson-Liljequist, Barbro; Wisell, Karin Tegmark; Monstein, Hans-Jürg; Nilsson, Lennart E; Schön, Thomas

2011-12-01

Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE.

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

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.

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.

Formation of curved micrometer-sized single crystals.

PubMed

Koifman Khristosov, Maria; Kabalah-Amitai, Lee; Burghammer, Manfred; Katsman, Alex; Pokroy, Boaz

2014-05-27

Crystals in nature often demonstrate curved morphologies rather than classical faceted surfaces. Inspired by biogenic curved single crystals, we demonstrate that gold single crystals exhibiting curved surfaces can be grown with no need of any fabrication steps. These single crystals grow from the confined volume of a droplet of a eutectic composition melt that forms via the dewetting of nanometric thin films. We can control their curvature by controlling the environment in which the process is carried out, including several parameters, such as the contact angle and the curvature of the drops, by changing the surface tension of the liquid drop during crystal growth. Here we present an energetic model that explains this phenomenon and predicts why and under what conditions crystals will be forced to grow with the curvature of the microdroplet even though the energetic state of a curved single crystal is very high.

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

High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

PubMed Central

Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob; Feld, Louise; Holben, William E.

2014-01-01

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. PMID:24610853

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hirano, Teruyuki; Sato, Bun'ei; Kobayashi, Atsushi

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} ∼more » 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.« less

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.

Melting, glass transition, and apparent heat capacity of α-D-glucose by thermal analysis.

PubMed

Magoń, A; Pyda, M

2011-11-29

The thermal behaviors of α-D-glucose in the melting and glass transition regions were examined utilizing the calorimetric methods of standard differential scanning calorimetry (DSC), standard temperature-modulated differential scanning calorimetry (TMDSC), quasi-isothermal temperature-modulated differential scanning calorimetry (quasi-TMDSC), and thermogravimetric analysis (TGA). The quantitative thermal analyses of experimental data of crystalline and amorphous α-D-glucose were performed based on heat capacities. The total, apparent and reversingheat capacities, and phase transitions were evaluated on heating and cooling. The melting temperature (T(m)) of a crystalline carbohydrate such as α-D-glucose, shows a heating rate dependence, with the melting peak shifted to lower temperature for a lower heating rate, and with superheating of around 25K. The superheating of crystalline α-D-glucose is observed as shifting the melting peak for higher heating rates, above the equilibrium melting temperature due to of the slow melting process. The equilibrium melting temperature and heat of fusion of crystalline α-D-glucose were estimated. Changes of reversing heat capacity evaluated by TMDSC at glass transition (T(g)) of amorphous and melting process at T(m) of fully crystalline α-D-glucose are similar. In both, the amorphous and crystalline phases, the same origin of heat capacity changes, in the T(g) and T(m) area, are attributable to molecular rotational motion. Degradation occurs simultaneously with the melting process of the crystalline phase. The stability of crystalline α-D-glucose was examined by TGA and TMDSC in the melting region, with the degradation shown to be resulting from changes of mass with temperature and time. The experimental heat capacities of fully crystalline and amorphous α-D-glucose were analyzed in reference to the solid, vibrational, and liquid heat capacities, which were approximated based on the ATHAS scheme and Data Bank. Copyright �

Detonation initiation of heterogeneous melt-cast high explosives

NASA Astrophysics Data System (ADS)

Chuzeville, V.; Baudin, G.; Lefrançois, A.; Genetier, M.; Barbarin, Y.; Jacquet, L.; Lhopitault, J.-L.; Peix, J.; Boulanger, R.; Catoire, L.

2017-01-01

2,4,6-trinitrotoluene (TNT) is widely used in conventional and insensitive munitions as a fusible binder, commonly melt-cast with other explosives such as 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) or 3-nitro-1,2,4-triazol-one (NTO). In this paper, we study the shock-to-detonation transition phenomenon in two melt-cast high explosives (HE). We have performed plate impact tests on wedge samples to measure run-distance and time-to-detonation in order to establish the Pop-plot relation for several melt-cast HE. Highlighting the existence of the single curve buildup, we propose a two phase model based on a Zeldovich, Von-Neumann, Döring (ZND) approach where the deflagration fronts grow from the explosive grain boundaries. Knowing the grain size distribution, we calculate the deflagration velocities of the explosive charges as a function of shock pressure and explore the possible grain fragmentation.

Origins of ultralow velocity zones through slab-derived metallic melt

PubMed Central

Liu, Jiachao; Li, Jie; Smith, Jesse S.

2016-01-01

Understanding the ultralow velocity zones (ULVZs) places constraints on the chemical composition and thermal structure of deep Earth and provides critical information on the dynamics of large-scale mantle convection, but their origin has remained enigmatic for decades. Recent studies suggest that metallic iron and carbon are produced in subducted slabs when they sink beyond a depth of 250 km. Here we show that the eutectic melting curve of the iron−carbon system crosses the current geotherm near Earth’s core−mantle boundary, suggesting that dense metallic melt may form in the lowermost mantle. If concentrated into isolated patches, such melt could produce the seismically observed density and velocity features of ULVZs. Depending on the wetting behavior of the metallic melt, the resultant ULVZs may be short-lived domains that are replenished or regenerated through subduction, or long-lasting regions containing both metallic and silicate melts. Slab-derived metallic melt may produce another type of ULVZ that escapes core sequestration by reacting with the mantle to form iron-rich postbridgmanite or ferropericlase. The hypotheses connect peculiar features near Earth's core−mantle boundary to subduction of the oceanic lithosphere through the deep carbon cycle. PMID:27143719

Thermal energy storage behaviour of nanoparticle enhanced PCM during freezing and melting

NASA Astrophysics Data System (ADS)

P, Murugan; P, Ganesh Kumar; V, Kumaresan; M, Meikandan; K, Malar Mohan; R, Velraj

2018-03-01

The present research work aimed to investigate the melting and solidification characteristics of NPCM. The NPCM was prepared using paraffin as the PCM and high conductive MWCNT as the nanomaterial without using any dispersant. The NPCM was prepared by dispersing MWCNTs with volume fractions of 0.3%, 0.6% and 0.9% in PCM as the base PCM. SEM morphology showed the uniform dispersion of MWCNTs in the paraffin wax. The MWCNT nano-additives PCMs showed two peaks in the heating curve by DSC measurement. Lessening in melting and solidification time of 30% and 43% was attained in the case of NPCM with 0.3% and 0.9%, respectively. It is observed from the DSC analysis that the latent heat of pure paraffin during freezing and melting cycle was 139.2 J/g (at 56.61 °C) and 131.8 J/g (at 57.55 °C), respectively. Whereas, the latent heat of NPCM with 0.9% of nanofluid was 150.7 J/g (at 56.36 °C) and 148.3 J/g (58.35 °C). It is construed that a maximum change in latent heat of 7.6% and 11% was observed between pure PCM and NPCM during freezing and melting cycle. For the lesser nanoparticle concentration (0.3% and 0.6%), the percentage change in latent heat was lesser than 0.9%.

Electro-physical properties of superconducting ceramic thick film prepared by partial melting method.

PubMed

Lee, Sang Heon

2013-05-01

BiSrCaCuO superconductor thick films were prepared at several curing temperatures, and their electro-physical properties were determined to find an optimum fabrication conditions. Critical temperatures of the superconductors were decreased with increasing melting temperature, which was related to the amount of equilibrium phases of the superconducting materials with temperature. The critical temperature of BiSrCaCuO bulk and thick film superconductors were 107 K and 96 K, respectively. The variation of susceptibility of the superconductor thick film formed at 950 degrees C had multi-step-type curve for 70 G externally applied field, whereas, a superconductor thick film formed at 885 degrees C had a single step-type curve like a bulk BiSrCaCuO ceramic superconductor in the temperature-susceptibility curves. A partial melting at 865 degrees C is one of optimum conditions for making a superconductor thick film with a relatively homogeneous phase.

PMAnalyzer: a new web interface for bacterial growth curve analysis.

PubMed

Cuevas, Daniel A; Edwards, Robert A

2017-06-15

Bacterial growth curves are essential representations for characterizing bacteria metabolism within a variety of media compositions. Using high-throughput, spectrophotometers capable of processing tens of 96-well plates, quantitative phenotypic information can be easily integrated into the current data structures that describe a bacterial organism. The PMAnalyzer pipeline performs a growth curve analysis to parameterize the unique features occurring within microtiter wells containing specific growth media sources. We have expanded the pipeline capabilities and provide a user-friendly, online implementation of this automated pipeline. PMAnalyzer version 2.0 provides fast automatic growth curve parameter analysis, growth identification and high resolution figures of sample-replicate growth curves and several statistical analyses. PMAnalyzer v2.0 can be found at https://edwards.sdsu.edu/pmanalyzer/ . Source code for the pipeline can be found on GitHub at https://github.com/dacuevas/PMAnalyzer . Source code for the online implementation can be found on GitHub at https://github.com/dacuevas/PMAnalyzerWeb . dcuevas08@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

High-Resolution Melting-Curve Analysis of Ligation-Mediated Real-Time PCR for Rapid Evaluation of an Epidemiological Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli ▿

PubMed Central

Woksepp, Hanna; Jernberg, Cecilia; Tärnberg, Maria; Ryberg, Anna; Brolund, Alma; Nordvall, Michaela; Olsson-Liljequist, Barbro; Wisell, Karin Tegmark; Monstein, Hans-Jürg; Nilsson, Lennart E.; Schön, Thomas

2011-01-01

Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated Escherichia coli isolates (n = 15) and control isolates (n = 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (n = 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing E. coli strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE. PMID:21956981

Analysis and Recognition of Curve Type as The Basis of Object Recognition in Image

NASA Astrophysics Data System (ADS)

Nugraha, Nurma; Madenda, Sarifuddin; Indarti, Dina; Dewi Agushinta, R.; Ernastuti

2016-06-01

An object in an image when analyzed further will show the characteristics that distinguish one object with another object in an image. Characteristics that are used in object recognition in an image can be a color, shape, pattern, texture and spatial information that can be used to represent objects in the digital image. The method has recently been developed for image feature extraction on objects that share characteristics curve analysis (simple curve) and use the search feature of chain code object. This study will develop an algorithm analysis and the recognition of the type of curve as the basis for object recognition in images, with proposing addition of complex curve characteristics with maximum four branches that will be used for the process of object recognition in images. Definition of complex curve is the curve that has a point of intersection. By using some of the image of the edge detection, the algorithm was able to do the analysis and recognition of complex curve shape well.

Process parameters, orientation, and functional properties of melt-processed bulk Y-Ba-Cu-O superconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakharchenko, I.V.; Terryll, K.M.; Rao, K.V.

1995-03-01

This study compared the microstructure, texturing, and functional properties (critical currents) of YBa{sub 2}Cu{sub 3}O{sub 7{minus}x}-based bulk pellets that were prepared by the quench-melt-growth-process (QMGP), melt-textured growth (MTG), and conventional solid-state reaction (SSR) approaches. Using two X-ray diffraction (XRD) methods, {theta}-2{theta}, and rocking curves, the authors found that the individual grains of two melt-processed pellets exhibited remarkable preferred orientational alignment (best rocking curve width = 3.2{degree}). However, the direction of the preferred orientation among the grains was random. Among the three types of bulk materials studied, the QMGP sample was found to have the best J{sub c} values, {approx} 4,500more » A/cm{sup 2} at 77 K in a field of 2 kG, as determined from SQUID magnetic data.« less

A comparison of the MeltPro® HPV Test with the Cobas® HPV Test for detecting and genotyping 14 high-risk human papillomavirus types.

PubMed

Tang, Zhiteng; Xu, Ye; Song, Najie; Zou, Dongqing; Liao, Yiqun; Li, Qingge; Pan, Chao

2018-03-01

The clinical performance of the newly developed MeltPro ® HPV Test, based on multicolor melting curve analysis, was evaluated and compared with the commercially available Cobas ® HPV Test for detection of HPV and genotyping of HPV-16 and HPV-18. A total of 1647 cervical samples were analyzed with both tests. The agreement values were 96.2% for HPV detection, 99.6% for HPV-16 identification, and 99.7% for HPV-18 identification. All genotyping results from MeltPro ® HPV Test showed that HPV-52, HPV-58, and HPV-16 were the most common types in this study. Intra-laboratory reproducibility studies showed 97.8% agreement while inter-laboratory reproducibility studies showed 96.9% agreement for the MeltPro ® HPV Test. The MeltPro ® HPV Test and Cobas ® HPV Test are highly correlative and are useful for monitoring HPV infection.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

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.

Competitive amplification of differentially melting amplicons (CADMA) enables sensitive and direct detection of all mutation types by high-resolution melting analysis.

PubMed

Kristensen, Lasse S; Andersen, Gitte B; Hager, Henrik; Hansen, Lise Lotte

2012-01-01

Sensitive and specific mutation detection is of particular importance in cancer diagnostics, prognostics, and individualized patient treatment. However, the majority of molecular methodologies that have been developed with the aim of increasing the sensitivity of mutation testing have drawbacks in terms of specificity, convenience, or costs. Here, we have established a new method, Competitive Amplification of Differentially Melting Amplicons (CADMA), which allows very sensitive and specific detection of all mutation types. The principle of the method is to amplify wild-type and mutated sequences simultaneously using a three-primer system. A mutation-specific primer is designed to introduce melting temperature decreasing mutations in the resulting mutated amplicon, while a second overlapping primer is designed to amplify both wild-type and mutated sequences. When combined with a third common primer very sensitive mutation detection becomes possible, when using high-resolution melting (HRM) as detection platform. The introduction of melting temperature decreasing mutations in the mutated amplicon also allows for further mutation enrichment by fast coamplification at lower denaturation temperature PCR (COLD-PCR). For proof-of-concept, we have designed CADMA assays for clinically relevant BRAF, EGFR, KRAS, and PIK3CA mutations, which are sensitive to, between 0.025% and 0.25%, mutated alleles in a wild-type background. In conclusion, CADMA enables highly sensitive and specific mutation detection by HRM analysis. © 2011 Wiley Periodicals, Inc.

Effects of porosity on shock-induced melting of honeycomb-shaped Cu nanofoams

NASA Astrophysics Data System (ADS)

Zhao, Fengpeng

Metallic foams are of fundamental and applied interests in various areas, including structure engineering (e.g., lightweight structural members and energy absorbers), and shock physics (e.g., as laser ablators involving shock-induced melting and vaporization).Honeycomb-shaped metallic foams consist of regular array of hexagonal cells in two dimensions and have extensive applications and represent a unique, simple yet useful model structure for exploring mechanisms and making quantitative assessment. We investigate shock-induced melting in honeycomb-shaped Cu nanofoams with extensive molecular dynamics simulations. A total of ten porosities (phi) are explored, ranging from 0 to 0.9 at an increment of 0.1. Upon shock compression, void collapse induces local melting followed by supercooling for sufficiently high porosity at low shock strengths. While superheating of solid remnants occurs for sufficiently strong shocks at phi<0.1. Both supercooling of melts and superheating of solid remnants are transient, and the equilibrated shock states eventually fall on the equilibrium melting curve for partial melting. However, phase equilibrium has not been achieved on the time scale of simulations in supercooled Cu liquid (from completely melted nanofoams). The temperatures for incipient and complete melting are related to porosity via a power law and approach the melting temperature at zero pressure as phi tends to 1.

Computerised curve deconvolution of TL/OSL curves using a popular spreadsheet program.

PubMed

Afouxenidis, D; Polymeris, G S; Tsirliganis, N C; Kitis, G

2012-05-01

This paper exploits the possibility of using commercial software for thermoluminescence and optically stimulated luminescence curve deconvolution analysis. The widely used software package Microsoft Excel, with the Solver utility has been used to perform deconvolution analysis to both experimental and reference glow curves resulted from the GLOw Curve ANalysis INtercomparison project. The simple interface of this programme combined with the powerful Solver utility, allows the analysis of complex stimulated luminescence curves into their components and the evaluation of the associated luminescence parameters.

High Resolution Melting (HRM) applied to wine authenticity.

PubMed

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

2017-02-01

Wine authenticity methods are in increasing demand mainly in Denomination of Origin designations. The DNA-based methodologies are a reliable means of tracking food/wine varietal composition. The main aim of this work was the study of High Resolution Melting (HRM) application as a screening method for must and wine authenticity. Three sample types (leaf, must and wine) were used to validate the three developed HRM assays (Vv1-705bp; Vv2-375bp; and Vv3-119bp). The Vv1 HRM assay was only successful when applied to leaf and must samples. The Vv2 HRM assay successfully amplified all sample types, allowing genotype discrimination based on melting temperature values. The smallest amplicon, Vv3, produced a coincident melting curve shape in all sample types (leaf and wine) with corresponding genotypes. This study presents sensitive, rapid and efficient HRM assays applied for the first time to wine samples suitable for wine authenticity purposes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Melting of Fe and Fe0.9Ni0.1 alloy at high pressures

NASA Astrophysics Data System (ADS)

Zhang, D.; Jackson, J. M.; Zhao, J.; Sturhahn, W.; Alp, E. E.; Hu, M. Y.; Toellner, T.

2014-12-01

Cosmochemical studies suggest that the cores of terrestrial planets are primarily composed of Fe alloyed with about 5 to 10 wt% Ni, plus some light elements (e.g., McDonough and Sun 1995). Thus, the high pressure melting curve of Fe0.9Ni0.1 is considered to be an important reference for characterizing the cores of terrestrial planets. We have determined the melting points of fcc-structured Fe and Fe0.9Ni0.1 up to 86 GPa using an in-situ method that monitors the atomic dynamics of the Fe atoms in the sample, synchrotron Mössbauer spectroscopy (Jackson et al. 2013). A laser heated diamond anvil cell is used to provide the high pressure-high temperature environmental conditions, and in-situ X-ray diffraction is used to constrain the pressure of the sample. To eliminate the influence of temperature fluctuations experienced by the sample on the determination of melting, we develop a Fast Temperature Readout (FasTeR) spectrometer. The FasTeR spectrometer features a fast reading rate (>100 Hz), a high sensitivity, a large dynamic range and a well-constrained focus. By combining the melting curve of fcc-structured Fe0.9Ni0.1 alloy determined in our study and the fcc-hcp phase boundary from Komabayashi et al. (2012), we calculate the fcc-hcp-liquid triple point of Fe0.9Ni0.1. Using this triple point and the thermophysical parameters from a nuclear resonant inelastic X-ray scattering study on hcp-Fe (Murphy et al. 2011), we compute the melting curve of hcp-structured Fe0.9Ni0.1. We will discuss our new experimental results with implications for the cores of Venus, Earth and Mars. Select references: McDonough & Sun (1995): The composition of the Earth. Chem. Geol. 120, 223-253. Jackson et al. (2013): Melting of compressed iron by monitoring atomic dynamics, EPSL, 362, 143-150. Komabayashi et al. (2012): In situ X-ray diffraction measurements of the fcc-hcp phase transition boundary of an Fe-Ni alloy in an internally heated diamond anvil cell, PCM, 39, 329-338. Murphy et al

High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh.

PubMed

Islam, Md Tarikul; Sarkar, Suprovath Kumar; Sultana, Nusrat; Begum, Mst Noorjahan; Bhuyan, Golam Sarower; Talukder, Shezote; Muraduzzaman, A K M; Alauddin, Md; Islam, Mohammad Sazzadul; Biswas, Pritha Promita; Biswas, Aparna; Qadri, Syeda Kashfi; Shirin, Tahmina; Banu, Bilquis; Sadya, Salma; Hussain, Manzoor; Sarwardi, Golam; Khan, Waqar Ahmed; Mannan, Mohammad Abdul; Shekhar, Hossain Uddin; Chowdhury, Emran Kabir; Sajib, Abu Ashfaqur; Akhteruzzaman, Sharif; Qadri, Syed Saleheen; Qadri, Firdausi; Mannoor, Kaiissar

2018-01-02

Bangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh necessitate a reliable DNA-based carrier screening approach that could supplement the use of hematological and electrophoretic indices to overcome the barriers of carrier screening. With this view in mind, the study aimed to establish a high resolution melting (HRM) curve-based rapid and reliable mutation screening method targeting the mutational hot-spot of South Asian and Southeast Asian countries that encompasses exon-1 (c.1 - c.92), intron-1 (c.92 + 1 - c.92 + 130) and a portion of exon-2 (c.93 - c.217) of the HBB gene which harbors more than 95% of mutant alleles responsible for beta-thalassemia in Bangladesh. Our HRM approach could successfully differentiate ten beta-globin gene mutations, namely c.79G > A, c.92 + 5G > C, c.126_129delCTTT, c.27_28insG, c.46delT, c.47G > A, c.92G > C, c.92 + 130G > C, c.126delC and c.135delC in heterozygous states from the wild type alleles, implying the significance of the approach for carrier screening as the first three of these mutations account for ~85% of total mutant alleles in Bangladesh. Moreover, different combinations of compound heterozygous mutations were found to generate melt curves that were distinct from the wild type alleles and from one another. Based on the findings, sixteen reference samples were run in parallel to 41 unknown specimens to perform direct genotyping of the beta-thalassemia specimens using HRM. The HRM-based genotyping of the unknown specimens showed 100% consistency with the sequencing result. Targeting the mutational hot-spot, the HRM approach could be successfully applied for screening of beta-thalassemia carriers in Bangladesh as well as in other countries of South Asia and Southeast Asia. The approach could be a useful supplement of hematological and

Rheology of multiphase polymer systems using novel "melt rigidity" evaluation approach

NASA Astrophysics Data System (ADS)

Kracalik, Milan

2015-04-01

Multiphase polymer systems like blends, composites and nanocomposites exhibit complex rheological behaviour due to physical and also possibly chemical interactions between individual phases. Up to now, rheology of heterogeneous polymer systems has been usually described by evaluation of viscosity curve (shear thinning phenomenon), storage modulus curve (formation of secondary plateau) or plotting information about damping behaviour (e.g. Van Gurp-Palmen-plot). On the contrary to evaluation of damping behaviour, "melt rigidity" approach has been introduced for description of physical network of rigid particles in polymer matrix as relation of ∫G'/∫G" over specific frequency range. This approach has been experimentally proved for polymer nanocomposites in order to compare shear flow characteristics with elongational flow field. In this contribution, LDPE-clay nanocomposites with different dispersion grades (physical networks) have been prepared and characterized by both conventional as well as novel "melt rigidity" approach.

Melting of genomic DNA: Predictive modeling by nonlinear lattice dynamics

NASA Astrophysics Data System (ADS)

Theodorakopoulos, Nikos

2010-08-01

The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the ϕX174 phage without any adjustable parameters are in good agreement with experiment. The calculated probabilities for single base-pair opening are consistent with values obtained from imino proton exchange experiments.

Temperature and composition dependencies of trace element partitioning - Olivine/melt and low-Ca pyroxene/melt

NASA Technical Reports Server (NTRS)

Colson, R. O.; Mckay, G. A.; Taylor, L. A.

1988-01-01

This paper presents a systematic thermodynamic analysis of the effects of temperature and composition on olivine/melt and low-Ca pyroxene/melt partitioning. Experiments were conducted in several synthetic basalts with a wide range of Fe/Mg, determining partition coefficients for Eu, Ca, Mn, Fe, Ni, Sm, Cd, Y, Yb, Sc, Al, Zr, and Ti and modeling accurately the changes in free energy for trace element exchange between crystal and melt as functions of the trace element size and charge. On the basis of this model, partition coefficients for olivine/melt and low-Ca pyroxene/melt can be predicted for a wide range of elements over a variety of basaltic bulk compositions and temperatures. Moreover, variations in partition coeffeicients during crystallization or melting can be modeled on the basis of changes in temperature and major element chemistry.

Origins of ultralow velocity zones through slab-derived metallic melt

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Jiachao; Li, Jie; Hrubiak, Rostislav

2016-05-03

Understanding the ultralow velocity zones (ULVZs) places constraints on the chemical composition and thermal structure of deep Earth and provides critical information on the dynamics of large-scale mantle convection, but their origin has remained enigmatic for decades. Recent studies suggest that metallic iron and carbon are produced in subducted slabs when they sink beyond a depth of 250 km. Here we show that the eutectic melting curve of the iron-carbon system crosses the current geotherm near Earth’s core-mantle boundary, suggesting that dense metallic melt may form in the lowermost mantle. If concentrated into isolated patches, such melt could produce themore » seismically observed density and velocity features of ULVZs. Depending on the wetting behavior of the metallic melt, the resultant ULVZs may be short-lived domains that are replenished or regenerated through subduction, or long-lasting regions containing both metallic and silicate melts. Slab-derived metallic melt may produce another type of ULVZ that escapes core sequestration by reacting with the mantle to form iron-rich post-bridgmanite or ferropericlase. The hypotheses connect peculiar features near Earth’s core-mantle boundary to subduction of the oceanic lithosphere through the deep carbon cycle.« less

Melting behavior of (Mg,Fe)O solid solutions at high pressure

NASA Astrophysics Data System (ADS)

Zhang, Li; Fei, Yingwei

2008-07-01

High pressure melting of (Mg,Fe)O ferropericlase, the second most abundant mineral in the Earth's lower mantle, is of fundamental importance for understanding the chemical differentiation, geodynamics and thermal evolution of the Earth's interior. We report the first systematic experimental study of melting behavior in the MgO-FeO system up to 3600 K and 7 GPa, indicating the ideal solution between solid and liquid (Mg,Fe)O in the MgO-rich portion. The zero pressure melting slope of MgO is ~221 K/GPa derived from our resistance heating measurements, which is several times higher than the value from the previous measurements in a CO2-laser heated diamond anvil cell, but consistent with the theoretically predicted melting curves. Our results combined with the previous first-principles simulations suggest that the melting temperature of MgO-rich (Mg,Fe)O is significantly higher than the geotherm through the lower mantle and this would place an upper bound on the solidus of the lower mantle.

Decision curve analysis: a novel method for evaluating prediction models.

PubMed

Vickers, Andrew J; Elkin, Elena B

2006-01-01

Diagnostic and prognostic models are typically evaluated with measures of accuracy that do not address clinical consequences. Decision-analytic techniques allow assessment of clinical outcomes but often require collection of additional information and may be cumbersome to apply to models that yield a continuous result. The authors sought a method for evaluating and comparing prediction models that incorporates clinical consequences,requires only the data set on which the models are tested,and can be applied to models that have either continuous or dichotomous results. The authors describe decision curve analysis, a simple, novel method of evaluating predictive models. They start by assuming that the threshold probability of a disease or event at which a patient would opt for treatment is informative of how the patient weighs the relative harms of a false-positive and a false-negative prediction. This theoretical relationship is then used to derive the net benefit of the model across different threshold probabilities. Plotting net benefit against threshold probability yields the "decision curve." The authors apply the method to models for the prediction of seminal vesicle invasion in prostate cancer patients. Decision curve analysis identified the range of threshold probabilities in which a model was of value, the magnitude of benefit, and which of several models was optimal. Decision curve analysis is a suitable method for evaluating alternative diagnostic and prognostic strategies that has advantages over other commonly used measures and techniques.

The Value of Hydrograph Partitioning Curves for Calibrating Hydrological Models in Glacierized Basins

NASA Astrophysics Data System (ADS)

He, Zhihua; Vorogushyn, Sergiy; Unger-Shayesteh, Katy; Gafurov, Abror; Kalashnikova, Olga; Omorova, Elvira; Merz, Bruno

2018-03-01

This study refines the method for calibrating a glacio-hydrological model based on Hydrograph Partitioning Curves (HPCs), and evaluates its value in comparison to multidata set optimization approaches which use glacier mass balance, satellite snow cover images, and discharge. The HPCs are extracted from the observed flow hydrograph using catchment precipitation and temperature gradients. They indicate the periods when the various runoff processes, such as glacier melt or snow melt, dominate the basin hydrograph. The annual cumulative curve of the difference between average daily temperature and melt threshold temperature over the basin, as well as the annual cumulative curve of average daily snowfall on the glacierized areas are used to identify the starting and end dates of snow and glacier ablation periods. Model parameters characterizing different runoff processes are calibrated on different HPCs in a stepwise and iterative way. Results show that the HPC-based method (1) delivers model-internal consistency comparably to the tri-data set calibration method; (2) improves the stability of calibrated parameter values across various calibration periods; and (3) estimates the contributions of runoff components similarly to the tri-data set calibration method. Our findings indicate the potential of the HPC-based approach as an alternative for hydrological model calibration in glacierized basins where other calibration data sets than discharge are often not available or very costly to obtain.

Erythritol: crystal growth from the melt.

PubMed

Lopes Jesus, A J; Nunes, Sandra C C; Ramos Silva, M; Matos Beja, A; Redinha, J S

2010-03-30

The structural changes occurring on erythritol as it is cooled from the melt to low temperature, and then heated up to the melting point have been investigated by differential scanning calorimetry (DSC), polarized light thermal microscopy (PLTM), X-ray powder diffraction (PXRD) and Fourier transform infrared spectroscopy (FTIR). By DSC, it was possible to set up the conditions to obtain an amorphous solid, a crystalline solid, or a mixture of both materials in different proportions. Two crystalline forms have been identified: a stable and a metastable one with melting points of 117 and 104 degrees C, respectively. The fusion curve decomposition of the stable form revealed the existence of three conformational structures. The main paths of the crystallization from the melt were followed by PLTM. The texture and colour changes allowed the characterization of the different phases and transitions in which they are involved on cooling as well as on heating processes. The type of crystallization front and its velocity were also followed by microscopic observation. These observations, together with the data provided by PXRD, allowed elucidating the transition of the metastable form into the stable one. The structural changes occurring upon the cooling and subsequent heating processes, namely those arising from intermolecular hydrogen bonds, were also accompanied by infrared spectroscopy. Particular attention was given to the spectral changes occurring in the OH stretching region. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Petrological Geodynamics of Mantle Melting II. AlphaMELTS + Multiphase Flow: Dynamic Fractional Melting

NASA Astrophysics Data System (ADS)

Tirone, Massimiliano

2018-03-01

In this second installment of a series that aims to investigate the dynamic interaction between the composition and abundance of the solid mantle and its melt products, the classic interpretation of fractional melting is extended to account for the dynamic nature of the process. A multiphase numerical flow model is coupled with the program AlphaMELTS, which provides at the moment possibly the most accurate petrological description of melting based on thermodynamic principles. The conceptual idea of this study is based on a description of the melting process taking place along a 1-D vertical ideal column where chemical equilibrium is assumed to apply in two local sub-systems separately on some spatial and temporal scale. The solid mantle belongs to a local sub-system (ss1) that does not interact chemically with the melt reservoir which forms a second sub-system (ss2). The local melt products are transferred in the melt sub-system ss2 where the melt phase eventually can also crystallize into a different solid assemblage and will evolve dynamically. The main difference with the usual interpretation of fractional melting is that melt is not arbitrarily and instantaneously extracted from the mantle, but instead remains a dynamic component of the model, hence the process is named dynamic fractional melting (DFM). Some of the conditions that may affect the DFM model are investigated in this study, in particular the effect of temperature, mantle velocity at the boundary of the mantle column. A comparison is made with the dynamic equilibrium melting (DEM) model discussed in the first installment. The implications of assuming passive flow or active flow are also considered to some extent. Complete data files of most of the DFM simulations, four animations and two new DEM simulations (passive/active flow) are available following the instructions in the supplementary material.

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

Functional principal component analysis of glomerular filtration rate curves after kidney transplant.

PubMed

Dong, Jianghu J; Wang, Liangliang; Gill, Jagbir; Cao, Jiguo

2017-01-01

This article is motivated by some longitudinal clinical data of kidney transplant recipients, where kidney function progression is recorded as the estimated glomerular filtration rates at multiple time points post kidney transplantation. We propose to use the functional principal component analysis method to explore the major source of variations of glomerular filtration rate curves. We find that the estimated functional principal component scores can be used to cluster glomerular filtration rate curves. Ordering functional principal component scores can detect abnormal glomerular filtration rate curves. Finally, functional principal component analysis can effectively estimate missing glomerular filtration rate values and predict future glomerular filtration rate values.

Microstructural evidence of melting in crustal rocks (Invited)

NASA Astrophysics Data System (ADS)

Holness, M. B.; Cesare, B.; Sawyer, E. W.

2010-12-01

The signature of the former presence of melt on a microscopic scale is highly variable, subject to modification both during the melting event and during its subsequent history. Static pyrometamorphism results in melt films on grain boundaries between reactant phases. If a volume increase is involved, melting results in hydrofracture. On a longer timescale, as demonstrated by fragments of the crustal source in lava flows at El Hoyazo (SE Spain), melt occurs throughout the rock. These examples are highly unusual: the great majority of rocks that underwent melting cooled more slowly, permitting microstructural modification driven by a combination of textural equilibration, reaction and deformation. In the absence of deformation, and at constant temperature, melt-bearing rocks approach textural equilibrium, characterised by uniform grain size, smoothly curved grain boundaries and the establishment at all three-grain junctions of the equilibrium dihedral angle. The dihedral angle controls melt connectivity, with consequences for melt mobility and rock rheology. However, deformation is the rule rather than the exception in regional metamorphic terrains with profound effects on melt distribution. If deformation occurs predominantly by diffusive processes, textural equilibration can keep pace. At higher deformation rates melt is squeezed into planar pockets aligned parallel to the shearing direction or perpendicular to the extensional stress. Microstructures formed during solidification are controlled by cooling rate, H2O, and the size of the melt pockets. Large pockets solidify to look like igneous rocks. In small pores the supersaturation required for crystal growth is high and melt persist to lower temperatures, even being preserved as tiny glassy inclusions (“nanogranites”) in regional terranes. The pore size effect changes crystallization order, resulting in small, highly cuspate grains on grain boundaries with low dihedral angles. Crystallisation microstructures

Light-curve Analysis of Neon Novae

NASA Astrophysics Data System (ADS)

Hachisu, Izumi; Kato, Mariko

2016-01-01

We analyzed light curves of five neon novae, QU Vul, V351 Pup, V382 Vel, V693 CrA, and V1974 Cyg, and determined their white dwarf (WD) masses and distance moduli on the basis of theoretical light curves composed of free-free and photospheric emission. For QU Vul, we obtained a distance of d ˜ 2.4 kpc, reddening of E(B - V) ˜ 0.55, and WD mass of MWD = 0.82-0.96 {M}⊙ . This suggests that an oxygen-neon WD lost a mass of more than ˜ 0.1 {M}⊙ since its birth. For V351 Pup, we obtained d˜ 5.5 {{kpc}}, E(B-V)˜ 0.45, and {M}{{WD}}=0.98-1.1 {M}⊙ . For V382 Vel, we obtained d˜ 1.6 {{kpc}}, E(B-V)˜ 0.15, and {M}{{WD}}=1.13-1.28 {M}⊙ . For V693 CrA, we obtained d˜ 7.1 {{kpc}}, E(B-V)˜ 0.05, and {M}{{WD}}=1.15-1.25 {M}⊙ . For V1974 Cyg, we obtained d˜ 1.8 {{kpc}}, E(B-V)˜ 0.30, and {M}{{WD}}=0.95-1.1 {M}⊙ . For comparison, we added the carbon-oxygen nova V1668 Cyg to our analysis and obtained d˜ 5.4 {{kpc}}, E(B-V)˜ 0.30, and {M}{{WD}}=0.98-1.1 {M}⊙ . In QU Vul, photospheric emission contributes 0.4-0.8 mag at most to the optical light curve compared with free-free emission only. In V351 Pup and V1974 Cyg, photospheric emission contributes very little (0.2-0.4 mag at most) to the optical light curve. In V382 Vel and V693 CrA, free-free emission dominates the continuum spectra, and photospheric emission does not contribute to the optical magnitudes. We also discuss the maximum magnitude versus rate of decline relation for these novae based on the universal decline law.

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

PubMed Central

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

2016-01-01

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

Vapor pressure and vapor fractionation of silicate melts of tektite composition

USGS Publications Warehouse

Walter, Louis S.; Carron, M.K.

1964-01-01

The total vapor pressure of Philippine tektite melts of approximately 70 per cent silica has been determined at temperatures ranging from 1500 to 2100??C. This pressure is 190 ?? 40 mm Hg at 1500??C, 450 ?? 50 mm at 1800??C and 850 ?? 70 mm at 2100?? C. Determinations were made by visually observing the temperature at which bubbles began to form at a constant low ambient pressure. By varying the ambient pressure, a boiling point curve was constructed. This curve differs from the equilibrium vapor pressure curve due to surface tension effects. This difference was evaluated by determining the equilibrium bubble size in the melt and calculating the pressure due to surface tension, assuming the latter to be 380 dyn/cm. The relative volatility from tektite melts of the oxides of Na, K, Fe, Al and Si has been determined as a function of temperature, total pressure arid roughly, of oxygen fugacity. The volatility of SiO2 is decreased and that of Na2O and K2O is increased in an oxygen-poor environment. Preliminary results indicate that volatilization at 2100??C under atmospheric pressure caused little or no change in the percentage Na2O and K2O. The ratio Fe3 Fe2 of the tektite is increased in ambient air at a pressure of 9 ?? 10-4 mm Hg (= 106.5 atm O2, partial pressure) at 2000??C. This suggests that tektites were formed either at lower oxygen pressures or that they are a product of incomplete oxidation of parent material with a still lower ferricferrous ratio. ?? 1964.

Molecular dynamics study of melting and fcc-bcc transitions in Xe.

PubMed

Belonoshko, A B; Ahuja, R; Johansson, B

2001-10-15

We have investigated the phase diagram of Xe over a wide pressure-temperature range by molecular dynamics. The calculated melting curve is in good agreement with earlier experimental data. At a pressure of around 25 GPa and a temperature of about 2700 K we find a triple fcc-bcc liquid point. The calculated fcc-bcc boundary is in nice agreement with the experimental points, which, however, were interpreted as melting. This finding suggests that the transition from close-packed to bcc structure might be more common at high pressure and high temperature than was previously anticipated.

Melting Processes at the Base of the Mantle Wedge: Melt Compositions and Melting Reactions for the First Melts of Vapor-Saturated Lherzolite

NASA Astrophysics Data System (ADS)

Grove, T. L.; Till, C. B.

2014-12-01

Vapor-saturated melting experiments have been performed at pressures near the base of the mantle wedge (3.2 GPa). The starting composition is a metasomatized lherzolite containing 3 wt. % H2O. Near-solidus melts and coexisting mineral phases have been characterized in experiments that span 925 to 1100 oC with melt % varying from 6 to 9 wt. %. Olivine, orthopyroxene, clinopyroxene and garnet coexist with melt over the entire interval and rutile is also present at < 1000 oC. Melt is andesitic in composition and varies from 60 wt. % SiO2 at 950 oC to 52 wt. % at 1075 oC. The Al2O3 contents of the melt are 13 to 14 wt. %, and CaO contents range from 1 and 4 wt. %. Melting is peritectic with orthopyroxene + liquid produced by melting of garnet + olivine + high-Ca pyroxene. In addition to quenched melt, we observe a quenched silicate component that is rhyolitic (>72 % SiO2) that we interpret as a precipitate from the coexisting supercritical H2O-rich vapor. Extrapolation of the measured compositional variation toward the solidus suggests that the first melt may be very SiO2 rich (i.e., granitic). We suggest that these granitic melts are the first melts of the mantle near the slab-wedge interface. As these SiO2-rich melts ascend into shallower, hotter overlying mantle, they continue to interact with the surrounding mantle and evolve in composition. These first melts may elucidate the geochemical and physical processes that accompany the beginnings of H2O flux melting.

Melting of Fe-Si-O alloys: the Fate of Coexisting Si and O in the Core

NASA Astrophysics Data System (ADS)

Arveson, S. M.; Lee, K. K. M.

2017-12-01

The light element budget of Earth's core plays an integral role in sustaining outer core convection, which powers the geodynamo. Many experiments have been performed on binary iron compounds, but the results do not robustly agree with seismological observations and geochemical constraints. Earth's core is almost certainly made up of multiple light elements, so the future of core composition studies lies in ternary (or higher order) systems in order to examine interactions between light elements. We perform melting experiments on Fe-Si-O alloys in a laser-heated diamond-anvil cell to 80 GPa and 4000 K. Using 2D multi- wavelength imaging radiometry together with textural and chemical analysis of quenched samples, we measure the high-pressure melting curves and determine partitioning of light elements between the melt and the coexisting solid. Quenched samples are analyzed both in map view and in cross section using scanning electron microscopy (SEM) and electron microprobe analysis (EPMA) to examine the 3D melt structure and composition. Partitioning of light elements between molten and solid alloys dictates (1) the density contrast at the ICB, which drives compositional convection in the outer core and (2) the temperature of the CMB, an integral parameter for understanding the deep Earth. Our experiments suggest silicon and oxygen do not simply coexist in the melt and instead show complex solubility based on temperature. Additionally, we do not find evidence of crystallization of SiO2 at low oxygen content as was recently reported.11 Hirose, K., et al., Crystallization of silicon dioxide and compositional evolution of the Earth's core. Nature, 2017. 543(7643): p. 99-102.

Formation of relief on Europa's surface and analysis of a melting probe movement through the ice

NASA Astrophysics Data System (ADS)

Erokhina, O. S.; Chumachenko, E. N.; Dunham, D. W.; Aksenov, S. A.; Logashina, I. V.

2013-12-01

These days, studies of planetary bodies' are of great interest. And of special interest are the icy moons of the giant planets like Jupiter and Saturn. Analysis of 'Voyager 1', 'Voyager 2', 'Galileo' and 'Cassini' spacecraft data showed that icy covers were observed on Jupiter's moons Ganymede, Europa and Calisto, and Saturn's moons Titan and Enceladus. Of particular interest is the relatively smooth surface of Europa. The entire surface is covered by a system of bands, valleys, and ridges. These structures are explained by the mobility of surface ice, and the impact of stress and large-scale tectonic processes. Also conditions on these moons allow speculation about possible life, considering these moons from an astrobiological point of view. To study the planetary icy body in future space missions, one of the problems to solve is the problem of design of a special device capable of penetrating through the ice, as well as the choice of the landing site of this probe. To select a possible landing site, analysis of Europa's surface relief formation is studied. This analysis showed that compression, extention, shearing, and bending can influence some arbitrarily separated section of Europe's icy surface. The computer simulation with the finite element method (FEM) was performed to see what types of defects could arise from such effects. The analysis showed that fractures and cracks could have various forms depending on the stress-strained state arising in their vicinity. Also the problem of a melting probe's movement through the ice is considered: How the probe will move in low gravity and low atmospheric pressure; whether the hole formed in the ice will be closed when the probe penetrates far enough or not; what is the influence of the probe's characteristics on the melting process; what would be the order of magnitude of the penetration velocity. This study explores the technique based on elasto-plastic theory and so-called 'solid water' theory to estimate the

Melting of Simple Solids and the Elementary Excitations of the Communal Entropy

NASA Astrophysics Data System (ADS)

Bongiorno, Angelo

2010-03-01

The melting phase transition of simple solids is addressed through the use of atomistic computer simulations. Three transition metals (Ni, Au, and Pt) and a semiconductor (Si) are considered in this study. Iso-enthalpic molecular dynamics simulations are used to compute caloric curves across the solid-to-liquid phase transition of a periodic crystalline system, to construct the free energy function of the solid and liquid phases, and thus to derive the thermodynamical limit of the melting point, latent heat and entropy of fusion of the material. The computational strategy used in this study yields accurate estimates of melting parameters, it consents to determine the superheating and supercooling temperature limits, and it gives access to the atomistic mechanisms mediating the melting process. In particular, it is found that the melting phase transition in simple solids is driven by exchange steps involving a few atoms and preserving the crystalline structure. These self-diffusion phenomena correspond to the elementary excitations of the communal entropy and, as their rate depends on the local material cohesivity, they mediate both the homogeneous and non-homogeneous melting process in simple solids.

Dependence of Ru2O3 Activity on Composition of Silicate Melts: Using Statistical Correlations to Infer Thermodynamic Behavior in the Melt

NASA Technical Reports Server (NTRS)

Colson, R. O.; Malum, K. M.

2005-01-01

Understanding variations in activity with composition is an essential step in improving prediction of partition coefficients during magma evolution. Variations in activity with composition are complex and do not generally exhibit ideal behavior relative to a traditional melt-component set. Although deviations from component ideality can be modeled numerically by simply fitting to compositional variables (such as in a regular or subregular solution model), such models have not been particularly successful for describing variations in trace component activities. A better approach might be to try to identify components that do a better job of describing the behavior of the species in the melt. Electrochemical Measurement of Ru2O3 activities: Electrodes were inserted into silicate melt beads of various compositions (Table 1) suspended on Ptwire loops in a 1-atm gas mixing furnace. An electrical potential was imposed between the electrodes, the imposed potential increasing along a step ramp with a pulse imposed on each step (Fig. 1). Current flows between electrodes when electroactive species in the melt are oxidized or reduced at the electrodes. The resulting current was measured at the top and bottom of the voltage pulse, and the difference (the differential current) was plotted against potential. The peak of the resulting curve is related to the activity coefficient for the particular electroactive species (Ru2O3) in the melt [1, 2, 3]. A significant part of the nonideal contribution to activity is due not to intrinsic properties of the component in the melt, but to our ignorance about the state and mixing properties of the component in the melt.

Analytical studies on the crystal melt interface shape in the Czochralski process for oxide single crystals

NASA Astrophysics Data System (ADS)

Jeong, Ja Hoon; Kang, In Seok

2000-09-01

Effects of the operating conditions on the crystal-melt interface shape are analytically investigated for the Czochralski process of the oxide single crystals. The ideas, which were used for the silicon single-crystal growth by Jeong et al. (J. Crystal Growth 177 (1997) 157), are extended to the oxide single-crystal growth problem by considering the internal radiation in the crystal phase and the melt phase heat transfer with the high Prandtl number. The interface shape is approximated in the simplest form as a quadratic function of radial position and an expression for the deviation from the flat interface shape is derived as a function of operating conditions. The radiative heat transfer rate between the interface and the ambient is computed by calculating the view factors for the curved interface shape with the assumption that the crystal phase is completely transparent. For the melt phase, the well-known results from the thermal boundary layer analysis are applied for the asymptotic case of high Prandtl number based on the idea that the flow field near the crystal-melt interface can be modeled as either a uniaxial or a biaxial flow. Through this work, essential information on the interface shape deformation and the effects of operating conditions are brought out for the oxide single-crystal growth.

Integrated System of Thermal/Dimensional Analysis for Quality Control of Metallic Melt and Ductile Iron Casting Solidification

NASA Astrophysics Data System (ADS)

Stan, Stelian; Chisamera, Mihai; Riposan, Iulian; Neacsu, Loredana; Cojocaru, Ana Maria; Stan, Iuliana

2018-03-01

The main objective of the present work is to introduce a specific experimental instrument and technique for simultaneously evaluating cooling curves and expansion or contraction of cast metals during solidification. Contraction/expansion analysis illustrates the solidification parameters progression, according to the molten cast iron characteristics, which are dependent on the melting procedure and applied metallurgical treatments, mold media rigidity and thermal behavior [heat transfer parameters]. The first part of the paper summarizes the performance of this two-mold device. Its function is illustrated by representative shrinkage tendency results in ductile cast iron as affected by mold rigidity (green sand and furan resin sand molds) and inoculant type (FeSi-based alloys), published in part previously. The second part of the paper illustrates an application of this equipment adapted for commercial foundry use. It conducts thermal analysis and volume change measurements in a single ceramic cup so that mold media as well as solidification conditions are constants, with cast iron quality as the variable. Experiments compared gray and ductile cast iron solidification patterns. Gray iron castings are characterized by higher undercooling at the beginning and at the end of solidification and lower graphitic expansion. Typically, ductile cast iron exhibits higher graphitic, initial expansion, conducive for shrinkage formation in soft molds.

Analysis of the curve of Spee and the curve of Wilson in adult Indian population: A three-dimensional measurement study.

PubMed

Surendran, Sowmya Velekkatt; Hussain, Sharmila; Bhoominthan, S; Nayar, Sanjna; Jayesh, Ragavendra

2016-01-01

When reconstructing the occlusal curvatures dentists often use a 4-inch radii arc as a rough standard based on Monson spherical theory. The use of an identical radius for the curve of Spee for all patients may not be appropriate because each patient is individually different. The validity of application of this theory in the Indian population and the present study has been undertaken. This study is an attempt to evaluate the curve of Spee and curve of Wilson in young Indian population using three dimensional analysis. This study compared the radius and the depth of right and left, maxillary and mandibular curves of Spee and the radius of maxillary and mandibular curves of Wilson in males and females. The cusp tips of canines, buccal cusp tips of premolars and molars and palatal/lingual cusp tips of second molars of 60 maxillary and 60 mandibular casts were obtained. Three-dimensional (x, y, z) coordinates of the cusp tips of the molars, premolars, and canines of the right and left sides of the maxilla and mandible were obtained with three dimensional coordinate measuring machine. The radius and the depth of right and left, maxillary and mandibular curves of Spee and the radius of maxillary and mandibular curves of Wilson were measured by means of computer software Metrologic-XG. Pearson's correlation test and Independent t-test were used to test the statistical significance (α=.05). The values of curve of Spee and curve of Wilson in Indian population obtained from this study were higher than the 4 inch (100 mm) radius proposed by Monson. These findings suggest ethnic differences in the radius of curve of Spee and curve of Wilson.

DNA melting analysis: application of the "open tube" format for detection of mutant KRAS.

PubMed

Botezatu, Irina V; Kondratova, Valentina N; Shelepov, Valery P; Lichtenstein, Anatoly V

2011-12-15

High-resolution melting (HRM) analysis is a very effective method for genotyping and mutation scanning that is usually performed just after PCR amplification (the "closed tube" format). Though simple and convenient, the closed tube format makes the HRM dependent on the PCR mix, not generally optimal for DNA melting analysis. Here, the "open tube" format, namely the post-PCR optimization procedure (amplicon shortening and solution chemistry modification), is proposed. As a result, mutation scanning of short amplicons becomes feasible on a standard real-time PCR instrument (not primarily designed for HRM) using SYBR Green I. This approach has allowed us to considerably enhance the sensitivity of detecting mutant KRAS using both low- and high-resolution systems (the Bio-Rad iQ5-SYBR Green I and Bio-Rad CFX96-EvaGreen, respectively). The open tube format, though more laborious than the closed tube one, can be used in situations when maximal sensitivity of the method is needed. It also permits standardization of DNA melting experiments and the introduction of instruments of a "lower level" into the range of those suitable for mutation scanning. Copyright © 2011 Elsevier Inc. All rights reserved.

New multicomponent solder alloys of low melting pointfor low-cost commercial electronic assembly

NASA Astrophysics Data System (ADS)

Al-Ganainy, G. S.; Sakr, M. S.

2003-09-01

The requirements of the telecommunications, automobile, electronics and aircraft industries for non-toxic solders with melting points close to that of near-eutectic Pb-Sn alloys has led to the development of new Sn-Zn-In solder alloys. Differential thermal analysis (DTA) shows melting points of 198, 195, 190 and 185 +/- 2 °C for the alloys Sn-9Zn, Sn-9Zn-2In, Sn-9Zn-4In and Sn-9Zn-6In, respectively. An equation that fits the data relating the melting point to the In content in the solders is derived. The X-ray diffraction patterns are analyzed to determine the phases that exist in each solder. The stress-strain curves are studied in the temperature range from 90 to 130 °C for all the solders except for those that contain 4 wt% of In, where the temperature range continues to 150 °C. The work-hardening parameters, y (the yield stress), f (the fracture stress), and the parabolic work-hardening coefficient X, increase with increasing indium content in the solders at all working temperatures. They decrease with increasing working temperature for each solder, and show two relaxation stages only for the Sn-9Zn-4In solder around a temperature of 120 °C. (

Rapid detection of pathological mutations and deletions of the haemoglobin beta gene (HBB) by High Resolution Melting (HRM) analysis and Gene Ratio Analysis Copy Enumeration PCR (GRACE-PCR).

PubMed

Turner, Andrew; Sasse, Jurgen; Varadi, Aniko

2016-10-19

Inherited disorders of haemoglobin are the world's most common genetic diseases, resulting in significant morbidity and mortality. The large number of mutations associated with the haemoglobin beta gene (HBB) makes gene scanning by High Resolution Melting (HRM) PCR an attractive diagnostic approach. However, existing HRM-PCR assays are not able to detect all common point mutations and have only a very limited ability to detect larger gene rearrangements. The aim of the current study was to develop a HBB assay, which can be used as a screening test in highly heterogeneous populations, for detection of both point mutations and larger gene rearrangements. The assay is based on a combination of conventional HRM-PCR and a novel Gene Ratio Analysis Copy Enumeration (GRACE) PCR method. HRM-PCR was extensively optimised, which included the use of an unlabelled probe and incorporation of universal bases into primers to prevent interference from common non-pathological polymorphisms. GRACE-PCR was employed to determine HBB gene copy numbers relative to a reference gene using melt curve analysis to detect rearrangements in the HBB gene. The performance of the assay was evaluated by analysing 410 samples. A total of 44 distinct pathological genotypes were detected. In comparison with reference methods, the assay has a sensitivity of 100 % and a specificity of 98 %. We have developed an assay that detects both point mutations and larger rearrangements of the HBB gene. This assay is quick, sensitive, specific and cost effective making it suitable as an initial screening test that can be used for highly heterogeneous cohorts.

The Kepler Light Curves of AGN: A Detailed Analysis

DOE PAGES

Smith, Krista Lynne; Mushotzky, Richard F.; Boyd, Patricia T.; ...

2018-04-25

Here, we present a comprehensive analysis of 21 light curves of Type 1 active galactic nuclei (AGN) from the Kepler spacecraft. First, we describe the necessity and development of a customized pipeline for treating Kepler data of stochastically variable sources like AGN. We then present the light curves, power spectral density functions (PSDs), and flux histograms. The light curves display an astonishing variety of behaviors, many of which would not be detected in ground-based studies, including switching between distinct flux levels. Six objects exhibit PSD flattening at characteristic timescales that roughly correlate with black hole mass. These timescales are consistentmore » with orbital timescales or free-fall accretion timescales. We check for correlations of variability and high-frequency PSD slope with accretion rate, black hole mass, redshift, and luminosity. We find that bolometric luminosity is anticorrelated with both variability and steepness of the PSD slope. We do not find evidence of the linear rms–flux relationships or lognormal flux distributions found in X-ray AGN light curves, indicating that reprocessing is not a significant contributor to optical variability at the 0.1%–10% level.« less

The Kepler Light Curves of AGN: A Detailed Analysis

NASA Astrophysics Data System (ADS)

Smith, Krista Lynne; Mushotzky, Richard F.; Boyd, Patricia T.; Malkan, Matt; Howell, Steve B.; Gelino, Dawn M.

2018-04-01

We present a comprehensive analysis of 21 light curves of Type 1 active galactic nuclei (AGN) from the Kepler spacecraft. First, we describe the necessity and development of a customized pipeline for treating Kepler data of stochastically variable sources like AGN. We then present the light curves, power spectral density functions (PSDs), and flux histograms. The light curves display an astonishing variety of behaviors, many of which would not be detected in ground-based studies, including switching between distinct flux levels. Six objects exhibit PSD flattening at characteristic timescales that roughly correlate with black hole mass. These timescales are consistent with orbital timescales or free-fall accretion timescales. We check for correlations of variability and high-frequency PSD slope with accretion rate, black hole mass, redshift, and luminosity. We find that bolometric luminosity is anticorrelated with both variability and steepness of the PSD slope. We do not find evidence of the linear rms–flux relationships or lognormal flux distributions found in X-ray AGN light curves, indicating that reprocessing is not a significant contributor to optical variability at the 0.1%–10% level.

The Kepler Light Curves of AGN: A Detailed Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Krista Lynne; Mushotzky, Richard F.; Boyd, Patricia T.

Here, we present a comprehensive analysis of 21 light curves of Type 1 active galactic nuclei (AGN) from the Kepler spacecraft. First, we describe the necessity and development of a customized pipeline for treating Kepler data of stochastically variable sources like AGN. We then present the light curves, power spectral density functions (PSDs), and flux histograms. The light curves display an astonishing variety of behaviors, many of which would not be detected in ground-based studies, including switching between distinct flux levels. Six objects exhibit PSD flattening at characteristic timescales that roughly correlate with black hole mass. These timescales are consistentmore » with orbital timescales or free-fall accretion timescales. We check for correlations of variability and high-frequency PSD slope with accretion rate, black hole mass, redshift, and luminosity. We find that bolometric luminosity is anticorrelated with both variability and steepness of the PSD slope. We do not find evidence of the linear rms–flux relationships or lognormal flux distributions found in X-ray AGN light curves, indicating that reprocessing is not a significant contributor to optical variability at the 0.1%–10% level.« less

Deep and persistent melt layer in the Archaean mantle

NASA Astrophysics Data System (ADS)

Andrault, Denis; Pesce, Giacomo; Manthilake, Geeth; Monteux, Julien; Bolfan-Casanova, Nathalie; Chantel, Julien; Novella, Davide; Guignot, Nicolas; King, Andrew; Itié, Jean-Paul; Hennet, Louis

2018-02-01

The transition from the Archaean to the Proterozoic eon ended a period of great instability at the Earth's surface. The origin of this transition could be a change in the dynamic regime of the Earth's interior. Here we use laboratory experiments to investigate the solidus of samples representative of the Archaean upper mantle. Our two complementary in situ measurements of the melting curve reveal a solidus that is 200-250 K lower than previously reported at depths higher than about 100 km. Such a lower solidus temperature makes partial melting today easier than previously thought, particularly in the presence of volatiles (H2O and CO2). A lower solidus could also account for the early high production of melts such as komatiites. For an Archaean mantle that was 200-300 K hotter than today, significant melting is expected at depths from 100-150 km to more than 400 km. Thus, a persistent layer of melt may have existed in the Archaean upper mantle. This shell of molten material may have progressively disappeared because of secular cooling of the mantle. Crystallization would have increased the upper mantle viscosity and could have enhanced mechanical coupling between the lithosphere and the asthenosphere. Such a change might explain the transition from surface dynamics dominated by a stagnant lid on the early Earth to modern-like plate tectonics with deep slab subduction.

Phase diagrams of block copolymer melts by dissipative particle dynamics simulations

NASA Astrophysics Data System (ADS)

Gavrilov, Alexey A.; Kudryavtsev, Yaroslav V.; Chertovich, Alexander V.

2013-12-01

Phase diagrams for monodisperse and polydisperse diblock copolymer melts and a random multiblock copolymer melt are constructed using dissipative particle dynamics simulations. A thorough visual analysis and calculation of the static structure factor in several hundreds of points at each of the diagrams prove the ability of mesoscopic molecular dynamics to predict the phase behavior of polymer systems as effectively as the self-consistent field-theory and Monte Carlo simulations do. It is demonstrated that the order-disorder transition (ODT) curve for monodisperse diblocks can be precisely located by a spike in the dependence of the mean square pressure fluctuation on χN, where χ is the Flory-Huggins parameter and N is the chain length. For two other copolymer types, the continuous ODTs are observed. Large polydispersity of both blocks obeying the Flory distribution in length does not shift the ODT curve but considerably narrows the domains of the cylindrical and lamellar phases partially replacing them with the wormlike micelle and perforated lamellar phases, respectively. Instead of the pure 3d-bicontinuous phase in monodisperse diblocks, which could be identified as the gyroid, a coexistence of the 3d phase and cylindrical micelles is detected in polydisperse diblocks. The lamellar domain spacing D in monodisperse diblocks follows the strong-segregation theory prediction, D/N1/2 ˜ (χN)1/6, whereas in polydisperse diblocks it is almost independent of χN at χN < 100. Completely random multiblock copolymers cannot form ordered microstructures other than lamellas at any composition.

Pyroxene-melt equilibria. [for lunar maria basalts

NASA Technical Reports Server (NTRS)

Nielsen, R. L.; Drake, M. J.

1979-01-01

A thermodynamic analysis of pyroxene-melt equilibria is performed through use of a literature survey of analyses of high-Ca pyroxene and coexisting silicate melt pairs and analyses of low-Ca pyroxene silicate melt pairs. Reference is made to a modified version of a model developed by Bottinga and Weill (1972) which more successfully accounts for variations in melt composition than does a model which considers the melt to be composed of simple oxides which mix ideally. By using a variety of pyroxene melt relations, several pyroxene-melt and low-Ca pyroxene-high-Ca pyroxene geothermometers are developed which have internally consistant precisions of approximately + or - 20 C. Finally, it is noted that these equations may have application in modeling the evolution of mineral compositions during differentiation of basaltic magmas.

Fault rheology beyond frictional melting.

PubMed

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

2015-07-28

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

Quantitative PCR high-resolution melting (qPCR-HRM) curve analysis, a new approach to simultaneously screen point mutations and large rearrangements: application to MLH1 germline mutations in Lynch syndrome.

PubMed

Rouleau, Etienne; Lefol, Cédrick; Bourdon, Violaine; Coulet, Florence; Noguchi, Tetsuro; Soubrier, Florent; Bièche, Ivan; Olschwang, Sylviane; Sobol, Hagay; Lidereau, Rosette

2009-06-01

Several techniques have been developed to screen mismatch repair (MMR) genes for deleterious mutations. Until now, two different techniques were required to screen for both point mutations and large rearrangements. For the first time, we propose a new approach, called "quantitative PCR (qPCR) high-resolution melting (HRM) curve analysis (qPCR-HRM)," which combines qPCR and HRM to obtain a rapid and cost-effective method suitable for testing a large series of samples. We designed PCR amplicons to scan the MLH1 gene using qPCR HRM. Seventy-six patients were fully scanned in replicate, including 14 wild-type patients and 62 patients with known mutations (57 point mutations and five rearrangements). To validate the detected mutations, we used sequencing and/or hybridization on a dedicated MLH1 array-comparative genomic hybridization (array-CGH). All point mutations and rearrangements detected by denaturing high-performance liquid chromatography (dHPLC)+multiplex ligation-dependent probe amplification (MLPA) were successfully detected by qPCR HRM. Three large rearrangements were characterized with the dedicated MLH1 array-CGH. One variant was detected with qPCR HRM in a wild-type patient and was located within the reverse primer. One variant was not detected with qPCR HRM or with dHPLC due to its proximity to a T-stretch. With qPCR HRM, prescreening for point mutations and large rearrangements are performed in one tube and in one step with a single machine, without the need for any automated sequencer in the prescreening process. In replicate, its reagent cost, sensitivity, and specificity are comparable to those of dHPLC+MLPA techniques. However, qPCR HRM outperformed the other techniques in terms of its rapidity and amount of data provided.

Downstream processing from melt granulation towards tablets: In-depth analysis of a continuous twin-screw melt granulation process using polymeric binders.

PubMed

Grymonpré, W; Verstraete, G; Vanhoorne, V; Remon, J P; De Beer, T; Vervaet, C

2018-03-01

The concept of twin-screw melt granulation (TSMG) has steadily (re)-gained interest in pharmaceutical formulation development as an intermediate step during tablet manufacturing. However, to be considered as a viable processing option for solid oral dosage forms there is a need to understand all critical sources of variability which could affect this granulation technique. The purpose of this study was to provide an in-depth analysis of the continuous TSMG process in order to expose the critical process parameters (CPP) and elucidate the impact of process and formulation parameters on the critical quality attributes (CQA) of granules and tablets during continuous TSMG. A first part of the study dealt with the screening of various amorphous polymers as binder for producing high-dosed melt granules of two model drug (i.e. acetaminophen and hydrochlorothiazide). The second part of this study described a quality-by-design (QbD) approach for melt granulation of hydrochlorothiazide in order to thoroughly evaluate TSMG, milling and tableting stage of the continuous TSMG line. Using amorphous polymeric binders resulted in melt granules with high milling efficiency due to their brittle behaviour without producing excessive amounts of fines, providing high granule yields with low friability. Therefore, it makes them extremely suitable for further downstream processing. One of the most important CPP during TSMG with polymeric binders was the granulation-torque, which - in case of polymers with high T g - increased during longer granulation runs to critical levels endangering the continuous process flow. However, by optimizing both screw speed and throughput or changing to polymeric binders with lower T g it was possible to significantly reduce this risk. This research paper highlighted that TSMG must be considered as a viable option during formulation development of solid oral dosage forms based on the robustness of the CQA of both melt granules and tablets. Copyright © 2017

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.

Dehydration melting studies in a 'Kyanite terrain', Manali, NW Himalayas

NASA Astrophysics Data System (ADS)

Verma, Pramod; Sengupta, Susmita; Chaddha, D. K.; Pant, N. C.

2005-05-01

The Beas valley section in Himachal Pradesh is characterized by the presence of kyanite as the alumino-silicate phase and a small extent of Neogene quartzo-feldspathic intrusives. The present paper explores the reasons for the lack of extensive granite occurrences through a detailed petrologic study on samples of a drill core (200 m, inclined 60° due ESE) close to Manali, the expected highest point in P-T space in this section. The highest assemblage encountered is quartz+muscovite+biotite+garnet+plagioclase+kyanite±apatite±zircon±tourmaline±ilmenite±rutile. The chemical analyses of mineral grains were carried out on a CAMECA SX51 EPMA. The following two reactions that constrain the P-T regime of the area have been established. St+Qtz→Alm+Ky+HO Bio+Plg+Qtz+Ksp→Gar+Ky+Liq. Our result, P=8.25±1 kbar, T=638±4 °C, falls in a region between curves representing aO=1.0 and aO=0.7 of the fluid in Thompson [Trans. Royal Soc. Edinb. 87 (1996) 1] diagram. The P-T estimate falls in the kyanite field and is very close to the mica dehydration-melting curve. The studies indicate that the core samples are a part of progressive metamorphic sequence. It implies that the absence of sillimanite and large scale melting is perhaps chance brought about by thrusting and erosion. The present section experienced single stage dehydration melting.

Rapid Detection Method for the Four Most Common CHEK2 Mutations Based on Melting Profile Analysis.

PubMed

Borun, Pawel; Salanowski, Kacper; Godlewski, Dariusz; Walkowiak, Jaroslaw; Plawski, Andrzej

2015-12-01

CHEK2 is a tumor suppressor gene, and the mutations affecting the functionality of the protein product increase cancer risk in various organs. The elevated risk, in a significant percentage of cases, is determined by the occurrence of one of the four most common mutations in the CHEK2 gene, including c.470T>C (p.I157T), c.444+1G>A (IVS2+1G>A), c.1100delC, and c.1037+1538_1224+328del5395 (del5395). We have developed and validated a rapid and effective method for their detection based on high-resolution melting analysis and comparative-high-resolution melting, a novel approach enabling simultaneous detection of copy number variations. The analysis is performed in two polymerase chain reactions followed by melting analysis, without any additional reagents or handling other than that used in standard high-resolution melting. Validation of the method was conducted in a group of 103 patients with diagnosed breast cancer, a group of 240 unrelated patients with familial history of cancer associated with the CHEK2 gene mutations, and a 100-person control group. The results of the analyses for all three groups were fully consistent with the results from other methods. The method we have developed improves the identification of the CHEK2 mutation carriers, reduces the cost of such analyses, as well as facilitates their implementation. Along with the increased efficiency, the method maintains accuracy and reliability comparable to other more labor-consuming techniques.

Extensions to decision curve analysis, a novel method for evaluating diagnostic tests, prediction models and molecular markers

PubMed Central

Vickers, Andrew J; Cronin, Angel M; Elkin, Elena B; Gonen, Mithat

2008-01-01

Background Decision curve analysis is a novel method for evaluating diagnostic tests, prediction models and molecular markers. It combines the mathematical simplicity of accuracy measures, such as sensitivity and specificity, with the clinical applicability of decision analytic approaches. Most critically, decision curve analysis can be applied directly to a data set, and does not require the sort of external data on costs, benefits and preferences typically required by traditional decision analytic techniques. Methods In this paper we present several extensions to decision curve analysis including correction for overfit, confidence intervals, application to censored data (including competing risk) and calculation of decision curves directly from predicted probabilities. All of these extensions are based on straightforward methods that have previously been described in the literature for application to analogous statistical techniques. Results Simulation studies showed that repeated 10-fold crossvalidation provided the best method for correcting a decision curve for overfit. The method for applying decision curves to censored data had little bias and coverage was excellent; for competing risk, decision curves were appropriately affected by the incidence of the competing risk and the association between the competing risk and the predictor of interest. Calculation of decision curves directly from predicted probabilities led to a smoothing of the decision curve. Conclusion Decision curve analysis can be easily extended to many of the applications common to performance measures for prediction models. Software to implement decision curve analysis is provided. PMID:19036144

Extensions to decision curve analysis, a novel method for evaluating diagnostic tests, prediction models and molecular markers.

PubMed

Vickers, Andrew J; Cronin, Angel M; Elkin, Elena B; Gonen, Mithat

2008-11-26

Decision curve analysis is a novel method for evaluating diagnostic tests, prediction models and molecular markers. It combines the mathematical simplicity of accuracy measures, such as sensitivity and specificity, with the clinical applicability of decision analytic approaches. Most critically, decision curve analysis can be applied directly to a data set, and does not require the sort of external data on costs, benefits and preferences typically required by traditional decision analytic techniques. In this paper we present several extensions to decision curve analysis including correction for overfit, confidence intervals, application to censored data (including competing risk) and calculation of decision curves directly from predicted probabilities. All of these extensions are based on straightforward methods that have previously been described in the literature for application to analogous statistical techniques. Simulation studies showed that repeated 10-fold crossvalidation provided the best method for correcting a decision curve for overfit. The method for applying decision curves to censored data had little bias and coverage was excellent; for competing risk, decision curves were appropriately affected by the incidence of the competing risk and the association between the competing risk and the predictor of interest. Calculation of decision curves directly from predicted probabilities led to a smoothing of the decision curve. Decision curve analysis can be easily extended to many of the applications common to performance measures for prediction models. Software to implement decision curve analysis is provided.

Relationship between the curve of Spee and craniofacial variables: A regression analysis.

PubMed

Halimi, Abdelali; Benyahia, Hicham; Azeroual, Mohamed-Faouzi; Bahije, Loubna; Zaoui, Fatima

2018-06-01

The aim of this regression analysis was to identify the determining factors, which impact the curve of Spee during its genesis, its therapeutic reconstruction, and its stability, within a continuously evolving craniofacial morphology throughout life. We selected a total of 107 patients, according to the inclusion criteria. A morphological and functional clinical examination was performed for each patient: plaster models, tracing of the curve of Spee, crowding, Angle's classification, overjet and overbite were thus recorded. Then, we made a cephalometric analysis based on the standardized lateral cephalograms. In the sagittal dimension, we measured the values of angles ANB, SNA, SNB, SND, I/i; and the following distances: AoBo, I/NA, i/NB, SE and SL. In the vertical dimension, we measured the values of angles FMA, GoGn/SN, the occlusal plane, and the following distances: SAr, ArD, Ar/Con, Con/Gn, GoPo, HFP, HFA and IF. The statistical analysis was performed using the SPSS software with a significance level of 0.05. Our sample including 107 subjects was composed of 77 female patients (71.3%) and 30 male patients (27.8%) 7 hypodivergent patients (6.5%), 56 hyperdivergent patients (52.3%) and 44 normodivergent patients (41.1%). Patients' mean age was 19.35±5.95 years. The hypodivergent patients presented more pronounced curves of Spee compared to the normodivergent and the hyperdivergent populations; patients in skeletal Class I presented less pronounced curves of Spee compared to patients in skeletal Class II and Class III. These differences were non significant (P>0.05). The curve of Spee was positively and moderately correlated with Angle's classification, overjet, overbite, sellion-articulare distance, and breathing type (P<0.05). We found no correlation between age, gender and the other parameters included in the study with the curve of Spee (P>0.05). Seventy five percent (75%) of the hyperdivergent patients with an oral breathing presented an overbite of 3mm

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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 inmore » 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.« less

The melting of subducted banded iron formations

NASA Astrophysics Data System (ADS)

Kang, Nathan; Schmidt, Max W.

2017-10-01

Banded iron formations (BIF) were common shelf and ocean basin sediments 3.5-1.8 Ga ago. To understand the fate of these dense rocks upon subduction, the melting relations of carbonated BIF were determined in Fe-Ca-(Mg)-Si-C-O2 at 950-1400 °C, 6 and 10 GPa, oxidizing (fO2 = hematite-magnetite, HM) and moderately reducing (fO2 ∼CO2-graphite/diamond, CCO) conditions. Solidus temperatures under oxidizing conditions are 950-1025 °C with H2O, and 1050-1150 °C anhydrous, but 250-175 °C higher at graphite saturation (values at 6-10 GPa). The combination of Fe3+ and carbonate leads to a strong melting depression. Solidus curves are steep with 17-20 °C/GPa. Near-solidus melts are ferro-carbonatites with ∼22 wt.% FeOtot, ∼48 wt% CO2 and 1-5 wt.% SiO2 at fO2 ∼ HM and ∼49 wt.% FeOtot, ∼20 wt% CO2 and 19-25 wt.% SiO2 at fO2 ∼ CCO . At elevated subduction geotherms, as likely for the Archean, C-bearing BIF could melt out all carbonate around 6 GPa. Fe-rich carbonatites would rise but stagnate gravitationally near the slab/mantle interface until they react with the mantle through Fe-Mg exchange and partial reduction. The latter would precipitate diamond and yield Fe- and C-rich mantle domains, yet, Fe-Mg is expected to diffusively re-equilibrate over Ga time scales. We propose that the oldest subduction derived diamonds stem from BIF derived melts.

First-principles melting of gallium clusters down to nine atoms: structural and electronic contributions to melting.

PubMed

Steenbergen, Krista G; Gaston, Nicola

2013-10-07

First-principles Born-Oppenheimer molecular dynamics simulations of small gallium clusters, including parallel tempering, probe the distinction between cluster and molecule in the size range of 7-12 atoms. In contrast to the larger sizes, dynamic measures of structural change at finite temperature demonstrate that Ga7 and Ga8 do not melt, suggesting a size limit to melting in gallium exists at 9 atoms. Analysis of electronic structure further supports this size limit, additionally demonstrating that a covalent nature cannot be identified for clusters larger than the gallium dimer. Ga9, Ga10 and Ga11 melt at greater-than-bulk temperatures, with no evident covalent character. As Ga12 represents the first small gallium cluster to melt at a lower-than-bulk temperature, we examine the structural properties of each cluster at finite temperature in order to probe both the origins of greater-than-bulk melting, as well as the significant differences in melting temperatures induced by a single atom addition. Size-sensitive melting temperatures can be explained by both energetic and entropic differences between the solid and liquid phases for each cluster. We show that the lower-than-bulk melting temperature of the 12-atom cluster can be attributed to persistent pair bonding, reminiscent of the pairing observed in α-gallium. This result supports the attribution of greater-than-bulk melting in gallium clusters to the anomalously low melting temperature of the bulk, due to its dimeric structure.

On the role of quantum ion dynamics for the anomalous melting of lithium

NASA Astrophysics Data System (ADS)

Elatresh, Sabri; Bonev, Stanimir

2011-03-01

Lithium has attracted a lot of interest in relation to a number of counterintuitive electronic and structural changes that it exhibits under pressure. One of the most remarkable properties of dense lithium is its anomalous melting. This behavior was first predicted theoretically based on first-principles molecular dynamics (FPMD) simulations, which treated the ions classically. The lowest melting temperature was determined to be about 275~K at 65~GPa. Recent experiments measured a melting temperature about 100~K lower at the same pressure. In this talk, we will present FPMD calculations of solid and liquid lithium free energies up to 100 GPa that take into account ion quantum dynamics. We examine the significance of the quantum effects for the finite-temperature phase boundaries of lithium and, in particular, its melting curve. Work supported by NSERC, Acenet, and LLNL under Contract DE-AC52-07NA27344.

Time Alignment as a Necessary Step in the Analysis of Sleep Probabilistic Curves

NASA Astrophysics Data System (ADS)

Rošt'áková, Zuzana; Rosipal, Roman

2018-02-01

Sleep can be characterised as a dynamic process that has a finite set of sleep stages during the night. The standard Rechtschaffen and Kales sleep model produces discrete representation of sleep and does not take into account its dynamic structure. In contrast, the continuous sleep representation provided by the probabilistic sleep model accounts for the dynamics of the sleep process. However, analysis of the sleep probabilistic curves is problematic when time misalignment is present. In this study, we highlight the necessity of curve synchronisation before further analysis. Original and in time aligned sleep probabilistic curves were transformed into a finite dimensional vector space, and their ability to predict subjects' age or daily measures is evaluated. We conclude that curve alignment significantly improves the prediction of the daily measures, especially in the case of the S2-related sleep states or slow wave sleep.

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.

Temperature of Earth's core constrained from melting of Fe and Fe0.9Ni0.1 at high pressures

NASA Astrophysics Data System (ADS)

Zhang, Dongzhou; Jackson, Jennifer M.; Zhao, Jiyong; Sturhahn, Wolfgang; Alp, E. Ercan; Hu, Michael Y.; Toellner, Thomas S.; Murphy, Caitlin A.; Prakapenka, Vitali B.

2016-08-01

The melting points of fcc- and hcp-structured Fe0.9Ni0.1 and Fe are measured up to 125 GPa using laser heated diamond anvil cells, synchrotron Mössbauer spectroscopy, and a recently developed fast temperature readout spectrometer. The onset of melting is detected by a characteristic drop in the time-integrated synchrotron Mössbauer signal which is sensitive to atomic motion. The thermal pressure experienced by the samples is constrained by X-ray diffraction measurements under high pressures and temperatures. The obtained best-fit melting curves of fcc-structured Fe and Fe0.9Ni0.1 fall within the wide region bounded by previous studies. We are able to derive the γ-ɛ-l triple point of Fe and the quasi triple point of Fe0.9Ni0.1 to be 110 ± 5GPa, 3345 ± 120K and 116 ± 5GPa, 3260 ± 120K, respectively. The measured melting temperatures of Fe at similar pressure are slightly higher than those of Fe0.9Ni0.1 while their one sigma uncertainties overlap. Using previously measured phonon density of states of hcp-Fe, we calculate melting curves of hcp-structured Fe and Fe0.9Ni0.1 using our (quasi) triple points as anchors. The extrapolated Fe0.9Ni0.1 melting curve provides an estimate for the upper bound of Earth's inner core-outer core boundary temperature of 5500 ± 200K. The temperature within the liquid outer core is then approximated with an adiabatic model, which constrains the upper bound of the temperature at the core side of the core-mantle boundary to be 4000 ± 200K. We discuss a potential melting point depression caused by light elements and the implications of the presented core-mantle boundary temperature bounds on phase relations in the lowermost part of the mantle.

Temperature of Earth's core constrained from melting of Fe and Fe 0.9Ni 0.1 at high pressures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Dongzhou; Jackson, Jennifer M.; Zhao, Jiyong

The melting points of fcc- and hcp-structured Fe 0.9Ni 0.1 and Fe are measured up to 125 GPa using laser heated diamond anvil cells, synchrotron Mossbauer spectroscopy, and a recently developed fast temperature readout spectrometer. The onset of melting is detected by a characteristic drop in the time integrated synchrotron Mfissbauer signal which is sensitive to atomic motion. The thermal pressure experienced by the samples is constrained by X-ray diffraction measurements under high pressures and temperatures. The obtained best-fit melting curves of fcc-structured Fe and Fe 0.9Ni 0.1 fall within the wide region bounded by previous studies. We are ablemore » to derive the gamma-is an element of-1 triple point of Fe and the quasi triple point of Fe0.9Ni0.1 to be 110 ± 5 GPa, 3345 ± 120 K and 116 ± 5 GPa, 3260 ± 120 K, respectively. The measured melting temperatures of Fe at similar pressure are slightly higher than those of Fe 0.9Ni 0.1 while their one sigma uncertainties overlap. Using previously measured phonon density of states of hcp-Fe, we calculate melting curves of hcp-structured Fe and Fe 0.9Ni 0.1 using our (quasi) triple points as anchors. The extrapolated Fe 0.9Ni 0.1 melting curve provides an estimate for the upper bound of Earth's inner core-outer core boundary temperature of 5500 ± 200 K. The temperature within the liquid outer core is then approximated with an adiabatic model, which constrains the upper bound of the temperature at the core side of the core -mantle boundary to be 4000 ± 200 K. We discuss a potential melting point depression caused by light elements and the implications of the presented core -mantle boundary temperature bounds on phase relations in the lowermost part of the mantle.« less

Solidus and liquidus profiles of chondritic mantle: Implication for melting of the Earth across its history

NASA Astrophysics Data System (ADS)

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

2011-04-01

We investigated the melting properties of a synthetic chondritic primitive mantle up to core-mantle boundary (CMB) pressures, using laser-heated diamond anvil cell. Melting criteria are essentially based on the use of X-rays provided by synchrotron radiation. We report a solidus melting curve lower than previously determined using optical methods. The liquidus curve is found between 300 and 600 K higher than the solidus over the entire lower mantle. At CMB pressures (135 GPa), the chondritic mantle solidus and liquidus reach 4150 (± 150) K and 4725 (± 150) K, respectively. We discuss that the lower mantle is unlikely to melt in the D″-layer, except if the highest estimate of the temperature profile at the base of the mantle, which is associated with a very hot core, is confirmed. Therefore, recent suggestions of partial melting in the lowermost mantle based on seismic observations of ultra-low velocity zones indicate either (1) a outer core exceeding 4150 K at the CMB or (2) the presence of chemical heterogeneities with high concentration of fusible elements. Our observations of a high liquidus temperature as well as a large gap between solidus and liquidus temperatures have important implications for the properties of the magma ocean during accretion. Not only complete melting of the lower mantle would require excessively high temperatures, but also, below liquidus temperatures partial melting should take place over a much larger depth interval than previously thought. In addition, magma adiabats suggest very high surface temperatures in case of a magma ocean that would extend to more than 40 GPa, as suggested by siderophile metal-silicate partitioning data. Such high surface temperature regime, where thermal blanketing is inefficient, points out to a transient character of the magma ocean, with a very fast cooling rate.

An Explanation for the Arctic Sea Ice Melt Pond Fractal Transition

NASA Astrophysics Data System (ADS)

Popovic, P.; Abbot, D. S.

2016-12-01

As Arctic sea ice melts during the summer, pools of melt water form on its surface. This decreases the ice's albedo, which signifcantly impacts its subsequent evolution. Understanding this process is essential for buiding accurate sea ice models in GCMs and using them to forecast future changes in sea ice. A feature of melt ponds that helps determine their impact on ice albedo is that they often form complex geometric shapes. One characteristic of their shape, the fractal dimension of the pond boundaries, D, has been shown to transition between the two fundamental limits of D = 1 and D = 2 at some critical pond size. Here, we provide an explanation for this behavior. First, using aerial photographs taken during the SHEBA mission, we show how this fractal transition curve changes with time, and show that there is a qualitative difference in the pond shape as ice transitions from impermeable to permeable. While ice is impermeable, the maximum fractal dimension is less than 2, whereas after it becomes permeable, the maximum fractal dimension becomes very close to 2. We then show how the fractal dimension of the boundary of a collection of overlapping circles placed randomly on a plane also transitions from D = 1 to D = 2 at a size equal to the average size of a single circle. We, therefore, conclude that this transition is a simple geometric consequence of regular shapes connecting. The one physical parameter that can be extracted from the fractal transition curve is the length scale at which transition occurs. Previously, this length scale has been associated with the typical size of snow dunes created on the ice surface during winter. We provide an alternative explanation by noting that the flexural wavelength of the ice poses a fundamental limit on the size of melt ponds on permeable ice. If this is true, melt ponds could be used as a proxy for ice thickness. Finally, we provide some remarks on how to observationally distinguish between the two ideas for what

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.

Toward a coherent model for the melting behavior of the deep Earth's mantle

NASA Astrophysics Data System (ADS)

Andrault, D.; Bolfan-Casanova, N.; Bouhifd, M. A.; Boujibar, A.; Garbarino, G.; Manthilake, G.; Mezouar, M.; Monteux, J.; Parisiades, P.; Pesce, G.

2017-04-01

Knowledge of melting properties is critical to predict the nature and the fate of melts produced in the deep mantle. Early in the Earth's history, melting properties controlled the magma ocean crystallization, which potentially induced chemical segregation in distinct reservoirs. Today, partial melting most probably occurs in the lowermost mantle as well as at mid upper-mantle depths, which control important aspects of mantle dynamics, including some types of volcanism. Unfortunately, despite major experimental and theoretical efforts, major controversies remain about several aspects of mantle melting. For example, the liquidus of the mantle was reported (for peridotitic or chondritic-type composition) with a temperature difference of ∼1000 K at high mantle depths. Also, the Fe partitioning coefficient (DFeBg/melt) between bridgmanite (Bg, the major lower mantle mineral) and a melt was reported between ∼0.1 and ∼0.5, for a mantle depth of ∼2000 km. Until now, these uncertainties had prevented the construction of a coherent picture of the melting behavior of the deep mantle. In this article, we perform a critical review of previous works and develop a coherent, semi-quantitative, model. We first address the melting curve of Bg with the help of original experimental measurements, which yields a constraint on the volume change upon melting (ΔVm). Secondly, we apply a basic thermodynamical approach to discuss the melting behavior of mineralogical assemblages made of fractions of Bg, CaSiO3-perovskite and (Mg,Fe)O-ferropericlase. Our analysis yields quantitative constraints on the SiO2-content in the pseudo-eutectic melt and the degree of partial melting (F) as a function of pressure, temperature and mantle composition; For examples, we find that F could be more than 40% at the solidus temperature, except if the presence of volatile elements induces incipient melting. We then discuss the melt buoyancy in a partial molten lower mantle as a function of pressure

Component Analysis of Remanent Magnetization Curves: A Revisit with a New Model Distribution

NASA Astrophysics Data System (ADS)

Zhao, X.; Suganuma, Y.; Fujii, M.

2017-12-01

Geological samples often consist of several magnetic components that have distinct origins. As the magnetic components are often indicative of their underlying geological and environmental processes, it is therefore desirable to identify individual components to extract associated information. This component analysis can be achieved using the so-called unmixing method, which fits a mixture model of certain end-member model distribution to the measured remanent magnetization curve. In earlier studies, the lognormal, skew generalized Gaussian and skewed Gaussian distributions have been used as the end-member model distribution in previous studies, which are performed on the gradient curve of remanent magnetization curves. However, gradient curves are sensitive to measurement noise as the differentiation of the measured curve amplifies noise, which could deteriorate the component analysis. Though either smoothing or filtering can be applied to reduce the noise before differentiation, their effect on biasing component analysis is vaguely addressed. In this study, we investigated a new model function that can be directly applied to the remanent magnetization curves and therefore avoid the differentiation. The new model function can provide more flexible shape than the lognormal distribution, which is a merit for modeling the coercivity distribution of complex magnetic component. We applied the unmixing method both to model and measured data, and compared the results with those obtained using other model distributions to better understand their interchangeability, applicability and limitation. The analyses on model data suggest that unmixing methods are inherently sensitive to noise, especially when the number of component is over two. It is, therefore, recommended to verify the reliability of component analysis by running multiple analyses with synthetic noise. Marine sediments and seafloor rocks are analyzed with the new model distribution. Given the same component

Non-invasive Prenatal Diagnosis of Feto-Maternal Platelet Incompatibility by Cold High Resolution Melting Analysis.

PubMed

Ferro, Marta; Macher, Hada C; Noguerol, Pilar; Jimenez-Arriscado, Pilar; Molinero, Patrocinio; Guerrero, Juan M; Rubio, Amalia

2016-01-01

Fetal and Neonatal alloimmune thrombocytopenia (FNAIT) is a condition which could occur when pregnant women develop an alloimmunization against paternally inherited antigens of the fetal platelets. Approximately 80 % of FNAIT cases are caused by anti-HPA-1a, about 15 % by anti-HPA-5b and 5 % by other HPA antibodies. Only 2 % of the total population is HPA-1a negative (HPA-1b1b). The HPA-1a allele differs by one single nucleotide from HPA-1b allele, yet it represents around 27 % of total severe thrombocytopenias. HPA-1 was studied in serum cDNA from 12 volunteer pregnant women to determine their HPA-1 genotype by HRM (high resolution melting) PCR. When an homozygous HPA-1 gene was detected in a mother, a COLD HRM was performed to determine whether or not the fetal genotype differs from the mother's.The differences in the melting curve shapes allow us to accurately distinguish the three pregnants genotypes. The fetal heterozygous genotype of homozygous pregnant women was correctly detected by COLD PCR HRM in maternal serum. HPA-1 genotyping by HRM may be a useful aproach for genotyping all pregnant women in inexpensively. Moreover, when HPA-1 homozygosis was detected in a pregnant woman, fetal heterozygosis may be diagnosed by COLD HRM to select pregnancies for preventive monitoring.

Non-isothermal elastoviscoplastic analysis of planar curved beams

NASA Technical Reports Server (NTRS)

Simitses, G. J.; Carlson, R. L.; Riff, R.

1988-01-01

The development of a general mathematical model and solution methodologies, to examine the behavior of thin structural elements such as beams, rings, and arches, subjected to large nonisothermal elastoviscoplastic deformations is presented. Thus, geometric as well as material type nonlinearities of higher order are present in the analysis. For this purpose a complete true abinito rate theory of kinematics and kinetics for thin bodies, without any restriction on the magnitude of the transformation is presented. A previously formulated elasto-thermo-viscoplastic material constitutive law is employed in the analysis. The methodology is demonstrated through three different straight and curved beams problems.

The melting and solidification of nanowires

NASA Astrophysics Data System (ADS)

Florio, B. J.; Myers, T. G.

2016-06-01

A mathematical model is developed to describe the melting of nanowires. The first section of the paper deals with a standard theoretical situation, where the wire melts due to a fixed boundary temperature. This analysis allows us to compare with existing results for the phase change of nanospheres. The equivalent solidification problem is also examined. This shows that solidification is a faster process than melting; this is because the energy transfer occurs primarily through the solid rather than the liquid which is a poorer conductor of heat. This effect competes with the energy required to create new solid surface which acts to slow down the process, but overall conduction dominates. In the second section, we consider a more physically realistic boundary condition, where the phase change occurs due to a heat flux from surrounding material. This removes the singularity in initial melt velocity predicted in previous models of nanoparticle melting. It is shown that even with the highest possible flux the melting time is significantly slower than with a fixed boundary temperature condition.

Melting temperatures of MgO under high pressure by micro-texture analysis

PubMed Central

Kimura, T.; Ohfuji, H.; Nishi, M.; Irifune, T.

2017-01-01

Periclase (MgO) is the second most abundant mineral after bridgmanite in the Earth's lower mantle, and its melting behaviour under pressure is important to constrain rheological properties and melting behaviours of the lower mantle materials. Significant discrepancies exist between the melting temperatures of MgO determined by laser-heated diamond anvil cell (LHDAC) and those based on dynamic compressions and theoretical predictions. Here we show the melting temperatures in earlier LHDAC experiments are underestimated due to misjudgment of melting, based on micro-texture observations of the quenched samples. The high melting temperatures of MgO suggest that the subducted cold slabs should have higher viscosities than previously thought, suggesting that the inter-connecting textural feature of MgO would not play important roles for the slab stagnation in the lower mantle. The present results also predict that the ultra-deep magmas produced in the lower mantle are peridotitic, which are stabilized near the core–mantle boundary. PMID:28580945

Defining the learning curve in laparoscopic paraesophageal hernia repair: a CUSUM analysis.

PubMed

Okrainec, Allan; Ferri, Lorenzo E; Feldman, Liane S; Fried, Gerald M

2011-04-01

There are numerous reports in the literature documenting high recurrence rates after laparoscopic paraesophageal hernia repair. The purpose of this study was to determine the learning curve for this procedure using the Cumulative Summation (CUSUM) technique. Forty-six consecutive patients with paraesophageal hernia were evaluated prospectively after laparoscopic paraesophageal hernia repair. Upper GI series was performed 3 months postoperatively to look for recurrence. Patients were stratified based on the surgeon's early (first 20 cases) and late experience (>20 cases). The CUSUM method was then used to further analyze the learning curve. Nine patients (21%) had anatomic recurrence. There was a trend toward a higher recurrence rate during the first 20 cases, although this did not achieve statistical significance (33% vs. 13%, p = 0.10). However, using a CUSUM analysis to plot the learning curve, we found that the recurrence rate diminishes after 18 cases and reaches an acceptable rate after 26 cases. Surgeon experience is an important predictor of recurrence after laparoscopic paraesophageal hernia repair. CUSUM analysis revealed there is a significant learning curve to become proficient at this procedure, with approximately 20 cases required before a consistent decrease in hernia recurrence rate is observed.

The Gao-Guenie impact melt breccia—Sampling a rapidly cooled impact melt dike on an H chondrite asteroid?

NASA Astrophysics Data System (ADS)

Schmieder, Martin; Kring, David A.; Swindle, Timothy D.; Bond, Jade C.; Moore, Carleton B.

2016-06-01

The Gao-Guenie H5 chondrite that fell on Burkina Faso (March 1960) has portions that were impact-melted on an H chondrite asteroid at ~300 Ma and, through later impact events in space, sent into an Earth-crossing orbit. This article presents a petrographic and electron microprobe analysis of a representative sample of the Gao-Guenie impact melt breccia consisting of a chondritic clast domain, quenched melt in contact with chondritic clasts, and an igneous-textured impact melt domain. Olivine is predominantly Fo80-82. The clast domain contains low-Ca pyroxene. Impact melt-grown pyroxene is commonly zoned from low-Ca pyroxene in cores to pigeonite and augite in rims. Metal-troilite orbs in the impact melt domain measure up to ~2 mm across. The cores of metal orbs in the impact melt domain contain ~7.9 wt% of Ni and are typically surrounded by taenite and Ni-rich troilite. The metallography of metal-troilite droplets suggest a stage I cooling rate of order 10 °C s-1 for the superheated impact melt. The subsolidus stage II cooling rate for the impact melt breccia could not be determined directly, but was presumably fast. An analogy between the Ni rim gradients in metal of the Gao-Guenie impact melt breccia and the impact-melted H6 chondrite Orvinio suggests similar cooling rates, probably on the order of ~5000-40,000 °C yr-1. A simple model of conductive heat transfer shows that the Gao-Guenie impact melt breccia may have formed in a melt injection dike ~0.5-5 m in width, generated during a sizeable impact event on the H chondrite parent asteroid.

The influence of partial melting and melt migration on the rheology of the continental crust

NASA Astrophysics Data System (ADS)

Cavalcante, Geane Carolina G.; Viegas, Gustavo; Archanjo, Carlos José; da Silva, Marcos Egydio

2016-11-01

analysis also suggests that the middle part of both belts contained large volumes of migmatites, attesting that the orogenic root was partially molten and encompassed more than 30% of granitic melt at the time of deformation.

Deriving injury risk curves using survival analysis from biomechanical experiments.

PubMed

Yoganandan, Narayan; Banerjee, Anjishnu; Hsu, Fang-Chi; Bass, Cameron R; Voo, Liming; Pintar, Frank A; Gayzik, F Scott

2016-10-03

Injury risk curves from biomechanical experimental data analysis are used in automotive studies to improve crashworthiness and advance occupant safety. Metrics such as acceleration and deflection coupled with outcomes such as fractures and anatomical disruptions from impact tests are used in simple binary regression models. As an improvement, the International Standards Organization suggested a different approach. It was based on survival analysis. While probability curves for side-impact-induced thorax and abdominal injuries and frontal impact-induced foot-ankle-leg injuries are developed using this approach, deficiencies are apparent. The objective of this study is to present an improved, robust and generalizable methodology in an attempt to resolve these issues. It includes: (a) statistical identification of the most appropriate independent variable (metric) from a pool of candidate metrics, measured and or derived during experimentation and analysis processes, based on the highest area under the receiver operator curve, (b) quantitative determination of the most optimal probability distribution based on the lowest Akaike information criterion, (c) supplementing the qualitative/visual inspection method for comparing the selected distribution with a non-parametric distribution with objective measures, (d) identification of overly influential observations using different methods, and (e) estimation of confidence intervals using techniques more appropriate to the underlying survival statistical model. These clear and quantified details can be easily implemented with commercial/open source packages. They can be used in retrospective analysis and prospective design of experiments, and in applications to different loading scenarios such as underbody blast events. The feasibility of the methodology is demonstrated using post mortem human subject experiments and 24 metrics associated with thoracic/abdominal injuries in side-impacts. Published by Elsevier Ltd.

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.

Laboratory plant study on the melting process of asbestos waste

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakai, Shinichi; Terazono, Atsushi; Takatsuki, Hiroshi

The melting process was studied as a method of changing asbestos into non-hazardous waste and recovering it as a reusable resource. In an initial effort, the thermal behaviors of asbestos waste in terms of physical and chemical structure have been studied. Then, 10 kg/h-scale laboratory plant experiments were carried out. By X-ray diffraction analysis, the thermal behaviors of sprayed-on asbestos waste revealed that chrysotile asbestos waste change in crystal structure at around 800 C, and becomes melted slag, mainly composed of magnesium silicate, at around 1,500 C. Laboratory plant experiments on the melting process of sprayed-on asbestos have shown thatmore » melted slag can be obtained. X-ray diffraction analysis of the melted slag revealed crystal structure change, and SEM analysis showed the slag to have a non-fibrous form. And more, TEM analysis proved the very high treatment efficiency of the process, that is, reduction of the asbestos content to 1/10{sup 6} as a weight basis. These analytical results indicate the effectiveness of the melting process for asbestos waste treatment.« less

Calculating Galactic Distances Through Supernova Light Curve Analysis (Abstract)

NASA Astrophysics Data System (ADS)

Glanzer, J.

2018-06-01

(Abstract only) The purpose of this project is to experimentally determine the distance to the galaxy M101 by using data that were taken on the type Ia supernova SN 2011fe at the Paul P. Feder Observatory. Type Ia supernovae are useful for determining distances in astronomy because they all have roughly the same luminosity at the peak of their outburst. Comparing the apparent magnitude to the absolute magnitude allows a measurement of the distance. The absolute magnitude is estimated in two ways: using an empirical relationship from the literature between the rate of decline and the absolute magnitude, and using sncosmo, a PYTHON package used for supernova light curve analysis that fits model light curves to the photometric data.

The application of depletion curves for parameterization of subgrid variability of snow

Treesearch

C. H. Luce; D. G. Tarboton

2004-01-01

Parameterization of subgrid-scale variability in snow accumulation and melt is important for improvements in distributed snowmelt modelling. We have taken the approach of using depletion curves that relate fractional snowcovered area to element-average snow water equivalent to parameterize the effect of snowpack heterogeneity within a physically based mass and energy...

Electron-Beam Atomic Spectroscopy for In Situ Measurements of Melt Composition for Refractory Metals: Analysis of Fundamental Physics and Plasma Models

NASA Astrophysics Data System (ADS)

Gasper, Paul Joseph; Apelian, Diran

2015-04-01

Electron-beam (EB) melting is used for the processing of refractory metals, such as Ta, Nb, Mo, and W. These metals have high value and are critical to many industries, including the semiconductor, aerospace, and nuclear industries. EB melting can also purify secondary feedstock, enabling the recovery and recycling of these materials. Currently, there is no method for measuring melt composition in situ during EB melting. Optical emission spectroscopy of the plasma generated by EB impact with vapor above the melt, a technique here termed electron-beam atomic spectroscopy, can be used to measure melt composition in situ, allowing for analysis of melt dynamics, facilitating improvement of EB melting processes and aiding recycling and recovery of these critical and high-value metals. This paper reviews the physics of the plasma generation by EB impact by characterizing the densities and energies of electrons, ions, and neutrals, and describing the interactions between them. Then several plasma models are introduced and their suitability to this application analyzed. Lastly, a potential method for calibration-free composition measurement is described and the challenges for implementation addressed.

Melting temperatures of MgO under high pressure determined by micro-texture observation

NASA Astrophysics Data System (ADS)

Kimura, T.; Ohfuji, H.; Nishi, M.; Irifune, T.

2016-12-01

Periclase (MgO) is the second abundant mineral after bridgmanite in the Earth's lower mantle, and its melting temperature (Tm) under pressure is important to constrain the chemical composition of ultra-deep magma formed near the mantle-core boundary. However, the melting behavior is highly controversial among previous studies: a laser-heated diamond anvil cell (LHDAC) study reported a melting curve with a dTm/dP of 30 K/GPa at zero pressure [1], while several theoretical computations gave substantially higher dTm/dP of 90 100 K/GPa [2,3]. We performed a series of LHDAC experiments for measurements of Tm of MgO under high pressure, using single crystal MgO as the starting material. The melting was detected by using micro-texture observations of the quenched samples. We found that the laser-heated area of the sample quenched from the Tm in previous LHDAC experiments [1] showed randomly aggregated granular crystals, which was not caused by melting, but by plastic deformation of the sample. This suggests that the Tms of their study were substantially underestimated. On the other hand, the sample recovered from the temperature higher by 1500-1700 K than the Tms in previous LHDAC experiments showed a characteristic internal texture comparable to the solidification texture typically shown in metal casting. We determined the Tms based on the observation of this texture up to 32 GPa. Fitting our Tms to the Simon equation yields dTm/dP of 82 K/GPa at zero pressure, which is consistent with those of the theoretical predictions (90 100 K/GPa) [2,3]. Extrapolation of the present melting curve of MgO to the pressure of the CMB (135 GPa) gives a melting temperature of 8900 K. The present steep melting slope offers the eutectic composition close to peridotite (in terms of Mg/Si ratio) throughout the lower mantle conditions. According to the model for sink/float relationship between the solid mantle and the magma [4], a considerable amount of iron (Fe/(Mg+Fe) > 0.24) is expected

Meta-analysis of Diagnostic Accuracy and ROC Curves with Covariate Adjusted Semiparametric Mixtures.

PubMed

Doebler, Philipp; Holling, Heinz

2015-12-01

Many screening tests dichotomize a measurement to classify subjects. Typically a cut-off value is chosen in a way that allows identification of an acceptable number of cases relative to a reference procedure, but does not produce too many false positives at the same time. Thus for the same sample many pairs of sensitivities and false positive rates result as the cut-off is varied. The curve of these points is called the receiver operating characteristic (ROC) curve. One goal of diagnostic meta-analysis is to integrate ROC curves and arrive at a summary ROC (SROC) curve. Holling, Böhning, and Böhning (Psychometrika 77:106-126, 2012a) demonstrated that finite semiparametric mixtures can describe the heterogeneity in a sample of Lehmann ROC curves well; this approach leads to clusters of SROC curves of a particular shape. We extend this work with the help of the [Formula: see text] transformation, a flexible family of transformations for proportions. A collection of SROC curves is constructed that approximately contains the Lehmann family but in addition allows the modeling of shapes beyond the Lehmann ROC curves. We introduce two rationales for determining the shape from the data. Using the fact that each curve corresponds to a natural univariate measure of diagnostic accuracy, we show how covariate adjusted mixtures lead to a meta-regression on SROC curves. Three worked examples illustrate the method.

Light Curve and Analysis of the Eclipsing Binary BF Centauri

NASA Astrophysics Data System (ADS)

Morris, M. A.; Wolf, G. W.

2003-12-01

The eclipsing binary star BF Centauri was observed photometrically by GWW in the uvby filter system from Mt. John Observatory in New Zealand during 1982, 1989 and 1998. It was also observed spectroscopically at 10 A/mm by W. A. Lawson in 1993 at Mt. Stromlo in Australia to obtain a radial velocity solution. The combined light curves and spectroscopic results have been analyzed using the 1998 version of Robert Wilson's WD light-curve programs. A consistent model for the system will be presented. This analysis was done as a part of a senior research project by MAM, who would like to acknowledge financial support from the Missouri Space Grant Consortium.

Partial Melting of the Indarch (EH4) Meteorite : A Textural, Chemical and Phase Relations View of Melting and Melt Migration

NASA Technical Reports Server (NTRS)

McCoy, Timothy J.; Dickinson, Tamara L.; Lofgren, Gary E.

2000-01-01

To Test whether Aubrites can be formed by melting of enstatite Chondrites and to understand igneous processes at very low oxygen fugacities, we have conducted partial melting experiments on the Indarch (EH4) chondrite at 1000-1500 C. Silicate melting begins at 1000 C. Substantial melt migration occurs at 1300-1400 C and metal migrates out of the silicate change at 1450 C and approx. 50% silicate partial melting. As a group, our experiments contain three immiscible metallic melts 9Si-, and C-rich), two immiscible sulfide melts(Fe-and FeMgMnCa-rich) and Silicate melt. Our partial melting experiments on the Indarch (EH4) enstatite Chondrite suggest that igneous processes at low fO2 exhibit serveral unique features. The complete melting of sulfides at 1000 C suggest that aubritic sulfides are not relicts. Aubritic oldhamite may have crystallized from Ca and S complexed in the silicate melt. Significant metal-sulfide melt migration might occur at relatively low degrees of silicate partial melting. Substantial elemental exchange occurred between different melts (e.g., between sulfide and silicate, Si between silicate and metal), a feature not observed during experiments at higher fO2. This exchange may help explain the formation of aubrites from known enstatite chondrites.

Eutectic melting temperature of the lowermost Earth's mantle

NASA Astrophysics Data System (ADS)

Andrault, D.; Lo Nigro, G.; Bolfan-Casanova, N.; Bouhifd, M.; Garbarino, G.; Mezouar, M.

2009-12-01

Partial melting of the Earth's deep mantle probably occurred at different stages of its formation as a consequence of meteoritic impacts and seismology suggests that it even continues today at the core-mantle boundary. Melts are important because they dominate the chemical evolution of the different Earth's reservoirs and more generally the dynamics of the whole planet. Unfortunately, the most critical parameter, that is the temperature profile inside the deep Earth, remains poorly constrained accross the planet history. Experimental investigations of the melting properties of materials representative of the deep Earth at relevant P-T conditions can provide anchor points to refine past and present temperature profiles and consequently determine the degree of melting at the different geological periods. Previous works report melting relations in the uppermost lower mantle region, using the multi-anvil press [1,2]. On the other hand, the pyrolite solidus was determined up to 65 GPa using optical observations in the laser-heated diamond anvil cell (LH-DAC) [3]. Finally, the melting temperature of (Mg,Fe)2SiO4 olivine is documented at core-mantle boundary (CMB) conditions by shock wave experiments [4]. Solely based on these reports, experimental data remain too sparse to draw a definite melting curve for the lower mantle in the relevant 25-135 GPa pressure range. We reinvestigated melting properties of lower mantle materials by means of in-situ angle dispersive X-ray diffraction measurements in the LH-DAC at the ESRF [5]. Experiments were performed in an extended P-T range for two starting materials: forsterite and a glass with chondrite composition. In both cases, the aim was to determine the onset of melting, and thus the eutectic melting temperatures as a function of pressure. Melting was evidenced from drastic changes of diffraction peak shape on the image plate, major changes in diffraction intensities in the integrated pattern, disappearance of diffraction rings

Method of Estimating Continuous Cooling Transformation Curves of Glasses

NASA Technical Reports Server (NTRS)

Zhu, Dongmei; Zhou, Wancheng; Ray, Chandra S.; Day, Delbert E.

2006-01-01

A method is proposed for estimating the critical cooling rate and continuous cooling transformation (CCT) curve from isothermal TTT data of glasses. The critical cooling rates and CCT curves for a group of lithium disilicate glasses containing different amounts of Pt as nucleating agent estimated through this method are compared with the experimentally measured values. By analysis of the experimental and calculated data of the lithium disilicate glasses, a simple relationship between the crystallized amount in the glasses during continuous cooling, X, and the temperature of undercooling, (Delta)T, was found to be X = AR(sup-4)exp(B (Delta)T), where (Delta)T is the temperature difference between the theoretical melting point of the glass composition and the temperature in discussion, R is the cooling rate, and A and B are constants. The relation between the amount of crystallisation during continuous cooling and isothermal hold can be expressed as (X(sub cT)/X(sub iT) = (4/B)(sup 4) (Delta)T(sup -4), where X(sub cT) stands for the crystallised amount in a glass during continuous cooling for a time t when the temperature comes to T, and X(sub iT) is the crystallised amount during isothermal hold at temperature T for a time t.

Stagnation-Point Shielding by Melting and Vaporization

NASA Technical Reports Server (NTRS)

Roberts, Leonard

1959-01-01

An approximate theoretical analysis was made of the shielding mechanism whereby the rate of heat transfer to the forward stagnation point of blunt bodies is reduced by melting and evaporation. General qualitative results are given and a numerical example, the melting and evaporation of ice, is presented and discussed in detail.

Study of the role of tumor necrosis factor-α (-308 G/A) and interleukin-10 (-1082 G/A) polymorphisms as potential risk factors to acute kidney injury in patients with severe sepsis using high-resolution melting curve analysis.

PubMed

Hashad, Doaa I; Elsayed, Eman T; Helmy, Tamer A; Elawady, Samier M

2017-11-01

Septic acute kidney injury (AKI) is a prevalent complication in intensive care units with an increased incidence of complications. The aim of the present study was to assess the use of high-resolution melting curve (HRM) analysis in investigating whether the genetic polymorphisms; -308 G/A of tumor necrosis factor-α (TNF-α), and -1082 G /A of Interleukin-10 (IL-10) genes may predispose patients diagnosed with severe sepsis to the development of AKI. One hundred and fifty patients with severe sepsis participated in the present study; only sixty-six developed AKI. Both polymorphisms were studied using HRM analysis. The low producer genotype of both studied polymorphism of TNF-α and IL-10 genes was associated with AKI. Using logistic regression analysis, the low producer genotypes remained an independent risk factor for AKI. A statistically significant difference was detected between both studied groups as regards the low producer genotype in both TNF-α (-308 G/A) and interleukin-10 (IL-10) (-1082 G/A) polymorphisms being prevalent in patients developing AKI. Principle conclusions: The low producer genotypes of both TNF-α (-308 G/A) and IL-10 (-1082 G/A) polymorphisms could be considered a risk factor for the development of AKI in critically ill patients with severe sepsis, thus management technique implemented for this category should be modulated rescuing this sector of patients from the grave deterioration to acute kidney injury. Using HRM for genotyping proved to be a highly efficient, simple, cost-effective genotyping technique that is most appropriate for the routine study of large-scale samples.

WHO Melting-Point Reference Substances

PubMed Central

Bervenmark, H.; Diding, N. Å.; Öhrner, B.

1963-01-01

Batches of 13 highly purified chemicals, intended for use as reference substances in the calibration of apparatus for melting-point determinations, have been subjected to a collaborative assay by 15 laboratories in 13 countries. All the laboratories performed melting-point determinations by the capillary methods described in the proposed text for the second edition of the Pharmacopoea Internationalis and some, in addition, carried out determinations by the microscope hot stage (Kofler) method, using both the “going-through” and the “equilibrium” technique. Statistical analysis of the data obtained by the capillary method showed that the within-laboratory variation was small and that the between-laboratory variation, though constituting the greatest part of the whole variance, was not such as to warrant the exclusion of any laboratory from the evaluation of the results. The average values of the melting-points obtained by the laboratories can therefore be used as constants for the substances in question, which have accordingly been established as WHO Melting-Point Reference Substances and included in the WHO collection of authentic chemical substances. As to the microscope hot stage method, analysis of the results indicated that the values obtained by the “going-through” technique did not differ significantly from those obtained by the capillary method, but the values obtained by the “equilibrium” technique were mostly significantly lower. PMID:20604137

Thermoluminescence glow curve analysis and CGCD method for erbium doped CaZrO{sub 3} phosphor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tiwari, Ratnesh, E-mail: 31rati@gmail.com; Chopra, Seema

2016-05-06

The manuscript report the synthesis, thermoluminescence study at fixed concentration of Er{sup 3+} (1 mol%) doped CaZrO{sub 3} 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.

Rapidly solidified titanium alloys by melt overflow

NASA Technical Reports Server (NTRS)

Gaspar, Thomas A.; Bruce, Thomas J., Jr.; Hackman, Lloyd E.; Brasmer, Susan E.; Dantzig, Jonathan A.; Baeslack, William A., III

1989-01-01

A pilot plant scale furnace was designed and constructed for casting titanium alloy strips. The furnace combines plasma arc skull melting techniques with melt overflow rapid solidification technology. A mathematical model of the melting and casting process was developed. The furnace cast strip of a suitable length and width for use with honeycomb structures. Titanium alloys Ti-6Al-4V and Ti-14Al-21 Nb were successfully cast into strips. The strips were evaluated by optical metallography, microhardness measurements, chemical analysis, and cold rolling.

Melt Heterogeneity and Degassing at MT Etna from Melt Inclusions

NASA Astrophysics Data System (ADS)

Salem, L. C.; Edmonds, M.; Maclennan, J.; Corsaro, R. A.

2014-12-01

The melts feeding Mt Etna, Italy, are rich in volatiles and drive long-lasting powerful eruptions of basaltic magma in both effusive and explosive styles of activity. The volatile systematics of the volcanic system are well understood through melt inclusion and volcanic gas studies. Etna's melts are generated from a complex mantle setting, with subduction-related chemical modifications as well as OIB-type features, and then the melts must travel through thick carbonate-rich crust. The continual influx of mantle-derived volatile-rich magma controls the major compositional and eruptive features of Mount Etna and magma mixing has been recognized as an important process driving large eruptions [Kamenetsky, 2007]. Our study focusses on the 1669 eruption, the largest in historical times. Olivine-hosted melt inclusions were analyzed for volatile, trace and major elements using electron microprobe and ion probe (SIMS). We use volatile systematics and geochemical data to deconvolve mantle-derived heterogeneity from melt mixing and crystal fractionation. Our data are well described by a mixing trend between two distinct melts: a CO2-rich (CO2~1000ppm), incompatible trace element depleted melt (La/Yb~16), and a CO2-poor, enriched melt. The mixing also generates a strong correlation between Sr and CO2 in the melt inclusions dataset, reflecting the presence of a strong Sr anomaly in one of the end-member melts. We investigate the origin of this Sr anomaly by considering plagioclase dissolution and crustal assimilation. We also investigate degassing processes in the crust and plumbing system of the volcano. We compare our results with similar studies of OIB and arc-related basalts elsewhere and assess the implications for linking eruption size and style with the nature of the mantle-derived melts. Kamenetsky et al. (2007) Geology 35, 255-258.

High-resolution melting analysis for detection of MYH9 mutations.

PubMed

Provaznikova, Dana; Kumstyrova, Tereza; Kotlin, Roman; Salaj, Peter; Matoska, Vaclav; Hrachovinova, Ingrid; Rittich, Simon

2008-09-01

May-Hegglin anomaly (MHA), Sebastian (SBS), Fechtner (FTNS) and Epstein (EPS) syndromes are rare autosomal dominant disorders with giant platelets and thrombocytopenia. Other manifestations of these disorders are combinations of the presence of granulocyte inclusions and deafness, cataracts and renal failure. Currently, MHA, SBS, FTNS and EPS are considered to be distinct clinical manifestation of a single illness caused by mutations of the MYH9 gene encoding the heavy chain of non-muscle myosin IIA (NMMHC-IIA). As the MYH9 gene has a high number of exons, it takes much time and material to use this method for the detection of MYH9 mutations. Recently, a new method has been introduced for scanning DNA mutations without the need for direct sequencing: high-resolution melting analysis (HRMA). Mutation detection with HRMA relies on the intercalation of the specific dye (LC Green plus) in double-strand DNA and fluorescence monitoring of PCR product melting profiles. In our study, we optimized the conditions and used HRMA for rapid screening of mutations in all MYH9 exons in seven affected individuals from four unrelated families with suspected MYH9 disorders. Samples identified by HRMA as positive for the mutation were analysed by direct sequencing. HRMA saved us over 85% of redundant sequencing.

Layering, melting, and recrystallization of a close-packed micellar crystal under steady and large-amplitude oscillatory shear flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

López-Barrón, Carlos R., E-mail: carlos.r.lopez-barron@exxonmobil.com; Wagner, Norman J.; Porcar, Lionel

2015-05-15

The rheology and three-dimensional microstructure of a concentrated viscoelastic solution of the triblock copolymer poly(ethylene oxide){sub 106}-poly(propylene oxide){sub 68}-poly(ethylene oxide){sub 106} (Pluronic F127) in the protic ionic liquid ethylammonium nitrate are measured by small angle neutron scattering (SANS) under flow in three orthogonal planes. This solution's shear-thinning viscosity is due to the formation of two-dimensional hexagonal close-packed (HCP) sliding layer structure. Shear-melting of the crystalline structure is observed without disruption of the self-assembled micelles, resulting in a change in flow properties. Spatially resolved measurements in the 1–2 plane reveal that both shear-melting and sliding are not uniform across the Couettemore » gap. Melting and recrystallization of the HCP layers occur cyclically during a single large amplitude oscillatory shear (LAOS) cycle, in agreement with the “stick-slip” flow mechanism proposed by Hamley et al. [Phys. Rev. E 58, 7620–7628 (1998)]. Analysis of 3D “structural” Lissajous curves show that the cyclic melting and sliding are direct functions of the strain rate amplitude and show perfect correlation with the cyclic stress response during LAOS. Both viscosity and structural order obey the Delaware–Rutgers rule. Combining rheology with in situ spatiotemporally resolved SANS is demonstrated to elucidate the structural origins of the nonlinear rheology of complex fluids.« less

Application of hot melt extrusion for improving bioavailability of artemisinin a thermolabile drug.

PubMed

Kulkarni, C; Kelly, A L; Gough, T; Jadhav, V; Singh, K K; Paradkar, A

2018-02-01

Hot melt extrusion has been used to produce a solid dispersion of the thermolabile drug artemisinin. Formulation and process conditions were optimized prior to evaluation of dissolution and biopharmaceutical performance. Soluplus ® , a low T g amphiphilic polymer especially designed for solid dispersions enabled melt extrusion at 110 °C although some drug-polymer incompatibility was observed. Addition of 5% citric acid as a pH modifier was found to suppress the degradation. The area under plasma concentration time curve (AUC 0-24h ) and peak plasma concentration (C max ) were four times higher for the modified solid dispersion compared to that of pure artemisinin.

A benchmark initiative on mantle convection with melting and melt segregation

NASA Astrophysics Data System (ADS)

Schmeling, Harro; Dannberg, Juliane; Dohmen, Janik; Kalousova, Klara; Maurice, Maxim; Noack, Lena; Plesa, Ana; Soucek, Ondrej; Spiegelman, Marc; Thieulot, Cedric; Tosi, Nicola; Wallner, Herbert

2016-04-01

In recent years a number of mantle convection models have been developed which include partial melting within the asthenosphere, estimation of melt volumes, as well as melt extraction with and without redistribution at the surface or within the lithosphere. All these approaches use various simplifying modelling assumptions whose effects on the dynamics of convection including the feedback on melting have not been explored in sufficient detail. To better assess the significance of such assumptions and to provide test cases for the modelling community we carry out a benchmark comparison. The reference model is taken from the mantle convection benchmark, cases 1a to 1c (Blankenbach et al., 1989), assuming a square box with free slip boundary conditions, the Boussinesq approximation, constant viscosity and Rayleigh numbers of 104 to 10^6. Melting is modelled using a simplified binary solid solution with linearly depth dependent solidus and liquidus temperatures, as well as a solidus temperature depending linearly on depletion. Starting from a plume free initial temperature condition (to avoid melting at the onset time) five cases are investigated: Case 1 includes melting, but without thermal or dynamic feedback on the convection flow. This case provides a total melt generation rate (qm) in a steady state. Case 2 is identical to case 1 except that latent heat is switched on. Case 3 includes batch melting, melt buoyancy (melt Rayleigh number Rm) and depletion buoyancy, but no melt percolation. Output quantities are the Nusselt number (Nu), root mean square velocity (vrms), the maximum and the total melt volume and qm approaching a statistical steady state. Case 4 includes two-phase flow, i.e. melt percolation, assuming a constant shear and bulk viscosity of the matrix and various melt retention numbers (Rt). These cases are carried out using the Compaction Boussinseq Approximation (Schmeling, 2000) or the full compaction formulation. For cases 1 - 3 very good agreement

Tin in granitic melts: The role of melting temperature and protolith composition

NASA Astrophysics Data System (ADS)

Wolf, Mathias; Romer, Rolf L.; Franz, Leander; López-Moro, Francisco Javier

2018-06-01

Granite bound tin mineralization typically is seen as the result of extreme magmatic fractionation and late exsolution of magmatic fluids. Mineralization, however, also could be obtained at considerably less fractionation if initial melts already had enhanced Sn contents. We present chemical data and results from phase diagram modeling that illustrate the dominant roles of protolith composition, melting conditions, and melt extraction/evolution for the distribution of Sn between melt and restite and, thus, the Sn content of melts. We compare the element partitioning between leucosome and restite of low-temperature and high-temperature migmatites. During low-temperature melting, trace elements partition preferentially into the restite with the possible exception of Sr, Cd, Bi, and Pb, that may be enriched in the melt. In high-temperature melts, Ga, Y, Cd, Sn, REE, Pb, Bi, and U partition preferentially into the melt whereas Sc, V, Cr, Co, Ni, Mo, and Ba stay in the restite. This contrasting behavior is attributed to the stability of trace element sequestering minerals during melt generation. In particular muscovite, biotite, titanite, and rutile act as host phases for Sn and, therefore prevent Sn enrichment in the melt as long as they are stable phases in the restite. As protolith composition controls both the mineral assemblage and modal contents of the various minerals, protolith composition eventually also controls the fertility of a rock during anatexis, restite mineralogy, and partitioning behavior of trace metals. If a particular trace element is sequestered in a phase that is stable during partial melting, the resulting melt is depleted in this element whereas the restite becomes enriched. Melt generation at high temperature may release Sn when Sn-hosts become unstable. If melt has not been lost before the breakdown of Sn-hosts, Sn contents in the melt will increase but never will be high. In contrast, if melt has been lost before the decomposition of Sn

Selective Laser Melting of Pure Copper

NASA Astrophysics Data System (ADS)

Ikeshoji, Toshi-Taka; Nakamura, Kazuya; Yonehara, Makiko; Imai, Ken; Kyogoku, Hideki

2017-12-01

Appropriate building parameters for selective laser melting of 99.9% pure copper powder were investigated at relatively high laser power of 800 W for hatch pitch in the range from 0.025 mm to 0.12 mm. The highest relative density of the built material was 99.6%, obtained at hatch pitch of 0.10 mm. Building conditions were also studied using transient heat analysis in finite element modeling of the liquidation and solidification of the powder layer. The estimated melt pool length and width were comparable to values obtained by observations using a thermoviewer. The trend for the melt pool width versus the hatch pitch agreed with experimental values.

Selective Laser Melting of Pure Copper

NASA Astrophysics Data System (ADS)

Ikeshoji, Toshi-Taka; Nakamura, Kazuya; Yonehara, Makiko; Imai, Ken; Kyogoku, Hideki

2018-03-01

Appropriate building parameters for selective laser melting of 99.9% pure copper powder were investigated at relatively high laser power of 800 W for hatch pitch in the range from 0.025 mm to 0.12 mm. The highest relative density of the built material was 99.6%, obtained at hatch pitch of 0.10 mm. Building conditions were also studied using transient heat analysis in finite element modeling of the liquidation and solidification of the powder layer. The estimated melt pool length and width were comparable to values obtained by observations using a thermoviewer. The trend for the melt pool width versus the hatch pitch agreed with experimental values.

Melting and Crystallization at Core Mantle Boundary

NASA Astrophysics Data System (ADS)

Fiquet, G.; Pradhan, G. K.; Siebert, J.; Auzende, A. L.; Morard, G.; Antonangeli, D.; Garbarino, G.

2015-12-01

Early crystallization of magma oceans may generate original compositional heterogeneities in the mantle. Dense basal melts may also be trapped in the lowermost mantle and explain mantle regions with ultralow seismic velocities (ULVZs) near the core-mantle boundary [1]. To test this hypothesis, we first constructed the solidus curve of a natural peridotite between 36 and 140 gigapascals using laser-heated diamond anvil cells. In our experiments, melting at core-mantle boundary pressures occurs around 4100 ± 150 K, which is a value that can match estimated mantle geotherms. Similar results were found for a chondritic mantle [2] whereas much lower pyrolitic melting temperatures were recently proposed from textural and chemical characterizations of quenched samples [3]. We also investigated the melting properties of natural mid ocean ridge basalt (MORB) up to core-mantle boundary (CMB) pressures. At CMB pressure (135 GPa), we obtain a MORB solidus temperature of 3950 ±150 K. If our solidus temperatures are in good agreement with recent results proposed for a similar composition [4], the textural and chemical characterizations of our recovered samples made by analytical transmission electron microscope indicate that CaSiO3 perovskite (CaPv) is the liquidus phase in the entire pressure range up to CMB. The partial melt composition is enriched in FeO, which suggests that such partial melts could be gravitationnally stable at the core mantle boundary. Our observations are tested against calculations made using a self-consistent thermodynamic database for the MgO-FeO-SiO2 system from 20 GPa to 140 GPa [5]. These observations and calculations provide a first step towards a consistent thermodynamic modelling of the crystallization sequence of the magma ocean, which shows that the existence of a dense iron rich and fusible layer above the CMB at the end of the crystallization is plausible [5], which is in contradiction with the conclusions drawn in [4]. [1] Williams

Isogeometric analysis of free-form Timoshenko curved beams including the nonlinear effects of large deformations

NASA Astrophysics Data System (ADS)

Hosseini, Seyed Farhad; Hashemian, Ali; Moetakef-Imani, Behnam; Hadidimoud, Saied

2018-03-01

In the present paper, the isogeometric analysis (IGA) of free-form planar curved beams is formulated based on the nonlinear Timoshenko beam theory to investigate the large deformation of beams with variable curvature. Based on the isoparametric concept, the shape functions of the field variables (displacement and rotation) in a finite element analysis are considered to be the same as the non-uniform rational basis spline (NURBS) basis functions defining the geometry. The validity of the presented formulation is tested in five case studies covering a wide range of engineering curved structures including from straight and constant curvature to variable curvature beams. The nonlinear deformation results obtained by the presented method are compared to well-established benchmark examples and also compared to the results of linear and nonlinear finite element analyses. As the nonlinear load-deflection behavior of Timoshenko beams is the main topic of this article, the results strongly show the applicability of the IGA method to the large deformation analysis of free-form curved beams. Finally, it is interesting to notice that, until very recently, the large deformations analysis of free-form Timoshenko curved beams has not been considered in IGA by researchers.

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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

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

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Melt containment member

DOEpatents

Rieken, Joel R.; Heidloff, Andrew J.

2014-09-09

A tubular melt containment member for transient containment of molten metals and alloys, especially reactive metals and alloys, includes a melt-contacting layer or region that comprises an oxygen-deficient rare earth oxide material that is less reactive as compared to the counterpart stoichiometric rare earth oxide. The oxygen-deficient (sub-stoichiometric) rare earth oxide can comprise oxygen-deficient yttria represented by Y.sub.2O.sub.3-x wherein x is from 0.01 to 0.1. Use of the oxygen-deficient rare earth oxide as the melt-contacting layer or region material reduces reaction with the melt for a given melt temperature and melt contact time.

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.

Methods for Melting Temperature Calculation

NASA Astrophysics Data System (ADS)

Hong, Qi-Jun

Melting temperature calculation has important applications in the theoretical study of phase diagrams and computational materials screenings. In this thesis, we present two new methods, i.e., the improved Widom's particle insertion method and the small-cell coexistence method, which we developed in order to capture melting temperatures both accurately and quickly. We propose a scheme that drastically improves the efficiency of Widom's particle insertion method by efficiently sampling cavities while calculating the integrals providing the chemical potentials of a physical system. This idea enables us to calculate chemical potentials of liquids directly from first-principles without the help of any reference system, which is necessary in the commonly used thermodynamic integration method. As an example, we apply our scheme, combined with the density functional formalism, to the calculation of the chemical potential of liquid copper. The calculated chemical potential is further used to locate the melting temperature. The calculated results closely agree with experiments. We propose the small-cell coexistence method based on the statistical analysis of small-size coexistence MD simulations. It eliminates the risk of a metastable superheated solid in the fast-heating method, while also significantly reducing the computer cost relative to the traditional large-scale coexistence method. Using empirical potentials, we validate the method and systematically study the finite-size effect on the calculated melting points. The method converges to the exact result in the limit of a large system size. An accuracy within 100 K in melting temperature is usually achieved when the simulation contains more than 100 atoms. DFT examples of Tantalum, high-pressure Sodium, and ionic material NaCl are shown to demonstrate the accuracy and flexibility of the method in its practical applications. The method serves as a promising approach for large-scale automated material screening in which

Analytical Problems and Suggestions in the Analysis of Behavioral Economic Demand Curves.

PubMed

Yu, Jihnhee; Liu, Liu; Collins, R Lorraine; Vincent, Paula C; Epstein, Leonard H

2014-01-01

Behavioral economic demand curves (Hursh, Raslear, Shurtleff, Bauman, & Simmons, 1988) are innovative approaches to characterize the relationships between consumption of a substance and its price. In this article, we investigate common analytical issues in the use of behavioral economic demand curves, which can cause inconsistent interpretations of demand curves, and then we provide methodological suggestions to address those analytical issues. We first demonstrate that log transformation with different added values for handling zeros changes model parameter estimates dramatically. Second, demand curves are often analyzed using an overparameterized model that results in an inefficient use of the available data and a lack of assessment of the variability among individuals. To address these issues, we apply a nonlinear mixed effects model based on multivariate error structures that has not been used previously to analyze behavioral economic demand curves in the literature. We also propose analytical formulas for the relevant standard errors of derived values such as P max, O max, and elasticity. The proposed model stabilizes the derived values regardless of using different added increments and provides substantially smaller standard errors. We illustrate the data analysis procedure using data from a relative reinforcement efficacy study of simulated marijuana purchasing.

Shape information from glucose curves: Functional data analysis compared with traditional summary measures

PubMed Central

2013-01-01

Background Plasma glucose levels are important measures in medical care and research, and are often obtained from oral glucose tolerance tests (OGTT) with repeated measurements over 2–3 hours. It is common practice to use simple summary measures of OGTT curves. However, different OGTT curves can yield similar summary measures, and information of physiological or clinical interest may be lost. Our mean aim was to extract information inherent in the shape of OGTT glucose curves, compare it with the information from simple summary measures, and explore the clinical usefulness of such information. Methods OGTTs with five glucose measurements over two hours were recorded for 974 healthy pregnant women in their first trimester. For each woman, the five measurements were transformed into smooth OGTT glucose curves by functional data analysis (FDA), a collection of statistical methods developed specifically to analyse curve data. The essential modes of temporal variation between OGTT glucose curves were extracted by functional principal component analysis. The resultant functional principal component (FPC) scores were compared with commonly used simple summary measures: fasting and two-hour (2-h) values, area under the curve (AUC) and simple shape index (2-h minus 90-min values, or 90-min minus 60-min values). Clinical usefulness of FDA was explored by regression analyses of glucose tolerance later in pregnancy. Results Over 99% of the variation between individually fitted curves was expressed in the first three FPCs, interpreted physiologically as “general level” (FPC1), “time to peak” (FPC2) and “oscillations” (FPC3). FPC1 scores correlated strongly with AUC (r=0.999), but less with the other simple summary measures (−0.42≤r≤0.79). FPC2 scores gave shape information not captured by simple summary measures (−0.12≤r≤0.40). FPC2 scores, but not FPC1 nor the simple summary measures, discriminated between women who did and did not develop

Shape information from glucose curves: functional data analysis compared with traditional summary measures.

PubMed

Frøslie, Kathrine Frey; Røislien, Jo; Qvigstad, Elisabeth; Godang, Kristin; Bollerslev, Jens; Voldner, Nanna; Henriksen, Tore; Veierød, Marit B

2013-01-17

Plasma glucose levels are important measures in medical care and research, and are often obtained from oral glucose tolerance tests (OGTT) with repeated measurements over 2-3  hours. It is common practice to use simple summary measures of OGTT curves. However, different OGTT curves can yield similar summary measures, and information of physiological or clinical interest may be lost. Our mean aim was to extract information inherent in the shape of OGTT glucose curves, compare it with the information from simple summary measures, and explore the clinical usefulness of such information. OGTTs with five glucose measurements over two hours were recorded for 974 healthy pregnant women in their first trimester. For each woman, the five measurements were transformed into smooth OGTT glucose curves by functional data analysis (FDA), a collection of statistical methods developed specifically to analyse curve data. The essential modes of temporal variation between OGTT glucose curves were extracted by functional principal component analysis. The resultant functional principal component (FPC) scores were compared with commonly used simple summary measures: fasting and two-hour (2-h) values, area under the curve (AUC) and simple shape index (2-h minus 90-min values, or 90-min minus 60-min values). Clinical usefulness of FDA was explored by regression analyses of glucose tolerance later in pregnancy. Over 99% of the variation between individually fitted curves was expressed in the first three FPCs, interpreted physiologically as "general level" (FPC1), "time to peak" (FPC2) and "oscillations" (FPC3). FPC1 scores correlated strongly with AUC (r=0.999), but less with the other simple summary measures (-0.42≤r≤0.79). FPC2 scores gave shape information not captured by simple summary measures (-0.12≤r≤0.40). FPC2 scores, but not FPC1 nor the simple summary measures, discriminated between women who did and did not develop gestational diabetes later in pregnancy. FDA of OGTT

Characterizing Decision-Analysis Performances of Risk Prediction Models Using ADAPT Curves.

PubMed

Lee, Wen-Chung; Wu, Yun-Chun

2016-01-01

The area under the receiver operating characteristic curve is a widely used index to characterize the performance of diagnostic tests and prediction models. However, the index does not explicitly acknowledge the utilities of risk predictions. Moreover, for most clinical settings, what counts is whether a prediction model can guide therapeutic decisions in a way that improves patient outcomes, rather than to simply update probabilities.Based on decision theory, the authors propose an alternative index, the "average deviation about the probability threshold" (ADAPT).An ADAPT curve (a plot of ADAPT value against the probability threshold) neatly characterizes the decision-analysis performances of a risk prediction model.Several prediction models can be compared for their ADAPT values at a chosen probability threshold, for a range of plausible threshold values, or for the whole ADAPT curves. This should greatly facilitate the selection of diagnostic tests and prediction models.

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

PubMed

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

2014-09-01

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

A benchmark initiative on mantle convection with melting and melt segregation

NASA Astrophysics Data System (ADS)

Schmeling, Harro; Dohmen, Janik; Wallner, Herbert; Noack, Lena; Tosi, Nicola; Plesa, Ana-Catalina; Maurice, Maxime

2015-04-01

In recent years a number of mantle convection models have been developed which include partial melting within the asthenosphere, estimation of melt volumes, as well as melt extraction with and without redistribution at the surface or within the lithosphere. All these approaches use various simplifying modelling assumptions whose effects on the dynamics of convection including the feedback on melting have not been explored in sufficient detail. To better assess the significance of such assumptions and to provide test cases for the modelling community we initiate a benchmark comparison. In the initial phase of this endeavor we focus on the usefulness of the definitions of the test cases keeping the physics as sound as possible. The reference model is taken from the mantle convection benchmark, case 1b (Blanckenbach et al., 1989), assuming a square box with free slip boundary conditions, the Boussinesq approximation, constant viscosity and a Rayleigh number of 1e5. Melting is modelled assuming a simplified binary solid solution with linearly depth dependent solidus and liquidus temperatures, as well as a solidus temperature depending linearly on depletion. Starting from a plume free initial temperature condition (to avoid melting at the onset time) three cases are investigated: Case 1 includes melting, but without thermal or dynamic feedback on the convection flow. This case provides a total melt generation rate (qm) in a steady state. Case 2 includes batch melting, melt buoyancy (melt Rayleigh number Rm), depletion buoyancy and latent heat, but no melt percolation. Output quantities are the Nusselt number (Nu), root mean square velocity (vrms) and qm approaching a statistical steady state. Case 3 includes two-phase flow, i.e. melt percolation, assuming a constant shear and bulk viscosity of the matrix and various melt retention numbers (Rt). These cases should be carried out using the Compaction Boussinseq Approximation (Schmeling, 2000) or the full compaction

Challenges in Melt Furnace Tests

NASA Astrophysics Data System (ADS)

Belt, Cynthia

2014-09-01

Measurement is a critical part of running a cast house. Key performance indicators such as energy intensity, production (or melt rate), downtime (or OEE), and melt loss must all be understood and monitored on a weekly or monthly basis. Continuous process variables such as bath temperature, flue temperature, and furnace pressure should be used to control the furnace systems along with storing the values in databases for later analysis. While using measurement to track furnace performance over time is important, there is also a time and place for short-term tests.

Melting along the Hugoniot and solid phase transition for Sn via sound velocity measurements

NASA Astrophysics Data System (ADS)

Song, Ping; Cai, Ling-cang; Tao, Tian-jiong; Yuan, Shuai; Chen, Hong; Huang, Jin; Zhao, Xin-wen; Wang, Xue-jun

2016-11-01

It is very important to determine the phase boundaries for materials with complex crystalline phase structures to construct their corresponding multi-phase equation of state. By measuring the sound velocity of Sn with different porosities, different shock-induced melting pressures along the solid-liquid phase boundary could be obtained. The incipient shock-induced melting of porous Sn samples with two different porosities occurred at a pressure of about 49.1 GPa for a porosity of 1.01 and 45.6 GPa for a porosity of 1.02, based on measurements of the sound velocity. The incipient shock-induced melting pressure of solid Sn was revised to 58.1 GPa using supplemental measurements of the sound velocity. Trivially, pores in Sn decreased the shock-induced melting pressure. Based on the measured longitudinal sound velocity data, a refined solid phase transition and the Hugoniot temperature-pressure curve's trend are discussed. No bcc phase transition occurs along the Hugoniot for porous Sn; further investigation is required to understand the implications of this finding.

New Equations for the Sublimation Pressure and Melting Pressure of H2O Ice Ih

NASA Astrophysics Data System (ADS)

Wagner, Wolfgang; Riethmann, Thomas; Feistel, Rainer; Harvey, Allan H.

2011-12-01

New reference equations, adopted by the International Association for the Properties of Water and Steam (IAPWS), are presented for the sublimation pressure and melting pressure of ice Ih as a function of temperature. These equations are based on input values derived from the phase-equilibrium condition between the IAPWS-95 scientific standard for thermodynamic properties of fluid H2O and the equation of state of H2O ice Ih adopted by IAPWS in 2006, making them thermodynamically consistent with the bulk-phase properties. Compared to the previous IAPWS formulations, which were empirical fits to experimental data, the new equations have significantly less uncertainty. The sublimation-pressure equation covers the temperature range from 50 K to the vapor-liquid-solid triple point at 273.16 K. The ice Ih melting-pressure equation describes the entire melting curve from 273.16 K to the ice Ih-ice III-liquid triple point at 251.165 K. For completeness, we also give the IAPWS melting-pressure equation for ice III, which is slightly adjusted to agree with the ice Ih melting-pressure equation at the corresponding triple point, and the unchanged IAPWS melting-pressure equations for ice V, ice VI, and ice VII.

Constraints on melt content of off-axis magma lenses at the East Pacific Rise from analysis of 3-D seismic amplitude variation with angle of incidence

NASA Astrophysics Data System (ADS)

Aghaei, Omid; Nedimović, Mladen R.; Marjanović, Milena; Carbotte, Suzanne M.; Pablo Canales, J.; Carton, Hélène; Nikić, Nikola

2017-06-01

We use 3-D multichannel seismic data to form partial angle P wave stacks and apply amplitude variation with angle (AVA) crossplotting to assess melt content and melt distribution within two large midcrustal off-axis magma lenses (OAMLs) found along the East Pacific Rise from 9°37.5'N to 9°57'N. The signal envelope of the partial angle stacks suggests that both OAMLs are partially molten with higher average melt content and more uniform melt distribution in the southern OAML than in the northern OAML. For AVA crossplotting, the OAMLs are subdivided into seven 1 km2 analysis windows. The AVA crossplotting results indicate that the OAMLs contain a smaller amount of melt than the axial magma lens (AML). For both OAMLs, a higher melt fraction is detected within analysis windows located close to the ridge axis than within the most distant windows. The highest average melt concentration is interpreted for the central sections of the OAMLs. The overall low OAML melt content could be indicative of melt lost due to recent off-axis eruptions, drainage to the AML, or limited mantle melt supply. Based on the results of this and earlier bathymetric, morphological, geochemical, and geophysical investigations, we propose that the melt-poor OAML state is largely the result of limited melt supply from the underlying mantle source reservoir with smaller contribution attributed to melt leakage to the AML. We hypothesize that the investigated OAMLs have a longer period of melt replenishment, lower eruption recurrence rates, and lower eruption volumes than the AML, though some could be single intrusion events.

Phase behavior and reactive transport of partial melt in heterogeneous mantle model

NASA Astrophysics Data System (ADS)

Jordan, J.; Hesse, M. A.

2013-12-01

The reactive transport of partial melt is the key process that leads to the chemical and physical differentiation of terrestrial planets and smaller celestial bodies. The essential role of the lithological heterogeneities during partial melting of the mantle is increasingly recognized. How far can enriched melts propagate while interacting with the ambient mantle? Can the melt flow emanating from a fertile heterogeneity be localized through a reactive infiltration feedback in a model without exogenous factors or contrived initial conditions? A full understanding of the role of heterogeneities requires reactive melt transport models that account for the phase behavior of major elements. Previous work on reactive transport in the mantle focuses on trace element partitioning; we present the first nonlinear chromatographic analysis of reactive melt transport in systems with binary solid solution. Our analysis shows that reactive melt transport in systems with binary solid solution leads to the formation of two separate reaction fronts: a slow melting/freezing front along which enthalpy change is dominant and a fast dissolution/precipitation front along which compositional changes are dominated by an ion-exchange process over enthalpy change. An intermediate state forms between these two fronts with a bulk-rock composition and enthalpy that are not necessarily bounded by the bulk-rock composition and enthalpy of either the enriched heterogeneity or the depleted ambient mantle. The formation of this intermediate state makes it difficult to anticipate the porosity changes and hence the stability of reaction fronts. Therefore, we develop a graphical representation for the solution that allows identification of the intermediate state by inspection, for all possible bulk-rock compositions and enthalpies of the heterogeneity and the ambient mantle. We apply the analysis to the partial melting of an enriched heterogeneity. This leads to the formation of moving precipitation

A retrospective analysis of compact fluorescent lamp experience curves and their correlations to deployment programs

DOE PAGES

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

2016-09-17

Experience curves are useful for understanding technology development and can aid in the design and analysis of market transformation programs. Here, we employ a novel approach to create experience curves, to examine both global and North American compact fluorescent lamp (CFL) data for the years 1990–2007. We move away from the prevailing method of fitting a single, constant, exponential curve to data and instead search for break points where changes in the learning rate may have occurred. Our analysis suggests a learning rate of approximately 21% for the period of 1990–1997, and 51% and 79% in global and North Americanmore » datasets, respectively, after 1998. We use price data for this analysis; therefore our learning rates encompass developments beyond typical “learning by doing”, including supply chain impacts such as market competition. We examine correlations between North American learning rates and the initiation of new programs, abrupt technological advances, and economic and political events, and find an increased learning rate associated with design advancements and federal standards programs. Our findings support the use of segmented experience curves for retrospective and prospective technology analysis, and may imply that investments in technology programs have contributed to an increase of the CFL learning rate.« less

A retrospective analysis of compact fluorescent lamp experience curves and their correlations to deployment programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

Experience curves are useful for understanding technology development and can aid in the design and analysis of market transformation programs. Here, we employ a novel approach to create experience curves, to examine both global and North American compact fluorescent lamp (CFL) data for the years 1990–2007. We move away from the prevailing method of fitting a single, constant, exponential curve to data and instead search for break points where changes in the learning rate may have occurred. Our analysis suggests a learning rate of approximately 21% for the period of 1990–1997, and 51% and 79% in global and North Americanmore » datasets, respectively, after 1998. We use price data for this analysis; therefore our learning rates encompass developments beyond typical “learning by doing”, including supply chain impacts such as market competition. We examine correlations between North American learning rates and the initiation of new programs, abrupt technological advances, and economic and political events, and find an increased learning rate associated with design advancements and federal standards programs. Our findings support the use of segmented experience curves for retrospective and prospective technology analysis, and may imply that investments in technology programs have contributed to an increase of the CFL learning rate.« less

Finite element modeling of melting and fluid flow in the laser-heated diamond-anvil cell

NASA Astrophysics Data System (ADS)

Gomez-Perez, N.; Rodriguez, J. F.; McWilliams, R. S.

2017-04-01

The laser-heated diamond anvil cell is widely used in the laboratory study of materials behavior at high-pressure and high-temperature, including melting curves and liquid properties at extreme conditions. Laser heating in the diamond cell has long been associated with fluid-like motion in samples, which is routinely used to determine melting points and is often described as convective in appearance. However, the flow behavior of this system is poorly understood. A quantitative treatment of melting and flow in the laser-heated diamond anvil cell is developed here to physically relate experimental motion to properties of interest, including melting points and viscosity. Numerical finite-element models are used to characterize the temperature distribution, melting, buoyancy, and resulting natural convection in samples. We find that continuous fluid motion in experiments can be explained most readily by natural convection. Fluid velocities, peaking near values of microns per second for plausible viscosities, are sufficiently fast to be detected experimentally, lending support to the use of convective motion as a criterion for melting. Convection depends on the physical properties of the melt and the sample geometry and is too sluggish to detect for viscosities significantly above that of water at ambient conditions, implying an upper bound on the melt viscosity of about 1 mPa s when convective motion is detected. A simple analytical relationship between melt viscosity and velocity suggests that direct viscosity measurements can be made from flow speeds, given the basic thermodynamic and geometric parameters of samples are known.

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

Production of Synthetic Nuclear Melt Glass

PubMed Central

Molgaard, Joshua J.; Auxier, John D.; Giminaro, Andrew V.; Oldham, Colton J.; Gill, Jonathan; Hall, Howard L.

2016-01-01

Realistic surrogate nuclear debris is needed within the nuclear forensics community to test and validate post-detonation analysis techniques. Here we outline a novel process for producing bulk surface debris using a high temperature furnace. The material developed in this study is physically and chemically similar to trinitite (the melt glass produced by the first nuclear test). This synthetic nuclear melt glass is assumed to be similar to the vitrified material produced near the epicenter (ground zero) of any surface nuclear detonation in a desert environment. The process outlined here can be applied to produce other types of nuclear melt glass including that likely to be formed in an urban environment. This can be accomplished by simply modifying the precursor matrix to which this production process is applied. The melt glass produced in this study has been analyzed and compared to trinitite, revealing a comparable crystalline morphology, physical structure, void fraction, and chemical composition. PMID:26779720

Movement of the Melt Metal Layer under Conditions Typical of Transient Events in ITER

NASA Astrophysics Data System (ADS)

Poznyak, I. M.; Safronov, V. M.; Zybenko, V. Yu.

2017-12-01

During the operation of ITER, protective coatings of the divertor and the first wall will be exposed to significant plasma heat loads which may cause a huge erosion. One of the major failure mechanisms of metallic armor is diminution of their thickness due to the melt layer displacement. New experimental data are required in order to develop and validate physical models of the melt layer movement. The paper presents the experiments where metal targets were irradiated by a plasma stream at the quasi-stationary high-current plasma accelerator QSPA-T. The obtained data allow one to determine the velocity and acceleration of the melt layer at various distances from the plasma stream axis. The force causing the radial movement of the melt layer is shown to create an acceleration whose order of magnitude is 1000g. The pressure gradient is not responsible for creating this large acceleration. To investigate the melt layer movement under a known force, the experiment with a rotating target was carried out. The influence of centrifugal and Coriolis forces led to appearance of curved elongated waves on the surface. The surface profile changed: there is no hill in the central part of the erosion crater in contrast to the stationary target. The experimental data clarify the trends in the melt motion that are required for development of theoretical models.

Evaluation of the MeltPro TB/STR assay for rapid detection of streptomycin resistance in Mycobacterium tuberculosis.

PubMed

Zhang, Ting; Hu, Siyu; Li, Guoli; Li, Hui; Liu, Xiaoli; Niu, Jianjun; Wang, Feng; Wen, Huixin; Xu, Ye; Li, Qingge

2015-03-01

Rapid and comprehensive detection of drug-resistance is essential for the control of tuberculosis, which has facilitated the development of molecular assays for the detection of drug-resistant mutations in Mycobacterium tuberculosis. We hereby assessed the analytical and clinical performance of an assay for streptomycin-resistant mutations. MeltPro TB/STR is a closed-tube, dual-color, melting curve analysis-based, real-time PCR test designed to detect 15 streptomycin-resistant mutations in rpsL 43, rpsL 88, rrs 513, rrs 514, rrs 517, and rrs 905-908 of M. tuberculosis. Analytical studies showed that the accuracy was 100%, the limit of detection was 50-500 bacilli per reaction, the reproducibility in the form of Tm variation was within 1.0 °C, and we could detect 20% STR resistance in mixed bacterial samples. The cross-platform study demonstrated that the assay could be performed on six models of real-time PCR instruments. A multicenter clinical study was conducted using 1056 clinical isolates, which were collected from three geographically different healthcare units, including 709 STR-susceptible and 347 STR-resistant isolates characterized on Löwenstein-Jensen solid medium by traditional drug susceptibility testing. The results showed that the clinical sensitivity and specificity of the MeltPro TB/STR was 88.8% and 95.8%, respectively. Sequencing analysis confirmed the accuracy of the mutation types. Among all the 8 mutation types detected, rpsL K43R (AAG → AGG), rpsL K88R (AAG → AGG) and rrs 514 A → C accounted for more than 90%. We concluded that MeltPro TB/STR represents a rapid and reliable assay for the detection of STR resistance in clinical isolates. Copyright © 2014. Published by Elsevier Ltd.

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

PubMed

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

2016-07-22

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

Integral equation theory study on the phase separation in star polymer nanocomposite melts.

PubMed

Zhao, Lei; Li, Yi-Gui; Zhong, Chongli

2007-10-21

The polymer reference interaction site model theory is used to investigate phase separation in star polymer nanocomposite melts. Two kinds of spinodal curves were obtained: classic fluid phase boundary for relatively low nanoparticle-monomer attraction strength and network phase boundary for relatively high nanoparticle-monomer attraction strength. The network phase boundaries are much more sensitive with nanoparticle-monomer attraction strength than the fluid phase boundaries. The interference among the arm number, arm length, and nanoparticle-monomer attraction strength was systematically investigated. When the arm lengths are short, the network phase boundary shows a marked shift toward less miscibility with increasing arm number. When the arm lengths are long enough, the network phase boundaries show opposite trends. There exists a crossover arm number value for star polymer nanocomposite melts, below which the network phase separation is consistent with that of chain polymer nanocomposite melts. However, the network phase separation shows qualitatively different behaviors when the arm number is larger than this value.

Experimental research of phase transitions in a melt of high-purity aluminum

NASA Astrophysics Data System (ADS)

Vorontsov, V. B.; Pershin, V. K.

2017-12-01

This scientific work is devoted to the studying of the genetic connection structures of solid and liquid phases. In this paper Fourier analysis of acoustic emission (AE) signals accompanying heating of high purity aluminum from the melting point up to 860 °C was performed. The experimental data allowed to follow the dynamics of disorder zones in the melt with increasing melt temperature up to their complete destruction. The presented results of spectral analysis of the signals were analyzed from the standpoint of the theory of cluster melting metals.

High resolution melting analysis: rapid and precise characterisation of recombinant influenza A genomes

PubMed Central

2013-01-01

Background High resolution melting analysis (HRM) is a rapid and cost-effective technique for the characterisation of PCR amplicons. Because the reverse genetics of segmented influenza A viruses allows the generation of numerous influenza A virus reassortants within a short time, methods for the rapid selection of the correct recombinants are very useful. Methods PCR primer pairs covering the single nucleotide polymorphism (SNP) positions of two different influenza A H5N1 strains were designed. Reassortants of the two different H5N1 isolates were used as a model to prove the suitability of HRM for the selection of the correct recombinants. Furthermore, two different cycler instruments were compared. Results Both cycler instruments generated comparable average melting peaks, which allowed the easy identification and selection of the correct cloned segments or reassorted viruses. Conclusions HRM is a highly suitable method for the rapid and precise characterisation of cloned influenza A genomes. PMID:24028349

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

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.

Simultaneous screening for JAK2 and calreticulin gene mutations in myeloproliferative neoplasms with high resolution melting.

PubMed

Matsumoto, Nariyoshi; Mori, Sayaka; Hasegawa, Hiroo; Sasaki, Daisuke; Mori, Hayato; Tsuruda, Kazuto; Imanishi, Daisuke; Imaizumi, Yoshitaka; Hata, Tomoko; Kaku, Norihito; Kosai, Kousuke; Uno, Naoki; Miyazaki, Yasushi; Yanagihara, Katsunori

2016-11-01

Recently, novel calreticulin (CALR) mutations were discovered in Janus kinase 2 (JAK2) non-mutated myelofibrosis (PMF) and essential thrombocythemia (ET) cases, with a frequency of 60-80%. We examined clinical correlations and CALR mutation frequency in our myeloproliferative neoplasms (MPN) cases, and introduce an effective test method for use in clinical practice. We examined 177 samples previously investigated for the JAK2 mutation for differential diagnosis of MPN. JAK2 and CALR mutations were analyzed using melting curve analysis and microchip electrophoresis, respectively. Next, we constructed a test for simultaneous screening of the JAK2 and CALR mutations utilizing high resolution melting (HRM). Among 99 MPN cases, 60 possessed the JAK2 mutation alone. Of the 39 MPN cases without the JAK2 mutation, 14 were positive for the CALR mutation, all of which were ET. Using our novel screening test for the JAK2 and CALR mutations by HRM, the concordance rate of conventional analysis with HRM was 96% for the JAK2 mutation and 95% for the CALR mutation. Our novel simultaneous screening test for the JAK2 and CALR gene mutations with HRM is useful for diagnosis of MPN. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Analysis of HD 73045 light curve data

NASA Astrophysics Data System (ADS)

Das, Mrinal Kanti; Bhatraju, Naveen Kumar; Joshi, Santosh

2018-04-01

In this work we analyzed the Kepler light curve data of HD 73045. The raw data has been smoothened using standard filters. The power spectrum has been obtained by using a fast Fourier transform routine. It shows the presence of more than one period. In order to take care of any non-stationary behavior, we carried out a wavelet analysis to obtain the wavelet power spectrum. In addition, to identify the scale invariant structure, the data has been analyzed using a multifractal detrended fluctuation analysis. Further to characterize the diversity of embedded patterns in the HD 73045 flux time series, we computed various entropy-based complexity measures e.g. sample entropy, spectral entropy and permutation entropy. The presence of periodic structure in the time series was further analyzed using the visibility network and horizontal visibility network model of the time series. The degree distributions in the two network models confirm such structures.

Temperature and pressure determination of the tin melt boundary from a combination of pyrometry, spectral reflectance, and velocity measurements along release paths

NASA Astrophysics Data System (ADS)

La Lone, Brandon; Asimow, Paul; Fatyanov, Oleg; Hixson, Robert; Stevens, Gerald

2017-06-01

Plate impact experiments were conducted on tin samples backed by LiF windows to determine the tin melt curve. Thin copper flyers were used so that a release wave followed the 30-40 GPa shock wave in the tin. The release wave at the tin-LiF interface was about 300 ns long. Two sets of experiments were conducted. In one set, spectral emissivity was measured at six wavelengths using a flashlamp illuminated integrating sphere. In the other set, thermal radiance was measured at two wavelengths. The emissivity and thermal radiance measurements were combined to obtain temperature histories of the tin-LiF interface during the release. PDV was used to obtain stress histories. All measurements were combined to obtain temperature vs. stress release paths. A kink or steepening in the release paths indicate where the releases merge onto the melt boundary, and release paths originating from different shock stresses overlap on the melt boundary. Our temperature-stress release path measurements provide a continuous segment of the tin melt boundary that is in good agreement with some of the published melt curves. This work was done by National Security Technologies, LLC, under Contract No. DE-AC52-06NA25946 with the U.S. Department of Energy, and supported by the Site-Directed Research and Development Program. DOE/NV/259463133.

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=1.86×10-8M⊙yr-1 and the minimal mass of the third body to be M3=0.31M⊙. 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.

Evaluation of High-Resolution Melting Curve Analysis of Ligation-Mediated Real-Time PCR, a Rapid Method for Epidemiological Typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) Pathogens

PubMed Central

Ryberg, Anna; Billström, Hanna; Hällgren, Anita; Nilsson, Lennart E.; Marklund, Britt-Inger; Olsson-Liljequist, Barbro; Schön, Thomas

2014-01-01

A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97% agreement (60/62 isolates) was achieved in comparison to pulsed-field gel electrophoresis (PFGE) results, which indicates that LMqPCR HRMA is a rapid and accurate screening tool for monitoring nosocomial outbreaks. PMID:25232168

Localized Principal Component Analysis based Curve Evolution: A Divide and Conquer Approach

PubMed Central

Appia, Vikram; Ganapathy, Balaji; Yezzi, Anthony; Faber, Tracy

2014-01-01

We propose a novel localized principal component analysis (PCA) based curve evolution approach which evolves the segmenting curve semi-locally within various target regions (divisions) in an image and then combines these locally accurate segmentation curves to obtain a global segmentation. The training data for our approach consists of training shapes and associated auxiliary (target) masks. The masks indicate the various regions of the shape exhibiting highly correlated variations locally which may be rather independent of the variations in the distant parts of the global shape. Thus, in a sense, we are clustering the variations exhibited in the training data set. We then use a parametric model to implicitly represent each localized segmentation curve as a combination of the local shape priors obtained by representing the training shapes and the masks as a collection of signed distance functions. We also propose a parametric model to combine the locally evolved segmentation curves into a single hybrid (global) segmentation. Finally, we combine the evolution of these semilocal and global parameters to minimize an objective energy function. The resulting algorithm thus provides a globally accurate solution, which retains the local variations in shape. We present some results to illustrate how our approach performs better than the traditional approach with fully global PCA. PMID:25520901

High-resolution melting PCR analysis for rapid genotyping of Burkholderia mallei.

PubMed

Girault, G; Wattiau, P; Saqib, M; Martin, B; Vorimore, F; Singha, H; Engelsma, M; Roest, H J; Spicic, S; Grunow, R; Vicari, N; De Keersmaecker, S C J; Roosens, N H C; Fabbi, M; Tripathi, B N; Zientara, S; Madani, N; Laroucau, K

2018-05-08

Burkholderia (B.) mallei is the causative agent of glanders. A previous work conducted on single-nucleotide polymorphisms (SNP) extracted from the whole genome sequences of 45 B. mallei isolates identified 3 lineages for this species. In this study, we designed a high-resolution melting (HRM) method for the screening of 15 phylogenetically informative SNPs within the genome of B. mallei that subtype the species into 3 lineages and 12 branches/sub-branches/groups. The present results demonstrate that SNP-based genotyping represent an interesting approach for the molecular epidemiology analysis of B. mallei. Copyright © 2018 Elsevier B.V. All rights reserved.

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

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. (c) 2015 APA, all rights reserved).

Compositions of Magmatic and Impact Melt Sulfides in Tissint And EETA79001: Precursors of Immiscible Sulfide Melt Blebs in Shergottite Impact Melts

NASA Technical Reports Server (NTRS)

Ross, D. K.; Rao, M. N.; Nyquist, L.; Agee, C.; Sutton, S.

2013-01-01

Immiscible sulfide melt spherules are locally very abundant in shergottite impact melts. These melts can also contain samples of Martian atmospheric gases [1], and cosmogenic nuclides [2] that are present in impact melt, but not in the host shergottite, indicating some components in the melt resided at the Martian surface. These observations show that some regolith components are, at least locally, present in the impact melts. This view also suggests that one source of the over-abundant sulfur in these impact melts could be sulfates that are major constituents of Martian regolith, and that the sulfates were reduced during shock heating to sulfide. An alternative view is that sulfide spherules in impact melts are produced solely by melting the crystalline sulfide minerals (dominantly pyrrhotite, Fe(1-x)S) that are present in shergottites [3]. In this abstract we report new analyses of the compositions of sulfide immiscible melt spherules and pyrrhotite in the shergottites Tissint, and EETA79001,507, and we use these data to investigate the possible origins of the immiscible sulfide melt spherules. In particular, we use the metal/S ratios determined in these blebs as potential diagnostic criteria for tracking the source material from which the numerous sulfide blebs were generated by shock in these melts.

The aluminum electrode in AlCl3-alkali-halide melts.

NASA Technical Reports Server (NTRS)

Holleck, G. L.; Giner, J.

1972-01-01

Passivation phenomena have been observed upon cathodic and anodic polarization of the Al electrode in AlCl3-KCl-NaCl melts between 100 and 160 C. They are caused by formation of a solid salt layer at the electrode surface resulting from concentration changes upon current flow. The anodic limiting currents increased with temperature and with decreasing AlCl3 content of the melt. Current voltage curves obtained on a rotating aluminum disk showed a linear relationship between the anodic limiting current and omega to the minus 1/2 power. Upon cathodic polarization, dendrite formation occurs at the Al electrode. The activation overvoltage in AlCl3-KCl-NaCl was determined by galvanostatic current step methods. An apparent exchange current density of 270 mA/sq cm at 130 C and a double layer capacity of 40 plus or minus 10 microfarad/sq cm were measured.

Melt production in large-scale impact events: Implications and observations at terrestrial craters

NASA Technical Reports Server (NTRS)

Grieve, Richard A. F.; Cintala, Mark J.

1992-01-01

The volume of impact melt relative to the volume of the transient cavity increases with the size of the impact event. Here, we use the impact of chondrite into granite at 15, 25, and 50 km s(sup -1) to model impact-melt volumes at terrestrial craters in crystalline targets and explore the implications for terrestrial craters. Figures are presented that illustrate the relationships between melt volume and final crater diameter D(sub R) for observed terrestrial craters in crystalline targets; also included are model curves for the three different impact velocities. One implication of the increase in melt volumes with increasing crater size is that the depth of melting will also increase. This requires that shock effects occurring at the base of the cavity in simple craters and in the uplifted peaks of central structures at complex craters record progressively higher pressures with increasing crater size, up to a maximum of partial melting (approx. 45 GPa). Higher pressures cannot be recorded in the parautochthonous rocks of the cavity floor as they will be represented by impact melt, which will not remain in place. We have estimated maximum recorded pressures from a review of the literature, using such observations as planar features in quartz and feldspar, diaplectic glasses of feldspar and quartz, and partial fusion and vesiculation, as calibrated with estimates of the pressures required for their formation. Erosion complicates the picture by removing the surficial (most highly shocked) rocks in uplifted structures, thereby reducing the maximum shock pressures observed. In addition, the range of pressures that can be recorded is limited. Nevertheless, the data define a trend to higher recorded pressures with crater diameter, which is consistent with the implications of the model. A second implication is that, as the limit of melting intersects the base of the cavity, central topographic peaks will be modified in appearance and ultimately will not occur. That is

Melting in Superheated Silicon Films Under Pulsed-Laser Irradiation

NASA Astrophysics Data System (ADS)

Wang, Jin Jimmy

This thesis examines melting in superheated silicon films in contact with SiO2 under pulsed laser irradiation. An excimer-laser pulse was employed to induce heating of the film by irradiating the film through the transparent fused-quartz substrate such that most of the beam energy was deposited near the bottom Si-SiO2 interface. Melting dynamics were probed via in situ transient reflectance measurements. The temperature profile was estimated computationally by incorporating temperature- and phase-dependent physical parameters and the time-dependent intensity profile of the incident excimer-laser beam obtained from the experiments. The results indicate that a significant degree of superheating occurred in the subsurface region of the film. Surface-initiated melting was observed in spite of the internal heating scheme, which resulted in the film being substantially hotter at and near the bottom Si-SiO2 interface. By considering that the surface melts at the equilibrium melting point, the solid-phase-only heat-flow analysis estimates that the bottom Si-SiO2 interface can be superheated by at least 220 K during excimer-laser irradiation. It was found that at higher laser fluences (i.e., at higher temperatures), melting can be triggered internally. At heating rates of 1010 K/s, melting was observed to initiate at or near the (100)-oriented Si-SiO2 interface at temperatures estimated to be over 300 K above the equilibrium melting point. Based on theoretical considerations, it was deduced that melting in the superheated solid initiated via a nucleation and growth process. Nucleation rates were estimated from the experimental data using Johnson-Mehl-Avrami-Kolmogorov (JMAK) analysis. Interpretation of the results using classical nucleation theory suggests that nucleation of the liquid phase occurred via the heterogeneous mechanism along the Si-SiO2 interface.

Melting Inside the Tibetan Crust? Constraint From Electrical Conductivity of Peraluminous Granitic Melt

NASA Astrophysics Data System (ADS)

Guo, Xuan; Zhang, Li; Su, Xue; Mao, Zhu; Gao, Xiao-Ying; Yang, Xiaozhi; Ni, Huaiwei

2018-05-01

Magnetotelluric and seismological studies suggested the presence of partial melts in the middle to lower Himalaya-Tibetan crust. However, the melt fractions inferred by previous work were based on presumed electrical conductivity of melts. We performed measurements on the electrical conductivity of peraluminous granitic melts with 0.16-8.4 wt % H2O (the expected compositions in the Tibetan crust) at 600-1,300°C and 0.5-1.0 GPa. Peraluminous melt exhibits lower electrical conductivity than peralkaline melt at dry condition, but this difference diminishes at H2O > 2 wt %. With our data, the observed electrical anomalies in the Tibetan crust could be explained by 2-33 vol % of peraluminous granitic melts with H2O > 6 wt %. Possible reasons for our inferred melt fractions being higher than seismological constraints include the following: (1) The real melts are more Na and H2O rich, (2) the effect of melt reducing seismic velocities was overestimated, and (3) the anomalies at some locations are due to fluids.

High Resolution Melting Analysis is Very Useful to Identify BRCA1 c.4964_4982del19 (rs80359876) Founder Calabrian Pathogenic Variant on Peripheral Blood and Buccal Swab DNA.

PubMed

Minucci, Angelo; De Bonis, Maria; De Paolis, Elisa; Gentile, Leonarda; Santonocito, Concetta; Concolino, Paola; Mignone, Flavio; Capoluongo, Ettore

2017-04-01

Detection of pathogenic variants in hereditary breast and ovarian cancer-related breast cancer type 1 and type 2 susceptibility proteins (BRCA1/2) genes is an effective strategy in cancer prevention and treatment. Some ethnic and geographical regions show different BRCA1/2 mutation spectrum and prevalence. In Italy, elucidation of founder effect in BRCA1/2 genes can have an impact on the management of hereditary cancer families on a healthcare system level, making genetic testing more affordable and cost effective in certain regions. The purpose of this paper is to develop a rapid, low-cost, high-throughput single-tube technology for genotyping the Italian founder mutation c.4964_4982del19 (rs80359876) in the BRCA1 gene, starting from peripheral blood and/or buccal swab DNA. Heterozygote samples for c.4964_4982del19 variant were easily and unambiguously identified by the altered shape of the melting curves and were clearly distinguished by a change in melting temperature that differed by approximately 5 °C. The same results were obtained both with DNA from peripheral blood than buccal swab. We provide evidence about application of high-resolution melting analysis (HRMA) in unambiguously genotyping of the founder BRCA1 c.4964_4982del19 variant (rs80359876) in individuals from the Calabria region of Italy. In fact, HRMA was confirmed to be particularly suitable for the identification of BRCA1 c.4964_4982del19 variant, making this approach useful in clinical molecular diagnostics.

Experimental study of eclogitization and melting of basic rocks at P = 4 GPa and T = 1200-1400°C

NASA Astrophysics Data System (ADS)

Gorbachev, N. S.; Shapovalov, Yu. B.; Kostyuk, A. V.

2017-06-01

Experimental study of gabbro-norite eclogitization and melting at P = 4 GPa has made it possible to reveal the effective influence of fluid and temperature on the phase relationships. The melt composition varies from andesite-dacite in "dry conditions" to phonolite and carbonate in the presence of a fluid. The Grt-containing melting curve is replaced by the Cpx-containing liquidus as the temperature changes or a fluid is added. Hence, the possible presence of "garnetitite" and "clinopyroxenite" in the upper mantle was proved experimentally. The ultimate pressure of the spinel facies at the depth of the eclogite upper mantle is controlled by the stability of Cht ≤ 4 GPa. The revealed similarity of the spectra of REE-adakite, tonalite-trondhjemite-granodiorite (TTG), and melts formed under the partial melting of eclogitized gabbro-norite does not contradict the existing ideas of the eclogite source of the TTG rocks. Wide variations in the interphase microelement distribution factors D (Grt, Cpx)/L are indicative of effective fractionation of the microelements in the course of eclogite melting and differentiation.

Rapakivi texture formation via disequilibrium melting in a contact partial melt zone, Antarctica

NASA Astrophysics Data System (ADS)

Currier, R. M.

2017-12-01

In the McMurdo Dry Valleys of Antarctica, a Jurassic aged dolerite sill induced partial melting of granite in the shallow crust. The melt zone can be traced in full, from high degrees of melting (>60%) along the dolerite contact, to no apparent signs of melting, 10s of meters above the contact. Within this melt zone, the well-known rapakivi texture is found, arrested in various stages of development. High above the contact, and at low degrees of melting, K-feldspar crystals are slightly rounded and unmantled. In the lower half of the melt zone, mantles of cellular textured plagioclase appear on K-feldspar, and thicken towards the contact heat source. At the highest degrees of melting, cellular-textured plagioclase completely replaces restitic K-feldspar. Because of the complete exposure and intact context, the leading models of rapakivi texture formation can be tested against this system. The previously proposed mechanisms of subisothermal decompression, magma-mixing, and hydrothermal exsolution all fail to adequately describe rapakivi generation in this melt zone. Preferred here is a closed system model that invokes the production of a heterogeneous, disequilibrium melt through rapid heating, followed by calcium and sodium rich melt reacting in a peritectic fashion with restitic K-feldspar crystals. This peritectic reaction results in the production of plagioclase of andesine-oligoclase composition—which is consistent with not just mantles in the melt zone, but globally as well. The thickness of the mantle is diffusion limited, and thus a measure of the diffusive length scale of sodium and calcium over the time scale of melting. Thermal modeling provides a time scale of melting that is consistent with the thickness of observed mantles. Lastly, the distribution of mantled feldspars is highly ordered in this melt zone, but if it were mobilized and homogenized—mixing together cellular plagioclase, mantled feldspars, and unmantled feldspars—the result would be

Electrical conductivity of basaltic and carbonatite melt-bearing peridotites at high pressures: Implications for melt distribution and melt fraction in the upper mantle

NASA Astrophysics Data System (ADS)

Yoshino, Takashi; Laumonier, Mickael; McIsaac, Elizabeth; Katsura, Tomoo

2010-07-01

Electrical impedance measurements were performed on two types of partial molten samples with basaltic and carbonatitic melts in a Kawai-type multi-anvil apparatus in order to investigate melt fraction-conductivity relationships and melt distribution of the partial molten mantle peridotite under high pressure. The silicate samples were composed of San Carlos olivine with various amounts of mid-ocean ridge basalt (MORB), and the carbonate samples were a mixture of San Carlos olivine with various amounts of carbonatite. High-pressure experiments on the silicate and carbonate systems were performed up to 1600 K at 1.5 GPa and up to at least 1650 K at 3 GPa, respectively. The sample conductivity increased with increasing melt fraction. Carbonatite-bearing samples show approximately one order of magnitude higher conductivity than basalt-bearing ones at the similar melt fraction. A linear relationship between log conductivity ( σbulk) and log melt fraction ( ϕ) can be expressed well by the Archie's law (Archie, 1942) ( σbulk/ σmelt = Cϕn) with parameters C = 0.68 and 0.97, n = 0.87 and 1.13 for silicate and carbonate systems, respectively. Comparison of the electrical conductivity data with theoretical predictions for melt distribution indicates that the model assuming that the grain boundary is completely wetted by melt is the most preferable melt geometry. The gradual change of conductivity with melt fraction suggests no permeability jump due to melt percolation at a certain melt fraction. The melt fraction of the partial molten region in the upper mantle can be estimated to be 1-3% and ˜ 0.3% for basaltic melt and carbonatite melt, respectively.

Analyzing Multiple-Choice Questions by Model Analysis and Item Response Curves

NASA Astrophysics Data System (ADS)

Wattanakasiwich, P.; Ananta, S.

2010-07-01

In physics education research, the main goal is to improve physics teaching so that most students understand physics conceptually and be able to apply concepts in solving problems. Therefore many multiple-choice instruments were developed to probe students' conceptual understanding in various topics. Two techniques including model analysis and item response curves were used to analyze students' responses from Force and Motion Conceptual Evaluation (FMCE). For this study FMCE data from more than 1000 students at Chiang Mai University were collected over the past three years. With model analysis, we can obtain students' alternative knowledge and the probabilities for students to use such knowledge in a range of equivalent contexts. The model analysis consists of two algorithms—concentration factor and model estimation. This paper only presents results from using the model estimation algorithm to obtain a model plot. The plot helps to identify a class model state whether it is in the misconception region or not. Item response curve (IRC) derived from item response theory is a plot between percentages of students selecting a particular choice versus their total score. Pros and cons of both techniques are compared and discussed.

Analysis of close-contact melting with inner wall temperature variation in a horizontal cylindrical capsule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saitoh, T.S.; Hoshi, Akira

1997-12-31

Melting and solidification of a phase change material (PCM) in a capsule is of practical importance in latent heat thermal energy storage (LHTES) systems which are considered to be very promising to reduce a peak demand of electricity in the summer season. Two melting modes are involved in melting in capsules. One is close-contact melting between the solid bulk and the capsule wall, and another is natural convection melting in the liquid region. In recent years, close-contact melting processes for a single enclosure have been solved using several numerical methods (e.g., Saitoh and Kato (1994)). However, there is no theoreticalmore » solution considering the inner wall temperature variation within cylindrical or spherical capsules. In this report close-contact melting heat transfer characteristics including melt flow in the liquid film under inner wall temperature distribution were analyzed and simple approximate equations are presented, which facilitates designing of the practical capsule bed LHTES systems. The effects of Stefan number and variable temperature profile etc. were clarified in detail. And the melting velocity of the solid bulk under various conditions was also studied theoretically. In addition, the effects of variable inner wall temperature on molten mass fraction were investigated.« less

The melting points of MgO up to 4 TPa predicted based on ab initio thermodynamic integration molecular dynamics

NASA Astrophysics Data System (ADS)

Taniuchi, Takashi; Tsuchiya, Taku

2018-03-01

The melting curve of MgO is extended up to 4 TPa, corresponding to the Jovian core pressure, based on the one-step thermodynamic integration method implemented on ab initio molecular dynamics. The calculated melting temperatures are 3100 and 16 000 K at 0 and 500 GPa, respectively, which are consistent with previous experimental results, and 20 600 K at 3900 GPa, which is inconsistent with a recent experimental extrapolation, which implies the molten Jovian core. A quite small Clapeyron slope (dT/dP ) of 0.0+/- 0.5 is found at 3900 GPa due to comparable densities of the liquid and B2 phases under extreme compression. The Mg-O coordination number in the liquid phase is saturated at around 7.5 above 1 TPa and remains smaller than that in the B2 phase (8) even at 4 TPa, suggesting no density crossover between liquid and crystal and thus no further denser crystalline phases. Dynamical properties (atomic diffusivity and viscosity) are also investigated along the melting curve to understand these behaviors in greater detail.

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.

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

PubMed

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

2016-10-04

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

Internal stress-induced melting below melting temperature at high-rate laser heating

NASA Astrophysics Data System (ADS)

Hwang, Yong Seok; Levitas, Valery I.

2014-06-01

In this Letter, continuum thermodynamic and phase field approaches (PFAs) predicted internal stress-induced reduction in melting temperature for laser-irradiated heating of a nanolayer. Internal stresses appear due to thermal strain under constrained conditions and completely relax during melting, producing an additional thermodynamic driving force for melting. Thermodynamic melting temperature for Al reduces from 933.67 K for a stress-free condition down to 898.1 K for uniaxial strain and to 920.8 K for plane strain. Our PFA simulations demonstrated barrierless surface-induced melt nucleation below these temperatures and propagation of two solid-melt interfaces toward each other at the temperatures very close to the corresponding predicted thermodynamic equilibrium temperatures for the heating rate Q ≤1.51×1010K/s. At higher heating rates, kinetic superheating competes with a reduction in melting temperature and melting under uniaxial strain occurs at 902.1 K for Q = 1.51 × 1011 K/s and 936.9 K for Q = 1.46 × 1012 K/s.

Phase Transitions and Melting in Magnesium to 200 GPa and 4500 K

NASA Astrophysics Data System (ADS)

Stinton, G.; MacLeod, S.; Cynn, H.; Errandonea, D.; Proctor, J.; Meng, Y.; McMahon, M.

2013-06-01

Magnesium is a ``simple'' nearly free-electron metal up to around 100 GPa. Despite similarly-simple group II metals being the subject of numerous studies that have revealed complex high-pressure behaviour, Mg has very few high-pressure diffraction studies, particularly above room temperature. Here we describe such studies to above 200 GPa at 300 K, combined with resistive- and laser-heating experiments to 4500 K and 100 GPa. The hcp-bcc transition at ~50 GPa exhibits a large region of phase co-existence at all temperatures up to 800 K, and the transition pressure is found to decrease with temperature at the rate of ~3.4 GPa per 100 K, somewhat smaller than the rate calculated by Mehta et al.,. At lower pressures, below the melting curve at 10 GPa, we find the dhcp phase to be stable, in agreement with Errandonea et al.. Laser heating studies to 4500 K and 100 GPa show that Mg remains bcc up to the melting curve, our measurement of which is in good agreement with the previous ``speckle'' studies of Errandonea et al.. This work was performed under the auspices of the US DOE by LLNL under Contract DE-AC52-07NA27344.

Are driving and overtaking on right curves more dangerous than on left curves?

PubMed

Othman, Sarbaz; Thomson, Robert; Lannér, Gunnar

2010-01-01

It is well known that crashes on horizontal curves are a cause for concern in all countries due to the frequency and severity of crashes at curves compared to road tangents. A recent study of crashes in western Sweden reported a higher rate of crashes in right curves than left curves. To further understand this result, this paper reports the results of novel analyses of the responses of vehicles and drivers during negotiating and overtaking maneuvers on curves for right hand traffic. The overall objectives of the study were to find road parameters for curves that affect vehicle dynamic responses, to analyze these responses during overtaking maneuvers on curves, and to link the results with driver behavior for different curve directions. The studied road features were speed, super-elevation, radius and friction including their interactions, while the analyzed vehicle dynamic factors were lateral acceleration and yaw angular velocity. A simulation program, PC-Crash, has been used to simulate road parameters and vehicle response interaction in curves. Overtaking maneuvers have been simulated for all road feature combinations in a total of 108 runs. Analysis of variances (ANOVA) was performed, using two sided randomized block design, to find differences in vehicle responses for the curve parameters. To study driver response, a field test using an instrumented vehicle and 32 participants was reviewed as it contained longitudinal speed and acceleration data for analysis. The simulation results showed that road features affect overtaking performance in right and left curves differently. Overtaking on right curves was sensitive to radius and the interaction of radius with road condition; while overtaking on left curves was more sensitive to super-elevation. Comparisons of lateral acceleration and yaw angular velocity during these maneuvers showed different vehicle response configurations depending on curve direction and maneuver path. The field test experiments also showed

The effect of melt refining upon inclusions in aluminum

NASA Astrophysics Data System (ADS)

Simensen, C. J.

1982-03-01

A series of aluminum melts has been refined with respect to inclusions by use of ALCOA 469, FILD, or SNIF. The content and size distribution of inclusions in the original-and the refined melts-have been measured by use of neutron activation (oxygen content), gas chromatography (carbide content), sedimentation analysis, and dissolution of metal in hydrochloric acid and subsequent analysis of oxides by means of a Coulter Counter. All the units tested have a beneficial effect and decrease the inclusion content, but the number of analyses are too few to make general conclusions. However, for melts cleaned by use of SNIF, it was found that oxides larger than 50 μm in cross section and borides larger than 20 μm in diameter were removed, while the smaller borides were agglomerated only. The effect of FILD and ALCOA 469 upon the melt tested was removal of borides larger than 5-10 μ m and oxides larger than 15μm in diameter, respectively.

Diameter-Dependent Modulus and Melting Behavior in Electrospun Semicrystalline Polymer Fibers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Y Liu; S Chen; E Zussman

2011-12-31

Confinement of the semicrystalline polymers, poly(ethylene-co-vinyl acetate) (PEVA) and low-density polyethylene (LDPE), produced by electrospinning has been observed to produce fibers with large protrusions, which have not been previously observed in fibers of comparable diameters produced by other methods. SAXS spectra confirmed the crystalline structure and determined that the lamellar spacing was almost unchanged from the bulk. Measurement of the mechanical properties of these fibers, by both shear modulation force microscopy (SMFM) and atomic force acoustic microscopy (AFAM), indicates that the modulii of these fibers increases with decreasing diameter, with the onset at {approx}10 {micro}m, which is an order ofmore » magnitude larger than previously reported. Melting point measurements indicate a decrease of more than 7% in T{sub m}/T{sub 0} (where T{sub m} is the melting point of semicrystalline polymer fibers and T{sub 0} is the melting point of the bulk polymer) for fibers ranging from 4 to 10 {micro}m in diameter. The functional form of the decrease followed a universal curve for PEVA, when scaled with T{sub 0}.« less

Analysis of the vitreoretinal surgery learning curve.

PubMed

Martín-Avià, J; Romero-Aroca, P

2017-06-01

To describe intra- and post-operative complications, as well as the evolution of the surgical technique in first 4years of work of a novice retina surgeon, and evaluate minimal learning time required to reduce its complications, deciding which pathologies should still be referred to higher level hospitals, until further experience may be achieved. A study was conducted on patients that had undergone vitreoretinal surgery by a novice surgeon in Tarragona between 23rd October 2007 and 31st December 2011. The primary diagnosis, surgeon learning time, surgical technique, intra-operative and post-operative complications were recorded. A total of 247 surgeries were studied. The percentage of use of 20G and 23G calibres during the time, marks a change towards trans-conjunctival surgery from the ninth trimester (98 surgeries). Surgical complications decreased towards twelfth trimester (130 surgeries) with an increase in the previous months. The shift towards 23G technique around 100 surgeries is interpreted as greater comfort and safety by the surgeon. Increased surgical complications during the following months until its decline around 130 surgeries can be interpreted as an 'overconfidence'. It is arguable that the learning curve is slower than what the surgeon believes. An individual analysis of the complications and surgical outcomes is recommended to ascertain the status of the learning curve. Copyright © 2016 Sociedad Española de Oftalmología. Publicado por Elsevier España, S.L.U. All rights reserved.

Universal digital high-resolution melt: a novel approach to broad-based profiling of heterogeneous biological samples.

PubMed

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

2013-10-01

Comprehensive profiling of nucleic acids in genetically heterogeneous samples is important for clinical and basic research applications. Universal digital high-resolution melt (U-dHRM) is a new approach to broad-based PCR diagnostics and profiling technologies that can overcome issues of poor sensitivity due to contaminating nucleic acids and poor specificity due to primer or probe hybridization inaccuracies for single nucleotide variations. The U-dHRM approach uses broad-based primers or ligated adapter sequences to universally amplify all nucleic acid molecules in a heterogeneous sample, which have been partitioned, as in digital PCR. Extensive assay optimization enables direct sequence identification by algorithm-based matching of melt curve shape and Tm to a database of known sequence-specific melt curves. We show that single-molecule detection and single nucleotide sensitivity is possible. The feasibility and utility of U-dHRM is demonstrated through detection of bacteria associated with polymicrobial blood infection and microRNAs (miRNAs) associated with host response to infection. U-dHRM using broad-based 16S rRNA gene primers demonstrates universal single cell detection of bacterial pathogens, even in the presence of larger amounts of contaminating bacteria; U-dHRM using universally adapted Lethal-7 miRNAs in a heterogeneous mixture showcases the single copy sensitivity and single nucleotide specificity of this approach.

Identification of a new genetic marker in Mycoplasma synoviae vaccine strain MS-H and development of a strategy using polymerase chain reaction and high-resolution melting curve analysis for differentiating MS-H from field strains.

PubMed

Zhu, Ling; Konsak, Barbara M; Olaogun, Olusola M; Agnew-Crumptona, Rebecca; Kanci, Anna; Marenda, Marc S; Browning, Glenn F; Noormohammadi, Amir H

2017-10-01

Mycoplasma synoviae (MS) is an economically important avian pathogen worldwide, causing subclinical respiratory tract infection and infectious synovitis in chickens and turkeys. A temperature-sensitive (ts + ) live attenuated vaccine MS-H, derived from the Australian field strain 86079/7NS, is now widely used in many countries to control the disease induced by MS. Differentiation of MS-H vaccine from field strains is crucial for monitoring vaccination programs in commercial poultry. Comparison of genomic sequences of MS-H and its parent strain revealed an adenine deletion at nucleotide position 468 of the MS-H oppF-1 gene. This mutation was shown to be unique to MS-H in further comparative analyses of oppF-1 genes of MS-H re-isolates and field strains from Australia and other countries. Based on this single nucleotide, a combination of nested PCR and high-resolution melting (HRM) curve analysis was used to evaluate its potential for use in differentiation of MS-H from field strains. The mean genotype confidence percentages of 99.27 and 48.20 for MS-H and field strains, respectively, demonstrated the high discriminative power of the newly developed assay (oppF PCR-HRM). A set of 13 tracheal swab samples collected from MS-H vaccinated specific pathogen free birds and commercial chicken flocks infected with MS were tested using the oppF PCR-HRM test and results were totally consistent with those obtained using vlhA genotyping. The nested-PCR HRM method established in this study proved to be a rapid, simple and cost effective tool for discriminating the MS-H vaccine strain from Australian and international strains in pure cultures and on tracheal swabs. Copyright © 2017 Elsevier B.V. All rights reserved.

Solidification microstructures in single-crystal stainless steel melt pools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sipf, J.B.; Boatner, L.A.; David, S.A.

1994-03-01

Development of microstructure of stationary melt pools of oriented stainless steel single crystals (70%Fe-15%Ni-15%Cr was analyzed. Stationary melt pools were formed by electron-beam and gas-tungsten-arc heating on (001), (011), and (111) oriented planes of the austenitic, fcc-alloy crystals. Characterization and analysis of resulting microstructure was carried out for each crystallographic plane and welding method. Results showed that crystallography which favors ``easy growth`` along the <100> family of directions is a controlling factor in the microstructural formation along with the melt-pool shape. The microstructure was found to depend on the melting method, since each method forms a unique melt-pool shape. Thesemore » results are used in making a three-dimensional reconstruction of the microstructure for each plane and melting method employed. This investigation also suggests avenues for future research into the microstructural properties of electron-beam welds as well as providing an experimental basis for mathematical models for the prediction of solidification microstructures.« less

Curve Boxplot: Generalization of Boxplot for Ensembles of Curves.

PubMed

Mirzargar, Mahsa; Whitaker, Ross T; Kirby, Robert M

2014-12-01

In simulation science, computational scientists often study the behavior of their simulations by repeated solutions with variations in parameters and/or boundary values or initial conditions. Through such simulation ensembles, one can try to understand or quantify the variability or uncertainty in a solution as a function of the various inputs or model assumptions. In response to a growing interest in simulation ensembles, the visualization community has developed a suite of methods for allowing users to observe and understand the properties of these ensembles in an efficient and effective manner. An important aspect of visualizing simulations is the analysis of derived features, often represented as points, surfaces, or curves. In this paper, we present a novel, nonparametric method for summarizing ensembles of 2D and 3D curves. We propose an extension of a method from descriptive statistics, data depth, to curves. We also demonstrate a set of rendering and visualization strategies for showing rank statistics of an ensemble of curves, which is a generalization of traditional whisker plots or boxplots to multidimensional curves. Results are presented for applications in neuroimaging, hurricane forecasting and fluid dynamics.

Detonation Initiation of Heterogeneous Melt-Cast High Explosives

NASA Astrophysics Data System (ADS)

Chuzeville, Vincent; Baudin, Gerard; Lefrancois, Alexandre; Boulanger, Remi; Catoire, Laurent

2015-06-01

The melt-cast explosives' shock initiation mechanisms are less investigated than pressed and cast-cured ones. If the existence of hot-spots is widely recognized, their formation mechanism is not yet established. We study here two melt-cast explosives, NTO-TNT 60:40 and RDX-TNT 60:40 in order to establish a relation between the microstructure and the reaction rate using a two-phase model based on a ZND approach. Such a model requires the reaction rate, the equations of state of the unreacted phase and of the detonation products and an interaction model between the two phases to describe the reaction zone thermodynamics. The reaction rate law can be written in a factorized form including the number of initiation sites, the explosive's deflagration velocity around hot spots and a function depending on gas volume fraction produced by the deflagration front propagation. The deflagration velocity mainly depends on pressure and is determined from pop-plot tests using the hypothesis of the single curve build-up. This hypothesis has been verified for our two melt-cast explosives. The function depending on gas volume fraction is deduced from microstructural observations and from an analogy with the solid nucleation and growth theory. It has been established for deflagration fronts growing from grain's surface and a given initial grain size distribution. The model requires only a few parameters, calibrated thanks to an inversion method. A good agreement is obtained between experiments and numerical simulations.

Statistical model to perform error analysis of curve fits of wind tunnel test data using the techniques of analysis of variance and regression analysis

NASA Technical Reports Server (NTRS)

Alston, D. W.

1981-01-01

The considered research had the objective to design a statistical model that could perform an error analysis of curve fits of wind tunnel test data using analysis of variance and regression analysis techniques. Four related subproblems were defined, and by solving each of these a solution to the general research problem was obtained. The capabilities of the evolved true statistical model are considered. The least squares fit is used to determine the nature of the force, moment, and pressure data. The order of the curve fit is increased in order to delete the quadratic effect in the residuals. The analysis of variance is used to determine the magnitude and effect of the error factor associated with the experimental data.

The impact pseudotachylitic breccia controversy: Insights from first isotope analysis of Vredefort impact-generated melt rocks

NASA Astrophysics Data System (ADS)

Reimold, Wolf Uwe; Hauser, Natalia; Hansen, Bent T.; Thirlwall, Matthew; Hoffmann, Marie

2017-10-01

Besides impact melt rock, several large terrestrial impact structures, notably the Sudbury (Canada) and Vredefort (South Africa) structures, exhibit considerable occurrences of a second type of impact-generated melt rock, so-called pseudotachylitic breccia (previously often termed ;pseudotachylite; - the term today reserved in structural geology for friction melt in shear or fault zones). At the Vredefort Dome, the eroded central uplift of the largest and oldest known terrestrial impact structure, pseudotachylitic breccia is well-exposed, with many massive occurrences of tens of meters width and many hundreds of meters extent. Genesis of these breccias has been discussed variably in terms of melt formation due to friction melting, melting due to decompression after initial shock compression, decompression melting upon formation/collapse of a central uplift, or a combination of these processes. In addition, it was recently suggested that they could have formed by the infiltration of impact melt into the crater floor, coming off a coherent melt sheet and under assimilation of wall rock; even seismic shaking has been invoked. Field evidence for generation of such massive melt bodies by friction on large shear/fault zones is missing. Also, no evidence for the generation of massive pseudotachylitic breccias in rocks of low to moderate shock degree by melting upon pressure release after shock compression has been demonstrated. The efficacy of seismic shaking to achieve sufficient melting as a foundation for massive pseudotachylitic melt generation as typified by the breccias of the Sudbury and Vredefort structures has so far remained entirely speculative. The available petrographic and chemical evidence has, thus, been interpreted to favor either decompression melting (i.e., in situ generation of melt) upon central uplift collapse, or the impact melt infiltration hypothesis. Importantly, all the past clast population and chemical analyses have invariably supported an