Design of primers for pertussis diagnosis by Real Time PCR and determination of its sensitivity and specificity in comparison with commercial kits.

Directory of Open Access Journals (Sweden)

Hamidreza Monavari

2013-12-01

Results: Performance of our home made primers for detecting pertussis using Real Time PCR in comparison with those by commercial kit was acceptable based on diagnostic classical guidance (WHO and the (CDC. Conclusions: Real time PCR test with new primers in comparison with culture techniques is more suitable, high sensitivity and can provide more informative values for pertussis detection.

Quantification of bacteria adherent to gastrointestinal mucosa by real-time PCR

NARCIS (Netherlands)

Huijsdens, Xander W.; Linskens, Ronald K.; Mak, Mariëtte; Meuwissen, Stephan G. M.; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

2002-01-01

The use of real-time quantitative PCR (5' nuclease PCR assay) as a tool to study the gastrointestinal microflora that adheres to the colonic mucosa was evaluated. We developed primers and probes based on the 16S ribosomal DNA gene sequences for the detection of Escherichia coli and Bacteroides

A plastome primer set for comprehensive quantitative real time RT-PCR analysis of Zea mays: a starter primer set for other Poaceae species

Directory of Open Access Journals (Sweden)

Dunn Sade N

2008-06-01

Full Text Available Abstract Background Quantitative Real Time RT-PCR (q2(RTPCR is a maturing technique which gives researchers the ability to quantify and compare very small amounts of nucleic acids. Primer design and optimization is an essential yet time consuming aspect of using q2(RTPCR. In this paper we describe the design and empirical optimization of primers to amplify and quantify plastid RNAs from Zea mays that are robust enough to use with other closely related species. Results Primers were designed and successfully optimized for 57 of the 104 reported genes in the maize plastome plus two nuclear genes. All 59 primer pairs produced single amplicons after end-point reverse transcriptase polymerase chain reactions (RT-PCR as visualized on agarose gels and subsequently verified by q2(RTPCR. Primer pairs were divided into several categories based on the optimization requirements or the uniqueness of the target gene. An in silico test suggested the majority of the primer sets should work with other members of the Poaceae family. An in vitro test of the primer set on two unsequenced species (Panicum virgatum and Miscanthus sinensis supported this assumption by successfully producing single amplicons for each primer pair. Conclusion Due to the highly conserved chloroplast genome in plant families it is possible to utilize primer pairs designed against one genomic sequence to detect the presence and abundance of plastid genes or transcripts from genomes that have yet to be sequenced. Analysis of steady state transcription of vital system genes is a necessary requirement to comprehensively elucidate gene expression in any organism. The primer pairs reported in this paper were designed for q2(RTPCR of maize chloroplast genes but should be useful for other members of the Poaceae family. Both in silico and in vitro data are presented to support this assumption.

Development of a primer–probe energy transfer based real-time PCR for the detection of Swine influenza virus

DEFF Research Database (Denmark)

Kowalczyk, Andrzej; Markowska-Daniel, Iwona; Rasmussen, Thomas Bruun

2013-01-01

Swine influenza virus (SIV) causes a contagious and requiring official notification disease of pigs and humans. In this study, a real-time reverse transcription-polymerase chain reaction (RT-PCR) assay based on primer–probe energy transfer (PriProET) for the detection of SIV RNA was developed...... of the specific product amplification. The assay is specific for influenza virus with a sensitivity of detection limit of approximately 10 copies of RNA by PCR. Based on serial dilutions of SIV, the detection limit of the assay was approximately 0.003 TCID50/ml for H1N1 A/Swine/Poland/KPR9/2004 virus. The Pri...

HybProbes-based real-time PCR assay for specific identification of Streptomyces scabies and Streptomyces europaeiscabiei, the potato common scab pathogens.

Science.gov (United States)

Xu, R; Falardeau, J; Avis, T J; Tambong, J T

2016-02-01

The aim of this study was to develop and validate a HybProbes-based real-time PCR assay targeting the trpB gene for specific identification of Streptomyces scabies and Streptomyces europaeiscabiei. Four primer pairs and a fluorescent probe were designed and evaluated for specificity in identifying S. scabies and Streptomyces europaeiscabiei, the potato common scab pathogens. The specificity of the HybProbes-based real-time PCR assay was evaluated using 46 bacterial strains, 23 Streptomyces strains and 23 non-Streptomyces bacterial species. Specific and strong fluorescence signals were detected from all nine strains of S. scabies and Streptomyces europaeiscabiei. No fluorescence signal was detected from 14 strains of other Streptomyces species and all non-Streptomyces strains. The identification was corroborated by the melting curve analysis that was performed immediately after the amplification step. Eight of the nine S. scabies and S. europaeiscabiei strains exhibited a unique melting peak, at Tm of 69·1°C while one strain, Warba-6, had a melt peak at Tm of 65·4°C. This difference in Tm peaks could be attributed to a guanine to cytosine mutation in strain Warba-6 at the region spanning the donor HybProbe. The reported HybProbes assay provides a more specific tool for accurate identification of S. scabies and S. europaeiscabiei strains. This study reports a novel assay based on HybProbes chemistry for rapid and accurate identification of the potato common scab pathogens. Since the HybProbes chemistry requires two probes for positive identification, the assay is considered to be more specific than conventional PCR or TaqMan real-time PCR. The developed assay would be a useful tool with great potential in early diagnosis and detection of common scab pathogens of potatoes in infected plants or for surveillance of potatoes grown in soil environment. © 2015 Her Majesty the Queen in Right of Canada © 2015 The Society for Applied Microbiology.

Simplified Pan-species Real-time PCR-based Detection of Plasmodium Spp. in Blood Smear.

Science.gov (United States)

Hassanpour, Gholamreza; Mirhendi, Hossein; Mohebali, Mehdi; Raeisi, Ahmad; Zeraati, Hojjat; Keshavarz, Hossein

2016-01-01

We aimed to quicken and simplify the detection of Plasmodium in blood samples by developing and testing a pan- Plasmodium real-time PCR for accurate screening of individuals suspected of malaria. A single primer/probe set for pan-species Plasmodium -specific real time PCR targeting a conserved region of the small subunit 18S ribosomal DNA was designed and evaluated for rapid diagnosis and screening of malaria infections using dried blood smears. FTA cards were used for rapid and simple DNA extraction. The primers and probes showed a positive response with the DNA extracted from bloods infected with P. falciparum and P. vivax but not with DNA extracted from various smears from uninfected blood samples. Seven positive cases positive by both microscopy and nested PCR were found among 280 blood samples taken from in South and Southeast Iran. Five samples were identified as positive for P. vivax and two as positive for P. falciparum . All positive samples were positive by real-time PCR. Furthermore, all 38-blood samples positive by microscopy were positive by real-time PCR. No microscopy-negative samples were positive by real-time PCR. By using a simple FTA card for DNA extraction and by application of the real-time PCR developed in this study, sensitivity similar to nested-PCR and microscopy was achieved. This format simplifies the detection of Plasmodium in large numbers of samples.

Searching for the best real-time RT-PCRs to detect Zika virus infections: the importance of comparing several protocols

Directory of Open Access Journals (Sweden)

F.M. de Moraes

2018-05-01

Full Text Available Clinical manifestations of Zika, dengue, and chikungunya virus infections are very similar, making it difficult to reach a diagnosis based only on clinical grounds. In addition, there is an intense cross-reactivity between antibodies directed to Zika virus and other flaviviruses, and an accurate Zika diagnosis is best achieved by real-time RT-PCR. However, some real-time RT-PCR show better performance than others. To reach the best possible Zika diagnosis, the analytic sensitivity of some probe-based real-time RT-PCR amplifying Zika virus RNA was evaluated in spiked and clinical samples. We evaluated primers and probes to detect Zika virus, which had been published before, and tested sensitivity using serum spiked and patient samples by real-time RT-PCR. When tested against spiked samples, the previously described primers showed different sensitivity, with very similar results when samples from patients (serum and urine were analyzed. Real-time RT-PCR designed to amplify Zika virus NS1 showed the best analytical sensitivity for all samples.

Real-time PCR assay using fine-needle aspirates and tissue biopsy specimens for rapid diagnosis of mycobacterial lymphadenitis in children

NARCIS (Netherlands)

Bruijnesteijn van Coppenraet, E. S.; Lindeboom, J. A.; Prins, J. M.; Peeters, M. F.; Claas, E. C. J.; Kuijper, E. J.

2004-01-01

A real-time PCR assay was developed to diagnose and identify the causative agents of suspected mycobacterial lymphadenitis. Primers and probes for the real-time PCR were designed on the basis of the internal transcribed spacer sequence, enabling the recognition of the genus Mycobacterium and the

Development of a non invasion real-time PCR assay for the quantitation of chicken parvovirus in fecal swabs

Science.gov (United States)

The present study describes the development of a real time Taqman polymerase chain reaction (PCR) assay using a fluorescent labeled probe for the detection and quantitation of chicken parvovirus (ChPV) in feces. The primers and probes were designed based on the nucleotide sequence of the non struct...

Multiplex real-time PCR (TaqMan) assay for the simultaneous detection and discrimination of potato powdery and common scab diseases and pathogens.

Science.gov (United States)

Qu, X S; Wanner, L A; Christ, B J

2011-03-01

To develop a multiplex real-time PCR assay using TaqMan probes for the simultaneous detection and discrimination of potato powdery scab and common scab, two potato tuber diseases with similar symptoms, and the causal pathogens Spongospora subterranea and plant pathogenic Streptomyces spp. Real-time PCR primers and a probe for S. subterranea were designed based on the DNA sequence of the ribosomal RNA ITS2 region. Primers and a probe for pathogenic Streptomyces were designed based on the DNA sequence of the txtAB genes. The two sets of primer pairs and probes were used in a single real-time PCR assay. The multiplex real-time PCR assay was confirmed to be specific for S. subterranea and pathogenic Streptomyces. The assay detected DNA quantities of 100 fg for each of the two pathogens and linear responses and high correlation coefficients between the amount of DNA and C(t) values for each pathogen were achieved. The presence of two sets of primer pairs and probes and of plant extracts did not alter the sensitivity and efficiency of multiplex PCR amplification. Using the PCR assay, we could discriminate between powdery scab and common scab tubers with similar symptoms. Common scab and powdery scab were detected in some tubers with no visible symptoms. Mixed infections of common scab and powdery scab on single tubers were also revealed. This multiplex real-time PCR assay is a rapid, cost efficient, specific and sensitive tool for the simultaneous detection and discrimination of the two pathogens on infected potato tubers when visual symptoms are inconclusive or not present. Accurate and quick identification and discrimination of the cause of scab diseases on potatoes will provide critical information to potato growers and researchers for disease management. This is important because management strategies for common and powdery scab diseases are very different. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Real-Time Probing of Structural Dynamics by Interaction between Chromophores

DEFF Research Database (Denmark)

Brogaard, Rasmus Y.; Møller, Klaus Braagaard; Sølling, Theis Ivan

2011-01-01

We present an investigation of structural dynamics in excited-state cations probed in real-time by femtosecond timeresolved ion photofragmentation spectroscopy. From photoelectron spectroscopy data on 1,3-dibromopropane we conclude that the pump pulse ionizes the molecule, populating an excited...

Simplified Pan-species Real-time PCR-based Detection of Plasmodium Spp. in Blood Smear

Directory of Open Access Journals (Sweden)

Gholamreza HASSANPOUR

2016-12-01

Full Text Available Background: We aimed to quicken and simplify the detection of Plasmodium in blood samples by developing and testing a pan-Plasmodium real-time PCR for accurate screening of individuals suspected of malaria.Methods: A single primer/probe set for pan-species Plasmodium-specific real time PCR targeting a conserved region of the small subunit 18S ribosomal DNA was designed and evaluated for rapid diagnosis and screening of malaria infections using dried blood smears. FTA cards were used for rapid and simple DNA extraction.Results: The primers and probes showed a positive response with the DNA extracted from bloods infected with P. falciparum and P. vivax but not with DNA extracted from various smears from uninfected blood samples. Seven positive cases positive by both microscopy and nested PCR were found among 280 blood samples taken from in South and Southeast Iran. Five samples were identified as positive for P. vivax and two as positive for P. falciparum. All positive samples were positive by real-time PCR. Furthermore, all 38-blood samples positive by microscopy were positive by real-time PCR. No microscopy-negative samples were positive by real-time PCR.Conclusion: By using a simple FTA card for DNA extraction and by application of the real-time PCR developed in this study, sensitivity similar to nested-PCR and microscopy was achieved. This format simplifies the detection of Plasmodium in large numbers of samples.

Improvement of a real-time RT-PCR assay for the detection of enterovirus RNA

Directory of Open Access Journals (Sweden)

Bruynseels Peggy

2009-07-01

Full Text Available Abstract We describe an improvement of an earlier reported real-time RT-PCR assay for the detection of enterovirus RNA, based on the 5' exonuclease digestion of a dual-labeled fluorogenic probe by Taq DNA polymerase. A different extraction method, real-time RT-PCR instrument and primer set were evaluated. Our data show that the optimized assay yields a higher sensitivity and reproducibility and resulted in a significant reduced hands-on time per sample.

Real time Faraday spectrometer

Science.gov (United States)

Smith, Jr., Tommy E.; Struve, Kenneth W.; Colella, Nicholas J.

1991-01-01

This invention uses a dipole magnet to bend the path of a charged particle beam. As the deflected particles exit the magnet, they are spatially dispersed in the bend-plane of the magnet according to their respective momenta and pass to a plurality of chambers having Faraday probes positioned therein. Both the current and energy distribution of the particles is then determined by the non-intersecting Faraday probes located along the chambers. The Faraday probes are magnetically isolated from each other by thin metal walls of the chambers, effectively providing real time current-versus-energy particle measurements.

Real time Faraday spectrometer

International Nuclear Information System (INIS)

Smith, T.E.; Struve, K.W.; Colella, N.J.

1991-01-01

This patent describes an invention which uses a dipole magnet to bend the path of a charged particle beam. As the deflected particles exit the magnet, they are spatially dispersed in the bend-plane of the magnet according to their respective momenta and pass to a plurality of chambers having Faraday probes positioned therein. Both the current and energy distribution of the particles is then determined by the non-intersecting Faraday probes located along the chambers. The Faraday probes are magnetically isolated from each other by thin metal walls of the chambers, effectively providing real time current-versus-energy particle measurements

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

Science.gov (United States)

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.

A novel duplex real-time reverse transcriptase-polymerase chain reaction assay for the detection of hepatitis C viral RNA with armored RNA as internal control

Directory of Open Access Journals (Sweden)

Meng Shuang

2010-06-01

Full Text Available Abstract Background The hepatitis C virus (HCV genome is extremely heterogeneous. Several HCV infections can not be detected using currently available commercial assays, probably because of mismatches between the template and primers/probes. By aligning the HCV sequences, we developed a duplex real-time reverse transcriptase-polymerase chain reaction (RT-PCR assay using 2 sets of primers/probes and a specific armored RNA as internal control. The 2 detection probes were labelled with the same fluorophore, namely, 6-carboxyfluorescein (FAM, at the 5' end; these probes could mutually combine, improving the power of the test. Results The limit of detection of the duplex primer/probe assay was 38.99 IU/ml. The sensitivity of the assay improved significantly, while the specificity was not affected. All HCV genotypes in the HCV RNA Genotype Panel for Nucleic Acid Amplification Techniques could be detected. In the testing of 109 serum samples, the performance of the duplex real-time RT-PCR assay was identical to that of the COBAS AmpliPrep (CAP/COBAS TaqMan (CTM assay and superior to 2 commercial HCV assay kits. Conclusions The duplex real-time RT-PCR assay is an efficient and effective viral assay. It is comparable with the CAP/CTM assay with regard to the power of the test and is appropriate for blood-donor screening and laboratory diagnosis of HCV infection.

[REAL TIME POLYMERASE CHAIN REACTION IN TULAREMIA LABORATORY DIAGNOSTICS].

Science.gov (United States)

Kormilitsyna, M I; Mescheryakova, I S; Mikhailova, T V; Dobrovolsky, A A

2015-01-01

Enhancement of tularemia laboratory diagnostics by F. tularensis DNA determination in blood sera of patients using real time polymerase chain reaction (RT-PCR). 39 blood sera of patients obtained during transmissive epidemic outbreak of tularemia in Khanty-Mansiysk in 2013 were studied in agglutination reaction, passive hemagglutination, RT-PCR. Specific primers and fluorescent probes were used: ISFTu2F/R+ISFTu2P, Tu14GF/R+tul4-PR2. Advantages of using RT-PCR for early diagnostics of tularemia, when specific antibodies are not detected using traditional immunologic methods, were established. Use of a combination of primers and ISFTu2F/R+ISFTu2P probe allowed to detect F. tularensis DNA in 100% of sera, whereas Tul4G F/R+tul4-PR2 combination--92% of sera. The data were obtained when DNA was isolated from sera using "Proba Rapid" express method. Clinical-epidemiologic diagnosis oftularemia was confirmed by both immune-serologic and RT-PCR methods when sera were studied 3-4 weeks after the onset of the disease. RT-PCR with ISFTu2F/R primers and fluorescent probe ISFTu2P, having high sensitivity and specificity, allows to determine F. tularensis DNA in blood sera of patients at both the early stage and 3-4 weeks after the onset of the disease.

Quantification of low-expressed mRNA using 5' LNA-containing real-time PCR primers

International Nuclear Information System (INIS)

Malgoyre, A.; Banzet, S.; Mouret, C.; Bigard, A.X.; Peinnequin, A.

2007-01-01

Real-time RT-PCR is the most sensitive and accurate method for mRNA quantification. Using specific recombinant DNA as a template, real-time PCR allows accurate quantification within a 7-log range and increased sensitivity below 10 copies. However, when using RT-PCR to quantify mRNA in biological samples, a stochastic off-targeted amplification can occur. Classical adjustments of assay parameters have minimal effects on such amplification. This undesirable amplification appears mostly to be dependent on specific to non-specific target ratio rather than on the absolute quantity of the specific target. This drawback, which decreases assay reliability, mostly appears when quantifying low-expressed transcript in a whole organ. An original primer design using properties of LNA allows to block off-target amplification. 5'-LNA substitution strengthens 5'-hybridization. Consequently on-target hybridization is stabilized and the probability for the off-target to lead to amplification is decreased

China Energy Primer

Energy Technology Data Exchange (ETDEWEB)

Ni, Chun Chun

2009-11-16

Based on extensive analysis of the 'China Energy Databook Version 7' (October 2008) this Primer for China's Energy Industry draws a broad picture of China's energy industry with the two goals of helping users read and interpret the data presented in the 'China Energy Databook' and understand the historical evolution of China's energy inustry. Primer provides comprehensive historical reviews of China's energy industry including its supply and demand, exports and imports, investments, environment, and most importantly, its complicated pricing system, a key element in the analysis of China's energy sector.

[A novel TaqMan® MGB probe for specifically detecting Streptococcus mutans].

Science.gov (United States)

Zheng, Hui; Lin, Jiu-Xiang; DU, Ning; Chen, Feng

2013-10-18

To design a new TaqMan® MGB probe for improving the specificity of Streptococcus mutans's detection. We extracted six DNA samples from different streptococcal strains for PCR reaction. Conventional nested PCR and TaqMan® MGB real-time PCR were applied independently. The first round of nested PCR was carried out with the bacterial universal primers, while a second PCR was conducted by using primers specific for the 16S rRNA gene of Streptococcus mutans. The TaqMan® MGB probe for Streptococcus mutans was designed from sequence analyses, and the primers were the same as nested PCR. Streptococcus mutans DNA with 2.5 mg/L was sequentially diluted at 5-fold intervals to 0.16 μg/L. Standard DNA samples were used to generate standard curves by TaqMan® MGB real-time PCR. In the nested PCR, the primers specific for Streptococcus mutans also detected Streptococcus gordonii with visible band of 282 bp, giving false-positive results. In the TaqMan® MGB real-time PCR reaction, only Streptococcus mutans was detected. The detection limitation of TaqMan® MGB real-time PCR for Streptococcus mutans 16S rRNA gene was 20 μg/L. We designed a new TaqMan® MGB probe, and successfully set up a PCR based method for detecting oral Streptococcus mutans. TaqMan® MGB real-time PCR is a both specific and sensitive bacterial detection method.

Mycoplasma detection by triplex real-time PCR in bronchoalveolar lavage fluid from bovine respiratory disease complex cases

NARCIS (Netherlands)

Cornelissen, Jan B.W.J.; Bree, de Freddy M.; Wal, van der Fimme J.; Kooij, Engbert A.; Koene, Miriam G.J.; Bossers, Alex; Smid, Bregtje; Antonis, Adriaan F.; Wisselink, Henk J.

2017-01-01

Background: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. bovis and M. bovirhinis, all three associated with bovine respiratory disease (BRD). Primers and probes of the RespoCheck

Quantitative Real-Time PCR using the Thermo Scientific Solaris qPCR Assay

Science.gov (United States)

Ogrean, Christy; Jackson, Ben; Covino, James

2010-01-01

The Solaris qPCR Gene Expression Assay is a novel type of primer/probe set, designed to simplify the qPCR process while maintaining the sensitivity and accuracy of the assay. These primer/probe sets are pre-designed to >98% of the human and mouse genomes and feature significant improvements from previously available technologies. These improvements were made possible by virtue of a novel design algorithm, developed by Thermo Scientific bioinformatics experts. Several convenient features have been incorporated into the Solaris qPCR Assay to streamline the process of performing quantitative real-time PCR. First, the protocol is similar to commonly employed alternatives, so the methods used during qPCR are likely to be familiar. Second, the master mix is blue, which makes setting the qPCR reactions easier to track. Third, the thermal cycling conditions are the same for all assays (genes), making it possible to run many samples at a time and reducing the potential for error. Finally, the probe and primer sequence information are provided, simplifying the publication process. Here, we demonstrate how to obtain the appropriate Solaris reagents using the GENEius product search feature found on the ordering web site (www.thermo.com/solaris) and how to use the Solaris reagents for performing qPCR using the standard curve method. PMID:20567213

Validation of a Non-Specific Dye Real-Time PCR Assay for Porcine Adulteration in Meatball Using ND5 Primer

Directory of Open Access Journals (Sweden)

Tri Joko Raharjo

2017-07-01

Full Text Available Porcine adulteration in meatball samples were analyzed using real-time polymerase chain reaction (RT-PCR, based on the ND5 primer obtained by previous study. This work consisted of three stages which were annealing temperature optimization, method validation, and application. DNA template was extracted using phenol-CIAA (chloroform-iso amyl alcohol method. The optimum annealing temperature for ND5 primers (forward primer 5'-CATTCGCCTCACTCACATTAACC-3' and reverse primer 5'-AAGAGAGAGTTCTACGGTCTGTAG-3' was 58.0 °C, obtained after testing annealing at 50.5 to 59.5 °C gradient temperature with 5 °C interval. Melting curve analysis was done at 65.0 to 95.0 °C, with increasing temperature for 0.5 °C per 2 sec. Method was validated for its specificity, precision and limit of detection. RT-PCR method with ND5 primers produced 227 bp DNA fragment with 78.50 °C Tm value. From eight commercial meatball samples, one was detected containing porcine. The methods showed high specificity and precision, with experimentally determined limits for porcine were no less than 1%.

Simultaneous quantitative assessment of circulating cell-free mitochondrial and nuclear DNA by multiplex real-time PCR

Directory of Open Access Journals (Sweden)

Peng Xia

2009-01-01

Full Text Available Quantification of circulating nucleic acids in plasma and serum could be used as a non-invasive diagnostic tool for monitoring a wide variety of diseases and conditions. We describe here a rapid, simple and accurate multiplex real-time PCR method for direct synchronized analysis of circulating cell-free (ccf mitochondrial (mtDNA and nuclear (nDNA DNA in plasma and serum samples. The method is based on one-step multiplex real-time PCR using a FAM-labeled MGB probe and primers to amplify the mtDNA sequence of the ATP 8 gene, and a VIC-labeled MGB probe and primers to amplify the nDNA sequence of the glycerinaldehyde-3-phosphate-dehydrogenase (GAPDH gene, in plasma and serum samples simultaneously. The efficiencies of the multiplex assays were measured in serial dilutions. Based on the simulation of the PCR reaction kinetics, the relative quantities of ccf mtDNA were calculated using a very simple equation. Using our optimised real-time PCR conditions, close to 100% efficiency was obtained from the two assays. The two assays performed in the dilution series showed very good and reproducible correlation to each other. This optimised multiplex real-time PCR protocol can be widely used for synchronized quantification of mtDNA and nDNA in different samples, with a very high rate of efficiency.

An Undergraduate Laboratory Experiment for Upper-Level Forensic Science, Biochemistry, or Molecular Biology Courses: Human DNA Amplification Using STR Single Locus Primers by Real-Time PCR with SYBR Green Detection

Science.gov (United States)

Elkins, Kelly M.; Kadunc, Raelynn E.

2012-01-01

In this laboratory experiment, real-time polymerase chain reaction (real-time PCR) was conducted using published human TPOX single-locus DNA primers for validation and various student-designed short tandem repeat (STR) primers for Combined DNA Index System (CODIS) loci. SYBR Green was used to detect the amplification of the expected amplicons. The…

TaqMan probe real-time polymerase chain reaction assay for the quantification of canine DNA in chicken nugget.

Science.gov (United States)

Rahman, Md Mahfujur; Hamid, Sharifah Bee Abd; Basirun, Wan Jefrey; Bhassu, Subha; Rashid, Nur Raifana Abdul; Mustafa, Shuhaimi; Mohd Desa, Mohd Nasir; Ali, Md Eaqub

2016-01-01

This paper describes a short-amplicon-based TaqMan probe quantitative real-time PCR (qPCR) assay for the quantitative detection of canine meat in chicken nuggets, which are very popular across the world, including Malaysia. The assay targeted a 100-bp fragment of canine cytb gene using a canine-specific primer and TaqMan probe. Specificity against 10 different animals and plants species demonstrated threshold cycles (Ct) of 16.13 ± 0.12 to 16.25 ± 0.23 for canine DNA and negative results for the others in a 40-cycle reaction. The assay was tested for the quantification of up to 0.01% canine meat in deliberately spiked chicken nuggets with 99.7% PCR efficiency and 0.995 correlation coefficient. The analysis of the actual and qPCR predicted values showed a high recovery rate (from 87% ± 28% to 112% ± 19%) with a linear regression close to unity (R(2) = 0.999). Finally, samples of three halal-branded commercial chicken nuggets collected from different Malaysian outlets were screened for canine meat, but no contamination was demonstrated.

Real-time scintillation probe measurement of left ventricular function

International Nuclear Information System (INIS)

Green, M.V.; Ostrow, H.G.; Bacharach, S.L.; Allen, S.I.; Bonow, R.O.; Johnston, G.S.

1981-01-01

The micro-processor based system described in this report was designed for maximum flexibility and utility. While the principle function of the system is to acquire, create, analyze and display (in real-time) left ventricular time activity (or volume) curves, provision is also made to acquire additional physiologic signals (e.g., ECG, flowmeter, etc.) and to calculate and display relationships between these various data. The system was designed for interactive use so that the system user can alter the course of a series of measurements based on previous results. These general capabilities are illustrated with several examples. In the first, LV function was measured continuously in a subject from (supine) rest through exercise and recovery. The second example illustrates the use of the system in acquiring (LV) pressure-volume loops. Several technical problems, such as correction for LV background radiation, appear at present to limit the probes applicability. Even now, however, probe systems are demonstrably useful in the study of global left ventricular function when this function is changing rapidly with time in response to various interventions. (orig.) [de

Sensitive detection of porcine DNA in processed animal proteins using a TaqMan real-time PCR assay.

Science.gov (United States)

Pegels, N; González, I; Fernández, S; García, T; Martín, R

2012-01-01

A TaqMan real-time PCR method was developed for specific detection of porcine-prohibited material in industrial feeds. The assay combines the use of a porcine-specific primer pair, which amplifies a 79 bp fragment of the mitochondrial (mt) 12 S rRNA gene, and a locked nucleic acid (LNA) TaqMan probe complementary to a target sequence lying between the porcine-specific primers. The nuclear 18 S rRNA gene system, yielding a 77 bp amplicon, was employed as a positive amplification control to monitor the total content of amplifiable DNA in the samples. The specificity of the porcine primers-probe system was verified against different animal and plant species, including mammals, birds and fish. The applicability of the real-time PCR protocol to detect the presence of porcine mt DNA in feeds was determined through the analysis of 190 industrial feeds (19 known reference and 171 blind samples) subjected to stringent processing treatments. The performance of the method allows qualitative and highly sensitive detection of short fragments from porcine DNA in all the industrial feeds declared to contain porcine material. Although the method has quantitative potential, the real quantitative capability of the assay is limited by the existing variability in terms of composition and processing conditions of the feeds, which affect the amount and quality of amplifiable DNA.

Establishment of a novel two-probe real-time PCR for simultaneously quantification of hepatitis B virus DNA and distinguishing genotype B from non-B genotypes.

Science.gov (United States)

Wang, Wei; Liang, Hongpin; Zeng, Yongbin; Lin, Jinpiao; Liu, Can; Jiang, Ling; Yang, Bin; Ou, Qishui

2014-11-01

Establishment of a simple, rapid and economical method for quantification and genotyping of hepatitis B virus (HBV) is of great importance for clinical diagnosis and treatment of chronic hepatitis B patients. We hereby aim to develop a novel two-probe real-time PCR for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes. Conserved primers and TaqMan probes for genotype B and non-B genotypes were designed. The linear range, detection sensitivity, specificity and repeatability of the method were assessed. 539 serum samples from HBV-infected patients were assayed, and the results were compared with commercial HBV quantification and HBV genotyping kits. The detection sensitivity of the two-probe real-time PCR was 500IU/ml; the linear range was 10(3)-10(9)IU/ml, and the intra-assay CVs and inter-assay CVs were between 0.84% and 2.80%. No cross-reaction was observed between genotypes B and non-B. Of the 539 detected samples, 509 samples were HBV DNA positive. The results showed that 54.0% (275/509) of the samples were genotype B, 39.5% (201/509) were genotype non-B and 6.5% (33/509) were mixed genotype. The coincidence rate between the method and a commercial HBV DNA genotyping kit was 95.9% (488/509, kappa=0.923, PDNA qPCR kit were achieved. A novel two-probe real-time PCR method for simultaneous quantification of HBV viral concentration and distinguishing genotype B from non-B genotypes was established. The assay was sensitive, specific and reproducible which can be applied to areas prevalent with HBV genotypes B and C, especially in China. Copyright © 2014 Elsevier B.V. All rights reserved.

Determination of the species specificity of the primers for the detection of chicken and turkey meat by realtime PCR method

Directory of Open Access Journals (Sweden)

Lenka Maršálková

2014-07-01

Full Text Available The aim of this work was to use TaqMan Real-Time PCR for quantitative authentication of chicken and turkey meat. To meet this purpose, a specific pair of primers and TaqMan probe was used. The test was aimed at identifying the reaction cycle of turkey and chicken meat using by two sets of primers. With first set of primer designed for chicken we obtained the following results: Cp = 16.18 for 100% chicken DNA Cp = 29, 18 100% turkey DNA It was also amplified DNA of pig that exceeded the detection threshold fluorescence intensities in the 31.07 cycle (Cp = 31.07. Using primers designed for turkey we obtained the following results Cp = 31.16 for 100% CHDNA, Cp =16.18 100% TDNA. It was also amplified the 100% DNA of rabbit in 31.63 cycle (Cp = 31.63 and deer in cycle 32 (Cp = 32. The DNA of all other animal species was amplificated after more than 35 cycles (Cp >35. It follows that the second detection primer pair is specific enough to unrelated species of animals by 30 cycles of the reaction. Species authentication based on DNA analysis from this perspective overcomes all the shortcomings of proteins. At present, DNA analysis use different types of PCR. Is the most progressive Real-time PCR, which is suitable for the specific use of detection (primers and TaqMan probe. The TaqMan Real-time PCR is within the sensitivity and specificity, clearly one of the best methods for identifying the species of chicken and turkey meat. The specificity of this method, however, depends primarily on the specificity of the primers and TaqMan probe. The 30 cycle reaction was chosen by us as the threshold for specificity using primers for authentication chicken and turkey meat.

Detection of Histoplasma capsulatum from clinical specimens by cycling probe-based real-time PCR and nested real-time PCR.

Science.gov (United States)

Muraosa, Yasunori; Toyotome, Takahito; Yahiro, Maki; Watanabe, Akira; Shikanai-Yasuda, Maria Aparecida; Kamei, Katsuhiko

2016-05-01

We developed new cycling probe-based real-time PCR and nested real-time PCR assays for the detection of Histoplasma capsulatum that were designed to detect the gene encoding N-acetylated α-linked acidic dipeptidase (NAALADase), which we previously identified as an H. capsulatum antigen reacting with sera from patients with histoplasmosis. Both assays specifically detected the DNAs of all H. capsulatum strains but not those of other fungi or human DNA. The limited of detection (LOD) of the real-time PCR assay was 10 DNA copies when using 10-fold serial dilutions of the standard plasmid DNA and 50 DNA copies when using human serum spiked with standard plasmid DNA. The nested real-time PCR improved the LOD to 5 DNA copies when using human serum spiked with standard plasmid DNA, which represents a 10-fold higher than that observed with the real-time PCR assay. To assess the ability of the two assays to diagnose histoplasmosis, we analyzed a small number of clinical specimens collected from five patients with histoplasmosis, such as sera (n = 4), formalin-fixed paraffin-embedded (FFPE) tissue (n = 4), and bronchoalveolar lavage fluid (BALF) (n = 1). Although clinical sensitivity of the real-time PCR assay was insufficiently sensitive (33%), the nested real-time PCR assay increased the clinical sensitivity (77%), suggesting it has a potential to be a useful method for detecting H. capsulatum DNA in clinical specimens. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Design and Validation of Real-Time PCR: Quantitative Diagnosis of Common Leishmania Species in Iran.

Science.gov (United States)

Fekri Soofi Abadi, Maryam; Dabiri, Shahriar; Fotouhi Ardakani, Reza; Fani Malaki, Lina; Amirpoor Rostami, Sahar; Ziasistani, Mahsa; Dabiri, Donya

2016-07-01

Design and validation of Real-time PCR on the protected gene region ITS2 to quantify the parasite load in common leishmania (L) species. Probe and primer were designed from the ITS2 region between the rRNA genes with minimum gene variation in three common leishmania species followed by a Real-time PCR using the Taq man probe method in the form of absolute quantification. A series of different concentrations of leishmania were analyzed. After the purified PCR product was successfully placed in a PTG19-T plasmid vector, specialized ITS2 region was cloned in this plasmid. In the last phase, the cloned gene was transferred to the Ecoli.Top10F bacteria. The standard plasmid was provided in 10(7) to 10(1) copies/rxn concentrations. The specification and clinical sensitivity of the data was analyzed using inter and intra scales. The probe and primer were designed using three species, including L. infantum, L. major, and L.tropica. Seven concentrations of purified parasite in culture media showed that the selected region for quantifying the parasite is suitable. Clinical and analytical specificity and sensitivity were both 100%, respectively. The Taq man method for the ITS2 region in leishmania is one the most sensitive diagnostic test for identifying the parasite load and is suggested as a tool for fast identification and quantification of species.

Real-time PCR array as a universal platform for the detection of genetically modified crops and its application in identifying unapproved genetically modified crops in Japan.

Science.gov (United States)

Mano, Junichi; Shigemitsu, Natsuki; Futo, Satoshi; Akiyama, Hiroshi; Teshima, Reiko; Hino, Akihiro; Furui, Satoshi; Kitta, Kazumi

2009-01-14

We developed a novel type of real-time polymerase chain reaction (PCR) array with TaqMan chemistry as a platform for the comprehensive and semiquantitative detection of genetically modified (GM) crops. Thirty primer-probe sets for the specific detection of GM lines, recombinant DNA (r-DNA) segments, endogenous reference genes, and donor organisms were synthesized, and a 96-well PCR plate was prepared with a different primer-probe in each well as the real-time PCR array. The specificity and sensitivity of the array were evaluated. A comparative analysis with the data and publicly available information on GM crops approved in Japan allowed us to assume the possibility of unapproved GM crop contamination. Furthermore, we designed a Microsoft Excel spreadsheet application, Unapproved GMO Checker version 2.01, which helps process all the data of real-time PCR arrays for the easy assumption of unapproved GM crop contamination. The spreadsheet is available free of charge at http://cse.naro.affrc.go.jp/jmano/index.html .

A method for automatically extracting infectious disease-related primers and probes from the literature

Directory of Open Access Journals (Sweden)

Pérez-Rey David

2010-08-01

Full Text Available Abstract Background Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1 convert each document into a tree of paper sections, (2 detect the candidate sequences using a set of finite state machine-based recognizers, (3 refine problem sequences using a rule-based expert system, and (4 annotate the extracted sequences with their related organism/gene information. Results We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. Conclusions We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch.

Evaluation of a duplex reverse-transcription real-time PCR assay for the detection of encephalomyocarditis virus.

Science.gov (United States)

Qin, Shaomin; Underwood, Darren; Driver, Luke; Kistler, Carol; Diallo, Ibrahim; Kirkland, Peter D

2018-06-01

We evaluated a fluorogenic probe-based assay for the detection of encephalomyocarditis virus (EMCV) by comparing a set of published primers and probe to a new set of primers and probe. The published reagents failed to amplify a range of Australian isolates and an Italian reference strain of EMCV. In contrast, an assay based on 2 new sets of primers and probes that were run in a duplex reverse-transcription real-time PCR (RT-rtPCR) worked well, with high amplification efficiency. The analytical sensitivity was ~100-fold higher than virus isolation in cell culture. The intra-assay variation was 0.21-4.90%. No cross-reactivity was observed with a range of other porcine viruses. One hundred and twenty-two clinical specimens were tested simultaneously by RT-rtPCR and virus isolation in cell culture; 72 specimens gave positive results by RT-rtPCR, and 63 of these were also positive by virus isolation. Of 245 archived cell culture isolates of EMCV that were tested in the RT-rtPCR, 242 samples were positive. The new duplex RT-rtPCR assay is a reliable tool for the detection of EMCV in clinical specimens and for use in epidemiologic investigations.

Improved real-time PCR assay for detection of the quarantine potato pathogen, Synchytrium endobioticum, in zonal centrifuge extracts from soil and in plants

NARCIS (Netherlands)

Gent-Pelzer, van M.P.E.; Krijger, M.C.; Bonants, P.J.M.

2010-01-01

Real-time PCR was used for quantitative detection of the potato pathogen, Synchytrium endobioticum, in different substrates: zonal centrifuge extracts, warts and different plant parts of potato. Specific primers and a TaqMan probe, designed from the internal transcribed spacer region of the

Early experience in centralized real time energy market

International Nuclear Information System (INIS)

Alaywan, Z.; Hernandez, L.; Martin, M.

2005-01-01

The current structure of the California Independent System Operator (ISO) was described. The study provided an outline of California's transition from a decentralized pool operation to a forward bilateral market through the implementation of a centralized real time market. Details of the institutional, economic and technological history of the power system were provided. Although the California real time market was implemented in order to simplify the power system, a number of operational challenges were observed. Discontinuities in the energy curve resulted in the implementation of a target price process, which aimed to resolve the overlap in energy bids. The design of the ISO's real time market did not provide a mechanism for bidders to execute real time energy trades. Regulation bidders also internalized energy in their regulation capacity bids. The real time market application (RTMA) provided the ISO with a substantial computer program to determine and account for nearly all aspects of generation unit scheduling and physical characteristics with a multiple ramp rate. The program combined optimal power flow (OPF) logic for energy flows in addition to mixed-integer nonlinear optimization of trading schedules, and system and security constraints. The RTMA used a multi-period security constrained economic dispatch (SCED) function to optimize energy dispatch schedules. Other features of the RTMA included security constrained unit commitment, security constrained economic dispatch, and dispatch schedule post processes. It was concluded that implementation of the RTMA has increased the efficiency of the ISO. A case study of the RTMA during an outage in November 2004 was provided. 5 refs., 1 tab., 2 figs

Real-time multiplex PCR assay for detection of Yersinia pestis and Yersinia pseudotuberculosis.

Science.gov (United States)

Matero, Pirjo; Pasanen, Tanja; Laukkanen, Riikka; Tissari, Päivi; Tarkka, Eveliina; Vaara, Martti; Skurnik, Mikael

2009-01-01

A multiplex real-time polymerase chain reaction (PCR) assay was developed for the detection of Yersinia pestis and Yersinia pseudotuberculosis. The assay includes four primer pairs, two of which are specific for Y. pestis, one for Y. pestis and Y. pseudotuberculosis and one for bacteriophage lambda; the latter was used as an internal amplification control. The Y. pestis-specific target genes in the assay were ypo2088, a gene coding for a putative methyltransferase, and the pla gene coding for the plasminogen activator. In addition, the wzz gene was used as a target to specifically identify both Y. pestis and the closely related Y. pseudotuberculosis group. The primer and probe sets described for the different genes can be used either in single or in multiplex PCR assays because the individual probes were designed with different fluorochromes. The assays were found to be both sensitive and specific; the lower limit of the detection was 10-100 fg of extracted Y. pestis or Y. pseudotuberculosis total DNA. The sensitivity of the tetraplex assay was determined to be 1 cfu for the ypo2088 and pla probe labelled with FAM and JOE fluorescent dyes, respectively.

A TaqMan real-time PCR-based assay for the identification of Fasciola spp.

Science.gov (United States)

Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Jowers, Michael J; Baños, Pablo Díez; Píriz, Ana; Fickel, Joerns; Zhu, Xing-Quan

2011-06-30

Real time quantitative PCR (qPCR) is one of the key technologies of the post-genome era, with clear advantages compared to normal end-point PCR. In this paper, we report the first qPCR-based assay for the identification of Fasciola spp. Based on sequences of the second internal transcribed spacers (ITS-2) of the ribosomal rRNA gene, we used a set of genus-specific primers for Fasciola ITS-2 amplification, and we designed species-specific internal TaqMan probes to identify F. hepatica and F. gigantica, as well as the hybrid 'intermediate'Fasciola. These primers and probes were used for the highly specific, sensitive, and simple identification of Fasciola species collected from different animal host from China, Spain, Niger and Egypt. The novel qPCR-based technique for the identification of Fasciola spp. may provide a useful tool for the epidemiological investigation of Fasciola infection, including their intermediate snail hosts. Copyright © 2011 Elsevier B.V. All rights reserved.

Development of Prevotella intermedia-specific PCR primers based on the nucleotide sequences of a DNA probe Pig27.

Science.gov (United States)

Kim, Min Jung; Hwang, Kyung Hwan; Lee, Young-Seok; Park, Jae-Yoon; Kook, Joong-Ki

2011-03-01

The aim of this study was to develop Prevotella intermedia-specific PCR primers based on the P. intermedia-specific DNA probe. The P. intermedia-specific DNA probe was screened by inverted dot blot hybridization and confirmed by Southern blot hybridization. The nucleotide sequences of the species-specific DNA probes were determined using a chain termination method. Southern blot analysis showed that the DNA probe, Pig27, detected only the genomic DNA of P. intermedia strains. PCR showed that the PCR primers, Pin-F1/Pin-R1, had species-specificity for P. intermedia. The detection limits of the PCR primer sets were 0.4pg of the purified genomic DNA of P. intermedia ATCC 49046. These results suggest that the PCR primers, Pin-F1/Pin-R1, could be useful in the detection of P. intermedia as well as in the development of a PCR kit in epidemiological studies related to periodontal diseases. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

Real time diagnosis of bladder cancer with probe-based confocal laser endomicroscopy

Science.gov (United States)

Liu, Jen-Jane; Wu, Katherine; Adams, Winifred; Hsiao, Shelly T.; Mach, Kathleen E.; Beck, Andrew H.; Jensen, Kristin C.; Liao, Joseph C.

2011-02-01

Probe-based confocal laser endomicroscopy (pCLE) is an emerging technology for in vivo optical imaging of the urinary tract. Particularly for bladder cancer, real time optical biopsy of suspected lesions will likely lead to improved management of bladder cancer. With pCLE, micron scale resolution is achieved with sterilizable imaging probes (1.4 or 2.6 mm diameter), which are compatible with standard cystoscopes and resectoscopes. Based on our initial experience to date (n = 66 patients), we have demonstrated the safety profile of intravesical fluorescein administration and established objective diagnostic criteria to differentiate between normal, benign, and neoplastic urothelium. Confocal images of normal bladder showed organized layers of umbrella cells, intermediate cells, and lamina propria. Low grade bladder cancer is characterized by densely packed monomorphic cells with central fibrovascular cores, whereas high grade cancer consists of highly disorganized microarchitecture and pleomorphic cells with indistinct cell borders. Currently, we are conducting a diagnostic accuracy study of pCLE for bladder cancer diagnosis. Patients scheduled to undergo transurethral resection of bladder tumor are recruited. Patients undergo first white light cystocopy (WLC), followed by pCLE, and finally histologic confirmation of the resected tissues. The diagnostic accuracy is determined both in real time by the operative surgeon and offline after additional image processing. Using histology as the standard, the sensitivity, specificity, positive and negative predictive value of WLC and WLC + pCLE are calculated. With additional validation, pCLE may prove to be a valuable adjunct to WLC for real time diagnosis of bladder cancer.

Real-time Energy Resource Scheduling considering a Real Portuguese Scenario

DEFF Research Database (Denmark)

Silva, Marco; Sousa, Tiago; Morais, Hugo

2014-01-01

The development in power systems and the introduction of decentralized gen eration and Electric Vehicles (EVs), both connected to distribution networks, represents a major challenge in the planning and operation issues. This new paradigm requires a new energy resources management approach which...... scheduling in smart grids, considering day - ahead, hour - ahead and real - time scheduling. The case study considers a 33 - bus distribution network with high penetration of distributed energy resources . The wind generation profile is base d o n a rea l Portuguese wind farm . Four scenarios are presented...... taking into account 0, 1, 2 and 5 periods (hours or minutes) ahead of the scheduling period in the hour - ahead and real - time scheduling...

Development and validation of a real-time PCR assay for the detection of anguillid herpesvirus 1.

Science.gov (United States)

van Beurden, S J; Voorbergen-Laarman, M A; Roozenburg, I; van Tellingen, J; Haenen, O L M; Engelsma, M Y

2016-01-01

Anguillid herpesvirus 1 (AngHV1) causes a haemorrhagic disease with increased mortality in wild and farmed European eel, Anguilla anguilla (L.) and Japanese eel Anguilla japonica, Temminck & Schlegel). Detection of AngHV1 is currently based on virus isolation in cell culture, antibody-based typing assays or conventional PCR. We developed, optimized and concisely validated a diagnostic TaqMan probe based real-time PCR assay for the detection of AngHV1. The primers and probe target AngHV1 open reading frame 57, encoding the capsid protease and scaffold protein. Compared to conventional PCR, the developed real-time PCR is faster, less labour-intensive and has a reduced risk of cross-contamination. The real-time PCR assay was shown to be analytically sensitive and specific and has a high repeatability, efficiency and r(2) -value. The diagnostic performance of the assay was determined by testing 10% w/v organ suspensions and virus cultures from wild and farmed European eels from the Netherlands by conventional and real-time PCR. The developed real-time PCR assay is a useful tool for the rapid and sensitive detection of AngHV1 in 10% w/v organ suspensions from wild and farmed European eels. © 2015 John Wiley & Sons Ltd.

Real-time RPA assay for rapid detection and differentiation of wild-type pseudorabies and gE-deleted vaccine viruses.

Science.gov (United States)

Wang, Jianchang; Liu, Libing; Wang, Jinfeng; Pang, Xiaoyu; Yuan, Wanzhe

2018-02-15

The objective of this study was to develop a dual real-time recombinase polymerase amplification (RPA) assay using exo probes for the detection and differentiation of pseudorabies virus (PRV). Specific RPA primers and probes were designed for gB and gE genes of PRV within the conserved region of viral genome. The reaction process can be completed in 20 min at 39 °C. The dual real-time RPA assay performed in the single tube was capable of specific detecting and differentiating of the wild-type PRV and gE-deleted vaccine strains, without cross-reactions with other non-targeted pig viruses. The analytical sensitivity of the assay was 10 2 copies for gB and gE genes. The dual real-time RPA demonstrated a 100% diagnostic agreement with the real-time PCR on 4 PRV strains and 37 clinical samples. Through the linear regression analysis, the R 2 value of the real-time RPA and the real-time PCR for gB and gE was 0.983 and 0.992, respectively. The dual real-time RPA assay provides an alternative useful tool for rapid, simple, and reliable detection and differentiation of PRV, especially in remote and rural areas. Copyright © 2017 Elsevier Inc. All rights reserved.

Novel TaqMan real-time polymerase chain reaction assay for verifying the authenticity of meat and commercial meat products from game birds.

Science.gov (United States)

Rojas, María; González, Isabel; Pavón, Miguel Angel; Pegels, Nicolette; Lago, Adriana; Hernández, Pablo E; García, Teresa; Martín, Rosario

2010-06-01

Species-specific real-time polymerase chain reaction (PCR) assays using TaqMan probes have been developed for verifying the labeling of meat and commercial meat products from game birds, including quail, pheasant, partridge, guinea fowl, pigeon, Eurasian woodcock and song thrush. The method combines the use of species-specific primers and TaqMan probes that amplify small fragments (amplicons meat products from the target species demonstrated the suitability of the assay for the detection of the target DNAs.

An advanced real time energy management system for microgrids

International Nuclear Information System (INIS)

Elsied, Moataz; Oukaour, Amrane; Youssef, Tarek; Gualous, Hamid; Mohammed, Osama

2016-01-01

This paper presents an advanced Real-Time Energy Management System (RT-EMS) for Microgrid (MG) systems. The proposed strategy of RT-EMS capitalizes on the power of Genetic Algorithms (GAs) to minimize the energy cost and carbon dioxide emissions while maximizing the power of the available renewable energy resources. MATLAB-dSPACE Real-Time Interface Libraries (MLIB/MTRACE) are used as new tools to run the optimization code in Real-Time Operation (RTO). The communication system is developed based on ZigBee communication network which is designed to work in harsh radio environment where the control system is developed based on Advanced Lead-Lag Compensator (ALLC) which its parameters are tuned online to achieve fast convergence and good tracking response. The proposed RT-EMS along with its control and communication systems is experimentally tested to validate the results obtained from the optimization algorithm in a real MG testbed. The simulation and experimental results using real-world data highlight the effectiveness of the proposed RT-EMS for MGs applications. - Highlights: • Real-time energy management system of a typical MG is developed, and analyzed. • RT-EMS considered the nonlinear cost function and emission constraints. • MLIB/MTRACE libraries in dSPACE are used as new tools to run the optimization code. • The communication system is developed based on a Zigbee communication network. • Control system parameters are tuned online to achieve good tracking response.

Novel 3′-Processing Integrase Activity Assay by Real-Time PCR for Screening and Identification of HIV-1 Integrase Inhibitors

Directory of Open Access Journals (Sweden)

Supachai Sakkhachornphop

2015-01-01

Full Text Available The 3′-end processing (3′P of each viral long terminal repeat (LTR during human immunodeficiency virus type-1 (HIV-1 integration is a vital step in the HIV life cycle. Blocking the 3′P using 3′P inhibitor has recently become an attractive strategy for HIV-1 therapeutic intervention. Recently, we have developed a novel real-time PCR based assay for the detection of 3′P activity in vitro. The methodology usually involves biotinylated HIV-1 LTR, HIV-1 integrase (IN, and specific primers and probe. In this novel assay, we designed the HIV-1 LTR substrate based on a sequence with a homology to HIV-1 LTR labeled at its 3′ end with biotin on the sense strand. Two nucleotides at the 3′ end were subsequently removed by IN activity. Only two nucleotides labeled biotin were captured on an avidin-coated tube; therefore, inhibiting the binding of primers and probe results in late signals in the real-time PCR. This novel assay has successfully detected both the 3′P activity of HIV-1 IN and the anti-IN activity by Raltegravir and sodium azide agent. This real-time PCR assay has been shown to be effective and inexpensive for a high-throughput screening of novel IN inhibitors.

Detection panel for identification of twelve hemorrhagic viruses using real-time RT-PCR.

Science.gov (United States)

Fajfr, M; Neubauerová, V; Pajer, P; Kubíčková, P; Růžek, D

2014-09-01

Viral hemorrhagic fevers are caused by viruses from four viral families and develop diseases with high fatality rates. However, no commercial diagnostic assay for these pathogens is available. We developed real-time RT-PCR assays for viruses Ebola, Marburg, Lassa, Guanarito, Machupo, Junin, Sabiá, Seoul, Puumala, Hantaan, Crimean-Congo hemorrhagic fever virus and Rift Valley fever virus. The assays were optimized for identical reaction conditions and can be performed using several types of real-time PCR instruments, both capillary and plate, including a portable Ruggedized Advanced Pathogen Identification Device (R.A.P.I.D.) (Idaho Technology, Inc.). In combination with primers and probes from previously published studies, we present a simple system for rapid identification of hemorrhagic filoviruses, arenaviruses and bunyaviruses with sufficient sensitivity for first contact laboratory and diagnosis under field conditions.

Rapid quantitative detection of Lactobacillus sakei in meat and fermented sausages by real-time PCR.

Science.gov (United States)

Martín, Belén; Jofré, Anna; Garriga, Margarita; Pla, Maria; Aymerich, Teresa

2006-09-01

A quick and simple method for quantitative detection of Lactobacillus sakei in fermented sausages was successfully developed. It is based on Chelex-100-based DNA purification and real-time PCR enumeration using a TaqMan fluorescence probe. Primers and probes were designed in the L. sakei 16S-23S rRNA intergenic transcribed spacer region, and the assay was evaluated using L. sakei genomic DNA and an artificially inoculated sausage model. The detection limit of this technique was approximately 3 cells per reaction mixture using both purified DNA and the inoculated sausage model. The quantification limit was established at 30 cells per reaction mixture in both models. The assay was then applied to enumerate L. sakei in real samples, and the results were compared to the MRS agar count method followed by confirmation of the percentage of L. sakei colonies. The results obtained by real-time PCR were not statistically significantly different than those obtained by plate count on MRS agar (P > 0.05), showing a satisfactory agreement between both methods. Therefore, the real-time PCR assay developed can be considered a promising rapid alternative method for the quantification of L. sakei and evaluation of the implantation of starter strains of L. sakei in fermented sausages.

Evaluation of a triplex real-time PCR system to detect the plant-pathogenic molds Alternaria spp., Fusarium spp. and C. purpurea.

Science.gov (United States)

Grube, Sabrina; Schönling, Jutta; Prange, Alexander

2015-12-01

This article describes the development of a triplex real-time PCR system for the simultaneous detection of three major plant-pathogenic mold genera (Alternaria spp., Fusarium spp. and the species Claviceps purpurea). The designed genus-specific primer-probe systems were validated for sensitivity, specificity and amplification in the presence of background DNA. Copyright © 2015 Elsevier B.V. All rights reserved.

Measurement of gas phase characteristics using new monofiber optical probes and real time signal processing

International Nuclear Information System (INIS)

Cartellier, A.

1998-01-01

Single optical or impedance phase detection probes are able to measure gas velocities provided that their sensitive length L is accurately known. In this paper, it is shown that L can be controlled during the manufacture of optical probes. Beside, for a probe geometry in the form of a cone + a cylinder + a cone, the corresponding rise time / velocity correlation becomes weakly sensitive to uncontrollable parameter such as the angle of impact on the interface. A real time signal processing performing phase detection as well as velocity measurements is described. Since its sensitivity to the operator inputs is less than the reproducibility of measurements, it is a fairly objective tool. Qualifications achieved in air/water flows with various optical probes demonstrate that the void fraction is detected with a relative error less than 10 %. For bubbly flows, the gas flux is accurate within ±10%, but this uncertainty increases when large bubbles are present in the flow. (author)

Energy-efficient fault tolerance in multiprocessor real-time systems

Science.gov (United States)

Guo, Yifeng

The recent progress in the multiprocessor/multicore systems has important implications for real-time system design and operation. From vehicle navigation to space applications as well as industrial control systems, the trend is to deploy multiple processors in real-time systems: systems with 4 -- 8 processors are common, and it is expected that many-core systems with dozens of processing cores will be available in near future. For such systems, in addition to general temporal requirement common for all real-time systems, two additional operational objectives are seen as critical: energy efficiency and fault tolerance. An intriguing dimension of the problem is that energy efficiency and fault tolerance are typically conflicting objectives, due to the fact that tolerating faults (e.g., permanent/transient) often requires extra resources with high energy consumption potential. In this dissertation, various techniques for energy-efficient fault tolerance in multiprocessor real-time systems have been investigated. First, the Reliability-Aware Power Management (RAPM) framework, which can preserve the system reliability with respect to transient faults when Dynamic Voltage Scaling (DVS) is applied for energy savings, is extended to support parallel real-time applications with precedence constraints. Next, the traditional Standby-Sparing (SS) technique for dual processor systems, which takes both transient and permanent faults into consideration while saving energy, is generalized to support multiprocessor systems with arbitrary number of identical processors. Observing the inefficient usage of slack time in the SS technique, a Preference-Oriented Scheduling Framework is designed to address the problem where tasks are given preferences for being executed as soon as possible (ASAP) or as late as possible (ALAP). A preference-oriented earliest deadline (POED) scheduler is proposed and its application in multiprocessor systems for energy-efficient fault tolerance is

In Silico PCR Tools for a Fast Primer, Probe, and Advanced Searching.

Science.gov (United States)

Kalendar, Ruslan; Muterko, Alexandr; Shamekova, Malika; Zhambakin, Kabyl

2017-01-01

The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching. Predicting sensitivity and specificity of primers and probes requires a search to determine whether they match a database with an optimal number of mismatches, similarity, and stability. In the development of in silico bioinformatics tools for nucleic acid amplification technologies, the prospects for the development of new NAAT or similar approaches should be taken into account, including forward-looking and comprehensive analysis that is not limited to only one PCR technique variant. The software FastPCR and the online Java web tool are integrated tools for in silico PCR of linear and circular DNA, multiple primer or probe searches in large or small databases and for advanced search. These tools are suitable for processing of batch files that are essential for automation when working with large amounts of data. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and the online Java version at http://primerdigital.com/tools/pcr.html .

Simultaneous detection of Legionella species and L. anisa, L. bozemanii, L. longbeachae and L. micdadei using conserved primers and multiple probes in a multiplex real-time PCR assay.

Science.gov (United States)

Cross, Kristen E; Mercante, Jeffrey W; Benitez, Alvaro J; Brown, Ellen W; Diaz, Maureen H; Winchell, Jonas M

2016-07-01

Legionnaires' disease is a severe respiratory disease that is estimated to cause between 8,000 and 18,000 hospitalizations each year, though the exact burden is unknown due to under-utilization of diagnostic testing. Although Legionella pneumophila is the most common species detected in clinical cases (80-90%), other species have also been reported to cause disease. However, little is known about Legionnaires' disease caused by these non-pneumophila species. We designed a multiplex real-time PCR assay for detection of all Legionella spp. and simultaneous specific identification of four clinically-relevant Legionella species, L. anisa, L. bozemanii, L. longbeachae, and L. micdadei, using 5'-hydrolysis probe real-time PCR. The analytical sensitivity for detection of nucleic acid from each target species was ≤50fg per reaction. We demonstrated the utility of this assay in spiked human sputum specimens. This assay could serve as a tool for understanding the scope and impact of non-pneumophila Legionella species in human disease. Published by Elsevier Inc.

Real time sensor for therapeutic radiation delivery

International Nuclear Information System (INIS)

Bliss, M.; Craig, R.A.; Reeder, P.L.

1998-01-01

The invention is a real time sensor for therapeutic radiation. A probe is placed in or near the patient that senses in real time the dose at the location of the probe. The strength of the dose is determined by either an insertion or an exit probe. The location is determined by a series of vertical and horizontal sensing elements that gives the operator a real time read out dose location relative to placement of the patient. The increased accuracy prevents serious tissue damage to the patient by preventing overdose or delivery of a dose to a wrong location within the body. 14 figs

A sensitive one-step real-time PCR for detection of avian influenza viruses using a MGB probe and an internal positive control

Directory of Open Access Journals (Sweden)

Delogu Mauro

2006-05-01

Full Text Available Abstract Background Avian influenza viruses (AIVs are endemic in wild birds and their introduction and conversion to highly pathogenic avian influenza virus in domestic poultry is a cause of serious economic losses as well as a risk for potential transmission to humans. The ability to rapidly recognise AIVs in biological specimens is critical for limiting further spread of the disease in poultry. The advent of molecular methods such as real time polymerase chain reaction has allowed improvement of detection methods currently used in laboratories, although not all of these methods include an Internal Positive Control (IPC to monitor for false negative results. Therefore we developed a one-step reverse transcription real time PCR (RRT-PCR with a Minor Groove Binder (MGB probe for the detection of different subtypes of AIVs. This technique also includes an IPC. Methods RRT-PCR was developed using an improved TaqMan technology with a MGB probe to detect AI from reference viruses. Primers and probe were designed based on the matrix gene sequences from most animal and human A influenza virus subtypes. The specificity of RRT-PCR was assessed by detecting influenza A virus isolates belonging to subtypes from H1–H13 isolated in avian, human, swine and equine hosts. The analytical sensitivity of the RRT-PCR assay was determined using serial dilutions of in vitro transcribed matrix gene RNA. The use of a rodent RNA as an IPC in order not to reduce the efficiency of the assay was adopted. Results The RRT-PCR assay is capable to detect all tested influenza A viruses. The detection limit of the assay was shown to be between 5 and 50 RNA copies per reaction and the standard curve demonstrated a linear range from 5 to 5 × 108 copies as well as excellent reproducibility. The analytical sensitivity of the assay is 10–100 times higher than conventional RT-PCR. Conclusion The high sensitivity, rapidity, reproducibility and specificity of the AIV RRT-PCR with

Cloud computing platform for real-time measurement and verification of energy performance

International Nuclear Information System (INIS)

Ke, Ming-Tsun; Yeh, Chia-Hung; Su, Cheng-Jie

2017-01-01

Highlights: • Application of PSO algorithm can improve the accuracy of the baseline model. • M&V cloud platform automatically calculates energy performance. • M&V cloud platform can be applied in all energy conservation measures. • Real-time operational performance can be monitored through the proposed platform. • M&V cloud platform facilitates the development of EE programs and ESCO industries. - Abstract: Nations worldwide are vigorously promoting policies to improve energy efficiency. The use of measurement and verification (M&V) procedures to quantify energy performance is an essential topic in this field. Currently, energy performance M&V is accomplished via a combination of short-term on-site measurements and engineering calculations. This requires extensive amounts of time and labor and can result in a discrepancy between actual energy savings and calculated results. In addition, the M&V period typically lasts for periods as long as several months or up to a year, the failure to immediately detect abnormal energy performance not only decreases energy performance, results in the inability to make timely correction, and misses the best opportunity to adjust or repair equipment and systems. In this study, a cloud computing platform for the real-time M&V of energy performance is developed. On this platform, particle swarm optimization and multivariate regression analysis are used to construct accurate baseline models. Instantaneous and automatic calculations of the energy performance and access to long-term, cumulative information about the energy performance are provided via a feature that allows direct uploads of the energy consumption data. Finally, the feasibility of this real-time M&V cloud platform is tested for a case study involving improvements to a cold storage system in a hypermarket. Cloud computing platform for real-time energy performance M&V is applicable to any industry and energy conservation measure. With the M&V cloud platform, real-time

Experimental validation of a method characterizing bow tie filters in CT scanners using a real-time dose probe

International Nuclear Information System (INIS)

McKenney, Sarah E.; Nosratieh, Anita; Gelskey, Dale; Yang Kai; Huang Shinying; Chen Lin; Boone, John M.

2011-01-01

Purpose: Beam-shaping or ''bow tie'' (BT) filters are used to spatially modulate the x-ray beam in a CT scanner, but the conventional method of step-and-shoot measurement to characterize a beam's profile is tedious and time-consuming. The theory for characterization of bow tie relative attenuation (COBRA) method, which relies on a real-time dosimeter to address the issues of conventional measurement techniques, was previously demonstrated using computer simulations. In this study, the feasibility of the COBRA theory is further validated experimentally through the employment of a prototype real-time radiation meter and a known BT filter. Methods: The COBRA method consisted of four basic steps: (1) The probe was placed at the edge of a scanner's field of view; (2) a real-time signal train was collected as the scanner's gantry rotated with the x-ray beam on; (3) the signal train, without a BT filter, was modeled using peak values measured in the signal train of step 2; and (4) the relative attenuation of the BT filter was estimated from filtered and unfiltered data sets. The prototype probe was first verified to have an isotropic and linear response to incident x-rays. The COBRA method was then tested on a dedicated breast CT scanner with a custom-designed BT filter and compared to the conventional step-and-shoot characterization of the BT filter. Using basis decomposition of dual energy signal data, the thickness of the filter was estimated and compared to the BT filter's manufacturing specifications. The COBRA method was also demonstrated with a clinical whole body CT scanner using the body BT filter. The relative attenuation was calculated at four discrete x-ray tube potentials and used to estimate the thickness of the BT filter. Results: The prototype probe was found to have a linear and isotropic response to x-rays. The relative attenuation produced from the COBRA method fell within the error of the relative attenuation measured with the step-and-shoot method

A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses.

Science.gov (United States)

Wadhwa, Ashutosh; Wilkins, Kimberly; Gao, Jinxin; Condori Condori, Rene Edgar; Gigante, Crystal M; Zhao, Hui; Ma, Xiaoyue; Ellison, James A; Greenberg, Lauren; Velasco-Villa, Andres; Orciari, Lillian; Li, Yu

2017-01-01

Rabies, resulting from infection by Rabies virus (RABV) and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA) test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR) based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N) coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses, its high

A Pan-Lyssavirus Taqman Real-Time RT-PCR Assay for the Detection of Highly Variable Rabies virus and Other Lyssaviruses.

Directory of Open Access Journals (Sweden)

Ashutosh Wadhwa

2017-01-01

Full Text Available Rabies, resulting from infection by Rabies virus (RABV and related lyssaviruses, is one of the most deadly zoonotic diseases and is responsible for up to 70,000 estimated human deaths worldwide each year. Rapid and accurate laboratory diagnosis of rabies is essential for timely administration of post-exposure prophylaxis in humans and control of the disease in animals. Currently, only the direct fluorescent antibody (DFA test is recommended for routine rabies diagnosis. Reverse-transcription polymerase chain reaction (RT-PCR based diagnostic methods have been widely adapted for the diagnosis of other viral pathogens, but there is currently no widely accepted rapid real-time RT-PCR assay for the detection of all lyssaviruses. In this study, we demonstrate the validation of a newly developed multiplex real-time RT-PCR assay named LN34, which uses a combination of degenerate primers and probes along with probe modifications to achieve superior coverage of the Lyssavirus genus while maintaining sensitivity and specificity. The primers and probes of the LN34 assay target the highly conserved non-coding leader region and part of the nucleoprotein (N coding sequence of the Lyssavirus genome to maintain assay robustness. The probes were further modified by locked nucleotides to increase their melting temperature to meet the requirements for an optimal real-time RT-PCR assay. The LN34 assay was able to detect all RABV variants and other lyssaviruses in a validation panel that included representative RABV isolates from most regions of the world as well as representatives of 13 additional Lyssavirus species. The LN34 assay was successfully used for both ante-mortem and post-mortem diagnosis of over 200 clinical samples as well as field derived surveillance samples. This assay represents a major improvement over previously published rabies specific RT-PCR and real-time RT-PCR assays because of its ability to universally detect RABV and other lyssaviruses

Identification of four squid species by quantitative real-time polymerase chain reaction.

Science.gov (United States)

Ye, Jian; Feng, Junli; Liu, Shasha; Zhang, Yanping; Jiang, Xiaona; Dai, Zhiyuan

2016-02-01

Squids are distributed worldwide, including many species of commercial importance, and they are often made into varieties of flavor foods. The rapid identification methods for squid species especially their processed products, however, have not been well developed. In this study, quantitative real-time PCR (qPCR) systems based on specific primers and TaqMan probes have been established for rapid and accurate identification of four common squid species (Ommastrephes bartramii, Dosidicus gigas, Illex argentinus, Todarodes pacificus) in Chinese domestic market. After analyzing mitochondrial genes reported in GenBank, the mitochondrial cytochrome b (Cytb) gene was selected for O. bartramii detection, cytochrome c oxidase subunit I (COI) gene for D. gigas and T. Pacificus detection, ATPase subunit 6 (ATPase 6) gene for I. Argentinus detection, and 12S ribosomal RNA (12S rDNA) gene for designing Ommastrephidae-specific primers and probe. As a result, all the TaqMan systems are of good performance, and efficiency of each reaction was calculated by making standard curves. This method could detect target species either in single or mixed squid specimen, and it was applied to identify 12 squid processed products successfully. Thus, it would play an important role in fulfilling labeling regulations and squid fishery control. Copyright © 2016 Elsevier Ltd. All rights reserved.

Real-time, in vivo measurement of radiation dose during radioimmunotherapy in mice using a miniature MOSFET dosimeter probe

International Nuclear Information System (INIS)

Gladstone, D.J.; Chin, L.M.

1995-01-01

This report presents the first real-time measurement of absorbed radiation dose during radioimmunotherapy in mice. Dose rate and total dose at the center of the tumor were measured after administration of 90 Y-labeled antibodies using a miniature metal oxide semiconductor field-effect transistor radiation dosimeter probe which was inserted into the center of the tumor volume. Continuous real-time measurements were made for as long as 23 h after injection of the radiolabeled antibodies. Comparison of the real-time dose-rate measurements with estimates based on the MIRD formalism indicates good agreement. The real-time measurements are further compared to measurements made in a second experiment in which groups of mice were sacrificed at individual times after injection of the same radiolabeled antibodies. The real-time measurements agree well with the measurements in excised tumors. The real-time measurements have greater time resolution and are much more efficient than traditional uptake measurements. 17 refs., 2 figs

Multiplex real-time PCR assay for Legionella species.

Science.gov (United States)

Kim, Seung Min; Jeong, Yoojung; Sohn, Jang Wook; Kim, Min Ja

2015-12-01

Legionella pneumophila serogroup 1 (sg1) accounts for the majority of infections in humans, but other Legionella species are also associated with human disease. In this study, a new SYBR Green I-based multiplex real-time PCR assay in a single reaction was developed to allow the rapid detection and differentiation of Legionella species by targeting specific gene sequences. Candidate target genes were selected, and primer sets were designed by referring to comparative genomic hybridization data of Legionella species. The Legionella species-specific groES primer set successfully detected all 30 Legionella strains tested. The xcpX and rfbA primers specifically detected L. pneumophila sg1-15 and L. pneumophila sg1, respectively. In addition, this assay was validated by testing clinical samples and isolates. In conclusion, this novel multiplex real-time PCR assay might be a useful diagnostic tool for the rapid detection and differentiation of Legionella species in both clinical and epidemiological studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

An immunomagnetic separation-real-time PCR system for the detection of Alicyclobacillus acidoterrestris in fruit products.

Science.gov (United States)

Wang, Zhouli; Cai, Rui; Yuan, Yahong; Niu, Chen; Hu, Zhongqiu; Yue, Tianli

2014-04-03

Alicyclobacillus acidoterrestris is the most important spoilage species within the Alicyclobacillus genus and has become a major issue in the pasteurized fruit juice industry. The aim of this study was to develop a method combining immunomagnetic separation (IMS) with real-time PCR system (IMS-PCR) for rapid and specific detection of A. acidoterrestris in fruit products. A real-time PCR with the TaqMan system was designed to target the 16S rDNA genes with specific primer and probe set. The specificity of the assay was confirmed using 9 A. acidoterrestris strains and 21 non-A. acidoterrestris strains. The results indicated that no combination of the designed primers and probe was found in any Alicyclobacillus genus except A. acidoterrestris. The detection limit of the established IMS-PCR was less than 10CFU/mL and the testing process was accomplished in 2-3h. For the three types of samples (sterile water, apple juice and kiwi juice), the correlation coefficient of standard curves was greater than 0.991, and the calculated PCR efficiencies were from 108% to 109%. As compared with the standard culture method performed concurrently on the same set of samples, the sensitivity, specificity and accuracy of IMS-PCR for 196 naturally contaminated fruit products were 90.0%, 98.3% and 97.5%, respectively. The results exhibited that the proposed IMS-PCR method was effective for the rapid detection of A. acidoterrestris in fruit products. Copyright © 2014. Published by Elsevier B.V.

2010 winter games tracks energy in real time

Energy Technology Data Exchange (ETDEWEB)

Anon.

2010-01-15

An online energy tracker was developed by BC Hydro to publicly monitor the real-time energy consumption at the Vancouver 2010 Olympic winter game sites within Vancouver, Richmond, Whistler and Whistler Blackcomb. The venues and associated sites participating in the live energy tracking project were the Richmond Olympic Oval, Canada Hockey Place, Vancouver Olympic/Paralympic Centre, South East False Creek Community Centre, Whistler Blackcomb Roundhouse Lodge and snowmaking facilities, and the Olympic and Paralympic Villages. The system was developed to allow venue managers to optimize their use of electricity on an hourly and daily basis. An energy tracking display board developed by Pulse Energy enabled them to compare their performance to similar facilities in real time, and to determine the greenhouse gas savings achieved as result of building and operating practices. Some venues had the potential to save as much as 15 to 20 per cent in energy costs with corresponding reductions in carbon emissions. Efficiency and conservation was built into the design of many new venues. The retrofits made to several existing buildings will continue to contribute to British Columbia's conservation goals long after the 2010 winter games are over.

Development of a highly sensitive one-tube nested real-time PCR for detecting Mycobacterium tuberculosis.

Science.gov (United States)

Choi, Yeonim; Jeon, Bo-Young; Shim, Tae Sun; Jin, Hyunwoo; Cho, Sang-Nae; Lee, Hyeyoung

2014-12-01

Rapid, accurate detection of Mycobacterium tuberculosis is crucial in the diagnosis of tuberculosis (TB), but conventional diagnostic methods have limited sensitivity and specificity or are time consuming. A new highly sensitive nucleic acid amplification test, combined nested and real-time polymerase chain reaction (PCR) in a single tube (one-tube nested real-time PCR), was developed for detecting M. tuberculosis, which takes advantage of two PCR techniques, i.e., nested PCR and real-time PCR. One-tube nested real-time PCR was designed to have two sequential reactions with two sets of primers and dual probes for the insertion sequence (IS) 6110 sequence of M. tuberculosis in a single closed tube. The minimum limits of detection of IS6110 real-time PCR and IS6110 one-tube nested real-time PCR were 100 fg/μL and 1 fg/μL of M. tuberculosis DNA, respectively. AdvanSure TB/non-tuberculous mycobacteria (NTM) real-time PCR, IS6110 real-time PCR, and two-tube nested real-time PCR showed 100% sensitivity and 100% specificity for clinical M. tuberculosis isolates and NTM isolates. In comparison, the sensitivities of AdvanSure TB/NTM real-time PCR, single IS6110 real-time PCR, and one-tube nested real-time PCR were 91% (152/167), 94.6% (158/167), and 100% (167/167) for sputum specimens, respectively. In conclusion, IS6110 one-tube nested real-time PCR is useful for detecting M. tuberculosis due to its high sensitivity and simple manipulation. Copyright © 2014 Elsevier Inc. All rights reserved.

Detection of Toxoplasma gondii and Epstein-Barr virus in HIV patients with clinical symptoms of suspected central nervous system infection using duplex real-time polymerase chain reaction

Science.gov (United States)

Rahmawati, E.; Ibrahim, F.; Imran, D.; Sudarmono, P.

2017-08-01

Focal brain lesion is a neurological complication in HIV, which is marked as a space occupying lesion (SOL) and needs rapid and effective treatment. This lesion is mainly caused by encephalitis toxoplasma and primary central nervous system lymphoma related to the Epstein-Barr virus (EBV) infection, which is difficult to distinguish using CT scan or magnetic resonance imaging (MRI). The gold standard of diagnosing focal brain lesion has been brain biopsy, but this examination is an invasive procedure that causes complications. The objective of this study is to obtain the rapid laboratory diagnosis of Toxoplasma gondii (T. gondii) and EBV infection. In this experimental study, blood and cerebrospinal fluid were obtained from HIV patients who were admitted to the Neurology Department of Cipto Mangunkusumo Hospital. The samples were examined using duplex real-time polymerase chain reaction (PCR) to detect T. gondii and EBV. The first step was the optimization of duplex real-time PCR, including the annealing temperature, primer and probe concentration, elution volume, and template volume. Minimal DNA detection was used to measure minimal T. gondii and EBV. Cross reactions were determined for technical specificity using the bacteria and viruses Staphylococcus aureus, Klebsiella pneumonia, Pseudomonas aeruginosa, Mycobacterium tuberculosis H37Rv, Candida spp, cytomegalovirus, herpes zoster virus, and varicella zoster virus. Duplex real-time PCR was applied optimally to patients. In the optimization of duplex real-time PCR, the annealing temperature of T. gondii and EBV were 58 °C, the concentration of primer forward and reverse for T. gondii and EBV were 0.2 μM, the concentration of probe for T. gondii and EBV were 0.4μM and 0.2 μM, respectively. Minimal DNA detection of T. gondii and EBV were 5.68 copy/ml and 1.31 copy/ml, respectively. There was no cross reaction between another bacteria and virus that were used as the primer and probe for T. gondii and EBV. The

Fluorescence probes for real-time remote cyanobacteria monitoring: A review of challenges and opportunities.

Science.gov (United States)

Bertone, Edoardo; Burford, Michele A; Hamilton, David P

2018-05-10

In recent years, there has been a widespread deployment of submersible fluorescence sensors by water utilities. They are used to measure diagnostic pigments and estimate algae and cyanobacteria abundance in near real-time. Despite being useful and promising tools, operators and decision-makers often rely on the data provided by these probes without a full understanding of their limitations. As a result, this may lead to wrong and misleading estimations which, in turn, means that researchers and technicians distrust these sensors. In this review paper, we list and discuss the main limitations of such probes, as well as identifying the effect of environmental factors on pigment production, and in turn, the conversion to cyanobacteria abundance estimation. We argue that a comprehensive calibration approach to obtain reliable readings goes well beyond manufacturers' recommendations, and should involve several context-specific experiments. We also believe that if such a comprehensive set of experiments is conducted, the data collected from fluorescence sensors could be used in artificial intelligence modelling approaches to reliably predict, in near real-time, the presence and abundance of different cyanobacteria species. This would have significant benefits for both drinking and recreational water management, given that cyanobacterial toxicity, and taste and odour compounds production, are species-dependent. Copyright © 2018 Elsevier Ltd. All rights reserved.

Evaluation of a new single-tube multiprobe real-time PCR for diagnosis of Entamoeba histolytica and Entamoeba dispar.

Science.gov (United States)

Liang, Shih-Yu; Hsia, Kan-Tai; Chan, Yun-Hsien; Fan, Chia-Kwung; Jiang, Donald Dah-Shyong; Landt, Olfert; Ji, Dar-Der

2010-08-01

A single-tube multiprobe real-time PCR assay for simultaneous detection of Entamoeba histolytica and Entamoeba dispar was developed. One primer pair with 2 species-specific probes was designed based on new SSU RNA regions of the ribosomal DNA-containing episome. The sensitivity is 1 parasite per milliliter of feces and thus superior to the conventional nested PCR and comparable to other published real-time PCR protocols. The applicability for clinical diagnosis was validated with 218 stool specimens from patients. A total of 51 E. histolytica and 39 E. dispar positive samples was detected by the multiprobe real-time PCR compared to 39 and 22 by routine nested PCR diagnosis. The detection rate of Entamoeba species for the multiprobe real-time PCR assays was significantly higher than the nested PCR (40.8% vs. 28.0%, P Entamoeba moshkovskii, Giardia lamblia , Cryptosporidium sp., Escherichia coli , or other nonpathogenic enteric parasites. The multiprobe real-time PCR assay is simple and rapid and has high specificity and sensitivity. The assay could streamline the laboratory diagnosis procedure and facilitate epidemiological investigation.

A NASBA on microgel-tethered molecular-beacon microarray for real-time microbial molecular diagnostics.

Science.gov (United States)

Ma, Y; Dai, X; Hong, T; Munk, G B; Libera, M

2016-12-19

Despite their many advantages and successes, molecular beacon (MB) hybridization probes have not been extensively used in microarray formats because of the complicating probe-substrate interactions that increase the background intensity. We have previously shown that tethering to surface-patterned microgels is an effective means for localizing MB probes to specific surface locations in a microarray format while simultaneously maintaining them in as water-like an environment as possible and minimizing probe-surface interactions. Here we extend this approach to include both real-time detection together with integrated NASBA amplification. We fabricate small (∼250 μm × 250 μm) simplex, duplex, and five-plex assays with microarray spots of controllable size (∼20 μm diameter), position, and shape to detect bacteria and fungi in a bloodstream-infection model. The targets, primers, and microgel-tethered probes can be combined in a single isothermal reaction chamber with no post-amplification labelling. We extract total RNA from clinical blood samples and differentiate between Gram-positive and Gram-negative bloodstream infection in a duplex assay to detect RNA- amplicons. The sensitivity based on our current protocols in a simplex assay to detect specific ribosomal RNA sequences within total RNA extracted from S. aureus and E. coli cultures corresponds to tens of bacteria per ml. We furthermore show that the platform can detect RNA- amplicons from synthetic target DNA with 1 fM sensitivity in sample volumes that contain about 12 000 DNA molecules. These experiments demonstrate an alternative approach that can enable rapid and real-time microarray-based molecular diagnostics.

Open Probe fast GC-MS - combining ambient sampling ultra-fast separation and in-vacuum ionization for real-time analysis.

Science.gov (United States)

Keshet, U; Alon, T; Fialkov, A B; Amirav, A

2017-07-01

An Open Probe inlet was combined with a low thermal mass ultra-fast gas chromatograph (GC), in-vacuum electron ionization ion source and a mass spectrometer (MS) of GC-MS for obtaining real-time analysis with separation. The Open Probe enables ambient sampling via sample vaporization in an oven that is open to room air, and the ultra-fast GC provides ~30-s separation, while if no separation is required, it can act as a transfer line with 2 to 3-s sample transfer time. Sample analysis is as simple as touching the sample, pushing the sample holder into the Open Probe oven and obtaining the results in 30 s. The Open Probe fast GC was mounted on a standard Agilent 7890 GC that was coupled with an Agilent 5977A MS. Open Probe fast GC-MS provides real-time analysis combined with GC separation and library identification, and it uses the low-cost MS of GC-MS. The operation of Open Probe fast GC-MS is demonstrated in the 30-s separation and 50-s full analysis cycle time of tetrahydrocannabinol and cannabinol in Cannabis flower, sub 1-min analysis of trace trinitrotoluene transferred from a finger onto a glass surface, vitamin E in canola oil, sterols in olive oil, polybrominated flame retardants in plastics, alprazolam in Xanax drug pill and free fatty acids and cholesterol in human blood. The extrapolated limit of detection for pyrene is Open Probe fast GC-MS is demonstrated in the analysis of heroin in its street drug powder. The use of Open Probe with the fast GC acting as a transfer line is demonstrated in <10-s analysis without separation of ibuprofen and estradiol. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Improved Safety for Molecular Diagnosis of Classical Rabies Viruses by Use of a TaqMan Real-Time Reverse Transcription-PCR "Double Check" Strategy

DEFF Research Database (Denmark)

Hoffmann, B.; Freuling, C. M.; Wakeley, P. R.

2010-01-01

To improve the diagnosis of classical rabies virus with molecular methods, a validated, ready-to-use, real-time reverse transcription-PCR (RT-PCR) assay was developed. In a first step, primers and 6-carboxyfluorescien-labeled TaqMan probes specific for rabies virus were selected from the consensus...... sequence of the nucleoprotein gene of 203 different rabies virus sequences derived from GenBank. The selected primer-probe combination was highly specific and sensitive. During validation using a sample set of rabies virus strains from the virus archives of the Friedrich-Loeffler-Institut (FLI; Germany......), the Veterinary Laboratories Agency (VLA; United Kingdom), and the DTU National Veterinary Institute (Lindholm, Denmark), covering the global diversity of rabies virus lineages, it was shown that both the newly developed assay and a previously described one had some detection failures. This was overcome...

Development and Validation of a P-35S, T-nos, T-35S and P-FMV Tetraplex Real-time PCR Screening Method to Detect Regulatory Genes of Genetically Modified Organisms in Food.

Science.gov (United States)

Eugster, Albert; Murmann, Petra; Kaenzig, Andre; Breitenmoser, Alda

2014-10-01

In routine analysis screening methods based on real-time PCR (polymerase chain reaction) are most commonly used for the detection of genetically modified (GM) plant material in food and feed. Screening tests are based on sequences frequently used for GM development, allowing the detection of a large number of GMOs (genetically modified organisms). Here, we describe the development and validation of a tetraplex real-time PCR screening assay comprising detection systems for the regulatory genes Cauliflower Mosaic Virus 35S promoter, Agrobacterium tumefaciens nos terminator, Cauliflower Mosaic Virus 35S terminator and Figwort Mosaic Virus 34S promoter. Three of the four primer and probe combinations have already been published elsewhere, whereas primers and probe for the 35S terminator have been developed in-house. Adjustment of primer and probe concentrations revealed a high PCR sensitivity with insignificant physical cross-talk between the four detection channels. The sensitivity of each PCR-system is sufficient to detect a GMO concentration as low as 0.05% of the containing respective element. The specificity of the described tetraplex is high when tested on DNA from GM maize, soy, rapeseed and tomato. We also demonstrate the robustness of the system by inter-laboratory tests. In conclusion, this method provides a sensitive and reliable screening procedure for the detection of the most frequently used regulatory elements present in GM crops either authorised or unauthorised for food.

Dynamic Reconfiguration in Real-Time Systems Energy, Performance, and Thermal Perspectives

CERN Document Server

Wang, Weixun; Ranka, Sanjay

2013-01-01

Given the widespread use of real-time multitasking systems, there are tremendous optimization opportunities if reconfigurable computing can be effectively incorporated while maintaining performance and other design constraints of typical applications. The focus of this book is to describe the dynamic reconfiguration techniques that can be safely used in real-time systems. This book provides comprehensive approaches by considering synergistic effects of computation, communication as well as storage together to significantly improve overall performance, power, energy and temperature.  Provides a comprehensive introduction to optimization and dynamic reconfiguration techniques in real-time embedded systems; Covers state-of-the-art techniques and ongoing research in reconfigurable architectures; Focuses on algorithms tuned for dynamic reconfiguration techniques in real-time systems;  Provides reference for anyone designing low-power systems, energy-/temperature-constrained devices, and power-performance efficie...

Development and utility of an internal threshold control (ITC real-time PCR assay for exogenous DNA detection.

Directory of Open Access Journals (Sweden)

Weiyi Ni

Full Text Available Sensitive and specific tests for detecting exogenous DNA molecules are useful for infectious disease diagnosis, gene therapy clinical trial safety, and gene doping surveillance. Taqman real-time PCR using specific sequence probes provides an effective approach to accurately and quantitatively detect exogenous DNA. However, one of the major challenges in these analyses is to eliminate false positive signals caused by either non-targeted exogenous or endogenous DNA sequences, or false negative signals caused by impurities that inhibit PCR. Although multiplex Taqman PCR assays have been applied to address these problems by adding extra primer-probe sets targeted to endogenous DNA sequences, the differences between targets can lead to different detection efficiencies. To avoid these complications, a Taqman PCR-based approach that incorporates an internal threshold control (ITC has been developed. In this single reaction format, the target sequence and ITC template are co-amplified by the same primers, but are detected by different probes each with a unique fluorescent dye. Sample DNA, a prescribed number of ITC template molecules set near the limit of sensitivity, a single pair of primers, target probe and ITC probe are added to one reaction. Fluorescence emission signals are obtained simultaneously to determine the cycle thresholds (Ct for amplification of the target and ITC sequences. The comparison of the target Ct with the ITC Ct indicates if a sample is a true positive for the target (i.e. Ct less than or equal to the ITC Ct or negative (i.e. Ct greater than the ITC Ct. The utility of this approach was demonstrated in a nonhuman primate model of rAAV vector mediated gene doping in vivo and in human genomic DNA spiked with plasmid DNA.

Detection and identification of Rift Valley fever virus in mosquito vectors by quantitative real-time PCR.

Science.gov (United States)

Mwaengo, D; Lorenzo, G; Iglesias, J; Warigia, M; Sang, R; Bishop, R P; Brun, A

2012-10-01

Diagnostic methods allowing for rapid identification of pathogens are crucial for controlling and preventing dissemination after disease outbreaks as well as for use in surveillance programs. For arboviruses, detection of the presence of virus in their arthropod hosts is important for monitoring of viral activity and quantitative information is useful for modeling of transmission dynamics. In this study, molecular detection of Rift Valley fever virus (RVFV) in mosquito samples from the 2006 to 2007 East African outbreaks was performed using quantitative real-time PCR assay (qRT-PCR). Specific RVFV sequence-based primer/fluorogenic (TaqMan) probe sets were derived from the L and S RNA segments of the virus. Both primer-probe L and S segment-based combinations detected genomic RVFV sequences, with generally comparable levels of sensitivity. Viral loads from three mosquito species, Aedes mcintoshi, Aedes ochraceus and Mansonia uniformis were estimated and significant differences of between 5- and 1000-fold were detected between Ae. mcintoshi and M. uniformis using both the L and S primer-probe-based assays. The genetic relationships of the viral sequences in mosquito samples were established by partial M segment sequencing and assigned to the two previously described viral lineages defined by analysis of livestock isolates obtained during the 2006-2007 outbreak, confirming that similar viruses were present in both the vector and mammalian host. The data confirms the utility of qRT-PCR for identification and initial quantification of virus in mosquito samples during RVFV outbreaks. Copyright © 2012 Elsevier B.V. All rights reserved.

Development and Characterization of Probe-Based Real Time Quantitative RT-PCR Assays for Detection and Serotyping of Foot-And-Mouth Disease Viruses Circulating in West Eurasia

DEFF Research Database (Denmark)

Jamal, Syed M.; Belsham, Graham

2015-01-01

Asia,A-Iran05 and Asia-1 (Group-II and Group-VII (Sindh-08)). In addition, field samples from Iran and Bulgaria, containing FMDVs belonging to the O-PanAsiaANT-10 subline-agewere also tested. Each of the three primer/probe sets was designed to be specific for just one of the serotypes O, A and Asia-1 of FMDV....... Due to the heterogeneity of FMD viruses (FMDVs) in different parts of the world, region specific diagnostic tests are required. In this study, hydrolysableprobe-based real time reverse transcription quantitative polymerase chain reaction (RTqPCR) assays were developed for specific detection...... and serotyping of the FMDVs currently circulating in West Eurasia. These assays were evaluated, in parallel with pan-FMDV diagnosticassays and earlier serotype-specific assays, using field samples originating from Pakistan and Afghanistan containing FMD viruses belonging to different sublineages of OPan...

Improved quantification accuracy for duplex real-time PCR detection of genetically modified soybean and maize in heat processed foods

Directory of Open Access Journals (Sweden)

CHENG Fang

2013-04-01

Full Text Available Real-time PCR technique has been widely used in quantitative GMO detection in recent years.The accuracy of GMOs quantification based on the real-time PCR methods is still a difficult problem,especially for the quantification of high processed samples.To develop the suitable and accurate real-time PCR system for high processed GM samples,we made ameliorations to several real-time PCR parameters,including re-designed shorter target DNA fragment,similar lengths of amplified endogenous and exogenous gene targets,similar GC contents and melting temperatures of PCR primers and TaqMan probes.Also,one Heat-Treatment Processing Model (HTPM was established using soybean flour samples containing GM soybean GTS 40-3-2 to validate the effectiveness of the improved real-time PCR system.Tested results showed that the quantitative bias of GM content in heat processed samples were lowered using the new PCR system.The improved duplex real-time PCR was further validated using processed foods derived from GM soybean,and more accurate GM content values in these foods was also achieved.These results demonstrated that the improved duplex real-time PCR would be quite suitable in quantitative detection of high processed food products.

MIB Probes for measurements of particle and energy fluxes in plasma of Wendelstein 7-X

Science.gov (United States)

Demidov, V. I.; Koepke, M. E.; Kurlyandskaya, I. P.; Raitses, Y.

2014-10-01

Magnetically insulated baffled (MIB) probes and probe arrays that share the simplicity of simple Langmuir probes but supersede them in their ability to make real-time measurements of plasma potential, temperature and energy/particle fluxes in W7-X stellarator plasma are being developed. The probes offer the advantages of direct measurements of the plasma fluid observables, while being non-emitting and electrically floating. The principle of operation of the probe is based on the dependence of the voltage drop in the plasma-probe sheath on the direction of the local magnetic field. The core technology for these probes rests with the use of a special baffling configuration such that electron current to the probe is fully controllable in the closed, open or partially open orientation, by a simple rotation of the baffle with respect to the magnetic field alignment in the plasma. The baffled-probe designs proposed for edge diagnostics will increase the capability to characterize separately plasma properties in real-time for understanding of underlying physics in the edge plasma.

Identification and genotyping of molluscum contagiosum virus from genital swab samples by real-time PCR and Pyrosequencing.

Science.gov (United States)

Trama, Jason P; Adelson, Martin E; Mordechai, Eli

2007-12-01

Laboratory diagnosis of molluscum contagiosum virus (MCV) is important as lesions can be confused with those caused by Cryptococcus neoformans, herpes simplex virus, human papillomavirus, and varicella-zoster virus. To develop a rapid method for identifying patients infected with MCV via swab sampling. Two dual-labeled probe real-time PCR assays, one homologous to the p43K gene and one to the MC080R gene, were designed. The p43K PCR was designed to be used in conjunction with Pyrosequencing for confirmation of PCR products and discrimination between MCV1 and MCV2. Both PCR assays were optimized with respect to reaction components, thermocycling parameters, and primer and probe concentrations. The specificities of both PCR assays were confirmed by non-amplification of 38 known human pathogens. Sensitivity assays demonstrated detection of as few as 10 copies per reaction. Testing 703 swabs, concordance between the two real-time PCR assays was 99.9%. Under the developed conditions, Pyrosequencing of the p43K PCR product was capable of providing enough nucleotide sequence to definitively differentiate MCV1 and MCV2. These real-time PCR assays can be used for the rapid, sensitive, and specific detection of MCV and, when combined with Pyrosequencing, can further discriminate between MCV1 and MCV2.

Development and implementation of real-time nucleic acid amplification for the detection of enterovirus infections in comparison to rapid culture of various clinical specimens

NARCIS (Netherlands)

van Doornum, G J J; Schutten, Martin; Voermans, J; Guldemeester, G J J; Niesters, H G M

2007-01-01

Several real-time PCR and nucleic acid sequence-based amplification (NASBA) primer pairs and a modified real-time PCR primer pair for the detection of enteroviruses were compared. The modified real-time PCR primer pair was evaluated on clinical samples in comparison with cell culture using the

Energy-aware embedded classifier design for real-time emotion analysis.

Science.gov (United States)

Padmanabhan, Manoj; Murali, Srinivasan; Rincon, Francisco; Atienza, David

2015-01-01

Detection and classification of human emotions from multiple bio-signals has a wide variety of applications. Though electronic devices are available in the market today that acquire multiple body signals, the classification of human emotions in real-time, adapted to the tight energy budgets of wearable embedded systems is a big challenge. In this paper we present an embedded classifier for real-time emotion classification. We propose a system that operates at different energy budgeted modes, depending on the available energy, where each mode is constrained by an operating energy bound. The classifier has an offline training phase where feature selection is performed for each operating mode, with an energy-budget aware algorithm that we propose. Across the different operating modes, the classification accuracy ranges from 95% - 75% and 89% - 70% for arousal and valence respectively. The accuracy is traded off for less power consumption, which results in an increased battery life of up to 7.7 times (from 146.1 to 1126.9 hours).

A real-time artifact reduction algorithm based on precise threshold during short-separation optical probe insertion in neurosurgery

Directory of Open Access Journals (Sweden)

Weitao Li

2017-01-01

Full Text Available During neurosurgery, an optical probe has been used to guide the micro-electrode, which is punctured into the globus pallidus (GP to create a lesion that can relieve the cardinal symptoms. Accurate target localization is the key factor to affect the treatment. However, considering the scattering nature of the tissue, the “look ahead distance (LAD” of optical probe makes the boundary between the different tissues blurred and difficult to be distinguished, which is defined as artifact. Thus, it is highly desirable to reduce the artifact caused by LAD. In this paper, a real-time algorithm based on precise threshold was proposed to eliminate the artifact. The value of the threshold was determined by the maximum error of the measurement system during the calibration procession automatically. Then, the measured data was processed sequentially only based on the threshold and the former data. Moreover, 100μm double-fiber probe and two-layer and multi-layer phantom models were utilized to validate the precision of the algorithm. The error of the algorithm is one puncture step, which was proved in the theory and experiment. It was concluded that the present method could reduce the artifact caused by LAD and make the real boundary sharper and less blurred in real-time. It might be potentially used for the neurosurgery navigation.

Development of a real-time TaqMan assay to detect mendocina sublineage Pseudomonas species in contaminated metalworking fluids.

Science.gov (United States)

Saha, Ratul; Donofrio, Robert S; Bagley, Susan T

2010-08-01

A TaqMan quantitative real-time polymerase chain reaction (qPCR) assay was developed for the detection and enumeration of three Pseudomonas species belonging to the mendocina sublineage (P. oleovorans, P. pseudoalcaligenes, and P. oleovorans subsp. lubricantis) found in contaminated metalworking fluids (MWFs). These microbes are the primary colonizers and serve as indicator organisms of biodegradation of used MWFs. Molecular techniques such as qPCR are preferred for the detection of these microbes since they grow poorly on typical growth media such as R2A agar and Pseudomonas isolation agar (PIA). Traditional culturing techniques not only underestimate the actual distribution of these bacteria but are also time-consuming. The primer-probe pair developed from gyrase B (gyrB) sequences of the targeted bacteria was highly sensitive and specific for the three species. qPCR was performed with both whole cell and genomic DNA to confirm the specificity and sensitivity of the assay. The sensitivity of the assay was 10(1) colony forming units (CFU)/ml for whole cell and 13.7 fg with genomic DNA. The primer-probe pair was successful in determining concentrations from used MWF samples, indicating levels between 2.9 x 10(3) and 3.9 x 10(6) CFU/ml. In contrast, the total count of Pseudomonas sp. recovered on PIA was in the range of <1.0 x 10(1) to 1.4 x 10(5) CFU/ml for the same samples. Based on these results from the qPCR assay, the designed TaqMan primer-probe pair can be efficiently used for rapid (within 2 h) determination of the distribution of these species of Pseudomonas in contaminated MWFs.

Development and implementation of a rapid real-time polymerase ...

African Journals Online (AJOL)

Final concentration in. PCR reactions. CtxA hydrolysis probe 5' Fam TGT TTC CAC CTC AAT TAG TTT GAG AAG TGC CC 3' BHQ. 0.25 µM. Gfp hydrolysis probe. 5' Vic TAC CTG TCC ACA CAA TCT GCC CTT TCG BHQ 3'. 0.25 µM. CtxA forward primer. 5'-GAC GGG ATT TGT TAG GCA CG-3'. 0.3 µM. CtxA reverse primer.

Detection of Mycobacterium avium subsp. paratuberculosis in bovine manure using Whatman FTA card technology and Lightcycler real-time PCR.

Science.gov (United States)

Jaravata, Carmela V; Smith, Wayne L; Rensen, Gabriel J; Ruzante, Juliana M; Cullor, James S

2006-01-01

A modified forensic DNA extraction and real-time fluorescent polymerase chain reaction assay has been evaluated for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) in bovine fecal samples using primers and fluorescent resonance energy transfer (FRET) probes targeting the IS900 gene sequence of MAP. DNA was successfully extracted from manure samples by utilizing the Whatman FTA card technology, which allows for simple processing and storage of samples at room temperature. The FTA cards were washed and subjected to a Chelex-100 incubation to remove any remaining polymerase chain reaction (PCR) inhibitors and to elute the DNA from the FTA card. This isolated DNA was then subjected to direct real time fluorescent PCR analysis. Detection of MAP DNA from bovine fecal samples spiked with known concentrations of viable MAP cells was obtained. The detection limits of the assay was consistently found to be between 10(2) and 10(4) colony forming units [CFU]/g, with some samples containing as low as 10 CFU/g, yielding positive assay results. This cost-efficient assay allows reporting of results as early as 4 h after fecal collection, which can be particularly useful in highthroughput herd screening.

Simplified Real-Time Multiplex Detection of Loop-Mediated Isothermal Amplification Using Novel Mediator Displacement Probes with Universal Reporters.

Science.gov (United States)

Becherer, Lisa; Bakheit, Mohammed; Frischmann, Sieghard; Stinco, Silvina; Borst, Nadine; Zengerle, Roland; von Stetten, Felix

2018-04-03

A variety of real-time detection techniques for loop-mediated isothermal amplification (LAMP) based on the change in fluorescence intensity during DNA amplification enable simultaneous detection of multiple targets. However, these techniques depend on fluorogenic probes containing target-specific sequences. That complicates the adaption to different targets leading to time-consuming assay optimization. Here, we present the first universal real-time detection technique for multiplex LAMP. The novel approach allows simple assay design and is easy to implement for various targets. The innovation features a mediator displacement probe and a universal reporter. During amplification of target DNA the mediator is displaced from the mediator displacement probe. Then it hybridizes to the reporter generating a fluorescence signal. The novel mediator displacement (MD) detection was validated against state-of-the-art molecular beacon (MB) detection by means of a HIV-1 RT-LAMP: MD surpassed MB detection by accelerated probe design (MD: 10 min, MB: 3-4 h), shorter times to positive (MD 4.1 ± 0.1 min shorter than MB, n = 36), improved signal-to-noise fluorescence ratio (MD: 5.9 ± 0.4, MB: 2.7 ± 0.4; n = 15), and showed equally good or better analytical performance parameters. The usability of one universal mediator-reporter set in different multiplex assays was successfully demonstrated for a biplex RT-LAMP of HIV-1 and HTLV-1 and a biplex LAMP of Haemophilus ducreyi and Treponema pallidum, both showing good correlation between target concentration and time to positive. Due to its simple implementation it is suggested to extend the use of the universal mediator-reporter sets to the detection of various other diagnostic panels.

Real-time changes in hippocampal energy demands during a spatial working memory task.

Science.gov (United States)

Kealy, John; Bennett, Rachel; Woods, Barbara; Lowry, John P

2017-05-30

Activity-dependent changes in hippocampal energy consumption have largely been determined using microdialysis. However, real-time recordings of brain energy consumption can be more accurately achieved using amperometric sensors, allowing for sensitive real-time monitoring of concentration changes. Here, we test the theory that systemic pre-treatment with glucose in rats prevents activity-dependent decreases in hippocampal glucose levels and thus enhances their performance in a spontaneous alternation task. Male Sprague Dawley rats were implanted into the hippocampus with either: 1) microdialysis probe; or 2) an oxygen sensor and glucose biosensor co-implanted together. Animals were pre-treated with either saline or glucose (250mg/kg) 30min prior to performing a single 20-min spontaneous alternation task in a +-maze. There were no significant differences found between either treatment group in terms of spontaneous alternation performance. Additionally, there was a significant difference found between treatment groups on hippocampal glucose levels measured using microdialysis (a decrease associated with glucose pre-treatment in control animals) but not amperometry. There were significant increases in hippocampal oxygen during +-maze exploration. Combining the findings from both methods, it appears that hippocampal activity in the spontaneous alternation task does not cause an increase in glucose consumption, despite an increase in regional cerebral blood flow (using oxygen supply as an index of blood flow) and, as such, pre-treatment with glucose does not enhance spontaneous alternation performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Investigating the Effect of Voltage-Switching on Low-Energy Task Scheduling in Hard Real-Time Systems

Science.gov (United States)

2005-01-01

We investigate the effect of voltage-switching on task execution times and energy consumption for dual-speed hard real - time systems , and present a...scheduling algorithm and apply it to two real-life task sets. Our results show that energy can be conserved in embedded real - time systems using energy...aware task scheduling. We also show that switching times have a significant effect on the energy consumed in hard real - time systems .

Single tube multiplex real-time PCR for the rapid detection of herpesvirus infections of the central nervous system.

Science.gov (United States)

Sankuntaw, Nipaporn; Sukprasert, Saovaluk; Engchanil, Chulapan; Kaewkes, Wanlop; Chantratita, Wasun; Pairoj, Vantanit; Lulitanond, Viraphong

2011-01-01

Human herpesvirus infection of immunocompromised hosts may lead to central nervous system (CNS) infection and diseases. In this study, a single tube multiplex real-time PCR was developed for the detection of five herpesviruses (HSV-1, HSV-2, VZV, EBV and CMV) in clinical cerebrospinal fluid (CSF) specimens. Two primer pairs specific for the herpesvirus polymerase gene and five hybridization probe pairs for the specific identification of the herpesvirus types were used in a LightCycler multiplex real-time PCR. A singleplex real-time PCR was first optimized and then applied to the multiplex real-time PCR. The singleplex and multiplex real-time PCRs showed no cross-reactivity. The sensitivity of the singleplex real-time PCR was 1 copy per reaction for each herpesvirus, while that of the multiplex real-time PCR was 1 copy per reaction for HSV-1 and VZV and 10 copies per reaction for HSV-2, EBV and CMV. Intra and inter-assay variations of the single tube multiplex assay were in the range of 0.02%-3.67% and 0.79%-4.35%, respectively. The assay was evaluated by testing 62 clinical CSF samples and was found to have equivalent sensitivity, specificity and agreement as the routine real-time PCR, but reducing time, cost and amount of used sample. Copyright © 2011 Elsevier Ltd. All rights reserved.

Rapid detection of Lactobacillus kefiranofaciens in kefir grain and kefir milk using newly developed real-time PCR.

Science.gov (United States)

Kim, Dong-Hyeon; Chon, Jung-Whan; Kim, Hong-Seok; Yim, Jin-Hyeok; Kim, Hyunsook; Seo, Kun-Ho

2015-04-01

Lactobacillus kefiranofaciens is an indicator microorganism for kefir and a key factor in kefir grain formation and kefiran production. We designed a novel real-time PCR primer and probe set, LKF_KU504, for the rapid detection of L. kefiranofaciens. In inclusivity and exclusivity tests, only 14 L. kefiranofaciens strains were positive among 61 microorganisms, indicating 100 % sensitivity and specificity. The LKF_KU504 set also differentiated kefir milk from 30 commercial nonkefir yogurts. The levels of L. kefiranofaciens in kefir grain and kefir milk were significantly different, indicating L. kefiranofaciens was more concentrated in kefir grain than in kefir milk.

Rapid diagnosis of sepsis with TaqMan-Based multiplex real-time PCR.

Science.gov (United States)

Liu, Chang-Feng; Shi, Xin-Ping; Chen, Yun; Jin, Ye; Zhang, Bing

2018-02-01

The survival rate of septic patients mainly depends on a rapid and reliable diagnosis. A rapid, broad range, specific and sensitive quantitative diagnostic test is the urgent need. Thus, we developed a TaqMan-Based Multiplex real-time PCR assays to identify bloodstream pathogens within a few hours. Primers and TaqMan probes were designed to be complementary to conserved regions in the 16S rDNA gene of different kinds of bacteria. To evaluate accurately, sensitively, and specifically, the known bacteria samples (Standard strains, whole blood samples) are determined by TaqMan-Based Multiplex real-time PCR. In addition, 30 blood samples taken from patients with clinical symptoms of sepsis were tested by TaqMan-Based Multiplex real-time PCR and blood culture. The mean frequency of positive for Multiplex real-time PCR was 96% at a concentration of 100 CFU/mL, and it was 100% at a concentration greater than 1000 CFU/mL. All the known blood samples and Standard strains were detected positively by TaqMan-Based Multiplex PCR, no PCR products were detected when DNAs from other bacterium were used in the multiplex assay. Among the 30 patients with clinical symptoms of sepsis, 18 patients were confirmed positive by Multiplex real-time PCR and seven patients were confirmed positive by blood culture. TaqMan-Based Multiplex real-time PCR assay with highly sensitivity, specificity and broad detection range, is a rapid and accurate method in the detection of bacterial pathogens of sepsis and should have a promising usage in the diagnosis of sepsis. © 2017 Wiley Periodicals, Inc.

Universal detection of phytoplasmas and Xylella spp. by TaqMan singleplex and multiplex real-time PCR with dual priming oligonucleotides.

Directory of Open Access Journals (Sweden)

Takao Ito

Full Text Available Phytoplasmas and Xylella spp. are bacteria that cause many economically important plant diseases worldwide. TaqMan probe-based quantitative real-time polymerase chain reaction (qPCR assays have been utilized to universally detect phytoplasmas or Xylella fastidiosa. To develop a superior universal qPCR method, we used a dual priming oligonucleotide (DPO with two annealing sites as a reverse primer to target the well-conserved bacterial 16S rDNA. The new qPCR assays universally detected various species of phytoplasmas and subspecies of X. fastidiosa as well as Xylella taiwanensis, and generally showed superior threshold cycle values when amplifying specific or non-specific products compared to current universal qPCR assays. The proposed qPCR assays were integrated to develop a multiplex qPCR assay that simultaneously detected phytoplasmas, Xylella spp., and an internal plant DNA positive control within 1 hour. This assay could detect a minimum of ten bacterial cells and was compatible with crude extractions used in the rapid screening of various plants. The amplicons were of sufficient lengths to be directly sequenced for preliminary identification, and the primers could be used in universal conventional PCR assays. Additionally, reverse DPO primers can be utilized to improve other probe-based qPCR assays.

Real-Time Energy Management Control for Hybrid Electric Powertrains

Directory of Open Access Journals (Sweden)

Mohamed Zaher

2013-01-01

Full Text Available This paper focuses on embedded control of a hybrid powertrain concepts for mobile vehicle applications. Optimal robust control approach is used to develop a real-time energy management strategy. The main idea is to store the normally wasted mechanical regenerative energy in energy storage devices for later usage. The regenerative energy recovery opportunity exists in any condition where the speed of motion is in the opposite direction to the applied force or torque. This is the case when the vehicle is braking, decelerating, the motion is driven by gravitational force, or load driven. There are three main concepts for energy storing devices in hybrid vehicles: electric, hydraulic, and mechanical (flywheel. The real-time control challenge is to balance the system power demands from the engine and the hybrid storage device, without depleting the energy storage device or stalling the engine in any work cycle. In the worst-case scenario, only the engine is used and the hybrid system is completely disabled. A rule-based control algorithm is developed and is tuned for different work cycles and could be linked to a gain scheduling algorithm. A gain scheduling algorithm identifies the cycle being performed by the work machine and its position via GPS and maps both of them to the gains.

Development of a novel real-time qPCR assay for the dual detection of canine and phocine distemper virus

DEFF Research Database (Denmark)

Nielsen, Linette Buxbom; Hjulsager, Charlotte Kristiane; Larsen, Helene

conventional PCR assays with real-time PCR assays to obtain a uniform assay palette. The present work describes the development of a novel real-time RT-qPCR assay for the dual detection of canine and phocine distemper virus. The assay is relevant for the future detection of outbreaks of canine distemper virus...... in e.g. in farmed mink and wildlife and phocine distemper in seals. A set of primers and dual labelled probe was designed based on an alignment of distemper sequences in GenBank from various species and in-house sequences from recent outbreaks in Danish farmed mink. The assay amplifies a segment of 151...... bp in the Phosphoprotein (P) gene of the distemper virus genome. The dynamic range and PCR efficiency (E) was experimentally determined using 10-fold dilutions of a specially designed distemper DNA-oligo in addition to extracted RNA from clinical samples. E of the real-time assay was shown to range...

Data-driven modeling and real-time distributed control for energy efficient manufacturing systems

International Nuclear Information System (INIS)

Zou, Jing; Chang, Qing; Arinez, Jorge; Xiao, Guoxian

2017-01-01

As manufacturers face the challenges of increasing global competition and energy saving requirements, it is imperative to seek out opportunities to reduce energy waste and overall cost. In this paper, a novel data-driven stochastic manufacturing system modeling method is proposed to identify and predict energy saving opportunities and their impact on production. A real-time distributed feedback production control policy, which integrates the current and predicted system performance, is established to improve the overall profit and energy efficiency. A case study is presented to demonstrate the effectiveness of the proposed control policy. - Highlights: • A data-driven stochastic manufacturing system model is proposed. • Real-time system performance and energy saving opportunity identification method is developed. • Prediction method for future potential system performance and energy saving opportunity is developed. • A real-time distributed feedback control policy is established to improve energy efficiency and overall system profit.

A real-time low energy electron calorimeter

International Nuclear Information System (INIS)

Mod Ali, N.; Smith, F.A.

1999-01-01

A real-time low energy electron calorimeter with a thin film window has been designed and fabricated to facilitate a reliable method of dose assessment for electron beam energies down to 200 keV. The work was initiated by the Radiation Physics Group of Queen Mary and Westfield College in collaboration with the National Physical Laboratory (NPL), Teddington. Irradiations were performed on the low and medium electron energy electron accelerators at the Malaysian Institute for Nuclear Technology Research (MINT). Calorimeter response was initially tested using the on-line temperature measurements for a 500-keV electron beam. The system was later redesigned by incorporating a data-logger to use on the self-shielded 200-keV beam. In use, the final version of the calorimeter could start logging temperature a short time before the calorimeter passed under the beam and continue measurements throughout the irradiation. Data could be easily retrieved at the end of the exposure. (author)

Integrative real-time geographic visualization of energy resources

International Nuclear Information System (INIS)

Sorokine, A.; Shankar, M.; Stovall, J.; Bhaduri, B.; King, T.; Fernandez, S.; Datar, N.; Omitaomu, O.

2009-01-01

'Full text:' Several models forecast that climatic changes will increase the frequency of disastrous events like droughts, hurricanes, and snow storms. Responding to these events and also to power outages caused by system errors such as the 2003 North American blackout require an interconnect-wide real-time monitoring system for various energy resources. Such a system should be capable of providing situational awareness to its users in the government and energy utilities by dynamically visualizing the status of the elements of the energy grid infrastructure and supply chain in geographic contexts. We demonstrate an approach that relies on Google Earth and similar standard-based platforms as client-side geographic viewers with a data-dependent server component. The users of the system can view status information in spatial and temporal contexts. These data can be integrated with a wide range of geographic sources including all standard Google Earth layers and a large number of energy and environmental data feeds. In addition, we show a real-time spatio-temporal data sharing capability across the users of the system, novel methods for visualizing dynamic network data, and a fine-grain access to very large multi-resolution geographic datasets for faster delivery of the data. The system can be extended to integrate contingency analysis results and other grid models to assess recovery and repair scenarios in the case of major disruption. (author)

Selective detection of viable seed-borne Acidovorax citrulli by real-time PCR with propidium monoazide.

Science.gov (United States)

Tian, Qian; Feng, Jian-Jun; Hu, Jie; Zhao, Wen-Jun

2016-10-14

In recent years, use of the DNA-intercalating dye propidium monoazide (PMA) in real-time PCR has been reported as a novel method to detect viable bacteria in different types of samples, such as food, environmental, and microbiological samples. In this study, viable cells of Acidovorax citrulli, the causal agent of bacterial seedling blight and fruit blotch, were selectively detected and differentiated from dead cells by real-time fluorescent polymerase chain reaction amplification after the bacterial solution was treated with the DNA-binding dye PMA. The primers and TaqMan probe were based on the A. citrulli genome (Aave_1909, Gene ID: 4669443) and were highly specific for A. citrulli. The detection threshold of this assay was 10 3 colony-forming units per mL (CFU/mL) in pure cell suspensions containing viable and dead cells and infected watermelon seeds. Application of this assay enables the selective detection of viable cells of A. citrulli and facilitates monitoring of the pathogen in watermelon and melon seeds.

Improving method of real-time offset tuning for arterial signal coordination using probe trajectory data

Directory of Open Access Journals (Sweden)

Jian Zhang

2016-12-01

Full Text Available In the environment of intelligent transportation systems, traffic condition data would have higher resolution in time and space, which is especially valuable for managing the interrupted traffic at signalized intersections. There exist a lot of algorithms for offset tuning, but few of them take the advantage of modern traffic detection methods such as probe vehicle data. This study proposes a method using probe trajectory data to optimize and adjust offsets in real time. The critical point, representing the changing vehicle dynamics, is first defined as the basis of this approach. Using the critical points related to different states of traffic conditions, such as free flow, queue formation, and dissipation, various traffic status parameters can be estimated, including actual travel speed, queue dissipation rate, and standing queue length. The offset can then be adjusted on a cycle-by-cycle basis. The performance of this approach is evaluated using a simulation network. The results show that the trajectory-based approach can reduce travel time of the coordinated traffic flow when compared with using well-defined offline offset.

Real-Time Tracking the Synthesis and Degradation of Albumin in Complex Biological Systems with a near-Infrared Fluorescent Probe.

Science.gov (United States)

Jin, Qiang; Feng, Lei; Zhang, Shui-Jun; Wang, Dan-Dan; Wang, Fang-Jun; Zhang, Yi; Cui, Jing-Nan; Guo, Wen-Zhi; Ge, Guang-Bo; Yang, Ling

2017-09-19

In this study, a novel fluorescent detection system for biological sensing of human albumin (HA) was developed on the basis of the pseudoesterase activity and substrate preference of HA. The designed near-infrared (NIR) fluorescent probe (DDAP) could be effectively hydrolyzed by HA, accompanied by significant changes in both color and fluorescence spectrum. The sensing mechanism was fully investigated by fluorescence spectroscopy, NMR, and mass spectra. DDAP exhibited excellent selectivity and sensitivity toward HA over a variety of human plasma proteins, hydrolases, and abundant biomolecules found in human body. The probe has been successfully applied to measure native HA in diluted plasma samples and the secreted HA in the hepatocyte culture supernatant. DDAP has also been used for fluorescence imaging of HA reabsorption in living renal cells, and the results show that the probe exhibits good cell permeability, low cytotoxicity and high imaging resolution. Furthermore, DDAP has been successfully used for real-time tracking the uptaking and degradation of albumin in ex vivo mouse kidney models for the first time. All these results clearly demonstrated that DDAP-based assay held great promise for real-time sensing and tracking HA in complex biological systems, which would be very useful for basic researches and clinical diagnosis of HA-associated diseases.

Comparison of real-time SYBR green dengue assay with real-time taqman RT-PCR dengue assay and the conventional nested PCR for diagnosis of primary and secondary dengue infection

Science.gov (United States)

Paudel, Damodar; Jarman, Richard; Limkittikul, Kriengsak; Klungthong, Chonticha; Chamnanchanunt, Supat; Nisalak, Ananda; Gibbons, Robert; Chokejindachai, Watcharee

2011-01-01

Background: Dengue fever and dengue hemorrhagic fever are caused by dengue virus. Dengue infection remains a burning problem of many countries. To diagnose acute dengue in the early phase we improve the low cost, rapid SYBR green real time assay and compared the sensitivity and specificity with real time Taqman® assay and conventional nested PCR assay. Aims: To develop low cost, rapid and reliable real time SYBR green diagnostic dengue assay and compare with Taqman real-time assay and conventional nested PCR (modified Lanciotti). Materials and Methods: Eight cultured virus strains were diluted in tenth dilution down to undetectable level by the PCR to optimize the primer, temperature (annealing, and extension and to detect the limit of detection of the assay. Hundred and ninety three ELISA and PCR proved dengue clinical samples were tested with real time SYBR® Green assay, real time Taqman® assay to compare the sensitivity and specificity. Results: Sensitivity and specificity of real time SYBR® green dengue assay (84% and 66%, respectively) was almost comparable to those (81% and 74%) of Taqman real time PCR dengue assay. Real time SYBR® green RT-PCR was equally sensitive in primary and secondary infection while real time Taqman was less sensitive in the secondary infection. Sensitivity of real time Taqman on DENV3 (87%) was equal to SYBR green real time PCR dengue assay. Conclusion: We developed low cost rapid diagnostic SYBR green dengue assay. Further study is needed to make duplex primer assay for the serotyping of dengue virus. PMID:22363089

Detection of Tomato black ring virus by real-time one-step RT-PCR.

Science.gov (United States)

Harper, Scott J; Delmiglio, Catia; Ward, Lisa I; Clover, Gerard R G

2011-01-01

A TaqMan-based real-time one-step RT-PCR assay was developed for the rapid detection of Tomato black ring virus (TBRV), a significant plant pathogen which infects a wide range of economically important crops. Primers and a probe were designed against existing genomic sequences to amplify a 72 bp fragment from RNA-2. The assay amplified all isolates of TBRV tested, but no amplification was observed from the RNA of other nepovirus species or healthy host plants. The detection limit of the assay was estimated to be around nine copies of the TBRV target region in total RNA. A comparison with conventional RT-PCR and ELISA, indicated that ELISA, the current standard test method, lacked specificity and reacted to all nepovirus species tested, while conventional RT-PCR was approximately ten-fold less sensitive than the real-time RT-PCR assay. Finally, the real-time RT-PCR assay was tested using five different RT-PCR reagent kits and was found to be robust and reliable, with no significant differences in sensitivity being found. The development of this rapid assay should aid in quarantine and post-border surveys for regulatory agencies. Copyright © 2010 Elsevier B.V. All rights reserved.

Laboratory validation of two real-time RT-PCR methods with 5'-tailed primers for an enhanced detection of foot-and-mouth disease virus.

Science.gov (United States)

Vandenbussche, Frank; Lefebvre, David J; De Leeuw, Ilse; Van Borm, Steven; De Clercq, Kris

2017-08-01

The 3D and 5UTR real-time RT-PCR assays (RT-qPCR) from Callahan et al. (2002) and Reid et al. (2002) are commonly used reference methods for the detection of foot-and-mouth disease virus (FMDV). For an optimal detection of FMDV in clinical samples, it is advised to use both assays simultaneously (King et al., 2006). Recently, Vandenbussche et al. (2016) showed that the addition of 5'-tails to the FMDV-specific primers enhances the detection of FMDV in both the 3D and the 5UTR RT-qPCR assay. To validate the 3D and 5UTR RT-qPCR assays with 5'-tailed primers for diagnostic purposes, both assays were run in parallel in a triplex one-step RT-qPCR protocol with beta-actin as an internal control and synthetic RNA as an external control. We obtained low limits of detection and high linearity's, high repeatability and reproducibility, near 100% analytical specificity and >99% diagnostic accuracy for both assays. It was concluded that the 3D and 5UTR RT-qPCR assays with 5'-tailed primers are particularly suited for the detection of FMDV as well as to exclude the presence of FMDV. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of a real-time PCR for the detection of pathogenic Leptospira spp. in California sea lions.

Science.gov (United States)

Wu, Qingzhong; Prager, Katherine C; Goldstein, Tracey; Alt, David P; Galloway, Renee L; Zuerner, Richard L; Lloyd-Smith, James O; Schwacke, Lori

2014-08-11

Several real-time PCR assays are currently used for detection of pathogenic Leptospira spp.; however, few methods have been described for the successful evaluation of clinical urine samples. This study reports a rapid assay for the detection of pathogenic Leptospira spp. in California sea lions Zalophus californianus using real-time PCR with primers and a probe targeting the lipL32 gene. The PCR assay had high analytic sensitivity-the limit of detection was 3 genome copies per PCR volume using L. interrogans serovar Pomona DNA and 100% analytic specificity; it detected all pathogenic leptospiral serovars tested and none of the non-pathogenic Leptospira species (L. biflexa and L. meyeri serovar Semaranga), the intermediate species L. inadai, or the non-Leptospira pathogens tested. Our assay had an amplification efficiency of 1.00. Comparisons between the real-time PCR assay and culture isolation for detection of pathogenic Leptospira spp. in urine and kidney tissue samples from California sea lions showed that samples were more often positive by real-time PCR than by culture methods. Inclusion of an internal amplification control in the real-time PCR assay showed no inhibitory effects in PCR negative samples. These studies indicated that our real-time PCR assay has high analytic sensitivity and specificity for the rapid detection of pathogenic Leptospira species in urine and kidney tissue samples.

Detection of subgenomic mRNA of feline coronavirus by real-time polymerase chain reaction based on primer-probe energy transfer (P-sg-QPCR)

DEFF Research Database (Denmark)

Hornyák, Ákos; Bálint, Ádám; Farsang, Attila

2012-01-01

Feline infectious peritonitis is one of the most severe devastating diseases of the Felidae. Upon the appearance of clinical signs, a cure for the infected animal is impossible. Therefore rapid and proper diagnosis for both the presence of the causative agent, feline coronavirus (FCo......V) and the manifestation of feline infectious peritonitis is of paramount importance. In the present work, a novel real-time RT-PCR method is described which is able to detect FCoV and to determine simultaneously the quantity of the viral RNA. The new assay combines the M gene subgenomic messenger RNA (sg-mRNA) detection...... assay was proven by positive amplification from a set of nine different FCoV strains and negative from the tested non-coronaviral targets. Examination of faecal samples of healthy young cats, organ samples of perished animals, which suffered from feline infectious peritonitis, and cat leukocytes from...

Real Energy Payback Time and Carbon Footprint of a GCPVS

Directory of Open Access Journals (Sweden)

Miguel de Simón-Martín

2017-01-01

Full Text Available Grid connected PV systems, or GCPVS, produce clean and renewable energy through the photovoltaic effect in the operation stage of the power plant. However, this is the penultimate stage of the facilities before its dismantlement. Before starting generating electricity with zero CO2 emissions, a negative energy balance exists mainly because of the embodied energy costs of the PV components manufacturing, transport and late dismantlement. First, a review of existing studies about energy life cycle assessment (LCA and Carbon Footprint of PV systems has been carried out in this paper. Then, a new method to evaluate the Real Energy Payback Time (REPBT, which includes power looses due to PV panels degradation is proposed and differences with traditional Energy Payback Time are analysed. Finally, a typical PV grid connected plant (100 kW nominal power located in Northern Spain is studied in these sustainability terms. This facility has been firstly completely modelled, including PV modules, inverters, structures and wiring. It has been also considerated the energy involved in the replacement of those components with shorter lifespan. The PV panels degradation has been analysed through the comparison of normalised flash test reports on a significant sample of the installed modules before and 5 years after installation. Results show that real PV degradation affect significantly to the Energy Payback Time of the installation increasing slightly a 4:2% more the EPBT value for the case study. However, along a lifespan of 30 years, the GCPVS under analysis will return only 5:6 times the inverted energy on components manufacturing, transport and installation, rather than the expected 9:1 times with the classical estimation.

Real time drift measurement for colloidal probe atomic force microscope: a visual sensing approach

Energy Technology Data Exchange (ETDEWEB)

Wang, Yuliang, E-mail: wangyuliang@buaa.edu.cn; Bi, Shusheng [Robotics Institute, School of Mechanical Engineering and Automation, Beihang University, Beijing 100191 (China); Wang, Huimin [Department of Materials Science and Engineering, The Ohio State University, 2041 College Rd., Columbus, OH 43210 (United States)

2014-05-15

Drift has long been an issue in atomic force microscope (AFM) systems and limits their ability to make long time period measurements. In this study, a new method is proposed to directly measure and compensate for the drift between AFM cantilevers and sample surfaces in AFM systems. This was achieved by simultaneously measuring z positions for beads at the end of an AFM colloidal probe and on sample surface through an off-focus image processing based visual sensing method. The working principle and system configuration are presented. Experiments were conducted to validate the real time drift measurement and compensation. The implication of the proposed method for regular AFM measurements is discussed. We believe that this technique provides a practical and efficient approach for AFM experiments requiring long time period measurement.

Short-Term Wave Forecasting for Real-Time Control of Wave Energy Converters

OpenAIRE

Fusco, Francesco; Ringwood, John

2010-01-01

Real-time control of wave energy converters requires knowledge of future incident wave elevation in order to approach optimal efficiency of wave energy extraction. We present an approach where the wave elevation is treated as a time series and it is predicted only from its past history. A comparison of a range of forecasting methodologies on real wave observations from two different locations shows how the relatively simple linear autoregressive model, which implicitly models the cyclical beh...

Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products.

Science.gov (United States)

Kaltenbrunner, Maria; Hochegger, Rupert; Cichna-Markl, Margit

2018-05-08

Since game meat is more valuable and expensive than meat from domesticated animal species it is a potential target for adulteration. Analytical methods must allow the identification and quantification of meat species to be applicable for the detection of fraudulent labelling. We developed a real-time PCR assay for the authentication of sika deer (Cervus nippon) and products thereof. The primer/probe system amplifies a 71 bp fragment of the kappa-casein precursor gene. Since the target sequence contained only one sika deer-specific base, we introduced a deliberate base mismatch in the forward primer. The real-time PCR assay did not show cross-reactivity with 19 animal and 49 plant species tested. Low cross-reactivity was observed with red deer, fallow deer, reindeer and moose. However, with a ΔCt value of ≥11.79 between sika deer and the cross-reacting species, cross-reactivity will not affect the accuracy of the method. LOD and LOQ, determined by analysing serial dilutions of a DNA extract containing 1% (w/w) sika deer DNA in pig DNA, were 0.3% and 0.5%, respectively. The accuracy was evaluated by analysing DNA mixtures and DNA isolates from meat extract mixtures and meat mixtures. In general, recoveries were in the range from 70 to 130%.

Real Time Energy Management Control Strategies for Hybrid Powertrains

Science.gov (United States)

Zaher, Mohamed Hegazi Mohamed

In order to improve fuel efficiency and reduce emissions of mobile vehicles, various hybrid power-train concepts have been developed over the years. This thesis focuses on embedded control of hybrid powertrain concepts for mobile vehicle applications. Optimal robust control approach is used to develop a real time energy management strategy for continuous operations. The main idea is to store the normally wasted mechanical regenerative energy in energy storage devices for later usage. The regenerative energy recovery opportunity exists in any condition where the speed of motion is in opposite direction to the applied force or torque. This is the case when the vehicle is braking, decelerating, or the motion is driven by gravitational force, or load driven. There are three main concepts for regernerative energy storing devices in hybrid vehicles: electric, hydraulic, and flywheel. The real time control challenge is to balance the system power demand from the engine and the hybrid storage device, without depleting the energy storage device or stalling the engine in any work cycle, while making optimal use of the energy saving opportunities in a given operational, often repetitive cycle. In the worst case scenario, only engine is used and hybrid system completely disabled. A rule based control is developed and tuned for different work cycles and linked to a gain scheduling algorithm. A gain scheduling algorithm identifies the cycle being performed by the machine and its position via GPS, and maps them to the gains.

Real-time pricing strategy of micro-grid energy centre considering price-based demand response

Science.gov (United States)

Xu, Zhiheng; Zhang, Yongjun; Wang, Gan

2017-07-01

With the development of energy conversion technology such as power to gas (P2G), fuel cell and so on, the coupling between energy sources becomes more and more closely. Centralized dispatch among electricity, natural gas and heat will become a trend. With the goal of maximizing the system revenue, this paper establishes the model of micro-grid energy centre based on energy hub. According to the proposed model, the real-time pricing strategy taking into account price-based demand response of load is developed. And the influence of real-time pricing strategy on the peak load shifting is discussed. In addition, the impact of wind power predicted inaccuracy on real-time pricing strategy is analysed.

Low-Energy Real-Time OS Using Voltage Scheduling Algorithm for Variable Voltage Processors

OpenAIRE

Okuma, Takanori; Yasuura, Hiroto

2001-01-01

This paper presents a real-time OS based on $ mu $ITRON using proposed voltage scheduling algorithm for variable voltage processors which can vary supply voltage dynamically. The proposed voltage scheduling algorithms assign voltage level for each task dynamically in order to minimize energy consumption under timing constraints. Using the presented real-time OS, running tasks with low supply voltage leads to drastic energy reduction. In addition, the presented voltage scheduling algorithm is ...

Development and Characterization of Probe-Based Real Time Quantitative RT-PCR Assays for Detection and Serotyping of Foot-And-Mouth Disease Viruses Circulating in West Eurasia.

Science.gov (United States)

Jamal, Syed M; Belsham, Graham J

2015-01-01

Rapid and accurate diagnosis of foot-and-mouth disease (FMD) and virus serotyping are of paramount importance for control of this disease in endemic areas where vaccination is practiced. Ideally this virus characterization should be achieved without the need for virus amplification in cell culture. Due to the heterogeneity of FMD viruses (FMDVs) in different parts of the world, region specific diagnostic tests are required. In this study, hydrolysable probe-based real time reverse transcription quantitative polymerase chain reaction (RT-qPCR) assays were developed for specific detection and serotyping of the FMDVs currently circulating in West Eurasia. These assays were evaluated, in parallel with pan-FMDV diagnostic assays and earlier serotype-specific assays, using field samples originating from Pakistan and Afghanistan containing FMD viruses belonging to different sublineages of O-PanAsia, A-Iran05 and Asia-1 (Group-II and Group-VII (Sindh-08)). In addition, field samples from Iran and Bulgaria, containing FMDVs belonging to the O-PanAsiaANT-10 sublineage were also tested. Each of the three primer/probe sets was designed to be specific for just one of the serotypes O, A and Asia-1 of FMDV and detected the RNA from the target viruses with cycle threshold (CT) values comparable with those obtained with the serotype-independent pan-FMDV diagnostic assays. No cross-reactivity was observed in these assays between the heterotypic viruses circulating in the region. The assays reported here have higher diagnostic sensitivity (100% each for serotypes O and Asia-1, and 92% [95% CI = 81.4-100%] for serotype A positive samples) and specificity (100% each for serotypes O, A and Asia-1 positive samples) for the viruses currently circulating in West Eurasia compared to the serotyping assays reported earlier. Comparisons of the sequences of the primers and probes used in these assays and the corresponding regions of the circulating viruses provided explanations for the poor

Development and Characterization of Probe-Based Real Time Quantitative RT-PCR Assays for Detection and Serotyping of Foot-And-Mouth Disease Viruses Circulating in West Eurasia.

Directory of Open Access Journals (Sweden)

Syed M Jamal

Full Text Available Rapid and accurate diagnosis of foot-and-mouth disease (FMD and virus serotyping are of paramount importance for control of this disease in endemic areas where vaccination is practiced. Ideally this virus characterization should be achieved without the need for virus amplification in cell culture. Due to the heterogeneity of FMD viruses (FMDVs in different parts of the world, region specific diagnostic tests are required. In this study, hydrolysable probe-based real time reverse transcription quantitative polymerase chain reaction (RT-qPCR assays were developed for specific detection and serotyping of the FMDVs currently circulating in West Eurasia. These assays were evaluated, in parallel with pan-FMDV diagnostic assays and earlier serotype-specific assays, using field samples originating from Pakistan and Afghanistan containing FMD viruses belonging to different sublineages of O-PanAsia, A-Iran05 and Asia-1 (Group-II and Group-VII (Sindh-08. In addition, field samples from Iran and Bulgaria, containing FMDVs belonging to the O-PanAsiaANT-10 sublineage were also tested. Each of the three primer/probe sets was designed to be specific for just one of the serotypes O, A and Asia-1 of FMDV and detected the RNA from the target viruses with cycle threshold (CT values comparable with those obtained with the serotype-independent pan-FMDV diagnostic assays. No cross-reactivity was observed in these assays between the heterotypic viruses circulating in the region. The assays reported here have higher diagnostic sensitivity (100% each for serotypes O and Asia-1, and 92% [95% CI = 81.4-100%] for serotype A positive samples and specificity (100% each for serotypes O, A and Asia-1 positive samples for the viruses currently circulating in West Eurasia compared to the serotyping assays reported earlier. Comparisons of the sequences of the primers and probes used in these assays and the corresponding regions of the circulating viruses provided explanations for

Optimal Real-time Dispatch for Integrated Energy Systems

DEFF Research Database (Denmark)

Anvari-Moghaddam, Amjad; Guerrero, Josep M.; Rahimi-Kian, Ashkan

2016-01-01

With the emerging of small-scale integrated energy systems (IESs), there are significant potentials to increase the functionality of a typical demand-side management (DSM) strategy and typical implementation of building-level distributed energy resources (DERs). By integrating DSM and DERs...... into a cohesive, networked package that fully utilizes smart energy-efficient end-use devices, advanced building control/automation systems, and integrated communications architectures, it is possible to efficiently manage energy and comfort at the end-use location. In this paper, an ontology-driven multi......-agent control system with intelligent optimizers is proposed for optimal real-time dispatch of an integrated building and microgrid system considering coordinated demand response (DR) and DERs management. The optimal dispatch problem is formulated as a mixed integer nonlinear programing problem (MINLP...

Linear-after-the-exponential polymerase chain reaction and allied technologies. Real-time detection strategies for rapid, reliable diagnosis from single cells.

Science.gov (United States)

Pierce, Kenneth E; Wangh, Lawrence J

2007-01-01

Accurate detection of gene sequences in single cells is the ultimate challenge to polymerase chain reaction (PCR) sensitivity. Unfortunately, commonly used conventional and real-time PCR techniques are often too unreliable at that level to provide the accuracy needed for clinical diagnosis. Here we provide details of linear-after-the-exponential-PCR (LATE-PCR), a method similar to asymmetric PCR in the use of primers at different concentrations, but with novel design criteria to ensure high efficiency and specificity. Compared with conventional PCR, LATE-PCR increases the signal strength and allele discrimination capability of oligonucleotide probes such as molecular beacons and reduces variability among replicate samples. The analysis of real-time kinetics of LATE-PCR signals provides a means for improving the accuracy of single cell genetic diagnosis.

Exploiting 16S rRNA gene for the detection and quantification of fish as a potential allergenic food: A comparison of two real-time PCR approaches.

Science.gov (United States)

Fernandes, Telmo J R; Costa, Joana; Oliveira, M Beatriz P P; Mafra, Isabel

2018-04-15

Fish is one of the most common allergenic foods that should be accurately labelled to protect the health of allergic consumers. In this work, two real-time PCR systems based on the EvaGreen dye and a TaqMan probe are proposed and compared. New primers were designed to target the 16S rRNA gene, as a universal maker for fish detection, with fully demonstrated specificity for a wide range of fish species. Both systems showed similar absolute sensitivities, down to 0.01 pg of fish DNA, and adequate real-time PCR performance parameters. The probe system showed higher relative sensitivity and dynamic range (0.0001-50%) than the EvaGreen (0.05-50%). They were both precise, but trueness was compromised at the highest tested level with the EvaGreen assay. Therefore, both systems were successful, although the probe one exhibited the best performance. Its application to verify labelling compliance of foodstuffs suggested a high level of mislabelling and/or fraudulent practices. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bias in the Cq value observed with hydrolysis probe based quantitative PCR can be corrected with the estimated PCR efficiency value

NARCIS (Netherlands)

Tuomi, Jari Michael; Voorbraak, Frans; Jones, Douglas L.; Ruijter, Jan M.

2010-01-01

For real-time monitoring of PCR amplification of DNA, quantitative PCR (qPCR) assays use various fluorescent reporters. DNA binding molecules and hybridization reporters (primers and probes) only fluoresce when bound to DNA and result in the non-cumulative increase in observed fluorescence.

RUCS: Rapid identification of PCR primers for unique core sequences

DEFF Research Database (Denmark)

Thomsen, Martin Christen Frølund; Hasman, Henrik; Westh, Henrik

2017-01-01

Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous, and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs...... for the targets in silico . Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex...... in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin...

A TaqMan real-time PCR assay for detection of Meloidogyne hapla in root galls and in soil

DEFF Research Database (Denmark)

Sapkota, Rumakanta; Skantar, Andrea M.; Nicolaisen, Mogens

2016-01-01

. haplaand showed no significant amplification of DNA from non-target nematodes. The assay was able to detect M. haplain a background of plant and soil DNA. A dilution series of M. haplaeggs in soil showed a high correlation ( R 2 = 0 . 95 , P ...Early detection and quantification of Meloidogyne haplain soil is essential for effective disease management. The purpose of this study was to develop a real-time PCR assay for detection of M. haplain soil. Primers and a TaqMan probe were designed for M. hapladetection. The assay detected M......-knot development in carrots by testing soils before planting. The assay could be useful for management decisions in carrot cultivation....

Detection of Balamuthia mandrillaris DNA by real-time PCR targeting the RNase P gene

Directory of Open Access Journals (Sweden)

Lewin Astrid

2008-12-01

Full Text Available Abstract Background The free-living amoeba Balamuthia mandrillaris may cause fatal encephalitis both in immunocompromised and in – apparently – immunocompetent humans and other mammalian species. Rapid, specific, sensitive, and reliable detection requiring little pathogen-specific expertise is an absolute prerequisite for a successful therapy and a welcome tool for both experimental and epidemiological research. Results A real-time polymerase chain reaction assay using TaqMan® probes (real-time PCR was established specifically targeting the RNase P gene of B. mandrillaris amoebae. The assay detected at least 2 (down to 0.5 genomes of B. mandrillaris grown in axenic culture. It did not react with DNA from closely related Acanthamoeba (3 species, nor with DNA from Toxoplasma gondii, Leishmania major, Pneumocystis murina, Mycobacterium bovis (BCG, human brain, various mouse organs, or from human and murine cell lines. The assay efficiently detected B. mandrillaris DNA in spiked cell cultures, spiked murine organ homogenates, B. mandrillaris-infected mice, and CNS tissue-DNA preparations from 2 patients with proven cerebral balamuthiasis. This novel primer set was successfully combined with a published set that targets the B. mandrillaris 18S rRNA gene in a duplex real-time PCR assay to ensure maximum specificity and as a precaution against false negative results. Conclusion A real-time PCR assay for B. mandrillaris amoebae is presented, that is highly specific, sensitive, and reliable and thus suited both for diagnosis and for research.

Dynamic, in vivo, real-time detection of retinal oxidative status in a model of elevated intraocular pressure using a novel, reversibly responsive, profluorescent nitroxide probe.

Science.gov (United States)

Rayner, Cassie L; Gole, Glen A; Bottle, Steven E; Barnett, Nigel L

2014-12-01

Changes to the redox status of biological systems have been implicated in the pathogenesis of a wide variety of disorders including cancer, Ischemia-reperfusion (I/R) injury and neurodegeneration. In times of metabolic stress e.g. ischaemia/reperfusion, reactive oxygen species (ROS) production overwhelms the intrinsic antioxidant capacity of the cell, damaging vital cellular components. The ability to quantify ROS changes in vivo, is therefore essential to understanding their biological role. Here we evaluate the suitability of a novel reversible profluorescent probe containing a redox-sensitive nitroxide moiety (methyl ester tetraethylrhodamine nitroxide, ME-TRN), as an in vivo, real-time reporter of retinal oxidative status. The reversible nature of the probe's response offers the unique advantage of being able to monitor redox changes in both oxidizing and reducing directions in real time. After intravitreal administration of the ME-TRN probe, we induced ROS production in rat retina using an established model of complete, acute retinal ischaemia followed by reperfusion. After restoration of blood flow, retinas were imaged using a Micron III rodent fundus fluorescence imaging system, to quantify the redox-response of the probe. Fluorescent intensity declined during the first 60 min of reperfusion. The ROS-induced change in probe fluorescence was ameliorated with the retinal antioxidant, lutein. Fluorescence intensity in non-Ischemia eyes did not change significantly. This new probe and imaging technology provide a reversible and real-time response to oxidative changes and may allow the in vivo testing of antioxidant therapies of potential benefit to a range of diseases linked to oxidative stress. Copyright © 2014 Elsevier Ltd. All rights reserved.

Real-Time Energy Management System for a Hybrid AC/DC Residential Microgrid

DEFF Research Database (Denmark)

Diaz, Enrique Rodriguez; Palacios-Garcia, Emilio J.; Anvari-Moghaddam, Amjad

2017-01-01

This paper proposes real-time Energy Management System (EMS) for a residential hybrid ac/dc microgrid. The residential microgrid is organized in two different distribution systems. A dc distribution bus which interconnect the renewable energy sources (RES), energy storage systems (ESS...... buildings. This architecture increases the overall efficiency of the distribution by interconnecting the RES and ESS thorough a dc distribution bus, and therefore avoiding unnecessary dc/ac conversion stages. The real-time EMS performs an 24 hours ahead optimization in order to schedule the charge...... setup. The results shown how the operational costs of the system are effectively decreased by 28%, even with non-accurate estimation of the RES generation or building parameters....

Fast real-time polymerase chain reaction for quantitative detection of Lactobacillus delbrueckii bacteriophages in milk.

Science.gov (United States)

Martín, Maria Cruz; del Rio, Beatriz; Martínez, Noelia; Magadán, Alfonso H; Alvarez, Miguel A

2008-12-01

One of the main microbiological problems of the dairy industry is the susceptibility of starter bacteria to virus infections. Lactobacillus delbrueckii, a component of thermophilic starter cultures used in the manufacture of several fermented dairy products, including yogurt, is also sensitive to bacteriophage attacks. To avoid the problems associated with these viruses, quick and sensitive detection methods are necessary. In the present study, a fast real-time quantitative polymerase chain reaction assay for the direct detection and quantification of L. delbrueckii phages in milk was developed. A set of primers and a TaqMan MGB probe was designed, based on the lysin gene sequence of different L. delbrueckii phages. The results show the proposed method to be a rapid (total processing time 30 min), specific and highly sensitive technique for detecting L. delbrueckii phages in milk.

The time domain triple probe method

International Nuclear Information System (INIS)

Meier, M.A.; Hallock, G.A.; Tsui, H.Y.W.; Bengtson, R.D.

1994-01-01

A new Langmuir probe technique based on the triple probe method is being developed to provide simultaneous measurement of plasma temperature, potential, and density with the temporal and spatial resolution required to accurately characterize plasma turbulence. When the conventional triple probe method is used in an inhomogeneous plasma, local differences in the plasma measured at each probe introduce significant error in the estimation of turbulence parameters. The Time Domain Triple Probe method (TDTP) uses high speed switching of Langmuir probe potential, rather than spatially separated probes, to gather the triple probe information thus avoiding these errors. Analysis indicates that plasma response times and recent electronics technology meet the requirements to implement the TDTP method. Data reduction techniques of TDTP data are to include linear and higher order correlation analysis to estimate fluctuation induced particle and thermal transport, as well as energy relationships between temperature, density, and potential fluctuations

A one-step, real-time PCR assay for rapid detection of rhinovirus.

Science.gov (United States)

Do, Duc H; Laus, Stella; Leber, Amy; Marcon, Mario J; Jordan, Jeanne A; Martin, Judith M; Wadowsky, Robert M

2010-01-01

One-step, real-time PCR assays for rhinovirus have been developed for a limited number of PCR amplification platforms and chemistries, and some exhibit cross-reactivity with genetically similar enteroviruses. We developed a one-step, real-time PCR assay for rhinovirus by using a sequence detection system (Applied Biosystems; Foster City, CA). The primers were designed to amplify a 120-base target in the noncoding region of picornavirus RNA, and a TaqMan (Applied Biosystems) degenerate probe was designed for the specific detection of rhinovirus amplicons. The PCR assay had no cross-reactivity with a panel of 76 nontarget nucleic acids, which included RNAs from 43 enterovirus strains. Excellent lower limits of detection relative to viral culture were observed for the PCR assay by using 38 of 40 rhinovirus reference strains representing different serotypes, which could reproducibly detect rhinovirus serotype 2 in viral transport medium containing 10 to 10,000 TCID(50) (50% tissue culture infectious dose endpoint) units/ml of the virus. However, for rhinovirus serotypes 59 and 69, the PCR assay was less sensitive than culture. Testing of 48 clinical specimens from children with cold-like illnesses for rhinovirus by the PCR and culture assays yielded detection rates of 16.7% and 6.3%, respectively. For a batch of 10 specimens, the entire assay was completed in 4.5 hours. This real-time PCR assay enables detection of many rhinovirus serotypes with the Applied Biosystems reagent-instrument platform.

A specific endogenous reference for genetically modified common bean (Phaseolus vulgaris L.) DNA quantification by real-time PCR targeting lectin gene.

Science.gov (United States)

Venturelli, Gustavo L; Brod, Fábio C A; Rossi, Gabriela B; Zimmermann, Naíra F; Oliveira, Jaison P; Faria, Josias C; Arisi, Ana C M

2014-11-01

The Embrapa 5.1 genetically modified (GM) common bean was approved for commercialization in Brazil. Methods for the quantification of this new genetically modified organism (GMO) are necessary. The development of a suitable endogenous reference is essential for GMO quantification by real-time PCR. Based on this, a new taxon-specific endogenous reference quantification assay was developed for Phaseolus vulgaris L. Three genes encoding common bean proteins (phaseolin, arcelin, and lectin) were selected as candidates for endogenous reference. Primers targeting these candidate genes were designed and the detection was evaluated using the SYBR Green chemistry. The assay targeting lectin gene showed higher specificity than the remaining assays, and a hydrolysis probe was then designed. This assay showed high specificity for 50 common bean samples from two gene pools, Andean and Mesoamerican. For GM common bean varieties, the results were similar to those obtained for non-GM isogenic varieties with PCR efficiency values ranging from 92 to 101 %. Moreover, this assay presented a limit of detection of ten haploid genome copies. The primers and probe developed in this work are suitable to detect and quantify either GM or non-GM common bean.

Rapid and Quantitative Detection of Leifsonia xyli subsp. xyli in Sugarcane Stalk Juice Using a Real-Time Fluorescent (TaqMan PCR Assay

Directory of Open Access Journals (Sweden)

Hua-Ying Fu

2016-01-01

Full Text Available Ratoon stunting disease (RSD of sugarcane, one of the most important diseases seriously affecting the productivity of sugarcane crops, was caused by the bacterial agent Leifsonia xyli subsp. xyli (Lxx. A TaqMan probe-based real-time quantitative polymerase chain reaction (qPCR assay was established in this study for the quantification of Lxx detection in sugarcane stalk juice. A pair of PCR primers (Pat1-QF/Pat1-QR and a fluorogenic probe (Pat1-QP targeting the Part1 gene of Lxx were used for the qPCR assay. The assay had a detection limit of 100 copies of plasmid DNA and 100 fg of Lxx genomic DNA, which was 100-fold more sensitive than the conventional PCR. Fifty (28.7% of 174 stalk juice samples from two field trials were tested to be positive by qPCR assay, whereas, by conventional PCR, only 12.1% (21/174 were tested to be positive with a published primer pair CxxITSf#5/CxxITSr#5 and 15.5% (27/174 were tested to be positive with a newly designed primer pair Pat1-F2/Pat1-R2. The new qPCR assay can be used as an alternative to current diagnostic methods for Lxx, especially when dealing with certificating a large number of healthy cane seedlings and determining disease incidence accurately in commercial fields.

Biocompatibility of RealSeal, its primer and AH Plus implanted in subcutaneous connective tissue of rats

Directory of Open Access Journals (Sweden)

Fabiana Soares Grecca

2011-02-01

Full Text Available OBJECTIVE: This study tested rat connective tissue response to RealSeal, RealSeal primer or AH Plus after 7, 15, 30, 60 and 90 days of implantation. MATERIAL AND METHODS: Thirty Wistar rats had subcutaneous sockets created on their back and received four implants each of polyethylene tubes containing one of the materials tested according to the groups: AH (AH Plus Sealer; RS (RealSeal Sealer; RP (RealSeal Primer; CG (control group - empty tube. After histological processing, sections were analyzed to identify the presence of neutrophils, lymphocytes and plasma cells, eosinophils, macrophages and giant cells, as well as fibrous capsule and abscesses, by an examiner using light microscope. Kruskal-Wallis and multiple-comparisons test were used for statistical analysis. Significance level was set at 5%. RESULTS: Lymphoplasmacytic infiltrate scores significantly higher than those of the control group were observed at 14 and 60 days in AH group, and at 90 days in RS group (p<0.05. There were no differences in terms of presence of macrophages, giant cells, eosinophils, neutrophils or fibrosis. AH Plus group scored higher for abscesses at 7 days than after any other period (p=0.031. RP group scored higher for lymphoplasmacytic infiltrate at 14 days than at 90 days (p=0.04. CONCLUSION: The main contribution of this study was to demonstrate that issues involved with tissue tolerance of a Resilon-containing sealer, RealSeal Sealer, cannot be attributed to its primer content.

Development of a hydrolysis probe-based real-time assay for the detection of tropical strains of Fusarium oxysporum f. sp. cubense race 4

Science.gov (United States)

Cerf-Wendling, Isabelle; Hostachy, Bruno; Viljoen, Altus; Ioos, Renaud

2017-01-01

Fusarium oxysporum f. sp. cubense (Foc) is one of the most important threats to global banana production. Strategies to control the pathogen are lacking, with plant resistance offering the only long-term solution, if sources of resistance are available. Prevention of introduction of Foc into disease-free areas thus remains a key strategy to continue sustainable banana production. In recent years, strains of Foc affecting Cavendish bananas have destroyed plantations in a number of countries in Asia and in the Middle East, and one African country. One vegetative compatibility group (VCG), 01213/16, is considered the major threat to bananas in tropical and subtropical climatic conditions. However, other genetically related VCGs, such as 0121, may potentially jeopardize banana cultures if they were introduced into disease-free areas. To prevent the introduction of these VCGs into disease-free Cavendish banana-growing countries, a real-time PCR test was developed to accurately detect both VCGs. A previously described putative virulence gene was used to develop a specific combination of hydrolysis probe/primers for the detection of tropical Foc race 4 strains. The real-time PCR parameters were optimized by following a statistical approach relying on orthogonal arrays and the Taguchi method in an attempt to enhance sensitivity and ensure high specificity of the assay. This study also assessed critical performance criteria, such as repeatability, reproducibility, robustness, and specificity, with a large including set of 136 F. oxysporum isolates, including 73 Foc pathogenic strains representing 24 VCGs. The validation data demonstrated that the new assay could be used for regulatory testing applications on banana plant material and can contribute to preventing the introduction and spread of Foc strains affecting Cavendish bananas in the tropics. PMID:28178348

A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus

Directory of Open Access Journals (Sweden)

Qin E-de

2010-06-01

Full Text Available Abstract A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009 influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02 TCID50 (50% tissue culture infective dose for H5N1 and 0.2 TCID50 for the pandemic H1N1, which was the same as that of each single-target RT-PCR for pandemic H1N1 and even more sensitive for H5N1 with the same primers and probes. No cross reactivity of detecting other subtype influenza viruses or respiratory tract viruses was observed. Two hundred and thirty-six clinical specimens were tested by comparing with single real-time RT-PCR and result from the duplex assay was 100% consistent with the results of single real-time RT-PCR and sequence analysis.

Scheduling for energy and reliability management on multiprocessor real-time systems

Science.gov (United States)

Qi, Xuan

Scheduling algorithms for multiprocessor real-time systems have been studied for years with many well-recognized algorithms proposed. However, it is still an evolving research area and many problems remain open due to their intrinsic complexities. With the emergence of multicore processors, it is necessary to re-investigate the scheduling problems and design/develop efficient algorithms for better system utilization, low scheduling overhead, high energy efficiency, and better system reliability. Focusing cluster schedulings with optimal global schedulers, we study the utilization bound and scheduling overhead for a class of cluster-optimal schedulers. Then, taking energy/power consumption into consideration, we developed energy-efficient scheduling algorithms for real-time systems, especially for the proliferating embedded systems with limited energy budget. As the commonly deployed energy-saving technique (e.g. dynamic voltage frequency scaling (DVFS)) will significantly affect system reliability, we study schedulers that have intelligent mechanisms to recuperate system reliability to satisfy the quality assurance requirements. Extensive simulation is conducted to evaluate the performance of the proposed algorithms on reduction of scheduling overhead, energy saving, and reliability improvement. The simulation results show that the proposed reliability-aware power management schemes could preserve the system reliability while still achieving substantial energy saving.

Development and characterization of a small electromembrane extraction probe coupled with mass spectrometry for real-time and online monitoring of in vitro drug metabolism

DEFF Research Database (Denmark)

Dugstad, Helene Bonkerud; Petersen, Nickolaj J.; Jensen, Henrik

2014-01-01

A small and very simple electromembrane extraction probe (EME-probe) was developed and coupled directly to electrospray ionization mass spectrometry (ESI-MS), and this system was used to monitor in real time in vitro metabolism by rat liver microsomes of drug substances from a small reaction...... (soft extraction). Soft extraction was mandatory in order not to affect the reaction kinetics by sample composition changes induced by the EME-probe. The EME-probe/MS-system was used to establish kinetic profiles for the in vitro metabolism of promethazine, amitriptyline and imipramine as model...

A real time Taqman RT-PCR for the detection of rabbit hemorrhagic disease virus 2 (RHDV2).

Science.gov (United States)

Duarte, Margarida Dias; Carvalho, Carina L; Barros, Silvia C; Henriques, Ana M; Ramos, Fernanda; Fagulha, Teresa; Luís, Tiago; Duarte, Elsa L; Fevereiro, Miguel

2015-07-01

A specific real time RT-PCR for the detection of RHDV2 was developed and validated using RHDV and RHDV2 RNA preparations from positive field samples. The system was designed to amplify a 127 nucleotide-long RNA region located within the vp60 gene, based on the alignment of six sequences originated in Portugal, obtained in our laboratory, and 11 sequences from France and Italy. The primers and probe target sequences are highly conserved in the vast majority of the RHDV2 sequences presently known. In the sequences showing variability, only one mismatch is found per strain, usually outlying the 3' end of the primer or probe hybridization sequences. The specificity of the method was demonstrated in vitro with a panel of common rabbit pathogens. Standardization was performed with RNA transcripts obtained from a recombinant plasmid harboring the target sequence. The method was able to detected nine RNA molecules with an efficiency of 99.4% and a R(2) value of 1. Repeatability and reproducibility of the method were very high, with coefficients of variation lower than 2.40%. The assay was proven a valuable tool to diagnose most of RDVH2 circulating strains, and may be also useful to monitor viral loads, and consequently, disease progression and vaccination efficacy. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of Candida-Specific Real-Time PCR Assays for the Detection and Identification of Eight Medically Important Candida Species.

Science.gov (United States)

Zhang, Jing; Hung, Guo-Chiuan; Nagamine, Kenjiro; Li, Bingjie; Tsai, Shien; Lo, Shyh-Ching

2016-01-01

Culture-based identification methods have been the gold standard for the diagnosis of fungal infection. Currently, molecular technologies such as real-time PCR assays with short turnaround time can provide desirable alternatives for the rapid detection of Candida microbes. However, most of the published PCR primer sets are not Candida specific and likely to amplify DNA from common environmental contaminants, such as Aspergillus microbes. In this study, we designed pan-Candida primer sets based on the ribosomal DNA-coding regions conserved within Candida but distinct from those of Aspergillus and Penicillium. We demonstrate that the final two selected pan-Candida primer sets would not amplify Aspergillus DNA and could be used to differentiate eight medically important Candida pathogens in real-time PCR assays based on their melting profiles, with a sensitivity of detection as low as 10 fg of Candida genomic DNA. Moreover, we further evaluated and selected species-specific primer sets covering Candida albicans, Candida glabrata, Candida tropicalis, and Candida dubliniensis and show that they had high sensitivity and specificity. These real-time PCR primer sets could potentially be assembled into a single PCR array for the rapid detection of Candida species in various clinical settings, such as corneal transplantation.

Quantitative Real-time PCR detection of putrescine-producing Gram-negative bacteria

Directory of Open Access Journals (Sweden)

Kristýna Maršálková

2017-01-01

Full Text Available Biogenic amines are indispensable components of living cells; nevertheless these compounds could be toxic for human health in higher concentrations. Putrescine is supposed to be the major biogenic amine associated with microbial food spoilage. Development of reliable, fast and culture-independent molecular methods to detect bacteria producing biogenic amines deserves the attention, especially of the food industry in purpose to protect health. The objective of this study was to verify the newly designed primer sets for detection of two inducible genes adiA and speF together in Salmonella enterica and Escherichia coli genome by Real-time PCR. These forenamed genes encode enzymes in the metabolic pathway which leads to production of putrescine in Gram-negative bacteria. Moreover, relative expression of these genes was studied in E. coli CCM 3954 strain using Real-time PCR. In this study, sets of new primers for the detection two inducible genes (speF and adiA in Salmonella enterica and E. coli by Real-time PCR were designed and tested. Amplification efficiency of a Real-time PCR was calculated from the slope of the standard curves (adiA, speF, gapA. An efficiency in a range from 95 to 105 % for all tested reactions was achieved. The gene expression (R of adiA and speF genes in E. coli was varied depending on culture conditions. The highest gene expression of adiA and speF was observed at 6, 24 and 36 h (RadiA ~ 3, 5, 9; RspeF ~11, 10, 9; respectively after initiation of growth of this bacteria in nutrient broth medium enchired with amino acids. The results show that these primers could be used for relative quantification analysis of E. coli.

Real time dose rate measurements with fiber optic probes based on the RL and OSL of beryllium oxide

International Nuclear Information System (INIS)

Teichmann, T.; Sponner, J.; Jakobi, Ch.; Henniger, J.

2016-01-01

This work covers the examination of fiber optical probes based on the radioluminescence and real time optically stimulated luminescence of beryllium oxide. Experiments are carried out to determine the fundamental dosimetric and temporal properties of the system and evaluate its suitability for dose rate measurements in brachytherapy and other applications using non-pulsed radiation fields. For this purpose the responses of the radioluminescence and optically stimulated luminescence signal have been investigated in the dose rate range of 20 mGy/h to 3.6 Gy/h and for doses of 1 mGy up to 6 Gy. Furthermore, a new, efficient analysis procedure, the double phase reference summing, is introduced, leading to a real time optically stimulated luminescence signal. This method allows a complete compensation of the stem effect during the measurement. In contrast to previous works, the stimulation of the 1 mm cylindrical beryllium oxide detectors is performed with a symmetric function during irradiation. The investigated dose rates range from 0.3 to 3.6 Gy/h. The real time optically stimulated luminescence signal of beryllium oxide shows a dependency on both the dose rate and the applied dose. To overcome the problem of dose dependency, further experiments using higher stimulation intensities have to follow. - Highlights: • RL and OSL measurements with BeO extended to low dose (rate) range. • A new method to obtain the real time OSL: Dual Phase Reference Summing. • Real time OSL signal shows both dose and dose rate dependency. • Real time OSL enables a complete discrimination of the stem effect.

Energy-Efficient Real-Time Human Activity Recognition on Smart Mobile Devices

Directory of Open Access Journals (Sweden)

Jin Lee

2016-01-01

Full Text Available Nowadays, human activity recognition (HAR plays an important role in wellness-care and context-aware systems. Human activities can be recognized in real-time by using sensory data collected from various sensors built in smart mobile devices. Recent studies have focused on HAR that is solely based on triaxial accelerometers, which is the most energy-efficient approach. However, such HAR approaches are still energy-inefficient because the accelerometer is required to run without stopping so that the physical activity of a user can be recognized in real-time. In this paper, we propose a novel approach for HAR process that controls the activity recognition duration for energy-efficient HAR. We investigated the impact of varying the acceleration-sampling frequency and window size for HAR by using the variable activity recognition duration (VARD strategy. We implemented our approach by using an Android platform and evaluated its performance in terms of energy efficiency and accuracy. The experimental results showed that our approach reduced energy consumption by a minimum of about 44.23% and maximum of about 78.85% compared to conventional HAR without sacrificing accuracy.

T-L Plane Abstraction-Based Energy-Efficient Real-Time Scheduling for Multi-Core Wireless Sensors

Directory of Open Access Journals (Sweden)

Youngmin Kim

2016-07-01

Full Text Available Energy efficiency is considered as a critical requirement for wireless sensor networks. As more wireless sensor nodes are equipped with multi-cores, there are emerging needs for energy-efficient real-time scheduling algorithms. The T-L plane-based scheme is known to be an optimal global scheduling technique for periodic real-time tasks on multi-cores. Unfortunately, there has been a scarcity of studies on extending T-L plane-based scheduling algorithms to exploit energy-saving techniques. In this paper, we propose a new T-L plane-based algorithm enabling energy-efficient real-time scheduling on multi-core sensor nodes with dynamic power management (DPM. Our approach addresses the overhead of processor mode transitions and reduces fragmentations of the idle time, which are inherent in T-L plane-based algorithms. Our experimental results show the effectiveness of the proposed algorithm compared to other energy-aware scheduling methods on T-L plane abstraction.

Real time observation of the excimer formation dynamics of a gas phase benzene dimer by picosecond pump-probe spectroscopy.

Science.gov (United States)

Miyazaki, Mitsuhiko; Fujii, Masaaki

2015-10-21

We observed the real-time excimer (EXC) formation dynamics of a gas phase benzene dimer (Bz2) cluster after photo-excitation to the S1 state by applying an ionization detected picosecond transient absorption method for probing the visible EXC absorption for the first time. The time evolution of the EXC absorption from the S1 0(0) level shows a rise that is well fitted by a single exponential function with a time constant of 18 ± 2 ps. The structure of the Bz dimer has a T-shaped structure in the ground electronic state, and that in the EXC state is a parallel sandwich (SW) structure. Thus, the observed rise time corresponds to the structural change from the T to the SW structures, which directly shows the EXC formation. On the other hand, the EXC formation after excitation of the S1 6(1) vibrational level of the stem site showed a faster rise of the time constant of 10 ± 2 ps. Supposing equilibrium between the EXC and the local excited states, it followed that the intramolecular vibrational energy redistribution rate of the 6(1) level is largely enhanced and becomes faster than the EXC formation reaction.

Bitmap-Wise Wireless M-Bus Coordination for Sustainable Real Time Energy Management

Directory of Open Access Journals (Sweden)

Kwang-il Hwang

2014-07-01

Full Text Available Even though WM-Bus is being considered to be the most promising network protocol for smart metering, it is not suitable for a sustainable real-time home energy management system (HEMS, which requires higher reliability and longer lifetime despite real time bi-directional communications. Therefore, in this paper we propose a Bitmap-wise WM-Bus (BWM-Bus, coping well with sustainable real-time HEMS. In particular, the proposed scheme addresses the several problems in WM-Bus for HEMS by introducing novel functions: asynchronous meter trigger, adaptive slot scheduling, and bitmap-wise retransmission request. Through experiments, we demonstrate that BWM-Bus guarantees higher data success ratio with lower data aggregation time, as well as longer lifetime than WM-Bus standard.

Pruning-Based, Energy-Optimal, Deterministic I/O Device Scheduling for Hard Real-Time Systems

Science.gov (United States)

2005-02-01

However, DPM via I/O device scheduling for hard real - time systems has received relatively little attention. In this paper,we present an offline I/O...polynomial time. We present experimental results to show that EDS and MDO reduce the energy consumption of I/O devices significantly for hard real - time systems .

Real-time PCR quantification of six periodontal pathogens in saliva samples from healthy young adults.

Science.gov (United States)

Zhou, Xiaodong; Liu, Xiaoli; Li, Jing; Aprecio, Raydolfo M; Zhang, Wu; Li, Yiming

2015-05-01

The use of saliva as a diagnostic fluid for the evaluation of periodontal health has gained attention recently. Most published real-time PCR assays focused on quantification of bacteria in subgingival plaque, not in saliva. The aims of this study were to develop a real-time PCR assay for quantification of six periodontal pathogens in saliva and to establish a relationship between the amount of DNA (fg) and colony-forming unit (CFU). TaqMan primers/probe sets were used for the detection of Aggregatibacter actinomycetemcomitans (Aa), Eikenella corrodens (Ec), Fusobacterium nucleatum (Fn), Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Tannerella forsythia (Tf), and total bacteria. Six periodontal pathogens and total bacteria in saliva from 24 periodontally healthy individuals were determined. The relationship between the amount of DNA (fg) and CFU was established by measuring the concentrations of extracted bacterial DNA and CFU per milliliter of bacteria on agar plates. Fn, Ec, and Pi were detected in all saliva samples, while 58.5, 45.8, and 33.3% were detected for Tf, Pg, and Aa, respectively. Numbers of Ec and Fn in saliva were highly correlated (R(2) = 0.93, P periodontal pathogens in saliva and estimate the number of live bacteria (CFU). This real-time PCR assay in combination with the relationship between DNA (fg) and CFU has the potential to be an adjunct in evaluation of periodontal health status.

Detection of Mycosphaerella graminicola in Wheat Leaves by a Microsatellite Dinucleotide Specific-Primer

Directory of Open Access Journals (Sweden)

Joseph-Alexander Verreet

2011-01-01

Full Text Available Early detection of infection is very important for efficient management of Mycosphaerella graminicola leaf blotch. To monitor and quantify the occurrence of this fungus during the growing season, a diagnostic method based on real-time PCR was developed. Standard and real-time PCR assays were developed using SYBR Green chemistry to quantify M. graminicola in vitro or in wheat samples. Microsatellite dinucleotide specific-primers were designed based on microsatellite repeats of sequences present in the genome of M. graminicola. Specificity was checked by analyzing DNA of 55 M. graminicola isolates obtained from different geographical origins. The method appears to be highly specific for detecting M. graminicola; no fluorescent signals were observed from 14 other closely related taxa. Primer (CT 7 G amplified a specific amplicon of 570 bp from all M. graminicola isolates. The primers did not amplify DNA extracted from 14 other fungal species. The approximate melting temperature (Tm of the (CT 7 G primer was 84.2 °C. The detection limit of the real-time PCR assay with the primer sets (CT 7 G is 10 fg/25 µL, as compared to 10 pg/25 µL using conventional PCR technology. From symptomless leaves, a PCR fragment could be generated two days after inoculation. Both conventional and real-time PCR could successfully detect the fungus from artificially inoculated wheat leaves. However, real-time PCR appeared much more sensitive than conventional PCR. The developed quantitative real-time PCR method proved to be rapid, sensitive, specific, cost-effective and reliable for the identification and quantification of M. graminicola in wheat.

Simultaneous Detection of Ricin and Abrin DNA by Real-Time PCR (qPCR

Directory of Open Access Journals (Sweden)

Roman Wölfel

2012-08-01

Full Text Available Ricin and abrin are two of the most potent plant toxins known and may be easily obtained in high yield from the seeds using rather simple technology. As a result, both toxins are potent and available toxins for criminal or terrorist acts. However, as the production of highly purified ricin or abrin requires sophisticated equipment and knowledge, it may be more likely that crude extracts would be used by non-governmental perpetrators. Remaining plant-specific nucleic acids in these extracts allow the application of a real-time PCR (qPCR assay for the detection and identification of abrin or ricin genomic material. Therefore, we have developed a duplex real-time PCR assays for simultaneous detection of ricin and abrin DNA based on the OmniMix HS bead PCR reagent mixture. Novel primers and hybridization probes were designed for detection on a SmartCycler instrument by using 5′-nuclease technology. The assay was thoroughly optimized and validated in terms of analytical sensitivity. Evaluation of the assay sensitivity by probit analysis demonstrated a 95% probability of detection at 3 genomes per reaction for ricin DNA and 1.2 genomes per reaction for abrin DNA. The suitability of the assays was exemplified by detection of ricin and abrin contaminations in a food matrix.

Real-Time PCR (qPCR) Primer Design Using Free Online Software

Science.gov (United States)

Thornton, Brenda; Basu, Chhandak

2011-01-01

Real-time PCR (quantitative PCR or qPCR) has become the preferred method for validating results obtained from assays which measure gene expression profiles. The process uses reverse transcription polymerase chain reaction (RT-PCR), coupled with fluorescent chemistry, to measure variations in transcriptome levels between samples. The four most…

A Short Interspersed Nuclear Element (SINE)-Based Real-Time PCR Approach to Detect and Quantify Porcine Component in Meat Products.

Science.gov (United States)

Zhang, Chi; Fang, Xin; Qiu, Haopu; Li, Ning

2015-01-01

Real-time PCR amplification of mitochondria gene could not be used for DNA quantification, and that of single copy DNA did not allow an ideal sensitivity. Moreover, cross-reactions among similar species were commonly observed in the published methods amplifying repetitive sequence, which hindered their further application. The purpose of this study was to establish a short interspersed nuclear element (SINE)-based real-time PCR approach having high specificity for species detection that could be used in DNA quantification. After massive screening of candidate Sus scrofa SINEs, one optimal combination of primers and probe was selected, which had no cross-reaction with other common meat species. LOD of the method was 44 fg DNA/reaction. Further, quantification tests showed this approach was practical in DNA estimation without tissue variance. Thus, this study provided a new tool for qualitative detection of porcine component, which could be promising in the QC of meat products.

Real-time optoacoustic monitoring of temperature in tissues

International Nuclear Information System (INIS)

Larina, Irina V; Larin, Kirill V; Esenaliev, Rinat O

2005-01-01

To improve the safety and efficacy of thermal therapy, it is necessary to map tissue temperature in real time with submillimetre spatial resolution. Accurate temperature maps may provide the necessary control of the boundaries of the heated regions and minimize thermal damage to surrounding normal tissues. Current imaging modalities fail to monitor tissue temperature in real time with high resolution and accuracy. We investigated a non-invasive optoacoustic method for accurate, real-time monitoring of tissue temperature during thermotherapy. In this study, we induced temperature gradients in tissue and tissue-like samples and monitored the temperature distribution using the optoacoustic technique. The fundamental harmonic of a Q-switched Nd : YAG laser (λ = 1064 nm) was used for optoacoustic wave generation and probing of tissue temperature. The tissue temperature was also monitored with a multi-sensor temperature probe inserted in the samples. Good agreement between optoacoustically measured and actual tissue temperatures was obtained. The accuracy of temperature monitoring was better than 1 0 C, while the spatial resolution was about 1 mm. These data suggest that the optoacoustic technique has the potential to be used for non-invasive, real-time temperature monitoring during thermotherapy

Real-Time Discrimination and Versatile Profiling of Spontaneous Reactive Oxygen Species in Living Organisms with a Single Fluorescent Probe.

Science.gov (United States)

Zhang, Ruilong; Zhao, Jun; Han, Guangmei; Liu, Zhengjie; Liu, Cui; Zhang, Cheng; Liu, Bianhua; Jiang, Changlong; Liu, Renyong; Zhao, Tingting; Han, Ming-Yong; Zhang, Zhongping

2016-03-23

Fluorescent probes are powerful tools for the investigations of reactive oxygen species (ROS) in living organisms by visualization and imaging. However, the multiparallel assays of several ROS with multiple probes are often limited by the available number of spectrally nonoverlapping chromophores together with large invasive effects and discrepant biological locations. Meanwhile, the spontaneous ROS profilings in various living organs/tissues are also limited by the penetration capability of probes across different biological barriers and the stability in reactive in vivo environments. Here, we report a single fluorescent probe to achieve the effective discrimination and profiling of hydroxyl radicals (•OH) and hypochlorous acid (HClO) in living organisms. The probe is constructed by chemically grafting an additional five-membered heterocyclic ring and a lateral triethylene glycol chain to a fluorescein mother, which does not only turn off the fluorescence of fluorescein, but also create the dual reactive sites to ROS and the penetration capability in passing through various biological barriers. The reactions of probe with •OH and HClO simultaneously result in cyan and green emissions, respectively, providing the real-time discrimination and quantitative analysis of the two ROS in cellular mitochondria. Surprisingly, the accumulation of probes in the intestine and liver of a normal-state zebrafish and the transfer pathway from intestine-to-blood-to-organ/tissue-to-kidney-to-excretion clearly present the profiling of spontaneous •OH and HClO in these metabolic organs. In particular, the stress generation of •OH at the fresh wound of zebrafish is successfully visualized for the first time, in spite of its extremely short lifetime.

Implementation of real-time duplex synthetic aperture ultrasonography

DEFF Research Database (Denmark)

Hemmsen, Martin Christian; Larsen, Lee; Kjeldsen, Thomas

2015-01-01

This paper presents a real-time duplex synthetic aperture imaging system, implemented on a commercially available tablet. This includes real-time wireless reception of ultrasound signals and GPU processing for B-mode and Color Flow Imaging (CFM). The objective of the work is to investigate the im...... and that the required bandwidth between the probe and processing unit is within the current Wi-Fi standards....

A Real-Time PCR Assay to Identify and Discriminate Among Wild-Type and Vaccine Strains of Varicella-Zoster Virus and Herpes Simplex Virus in Clinical Specimens, and Comparison With the Clinical Diagnoses

Science.gov (United States)

Harbecke, Ruth; Oxman, Michael N.; Arnold, Beth A.; Ip, Charlotte; Johnson, Gary R.; Levin, Myron J.; Gelb, Lawrence D.; Schmader, Kenneth E.; Straus, Stephen E.; Wang, Hui; Wright, Peter F.; Pachucki, Constance T.; Gershon, Anne A.; Arbeit, Robert D.; Davis, Larry E.; Simberkoff, Michael S.; Weinberg, Adriana; Williams, Heather M.; Cheney, Carol; Petrukhin, Luba; Abraham, Katalin G.; Shaw, Alan; Manoff, Susan; Antonello, Joseph M.; Green, Tina; Wang, Yue; Tan, Charles; Keller, Paul M.

2014-01-01

A real-time PCR assay was developed to identify varicella-zoster virus (VZV) and herpes simplex virus (HSV) DNA in clinical specimens from subjects with suspected herpes zoster (HZ; shingles). Three sets of primers and probes were used in separate PCR reactions to detect and discriminate among wild-type VZV (VZV-WT), Oka vaccine strain VZV (VZV-Oka), and HSV DNA, and the reaction for each virus DNA was multiplexed with primers and probe specific for the human β-globin gene to assess specimen adequacy. Discrimination of all VZV-WT strains, including Japanese isolates and the Oka parent strain, from VZV-Oka was based upon a single nucleotide polymorphism at position 106262 in ORF 62, resulting in preferential amplification by the homologous primer pair. The assay was highly sensitive and specific for the target virus DNA, and no cross-reactions were detected with any other infectious agent. With the PCR assay as the gold standard, the sensitivity of virus culture was 53% for VZV and 77% for HSV. There was 92% agreement between the clinical diagnosis of HZ by the Clinical Evaluation Committee and the PCR assay results. PMID:19475609

Real-time control and data-acquisition system for high-energy neutral-beam injectors

International Nuclear Information System (INIS)

Glad, A.S.; Jacobson, V.

1981-12-01

The need for a real-time control system and a data acquisition, processing and archiving system operating in parallel on the same computer became a requirement on General Atomic's Doublet III fusion energy project with the addition of high energy neutral beam injectors. The data acquisition processing and archiving system is driven from external events and is sequenced through each experimental shot utilizing ModComp's intertask message service. This system processes, archives and displays on operator console CRTs all physics diagnostic data related to the neutral beam injectores such as temperature, beam alignment, etc. The real-time control system is data base driven and provides periodic monitoring and control of the numerous dynamic subsystems of the neutral beam injectors such as power supplies, timing, water cooling, etc

[Development and application of real-time PCR for identification and detection of horse meat in animal-origin products].

Science.gov (United States)

Li, Nan; Wang, Jiahui; Shen, Qing; Han, Chunhui; Zhang, Jing; Li, Fengqin; Xu, Jin; Jiang, Tao

2013-11-01

To develop a real-time PCR method for identification and detection of domestic horse meat (Equus caballus) in animal-origin products. The primer and TaqMan-probe was designed and synthesized according to the EU reference laboratory and 87 bp fragments was amplified for horse ingredients. The specificity and sensitivity was tested by artificially spiked horse meat into other domestic meat, such as cattle, sheep, pork, chicken, duck and rabbit. 122 samples of cattle and sheep products were random collected in Beijing market and the detection of horse meat was carried out. The real-time PCR in this study has high specificity and sensitivity for horse meat. No cross-reaction was observed between the horse and sheep, pork, chicken, duck and rabbit meat. There was little cross reaction between horse and cattle when the CT value reach 33. 81. The method can detect 0.1% of horse meat mixed with other domestic animal-origin products. No horse meat ingredients were detected in 122 samples in this survey. There was no horse meat mixed into cattle and sheep products in Beijing marked.

Big IoT data mining for real-time energy disaggregation in buildings

NARCIS (Netherlands)

Mocanu, D.C.; Mocanu, E.; Nguyen, H.P.; Gibescu, M.; Liotta, A.

2017-01-01

In the smart grid context, the identification and prediction of building energy flexibility is a challenging open question, thus paving the way for new optimized behaviors from the demand side. At the same time, the latest smart meters developments allow us to monitor in real-time the power

A real-time PCR approach to detect predation on anchovy and sardine early life stages

Science.gov (United States)

Cuende, Elsa; Mendibil, Iñaki; Bachiller, Eneko; Álvarez, Paula; Cotano, Unai; Rodriguez-Ezpeleta, Naiara

2017-12-01

Recruitment of sardine (Sardina pilchardus Walbaum, 1792) and anchovy (Engraulis encrasicolus Linnaeus, 1758) is thought to be regulated by predation of their eggs and larvae. Predators of sardine and anchovy can be identified by visual taxonomic identification of stomach contents, but this method is time consuming, tedious and may underestimate predation, especially in small predators such as fish larvae. Alternatively, genetic tools may offer a more cost-effective and accurate alternative. Here, we have developed a multiplex real-time polymerase chain reaction (RT-PCR) assay based on TaqMan probes to simultaneously detect sardine and anchovy remains in gut contents of potential predators. The assay combines previously described and newly generated species-specific primers and probes for anchovy and sardine detection respectively, and allows the detection of 0,001 ng of target DNA (which corresponds to about one hundredth of the total DNA present in a single egg). We applied the method to candidate anchovy and sardine egg predators in the Bay of Biscay, Atlantic Mackerel (Scomber scombrus) larvae. Egg predation observed was limited primarily to those stations where sardine and/or anchovy eggs were present. Our developed assay offers a suitable tool to understand the effects of predation on the survival of anchovy and sardine early life stages.

Development of field-based real-time reverse transcription-polymerase chain reaction assays for detection of Chikungunya and O'nyong-nyong viruses in mosquitoes.

Science.gov (United States)

Smith, Darci R; Lee, John S; Jahrling, Jordan; Kulesh, David A; Turell, Michael J; Groebner, Jennifer L; O'Guinn, Monica L

2009-10-01

Chikungunya (CHIK) and O'nyong-nyong (ONN) are important emerging arthropod-borne diseases. Molecular diagnosis of these two viruses in mosquitoes has not been evaluated, and the effects of extraneous mosquito tissue on assay performance have not been tested. Additionally, no real-time reverse transcription-polymerase chain reaction (RT-PCR) assay exists for detecting ONN virus (ONNV) RNA. We describe the development of sensitive and specific real-time RT-PCR assays for detecting CHIK and ONN viral RNA in mosquitoes, which have application for field use. In addition, we compared three methods for primer/probe design for assay development by evaluating their sensitivity and specificity. This comparison resulted in development of virus-specific assays that could detect less than one plaque-forming unit equivalent of each of the viruses in mosquitoes. The use of these assays will aid in arthropod-borne disease surveillance and in the control of the associated diseases.

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.

Science.gov (United States)

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.

Real time implementation and control validation of the wind energy conversion system

Science.gov (United States)

Sattar, Adnan

The purpose of the thesis is to analyze dynamic and transient characteristics of wind energy conversion systems including the stability issues in real time environment using the Real Time Digital Simulator (RTDS). There are different power system simulation tools available in the market. Real time digital simulator (RTDS) is one of the powerful tools among those. RTDS simulator has a Graphical User Interface called RSCAD which contains detail component model library for both power system and control relevant analysis. The hardware is based upon the digital signal processors mounted in the racks. RTDS simulator has the advantage of interfacing the real world signals from the external devices, hence used to test the protection and control system equipments. Dynamic and transient characteristics of the fixed and variable speed wind turbine generating systems (WTGSs) are analyzed, in this thesis. Static Synchronous Compensator (STATCOM) as a flexible ac transmission system (FACTS) device is used to enhance the fault ride through (FRT) capability of the fixed speed wind farm. Two level voltage source converter based STATCOM is modeled in both VSC small time-step and VSC large time-step of RTDS. The simulation results of the RTDS model system are compared with the off-line EMTP software i.e. PSCAD/EMTDC. A new operational scheme for a MW class grid-connected variable speed wind turbine driven permanent magnet synchronous generator (VSWT-PMSG) is developed. VSWT-PMSG uses fully controlled frequency converters for the grid interfacing and thus have the ability to control the real and reactive powers simultaneously. Frequency converters are modeled in the VSC small time-step of the RTDS and three phase realistic grid is adopted with RSCAD simulation through the use of optical analogue digital converter (OADC) card of the RTDS. Steady state and LVRT characteristics are carried out to validate the proposed operational scheme. Simulation results show good agreement with real

Quantification of the biocontrol agent Trichoderma harzianum with real-time TaqMan PCR and its potential extrapolation to the hyphal biomass.

Science.gov (United States)

López-Mondéjar, Rubén; Antón, Anabel; Raidl, Stefan; Ros, Margarita; Pascual, José Antonio

2010-04-01

The species of the genus Trichoderma are used successfully as biocontrol agents against a wide range of phytopathogenic fungi. Among them, Trichoderma harzianum is especially effective. However, to develop more effective fungal biocontrol strategies in organic substrates and soil, tools for monitoring the control agents are required. Real-time PCR is potentially an effective tool for the quantification of fungi in environmental samples. The aim of this study consisted of the development and application of a real-time PCR-based method to the quantification of T. harzianum, and the extrapolation of these data to fungal biomass values. A set of primers and a TaqMan probe for the ITS region of the fungal genome were designed and tested, and amplification was correlated to biomass measurements obtained with optical microscopy and image analysis, of the hyphal length of the mycelium of the colony. A correlation of 0.76 between ITS copies and biomass was obtained. The extrapolation of the quantity of ITS copies, calculated based on real-time PCR data, into quantities of fungal biomass provides potentially a more accurate value of the quantity of soil fungi. Copyright 2009 Elsevier Ltd. All rights reserved.

Real-time sequence-validated loop-mediated isothermal amplification assays for detection of Middle East respiratory syndrome coronavirus (MERS-CoV.

Directory of Open Access Journals (Sweden)

Sanchita Bhadra

Full Text Available The Middle East respiratory syndrome coronavirus (MERS-CoV, an emerging human coronavirus, causes severe acute respiratory illness with a 35% mortality rate. In light of the recent surge in reported infections we have developed asymmetric five-primer reverse transcription loop-mediated isothermal amplification (RT-LAMP assays for detection of MERS-CoV. Isothermal amplification assays will facilitate the development of portable point-of-care diagnostics that are crucial for management of emerging infections. The RT-LAMP assays are designed to amplify MERS-CoV genomic loci located within the open reading frame (ORF1a and ORF1b genes and upstream of the E gene. Additionally we applied one-step strand displacement probes (OSD for real-time sequence-specific verification of LAMP amplicons. Asymmetric amplification effected by incorporating a single loop primer in each assay accelerated the time-to-result of the OSD-RT-LAMP assays. The resulting assays could detect 0.02 to 0.2 plaque forming units (PFU (5 to 50 PFU/ml of MERS-CoV in infected cell culture supernatants within 30 to 50 min and did not cross-react with common human respiratory pathogens.

Quantitative (real-time) PCR

International Nuclear Information System (INIS)

Denman, S.E.; McSweeney, C.S.

2005-01-01

Many nucleic acid-based probe and PCR assays have been developed for the detection tracking of specific microbes within the rumen ecosystem. Conventional PCR assays detect PCR products at the end stage of each PCR reaction, where exponential amplification is no longer being achieved. This approach can result in different end product (amplicon) quantities being generated. In contrast, using quantitative, or real-time PCR, quantification of the amplicon is performed not at the end of the reaction, but rather during exponential amplification, where theoretically each cycle will result in a doubling of product being created. For real-time PCR, the cycle at which fluorescence is deemed to be detectable above the background during the exponential phase is termed the cycle threshold (Ct). The Ct values obtained are then used for quantitation, which will be discussed later

Improvements for real-time magnetic equilibrium reconstruction on ASDEX Upgrade

International Nuclear Information System (INIS)

Giannone, L.; Fischer, R.; McCarthy, P.J.; Odstrcil, T.; Zammuto, I.; Bock, A.; Conway, G.; Fuchs, J.C.; Gude, A.; Igochine, V.; Kallenbach, A.; Lackner, K.; Maraschek, M.; Rapson, C.; Ruan, Q.; Schuhbeck, K.H.; Suttrop, W.; Wenzel, L.

2015-01-01

Highlights: • Spline basis current functions with second-order linear regularisation. • Perturbations of magnetic probe measurements due to ferromagnetic tiles on the inner wall and from oscillations in the fast position coil current are corrected. • A constraint of the safety factor on the magnetic axis is introduced. Soft X-ray tomography is used to assess the quality of the real-time magnetic equilibrium reconstruction. • External loop voltage measurements and magnetic probe pairs inside and outside the vessel wall were used to measure the vacuum vessel wall resistivity. - Abstract: Real-time magnetic equilibria are needed for NTM stabilization and disruption avoidance experiments on ASDEX Upgrade. Five improvements to real-time magnetic equilibrium reconstruction on ASDEX Upgrade have been investigated. The aim is to include as many features of the offline magnetic equilibrium reconstruction code in the real-time equilibrium reconstruction code. Firstly, spline current density basis functions with regularization are used in the offline equilibrium reconstruction code, CLISTE [1]. It is now possible to have the same number of spline basis functions in the real-time code. Secondly, in the presence of edge localized modes, (ELM's), it is found to be necessary to include the low pass filter effect of the vacuum vessel on the fast position control coil currents to correctly compensate the magnetic probes for current oscillations in these coils. Thirdly, the introduction of ferromagnetic tiles in ASDEX Upgrade means that a real-time algorithm for including the perturbations of the magnetic equilibrium generated by these tiles is required. A methodology based on tile surface currents is described. Fourthly, during current ramps it was seen that the difference between fitted and measured magnetic measurements in the equilibrium reconstruction were larger than in the constant current phase. External loop voltage measurements and magnetic probe pairs inside and

Improvements for real-time magnetic equilibrium reconstruction on ASDEX Upgrade

Energy Technology Data Exchange (ETDEWEB)

Giannone, L.; Fischer, R. [Max Planck Institute for Plasma Physics, 85748 Garching (Germany); McCarthy, P.J. [Department of Physics, University College Cork, Cork (Ireland); Odstrcil, T.; Zammuto, I.; Bock, A.; Conway, G.; Fuchs, J.C.; Gude, A.; Igochine, V.; Kallenbach, A.; Lackner, K.; Maraschek, M.; Rapson, C. [Max Planck Institute for Plasma Physics, 85748 Garching (Germany); Ruan, Q. [National Instruments, Austin, TX 78759-3504 (United States); Schuhbeck, K.H.; Suttrop, W. [Max Planck Institute for Plasma Physics, 85748 Garching (Germany); Wenzel, L. [National Instruments, Austin, TX 78759-3504 (United States)

2015-11-15

Highlights: • Spline basis current functions with second-order linear regularisation. • Perturbations of magnetic probe measurements due to ferromagnetic tiles on the inner wall and from oscillations in the fast position coil current are corrected. • A constraint of the safety factor on the magnetic axis is introduced. Soft X-ray tomography is used to assess the quality of the real-time magnetic equilibrium reconstruction. • External loop voltage measurements and magnetic probe pairs inside and outside the vessel wall were used to measure the vacuum vessel wall resistivity. - Abstract: Real-time magnetic equilibria are needed for NTM stabilization and disruption avoidance experiments on ASDEX Upgrade. Five improvements to real-time magnetic equilibrium reconstruction on ASDEX Upgrade have been investigated. The aim is to include as many features of the offline magnetic equilibrium reconstruction code in the real-time equilibrium reconstruction code. Firstly, spline current density basis functions with regularization are used in the offline equilibrium reconstruction code, CLISTE [1]. It is now possible to have the same number of spline basis functions in the real-time code. Secondly, in the presence of edge localized modes, (ELM's), it is found to be necessary to include the low pass filter effect of the vacuum vessel on the fast position control coil currents to correctly compensate the magnetic probes for current oscillations in these coils. Thirdly, the introduction of ferromagnetic tiles in ASDEX Upgrade means that a real-time algorithm for including the perturbations of the magnetic equilibrium generated by these tiles is required. A methodology based on tile surface currents is described. Fourthly, during current ramps it was seen that the difference between fitted and measured magnetic measurements in the equilibrium reconstruction were larger than in the constant current phase. External loop voltage measurements and magnetic probe pairs inside

Detection of infectious bronchitis virus with the use of real-time quantitative reverse transcriptase-PCR and correlation with virus detection in embryonated eggs.

Science.gov (United States)

Roh, Ha-Jung; Hilt, Deborah A; Jackwood, Mark W

2014-09-01

Real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assays have been used to detect the presence of challenge virus when the efficacy of infectious bronchitis virus (IBV) vaccine against field viruses is being experimentally evaluated. However, federal guidelines for licensing IBV vaccines indicate that challenge-virus detection following vaccination is to be conducted in embryonated eggs. In this study, we examined qRT-PCR data with the use of universal and type-specific primers and probe sets for IBV detection and compared those data with challenge-virus detection in embryonated eggs to determine if the two methods of evaluating vaccine efficacy are comparable. In addition, we tested the qRT-PCR assays on thermocyclers from two different manufacturers. We found the universal IBV primers and probe set to be comparable to challenge-virus detection in embryonated eggs. However, for some IBV types (Mass41 and Conn on the SmartCycler II and Ark, Mass41, Conn, and GA98 on the ABI 7500) the qRT-PCR assay was more sensitive than virus detection in embryonated eggs. This may simply be due to the universal IBV qRT-PCR assay being more sensitive than virus detection in eggs or to the assay detecting nucleic acid from nonviable virus. This finding is important and needs to be considered when evaluating challenge-virus detection for vaccination and challenge studies, because qRT-PCR could potentially identify positive birds that would otherwise be negative by virus detection in embryonated eggs; thus it could lead to a more stringent measure of vaccine efficacy. We also found that the IBV type-specific primers and probe sets designed in this study were in general less sensitive than the universal IBV primers and probe set. Only the Ark-DPI-spedcific assay on the SmartCycler II and the Ark-DPI-, Mass41-, and DE072/GA98- (for detection of GA98 virus only) specific assays on the ABI 7500 were comparable in sensitivity to virus detection in eggs. We

Power in the loop real time simulation platform for renewable energy generation

Science.gov (United States)

Li, Yang; Shi, Wenhui; Zhang, Xing; He, Guoqing

2018-02-01

Nowadays, a large scale of renewable energy sources has been connecting to power system and the real time simulation platform is widely used to carry out research on integration control algorithm, power system stability etc. Compared to traditional pure digital simulation and hardware in the loop simulation, power in the loop simulation has higher accuracy and degree of reliability. In this paper, a power in the loop analog digital hybrid simulation platform has been built and it can be used not only for the single generation unit connecting to grid, but also for multiple new energy generation units connecting to grid. A wind generator inertia control experiment was carried out on the platform. The structure of the inertia control platform was researched and the results verify that the platform is up to need for renewable power in the loop real time simulation.

Development of a Rapid Real-Time PCR Method as a Tool To Quantify Viable Photobacterium phosphoreum Bacteria in Salmon (Salmo salar) Steaks

DEFF Research Database (Denmark)

Macé, Sabrina; Mamlouk, Kelthoum; Chipchakova, Stoyka

2013-01-01

A specific real-time PCR quantification method combined with a propidium monoazide sample treatment step was developed to determine quantitatively the viable population of the Photobacterium phosphoreum species group in raw modified-atmosphere-packed salmon. Primers were designed to amplify a 350......-bp fragment of the gyrase subunit B gene (gyrB) of P. phosphoreum. The specificity of the two primers was demonstrated by using purified DNA from 81 strains of 52 different bacterial species. When these primers were used for real-time PCR in pure culture, a good correlation (R2 of 0.99) was obtained...... between this method and conventional enumeration on marine agar (MA). Quantification was linear over 5 log units as confirmed by using inoculated salmon samples. On naturally contaminated fresh salmon, the new real-time PCR method performed successfully with a quantification limit of 3 log CFU...

[Real time 3D echocardiography

Science.gov (United States)

Bauer, F.; Shiota, T.; Thomas, J. D.

2001-01-01

Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients.

Comparison among amoA Primers Suited for Quantification and Diversity Analyses of Ammonia-Oxidizing Bacteria in Soil

Science.gov (United States)

Shimomura, Yumi; Morimoto, Sho; Hoshino, Yuko Takada; Uchida, Yoshitaka; Akiyama, Hiroko; Hayatsu, Masahito

2012-01-01

Ammonia monooxygenase subunit A gene (amoA) is frequently used as a functional gene marker for diversity analysis of ammonia-oxidizing bacteria (AOB). To select a suitable amoA primer for real-time PCR and PCR-denaturing gradient gel electrophoresis (DGGE), three reverse primers (degenerate primer amoA-2R; non-degenerate primers amoA-2R-GG and amoA-2IR) were examined. No significant differences were observed among the three primers in terms of quantitative values of amoA from environmental samples using real-time PCR. We found that PCR-DGGE analysis with the amoA-2IR primer gave the best results in this studied soil. These results indicate that amoA-2IR is a suitable primer for community analysis of AOB in the environment. PMID:22075625

Real-time PCR-based method for rapid detection of Aspergillus niger and Aspergillus welwitschiae isolated from coffee.

Science.gov (United States)

von Hertwig, Aline Morgan; Sant'Ana, Anderson S; Sartori, Daniele; da Silva, Josué José; Nascimento, Maristela S; Iamanaka, Beatriz Thie; Pelegrinelli Fungaro, Maria Helena; Taniwaki, Marta Hiromi

2018-05-01

Some species from Aspergillus section Nigri are morphologically very similar and altogether have been called A. niger aggregate. Although the species included in this group are morphologically very similar, they differ in their ability to produce mycotoxins and other metabolites and their taxonomical status has evolved continuously. Among them, A. niger and A. welwitschiae are ochratoxin A and fumonisin B 2 producers and their detection and/or identification is of crucial importance for food safety. The aim of this study was the development of a real-time PCR-based method for simultaneous discrimination of A. niger and A. welwitschiae from other species of the A. niger aggregate isolated from coffee beans. One primer pair and a hybridization probe specific for detection of A. niger and A. welwitschiae strains were designed based on the BenA gene sequences, and used in a Real-time PCR assay for the rapid discrimination between both these species from all others of the A. niger aggregate. The Real-time PCR assay was shown to be 100% efficient in discriminating the 73 isolates of A. niger/A. welwitschiae from the other A. niger aggregate species analyzed as a negative control. This result testifies to the use of this technique as a good tool in the rapid detection of these important toxigenic species. Copyright © 2018 Elsevier B.V. All rights reserved.

A two-step lyssavirus real-time polymerase chain reaction using degenerate primers with superior sensitivity to the fluorescent antigen test.

Science.gov (United States)

Suin, Vanessa; Nazé, Florence; Francart, Aurélie; Lamoral, Sophie; De Craeye, Stéphane; Kalai, Michael; Van Gucht, Steven

2014-01-01

A generic two-step lyssavirus real-time reverse transcriptase polymerase chain reaction (qRT-PCR), based on a nested PCR strategy, was validated for the detection of different lyssavirus species. Primers with 17 to 30% of degenerate bases were used in both consecutive steps. The assay could accurately detect RABV, LBV, MOKV, DUVV, EBLV-1, EBLV-2, and ABLV. In silico sequence alignment showed a functional match with the remaining lyssavirus species. The diagnostic specificity was 100% and the sensitivity proved to be superior to that of the fluorescent antigen test. The limit of detection was ≤ 1 50% tissue culture infectious dose. The related vesicular stomatitis virus was not recognized, confirming the selectivity for lyssaviruses. The assay was applied to follow the evolution of rabies virus infection in the brain of mice from 0 to 10 days after intranasal inoculation. The obtained RNA curve corresponded well with the curves obtained by a one-step monospecific RABV-qRT-PCR, the fluorescent antigen test, and virus titration. Despite the presence of degenerate bases, the assay proved to be highly sensitive, specific, and reproducible.

Rapid and sensitive detection of canine distemper virus by real-time reverse transcription recombinase polymerase amplification.

Science.gov (United States)

Wang, Jianchang; Wang, Jinfeng; Li, Ruiwen; Liu, Libing; Yuan, Wanzhe

2017-08-15

Canine distemper, caused by Canine distemper virus (CDV), is a highly contagious and fatal systemic disease in free-living and captive carnivores worldwide. Recombinase polymerase amplification (RPA), as an isothermal gene amplification technique, has been explored for the molecular detection of diverse pathogens. A real-time reverse transcription RPA (RT-RPA) assay for the detection of canine distemper virus (CDV) using primers and exo probe targeting the CDV nucleocapsid protein gene was developed. A series of other viruses were tested by the RT-RPA.Thirty-two field samples were further tested by RT-RPA, and the resuts were compared with those obtained by the real-time RT-PCR. The RT-RPA assay was performed successfully at 40 °C, and the results were obtained within 3 min-12 min. The assay could detect CDV, but did not show cross-detection of canine parvovirus-2 (CPV-2), canine coronavirus (CCoV), canine parainfluenza virus (CPIV), pseudorabies virus (PRV) or Newcastle disease virus (NDV), demonstrating high specificity. The analytical sensitivity of RT-RPA was 31.8 copies in vitro transcribed CDV RNA, which is 10 times lower than the real-time RT-PCR. The assay performance was validated by testing 32 field samples and compared to real-time RT-PCR. The results indicated an excellent correlation between RT-RPA and a reference real-time RT-PCR method. Both assays provided the same results, and R 2 value of the positive results was 0.947. The results demonstrated that the RT-RPA assay offers an alternative tool for simple, rapid, and reliable detection of CDV both in the laboratory and point-of-care facility, especially in the resource-limited settings.

Energy-Aware Synthesis of Fault-Tolerant Schedules for Real-Time Distributed Embedded Systems

DEFF Research Database (Denmark)

Poulsen, Kåre Harbo; Pop, Paul; Izosimov, Viacheslav

2007-01-01

This paper presents a design optimisation tool for distributed embedded real-time systems that 1) decides mapping, fault-tolerance policy and generates a fault-tolerant schedule, 2) is targeted for hard real-time, 3) has hard reliability goal, 4) generates static schedule for processes and messages......, 5) provides fault-tolerance for k transient/soft faults, 6) optimises for minimal energy consumption, while considering impact of lowering voltages on the probability of faults, 7) uses constraint logic programming (CLP) based implementation....

Real-time simulation of energy management in a domestic consumer

DEFF Research Database (Denmark)

Fernandes, F.; Silva, M.; Faria, P.

2013-01-01

Recent and future changes in power systems, mainly in the smart grid operation context, are related to a high complexity of power networks operation. This leads to more complex communications and to higher network elements monitoring and control levels, both from network’s and consumers’ standpoi......-time simulation from Opal RT. This makes possible the integration of Matlab®/Simulink® real-time simulation models. The main goal of the present paper is to compare the advantages of the resulting improved system, while managing the energy consumption of a domestic consumer....

Real-time PCR method applied to seafood products for authentication of European sole (Solea solea) and differentiation of common substitute species.

Science.gov (United States)

Herrero, Beatriz; Lago, Fátima C; Vieites, Juan M; Espiñeira, Montserrat

2012-01-01

Judged by quality and taste, the European sole (Solea solea) is considered one of the finest flatfish and is, thus, of considerable commercial value. In the present work, a specific fast real-time PCR was developed for the authentication of S. solea, i.e. to distinguish it from other related species and avoid substitution of this species, either deliberately or unintentionally. The method is based on a species-specific set of primers and MGB Taqman probe which amplifies a 116-bp fragment of the internal transcribed spacer 1 (ITS 1) ribosomal DNA region. This assay combines the high specificity and sensitivity of real-time PCR with the rapidity of the fast mode, allowing the detection of S. solea in a short period of time. The present methodology was validated for application to all types of manufactured products for the presence of S. solea, with successful results. Subsequently, the method was applied to 40 commercial samples to determine whether correct labeling had been employed in the market. It was demonstrated that the assay is a useful tool in monitoring and verifying food labeling regulations.

Sentinel Wraps: Real-Time Monitoring of Food Contamination by Printing DNAzyme Probes on Food Packaging.

Science.gov (United States)

Yousefi, Hanie; Ali, M Monsur; Su, Hsuan-Ming; Filipe, Carlos D M; Didar, Tohid F

2018-04-24

Here, we report the development of a transparent, durable, and flexible sensing surface that generates a fluorescence signal in the presence of a specific target bacterium. This material can be used in packaging, and it is capable of monitoring microbial contamination in various types of food products in real time without having to remove the sample or the sensor from the package. The sensor was fabricated by covalently attaching picoliter-sized microarrays of an E. coli-specific RNA-cleaving fluorogenic DNAzyme probe (RFD-EC1) to a thin, flexible, and transparent cyclo-olefin polymer (COP) film. Our experimental results demonstrate that the developed (RFD-EC1)-COP surface is specific, stable for at least 14 days under various pH conditions (pH 3-9), and can detect E. coli in meat and apple juice at concentrations as low as 10 3 CFU/mL. Furthermore, we demonstrate that our sensor is capable of detecting bacteria while still attached to the food package, which eliminates the need to manipulate the sample. The developed biosensors are stable for at least the shelf life of perishable packaged food products and provide a packaging solution for real-time monitoring of pathogens. These sensors hold the potential to make a significant contribution to the ongoing efforts to mitigate the negative public-health-related impacts of food-borne illnesses.

Culture-independent identification and quantification of Gallibacterium anatis (G. anatis) by real-time quantitative PCR

DEFF Research Database (Denmark)

Wang, Chong; Robles, Francisco; Ramirez, Saul

2016-01-01

Gallibacterium is a genus within the family Pasteurellaceae characterized by a high level of phenotypic and genetic diversity. No diagnostic method has yet been described, which allows species-specific identification of Gallibacterium anatis. The aim of this study was to develop a real...... published conventional PCR method and culture-based identification, respectively. The detection rates were 97%, 78% and 34% for the current qPCR, the conventional PCR and the culture-based identification method, respectively. The qPCR assay was able to detect the gene gyrB in serial dilutions of 10......-time quantitative PCR (qPCR) method allowing species-specific identification and quantification of G. anatis. A G. anatis specific DNA sequence was identified in the gyrase subunit B gene (gyrB) and used to design a TaqMan probe and corresponding primers. The specificity of the assay was tested on 52 bacterial...

A Multiplex Real-Time PCR Assay to Diagnose and Separate Helicoverpa armigera and H. zea (Lepidoptera: Noctuidae) in the New World.

Science.gov (United States)

Gilligan, Todd M; Tembrock, Luke R; Farris, Roxanne E; Barr, Norman B; van der Straten, Marja J; van de Vossenberg, Bart T L H; Metz-Verschure, Eveline

2015-01-01

The Old World bollworm, Helicoverpa armigera (Hübner), and the corn earworm, H. zea (Boddie), are two of the most important agricultural pests in the world. Diagnosing these two species is difficult-adults can only be separated with a complex dissection, and larvae cannot be identified to species using morphology, necessitating the use of geographic origin for identification in most instances. With the discovery of H. armigera in the New World, identification of immature Helicoverpa based on origin is no longer possible because H. zea also occurs in all of the geographic regions where H. armigera has been discovered. DNA barcoding and restriction fragment length polymorphism (RFLP) analyses have been reported in publications to distinguish these species, but these methods both require post-PCR processing (i.e., DNA sequencing or restriction digestion) to complete. We report the first real-time PCR assay to distinguish these pests based on two hydrolysis probes that bind to a segment of the internal transcribed spacer region 2 (ITS2) amplified using a single primer pair. One probe targets H. armigera, the second probe targets H. zea, and a third probe that targets a conserved segment of 18S rDNA is used as a control of DNA quality. The assay can be completed in 50 minutes when using isolated DNA and is successfully tested on larvae intercepted at ports of entry and adults captured during domestic surveys. We demonstrate that the assay can be run in triplex with no negative effects on sensitivity, can be run using alternative real-time PCR reagents and instruments, and does not cross react with other New World Heliothinae.

A Multiplex Real-Time PCR Assay to Diagnose and Separate Helicoverpa armigera and H. zea (Lepidoptera: Noctuidae in the New World.

Directory of Open Access Journals (Sweden)

Todd M Gilligan

Full Text Available The Old World bollworm, Helicoverpa armigera (Hübner, and the corn earworm, H. zea (Boddie, are two of the most important agricultural pests in the world. Diagnosing these two species is difficult-adults can only be separated with a complex dissection, and larvae cannot be identified to species using morphology, necessitating the use of geographic origin for identification in most instances. With the discovery of H. armigera in the New World, identification of immature Helicoverpa based on origin is no longer possible because H. zea also occurs in all of the geographic regions where H. armigera has been discovered. DNA barcoding and restriction fragment length polymorphism (RFLP analyses have been reported in publications to distinguish these species, but these methods both require post-PCR processing (i.e., DNA sequencing or restriction digestion to complete. We report the first real-time PCR assay to distinguish these pests based on two hydrolysis probes that bind to a segment of the internal transcribed spacer region 2 (ITS2 amplified using a single primer pair. One probe targets H. armigera, the second probe targets H. zea, and a third probe that targets a conserved segment of 18S rDNA is used as a control of DNA quality. The assay can be completed in 50 minutes when using isolated DNA and is successfully tested on larvae intercepted at ports of entry and adults captured during domestic surveys. We demonstrate that the assay can be run in triplex with no negative effects on sensitivity, can be run using alternative real-time PCR reagents and instruments, and does not cross react with other New World Heliothinae.

Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY® FL-labeled probe or primer

Science.gov (United States)

Kurata, Shinya; Kanagawa, Takahiro; Yamada, Kazutaka; Torimura, Masaki; Yokomaku, Toyokazu; Kamagata, Yoichi; Kurane, Ryuichiro

2001-01-01

We have developed a simple method for the quantitative detection of specific DNA or RNA molecules based on the finding that BODIPY® FL fluorescence was quenched by its interaction with a uniquely positioned guanine. This approach makes use of an oligonucleotide probe or primer containing a BODIPY® FL-modified cytosine at its 5′-end. When such a probe was hybridized with a target DNA, its fluorescence was quenched by the guanine in the target, complementary to the modified cytosine, and the quench rate was proportional to the amount of target DNA. This widely applicable technique will be used directly with larger samples or in conjunction with the polymerase chain reaction to quantify small DNA samples. PMID:11239011

Sensitive detection of novel Indian isolate of BTV 21 using ns1 gene based real-time PCR assay

Directory of Open Access Journals (Sweden)

Gaya Prasad

2013-06-01

Full Text Available Aim: The study was conducted to develop ns1 gene based sensitive real-time RT-PCR assay for diagnosis of India isolates of bluetongue virus (BTV. Materials and Methods: The BTV serotype 21 isolate (KMNO7 was isolated from Andhra Pradesh and propagated in BHK-21 cell line in our laboratory. The Nucleic acid (dsRNA of virus was extracted using Trizol method and cDNA was prepared using a standard protocol. The cDNA was allowed to ns1 gene based group specific PCR to confirm the isolate as BTV. The viral RNA was diluted 10 folds and the detection limit of ns1 gene based RT-PCR was determined. Finally the tenfold diluted viral RNA was subjected to real-time RT-PCR using ns1 gene primer and Taq man probe to standardized the reaction and determine the detection limit. Results: The ns1 gene based group specific PCR showed a single 366bp amplicon in agarose gel electrophoresis confirmed the sample as BTV. The ns1 gene RT-PCR using tenfold diluted viral RNA showed the detection limit of 70.0 fg in 1%agarose gel electrophoresis. The ns1 gene based real time RT-PCR was successfully standardized and the detection limit was found to be 7.0 fg. Conclusion: The ns1 gene based real-time RT-PCR was successfully standardized and it was found to be 10 times more sensitive than conventional RT-PCR. Key words: bluetongue, BTV21, RT-PCR, Real time RT-PCR, ns1 gene [Vet World 2013; 6(8.000: 554-557

Energy and Reserve under Distributed Energy Resources Management-Day-Ahead, Hour-Ahead and Real-Time

DEFF Research Database (Denmark)

Soares, Tiago; Silva, Marco; Sousa, Tiago

2017-01-01

and evaluates a generic model for day-ahead, intraday (hour-ahead) and real-time scheduling, considering the joint optimization of energy and reserve in the scope of the virtual power player concept. The model aims to minimize the operation costs in the point of view of one aggregator agent taking into account...

Real-time distributed economic model predictive control for complete vehicle energy management

NARCIS (Netherlands)

Romijn, Constantijn; Donkers, Tijs; Kessels, John; Weiland, Siep

2017-01-01

In this paper, a real-time distributed economic model predictive control approach for complete vehicle energy management (CVEM) is presented using a receding control horizon in combination with a dual decomposition. The dual decomposition allows the CVEM optimization problem to be solved by solving

Molecular beacon probes-base multiplex NASBA Real-time for detection of HIV-1 and HCV.

Science.gov (United States)

Mohammadi-Yeganeh, S; Paryan, M; Mirab Samiee, S; Kia, V; Rezvan, H

2012-06-01

Developed in 1991, nucleic acid sequence-based amplification (NASBA) has been introduced as a rapid molecular diagnostic technique, where it has been shown to give quicker results than PCR, and it can also be more sensitive. This paper describes the development of a molecular beacon-based multiplex NASBA assay for simultaneous detection of HIV-1 and HCV in plasma samples. A well-conserved region in the HIV-1 pol gene and 5'-NCR of HCV genome were used for primers and molecular beacon design. The performance features of HCV/HIV-1 multiplex NASBA assay including analytical sensitivity and specificity, clinical sensitivity and clinical specificity were evaluated. The analysis of scalar concentrations of the samples indicated that the limit of quantification of the assay was beacon probes detected all HCV genotypes and all major variants of HIV-1. This method may represent a relatively inexpensive isothermal method for detection of HIV-1/HCV co-infection in monitoring of patients.

Direct Detection and Differentiation of Pathogenic Leptospira Species Using a Multi-Gene Targeted Real Time PCR Approach

Science.gov (United States)

Ferreira, Ana Sofia; Costa, Pedro; Rocha, Teresa; Amaro, Ana; Vieira, Maria Luísa; Ahmed, Ahmed; Thompson, Gertrude; Hartskeerl, Rudy A.; Inácio, João

2014-01-01

Leptospirosis is a growing public and veterinary health concern caused by pathogenic species of Leptospira. Rapid and reliable laboratory tests for the direct detection of leptospiral infections in animals are in high demand not only to improve diagnosis but also for understanding the epidemiology of the disease. In this work we describe a novel and simple TaqMan-based multi-gene targeted real-time PCR approach able to detect and differentiate Leptospira interrogans, L. kirschneri, L. borgpeteresenii and L. noguchii, which constitute the veterinary most relevant pathogenic species of Leptospira. The method uses sets of species-specific probes, and respective flanking primers, designed from ompL1 and secY gene sequences. To monitor the presence of inhibitors, a duplex amplification assay targeting both the mammal β-actin and the leptospiral lipL32 genes was implemented. The analytical sensitivity of all primer and probe sets was estimated to be <10 genome equivalents (GE) in the reaction mixture. Application of the amplification reactions on genomic DNA from a variety of pathogenic and non-pathogenic Leptospira strains and other non-related bacteria revealed a 100% analytical specificity. Additionally, pathogenic leptospires were successfully detected in five out of 29 tissue samples from animals (Mus spp., Rattus spp., Dolichotis patagonum and Sus domesticus). Two samples were infected with L. borgpetersenii, two with L. interrogans and one with L. kirschneri. The possibility to detect and identify these pathogenic agents to the species level in domestic and wildlife animals reinforces the diagnostic information and will enhance our understanding of the epidemiology of leptopirosis. PMID:25398140

Probe-based real-time PCR method for multilocus melt typing of Xylella fastidiosa strains.

Science.gov (United States)

Brady, Jeff A; Faske, Jennifer B; Ator, Rebecca A; Castañeda-Gill, Jessica M; Mitchell, Forrest L

2012-04-01

Epidemiological studies of Pierce's disease (PD) can be confounded by a lack of taxonomic detail on the bacterial causative agent, Xylella fastidiosa (Xf). PD in grape is caused by strains of Xylella fastidiosa subsp. fastidiosa, but is not caused by other subspecies of Xf that typically colonize plants other than grape. Detection assays using ELISA and qPCR are effective at detecting and quantifying Xf presence or absence, but offer no information on Xf subspecies or strain identity. Surveying insects or host plants for Xf by current ELISA or qPCR methods provides only presence/absence and quantity information for any and all Xf subspecies, potentially leading to false assessments of disease threat. This study uses a series of adjacent-hybridizing DNA melt analysis probes that are capable of efficiently discriminating Xf subspecies and strain relationships in rapid real-time PCR reactions. Copyright © 2012 Elsevier B.V. All rights reserved.

Sensitive detection of African swine fever virus using real-time PCR with a 5' conjugated minor groove binding probe

DEFF Research Database (Denmark)

McKillan, John; McMenamy, Michael; Hjertner, Bernt

2010-01-01

sensitive than the conventional PCR recommended by the OIE. Linear range was ten logs from 2 × 101 to 2 × 1010. The assay is rapid with an amplification time just over 2 h. The development of this assay provides a useful tool for the specific diagnosis of ASF in statutory or emergency testing programs......The design of a 5′ conjugated minor groove binder (MGB) probe real-time PCR assay is described for the rapid, sensitive and specific detection of African swine fever virus (ASFV) DNA. The assay is designed against the 9GL region and is capable of detecting 20 copies of a DNA standard. It does...

A quick method for species identification of Japanese eel (Anguilla japonica) using real-time PCR: an onboard application for use during sampling surveys.

Science.gov (United States)

Watanabe, Shun; Minegishi, Yuki; Yoshinaga, Tatsuki; Aoyama, Jun; Tsukamoto, Katsumi

2004-01-01

To compensate for the limited number of morphological characteristics of fish eggs and larvae, we established a convenient and robust method of species identification for eggs of the Japanese eel (Anguilla japonica) using a real-time polymerase chain reaction (PCR) that can be performed onboard research ships at sea. A total of about 1.2 kbp of the mitochondrial 16S ribosomal RNA gene sequences from all species of Anguilla and 3 other anguilliform species were compared to design specific primer pairs and a probe for A. japonica. This real-time PCR amplification was conducted for a total of 44 specimens including A. japonica, A. marmorata, A. bicolor pacifica, and 6 other anguilliform species. Immediate PCR amplification was only observed in A. japonica. We then tested this method under onboard conditions and obtained the same result as had been produced in the laboratory. These results suggest that real-time PCR can be a powerful tool for detecting Japanese eel eggs and newly hatched larvae immediately after onboard sampling during research cruises and will allow targeted sampling efforts to occur rapidly in response to any positive onboard identification of the eggs and larvae of this species.

The Role of Smart Meters in Enabling Real-Time Energy Services for Households: The Italian Case

Directory of Open Access Journals (Sweden)

Alessandro Pitì

2017-02-01

Full Text Available The Smart Meter (SM is an essential tool for successful balancing the demand-offer energy curve. It allows the linking of the consumption and production measurements with the time information and the customer’s identity, enabling the substitution of flat-price billing with smarter solutions, such as Time-of-Use or Real-Time Pricing. In addition to sending data to the energy operators for billing and monitoring purposes, Smart Meters must be able to send the same data to customer devices in near-real-time conditions, enabling new services such as instant energy awareness and home automation. In this article, we review the ongoing situation in Europe regarding real-time services for the final customers. Then, we review the architectural and technological options that have been considered for the roll-out phase of the Italian second generation of Smart Meters. Finally, we identify a collection of use cases, along with their functional and performance requirements, and discuss what architectures and communications technologies can meet these requirements.

An Energy Efficient Neuromorphic Computing System Using Real Time Sensing Method

DEFF Research Database (Denmark)

Farkhani, Hooman; Tohidi, Mohammad; Farkhani, Sadaf

2017-01-01

In spintronic-based neuromorphic computing systems (NCS), the switching of magnetic moment in a magnetic tunnel junction (MTJ) is used to mimic neuron firing. However, the stochastic switching behavior of the MTJ and process variations effect leads to extra stimulation time. This leads to extra...... energy consumption and delay of such NCSs. In this paper, a new real-time sensing (RTS) circuit is proposed to track the MTJ state and terminate stimulation phase immediately after MTJ switching. This leads to significant degradation in energy consumption and delay of NCS. The simulation results using...... a 65-nm CMOS technology and a 40-nm MTJ technology confirm that the energy consumption of a RTS-based NCS is improved by 50% in comparison with a typical NCS. Moreover, utilizing RTS circuit improves the overall speed of an NCS by 2.75x....

Development of duplex real-time RT-PCR based on Taqman technology for detecting simultaneously the genome of pan-enterovirus and enterovirus 71.

Science.gov (United States)

Hwang, Seoyeon; Kang, Byunghak; Hong, Jiyoung; Kim, Ahyoun; Kim, Hyejin; Kim, Kisang; Cheon, Doo-Sung

2013-07-01

Human enterovirus (EV) 71 is the main etiological agent of hand, foot, and mouth disease (HFMD). It is associated with neurological complications, and caused fatalities during recent outbreaks in the Asia-Pacific region. Infections caused by EV71 could lead to many complications, ranging from brainstem encephalitis to pulmonary oedema, resulting in high mortality. In this study, a duplex real-time RT-PCR assay was developed in order to simultaneously detect pan-EV and EV71. EV71-specific primers and probes were designed based on the highly conserved VP1 region of EV71. Five EV71 strains were detected as positive, and no positive fluorescence signal was observed in the duplex real-time RT-PCR for other viral RNA, which showed 100% specificity for the selected panel, and no cross-reactions were observed in this duplex real-time RT-PCR. The EV71-specific duplex real-time RT-PCR was more sensitive than conventional RT-PCR, and detected viral titers that were 10-fold lower than those measured by the latter. Of the 381 HFMD clinical specimens, 196 (51.4%) cases were pan-EV-positive, of which 170 (86.7%) were EV71-positive when tested by pan-EV and EV71-specific duplex real-time RT-PCR. EV71-specific duplex real-time RT-PCR offers a rapid and sensitive method to detect EV71 from clinical specimens, and will allow quarantine measures to be taken more effectively during outbreaks. Copyright © 2013 Wiley Periodicals, Inc.

Slow down or race to halt: towards managing complexity of real-time energy management decisions

OpenAIRE

Petters, Stefan M.; Awan, Muhammad Ali

2010-01-01

Existing work in the context of energy management for real-time systems often ignores the substantial cost of making DVFS and sleep state decisions in terms of time and energy and/or assume very simple models. Within this paper we attempt to explore the parameter space for such decisions and possible constraints faced.

Rapid screening of β-Globin gene mutations by Real-Time PCR in ...

African Journals Online (AJOL)

Introduction of the real time PCR has made a revolution in the time taken for the PCR reactions. We present a method for the diagnosis of the common mutations of the B-thalassemia in Egyptian children & families. The procedure depends on the real-time PCR using specific fluorescently labeled hybridization probes.

Real-Time Vehicle Energy Management System Based on Optimized Distribution of Electrical Load Power

Directory of Open Access Journals (Sweden)

Yuefei Wang

2016-10-01

Full Text Available As a result of severe environmental pressure and stringent government regulations, refined energy management for vehicles has become inevitable. To improve vehicle fuel economy, this paper presents a bus-based energy management system for the electrical system of internal combustion engine vehicles. Both the model of an intelligent alternator and the model of a lead-acid battery are discussed. According to these models, the energy management for a vehicular electrical system is formulated as a global optimal control problem which aims to minimize fuel consumption. Pontryagin’s minimum principle is applied to solve the optimal control problem to realize a real-time control strategy for electrical energy management in vehicles. The control strategy can change the output of the intelligent alternator and the battery with the changes of electrical load and driving conditions in real-time. Experimental results demonstrate that, compared to the traditional open-loop control strategy, the proposed control strategy for vehicle energy management can effectively reduce fuel consumption and the fuel consumption per 100 km is decreased by approximately 1.7%.

Sparse Beamforming for Real-time Resource Management and Energy Trading in Green C-RAN

OpenAIRE

Wan Ariffin, Wan Nur Suryani Firuz; Zhang, Xinruo; Nakhai, Mohammad Reza

2017-01-01

This paper considers cloud radio access network with simultaneous wireless information and power transfer and finite capacity fronthaul, where the remote radio heads are equipped with renewable energy resources and can trade energy with the grid. Due to uneven distribution of mobile radio traffic and inherent intermittent nature of renewable energy resources, the remote radio heads may need real-time energy provisioning to meet the users’ demands. Given the amount of available energy resource...

Energy-Aware Real-Time Task Scheduling for Heterogeneous Multiprocessors with Particle Swarm Optimization Algorithm

Directory of Open Access Journals (Sweden)

Weizhe Zhang

2014-01-01

Full Text Available Energy consumption in computer systems has become a more and more important issue. High energy consumption has already damaged the environment to some extent, especially in heterogeneous multiprocessors. In this paper, we first formulate and describe the energy-aware real-time task scheduling problem in heterogeneous multiprocessors. Then we propose a particle swarm optimization (PSO based algorithm, which can successfully reduce the energy cost and the time for searching feasible solutions. Experimental results show that the PSO-based energy-aware metaheuristic uses 40%–50% less energy than the GA-based and SFLA-based algorithms and spends 10% less time than the SFLA-based algorithm in finding the solutions. Besides, it can also find 19% more feasible solutions than the SFLA-based algorithm.

A Two-Step Lyssavirus Real-Time Polymerase Chain Reaction Using Degenerate Primers with Superior Sensitivity to the Fluorescent Antigen Test

Directory of Open Access Journals (Sweden)

Vanessa Suin

2014-01-01

Full Text Available A generic two-step lyssavirus real-time reverse transcriptase polymerase chain reaction (qRT-PCR, based on a nested PCR strategy, was validated for the detection of different lyssavirus species. Primers with 17 to 30% of degenerate bases were used in both consecutive steps. The assay could accurately detect RABV, LBV, MOKV, DUVV, EBLV-1, EBLV-2, and ABLV. In silico sequence alignment showed a functional match with the remaining lyssavirus species. The diagnostic specificity was 100% and the sensitivity proved to be superior to that of the fluorescent antigen test. The limit of detection was ≤1 50% tissue culture infectious dose. The related vesicular stomatitis virus was not recognized, confirming the selectivity for lyssaviruses. The assay was applied to follow the evolution of rabies virus infection in the brain of mice from 0 to 10 days after intranasal inoculation. The obtained RNA curve corresponded well with the curves obtained by a one-step monospecific RABV-qRT-PCR, the fluorescent antigen test, and virus titration. Despite the presence of degenerate bases, the assay proved to be highly sensitive, specific, and reproducible.

Real-Time PCR Detection and QUantification of Soilborne Fungal Pathogens : the Case of Rosellinia necatrix, Phytophthora nicotianae, P. citrophthora and Verticillium dahliae

Directory of Open Access Journals (Sweden)

L. Schena

2004-08-01

Full Text Available Conventional and Scorpion primers were designed from the ITS regions to identify Rosellinia necatrix, Phytophthora nicotianae, and P. citrophthora and from the IGS regions to identify Verticillium dahliae and V. alboatrum. Specificity of primers and probes was assessed using genomic DNA from a large number of fungi from several hosts and by means of BLAST analyses, to exclude the presence of similar sequences in other micro-organisms among available DNA databases (GenBank. Simple and rapid procedures for DNA extraction from naturally infected matrices (soils, roots, bark, and/or woody tissues were utilised to yield DNA of a purity and quality suitable for PCR assays. Combining these protocols with a double amplification (nested Scorpion-PCR, the real-time detection of these pathogens was possible from naturally infested soils and from infected citrus roots (P. nicotianae and P. citrophthora, from the roots and bark of stone fruits and olive (R. necatrix and from olive branches (V. dahliae. For target pathogens, the limit of detection was 1 pg µl-1 in Scorpion-PCR and 1 fg µl-1 in nested Scorpion-PCR. High and significant correlations between pathogen propagule concentrations and real-time PCR cycle thresholds (Ct were obtained. Moreover, specific tests with R. necatrix seem to indicate that its DNA is quite rapidly degraded in the soil, excluding the risk of false positives due to the presence of dead cells.

Development of a panel of seven duplex real-time PCR assays for detecting 13 streptococcal superantigens.

Science.gov (United States)

Yang, Peng; Peng, Xiaomin; Cui, Shujuan; Shao, Junbin; Zhu, Xuping; Zhang, Daitao; Liang, Huijie; Wang, Quanyi

2013-07-30

Streptococcal superantigens (SAgs) are the major virulence factors of infection in humans for group A Streptococcus (GAS) bacteria. A panel consisting of seven duplex real-time PCR assays was developed to simultaneously detect 13 streptococcal SAgs and one internal control which may be important in the control of GAS-mediated diseases. Primer and probe sequences were selected based on the highly conserved region from an alignment of nucleotide sequences of the 13 streptococcal SAgs. The reaction conditions of the duplex real-time PCR were optimized and the specificity of the duplex assays was evaluated using SAg positive strains. The limit of detection of the duplex assays was determined by using 10-fold serial dilutions of the DNA of 13 streptococcal SAgs and compared to a conventional polymerase chain reaction (PCR) method for evaluating the duplex assays sensitivity. Using the duplex assays, we were able to differentiate between 13 SAgs from Streptococcus strains and other non-Streptococcus bacteria without cross-reaction. On the other hand, the limit of detection of the duplex assays was at least one or two log dilutions lower than that of the conventional PCR. The panel was highly specific (100%) and the limit of detection of these duplex groups was at least ten times lower than that obtained by using a conventional PCR method.

Energy efficient approach for transient fault recovery in real time ...

African Journals Online (AJOL)

DR OKE

Keywords: DVS, Fault tolerance, Real Time System, Transient Fault. ... in which missing the deadline may cause a failure and soft real time system, ..... Pillai, P., Shin, K., Real-time dynamic voltage scaling for low-power embedded operating ...

Real-time Pricing in Power Markets

DEFF Research Database (Denmark)

Boom, Anette; Schwenen, Sebastian

We examine welfare e ects of real-time pricing in electricity markets. Before stochastic energy demand is known, competitive retailers contract with nal consumers who exogenously do not have real-time meters. After demand is realized, two electricity generators compete in a uniform price auction...... to satisfy demand from retailers acting on behalf of subscribed customers and from consumers with real-time meters. Increasing the number of consumers on real-time pricing does not always increase welfare since risk-averse consumers dislike uncertain and high prices arising through market power...

Real-time Pricing in Power Markets

DEFF Research Database (Denmark)

Boom, Anette; Schwenen, Sebastian

We examine welfare eects of real-time pricing in electricity markets. Before stochastic energy demand is known, competitive retailers contract with nal consumers who exogenously do not have real-time meters. After demand is realized, two electricity generators compete in a uniform price auction...... to satisfy demand from retailers acting on behalf of subscribed customers and from consumers with real-time meters. Increasing the number of consumers on real-time pricing does not always increase welfare since risk-averse consumers dislike uncertain and high prices arising through market power...

Modern Energy Markets Real-Time Pricing, Renewable Resources and Efficient Distribution

CERN Document Server

Kopsakangas-Savolainen, Maria

2012-01-01

Energy has moved to the forefront in terms of societal and economic development. Modern Energy Markets is a comprehensive, economically oriented, exploration of modern electricity networks from production and distribution to deregulation and liberalization processes. Updating previous work by the authors, different aspects are considered resulting in a complete and detailed picture of  the systems and characteristics of modern electricity markets. Modern Energy Markets provides clear detail whilst encompassing a broad scope of topics and includes: •A method to model energy production systems including the main characteristics of future demand side management, •Different applications of this model in nuclear and renewable energy scenarios, •An analysis of Real-Time Pricing of electricity and its potential effects across the market, and, •A discussion of the need for regulation in an easily monopolized industry. Engineering and Economics students alike will find that Modern Energy Markets is a succinct...

Real-time polymerase chain reaction assay for endogenous reference gene for specific detection and quantification of common wheat-derived DNA (Triticum aestivum L.).

Science.gov (United States)

Vautrin, Sonia; Zhang, David

2007-01-01

A species-specific endogenous reference gene system was developed for polymerase chain reaction (PCR)-based analysis in common wheat (Triticum aestivum L.) by targeting the ALMT1 gene, an aluminium-activated malate transporter. The primers and probe were elaborated for real-time PCR-based qualitative and quantitative assay. The size of amplified product is 95 base pairs. The specificity was assessed on 17 monocot and dicot plant species. The established real-time PCR assay amplified only T. aestivum-derived DNA; no amplification occurred on other phylogenetically related species, including durum wheat (T. durum). The robustness of the system was tested on the DNA of 15 common wheat cultivars using 20 000 genomic copies per PCR the mean cycle threshold (Ct) values of 24.02 +/- 0.251 were obtained. The absolute limits of detection and quantification of the real-time PCR assay were estimated to 2 and 20 haploid genome copies of common wheat, respectively. The linearity was experimentally validated on 2-fold serial dilutions of DNA from 650 to 20 000 haploid genome copies. All these results show that the real-time PCR assay developed on the ALMT1 gene is suitable to be used as an endogenous reference gene for PCR-based specific detection and quantification of T. aestivum-derived DNA in various applications, in particular for the detection and quantification of genetically modified materials in common wheat.

[Development of a novel real-time PCR method for detection of HSV types 1 and 2 DNA using HybProbe chemistry].

Science.gov (United States)

Chudzik, Emilia; Karabin, Karolina; Dzieciątkowski, Tomasz; Majewska, Anna; Przybylski, Maciej; Midak-Siewirska, Anna; Łuczak, Mirosław; Młynarczyk, Grazyna

2010-01-01

Herpes simplex viruses types 1 and 2 are members of the Alphaherpesviridae subfamily, as they can infect both skin and nerves and develop latent infection within the dorsal root and trigeminal ganglia. Infections with these viruses are common worldwide and cause wide range of clinical syndromes. Although HSV-1/2 infect healthy children and adults, disease is more severe and extensive in the immunocompromised individuals and/or during neuroinfections. The aim of the study was development of real-time PCR assay for detection and differentiation of herpes simplex viruses type 1 and 2. DNA in clinical samples, using specific dual-channel HybProbe chemistry. The nalytical sensitivity of assay was tested using serial dilutions of HSV-1 and HSV-2 DNA in range between 10 degrees and 10(-5). (4.35 x 10(5)-4.00 x 10(2) copies/ml and 4.18 x 10(5)-3.82 x 10(2) copies/ml, respectively). Thirty four cell line isolates and sixteen clinical samples taken from a group of adult patients with neurological signs were tested for the presence of HSV-1/2 DNA in the LightCycler instrument. Described in-house real-time PCR assay detected herpesviral DNA in all cell line isolates (31 of them were HSV-1 positive; 3 were HSV-2 positive) and in 10 clinical samples (positive only for HSV-1). The conclusion is that developed HybProbe-based real-time PCR test is very reliable and valuable tool for detection and differentiation of HSV-1/2 viremia in different kind of samples. The high level of sensitivity and accuracy provided by this assay is favorable for the quantification of herpes simplex virus 1 and 2 DNA in clinical specimens, especially during low-copy infections.

Identification of differentially expressed genes induced by energy restriction using annealing control primer system from the liver and adipose tissues of broilers.

Science.gov (United States)

Wang, J W; Chen, W; Kang, X T; Huang, Y Q; Tian, Y D; Wang, Y B

2012-04-01

Female Arbor Acre broilers were divided into 2 groups at 18 d of age. One group of chickens had free access to feed (AL), and the other group of chickens had 30% energy restriction (ER). Adipose and hepatic RNA samples were collected at 48 d of age. We employed an accurate reverse-transcription (RT) PCR method that involves annealing control primers to identify the differentially expressed genes (DEG) between ER and AL groups. Using 20 annealing control primers, 43 differentially expressed bands (40 downregulated and 3 upregulated in the ER group) were detected from the hepatic tissue, whereas no differentially expressed bands were detected from the adipose tissue. It seems that energy restriction could induce more DEG in hepatic tissue than that in adipose tissue and could result in more gene-expression downregulation in hepatic tissue. Eight DEG (6 known and 2 unknown genes) were gained from hepatic tissue and confirmed by RT-PCR, which were all supported by released expressed sequence tag sequences. Their expressions were all downregulated by energy restriction in hepatic tissues. Six known genes are RPL7, RPLP1, FBXL12, ND1, ANTXR2, and SLC22A18, respectively, which seem to play essential roles in the protein translation, energy metabolism, and tumor inhibition. The alterations of gene expression in 3 selected genes, including ND1 (P < 0.01), FBXL12 (P < 0.01), and RPLP1 (P < 0.05), were supported by real-time quantitative RT-PCR reaction. Our data provide new insights on the metabolic state of broilers changed by energy restriction.

Staged Inference using Conditional Deep Learning for energy efficient real-time smart diagnosis.

Science.gov (United States)

Parsa, Maryam; Panda, Priyadarshini; Sen, Shreyas; Roy, Kaushik

2017-07-01

Recent progress in biosensor technology and wearable devices has created a formidable opportunity for remote healthcare monitoring systems as well as real-time diagnosis and disease prevention. The use of data mining techniques is indispensable for analysis of the large pool of data generated by the wearable devices. Deep learning is among the promising methods for analyzing such data for healthcare applications and disease diagnosis. However, the conventional deep neural networks are computationally intensive and it is impractical to use them in real-time diagnosis with low-powered on-body devices. We propose Staged Inference using Conditional Deep Learning (SICDL), as an energy efficient approach for creating healthcare monitoring systems. For smart diagnostics, we observe that all diagnoses are not equally challenging. The proposed approach thus decomposes the diagnoses into preliminary analysis (such as healthy vs unhealthy) and detailed analysis (such as identifying the specific type of cardio disease). The preliminary diagnosis is conducted real-time with a low complexity neural network realized on the resource-constrained on-body device. The detailed diagnosis requires a larger network that is implemented remotely in cloud and is conditionally activated only for detailed diagnosis (unhealthy individuals). We evaluated the proposed approach using available physiological sensor data from Physionet databases, and achieved 38% energy reduction in comparison to the conventional deep learning approach.

Designing a time-effective TaqMan probe-based real-time polymerase chain reaction protocol for the identification of Yersinia enterocolitica in raw pork meat

Directory of Open Access Journals (Sweden)

Milena Alicja Stachelska

2017-01-01

Full Text Available The aim of this study was to design a time-effective method comprising a short pre-enrichment step in a non-selective broth in combination with the TaqMan probe applied in the real-time polymerase chain reaction to detect Yersinia enterocolitica strains in raw pork meat. The method enabled to detect 1 colony forming unit per 25 mg of Yersinia enterocolitica in pork meat. The specificity and reliability of the method was not diminished by the company of microflora naturally present in meat. The method was found successful to detect pathogenic Yersinia enterocolitica strains in pork meat. It is advised to be used for assessing the microbial risk and for controlling the microbial quality of meat and meat products.

Perturbing Tandem Energy Transfer in Luminescent Heterobinuclear Lanthanide Coordination Polymer Nanoparticles Enables Real-Time Monitoring of Release of the Anthrax Biomarker from Bacterial Spores.

Science.gov (United States)

Gao, Nan; Zhang, Yunfang; Huang, Pengcheng; Xiang, Zhehao; Wu, Fang-Ying; Mao, Lanqun

2018-06-05

Lanthanide-based luminescent sensors have been widely used for the detection of the anthrax biomarker dipicolinic acid (DPA). However, mainly based on DPA sensitization to the lanthanide core, most of them failed to realize robust detection of DPA in bacterial spores. We proposed a new strategy for reliable detection of DPA by perturbing a tandem energy transfer in heterobinuclear lanthanide coordination polymer nanoparticles simply constructed by two kinds of lanthanide ions, Tb 3+ and Eu 3+ , and guanosine 5'-monophosphate. This smart luminescent probe was demonstrated to exhibit highly sensitive and selective visual luminescence color change upon exposure to DPA, enabling accurate detection of DPA in complex biosystems such as bacterial spores. DPA release from bacterial spores on physiological germination was also successfully monitored in real time by confocal imaging. This probe is thus expected to be a powerful tool for efficient detection of bacterial spores in responding to anthrax threats.

Quantitative Microbiological Study of Human Carious Dentine by Culture and Real-Time PCR: Association of Anaerobes with Histopathological Changes in Chronic Pulpitis

Science.gov (United States)

Martin, F. Elizabeth; Nadkarni, Mangala A.; Jacques, Nicholas A.; Hunter, Neil

2002-01-01

The bacteria found in carious dentine were correlated with the tissue response of the dental pulps of 65 teeth extracted from patients with advanced caries and pulpitis. Standardized homogenates of carious dentine were plated onto selective and nonselective media under anaerobic and microaerophilic conditions. In addition, real-time PCR was used to quantify the recovery of anaerobic bacteria. Primers and fluorogenic probes were designed to detect the total anaerobic microbial load, the genera Prevotella and Fusobacterium, and the species Prevotella melaninogenica, Porphyromonas endodontalis, Porphyromonas gingivalis, and Micromonas (formerly Peptostreptococcus) micros. The pulpal pathology was categorized according to the cellular response and degenerative changes. Analysis of cultured bacteria showed a predominance of gram-positive microorganisms, particularly lactobacilli. Gram-negative bacteria were also present in significant numbers with Prevotella spp., the most numerous anaerobic group cultured. Real-time PCR analysis indicated a greater microbial load than that determined by colony counting. The total number of anaerobes detected was 41-fold greater by real-time PCR than by colony counting, while the numbers of Prevotella and Fusobacterium spp. detected were 82- and 2.4-fold greater by real-time PCR than by colony counting, respectively. Real-time PCR also identified M. micros, P. endodontalis, and P. gingivalis in 71, 60, and 52% of carious samples, respectively. Correlation matrices of the real-time PCR data revealed significant positive associations between M. micros and P. endodontalis detection and inflammatory degeneration of pulpal tissues. These anaerobes have been strongly implicated in endodontic infections that occur as sequelae to carious pulpitis. Accordingly, the data suggest that the presence of high levels of these bacteria in carious lesions may be indicative of irreversible pulpal pathology. PMID:11980945

The use of real-time polymerase chain reaction with high resolution melting (real-time PCR-HRM) analysis for the detection and discrimination of nematodes Bursaphelenchus xylophilus and Bursaphelenchus mucronatus.

Science.gov (United States)

Filipiak, Anna; Hasiów-Jaroszewska, Beata

2016-04-01

The real-time PCR-HRM analysis was developed for the detection and discrimination of the quarantine nematode Bursaphelenchus xylophilus and Bursaphelenchus mucronatus. A set of primers was designed to target the ITS region of rDNA. The results have demonstrated that this analysis is a valuable tool for differentiation of these both species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ratiometric Time-Gated Luminescence Probe for Nitric Oxide Based on an Apoferritin-Assembled Lanthanide Complex-Rhodamine Luminescence Resonance Energy Transfer System.

Science.gov (United States)

Tian, Lu; Dai, Zhichao; Liu, Xiangli; Song, Bo; Ye, Zhiqiang; Yuan, Jingli

2015-11-03

Using apoferritin (AFt) as a carrier, a novel ratiometric luminescence probe based on luminescence resonance energy transfer (LRET) between a Tb(3+) complex (PTTA-Tb(3+)) and a rhodamine derivative (Rh-NO), PTTA-Tb(3+)@AFt-Rh-NO, has been designed and prepared for the specific recognition and time-gated luminescence detection of nitric oxide (NO) in living samples. In this LRET probe, PTTA-Tb(3+) encapsulated in the core of AFt is the energy donor, and Rh-NO, a NO-responsive rhodamine derivative, bound on the surface of AFt is the energy acceptor. The probe only emits strong Tb(3+) luminescence because the emission of rhodamine is switched off in the absence of NO. Upon reaction with NO, accompanied by the turn-on of rhodamine emission, the LRET from Tb(3+) complex to rhodamine occurs, which results in the remarkable increase and decrease of the long-lived emissions of rhodamine and PTTA-Tb(3+), respectively. After the reaction, the intensity ratio of rhodamine emission to Tb(3+) emission, I565/I539, is ∼24.5-fold increased, and the dose-dependent enhancement of I565/I539 shows a good linearity in a wide concentration range of NO. This unique luminescence response allowed PTTA-Tb(3+)@AFt-Rh-NO to be conveniently used as a ratiometric probe for the time-gated luminescence detection of NO with I565/I539 as a signal. Taking advantages of high specificity and sensitivity of the probe as well as its good water-solubility, biocompatibility, and cell membrane permeability, PTTA-Tb(3+)@AFt-Rh-NO was successfully used for the luminescent imaging of NO in living cells and Daphnia magna. The results demonstrated the efficacy of the probe and highlighted it's advantages for the ratiometric time-gated luminescence bioimaging application.

A platform for development and evaluation of real - time wind energy conversion strategies

International Nuclear Information System (INIS)

Toccaceli, G; Cendoya, M; Battaiotto, P

2005-01-01

Wind energy is one of the most promising power generation alternatives, and one of the most dynamic scenarios for novel control strategies. The particular characteristics of each geographical zone, and the inherent randomness of the wind impose important constrains for the evaluation of a wind energy conversion system (WECS). This is particularly true for wind turbines and their associated instrumentation. A wind turbine emulator (WTE) can be used to help in the evaluation of hardware-software alternatives, avoiding difficult field tests by recreating real environments on a controlled testbed. It consists of an electrical machine driven by a solid-state converter. WTEs are controlled to provide a desired dynamic Torque-Speed characteristic, equivalent to a real wind turbine under prescribed external conditions. The control system provides a desired torque value as a function of wind and turbine shaft speeds. This work presents the hardware / software development of a WECS emulator to be used in analysis and design of Real-Time control strategies for different types of electric generators. The proposed system is composed by a wind turbine emulator connected to an AC generator. The Wind Turbine Emulator consists of a direct current (DC) motor that is driven by a four-quadrant DC/DC converter or chopper. It is made of a MOSFET H-Bridge, with a current control loop. The generator block consists of an asynchronous AC machine, driven by static converters tailored to particular applications (autonomous or grid-connected WECS).With the objective to have a versatile system, the control of WTE and WECS generator is carried out by a Pentium PC equipped with an I/O multifunction acquisition board. It generates reference values for the current control loop driving the chopper and measures the shaft rotation speed using an incremental optical encoder. Software for the PC is developed in MatLab/Simulink, using Real Time WorkShop (RTW) and Real Time Windows Target (RTWT). This

Real time ultrasonography in obstructive jaundice

International Nuclear Information System (INIS)

Cho, Kyung Sik; Kim, Ho Kyun; Sung, Nak Kwan; Kim, Soon Yong

1982-01-01

Ultrasonography is a predominantly accurate, relatively simple unique diagnostic method of obstructive jaundice. The ultrasonographic findings of obstructive jaundice are dilated intra- and extrahepatic duct with intraluminal hyper reflective echo or mass in and/ or around the bile duct. The superiority of high resolution real time ultrasonography for the diagnosis of obstructive jaundice is bases on the easy detectability of extra- and intrahepatic bile ducts by its multiple sectional images in a short time, the flexibility of probe and small crystal size. Author evaluated real time sonographic findings 46 obstructive jaundice patients confirmed by surgery or radiographical examinations. The results were: 1. Diameter of extrahepatic duct in obstructive jaundice were varied from normal to 4.0 Cm, mostly 8 to 10 mm in diameter (26%). Degree of dilatation of biliary duct appeared more prominent in cancer patients than other causes of obstruction. 2. The site of obstruction was detected in 85% (39/46) and its common site was common bile duct in 63% (29/46). 3. The diagnostic accuracy of choledocholithiasis and cancer was 82% (22/27) and 44% (4/9), respectively. Diagnostic accuracy of the real time ultrasonography in obstructive jaundice was over all 75% (34/46)

Investigating the Effect of Voltage-Switching on Low-Energy Task Scheduling in Hard Real-Time Systems

National Research Council Canada - National Science Library

Swaminathan, Vishnu; Chakrabarty, Krishnendu

2005-01-01

We investigate the effect of voltage-switching on task execution times and energy consumption for dual-speed hard real-time systems, and present a new approach for scheduling workloads containing periodic tasks...

Using dual-energy x-ray imaging to enhance automated lung tumor tracking during real-time adaptive radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Menten, Martin J., E-mail: martin.menten@icr.ac.uk; Fast, Martin F.; Nill, Simeon; Oelfke, Uwe, E-mail: uwe.oelfke@icr.ac.uk [Joint Department of Physics at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust, London SM2 5NG (United Kingdom)

2015-12-15

Purpose: Real-time, markerless localization of lung tumors with kV imaging is often inhibited by ribs obscuring the tumor and poor soft-tissue contrast. This study investigates the use of dual-energy imaging, which can generate radiographs with reduced bone visibility, to enhance automated lung tumor tracking for real-time adaptive radiotherapy. Methods: kV images of an anthropomorphic breathing chest phantom were experimentally acquired and radiographs of actual lung cancer patients were Monte-Carlo-simulated at three imaging settings: low-energy (70 kVp, 1.5 mAs), high-energy (140 kVp, 2.5 mAs, 1 mm additional tin filtration), and clinical (120 kVp, 0.25 mAs). Regular dual-energy images were calculated by weighted logarithmic subtraction of high- and low-energy images and filter-free dual-energy images were generated from clinical and low-energy radiographs. The weighting factor to calculate the dual-energy images was determined by means of a novel objective score. The usefulness of dual-energy imaging for real-time tracking with an automated template matching algorithm was investigated. Results: Regular dual-energy imaging was able to increase tracking accuracy in left–right images of the anthropomorphic phantom as well as in 7 out of 24 investigated patient cases. Tracking accuracy remained comparable in three cases and decreased in five cases. Filter-free dual-energy imaging was only able to increase accuracy in 2 out of 24 cases. In four cases no change in accuracy was observed and tracking accuracy worsened in nine cases. In 9 out of 24 cases, it was not possible to define a tracking template due to poor soft-tissue contrast regardless of input images. The mean localization errors using clinical, regular dual-energy, and filter-free dual-energy radiographs were 3.85, 3.32, and 5.24 mm, respectively. Tracking success was dependent on tumor position, tumor size, imaging beam angle, and patient size. Conclusions: This study has highlighted the influence of

Using dual-energy x-ray imaging to enhance automated lung tumor tracking during real-time adaptive radiotherapy

International Nuclear Information System (INIS)

Menten, Martin J.; Fast, Martin F.; Nill, Simeon; Oelfke, Uwe

2015-01-01

Purpose: Real-time, markerless localization of lung tumors with kV imaging is often inhibited by ribs obscuring the tumor and poor soft-tissue contrast. This study investigates the use of dual-energy imaging, which can generate radiographs with reduced bone visibility, to enhance automated lung tumor tracking for real-time adaptive radiotherapy. Methods: kV images of an anthropomorphic breathing chest phantom were experimentally acquired and radiographs of actual lung cancer patients were Monte-Carlo-simulated at three imaging settings: low-energy (70 kVp, 1.5 mAs), high-energy (140 kVp, 2.5 mAs, 1 mm additional tin filtration), and clinical (120 kVp, 0.25 mAs). Regular dual-energy images were calculated by weighted logarithmic subtraction of high- and low-energy images and filter-free dual-energy images were generated from clinical and low-energy radiographs. The weighting factor to calculate the dual-energy images was determined by means of a novel objective score. The usefulness of dual-energy imaging for real-time tracking with an automated template matching algorithm was investigated. Results: Regular dual-energy imaging was able to increase tracking accuracy in left–right images of the anthropomorphic phantom as well as in 7 out of 24 investigated patient cases. Tracking accuracy remained comparable in three cases and decreased in five cases. Filter-free dual-energy imaging was only able to increase accuracy in 2 out of 24 cases. In four cases no change in accuracy was observed and tracking accuracy worsened in nine cases. In 9 out of 24 cases, it was not possible to define a tracking template due to poor soft-tissue contrast regardless of input images. The mean localization errors using clinical, regular dual-energy, and filter-free dual-energy radiographs were 3.85, 3.32, and 5.24 mm, respectively. Tracking success was dependent on tumor position, tumor size, imaging beam angle, and patient size. Conclusions: This study has highlighted the influence of

Using dual-energy x-ray imaging to enhance automated lung tumor tracking during real-time adaptive radiotherapy.

Science.gov (United States)

Menten, Martin J; Fast, Martin F; Nill, Simeon; Oelfke, Uwe

2015-12-01

Real-time, markerless localization of lung tumors with kV imaging is often inhibited by ribs obscuring the tumor and poor soft-tissue contrast. This study investigates the use of dual-energy imaging, which can generate radiographs with reduced bone visibility, to enhance automated lung tumor tracking for real-time adaptive radiotherapy. kV images of an anthropomorphic breathing chest phantom were experimentally acquired and radiographs of actual lung cancer patients were Monte-Carlo-simulated at three imaging settings: low-energy (70 kVp, 1.5 mAs), high-energy (140 kVp, 2.5 mAs, 1 mm additional tin filtration), and clinical (120 kVp, 0.25 mAs). Regular dual-energy images were calculated by weighted logarithmic subtraction of high- and low-energy images and filter-free dual-energy images were generated from clinical and low-energy radiographs. The weighting factor to calculate the dual-energy images was determined by means of a novel objective score. The usefulness of dual-energy imaging for real-time tracking with an automated template matching algorithm was investigated. Regular dual-energy imaging was able to increase tracking accuracy in left-right images of the anthropomorphic phantom as well as in 7 out of 24 investigated patient cases. Tracking accuracy remained comparable in three cases and decreased in five cases. Filter-free dual-energy imaging was only able to increase accuracy in 2 out of 24 cases. In four cases no change in accuracy was observed and tracking accuracy worsened in nine cases. In 9 out of 24 cases, it was not possible to define a tracking template due to poor soft-tissue contrast regardless of input images. The mean localization errors using clinical, regular dual-energy, and filter-free dual-energy radiographs were 3.85, 3.32, and 5.24 mm, respectively. Tracking success was dependent on tumor position, tumor size, imaging beam angle, and patient size. This study has highlighted the influence of patient anatomy on the success rate of real-time

Impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott RealTime HCV Genotype II assay for hepatitis C genotyping.

Science.gov (United States)

Sridhar, Siddharth; Yip, Cyril C Y; Chan, Jasper F W; To, Kelvin K W; Cheng, Vincent C C; Yuen, Kwok-Yung

2018-05-01

The Abbott RealTime HCV Genotype II assay (Abbott-RT-HCV assay) is a real-time PCR based genotyping method for hepatitis C virus (HCV). This study measured the impact of inter-genotypic recombination and probe cross-reactivity on the performance of the Abbott-RT-HCV assay. 517 samples were genotyped using the Abbott-RT-HCV assay over a one-year period, 34 (6.6%) were identified as HCV genotype 1 without further subtype designation raising the possibility of inaccurate genotyping. These samples were subjected to confirmatory sequencing. 27 of these 34 (79%) samples were genotype 1b while five (15%) were genotype 6. One HCV isolate was an inter-genotypic 1a/4o recombinant. This is a novel natural HCV recombinant that has never been reported. Inter-genotypic recombination and probe cross-reactivity can affect the accuracy of the Abbott-RT-HCV assay, both of which have significant implications on antiviral regimen choice. Confirmatory sequencing of ambiguous results is crucial for accurate genotyping. Copyright © 2018 Elsevier Inc. All rights reserved.

Multiplex hydrolysis probe real-time PCR for simultaneous detection of hepatitis A virus and hepatitis E virus.

Science.gov (United States)

Qiu, Feng; Cao, Jingyuan; Su, Qiudong; Yi, Yao; Bi, Shengli

2014-05-30

Detection of hepatitis viral infections has traditionally relied on the circulating antibody test using the enzyme-linked immunosorbent assay. However, multiplex real-time PCR has been increasingly used for a variety of viral nucleic acid detections and has proven to be superior to traditional methods. Hepatitis A virus (HAV) and hepatitis E virus (HEV) are the major causes of acute hepatitis worldwide; both HAV and HEV infection are a main public health problem. In the present study, a one-step multiplex reverse transcriptase quantitative polymerase chain reaction assay using hydrolysis probes was developed for simultaneously detecting HAV and HEV. This novel detection system proved specific to the target viruses, to be highly sensitive and to be applicable to clinical sera samples, making it useful for rapid, accurate and feasible identification of HAV and HEV.

Energy and Reserve under Distributed Energy Resources Management—Day-Ahead, Hour-Ahead and Real-Time

Directory of Open Access Journals (Sweden)

Tiago Soares

2017-11-01

Full Text Available The increasing penetration of distributed energy resources based on renewable energy sources in distribution systems leads to a more complex management of power systems. Consequently, ancillary services become even more important to maintain the system security and reliability. This paper proposes and evaluates a generic model for day-ahead, intraday (hour-ahead and real-time scheduling, considering the joint optimization of energy and reserve in the scope of the virtual power player concept. The model aims to minimize the operation costs in the point of view of one aggregator agent taking into account the balance of the distribution system. For each scheduling stage, previous scheduling results and updated forecasts are considered. An illustrative test case of a distribution network with 33 buses, considering a large penetration of distribution energy resources allows demonstrating the benefits of the proposed model.

Evaluation of Subgingival Dental Plaque Microbiota Changes In Fixed Orthodontic Patients with Syber Green Real Time PCR

Directory of Open Access Journals (Sweden)

Naser Sargolzaie

2014-06-01

Full Text Available Introduction: One of the most common problems we confront in orthodontic therapy is periodontal diseases. Initial factor which causes these diseases is colonization of anaerobic microorganisms in subgingival plaque. Technically, local environmental changes related to orthodontic band and brackets may influence the bacterial species in periodontal plaque. However, it seems necessary to assess variations in subgingival plaque caused by orthodontic appliances. The aim of this study was to investigate changes in subgingival microbiota and clinical parameters before and after bracket placement. Methods: Clinical parameters including probing depth (PD, plaque index (PI, clinical attachment level (CAL, bleeding on probing (BOP and gingival index (GI were recorded and subgingival microbial samples were collected in 30 people aged between 13 and 25. As a control group, 15 persons getting matched as to their age and sex with no need to orthodontic treatment were opted using specific primers, SYBER Green Real-Time PCR was carried out in order to determine bacterial flora in stored samples. All mentioned procedures were reassessed in experimental group and in control group three months after band and bracket bonding. A descriptive analysis was conducted, and paired t test and Wilcoxon test were used for differences between groups (P

An energy saving mechanism of EPON networks for real time video transmission

Science.gov (United States)

Liu, Chien-Ping; Wu, Ho-Ting; Chiang, Yun-Ting; Chien, Shieh-Chieh; Ke, Kai-Wei

2015-07-01

Modern access networks are constructed widely by passive optical networks (PONs) to meet the growing bandwidth demand. However, higher bandwidth means more energy consumption. To save energy, a few research works propose the dual-mode energy saving mechanism that allows the ONU to operate between active and sleep modes periodically. However, such dual-mode energy saving design may induce unnecessary power consumption or packet delay increase in the case where only downstream data exist for most of the time. In this paper, we propose a new tri-mode energy saving scheme for Ethernet PON (EPON). The new tri-mode energy saving design, combining the dual-mode saving mechanism with the doze mode, allows the ONU to switch among these three modes alternatively. In the doze mode, the ONU may receive downstream data while keeping its transmitter close. Such scenario is often observed for real time video downstream transmission. Furthermore, the low packet delay of high priority upstream data can be attained through the use of early wake-up mechanism employed in both energy saving modes. The energy saving and system efficiency can thus be achieved jointly while maintaining the differentiated QoS for data with various priorities. Performance results via simulation have demonstrated the effectiveness of such mechanism.

Real - time Optimization of Distributed Energy Storage System Operation Strategy Based on Peak Load Shifting

Science.gov (United States)

Wang, Qian; Lu, Guangqi; Li, Xiaoyu; Zhang, Yichi; Yun, Zejian; Bian, Di

2018-01-01

To take advantage of the energy storage system (ESS) sufficiently, the factors that the service life of the distributed energy storage system (DESS) and the load should be considered when establishing optimization model. To reduce the complexity of the load shifting of DESS in the solution procedure, the loss coefficient and the equal capacity ratio distribution principle were adopted in this paper. Firstly, the model was established considering the constraint conditions of the cycles, depth, power of the charge-discharge of the ESS, the typical daily load curves, as well. Then, dynamic programming method was used to real-time solve the model in which the difference of power Δs, the real-time revised energy storage capacity Sk and the permission error of depth of charge-discharge were introduced to optimize the solution process. The simulation results show that the optimized results was achieved when the load shifting in the load variance was not considered which means the charge-discharge of the energy storage system was not executed. In the meantime, the service life of the ESS would increase.

MIROS: a hybrid real-time energy-efficient operating system for the resource-constrained wireless sensor nodes.

Science.gov (United States)

Liu, Xing; Hou, Kun Mean; de Vaulx, Christophe; Shi, Hongling; El Gholami, Khalid

2014-09-22

Operating system (OS) technology is significant for the proliferation of the wireless sensor network (WSN). With an outstanding OS; the constrained WSN resources (processor; memory and energy) can be utilized efficiently. Moreover; the user application development can be served soundly. In this article; a new hybrid; real-time; memory-efficient; energy-efficient; user-friendly and fault-tolerant WSN OS MIROS is designed and implemented. MIROS implements the hybrid scheduler and the dynamic memory allocator. Real-time scheduling can thus be achieved with low memory consumption. In addition; it implements a mid-layer software EMIDE (Efficient Mid-layer Software for User-Friendly Application Development Environment) to decouple the WSN application from the low-level system. The application programming process can consequently be simplified and the application reprogramming performance improved. Moreover; it combines both the software and the multi-core hardware techniques to conserve the energy resources; improve the node reliability; as well as achieve a new debugging method. To evaluate the performance of MIROS; it is compared with the other WSN OSes (TinyOS; Contiki; SOS; openWSN and mantisOS) from different OS concerns. The final evaluation results prove that MIROS is suitable to be used even on the tight resource-constrained WSN nodes. It can support the real-time WSN applications. Furthermore; it is energy efficient; user friendly and fault tolerant.

MIROS: A Hybrid Real-Time Energy-Efficient Operating System for the Resource-Constrained Wireless Sensor Nodes

Science.gov (United States)

Liu, Xing; Hou, Kun Mean; de Vaulx, Christophe; Shi, Hongling; Gholami, Khalid El

2014-01-01

Operating system (OS) technology is significant for the proliferation of the wireless sensor network (WSN). With an outstanding OS; the constrained WSN resources (processor; memory and energy) can be utilized efficiently. Moreover; the user application development can be served soundly. In this article; a new hybrid; real-time; memory-efficient; energy-efficient; user-friendly and fault-tolerant WSN OS MIROS is designed and implemented. MIROS implements the hybrid scheduler and the dynamic memory allocator. Real-time scheduling can thus be achieved with low memory consumption. In addition; it implements a mid-layer software EMIDE (Efficient Mid-layer Software for User-Friendly Application Development Environment) to decouple the WSN application from the low-level system. The application programming process can consequently be simplified and the application reprogramming performance improved. Moreover; it combines both the software and the multi-core hardware techniques to conserve the energy resources; improve the node reliability; as well as achieve a new debugging method. To evaluate the performance of MIROS; it is compared with the other WSN OSes (TinyOS; Contiki; SOS; openWSN and mantisOS) from different OS concerns. The final evaluation results prove that MIROS is suitable to be used even on the tight resource-constrained WSN nodes. It can support the real-time WSN applications. Furthermore; it is energy efficient; user friendly and fault tolerant. PMID:25248069

Probing the pomeron structure with quasi-real photons

International Nuclear Information System (INIS)

Arteaga-Romero, N.; Kessler, P.

1986-03-01

Following a recent suggestion of Ingelman and Schlein, we here consider the possibility of probing the gluonic structure of the pomeron with quasi-real photons, i.e. in reactions e p → e p + 2 jets + X taking place at an ep collider such as HERA

A fully automated and scalable timing probe-based method for time alignment of the LabPET II scanners

Science.gov (United States)

Samson, Arnaud; Thibaudeau, Christian; Bouchard, Jonathan; Gaudin, Émilie; Paulin, Caroline; Lecomte, Roger; Fontaine, Réjean

2018-05-01

A fully automated time alignment method based on a positron timing probe was developed to correct the channel-to-channel coincidence time dispersion of the LabPET II avalanche photodiode-based positron emission tomography (PET) scanners. The timing probe was designed to directly detect positrons and generate an absolute time reference. The probe-to-channel coincidences are recorded and processed using firmware embedded in the scanner hardware to compute the time differences between detector channels. The time corrections are then applied in real-time to each event in every channel during PET data acquisition to align all coincidence time spectra, thus enhancing the scanner time resolution. When applied to the mouse version of the LabPET II scanner, the calibration of 6 144 channels was performed in less than 15 min and showed a 47% improvement on the overall time resolution of the scanner, decreasing from 7 ns to 3.7 ns full width at half maximum (FWHM).

Real-time boronization in PBX-M using erosion of solid boronized targets

International Nuclear Information System (INIS)

Kugel, H.W.; Timberlake, J.; Bell, R.; LeBlanc, B.; Okabayashi, M.; Paul, S.; Tighe, W.; Hirooka, Y.

1994-11-01

Thirty one real-time boronizations were applied to PBX-M using the plasma erosion of solid target probes. More than 17 g of boron were deposited in PBX-M using this technique. The probes were positioned at the edge plasma to optimize vaporization and minimize spallation. Auger depth profile analysis of poloidal and toroidal deposition sample coupon arrays indicate that boron was transported by the plasma around the torus and deep into the divertors. During discharges with continuous real-time boronization, low-Z and high-Z impurities decreased rapidly as plasma surfaces were covered during the first 20-30 discharges. After boronization, a short-term improvement in plasma conditions persisted prior to significant boron erosion from plasma surfaces, and a longer term, but less significant improvement persisted as boron farther from the edge continued gettering. Real-time solid target boronization has been found to be very effective for accelerating conditioning to new regimes and maintaining high performance plasma conditions

An Experimental Evaluation of Real-Time DVFS Scheduling Algorithms

OpenAIRE

Saha, Sonal

2011-01-01

Dynamic voltage and frequency scaling (DVFS) is an extensively studied energy manage- ment technique, which aims to reduce the energy consumption of computing platforms by dynamically scaling the CPU frequency. Real-Time DVFS (RT-DVFS) is a branch of DVFS, which reduces CPU energy consumption through DVFS, while at the same time ensures that task time constraints are satisfied by constructing appropriate real-time task schedules. The literature presents numerous RT-DVFS schedul...

Development of a real time polymerase chain reaction for quantitation of Schistosoma mansoni DNA

Directory of Open Access Journals (Sweden)

Ana Lisa do Vale Gomes

2006-10-01

Full Text Available This report describes the development of a SYBR Green I based real time polymerase chain reaction (PCR protocol for detection on the ABI Prism 7000 instrument. Primers targeting the gene encoding the SSU rRNA were designed to amplify with high specificity DNA from Schistosoma mansoni, in a real time quantitative PCR system. The limit of detection of parasite DNA for the system was 10 fg of purified genomic DNA, that means less than the equivalent to one parasite cell (genome ~580 fg DNA. The efficiency was 0.99 and the correlation coefficient (R² was 0.97. When different copy numbers of the target amplicon were used as standards, the assay could detect at least 10 copies of the specific target. The primers used were designed to amplify a 106 bp DNA fragment (Tm 83ºC. The assay was highly specific for S. mansoni, and did not recognize DNA from closely related non-schistosome trematodes. The real time PCR allowed for accurate quantification of S. mansoni DNA and no time-consuming post-PCR detection of amplification products by gel electrophoresis was required. The assay is potentially able to quantify S. mansoni DNA (and indirectly parasite burden in a number of samples, such as snail tissue, serum and feces from patients, and cercaria infested water. Thus, these PCR protocols have potential to be used as tools for monitoring of schistosome transmission and quantitative diagnosis of human infection.

Development of a real-time PCR for detection of Staphylococcus pseudintermedius using a novel automated comparison of whole-genome sequences.

Directory of Open Access Journals (Sweden)

Koen M Verstappen

Full Text Available Staphylococcus pseudintermedius is an opportunistic pathogen in dogs and cats and occasionally causes infections in humans. S. pseudintermedius is often resistant to multiple classes of antimicrobials. It requires a reliable detection so that it is not misidentified as S. aureus. Phenotypic and currently-used molecular-based diagnostic assays lack specificity or are labour-intensive using multiplex PCR or nucleic acid sequencing. The aim of this study was to identify a specific target for real-time PCR by comparing whole genome sequences of S. pseudintermedius and non-pseudintermedius.Genome sequences were downloaded from public repositories and supplemented by isolates that were sequenced in this study. A Perl-script was written that analysed 300-nt fragments from a reference genome sequence of S. pseudintermedius and checked if this sequence was present in other S. pseudintermedius genomes (n = 74 and non-pseudintermedius genomes (n = 138. Six sequences specific for S. pseudintermedius were identified (sequence length between 300-500 nt. One sequence, which was located in the spsJ gene, was used to develop primers and a probe. The real-time PCR showed 100% specificity when testing for S. pseudintermedius isolates (n = 54, and eight other staphylococcal species (n = 43. In conclusion, a novel approach by comparing whole genome sequences identified a sequence that is specific for S. pseudintermedius and provided a real-time PCR target for rapid and reliable detection of S. pseudintermedius.

Is Advanced Real-Time Energy Metering Sufficient to Persuade People to Save Energy?

Science.gov (United States)

Ting, L.; Leite, H.; Ponce de Leão, T.

2012-10-01

In order to promote a low-carbon economy, EU citizens may soon be able to check their electricity consumption from smart meter. It is hoped that smart meter can, by providing real-time consumption and pricing information to residential users, help reducing demand for electricity. It is argued in this paper that, according the Elaborative Likelihood Model (ELM), these methods are most likely to be effective when consumers perceive the issue of energy conservation relevant to their lives. Nevertheless, some fundamental characteristics of these methods result in limited amount of perceived personal relevance; for instance, energy expenditure expense may be relatively small comparing to other household expenditure like mortgage and consumption information does not enhance interpersonal trust. In this paper, it is suggested that smart meter can apply the "nudge" approaches which respond to ELM as the use of simple rules to make decision, which include the change of feedback delivery and device design.

Is Advanced Real-Time Energy Metering Sufficient to Persuade People to Save Energy?

Directory of Open Access Journals (Sweden)

Leite H.

2012-10-01

Full Text Available In order to promote a low-carbon economy, EU citizens may soon be able to check their electricity consumption from smart meter. It is hoped that smart meter can, by providing real-time consumption and pricing information to residential users, help reducing demand for electricity. It is argued in this paper that, according the Elaborative Likelihood Model (ELM, these methods are most likely to be effective when consumers perceive the issue of energy conservation relevant to their lives. Nevertheless, some fundamental characteristics of these methods result in limited amount of perceived personal relevance; for instance, energy expenditure expense may be relatively small comparing to other household expenditure like mortgage and consumption information does not enhance interpersonal trust. In this paper, it is suggested that smart meter can apply the “nudge” approaches which respond to ELM as the use of simple rules to make decision, which include the change of feedback delivery and device design.

Real-time systems

OpenAIRE

Badr, Salah M.; Bruztman, Donald P.; Nelson, Michael L.; Byrnes, Ronald Benton

1992-01-01

This paper presents an introduction to the basic issues involved in real-time systems. Both real-time operating sys and real-time programming languages are explored. Concurrent programming and process synchronization and communication are also discussed. The real-time requirements of the Naval Postgraduate School Autonomous Under Vehicle (AUV) are then examined. Autonomous underwater vehicle (AUV), hard real-time system, real-time operating system, real-time programming language, real-time sy...

Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen.

Science.gov (United States)

Denman, Stuart E; McSweeney, Christopher S

2006-12-01

Traditional methods for enumerating and identifying microbial populations within the rumen can be time consuming and cumbersome. Methods that involve culturing and microscopy can also be inconclusive, particularly when studying anaerobic rumen fungi. A real-time PCR SYBR Green assay, using PCR primers to target total rumen fungi and the cellulolytic bacteria Ruminococcus flavefaciens and Fibrobacter succinogenes, is described, including design and validation. The DNA and crude protein contents with respect to the fungal biomass of both polycentric and monocentric fungal isolates were investigated across the fungal growth stages to aid in standard curve generation. The primer sets used were found to be target specific with no detectable cross-reactivity. Subsequently, the real-time PCR assay was employed in a study to detect these populations within cattle rumen. The anaerobic fungal target was observed to increase 3.6-fold from 0 to 12 h after feeding. The results also indicated a 5.4-fold increase in F. succinogenes target between 0 and 12 h after feeding, whereas R. flavefaciens was observed to maintain more or less consistent levels. This is the first report of a real-time PCR assay to estimate the rumen anaerobic fungal population.

Real time monitoring of filament-assisted chemically vapor deposited diamond by spectroscopic ellipsometry

International Nuclear Information System (INIS)

Yue Cong; An, I.; Vedam, K.; Collins, R.W.; Nguyen, H.V.; Messier, R.

1991-01-01

Spectroscopic ellipsometry over the range 1.5-4.5 eV was applied as a real time probe of the processes occurring in the initial nucleation of thin film diamond by heated-filament assisted chemical vapor deposition. Using both untreated and diamond-polished c-Si substrates, as well as both carburized and uncarburized tungsten filaments, it was possible to separate and characterize competing phenomena, including the increase in surface temperature induced by filament ignition, the formation of carbide layers, contamination of the substrate by tungsten from the filament, annealing of diamond polishing damage, and, finally, diamond nucleation. An accurate measurement of the true temperature of the substrate surface averaged over the top 500 A can be obtained from the energy position of critical points in the c-Si band structure. For diamond deposition, we operated with an initial excess flow of CH 4 to stimulate nucleation. We applied real time feedback and manual control to reduce the CH 4 flow in the first monolayers of deposition. The thickness of diamond and an estimate of its nucleation density can be obtained from real time spectra, and the latter was in good agreement with that obtained from scanning electron microscopy. (orig.)

Microsatellite instability typing in serum and tissue of patients with colorectal cancer: comparing real time PCR with hybridization probe and high-performance liquid chromatography.

Science.gov (United States)

Mokarram, P; Rismanchi, M; Alizadeh Naeeni, M; Mirab Samiee, S; Paryan, M; Alipour, A; Honardar, Z; Kavousipour, S; Naghibalhossaini, F; Mostafavi-Pour, Z; Monabati, A; Hosseni, S V; Shamsdin, S A

2014-05-01

Allelic variation of BAT-25 (a 25-repeat quasimonomorphic poly T) and BAT-26 (a 26-repeat quasimonomorphic polyA) loci as two mononucleotide microsatellite markers, were analyzed with high-performance liquid chromatography (HPLC) compared with Real-Time PCR using hybridization probes. BAT-26 and BAT-25 markers were used to determine an appropriate screening technique with high sensitivity and specificity to diagnose microsatellite instability (MSI) status in patients with colorectal cancer (CRC). One of the pathways in colorectal tumor genesis is microsatellite instability (MSI+). MSI is detected in about 15% of all CRCs; 3% are of these are associated with Lynch syndrome and the other 12% are caused by sporadic. Colorectal tumors with MSI have distinctive features compared with microsatellite stable tumors. Due to the high percentage of MSI+ CRC in Iran, screening of this type of CRC is imperative. Two markers were analyzed in tissues and sera of 44 normal volunteers and tumor and matched normal mucosal tissues as well as sera of 44 patients with sporadic CRC. The sensitivity and specificity of BAT-26 with real time PCR method (Hybridization probe) were 100% in comparison with sequencing method as the gold standard, while HPLC had a lower sensitivity and specificity. According to HPLC data, BAT-26 was more sensitive than BAT-25 in identifying MSI tumors. Therefore, MSI typing using the BAT-26 hybridization probe method compared to HPLC could be considered as an accurate method for diagnosing MSI in CRC tumors but not in serum circulating DNAs.

Real-Time Vision-Based Stiffness Mapping †.

Science.gov (United States)

Faragasso, Angela; Bimbo, João; Stilli, Agostino; Wurdemann, Helge Arne; Althoefer, Kaspar; Asama, Hajime

2018-04-26

This paper presents new findings concerning a hand-held stiffness probe for the medical diagnosis of abnormalities during palpation of soft-tissue. Palpation is recognized by the medical community as an essential and low-cost method to detect and diagnose disease in soft-tissue. However, differences are often subtle and clinicians need to train for many years before they can conduct a reliable diagnosis. The probe presented here fills this gap providing a means to easily obtain stiffness values of soft tissue during a palpation procedure. Our stiffness sensor is equipped with a multi degree of freedom (DoF) Aurora magnetic tracker, allowing us to track and record the 3D position of the probe whilst examining a tissue area, and generate a 3D stiffness map in real-time. The stiffness probe was integrated in a robotic arm and tested in an artificial environment representing a good model of soft tissue organs; the results show that the sensor can accurately measure and map the stiffness of a silicon phantom embedded with areas of varying stiffness.

Real-Time Vision-Based Stiffness Mapping †

Directory of Open Access Journals (Sweden)

Angela Faragasso

2018-04-01

Full Text Available This paper presents new findings concerning a hand-held stiffness probe for the medical diagnosis of abnormalities during palpation of soft-tissue. Palpation is recognized by the medical community as an essential and low-cost method to detect and diagnose disease in soft-tissue. However, differences are often subtle and clinicians need to train for many years before they can conduct a reliable diagnosis. The probe presented here fills this gap providing a means to easily obtain stiffness values of soft tissue during a palpation procedure. Our stiffness sensor is equipped with a multi degree of freedom (DoF Aurora magnetic tracker, allowing us to track and record the 3D position of the probe whilst examining a tissue area, and generate a 3D stiffness map in real-time. The stiffness probe was integrated in a robotic arm and tested in an artificial environment representing a good model of soft tissue organs; the results show that the sensor can accurately measure and map the stiffness of a silicon phantom embedded with areas of varying stiffness.

Innovative SPM Probes for Energy-Storage Science: MWCNT-Nanopipettes to Nanobattery Probes

Science.gov (United States)

Larson, Jonathan; Talin, Alec; Pearse, Alexander; Kozen, Alexander; Reutt-Robey, Janice

As energy-storage materials and designs continue to advance, new tools are needed to direct and explore ion insertion/de-insertion at well-defined battery materials interfaces. Scanned probe tips, assembled from actual energy-storage materials, permit SPM measures of local cathode-anode (tip-sample) interactions, including ion transfer. We present examples of ``cathode'' MWCNT-terminated STM probe tips interacting with Li(s)/Si(111) anode substrates. The MWCNT tip functions as both SPM probe and Li-nanopipette,[1] for controlled transport and manipulation of Li. Local field conditions for lithium ionization and transfer are determined and compared to electrostatic models. Additional lithium metallic and oxide tips have been prepared by thin film deposition on conventional W tips, the latter of which effectively functions as a nanobattery. We demonstrate use of these novel probe materials in the local lithiation of low-index Si anode interfaces, probing local barriers for lithium insertion. Prospects and limitations of these novel SPM probes will be discussed. U.S. Department of Energy Award Number DESC0001160.

A closed-loop energy price controlling method for real-time energy balancing in a smart grid energy market

International Nuclear Information System (INIS)

Alagoz, B. Baykant; Kaygusuz, Asim; Akcin, Murat; Alagoz, Serkan

2013-01-01

Future smart grids will require a flexible, observable, and controllable network for reliable and efficient energy delivery under uncertain generation and demand conditions. One of the mechanisms for efficient and reliable energy generation is dynamic demand-responsive generation management based on energy price adjustments that creates a balance in energy markets. This study presents a closed-loop PID (proportional–integral–derivative) controller-based price control method for autonomous and real-time balancing of energy demand and generation in smart grid electricity markets. The PID control system can regulate energy prices online to respond dynamically and instantaneously to the varying energy demands of grid consumers. Independent energy suppliers in the smart grid decide whether to sell their energy to the grid according to the energy prices declared by the closed-loop PID controller system. Energy market simulations demonstrate that PID-controlled energy price regulation can effectively maintain an energy balance for hourly demand fluctuations of consumers. - Highlights: • This study presents a control theoretic approach for management of energy balance. • A closed-loop PID controller-based price controlling method is used in smart grid. • The simulation results demonstrate advantages of PID-based energy price control. • This method is appropriate for demand responsive management of smart grid markets

Integration of multidisciplinary technologies for real time target visualization and verification for radiotherapy.

Science.gov (United States)

Chang, Wen-Chung; Chen, Chin-Sheng; Tai, Hung-Chi; Liu, Chia-Yuan; Chen, Yu-Jen

2014-01-01

The current practice of radiotherapy examines target coverage solely from digitally reconstructed beam's eye view (BEV) in a way that is indirectly accessible and that is not in real time. We aimed to visualize treatment targets in real time from each BEV. The image data of phantom or patients from ultrasound (US) and computed tomography (CT) scans were captured to perform image registration. We integrated US, CT, US/CT image registration, robotic manipulation of US, a radiation treatment planning system, and a linear accelerator to constitute an innovative target visualization system. The performance of this algorithm segmented the target organ in CT images, transformed and reconstructed US images to match each orientation, and generated image registration in real time mode with acceptable accuracy. This image transformation allowed physicians to visualize the CT image-reconstructed target via a US probe outside the BEV that was non-coplanar to the beam's plane. It allowed the physicians to remotely control the US probe that was equipped on a robotic arm to dynamically trace and real time monitor the coverage of the target within the BEV during a simulated beam-on situation. This target visualization system may provide a direct remotely accessible and real time way to visualize, verify, and ensure tumor targeting during radiotherapy.

Quantum dots-hyperbranched polyether hybrid nanospheres towards delivery and real-time detection of nitric oxide

Energy Technology Data Exchange (ETDEWEB)

Liu, Shuiping; Gu, Tianxun; Fu, Jiajia [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China); Li, Xiaoqiang, E-mail: leecaiwei@163.com [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China); Technical University of Denmark, DTU Food, Søltofts plads, B227, 2800 Kgs. Lyngby (Denmark); Chronakis, Ioannis S. [Technical University of Denmark, DTU Food, Søltofts plads, B227, 2800 Kgs. Lyngby (Denmark); Ge, Mingqiao [Key Laboratory of Eco-Textiles, Ministry of Education (Jiangnan University), Wuxi 214122 (China); College of Textile and Clothing, Jiangnan University, Wuxi 214122 (China)

2014-12-01

In this work, novel hybrid nanosphere vehicles were synthesized for nitric oxide (NO) donating and real-time detection. The hybrid nanosphere vehicles consist of cadmium selenide quantum dots (CdSe QDs) as NO fluorescent probes, and the modified hyperbranched polyether (mHP)-based diazeniumdiolates as NO donors, respectively. The nanospheres have spherical outline with dimension of ∼ 127 nm. The data of systematic characterization demonstrated that the mHP-based hybrid nanosphere vehicles (QDs-mHP-NO) can release and real-time detect NO with the low limit of 25 nM, based on fluorescence quenching mechanism. The low cell-toxicity of QDs-mHP-NO nanospheres was verified by means of MTT assay on L929 cells viability. The QDs-mHP-NO nanospheres provide perspectives for designing a new class of biocompatible NO donating and imaging systems. - Highlights: • QDs-mHP-NO fluorescent probe was prepared. • The QDs-mHP-NO probe is capable of releasing NO. • The QDs-mHP-NO probe can quantitatively detecting the release of NO in real time. • The low cell-toxicity of QDs-mHP-NO nanospheres was verified.

Diagnosing Human Papillomavirus and Human Papillomavirus Type 16 By Real-Time PCR in Patient Undergone to Colposcopy and Significance of the Diagnosis

Directory of Open Access Journals (Sweden)

Sibel Özdaş

2013-06-01

Full Text Available Objective: It is aimed to determine presence of HPV and HPV 16 by Real-Time PCR in cervical smears obtained from patients during colposcopic examination who had referred to outpatient clinic of Gynecology and Obstetrics Department due to various complaints and to examine interrelation between positive test results and clinical data. Method: Sixty patients were included in the study who were referred to outpatient clinic due to vary complaints and who had been decided to undergo to colposcopic examination. DNA was obtained from each smear sample by phenol-chloroform-isoamylalcohol method. L1 region was replicated in amplification process using MY09/MY11 primers. Products for Nested Real time PCR were studied in Ligth Cycler equipment by GP5+/GP6+ primers and Cyanine-5 labeled HPV 16 DNA specific probe. Real time PCR products were undergone melting curve analysis by LigthCycler software version 3.5.3. HPV DNA positivity and HPV 16 positivity were determined at 78-82°C and 68°C, respectively. Results: No statistically significant difference could be detected between HPV positivity, HPV 16 in and types other than HPV 16 control group and patients with positive test result as a consequence of colposcopic examination. Again, no statistically significant difference could be detected between HPV positivity and status of parity, result of PAP test, marital status and age of patient. Conclusion: No statistically significant difference could be detected between HPV positivity, HPV 16 in and types other than HPV 16 control group and patients with positive test result as a consequence of colposcopic examination. Again, no statistically difference could be detected between HPV positivity and result of PAP smear test, marital status, age of patient and smoking but statistically significant difference could be detected between types other than HPV 16 and status of parity (respectively; χ2=0.821, p=0.365; χ2=0.752, p=0.564; χ2=0.364, p=0.834; χ2= 6.835, p

Real time monitoring automation of dose rate absorbed in air due to environmental gamma radiation

International Nuclear Information System (INIS)

Dominguez Ley, Orlando; Capote Ferrera, Eduardo; Carrazana Gonzalez, Jorge A.; Manzano de Armas, Jose F.; Alonso Abad, Dolores; Prendes Alonso, Miguel; Tomas Zerquera, Juan; Caveda Ramos, Celia A.; Kalber, Olof; Fabelo Bonet, Orlando; Montalvan Estrada, Adelmo; Cartas Aguila, Hector; Leyva Fernandez, Julio C.

2005-01-01

The Center of Radiation Protection and Hygiene (CPHR) as the head institution of the National Radiological Environmental Surveillance Network (RNVRA) has strengthened its detection and response capacity for a radiological emergency situation. The measurements of gamma dose rate at the main point of the RNVRA are obtained in real time and the CPHR receives the data coming from those points in a short time. To achieve the operability of the RNVRA it was necessary to complete the existent monitoring facilities using 4 automatic gamma probes, implementing in this way a real time measurement system. The software, GenitronProbe for obtaining the data automatically from the probe, Data Mail , for sending the data via e-mail, and Gamma Red , for receiving and processing the data in the head institution ,were developed

Distributed Resource Energy Analysis and Management System (DREAMS) Development for Real-time Grid Operations

Energy Technology Data Exchange (ETDEWEB)

Nakafuji, Dora [Hawaiian Electric Company, Honululu, HI (United States); Gouveia, Lauren [Hawaiian Electric Company, Honululu, HI (United States)

2016-10-24

This project supports development of the next generation, integrated energy management infrastructure (EMS) able to incorporate advance visualization of behind-the-meter distributed resource information and probabilistic renewable energy generation forecasts to inform real-time operational decisions. The project involves end-users and active feedback from an Utility Advisory Team (UAT) to help inform how information can be used to enhance operational functions (e.g. unit commitment, load forecasting, Automatic Generation Control (AGC) reserve monitoring, ramp alerts) within two major EMS platforms. Objectives include: Engaging utility operations personnel to develop user input on displays, set expectations, test and review; Developing ease of use and timeliness metrics for measuring enhancements; Developing prototype integrated capabilities within two operational EMS environments; Demonstrating an integrated decision analysis platform with real-time wind and solar forecasting information and timely distributed resource information; Seamlessly integrating new 4-dimensional information into operations without increasing workload and complexities; Developing sufficient analytics to inform and confidently transform and adopt new operating practices and procedures; Disseminating project lessons learned through industry sponsored workshops and conferences;Building on collaborative utility-vendor partnership and industry capabilities

A TaqMan-based real time PCR assay for specific detection and quantification of Xylella fastidiosa strains causing bacterial leaf scorch in oleander.

Science.gov (United States)

Guan, Wei; Shao, Jonathan; Singh, Raghuwinder; Davis, Robert E; Zhao, Tingchang; Huang, Qi

2013-02-15

A TaqMan-based real-time PCR assay was developed for specific detection of strains of X. fastidiosa causing oleander leaf scorch. The assay uses primers WG-OLS-F1 and WG-OLS-R1 and the fluorescent probe WG-OLS-P1, designed based on unique sequences found only in the genome of oleander strain Ann1. The assay is specific, allowing detection of only oleander-infecting strains, not other strains of X. fastidiosa nor other plant-associated bacteria tested. The assay is also sensitive, with a detection limit of 10.4fg DNA of X. fastidiosa per reaction in vitro and in planta. The assay can also be applied to detect low numbers of X. fastidiosa in insect samples, or further developed into a multiplex real-time PCR assay to simultaneously detect and distinguish diverse strains of X. fastidiosa that may occupy the same hosts or insect vectors. Specific and sensitive detection and quantification of oleander strains of X. fastidiosa should be useful for disease diagnosis, epidemiological studies, management of oleander leaf scorch disease, and resistance screening for oleander shrubs. Published by Elsevier B.V.

Light Driven Energy Research at LCLS: Planned Pump-Probe X-ray Spectroscopy Studies on Photosynthetic Water Splitting

Science.gov (United States)

Bergmann, Uwe

2010-02-01

Arguably the most important chemical reaction on earth is the photosynthetic splitting of water to molecular oxygen by the Mn-containing oxygen-evolving complex (Mn-OEC) in the protein known as photosystem II (PSII). It is this reaction which has, over the course of some 3.8 billion years, gradually filled our atmosphere with O2 and consequently enabled and sustained the evolution of complex aerobic life. Coupled to the reduction of carbon dioxide, biological photosynthesis contributes foodstuffs for nutrition while recycling CO2 from the atmosphere and replacing it with O2. By utilizing sunlight to power these energy-requiring reactions, photosynthesis also serves as a model for addressing societal energy needs as we enter an era of diminishing fossil hydrocarbon resources. Understanding, at the molecular level, the dynamics and mechanism of how nature has solved this problem is of fundamental importance and could be critical to aid in the design of manufactured devices to accomplish the conversion of sunlight into useful electrochemical energy and transportable fuel in the foreseeable future. In order to understand the photosynthetic splitting of water by the Mn-OEC we need to be able to follow the reaction in real time at an atomic level. A powerful probe to study the electronic and molecular structure of the Mn-OEC is x-ray spectroscopy. Here, in particular x-ray emission spectroscopy (XES) has two crucial qualities for LCLS based time-dependent pump-probe studies of the Mn-OEC: a) it directly probes the Mn oxidation state and ligation, b) it can be performed with wavelength dispersive optics to avoid the necessity of scanning in pump probe experiments. Recent results and the planned time dependent experiments at LCLS will be discussed. )

Implementation of real-time energy management strategy based on reinforcement learning for hybrid electric vehicles and simulation validation.

Science.gov (United States)

Kong, Zehui; Zou, Yuan; Liu, Teng

2017-01-01

To further improve the fuel economy of series hybrid electric tracked vehicles, a reinforcement learning (RL)-based real-time energy management strategy is developed in this paper. In order to utilize the statistical characteristics of online driving schedule effectively, a recursive algorithm for the transition probability matrix (TPM) of power-request is derived. The reinforcement learning (RL) is applied to calculate and update the control policy at regular time, adapting to the varying driving conditions. A facing-forward powertrain model is built in detail, including the engine-generator model, battery model and vehicle dynamical model. The robustness and adaptability of real-time energy management strategy are validated through the comparison with the stationary control strategy based on initial transition probability matrix (TPM) generated from a long naturalistic driving cycle in the simulation. Results indicate that proposed method has better fuel economy than stationary one and is more effective in real-time control.

Implementation of real-time energy management strategy based on reinforcement learning for hybrid electric vehicles and simulation validation.

Directory of Open Access Journals (Sweden)

Zehui Kong

Full Text Available To further improve the fuel economy of series hybrid electric tracked vehicles, a reinforcement learning (RL-based real-time energy management strategy is developed in this paper. In order to utilize the statistical characteristics of online driving schedule effectively, a recursive algorithm for the transition probability matrix (TPM of power-request is derived. The reinforcement learning (RL is applied to calculate and update the control policy at regular time, adapting to the varying driving conditions. A facing-forward powertrain model is built in detail, including the engine-generator model, battery model and vehicle dynamical model. The robustness and adaptability of real-time energy management strategy are validated through the comparison with the stationary control strategy based on initial transition probability matrix (TPM generated from a long naturalistic driving cycle in the simulation. Results indicate that proposed method has better fuel economy than stationary one and is more effective in real-time control.

Analysis of conditional gene deletion using probe based Real-Time PCR

Directory of Open Access Journals (Sweden)

Lyko Frank

2010-12-01

Full Text Available Abstract Following publication of this article 1 the authors noticed that an incorrect probe reference was cited on page 3, 4, 5 and 6 ("UP #69, Roche Applied Science". The correct probe that was used for the 1lox/2lox allele ratio analysis in the paper is as follows Probe for 1lox/2lox allele quantification: 5'-6-FAM-atAaCtTCgtatagCATaCattatac-BHQ-1 -3' (uppercase letters = LNA bases Manufacturer: EUROGENTEC, Seraing, Belgium All other information and reaction conditions in the paper are correct as stated.

Dynamic I/O Power Management for Hard Real-Time Systems

Science.gov (United States)

2005-01-01

recently emerged as an attractive alternative to inflexible hardware solutions. DPM for hard real - time systems has received relatively little attention...In particular, energy-driven I/O device scheduling for real - time systems has not been considered before. We present the first online DPM algorithm...which we call Low Energy Device Scheduler (LEDES), for hard real - time systems . LEDES takes as inputs a predetermined task schedule and a device-usage

Real-time image parameterization in high energy gamma-ray astronomy using transputers

International Nuclear Information System (INIS)

Punch, M.; Fegan, D.J.

1991-01-01

Recently, significant advances in Very-High-Energy gamma-ray astronomy have been made by parameterization of the Cherenkov images arising from gamma-ray initiated showers in the Earth's atmosphere. A prototype system to evaluate the use of Transputers as a parallel-processing elements for real-time analysis of data from a Cherenkov imaging camera is described in this paper. The operation of and benefits resulting from such a system are described, and the viability of an applicaiton of the prototype system is discussed

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.

Science.gov (United States)

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.

Real-time particle image velocimetry based on FPGA technology;Velocimetria PIV en tiempo real basada en logica programable FPGA

Energy Technology Data Exchange (ETDEWEB)

Iriarte Munoz, Jose Miguel [Universidad Nacional de Cuyo, Instituto Balseiro, Centro Atomico Bariloche (Argentina)

2008-07-01

Particle image velocimetry (PIV), based on laser sheet, is a method for image processing and calculation of distributed velocity fields.It is well established as a fluid dynamics measurement tool, being applied to liquid, gases and multiphase flows.Images of particles are processed by means of computationally demanding algorithms, what makes its real-time implementation difficult.The most probable displacements are found applying two dimensional cross-correlation function. In this work, we detail how it is possible to achieve real-time visualization of PIV method by designing an adaptive embedded architecture based on FPGA technology.We show first results of a physical field of velocity calculated by this platform system in a real-time approach.;La velocimetria por imagenes de particulas (PIV), basada en plano laser, es una potente herramienta de medicion en dinamica de fluidos, capaz de medir sin grandes errores, un campo de velocidades distribuido en liquidos, gases y flujo multifase.Los altos requerimientos computacionales de los algoritmos PIV dificultan su empleo en tiempo-real.En este trabajo presentamos el diseno de una plataforma basada en tecnologia FPGA para capturar video y procesar en tiempo real el algoritmo de correlacion cruzada bidimensional.Mostramos resultados de un primer abordaje de la captura de imagenes y procesamiento de un campo fisico de velocidades en tiempo real.

Real Time Conference 2016 Overview

Science.gov (United States)

Luchetta, Adriano

2017-06-01

This is a special issue of the IEEE Transactions on Nuclear Science containing papers from the invited, oral, and poster presentation of the 20th Real Time Conference (RT2016). The conference was held June 6-10, 2016, at Centro Congressi Padova “A. Luciani,” Padova, Italy, and was organized by Consorzio RFX (CNR, ENEA, INFN, Università di Padova, Acciaierie Venete SpA) and the Istituto Nazionale di Fisica Nucleare. The Real Time Conference is multidisciplinary and focuses on the latest developments in real-time techniques in high-energy physics, nuclear physics, astrophysics and astroparticle physics, nuclear fusion, medical physics, space instrumentation, nuclear power instrumentation, general radiation instrumentation, and real-time security and safety. Taking place every second year, it is sponsored by the Computer Application in Nuclear and Plasma Sciences technical committee of the IEEE Nuclear and Plasma Sciences Society. RT2016 attracted more than 240 registrants, with a large proportion of young researchers and engineers. It had an attendance of 67 students from many countries.

Review of Real-time Electricity Markets for Integrating Distributed Energy Resources and Demand Response

DEFF Research Database (Denmark)

Wang, Qi; Zhang, Chunyu; Ding, Yi

2015-01-01

The high penetration of both Distributed Energy Resources (DER) and Demand Response (DR) in modern power systems requires a sequence of advanced strategies and technologies for maintaining system reliability and flexibility. Real-time electricity markets (RTM) are the nondiscriminatory transaction...... platforms for providing necessary balancing services, where the market clearing (nodal or zonal prices depending on markets) is very close to real time operations of power systems. One of the primary functions of RTMs in modern power systems is establishing an efficient and effective mechanism for small DER...... and DR to participate in balancing market transactions, while handling their meteorological or intermittent characteristics, facilitating asset utilization, and stimulating their active responses. Consequently, RTMs are dedicated to maintaining the flexibility and reliability of power systems. This paper...

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

Directory of Open Access Journals (Sweden)

Hany Sady

2015-07-01

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

Multicolor probe-based confocal laser endomicroscopy: a new world for in vivo and real-time cellular imaging

Science.gov (United States)

Vercauteren, Tom; Doussoux, François; Cazaux, Matthieu; Schmid, Guillaume; Linard, Nicolas; Durin, Marie-Amélie; Gharbi, Hédi; Lacombe, François

2013-03-01

Since its inception in the field of in vivo imaging, endomicroscopy through optical fiber bundles, or probe-based Confocal Laser Endomicroscopy (pCLE), has extensively proven the benefit of in situ and real-time examination of living tissues at the microscopic scale. By continuously increasing image quality, reducing invasiveness and improving system ergonomics, Mauna Kea Technologies has turned pCLE not only into an irreplaceable research instrument for small animal imaging, but also into an accurate clinical decision making tool with applications as diverse as gastrointestinal endoscopy, pulmonology and urology. The current implementation of pCLE relies on a single fluorescence spectral band making different sources of in vivo information challenging to distinguish. Extending the pCLE approach to multi-color endomicroscopy therefore appears as a natural plan. Coupling simultaneous multi-laser excitation with minimally invasive, microscopic resolution, thin and flexible optics, allows the fusion of complementary and valuable biological information, thus paving the way to a combination of morphological and functional imaging. This paper will detail the architecture of a new system, Cellvizio Dual Band, capable of video rate in vivo and in situ multi-spectral fluorescence imaging with a microscopic resolution. In its standard configuration, the system simultaneously operates at 488 and 660 nm, where it automatically performs the necessary spectral, photometric and geometric calibrations to provide unambiguously co-registered images in real-time. The main hardware and software features, including calibration procedures and sub-micron registration algorithms, will be presented as well as a panorama of its current applications, illustrated with recent results in the field of pre-clinical imaging.

Acquisition of Real Time Simulator for Intelligent Power Networks in Operational Energy Applications

Science.gov (United States)

2017-12-05

and fixed power installations to enhance DoD mission effectiveness. The long term goal of this effort is to create a strong research and education ...effort is to create a strong research and education center at UTSA focused on innovative technologies and solutions for Energy-Systems Management...in Real-Time. , Grid Low voltage dc = ~ Dual Active Bridge (DAB) With 3-Level NPC HV bridge and High frequency transformer High voltage dc

Optimal Real-time Dispatch for Integrated Energy Systems

Energy Technology Data Exchange (ETDEWEB)

Firestone, Ryan Michael [Univ. of California, Berkeley, CA (United States)

2007-05-31

This report describes the development and application of a dispatch optimization algorithm for integrated energy systems (IES) comprised of on-site cogeneration of heat and electricity, energy storage devices, and demand response opportunities. This work is intended to aid commercial and industrial sites in making use of modern computing power and optimization algorithms to make informed, near-optimal decisions under significant uncertainty and complex objective functions. The optimization algorithm uses a finite set of randomly generated future scenarios to approximate the true, stochastic future; constraints are included that prevent solutions to this approximate problem from deviating from solutions to the actual problem. The algorithm is then expressed as a mixed integer linear program, to which a powerful commercial solver is applied. A case study of United States Postal Service Processing and Distribution Centers (P&DC) in four cities and under three different electricity tariff structures is conducted to (1) determine the added value of optimal control to a cogeneration system over current, heuristic control strategies; (2) determine the value of limited electric load curtailment opportunities, with and without cogeneration; and (3) determine the trade-off between least-cost and least-carbon operations of a cogeneration system. Key results for the P&DC sites studied include (1) in locations where the average electricity and natural gas prices suggest a marginally profitable cogeneration system, optimal control can add up to 67% to the value of the cogeneration system; optimal control adds less value in locations where cogeneration is more clearly profitable; (2) optimal control under real-time pricing is (a) more complicated than under typical time-of-use tariffs and (b) at times necessary to make cogeneration economic at all; (3) limited electric load curtailment opportunities can be more valuable as a compliment to the cogeneration system than alone; and

Development of Real-Time Dual-Display Handheld and Bench-Top Hybrid-Mode SD-OCTs

Directory of Open Access Journals (Sweden)

Nam Hyun Cho

2014-01-01

Full Text Available Development of a dual-display handheld optical coherence tomography (OCT system for retina and optic-nerve-head diagnosis beyond the volunteer motion constraints is reported. The developed system is portable and easily movable, containing the compact portable OCT system that includes the handheld probe and computer. Eye posterior chambers were diagnosed using the handheld probe, and the probe could be fixed to the bench-top cradle depending on the volunteers’ physical condition. The images obtained using this handheld probe were displayed in real time on the computer monitor and on a small secondary built-in monitor; the displayed images were saved using the handheld probe’s built-in button. Large-scale signal-processing procedures such as k-domain linearization, fast Fourier transform (FFT, and log-scaling signal processing can be rapidly applied using graphics-processing-unit (GPU accelerated processing rather than central-processing-unit (CPU processing. The Labview-based system resolution is 1,024 × 512 pixels, and the frame rate is 56 frames/s, useful for real-time display. The 3D images of the posterior chambers including the retina, optic-nerve head, blood vessels, and optic nerve were composed using real-time displayed images with 500 × 500 × 500 pixel resolution. A handheld and bench-top hybrid mode with a dual-display handheld OCT was developed to overcome the drawbacks of the conventional method.

Real-time PCR detection of Ochroconis lascauxensis involved in the formation of black stains in the Lascaux Cave, France.

Science.gov (United States)

Martin-Sanchez, Pedro M; Bastian, Fabiola; Alabouvette, Claude; Saiz-Jimenez, Cesareo

2013-01-15

A real-time Polymerase Chain Reaction (PCR) assay was developed to detect and quantify Ochroconis lascauxensis in the Lascaux Cave in France. This fungus is the principal causal agent of the black stains threatening the Paleolithic paintings of this UNESCO World Heritage Site. The black stains outbreak could not be stopped in spite of using intensive biocide treatments. A sensitive and time-saving protocol is needed for determining the extent of the colonization. Sets of primers that target the ITS and RPB2 regions were designed and evaluated for specificity against O. lascauxensis. Genomic DNA extracted from five species of Ochroconis and 13 other fungal species frequently isolated from caves were used to test the specificity of each primer set. The specific and sensitive real-time PCR assay using the primers 347F/493R targeting a 147-bp fragment from the RPB2 gene was useful for quantifying the presence of O. lascauxensis in the stains on the walls, sediments and air of the cavity. The results confirmed the association of this fungus with the black stains and its wide dissemination in all cave compartments. The suitability of this method for monitoring fungal outbreaks in cave environments is discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

Detection by real-time PCR and pyrosequencing of the cry1Ab and cry1Ac genes introduced in genetically modified (GM) constructs.

Science.gov (United States)

Debode, Frederic; Janssen, Eric; Bragard, Claude; Berben, Gilbert

2017-08-01

The presence of genetically modified organisms (GMOs) in food and feed is mainly detected by the use of targets focusing on promoters and terminators. As some genes are frequently used in genetically modified (GM) construction, they also constitute excellent screening elements and their use is increasing. In this paper we propose a new target for the detection of cry1Ab and cry1Ac genes by real-time polymerase chain reaction (PCR) and pyrosequencing. The specificity, sensitivity and robustness of the real-time PCR method were tested following the recommendations of international guidelines and the method met the expected performance criteria. This paper also shows how the robustness testing was assessed. This new cry1Ab/Ac method can provide a positive signal with a larger number of GM events than do the other existing methods using double dye-probes. The method permits the analysis of results with less ambiguity than the SYBRGreen method recommended by the European Reference Laboratory (EURL) GM Food and Feed (GMFF). A pyrosequencing method was also developed to gain additional information thanks to the sequence of the amplicon. This method of sequencing-by-synthesis can determine the sequence between the primers used for PCR. Pyrosequencing showed that the sequences internal to the primers present differences following the GM events considered and three different sequences were observed. The sensitivity of the pyrosequencing was tested on reference flours with a low percentage GM content and different copy numbers. Improvements in the pyrosequencing protocol provided correct sequences with 50 copies of the target. Below this copy number, the quality of the sequence was more random.

Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene.

Science.gov (United States)

Zuccaro, Laura; Tesauro, Cinzia; Kurkina, Tetiana; Fiorani, Paola; Yu, Hak Ki; Knudsen, Birgitta R; Kern, Klaus; Desideri, Alessandro; Balasubramanian, Kannan

2015-11-24

Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.

Real-time control of ion density and ion energy in chlorine inductively coupled plasma etch processing

International Nuclear Information System (INIS)

Chang, C.-H.; Leou, K.-C.; Lin Chaung; Lin, T.-L.; Tseng, C.-W.; Tsai, C.-H.

2003-01-01

In this study, we have experimentally demonstrated the real-time closed-loop control of both ion density and ion energy in a chlorine inductively coupled plasma etcher. To measure positive ion density, the trace rare gases-optical emission spectroscopy is used to measure the chlorine positive ion density. An rf voltage probe is adopted to measure the root-mean-square rf voltage on the electrostatic chuck which is linearly dependent on sheath voltage. One actuator is a 13.56 MHz rf generator to drive the inductive coil seated on a ceramic window. The second actuator is also a 13.56 MHz rf generator to power the electrostatic chuck. The closed-loop controller is designed to compensate for process drift, process disturbance, and pilot wafer effect and to minimize steady-state error of plasma parameters. This controller has been used to control the etch process of unpatterned polysilicon. The experimental results showed that the closed-loop control had a better repeatability of plasma parameters compared with open-loop control. The closed-loop control can eliminate the process disturbance resulting from reflected power. In addition, experimental results also demonstrated that closed-loop control has a better reproducibility in etch rate as compared with open-loop control

Real time monitoring of electron processors

International Nuclear Information System (INIS)

Nablo, S.V.; Kneeland, D.R.; McLaughlin, W.L.

1995-01-01

A real time radiation monitor (RTRM) has been developed for monitoring the dose rate (current density) of electron beam processors. The system provides continuous monitoring of processor output, electron beam uniformity, and an independent measure of operating voltage or electron energy. In view of the device's ability to replace labor-intensive dosimetry in verification of machine performance on a real-time basis, its application to providing archival performance data for in-line processing is discussed. (author)

Real time magnetic field and flux measurements for tokamak control using a multi-core PCI Express system

International Nuclear Information System (INIS)

Giannone, L.; Schneider, W.; McCarthy, P.J.; Sips, A.C.C.; Treutterer, W.; Behler, K.; Eich, T.; Fuchs, J.C.; Hicks, N.; Kallenbach, A.; Maraschek, M.; Mlynek, A.; Neu, G.; Pautasso, G.; Raupp, G.; Reich, M.; Schuhbeck, K.H.; Stober, J.; Volpe, F.; Zehetbauer, T.

2009-01-01

The existing real time system for the position and shape control in ASDEX Upgrade has been extended to calculate magnetic flux surfaces in real time using a multi-core PCI Express system running LabVIEW RT. The availability of reflective memory for LabVIEW RT will allow this system to be connected to the control system and other diagnostics in a multi-platform real time network. The measured response of each magnetic probe to the individual poloidal field coil currents in the absence of plasma current is compared to the calculated value. Prior to a tokamak discharge this comparison can be used to check for failure of the magnetic probe, flux loop or integrator.

Real-Time PCR in Clinical Microbiology: Applications for Routine Laboratory Testing

Science.gov (United States)

Espy, M. J.; Uhl, J. R.; Sloan, L. M.; Buckwalter, S. P.; Jones, M. F.; Vetter, E. A.; Yao, J. D. C.; Wengenack, N. L.; Rosenblatt, J. E.; Cockerill, F. R.; Smith, T. F.

2006-01-01

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory. PMID:16418529

Optimized Pan-species and speciation duplex real-time PCR assays for Plasmodium parasites detection in malaria vectors.

Directory of Open Access Journals (Sweden)

Maurice Marcel Sandeu

Full Text Available BACKGROUND: An accurate method for detecting malaria parasites in the mosquito's vector remains an essential component in the vector control. The Enzyme linked immunosorbent assay specific for circumsporozoite protein (ELISA-CSP is the gold standard method for the detection of malaria parasites in the vector even if it presents some limitations. Here, we optimized multiplex real-time PCR assays to accurately detect minor populations in mixed infection with multiple Plasmodium species in the African malaria vectors Anopheles gambiae and Anopheles funestus. METHODS: Complementary TaqMan-based real-time PCR assays that detect Plasmodium species using specific primers and probes were first evaluated on artificial mixtures of different targets inserted in plasmid constructs. The assays were further validated in comparison with the ELISA-CSP on 200 field caught Anopheles gambiae and Anopheles funestus mosquitoes collected in two localities in southern Benin. RESULTS: The validation of the duplex real-time PCR assays on the plasmid mixtures demonstrated robust specificity and sensitivity for detecting distinct targets. Using a panel of mosquito specimen, the real-time PCR showed a relatively high sensitivity (88.6% and specificity (98%, compared to ELISA-CSP as the referent standard. The agreement between both methods was "excellent" (κ=0.8, P<0.05. The relative quantification of Plasmodium DNA between the two Anopheles species analyzed showed no significant difference (P=0, 2. All infected mosquito samples contained Plasmodium falciparum DNA and mixed infections with P. malariae and/or P. ovale were observed in 18.6% and 13.6% of An. gambiae and An. funestus respectively. Plasmodium vivax was found in none of the mosquito samples analyzed. CONCLUSION: This study presents an optimized method for detecting the four Plasmodium species in the African malaria vectors. The study highlights substantial discordance with traditional ELISA-CSP pointing out the

Multiplex real-time PCR for detection, identification and quantification of 'Candidatus Liberibacter solanacearum' in potato plants with zebra chip.

Science.gov (United States)

Li, Wenbin; Abad, Jorge A; French-Monar, Ronald D; Rascoe, John; Wen, Aimin; Gudmestad, Neil C; Secor, Gary A; Lee, Ing-Ming; Duan, Yongping; Levy, Laurene

2009-07-01

The new Liberibacter species, 'Candidatus Liberibacter solanacearum' (Lso) recently associated with potato/tomato psyllid-transmitted diseases in tomato and capsicum in New Zealand, was found to be consistently associated with a newly emerging potato zebra chip (ZC) disease in Texas and other southwestern states in the USA. A species-specific primer LsoF was developed for both quantitative real-time PCR (qPCR) and conventional PCR (cPCR) to detect and quantify Lso in infected samples. In multiplex qPCR, a plant cytochrome oxidase (COX)-based probe-primer set was used as a positive internal control for host plants, which could be used to reliably access the DNA extraction quality and to normalize qPCR data for accurate quantification of the bacterial populations in environment samples. Neither the qPCR nor the cPCR using the primer and/or probe sets with LsoF reacted with other Liberibacter species infecting citrus or other potato pathogens. The low detection limit of the multiplex qPCR was about 20 copies of the target 16S rDNA templates per reaction for field samples. Lso was readily detected and quantified in various tissues of ZC-affected potato plants collected from fields in Texas. A thorough but uneven colonization of Lso was revealed in various tissues of potato plants. The highest Lso populations were about 3x10(8) genomes/g tissue in the root, which were 3-order higher than those in the above-ground tissues of potato plants. The Lso bacterial populations were normally distributed across the ZC-affected potato plants collected from fields in Texas, with 60% of ZC-affected potato plants harboring an average Lso population from 10(5) to 10(6) genomes/g tissue, 4% of plants hosting above 10(7) Lso genomes/g tissue, and 8% of plants holding below 10(3) Lso genomes/g tissue. The rapid, sensitive, specific and reliable multiplex qPCR showed its potential to become a powerful tool for early detection and quantification of the new Liberibacter species associated

Standardisation and evaluation of a quantitative multiplex real-time PCR assay for the rapid identification of Streptococcus pneumoniae

Directory of Open Access Journals (Sweden)

Feroze Ahmed Ganaie

2015-01-01

Full Text Available Rapid diagnosis of Streptococcus pneumoniae can play a significant role in decreasing morbidity and mortality of infection. The accurate diagnosis of pneumococcal disease is hampered by the difficulties in growing the isolates from clinical specimens and also by misidentification. Molecular methods have gained popularity as they offer improvement in the detection of causative pathogens with speed and ease. The present study aims at validating and standardising the use of 4 oligonucleotide primer-probe sets (pneumolysin [ply], autolysin [lytA], pneumococcal surface adhesion A [psaA] and Spn9802 [DNA fragment] in a single-reaction mixture for the detection and discrimination of S. pneumoniae. Here, we validate a quantitative multiplex real-time PCR (qmPCR assay with a panel consisting of 43 S. pneumoniae and 29 non-pneumococcal isolates, 20 culture positive, 26 culture negative and 30 spiked serum samples. A standard curve was obtained using S. pneumoniae ATCC 49619 strain and glyceraldehyde 3-phosphate dehydrogenase (GAPDH gene was used as an endogenous internal control. The experiment showed high sensitivity with lower limit of detection equivalent to 4 genome copies/µl. The efficiency of the reaction was 100% for ply, lytA, Spn9802 and 97% for psaA. The test showed sensitivity and specificity of 100% with culture isolates and serum specimens. This study demonstrates that qmPCR analysis of sera using 4 oligonucleotide primers appears to be an appropriate method for the genotypic identification of S. pneumoniae infection.

Performance Evaluation of a Synthetic Aperture Real-Time Ultrasound System

DEFF Research Database (Denmark)

Stuart, Matthias Bo; Tomov, Borislav Gueorguiev; Jensen, Jørgen Arendt

2011-01-01

This paper evaluates the signal-to-noise ratio, the time stability, and the phase difference of the sampling in the experimental ultrasound scanner SARUS: A synthetic aperture, real-time ultrasound system. SARUS has 1024 independent transmit and receive channels and is capable of handling 2D probes...... arrays (FPGAs) making it very flexible and allowing implementation of other real-time ultrasound processing methods in the future. For conventional B-mode imaging, a penetration depth around 7 cm for a 7 MHz transducer is obtained (signal-tonoise ratio of 0 dB), which is comparable to commercial...... for 3D ultrasound imaging. It samples at 12 bits per sample and has a sampling rate of 70 MHz with the possibility of decimating the sampling frequency at the input. SARUS is capable of advanced real-time computations such as synthetic aperture imaging. The system is built using fieldprogrammable gate...

Evaluation of the PrimerDesign™ genesig real-time reverse transcription-polymerase chain reaction assay and the INFINITI® Respiratory Viral Panel Plus assay for the detection of human metapneumovirus in Kuwait.

Science.gov (United States)

Al-Turab, Mariam; Chehadeh, Wassim; Al-Mulla, Fahd; Al-Nakib, Widad

2012-04-01

Human metapneumovirus (hMPV) is a respiratory pathogen that was discovered in 2001 and is considered a major cause of both upper and lower respiratory tract infections. A sensitive, fast, and high-throughput diagnostic test is needed for the detection of hMPV that may assist in the clinical management as well as in the reduction of inappropriate therapy. Therefore, a comparison assessment was performed in this study between the PrimerDesign™ genesig real-time reverse transcription-polymerase chain reaction (RT-PCR) Assay and the INFINITI(®) Respiratory Viral Panel Plus Assay (RVP-Plus) for the detection of hMPV infection in patients with respiratory tract infections. A total of 200 respiratory samples were collected from 185 hospitalized patients, during the winter season in Kuwait. Of 185 patients, 10 (5.4%) were positive for hMPV RNA by the in-house RT-PCR assay, while 7 (4%) were positive for hMPV RNA by the real-time RT-PCR assay and 9 (5%) were positive for hMPV RNA by the INFINITI(®) RVP-Plus assay. The high incidence rate (60%) of hMPV infection was in January 2011. The sensitivity of the real-time RT-PCR and INFINITI(®) RVP-Plus assays was 70% and 90%, respectively, with specificity of 100% for both assays. hMPV types A and B could be identified in this study; however, discordant genotyping results were found between the direct sequencing method and the INFINITI(®) RVP-Plus assay in 33% of hMPV-positive patients. Copyright © 2012 Elsevier Inc. All rights reserved.

Detection of the clostridial hydrogenase gene activity as a bio-index in a molasses wastewater bio-hydrogen producing system by real time PCR and FISH/ flow cytometry

International Nuclear Information System (INIS)

Jui-Jen Chang; Ping-Chi Hsu; Chi-Wa Choi; Sian-Jhong Yu; Cheng-Yu Ho; Wei-En Chen; Jiunn-Jyi Lay; Chieh-Chen Huang; Fu-Shyan Wen

2006-01-01

Hydrogenase is a key enzyme that is used by obligate, anaerobic clostridial to produce hydrogen. In this study a fermentative system with molasses wastewater as nutrient was used to produce hydrogen. For establishing the relationship between the vicissitude of clostridial hydrogenase gene activity and the hydrogen production of this system during the culturing period, total cellular RNA isolated at different growing stages were subjected to real time PCR using primer pair, which were designed according to the conserved sequence of clostridial hydrogenase genes. Cell samples at corresponding growing stages were subjected to in situ reverse transcriptase polymerase chain reaction (in situ RT-PCR) using the same primers and then to fluorescence in situ hybridization (FISH) using clostridial hydrogenase gene-specific DNA probe. Those clostridial cells expressed hydrogenase gene activity could be detected by fluorescence microscopy. This is the first time hydrogen-producing activity in a mixed culture could be successfully studied by means of FISH of hydrogenase mRNA. Besides, 16S rDNA was amplified from total cellular DNA analyzed by denaturing gradient gel electrophoresis (DGGE) to reveal the bacterial diversity in the fermentative system; FISH and flow cytometry aiming at 16S rRNA were also carried out to calculate the population of clostridia and total eubacteria in the system. (authors)

Development and evaluation of a real-time one step Reverse-Transcriptase PCR for quantitation of Chandipura Virus

Directory of Open Access Journals (Sweden)

Tandale Babasaheb V

2008-12-01

Full Text Available Abstract Background Chandipura virus (CHPV, a member of family Rhabdoviridae was attributed to an explosive outbreak of acute encephalitis in children in Andhra Pradesh, India in 2003 and a small outbreak among tribal children from Gujarat, Western India in 2004. The case-fatality rate ranged from 55–75%. Considering the rapid progression of the disease and high mortality, a highly sensitive method for quantifying CHPV RNA by real-time one step reverse transcriptase PCR (real-time one step RT-PCR using TaqMan technology was developed for rapid diagnosis. Methods Primers and probe for P gene were designed and used to standardize real-time one step RT-PCR assay for CHPV RNA quantitation. Standard RNA was prepared by PCR amplification, TA cloning and run off transcription. The optimized real-time one step RT-PCR assay was compared with the diagnostic nested RT-PCR and different virus isolation systems [in vivo (mice in ovo (eggs, in vitro (Vero E6, PS, RD and Sand fly cell line] for the detection of CHPV. Sensitivity and specificity of real-time one step RT-PCR assay was evaluated with diagnostic nested RT-PCR, which is considered as a gold standard. Results Real-time one step RT-PCR was optimized using in vitro transcribed (IVT RNA. Standard curve showed linear relationship for wide range of 102-1010 (r2 = 0.99 with maximum Coefficient of variation (CV = 5.91% for IVT RNA. The newly developed real-time RT-PCR was at par with nested RT-PCR in sensitivity and superior to cell lines and other living systems (embryonated eggs and infant mice used for the isolation of the virus. Detection limit of real-time one step RT-PCR and nested RT-PCR was found to be 1.2 × 100 PFU/ml. RD cells, sand fly cells, infant mice, and embryonated eggs showed almost equal sensitivity (1.2 × 102 PFU/ml. Vero and PS cell-lines (1.2 × 103 PFU/ml were least sensitive to CHPV infection. Specificity of the assay was found to be 100% when RNA from other viruses or healthy

Reflection-mode micro-spherical fiber-optic probes for in vitro real-time and single-cell level pH sensing.

Science.gov (United States)

Yang, Qingbo; Wang, Hanzheng; Lan, Xinwei; Cheng, Baokai; Chen, Sisi; Shi, Honglan; Xiao, Hai; Ma, Yinfa

2015-02-01

pH sensing at the single-cell level without negatively affecting living cells is very important but still a remaining issue in the biomedical studies. A 70 μm reflection-mode fiber-optic micro-pH sensor was designed and fabricated by dip-coating thin layer of organically modified aerogel onto a tapered spherical probe head. A pH sensitive fluorescent dye 2', 7'-Bis (2-carbonylethyl)-5(6)-carboxyfluorescein (BCECF) was employed and covalently bonded within the aerogel networks. By tuning the alkoxide mixing ratio and adjusting hexamethyldisilazane (HMDS) priming procedure, the sensor can be optimized to have high stability and pH sensing ability. The in vitro real-time sensing capability was then demonstrated in a simple spectroscopic way, and showed linear measurement responses with a pH resolution up to an average of 0.049 pH unit within a narrow, but biological meaningful pH range of 6.12-7.81. Its novel characterizations of high spatial resolution, reflection mode operation, fast response and high stability, great linear response within biological meaningful pH range and high pH resolutions, make this novel pH probe a very cost-effective tool for chemical/biological sensing, especially within the single cell level research field.

Performance of the Abbott RealTime CT/NG for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae▿

Science.gov (United States)

Gaydos, C. A.; Cartwright, C. P.; Colaninno, P.; Welsch, J.; Holden, J.; Ho, S. Y.; Webb, E. M.; Anderson, C.; Bertuzis, R.; Zhang, L.; Miller, T.; Leckie, G.; Abravaya, K.; Robinson, J.

2010-01-01

A multicenter clinical study was conducted to evaluate the performance characteristics of the Abbott RealTime CT/NG assay, a multiplex real-time PCR assay, for simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae. The specimens were collected from a total of 3,832 male and female subjects at 16 geographically diverse sites. Specimens included male and female urine samples, male urethral swabs, female endocervical swabs, and self-collected and clinician-collected vaginal swabs. Specimens were tested with the automated Abbott RealTime CT/NG assay, Aptima Combo 2 assay (Gen-Probe), ProbeTec ET CT/GC assay (Becton Dickinson), and culture for N. gonorrhoeae. The Aptima Combo 2 assay, the ProbeTec assay, and the N. gonorrhoeae culture were used as the reference assays. For each subject, a patient infected status (PIS) was determined based on the combined results from the reference assays. The overall prevalence in female subjects was 8.9% for C. trachomatis and 3.8% for N. gonorrhoeae. The overall male prevalence was 18.2% for C. trachomatis and 16.7% for N. gonorrhoeae. The overall sensitivity and specificity of the Abbott RealTime CT/NG assay were 92.4% and 99.2% for C. trachomatis and 96.9% and 99.7% for N. gonorrhoeae, respectively. In comparison, the sensitivity and specificity, respectively, for the Aptima Combo 2 assay were 94.5% and 99.0% for C. trachomatis and 96.1% and 99.5% for N. gonorrhoeae, and those for the ProbeTec ET assay were 90.3% and 99.5% for C. trachomatis and 92.0% and 97.3% for N. gonorrhoeae in this study. The Abbott RealTime CT/NG assay offers C. trachomatis and N. gonorrhoeae dual detection with high sensitivity and specificity. The automated assay provides a useful alternative nucleic acid amplification assay for clinical laboratories and clinicians. PMID:20668135

Performance of the Abbott RealTime CT/NG for detection of Chlamydia trachomatis and Neisseria gonorrhoeae.

Science.gov (United States)

Gaydos, C A; Cartwright, C P; Colaninno, P; Welsch, J; Holden, J; Ho, S Y; Webb, E M; Anderson, C; Bertuzis, R; Zhang, L; Miller, T; Leckie, G; Abravaya, K; Robinson, J

2010-09-01

A multicenter clinical study was conducted to evaluate the performance characteristics of the Abbott RealTime CT/NG assay, a multiplex real-time PCR assay, for simultaneous detection of Chlamydia trachomatis and Neisseria gonorrhoeae. The specimens were collected from a total of 3,832 male and female subjects at 16 geographically diverse sites. Specimens included male and female urine samples, male urethral swabs, female endocervical swabs, and self-collected and clinician-collected vaginal swabs. Specimens were tested with the automated Abbott RealTime CT/NG assay, Aptima Combo 2 assay (Gen-Probe), ProbeTec ET CT/GC assay (Becton Dickinson), and culture for N. gonorrhoeae. The Aptima Combo 2 assay, the ProbeTec assay, and the N. gonorrhoeae culture were used as the reference assays. For each subject, a patient infected status (PIS) was determined based on the combined results from the reference assays. The overall prevalence in female subjects was 8.9% for C. trachomatis and 3.8% for N. gonorrhoeae. The overall male prevalence was 18.2% for C. trachomatis and 16.7% for N. gonorrhoeae. The overall sensitivity and specificity of the Abbott RealTime CT/NG assay were 92.4% and 99.2% for C. trachomatis and 96.9% and 99.7% for N. gonorrhoeae, respectively. In comparison, the sensitivity and specificity, respectively, for the Aptima Combo 2 assay were 94.5% and 99.0% for C. trachomatis and 96.1% and 99.5% for N. gonorrhoeae, and those for the ProbeTec ET assay were 90.3% and 99.5% for C. trachomatis and 92.0% and 97.3% for N. gonorrhoeae in this study. The Abbott RealTime CT/NG assay offers C. trachomatis and N. gonorrhoeae dual detection with high sensitivity and specificity. The automated assay provides a useful alternative nucleic acid amplification assay for clinical laboratories and clinicians.

Real-time ultrafast dynamics of dense, hot matter measured by pump-probe Doppler spectrometry

Energy Technology Data Exchange (ETDEWEB)

Lad, Amit D; Mondal, S; Narayanan, V; Ahmed, Saima; Kumar, G Ravindra; Rajeev, P P; Robinson, A P L [Central Laser Facility, Rutherford-Appleton Laboratory, Chilton, Oxfordshire (United Kingdom); Pasley, J, E-mail: amitlad@tifr.res.i [Department of Physics, University of York, Heslington, York (United Kingdom)

2010-08-01

A detailed understanding of the critical surface motion of high intensity laser produced plasma is very crucial for understanding the interaction. We employ the two colour pump-probe technique to report the first ever femtosecond scale ultrafast dynamics measurement of the critical surface of a solid plasma produced by a relativistically intense, femtosecond pump laser beam (10{sup 18} W/cm{sup 2}, 30 fs, 800 nm) on an aluminium target. We observe the Doppler shift of a time delayed probe laser beam (10{sup 12} W/cm{sup 2}, 80 fs, 400 nm) up to delays of 30 ps. Such unravelling of dynamics has not been possible in earlier measurements, which typically used the self reflection of a powerful pump pulse. We observe time dependent red and blue shifts and measure their magnitudes to infer plasma expansion velocity and acceleration and thereby the plasma profile. Our results are very well reproduced by 1D hydrodynamic simulation (HYADES code).

Real-time UNIX in HEP data acquisition

International Nuclear Information System (INIS)

Buono, S.; Gaponenko, I.; Jones, R.; Mapelli, L.; Mornacchi, G.; Prigent, D.; Sanchez-Corral, E.; Skiadelli, M.; Toppers, A.; Duval, P.Y.; Ferrato, D.; Le Van Suu, A.; Qian, Z.; Rondot, C.; Ambrosini, G.; Fumagalli, G.; Aguer, M.; Huet, M.

1994-01-01

Today's experimentation in high energy physics is characterized by an increasing need for sensitivity to rare phenomena and complex physics signatures, which require the use of huge and sophisticated detectors and consequently a high performance readout and data acquisition. Multi-level triggering, hierarchical data collection and an always increasing amount of processing power, distributed throughout the data acquisition layers, will impose a number of features on the software environment, especially the need for a high level of standardization. Real-time UNIX seems, today, the best solution for the platform independence, operating system interface standards and real-time features necessary for data acquisition in HEP experiments. We present the results of the evaluation, in a realistic application environment, of a Real-Time UNIX operating system: the EP/LX real-time UNIX system. ((orig.))

Radiation environmental real-time monitoring and dispersion modelling

International Nuclear Information System (INIS)

Kovacik, Andrej; Bartokova, Ivana; Melicherova, Terezia; Omelka, Jozef

2015-01-01

The MicroStep-MIS system of real-time radiation monitoring, which provides a turn-key solution for measurement, acquisition, processing, reporting, archiving and displaying of various radiation data, is described and discussed in detail. The qualities, long-term stability of measurement and sensitivity of the RPSG-05 probe are illustrated on its use within the radiation monitoring network of the Slovak Hydrometeorological Institute and within the monitoring network in the United Arab Emirates. (orig.)

Real-time monitoring energy efficiency and performance degradation of condensing boilers

International Nuclear Information System (INIS)

Baldi, Simone; Quang, Thuan Le; Holub, Ondrej; Endel, Petr

2017-01-01

Highlights: • Fully-fledged set of fault detection and diagnosis tools for condensing boilers. • Detection of boiler performance degradation in condensing and noncondensing mode. • Virtual sensing for estimation of water mass flow rate. • Optimal Kalman detection of actuator and sensor faults. • Structural properties for detection and isolation of faults. - Abstract: Condensing boilers achieve higher efficiency than traditional boilers by using waste heat in flue gases to preheat cold return water entering the boiler. Water vapor produced during combustion is condensed into liquid form, thus recovering its latent heat of vaporization, leading to around 10–12% increased efficiency. Many countries have encouraged the use of condensing boilers with financial incentives. It is thus important to develop software tools to assess the correct functioning of the boiler and eventually detect problems. Current monitoring tools are based on boiler static maps and on large sets of historical data, and are unable to assess timely loss of performance due to degradation of the efficiency curve or water leakages. This work develops a set of fault detection and diagnosis tools for dynamic energy efficiency monitoring and assessment in condensing boilers, i.e. performance degradation and faults can be detected using real-time measurements: this real-time feature is particularly relevant because of the limited amount of data that can be stored by state-of-the-art building energy management systems. The monitoring tools are organized as follows: a bimodal parameter estimator to detect deviations of the efficiency of the boiler from nominal values in both condensing and noncondensing mode; a virtual sensor for the estimation of the water mass flow rate; filters to detect actuator and sensor faults, possibly due to control and sensing problems. Most importantly, structural properties for detection and isolation of actuators and sensing faults are given: these properties are

Robotic 4D ultrasound solution for real-time visualization and teleoperation

Directory of Open Access Journals (Sweden)

Al-Badri Mohammed

2017-09-01

Full Text Available Automation of the image acquisition process via robotic solutions offer a large leap towards resolving ultrasound’s user-dependency. This paper, as part of a larger project aimed to develop a multipurpose 4d-ultrasonic force-sensitive robot for medical applications, focuses on achieving real-time remote visualisation for 4d ultrasound image transfer. This was possible through implementing our software modification on a GE Vivid 7 Dimension workstation, which operates a matrix array probe controlled by a KUKA LBR iiwa 7 7-DOF robotic arm. With the help of robotic positioning and the matrix array probe, fast volumetric imaging of target regions was feasible. By testing ultrasound volumes, which were roughly 880 kB in size, while using gigabit Ethernet connection, a latency of ∼57 ms was achievable for volume transfer between the ultrasound station and a remote client application, which as a result allows a frame count of 17.4 fps. Our modification thus offers for the first time real-time remote visualization, recording and control of 4d ultrasound data, which can be implemented in teleoperation.

Time-resolved measurements with intense ultrashort laser pulses: a 'molecular movie' in real time

International Nuclear Information System (INIS)

Rudenko, A; Ergler, Th; Feuerstein, B; Zrost, K; Schroeter, C D; Moshammer, R; Ullrich, J

2007-01-01

We report on the high-resolution multidimensional real-time mapping of H 2 + and D 2 + nuclear wave packets performed employing time-resolved three-dimensional Coulomb explosion imaging with intense laser pulses. Exploiting a combination of a 'reaction microscope' spectrometer and a pump-probe setup with two intense 6-7 fs laser pulses, we simultaneously visualize both vibrational and rotational motion of the molecule, and obtain a sequence of snapshots of the squared ro-vibrational wave function with time-step resolution of ∼ 0.3 fs, allowing us to reconstruct a real-time movie of the ultrafast molecular motion. We observe fast dephasing, or 'collapse' of the vibrational wave packet and its subsequent revival, as well as signatures of rotational excitation. For D 2 + we resolve also the fractional revivals resulting from the interference between the counter-propagating parts of the wave packet

Real Time Revisited

Science.gov (United States)

Allen, Phillip G.

1985-12-01

The call for abolishing photo reconnaissance in favor of real time is once more being heard. Ten years ago the same cries were being heard with the introduction of the Charge Coupled Device (CCD). The real time system problems that existed then and stopped real time proliferation have not been solved. The lack of an organized program by either DoD or industry has hampered any efforts to solve the problems, and as such, very little has happened in real time in the last ten years. Real time is not a replacement for photo, just as photo is not a replacement for infra-red or radar. Operational real time sensors can be designed only after their role has been defined and improvements made to the weak links in the system. Plodding ahead on a real time reconnaissance suite without benefit of evaluation of utility will allow this same paper to be used ten years from now.

Kinetics of the main phase transition of hydrated lecithin monitored by real-time x-ray diffraction

International Nuclear Information System (INIS)

Caffrey, M.; Bilderback, D.H.

1984-01-01

A method is described for observing and recording in real-time x-ray diffraction from an unoriented hydrated membrane lipid, dipalmitoylphosphatidylcholine (DPPC), through its thermotropic gel/liquid crystal phase transition. Synchrotron radiation from the Cornell High Energy Synchrotron Source (Ithaca, New York) was used as an x-ray source of extremely high brilliance and the dynamic display of the diffraction image was effected using a three-stage image intensifier tube coupled to an external fluorescent screen. The image on the output phosphor was sufficiently intense to be recorded cinematographically and to be displayed on a television monitor using a vidicon camera at 30 frames x s -1 . These measurements set an upper limit of 2 s on the DPPC gel → liquid crystal phase transition and indicate that the transition is a two-state process. The real-time method couples the power of x-ray diffraction as a structural probe with the ability to follow kinetics of structural changes. The method does not require an exogenous probe, is relatively nonperturbing, and can be used with membranes in a variety of physical states and with unstable samples. The method has the additional advantage over its static measurement counterpart in that it is more likely to detect transiently stable intermediates if present

A Method for Measuring Fast Time Evolutions of the Plasma Potential by Means of a Simple Emissive Probe

DEFF Research Database (Denmark)

Iizuka, S.; Michelsen, Poul; Juul Rasmussen, Jens

1981-01-01

potential is measured across a high resistance. During each sweep of the probe voltage, the changing of the sign of the probe current, which is sampled at a specific time, gives rise to a negative pulse, driving the pen-lift of an X-Y recorder. Since the real floating potential is measured where the probe......A method is presented for obtaining the temporal evolution of the plasma potential, which is assumed to be given by the floating potential of a simple emissive probe. The construction of the probe is also described. The method avoids the slow time response of the usual technique where the floating...

Advantages of Real-Time Spectrum Analyzers in High-Energy Physics Applications

International Nuclear Information System (INIS)

Parker, Louis

2004-01-01

Typically, particles are injected into the ring at low energy levels and then 'ramped up' to higher levels. During ramping, it is important that the horizontal and vertical tune frequencies do not shift, lest they hit upon a resonant combination that causes beam instability or sudden total loss of ring beam current (beam blow up). Beam instabilities can be caused by a number of factors. Non-linearities and/or different response times of independent controls such as beam position monitor (BPM) cables and circuits, magnets for guidance and focusing of the beam, Klystrons or Tetrodes (which provide power to RF cavities that transmit energy to the beam), and vacuum pumps and monitors can all cause beam instabilities. Vibrations and lack of proper shielding are other factors. The challenge for operators and researchers is to correctly identify the factors causing beam instabilities and blow up so that costly accelerator time is not interrupted and experimental results are not compromised. The instrument often used to identify problems in particle accelerator applications is the spectrum analyzer. This paper will discuss the advantages of real time spectrum analyzers (RSA) versus swept frequency spectrum analyzers in HEP applications. The main focus will be on monitoring beam position and stability, especially during ramp-up. Also covered will be use of RSA for chromaticity measurements, Phase Locked Loop (PLL) diagnostics, and vibration analysis

Detection of polyoma virus in brain tissue of patients with progressive multifocal leukoencephalopathy by real-time PCR and pyrosequencing.

Science.gov (United States)

Beck, Rose C; Kohn, Debra J; Tuohy, Marion J; Prayson, Richard A; Yen-Lieberman, Belinda; Procop, Gary W

2004-03-01

We evaluated 2 methods, a LightCycler PCR assay and pyrosequencing for the detection of the JC polyoma virus (JCV) in fixed brain tissue of 10 patients with and 3 control patients without progressive multifocal leukoencephalopathy (PML). Nucleic acid extraction was performed after deparaffinization and proteinase K digestion. The LightCycler assay differentiates the BK virus (BKV), JCV, and SV40 using melt curve analysis. Conventional PCR was used with the same primers to generate products for pyrosequencing. Two sequencing primers were used that differentiate the polyoma viruses. Seven of 11 biopsies (1 patient had 2 biopsies) with PML were positive for JCV by real-time PCR and/or PCR/pyrosequencing. Three of 4 remaining biopsies were positive by real-time PCR but had melting points between JCV and SV40. The 4 specimens that were negative or atypical by LightCycler PCR were positive by traditional PCR, but 1 had an amplicon of lower molecular weight by gel electrophoresis. These were shown to represent JCV by at least 1 of the 2 pyrosequencing primers. The biopsies from patients without PML were PCR negative. Both the LightCycler and pyrosequencing assays are useful for confirming JCV in brain biopsies from patients with PML, but variant JCVs may require supplementary methods to confirm JCV infection.

Towards a real-time Energy Management System for a Microgrid using a multi-objective genetic algorithm

DEFF Research Database (Denmark)

Vergara, Pedro P.; Torquato, Ricardo; Da Silva, Luiz C.P.

2015-01-01

This paper proposes a real-time Energy Management System (EMS) for a low voltage (LV) Microgrid (MG). The system operation consists in solving the Unit Commitment (UC) and Economic Load Dispatch (ELD) simultaneously for 24 hours ahead at every 15-minute period. This operation is formulated...

Competitive Reporter Monitored Amplification (CMA) - Quantification of Molecular Targets by Real Time Monitoring of Competitive Reporter Hybridization

Science.gov (United States)

Ullrich, Thomas; Ermantraut, Eugen; Schulz, Torsten; Steinmetzer, Katrin

2012-01-01

Background State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. Methodology and Principal Findings The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. Conclusions and Significance The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2), we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls and targets into a

Competitive reporter monitored amplification (CMA--quantification of molecular targets by real time monitoring of competitive reporter hybridization.

Directory of Open Access Journals (Sweden)

Thomas Ullrich

Full Text Available BACKGROUND: State of the art molecular diagnostic tests are based on the sensitive detection and quantification of nucleic acids. However, currently established diagnostic tests are characterized by elaborate and expensive technical solutions hindering the development of simple, affordable and compact point-of-care molecular tests. METHODOLOGY AND PRINCIPAL FINDINGS: The described competitive reporter monitored amplification allows the simultaneous amplification and quantification of multiple nucleic acid targets by polymerase chain reaction. Target quantification is accomplished by real-time detection of amplified nucleic acids utilizing a capture probe array and specific reporter probes. The reporter probes are fluorescently labeled oligonucleotides that are complementary to the respective capture probes on the array and to the respective sites of the target nucleic acids in solution. Capture probes and amplified target compete for reporter probes. Increasing amplicon concentration leads to decreased fluorescence signal at the respective capture probe position on the array which is measured after each cycle of amplification. In order to observe reporter probe hybridization in real-time without any additional washing steps, we have developed a mechanical fluorescence background displacement technique. CONCLUSIONS AND SIGNIFICANCE: The system presented in this paper enables simultaneous detection and quantification of multiple targets. Moreover, the presented fluorescence background displacement technique provides a generic solution for real time monitoring of binding events of fluorescently labelled ligands to surface immobilized probes. With the model assay for the detection of human immunodeficiency virus type 1 and 2 (HIV 1/2, we have been able to observe the amplification kinetics of five targets simultaneously and accommodate two additional hybridization controls with a simple instrument set-up. The ability to accommodate multiple controls

Real-time energy resources scheduling considering short-term and very short-term wind forecast

Energy Technology Data Exchange (ETDEWEB)

Silva, Marco; Sousa, Tiago; Morais, Hugo; Vale, Zita [Polytechnic of Porto (Portugal). GECAD - Knowledge Engineering and Decision Support Research Center

2012-07-01

This paper proposes an energy resources management methodology based on three distinct time horizons: day-ahead scheduling, hour-ahead scheduling, and real-time scheduling. In each scheduling process the update of generation and consumption operation and of the storage and electric vehicles storage status are used. Besides the new operation conditions, the most accurate forecast values of wind generation and of consumption using results of short-term and very short-term methods are used. A case study considering a distribution network with intensive use of distributed generation and electric vehicles is presented. (orig.)

Optimal Energy Management for the Integrated Power and Gas Systems via Real-time Pricing

DEFF Research Database (Denmark)

Shu, KangAn; Ai, Xiaomeng; Wen, Jinyu

2018-01-01

This work proposed a bi-level formulation for energy management in the integrated power and natural gas system via real-time price signals. The upper-level problem minimizes the operational cost, in which dynamic electricity price and dynamic gas tariff are proposed. The lower level problem...... and P2Gs plants follow the system operator’s preferences such as wind power accommodation, mitigation of unsupplied load and relieving the network congestion....

Main real time software for high-energy physics experiments

International Nuclear Information System (INIS)

Tikhonov, A.N.

1985-01-01

The general problems of organization of software complexes, as well as development of typical algorithms and packages of applied programs for real time systems used in experiments with charged particle accelerators are discussed. It is noted that numerous qualitatively different real time tasks are solved by parallel programming of the processes of data acquisition, equipment control, data exchange with remote terminals, data express processing and accumulation, operator's instruction interpretation, generation and buffering of resulting files for data output and information processing which is realized on the basis of multicomputer system utilization. Further development of software for experiments is associated with improving the algorithms for automatic recognition and analysis of events with complex topology and standardization of applied program packages

Real-time energy monitoring system : Web-Keruu; Energian tosiaikainen seurantapalvelu : Web-Keruu

Energy Technology Data Exchange (ETDEWEB)

Serkkola, A. (Aalto University, Espoo (Finland)); Nyman, J.; Fraemling, K.; Kaustell, A.

2011-07-01

Climate action and reducing greenhouse gases have become a top topics in EU and all over the world. But how can an individual consumer reduce his or her energy consumption, if he does not even know how much energy he or she is consuming and when? Or how can he know if an electrical device is not working properly and needs to be fixed to avoid extra electricity bills or other harms? One solution is to make the invisible energy consumption visible, by visualizing the consumption on the web. In the Housing Eco-Monitoring Service (Asemo) project funded by the EU's Regional Development fund, Southern Finland program, the STOK electrical building services center, Posintra Oy in Porvoo (Finland) and the Aalto University School of Engineering Lahti Center (Finland) are developing an energy monitoring system that visualizes the actual energy consumption of a house or a flat in real time. A resident may instantly 'see' his or her energy consumption as a constantly updating graph on a web page. The graph makes it easy to understand the effect of various energy savings measures. One instantly gets feedback on how energy consumption is affected by switching on and off electrical devices, for instance a television set. The users of the system can also write blog-type comments, and share them with other users. The system itself is flexible and cheap. It is a stand-alone, plug-and-play type of solution, based on off-the-shelf consumer hardware supplemented by software created in the project. The system reads data from an electricity meter, channels it through the Internet using the residence's broadband connection, and stores the data in a database. This energy monitoring system will be used to monitor energy usage in Finland in Porvoo's new Skaftkaerr housing area, where this system will be set-up in residences, or LivingLabs. Currently we are in the initial testing phase with half a dozen LivingLabs. The residences are inhabited by real families, so that

Short-Term Wave Forecasting with AR models in Real-Time Optimal Control of Wave Energy Converters

OpenAIRE

Fusco, Francesco; Ringwood, John

2010-01-01

Time domain control of wave energy converters requires knowledge of future incident wave elevation in order to approach conditions for optimal energy extraction. Autoregressive models revealed to be a promising approach to the prediction of future values of the wave elevation only from its past history. Results on real wave observations from different ocean locations show that AR models allow to achieve very good predictions for more than one wave period in the future if ...

Time- and energy resolved photoemission electron microscopy-imaging of photoelectron time-of-flight analysis by means of pulsed excitations

International Nuclear Information System (INIS)

Oelsner, Andreas; Rohmer, Martin; Schneider, Christian; Bayer, Daniela; Schoenhense, Gerd; Aeschlimann, Martin

2010-01-01

The present work enlightens the developments in time- and energy resolved photoemission electron microscopy over the past few years. We describe basic principles of the technique and demonstrate different applications. An energy- and time-filtering photoemission electron microscopy (PEEM) for real-time spectroscopic imaging can be realized either by a retarding field or hemispherical energy analyzer or by using time-of-flight optics with a delay line detector. The latter method has the advantage of no data loss at all as all randomly incoming particles are measured not only by position but also by time. This is of particular interest for pump-probe experiments in the femtosecond and attosecond time scale where space charge processes drastically limit the maximum number of photoemitted electrons per laser pulse. This work focuses particularly on time-of-flight analysis using a novel delay line detector. Time and energy resolved PEEM instruments with delay line detectors enable 4D imaging (x, y, Δt, E Kin ) on a true counting basis. This allows a broad range of applications from real-time observation of dynamic phenomena at surfaces to fs time-of-flight spectro-microscopy and even aberration correction. By now, these time-of-flight analysis instruments achieve intrinsic time resolutions of 108 ps absolute and 13.5 ps relative. Very high permanent measurement speeds of more than 4 million events per second in random detection regimes have been realized using a standard USB2.0 interface. By means of this performance, the time-resolved PEEM technique enables to display evolutions of spatially resolved (<25 nm) and temporal sliced images life on any modern computer. The method allows dynamics investigations of variable electrical, magnetic, and optical near fields at surfaces and great prospects in dynamical adaptive photoelectron optics. For dynamical processes in the ps time scale such as magnetic domain wall movements, the time resolution of the delay line detectors

Incorporating travel-time reliability into the congestion management process : a primer.

Science.gov (United States)

2015-02-01

This primer explains the value of incorporating travel-time reliability into the Congestion Management Process (CMP) : and identifies the most current tools available to assist with this effort. It draws from applied research and best practices : fro...

Molecular Properties of Poliovirus Isolates: Nucleotide Sequence Analysis, Typing by PCR and Real-Time RT-PCR.

Science.gov (United States)

Burns, Cara C; Kilpatrick, David R; Iber, Jane C; Chen, Qi; Kew, Olen M

2016-01-01

Virologic surveillance is essential to the success of the World Health Organization initiative to eradicate poliomyelitis. Molecular methods have been used to detect polioviruses in tissue culture isolates derived from stool samples obtained through surveillance for acute flaccid paralysis. This chapter describes the use of realtime PCR assays to identify and serotype polioviruses. In particular, a degenerate, inosine-containing, panpoliovirus (panPV) PCR primer set is used to distinguish polioviruses from NPEVs. The high degree of nucleotide sequence diversity among polioviruses presents a challenge to the systematic design of nucleic acid-based reagents. To accommodate the wide variability and rapid evolution of poliovirus genomes, degenerate codon positions on the template were matched to mixed-base or deoxyinosine residues on both the primers and the TaqMan™ probes. Additional assays distinguish between Sabin vaccine strains and non-Sabin strains. This chapter also describes the use of generic poliovirus specific primers, along with degenerate and inosine-containing primers, for routine VP1 sequencing of poliovirus isolates. These primers, along with nondegenerate serotype-specific Sabin primers, can also be used to sequence individual polioviruses in mixtures.

Frequency Based Real-time Pricing for Residential Prosumers

Science.gov (United States)

Hambridge, Sarah Mabel

This work is the first to explore frequency based pricing for secondary frequency control as a price-reactive control mechanism for residential prosumers. A frequency based real-time electricity rate is designed as an autonomous market control mechanism for residential prosumers to provide frequency support as an ancillary service. In addition, prosumers are empowered to participate in dynamic energy transactions, therefore integrating Distributed Energy Resources (DERs), and increasing distributed energy storage onto the distributed grid. As the grid transitions towards DERs, a new market based control system will take the place of the legacy distributed system and possibly the legacy bulk power system. DERs provide many benefits such as energy independence, clean generation, efficiency, and reliability to prosumers during blackouts. However, the variable nature of renewable energy and current lack of installed energy storage on the grid will create imbalances in supply and demand as uptake increases, affecting the grid frequency and system operation. Through a frequency-based electricity rate, prosumers will be encouraged to purchase energy storage systems (ESS) to offset their neighbor's distributed generation (DG) such as solar. Chapter 1 explains the deregulation of the power system and move towards Distributed System Operators (DSOs), as prosumers become owners of microgrids and energy cells connected to the distributed system. Dynamic pricing has been proposed as a benefit to prosumers, giving them the ability to make decisions in the energy market, while also providing a way to influence and control their behavior. Frequency based real-time pricing is a type of dynamic pricing which falls between price-reactive control and transactive control. Prosumer-to-prosumer transactions may take the place of prosumer-to-utility transactions, building The Energy Internet. Frequency based pricing could be a mechanism for determining prosumer prices and supporting

Real-Time Framework for Energy Management System of a Smart Microgrid Using Multiagent Systems

Directory of Open Access Journals (Sweden)

Roberto S. Netto

2018-03-01

Full Text Available This paper presents a framework to analyze the problem of real-time management of Smart Grids. For this purpose, the energy management is integrated with the power system through a telecommunication system. The use of Multiagent Systems (MAS leads the proposed algorithm to find the best-integrated solution, taking into consideration the operating scenario and the system characteristics. With this framework it was possible to evaluate the design of the energy management and the impact of the algorithm developed in the MAS. In the same way, the data sent from the power system to be used for energy management have a direct impact on his behavior. The proposed framework is tested with the help of a microgrid, so the results may be replicated.

Merit-order effects of renewable energy and price divergence in California’s day-ahead and real-time electricity markets

International Nuclear Information System (INIS)

Woo, C.K.; Moore, J.; Schneiderman, B.; Ho, T.; Olson, A.; Alagappan, L.; Chawla, K.; Toyama, N.; Zarnikau, J.

2016-01-01

We answer two policy questions: (1) what are the estimated merit-order effects of renewable energy in the California Independent System Operator’s (CAISO’s) day-ahead market (DAM) and real-time market (RTM)? and (2) what causes the hourly DAM and RTM prices to systematically diverge? The first question is timely and relevant because if the merit-order effect estimates are small, California’s renewable energy development is of limited help in cutting electricity consumers’ bills but also has a lesser adverse impact on the state’s investment incentive for natural-gas-fired generation. The second question is related to the efficient market hypothesis under which the hourly RTM and DAM prices tend to converge. Using a sample of about 21,000 hourly observations of CAISO market prices and their fundamental drivers during 12/12/2012–04/30/2015, we document statistically significant estimates (p-value≤0.01) for the DAM and RTM merit-order effects. This finding lends support to California’s adopted procurement process to provide sufficient investment incentives for natural-gas-fired generation. We document that the RTM-DAM price divergence partly depends on the CASIO’s day-ahead forecast errors for system loads and renewable energy. This finding suggests that improving the performance of the CAISO’s day-ahead forecasts can enhance trading efficiency in California’s DAM and RTM electricity markets. - Highlights: •Estimate the day-ahead and real-time merit-order effects of renewable energy in California. •Document statistically significant merit-order effects of solar and wind energy. •Document the difference between the day-ahead and real-time prices. •Attribute the price differences to forecast errors for load, solar and wind energy. •Discuss the evidence’s implications for California’s energy policy.

Short recovery time NMR probe

International Nuclear Information System (INIS)

Ramia, M.E.; Martin, C.A.; Jeandrevin, S.

2011-01-01

A NMR probe for low frequency and short recovery time is presented in this work. The probe contains the tuning circuit, diode expanders and quarter wavelength networks to protect the receiver from both the amplifier noise and the coil ringing following the transmitter power pulse. It also possesses a coil damper which is activated by of non active components. The probe performance shows a recovery time of about of 15μs a sensitive Q factor reduction and an increase of the signal to noise ratio of about 68% during the reception at a work frequency of 2 MHz. (author)

The time resolved measurement of ultrashort terahertz-band electric fields without an ultrashort probe

International Nuclear Information System (INIS)

Walsh, D. A.; Snedden, E. W.; Jamison, S. P.

2015-01-01

The time-resolved detection of ultrashort pulsed THz-band electric field temporal profiles without an ultrashort laser probe is demonstrated. A non-linear interaction between a narrow-bandwidth optical probe and the THz pulse transposes the THz spectral intensity and phase information to the optical region, thereby generating an optical pulse whose temporal electric field envelope replicates the temporal profile of the real THz electric field. This optical envelope is characterised via an autocorrelation based FROG (frequency resolved optical gating) measurement, hence revealing the THz temporal profile. The combination of a narrow-bandwidth, long duration, optical probe, and self-referenced FROG makes the technique inherently immune to timing jitter between the optical probe and THz pulse and may find particular application where the THz field is not initially generated via ultrashort laser methods, such as the measurement of longitudinal electron bunch profiles in particle accelerators

Collection and evaluation of salt mixing data with the real time data acquisition system. [LMFBR

Energy Technology Data Exchange (ETDEWEB)

Glazer, S.; Chiu, C.; Todreas, N.E.

1977-09-01

A minicomputer based real time data acquisition system was designed and built to facilitate data collection during salt mixing tests in mock ups of LMFBR rod bundles. The system represents an expansion of data collection capabilities over previous equipment. It performs steady state and transient monitoring and recording of up to 512 individual electrical resistance probes. Extensive real time software was written to govern all phases of the data collection procedure, including probe definition, probe calibration, salt mixing test data acquisition and storage, and data editing. Offline software was also written to permit data examination and reduction to dimensionless salt concentration maps. Finally, the computer program SUPERENERGY was modified to permit rapid extraction of parameters from dimensionless salt concentration maps. The document describes the computer system, and includes circuit diagrams of all custom built components. It also includes descriptions and listings of all software written, as well as extensive user instructions.

Real-time spot size camera for pulsed high-energy radiographic machines

International Nuclear Information System (INIS)

Watson, S.A.

1993-01-01

The focal spot size of an x-ray source is a critical parameter which degrades resolution in a flash radiograph. For best results, a small round focal spot is required. Therefore, a fast and accurate measurement of the spot size is highly desirable to facilitate machine tuning. This paper describes two systems developed for Los Alamos National Laboratory's Pulsed High-Energy Radiographic Machine Emitting X-rays (PHERMEX) facility. The first uses a CCD camera combined with high-brightness floors, while the second utilizes phosphor storage screens. Other techniques typically record only the line spread function on radiographic film, while systems in this paper measure the more general two-dimensional point-spread function and associated modulation transfer function in real time for shot-to-shot comparison

Development and evaluation of the quantitative real-time PCR assay in detection and typing of herpes simplex virus in swab specimens from patients with genital herpes.

Science.gov (United States)

Liu, Junlian; Yi, Yong; Chen, Wei; Si, Shaoyan; Yin, Mengmeng; Jin, Hua; Liu, Jianjun; Zhou, Jinlian; Zhang, Jianzhong

2015-01-01

Genital herpes (GH), which is caused mainly by herpes simplex virus (HSV)-2 and HSV-1, remains a worldwide problem. Laboratory confirmation of GH is important, particularly as there are other conditions which present similarly to GH, while atypical presentations of GH also occur. Currently, virus culture is the classical method for diagnosis of GH, but it is time consuming and with low sensitivity. A major advance for diagnosis of GH is to use Real-time polymerase chain reaction (PCR). In this study, to evaluate the significance of the real-time PCR method in diagnosis and typing of genital HSV, the primers and probes targeted at HSV-1 DNA polymerase gene and HSV-2 glycoprotein D gene fraction were designed and applied to amplify DNA from HSV-1 or HSV-2 by employing the real-time PCR technique. Then the PCR reaction system was optimized and evaluated. HSV in swab specimens from patients with genital herpes was detected by real-time PCR. The real-time PCR assay showed good specificity for detection and typing of HSV, with good linear range (5×10(2)~5×10(8) copies/ml, r=0.997), a sensitivity of 5×10(2) copies/ml, and good reproducibility (intra-assay coefficients of variation 2.29% and inter-assay coefficients of variation 4.76%). 186 swab specimens were tested for HSV by real-time PCR, and the positive rate was 23.7% (44/186). Among the 44 positive specimens, 8 (18.2%) were positive for HSV-1 with a viral load of 8.5546×10(6) copies/ml and 36 (81.2%) were positive for HSV-2 with a viral load of 1.9861×10(6) copies/ml. It is concluded that the real-time PCR is a specific, sensitive and rapid method for the detection and typing of HSV, which can be widely used in clinical diagnosis of GH.

Integration of multidisciplinary technologies for real time target visualization and verification for radiotherapy

Directory of Open Access Journals (Sweden)

Chang WC

2014-06-01

Full Text Available Wen-Chung Chang,1,* Chin-Sheng Chen,2,* Hung-Chi Tai,3 Chia-Yuan Liu,4,5 Yu-Jen Chen3 1Department of Electrical Engineering, National Taipei University of Technology, Taipei, Taiwan; 2Graduate Institute of Automation Technology, National Taipei University of Technology, Taipei, Taiwan; 3Department of Radiation Oncology, Mackay Memorial Hospital, Taipei, Taiwan; 4Department of Internal Medicine, Mackay Memorial Hospital, Taipei, Taiwan; 5Department of Medicine, Mackay Medical College, New Taipei City, Taiwan  *These authors contributed equally to this work Abstract: The current practice of radiotherapy examines target coverage solely from digitally reconstructed beam's eye view (BEV in a way that is indirectly accessible and that is not in real time. We aimed to visualize treatment targets in real time from each BEV. The image data of phantom or patients from ultrasound (US and computed tomography (CT scans were captured to perform image registration. We integrated US, CT, US/CT image registration, robotic manipulation of US, a radiation treatment planning system, and a linear accelerator to constitute an innovative target visualization system. The performance of this algorithm segmented the target organ in CT images, transformed and reconstructed US images to match each orientation, and generated image registration in real time mode with acceptable accuracy. This image transformation allowed physicians to visualize the CT image-reconstructed target via a US probe outside the BEV that was non-coplanar to the beam's plane. It allowed the physicians to remotely control the US probe that was equipped on a robotic arm to dynamically trace and real time monitor the coverage of the target within the BEV during a simulated beam-on situation. This target visualization system may provide a direct remotely accessible and real time way to visualize, verify, and ensure tumor targeting during radiotherapy. Keywords: ultrasound, computerized tomography

A Canadian case study : the value of real time electricity monitoring : a real-time cost utility management solution

International Nuclear Information System (INIS)

Rouse, S.; Dittburner, D.

2006-01-01

Energy prices can vary significantly over the course of a single day in response to changing levels in energy demand and availability of supply. The impacts of varying energy prices on business and industry means that hourly electricity costs can fluctuate widely over the course of a day even though energy use remains stable. This presentation gave details of an energy efficiency initiative at Unilever's Rexdale site which has resulted in $4 million saved through reductions in energy consumption and equipment retrofits. The Rexdale plant won an energy efficiency award in 2005, and the success of the initiative was attributed to the use of Utility 3 + , an energy management software tool. A turn key system with integrated software and hardware, Utility 3 + is capable of measuring how much energy is being used and can provide details of costs using a combination of historical and forecast prices. The tool is equipped with alarms with pre-set thresholds to match real-time rises in energy prices. Real-time prices are relayed from the Internet along with a 2 way data communication system. It was concluded that use of the tool has resulted in improved cash flow management and greater control of energy costs. A system description of the tool was provided, as well as details of various equipment retrofits. refs.., tabs., figs

A Canadian case study : the value of real time electricity monitoring : a real-time cost utility management solution

Energy Technology Data Exchange (ETDEWEB)

Rouse, S. [Energy at Work, Toronto, ON (Canada); Dittburner, D. [Unilever Canada, Toronto, ON (Canada)

2006-07-01

Energy prices can vary significantly over the course of a single day in response to changing levels in energy demand and availability of supply. The impacts of varying energy prices on business and industry means that hourly electricity costs can fluctuate widely over the course of a day even though energy use remains stable. This presentation gave details of an energy efficiency initiative at Unilever's Rexdale site which has resulted in $4 million saved through reductions in energy consumption and equipment retrofits. The Rexdale plant won an energy efficiency award in 2005, and the success of the initiative was attributed to the use of Utility 3{sup +}, an energy management software tool. A turn key system with integrated software and hardware, Utility 3{sup +} is capable of measuring how much energy is being used and can provide details of costs using a combination of historical and forecast prices. The tool is equipped with alarms with pre-set thresholds to match real-time rises in energy prices. Real-time prices are relayed from the Internet along with a 2 way data communication system. It was concluded that use of the tool has resulted in improved cash flow management and greater control of energy costs. A system description of the tool was provided, as well as details of various equipment retrofits. refs.., tabs., figs.

Development of Real-Time PCR to Monitor Groundwater Contaminated by Fecal Sources and Leachate from the Carcass

Science.gov (United States)

Park, S.; Kim, H.; Kim, M.; Lee, Y.; Han, J.

2011-12-01

The 2010 outbreak of foot and mouth disease (FMD) in South Korea caused about 4,054 carcass burial sites to dispose the carcasses. Potential environmental impacts by leachate of carcass on groundwater have been issued and it still needs to be studied. Therefore, we tried to develop robust and sensitive tool to immediately determine a groundwater contamination by the leachate from carcass burial. For tracking both an agricultural fecal contamination source and the leachate in groundwater, competitive real-time PCR and PCR method were developed using various PCR primer sets designed to detect E. Coli uidA gene and mtDNA(cytochrome B, cytB) of the animal species such as ovine, porcine, caprine, and bovine. The designed methods were applied to tract the animal species in livestock wastewater and leachate of carcass under appropriate PCR or real-time PCR condition. In the result, mtDNA primer sets for individual (Cow or Pig) and multiple (Cow and Pig) amplification, and E. Coli uidA primers for fecal source amplification were specific and sensitive to target genes. To determine contamination source, concentration of amplified mtDNA and uidA was competitively quantified in Livestock wastewater, leachate of carcass, and groundwater. The highest concentration of mtDNA and uidA showed in leachate of carcass and livestock wastewater, respectively. Groundwater samples possibly contaminated by leachate of carcass were analyzed by this assay and it was able to prove contamination source.

Continuously tunable nucleic acid hybridization probes.

Science.gov (United States)

Wu, Lucia R; Wang, Juexiao Sherry; Fang, John Z; Evans, Emily R; Pinto, Alessandro; Pekker, Irena; Boykin, Richard; Ngouenet, Celine; Webster, Philippa J; Beechem, Joseph; Zhang, David Yu

2015-12-01

In silico-designed nucleic acid probes and primers often do not achieve favorable specificity and sensitivity tradeoffs on the first try, and iterative empirical sequence-based optimization is needed, particularly in multiplexed assays. We present a novel, on-the-fly method of tuning probe affinity and selectivity by adjusting the stoichiometry of auxiliary species, which allows for independent and decoupled adjustment of the hybridization yield for different probes in multiplexed assays. Using this method, we achieved near-continuous tuning of probe effective free energy. To demonstrate our approach, we enforced uniform capture efficiency of 31 DNA molecules (GC content, 0-100%), maximized the signal difference for 11 pairs of single-nucleotide variants and performed tunable hybrid capture of mRNA from total RNA. Using the Nanostring nCounter platform, we applied stoichiometric tuning to simultaneously adjust yields for a 24-plex assay, and we show multiplexed quantitation of RNA sequences and variants from formalin-fixed, paraffin-embedded samples.

Trial of real-time locating and messaging system with Bluetooth low energy.

Science.gov (United States)

Arisaka, Naoya; Mamorita, Noritaka; Isonaka, Risa; Kawakami, Tadashi; Takeuchi, Akihiro

2016-09-14

Hospital real-time location systems (RTLS) are increasing efficiency and reducing operational costs, but room access tags are necessary. We developed three iPhone 5 applications for an RTLS and communications using Bluetooth low energy (BLE). The applications were: Peripheral device tags, Central beacons, and a Monitor. A Peripheral communicated with a Central using BLE. The Central communicated with a Monitor using sockets on TCP/IP (Transmission Control Protocol/Internet Protocol) via a WLAN (wireless local area network). To determine a BLE threshold level for the received signal strength indicator (RSSI), relationships between signal strength and distance were measured in our laboratory and on the terrace. The BLE RSSI threshold was set at -70 dB, about 10 m. While an individual with a Peripheral moved around in a concrete building, the Peripheral was captured in a few 10-sec units at about 10 m from a Central. The Central and Monitor showed and saved the approach events, location, and Peripheral's nickname sequentially in real time. Remote Centrals also interactively communicate with Peripherals by intermediating through Monitors that found the nickname in the event database. Trial applications using BLE on iPhones worked well for patient tracking, and messaging in indoor environments.

[Quantitative fluorogenic real-time PCR assay for respiratory syncytial virus detection].

Science.gov (United States)

Zhang, Qi-wei; You, Shang-you; Sun, Ji-min; Wu, Qi; Yu, Chun-hua; Zhang, Chu-yu

2005-07-01

To Establish a rapid and objective quantitative fluorogenic real-time PCR assay for early detection of human respiratory syncytial virus (hRSV). Two pairs of primers and one TaqMan Fluorogenic probe that are specific for the recognition of the most conservative N gene of hRSV for virus detection with LighCycler PCR in 93 nasopharyngeal secretion specimens collected from infants and young children. The assay was compared with virus isolation, routine PCR, nested PCR, and enzyme-linked immunosorbent assay (ELISA). This TaqMan assay had a sensitivity of 1 x 10(2) cDNA copies/microl with a dynamic range between 1 x 10(2) and 1 x 10(7) cDNA copies/microl, which was the same as that of nested PCR, but 10 times more sensitive than routine PCR. The specificity of the assay was evaluated by comparing hRSV with polivirus type 1, coxsackie virus type 2, influenza A, influenza B and adenovirus type 7. A PCR product of the expected size (195 bp) was produced and fluorescence signal detected for hRSV, but not for any of the other viruses. The results in LightCycler and Rotor-Gene instrument were consistent. Forty-four specimens (43.9%) were hRSV-positive with this assay and 4 (4/93,4.3%) were hRSV-positive with ELISA, showing rather low correlation between the two methods. No visible relation was found between the concentration of hRSV RNA and severity of the disease. This assay is rapid, sensitive, specific and quantitative, and has the potential of wide application for early diagnosis of hRSV infection and evaluation of the therapeutic effect.

Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants.

Science.gov (United States)

Liu, Weipeng; Zhu, Minjun; Liu, Hongxing; Wei, Jitao; Zhou, Xiaoming; Xing, Da

2016-07-15

Searching for a strategy to enhance the efficiency of nucleic acid amplification and achieve exquisite discrimination of nucleic acids at the single-base level for biological detection has become an exciting research direction in recent years. Here, we have developed a simple and universal primer design strategy which produces a fascinating effect on isothermal strand displacement amplification (iSDA). We refer to the resultant primer as "invading stacking primer (IS-Primer)" which is based on contiguous stacking hybridization and toehold-mediated exchange reaction and function by merely changing the hybridization location of the primer. Using the IS-Primer, the sensitivity in detecting the target miR-21 is improved approximately five fold compared with the traditional iSDA reaction. It was further demonstrated that the IS-Primer acts as an invading strand to initiate branch migration which can increase the efficiency of the untwisting of the hairpin probe. This effect is equivalent to reducing the free energy of the stem, and the technique shows superior selectivity for single-base mismatches. By demonstrating the enhanced effect of the IS-Primer in the iSDA reaction, this work may provide a potentially new avenue for developing more sensitive and selective nucleic acids assays. Copyright © 2016 Elsevier B.V. All rights reserved.

Species-specific detection and quantification of common barnacle larvae from the Japanese coast using quantitative real-time PCR.

Science.gov (United States)

Endo, Noriyuki; Sato, Kana; Matsumura, Kiyotaka; Yoshimura, Erina; Odaka, Yukiko; Nogata, Yasuyuki

2010-11-01

Species-specific detection and quantification methods for barnacle larvae using quantitative real-time polymerase chain reaction (qPCR) were developed. Species-specific primers for qPCR were designed for 13 barnacle species in the mitochondrial 12S ribosomal RNA gene region. Primer specificity was examined by PCR using template DNA extracted from each of the 13 barnacle species, other unidentified barnacle species, and field collected zooplankton samples. The resulting PCR products comprised single bands following agarose gel electrophoresis when the templates corresponded to primers. The amplifications were highly species-specific even for the field plankton samples. The field plankton samples were subjected to qPCR assay. The calculated DNA contents for each barnacle species were closely correlated with the number of larvae measured by microscopic examination. The method could be applied to quantify barnacle larvae in natural plankton samples.

Real-time in vivo luminescence dosimetry in radiotherapy and mammography using Al2O3:C

International Nuclear Information System (INIS)

Aznar, M.C.

2005-07-01

New treatment and clinical imaging techniques have created a need for accurate and practical in vivo dosimeters in radiation medicine. This work describes the development of a new optical-fiber radiation dosimeter system, based on radioluminescence (RL) and optically stimulated luminescence (OSL) from carbon-doped aluminium oxide (Al2O3:C), for applications in radiotherapy and mammography. This system offers several features, such as a small detector, high sensitivity, real-time read-out, and the ability to measure both dose rate and absorbed dose. Measurement protocols and algorithms for the correction of responses were developed to enable a reliable absorbed dose assessment from the RL and OSL signals. At radiotherapy energies, the variation of the signal with beam parameters was smaller than 1% (1 SD). Treatment-like experiments in phantoms, and in vivo measurements during complex patient treatments (such as intensity-modulated radiation therapy) indicate that the RL/OSL dosimetry system can reliably measure the absorbed dose within 2%. The real-time RL signal also enables an individual dose assessment from each field. The RL/OSL dosimetry system was also used during mammography examinations. In such conditions, the reproducibility of the measurements showed to be around 3%. In vivo measurements on three patients showed that the presence of the RL/OSL probes did not degrade the diagnostic quality of the radiograph and that the system could be used to measure exit doses (i.e., absorbed doses on the inferior surface of the breast). A Monte Carlo study proved that the energy dependence of the RL/OSL system at these low energies could be reduced by optimizing the design of the probes. It is concluded that the new RL/OSL dosimetry system shows considerable potential for applications in both radiotherapy and mammography. (au)

Power minimisation for real-time dataflow applications.

NARCIS (Netherlands)

Nelson, Andrew; Moreira, O.; Molnos, A.M.; Stuijk, S.; Nguyen, B.T.; Goossens, K.G.W.; Kitsos, P.

2011-01-01

Energy efficient execution of applications is important for many reasons, e.g. time between battery charges, device temperature. Voltage and Frequency Scaling (VFS) enables applications to be run at lower frequencies on hardware resources thereby consuming less power. Real-time applications have

Real-time appraisal of the spatially distributed heat related health risk and energy demand of cities

Science.gov (United States)

Keramitsoglou, Iphigenia; Kiranoudis, Chris T.; Sismanidis, Panagiotis

2016-08-01

The Urban Heat Island (UHI) is an adverse environmental effect of urbanization that increases the energy demand of cities, impacts the human health, and intensifies and prolongs heatwave events. To facilitate the study of UHIs the Institute for Astronomy, Astrophysics, Space Applications and Remote Sensing of the National Observatory of Athens (IAASARS/NOA) has developed an operational real-time system that exploits remote sensing image data from Meteosat Second Generation - Spinning Enhanced Visible and Infrared Imager (MSG-SEVIRI) and generates high spatiotemporal land surface temperature (LST) and 2 m air temperature (TA) time series. These datasets form the basis for the generation of higher value products and services related to energy demand and heat-related health issues. These products are the heatwave hazard (HZ); the HUMIDEX (i.e. an index that describes the temperature felt by an individual exposed to heat and humidity); and the cooling degrees (CD; i.e. a measure that reflects the energy needed to cool a building). The spatiotemporal characteristics of HZ, HUMIDEX and CD are unique (1 km/5 min) and enable the appraisal of the spatially distributed heat related health risk and energy demand of cities. In this paper, the real time generation of the high spatiotemporal HZ, HUMIDEX and CD products is discussed. In addition, a case study corresponding to Athens' September 2015 heatwave is presented so as to demonstrate their capabilities. The overall aim of the system is to provide high quality data to several different end users, such as health responders, and energy suppliers. The urban thermal monitoring web service is available at http://snf-652558.vm.okeanos.grnet.gr/treasure/portal/info.html.

A centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria.

Science.gov (United States)

Choi, Goro; Jung, Jae Hwan; Park, Byung Hyun; Oh, Seung Jun; Seo, Ji Hyun; Choi, Jong Seob; Kim, Do Hyun; Seo, Tae Seok

2016-06-21

In this study, we developed a centrifugal direct recombinase polymerase amplification (direct-RPA) microdevice for multiplex and real-time identification of food poisoning bacteria contaminated milk samples. The microdevice was designed to contain identical triplicate functional units and each unit has four reaction chambers, thereby making it possible to perform twelve direct-RPA reactions simultaneously. The integrated microdevice consisted of two layers: RPA reagents were injected in the top layer, while spiked milk samples with food poisoning bacteria were loaded into sample reservoirs in the bottom layer. For multiplex bacterial detection, the target gene-specific primers and probes were dried in each reaction chamber. The introduced samples and reagents could be equally aliquoted and dispensed into each reaction chamber by centrifugal force, and then the multiplex direct-RPA reaction was executed. The target genes of bacteria spiked in milk could be amplified at 39 °C without a DNA extraction step by using the direct-RPA cocktails, which were a combination of a direct PCR buffer and RPA enzymes. As the target gene amplification proceeded, the increased fluorescence signals coming from the reaction chambers were recorded in real-time at an interval of 2 min. The entire process, including the sample distribution, the direct-RPA reaction, and the real-time analysis, was accomplished with a custom-made portable genetic analyzer and a miniaturized optical detector. Monoplex, duplex, and triplex food poisoning bacteria (Salmonella enterica, Escherichia coli O157:H7, and Vibrio parahaemolyticus) detection was successfully performed with a detection sensitivity of 4 cells per 3.2 μL of milk samples within 30 min. By implementing the direct-PRA on the miniaturized centrifugal microsystem, the on-site food poisoning bacteria analysis would be feasible with high speed, sensitivity, and multiplicity.

Quantification of organellar DNA and RNA using real-time PCR.

Science.gov (United States)

Weihe, Andreas

2014-01-01

Quantitative (real-time) polymerase chain reaction (PCR) allows the measurement of relative organellar gene copy numbers as well as transcript abundance of individual mitochondrial or plastidial genes. Requiring only minute amounts of total DNA or RNA, the described method can replace traditional analyses like Southern or Northern hybridization which require large amounts of organellar nucleic acids and usually provide only semiquantitative data. Here we describe prerequisites, reaction conditions, and data analysis principles, which should be applicable for a wide range of plant species and experimental situations where comparative and precise determination of gene copy numbers or transcript abundance is requested. Sequences of amplification primers for qPCR of organellar genes from Arabidopsis are provided.

Design and Validation of Real-Time Optimal Control with ECMS to Minimize Energy Consumption for Parallel Hybrid Electric Vehicles

Directory of Open Access Journals (Sweden)

Aiyun Gao

2017-01-01

Full Text Available A real-time optimal control of parallel hybrid electric vehicles (PHEVs with the equivalent consumption minimization strategy (ECMS is presented in this paper, whose purpose is to achieve the total equivalent fuel consumption minimization and to maintain the battery state of charge (SOC within its operation range at all times simultaneously. Vehicle and assembly models of PHEVs are established, which provide the foundation for the following calculations. The ECMS is described in detail, in which an instantaneous cost function including the fuel energy and the electrical energy is proposed, whose emphasis is the computation of the equivalent factor. The real-time optimal control strategy is designed through regarding the minimum of the total equivalent fuel consumption as the control objective and the torque split factor as the control variable. The validation of the control strategy proposed is demonstrated both in the MATLAB/Simulink/Advisor environment and under actual transportation conditions by comparing the fuel economy, the charge sustainability, and parts performance with other three control strategies under different driving cycles including standard, actual, and real-time road conditions. Through numerical simulations and real vehicle tests, the accuracy of the approach used for the evaluation of the equivalent factor is confirmed, and the potential of the proposed control strategy in terms of fuel economy and keeping the deviations of SOC at a low level is illustrated.

Urethral alarm probe for permanent prostate implants

International Nuclear Information System (INIS)

Cutajar, D.; Lerch, M.; Takacs, G.

2008-01-01

We have developed a urethral dosimetry system for real time dose verification along the urethra during permanent implant prostate brachytherapy. The urethral alarm uses 'spectroscopic dosimetry' to calculate the dose rate along the urethra in real time. The application of spectroscopic dosimetry for the urethral alarm probe was verified using Monte Carlo calculations. In phantom depth dose measurements as well as isotropy measurements were performed to verify the usefulness of the urethra alarm probe as an in vivo real time dosimeter. (author)

A SiPM based real time dosimeter for radiotherapic beams

Energy Technology Data Exchange (ETDEWEB)

Berra, A., E-mail: alessandro.berra@gmail.it [Università degli Studi dell' Insubria e INFN sezione di Milano Bicocca, Via Valleggio, 11 22100 Como (Italy); Conti, V. [Ospedale Sant' Anna, Servizio di Fisica Sanitaria, Como (Italy); Lietti, D.; Milan, L.; Novati, C. [Università degli Studi dell' Insubria e INFN sezione di Milano Bicocca, Via Valleggio, 11 22100 Como (Italy); Ostinelli, A. [Ospedale Sant' Anna, Servizio di Fisica Sanitaria, Como (Italy); Prest, M.; Romanó, C. [Università degli Studi dell' Insubria e INFN sezione di Milano Bicocca, Via Valleggio, 11 22100 Como (Italy); Vallazza, E. [INFN sezione di Trieste (Italy)

2015-02-11

This paper describes the development of a scintillator dosimeter prototype for radiotherapic applications based on plastic scintillating fibers readout by Silicon PhotoMultipliers. The dosimeter, whose probes are water equivalent, could be used for quality control measurements, beam characterization and in vivo dosimetry, allowing a real time measurement of the dose spatial distribution. This paper describes the preliminary percentual depth dose scan performed with clinical 6 and 18 MV photon beams, comparing the results with a reference curve. The measurements were performed using a Varian Clinac iX linear accelerator at the Radiotherapy Department of the St. Anna Hospital in Como (IT). The prototype has given promising results, allowing real time measurements of relative dose without applying any correction factors.

UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes

Directory of Open Access Journals (Sweden)

Nomin Batnyam

2012-01-01

Full Text Available Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

Development and validation of a SYBR Green I-based real-time polymerase chain reaction method for detection of haptoglobin gene deletion in clinical materials.

Science.gov (United States)

Soejima, Mikiko; Tsuchiya, Yuji; Egashira, Kouichi; Kawano, Hiroyuki; Sagawa, Kimitaka; Koda, Yoshiro

2010-06-01

Anhaptoglobinemic patients run the risk of severe anaphylactic transfusion reaction because they produce serum haptoglobin (Hp) antibodies. Being homozygous for the Hp gene deletion (HP(del)) is the only known cause of congenital anhaptoglobinemia, and clinical diagnosis of HP(del) before transfusion is important to prevent anaphylactic shock. We recently developed a 5'-nuclease (TaqMan) real-time polymerase chain reaction (PCR) method. A SYBR Green I-based duplex real-time PCR assay using two forward primers and a common reverse primer followed by melting curve analysis was developed to determine HP(del) zygosity in a single tube. In addition, to obviate initial DNA extraction, we examined serially diluted blood samples as PCR templates. Allelic discrimination of HP(del) yielded optimal results at blood sample dilutions of 1:64 to 1:1024. The results from 2231 blood samples were fully concordant with those obtained by the TaqMan-based real-time PCR method. The detection rate of the HP(del) allele by the SYBR Green I-based method is comparable with that using the TaqMan-based method. This method is readily applicable due to its low initial cost and analyzability using economical real-time PCR machines and is suitable for high-throughput analysis as an alternative method for allelic discrimination of HP(del).

Direct quantification of fungal DNA from soil substrate using real-time PCR.

Science.gov (United States)

Filion, Martin; St-Arnaud, Marc; Jabaji-Hare, Suha H

2003-04-01

Detection and quantification of genomic DNA from two ecologically different fungi, the plant pathogen Fusarium solani f. sp. phaseoli and the arbuscular mycorrhizal fungus Glomus intraradices, was achieved from soil substrate. Specific primers targeting a 362-bp fragment from the SSU rRNA gene region of G. intraradices and a 562-bp fragment from the F. solani f. sp. phaseoli translation elongation factor 1 alpha gene were used in real-time polymerase chain reaction (PCR) assays conjugated with the fluorescent SYBR(R) Green I dye. Standard curves showed a linear relation (r(2)=0.999) between log values of fungal genomic DNA of each species and real-time PCR threshold cycles and were quantitative over 4-5 orders of magnitude. Real-time PCR assays were applied to in vitro-produced fungal structures and sterile and non-sterile soil substrate seeded with known propagule numbers of either fungi. Detection and genomic DNA quantification was obtained from the different treatments, while no amplicon was detected from non-seeded non-sterile soil samples, confirming the absence of cross-reactivity with the soil microflora DNA. A significant correlation (Pgenomic DNA of F. solani f. sp. phaseoli or G. intraradices detected and the number of fungal propagules present in seeded soil substrate. The DNA extraction protocol and real-time PCR quantification assay can be performed in less than 2 h and is adaptable to detect and quantify genomic DNA from other soilborne fungi.

ENERGY CONSUMPTION AND REAL GDP IN IRAN

Directory of Open Access Journals (Sweden)

Ali Akbar Naji Meidani

2014-01-01

Full Text Available As one of the most important production factors and one of the most urgent final products, energy has a special position in the growth and development of the country. This paper examines the causal relationship between Real GDP and energy consumption in various economic sectors including (household and commercial, industry, transportation and agriculture sectors for Iran during 1967–2010 using the time series technique known as the Toda-Yamamoto method. Moreover, an error correction model is also estimated so that the results of these two methods are compared. We found a strong unidirectional causality from energy consumption in industry sector to real gross domestic product. Energy consumption in industry sector can observably promote the development of economy.

The detection of T-Nos, a genetic element present in GMOs, by cross-priming isothermal amplification with real-time fluorescence.

Science.gov (United States)

Zhang, Fang; Wang, Liu; Fan, Kai; Wu, Jian; Ying, Yibin

2014-05-01

An isothermal cross-priming amplification (CPA) assay for Agrobacterium tumefaciens nopaline synthase terminator (T-Nos) was established and investigated in this work. A set of six specific primers, recognizing eight distinct regions on the T-Nos sequence, was designed. The CPA assay was performed at a constant temperature, 63 °C, and detected by real-time fluorescence. The results indicated that real-time fluorescent CPA had high specificity, and the limit of detection was 1.06 × 10(3) copies of rice genomic DNA, which could be detected in 40 min. Comparison of real-time fluorescent CPA and conventional polymerase chain reaction (PCR) was also performed. Results revealed that real-time fluorescent CPA had a comparable sensitivity to conventional real-time PCR and had taken a shorter time. In addition, different contents of genetically modified (GM)-contaminated rice seed powder samples were detected for practical application. The result showed real-time fluorescent CPA could detect 0.5 % GM-contaminated samples at least, and the whole reaction could be finished in 35 min. Real-time fluorescent CPA is sensitive enough to monitor labeling systems and provides an attractive method for the detection of GMO.

Development of a real-time PCR assay for detection of planktonic red king crab (Paralithodes camtschaticus (Tilesius 1815)) larvae

Science.gov (United States)

Jensen, Pamela C.; Purcell, Maureen K.; Morado, J. Frank; Eckert, Ginny L.

2012-01-01

The Alaskan red king crab (Paralithodes camtschaticus) fishery was once one of the most economically important single-species fisheries in the world, but is currently depressed. This fishery would benefit from improved stock assessment capabilities. Larval crab distribution is patchy temporally and spatially, requiring extensive sampling efforts to locate and track larval dispersal. Large-scale plankton surveys are generally cost prohibitive because of the effort required for collection and the time and taxonomic expertise required to sort samples to identify plankton individually via light microscopy. Here, we report the development of primers and a dual-labeled probe for use in a DNA-based real-time polymerase chain reaction assay targeting the red king crab, mitochondrial gene cytochrome oxidase I for the detection of red king crab larvae DNA in plankton samples. The assay allows identification of plankton samples containing crab larvae DNA and provides an estimate of DNA copy number present in a sample without sorting the plankton sample visually. The assay was tested on DNA extracted from whole red king crab larvae and plankton samples seeded with whole larvae, and it detected DNA copies equivalent to 1/10,000th of a larva and 1 crab larva/5mL sieved plankton, respectively. The real-time polymerase chain reaction assay can be used to screen plankton samples for larvae in a fraction of the time required for traditional microscopial methods, which offers advantages for stock assessment methodologies for red king crab as well as a rapid and reliable method to assess abundance of red king crab larvae as needed to improve the understanding of life history and population processes, including larval population dynamics.

Some selection criteria for computers in real-time systems for high energy physics

International Nuclear Information System (INIS)

Kolpakov, I.F.

1980-01-01

The right choice of program source is for the organization of real-time systems of great importance as cost and reliability are decisive factors. Some selection criteria for program sources for high energy physics multiwire chamber spectrometers (MWCS) are considered in this report. MWCS's accept bits of information from event pattens. Large and small computers, microcomputers and intelligent controllers in CAMAC crates are compared with respect to the following characteristics: data exchange speed, number of addresses for peripheral devices, cost of interfacing a peripheral device, sizes of buffer and mass memory, configuration costs, and the mean time between failures (MTBF). The results of comparisons are shown by plots and histograms which allow the selection of program sources according to the above criteria. (Auth.)

The effects of combining dynamic pricing, AC load control, and real-time energy feedback. SMUD'S 2011 Residential Summer Solutions Study

Energy Technology Data Exchange (ETDEWEB)

Herter, K. [Herter Energy Research Solutions, El Dorado Hills, CA (United States); Wood, V. [Sacramento Municipal Utility District, Sacramento, CA (United States); Blozis, S. [University of California, Davis, CA (United States)

2013-11-15

The 2011 Residential Summer Solutions Study compared the hourly load effects of three different real-time information treatments and two program options. The information treatments included: Baseline information (no real-time data), real-time Home information (whole-house data), and real-time Appliance information (data for the whole house plus three individual appliances). Compared to the Baseline group, real-time Home information lowered overall energy use by about 4 %. Real-time information at both the Home and Appliance levels had a significant effect on non-event peak loads: compared to the Baseline group, real-time Home data lowered peak load by 5 %, while Appliance data lowered peak load by 7 %. All three information treatments averaged a 1-kW (40 %) load shed during events. The customer-chosen program options included a dynamic time-of-use rate and a load control incentive program. Customers were more likely to sign up for the dynamic rate, and those who did saved significantly more peak load on both event days (>50 % savings) and non-event days (>20 % savings) than did those on the load control program alone. In addition, those on the dynamic rate saved twice as much on their summer bills as did those who chose to remain on the standard tiered rate. At the end of the summer, more than 90 % of participants signed up to participate again the following year.

Real-time PCR protocols for the quantification of the begomovirus tomato yellow leaf curl Sardinia virus in tomato plants and in its insect vector.

Science.gov (United States)

Noris, Emanuela; Miozzi, Laura

2015-01-01

Tomato yellow leaf curl Sardinia virus (TYLCSV) (Geminiviridae) is an important pathogen, transmitted by the whitefly Bemisia tabaci, that severely affects the tomato production in the Mediterranean basin. Here, we describe real-time PCR protocols suitable for relative and absolute quantification of TYLCSV in tomato plants and in whitefly extracts. Using primers and probe specifically designed for TYLCSV, the protocols for relative quantification allow to compare the amount of TYLCSV present in different plant or whitefly samples, normalized to the amount of DNA present in each sample using endogenous tomato or Bemisia genes as internal references. The absolute quantification protocol allows to calculate the number of genomic units of TYLCSV over the genomic units of the plant host (tomato), with a sensitivity of as few as ten viral genome copies per sample. The described protocols are potentially suitable for several applications, such as plant breeding for resistance, analysis of virus replication, and virus-vector interaction studies.

Development of a real-time PCR assay for Penicillium expansum quantification and patulin estimation in apples

International Nuclear Information System (INIS)

Atoui, A.; Tannous, J.; El Khoury, A.; Kantar, S.; Chdid, N.; Lteif, R.; Oswald, I.; Puel, O.

2015-01-01

Due to the occurrence and spread of the fungal contaminants in food and the difficulties to remove their resulting mycotoxins, rapid and accurate methods are needed for early detection of these mycotoxigenic fungi. The polymerase chain reaction and the real time PCR have been widely used for this purpose. Apples are suitable substrates for fungal colonization mostly caused by Penicillium expansum, which produces the mycotoxin patulin during fruit infection. This study describes the development of a realtime PCR assay incorporating an internal amplification control (IAC) to specifically detect and quantify P. expansum. A specific primer pair was designed from the patF gene, involved in patulin biosynthesis. The selected primer set showed a high specificity for P. expansum and was successfully employed in a standardized real-time PCR for the direct quantification of this fungus in apples. Using the developed system, twenty eight apples were analyzed for their DNA content. Apples were also analyzed for patulin content by HPLC. Interestingly, a positive correlation (R"2 = 0.701) was found between P. expansum DNA content and patulin concentration. This work offers an alternative to conventional methods of patulin quantification and mycological detection of P. expansum and could be very useful for the screening of patulin in fruits through the application of industrial quality control. (author)

A field based detection method for Rose rosette virus using isothermal probe-based Reverse transcription-recombinase polymerase amplification assay.

Science.gov (United States)

Babu, Binoy; Washburn, Brian K; Ertek, Tülin Sarigül; Miller, Steven H; Riddle, Charles B; Knox, Gary W; Ochoa-Corona, Francisco M; Olson, Jennifer; Katırcıoğlu, Yakup Zekai; Paret, Mathews L

2017-09-01

Rose rosette disease, caused by Rose rosette virus (RRV; genus Emaravirus) is a major threat to the rose industry in the U.S. The only strategy currently available for disease management is early detection and eradication of the infected plants, thereby limiting its potential spread. Current RT-PCR based diagnostic methods for RRV are time consuming and are inconsistent in detecting the virus from symptomatic plants. Real-time RT-qPCR assay is highly sensitive for detection of RRV, but it is expensive and requires well-equipped laboratories. Both the RT-PCR and RT-qPCR cannot be used in a field-based testing for RRV. Hence a novel probe based, isothermal reverse transcription-recombinase polymerase amplification (RT-exoRPA) assay, using primer/probe designed based on the nucleocapsid gene of the RRV has been developed. The assay is highly specific and did not give a positive reaction to other viruses infecting roses belonging to both inclusive and exclusive genus. Dilution assays using the in vitro transcript showed that the primer/probe set is highly sensitive, with a detection limit of 1 fg/μl. In addition, a rapid technique for the extraction of viral RNA (rose varieties, collected from different states in the U.S. The entire process, including the extraction can be completed in 25min, with less sophisticated equipments. The developed assay can be used with high efficiency in large scale field testing for rapid detection of RRV in commercial nurseries and landscapes. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis on the arcelin expression in bruchid pest resistant wild pulses using real time RT-qPCR.

Science.gov (United States)

Sakthivelkumar, Shanmugavel; Veeramani, Velayutham; Hilda, Karuppiah; Arumugam, Munusamy; Janarthanan, Sundaram

2014-12-01

Arcelin, the antimetabolic protein from wild pulses is a known natural insecticidal molecule. Wild pulses with high arcelin content could serve as potential source to. increase the levels of insect resistance in cultivated pulse crops. In this study, arcelin (Arl) gene expression was screened in seven stored product insect pest resistant wild pulse varieties using real time RT-qPCR. Arcelin gene specific real time PCR primers were synthesized from arcelin mRNA sequence of the wild pulse variety, Lablab purpureus. The results revealed different levels of arcelin gene expression in the tested varieties. Canavalia virosa registered significantly high content indicating its suitability for utilization of arcelin gene in developing stored product insect pest resistance with other cultivated pulses.

Supporting Development of Energy-Optimised Java Real-Time Systems using TetaSARTS

DEFF Research Database (Denmark)

Luckow, Kasper Søe; Bøgholm, Thomas; Thomsen, Bent

2013-01-01

This paper presents how the tool TetaSARTS can be used to support the development of embedded hard real-time systems written in Java using the emerging Safety Critical Java (SCJ) profile. TetaSARTS facilitates control-flow sensitive schedulability analysis of a set of real-time tasks, and features...

SU-G-JeP1-11: Feasibility Study of Markerless Tracking Using Dual Energy Fluoroscopic Images for Real-Time Tumor-Tracking Radiotherapy System

Energy Technology Data Exchange (ETDEWEB)

Shiinoki, T; Shibuya, K [Yamaguchi University, Ube, Yamaguchi (Japan); Sawada, A [Kyoto college of medical science, Nantan, Kyoto (Japan); Uehara, T; Yuasa, Y; Koike, M; Kawamura, S [Yamaguchi University Hospital, Ube, Yamaguchi (Japan)

2016-06-15

Purpose: The new real-time tumor-tracking radiotherapy (RTRT) system was installed in our institution. This system consists of two x-ray tubes and color image intensifiers (I.I.s). The fiducial marker which was implanted near the tumor was tracked using color fluoroscopic images. However, the implantation of the fiducial marker is very invasive. Color fluoroscopic images enable to increase the recognition of the tumor. However, these images were not suitable to track the tumor without fiducial marker. The purpose of this study was to investigate the feasibility of markerless tracking using dual energy colored fluoroscopic images for real-time tumor-tracking radiotherapy system. Methods: The colored fluoroscopic images of static and moving phantom that had the simulated tumor (30 mm diameter sphere) were experimentally acquired using the RTRT system. The programmable respiratory motion phantom was driven using the sinusoidal pattern in cranio-caudal direction (Amplitude: 20 mm, Time: 4 s). The x-ray condition was set to 55 kV, 50 mA and 105 kV, 50 mA for low energy and high energy, respectively. Dual energy images were calculated based on the weighted logarithmic subtraction of high and low energy images of RGB images. The usefulness of dual energy imaging for real-time tracking with an automated template image matching algorithm was investigated. Results: Our proposed dual energy subtraction improve the contrast between tumor and background to suppress the bone structure. For static phantom, our results showed that high tracking accuracy using dual energy subtraction images. For moving phantom, our results showed that good tracking accuracy using dual energy subtraction images. However, tracking accuracy was dependent on tumor position, tumor size and x-ray conditions. Conclusion: We indicated that feasibility of markerless tracking using dual energy fluoroscopic images for real-time tumor-tracking radiotherapy system. Furthermore, it is needed to investigate the

Real-time monitoring of caspase cascade activation in living cells.

Science.gov (United States)

Zhu, Lei; Huang, Xinglu; Choi, Ki Young; Ma, Ying; Zhang, Fan; Liu, Gang; Lee, Seulki; Chen, Xiaoyuan

2012-10-10

We introduce a simple, versatile and robust one-step technique that enables real-time imaging of multiple intracellular caspase activities in living cells without the need for complicated synthetic protocols. Conventional fluorogenic probes or recently reported activatable probes have been designed to target various proteases but are limited to extracellular molecules. Only a few have been applied to image intracellular proteases in living cells because most of these probes have limited cell-permeability. Our platform does not need complicated synthetic processes; instead it involves a straightforward peptide synthesis and a simple mixing step with a commercial transfection agent. The transfection agent efficiently delivered the highly quenched fluorogenic probes, comprised of distinctive pairs of dyes and quenchers, to the initiator caspase-8 and the effector caspase-3 in MDA-MB-435 cells, allowing dual-imaging of the activities of both caspases during the apoptotic process induced by TNF-related apoptosis induced ligand (TRAIL). With the combination of multiple fluorogenic probes, this simple platform can be applied to multiplexed imaging of selected intracellular proteases to study apoptotic processes in pathologies or for cell-based high throughput screening systems for drug discovery. Published by Elsevier B.V.

Real Time Grid Reliability Management 2005

Energy Technology Data Exchange (ETDEWEB)

Eto, Joe; Eto, Joe; Lesieutre, Bernard; Lewis, Nancy Jo; Parashar, Manu

2008-07-07

The increased need to manage California?s electricity grid in real time is a result of the ongoing transition from a system operated by vertically-integrated utilities serving native loads to one operated by an independent system operator supporting competitive energy markets. During this transition period, the traditional approach to reliability management -- construction of new transmission lines -- has not been pursued due to unresolved issues related to the financing and recovery of transmission project costs. In the absence of investments in new transmission infrastructure, the best strategy for managing reliability is to equip system operators with better real-time information about actual operating margins so that they can better understand and manage the risk of operating closer to the edge. A companion strategy is to address known deficiencies in offline modeling tools that are needed to ground the use of improved real-time tools. This project: (1) developed and conducted first-ever demonstrations of two prototype real-time software tools for voltage security assessment and phasor monitoring; and (2) prepared a scoping study on improving load and generator response models. Additional funding through two separate subsequent work authorizations has already been provided to build upon the work initiated in this project.

Real time event selection and flash analog-to-digital converters

International Nuclear Information System (INIS)

Imori, Masatosi

1983-01-01

In high-energy particle experiments, high-speed analog logic is employed to select events on a real-time basis. Flash analog-to-digital converters replace the high-speed analog logic with digital logic. The digital logic gives great flexibility to the scheme for real-time event selection. This paper proposes the use of flash A/D converters for the logic used to obtain the total sum of the energy deposited in individual counters in a shower detector. (author)

Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: applications and considerations.

Science.gov (United States)

Kim, Jaai; Lim, Juntaek; Lee, Changsoo

2013-12-01

Quantitative real-time PCR (qPCR) has been widely used in recent environmental microbial ecology studies as a tool for detecting and quantifying microorganisms of interest, which aids in better understandings of the complexity of wastewater microbial communities. Although qPCR can be used to provide more specific and accurate quantification than other molecular techniques, it does have limitations that must be considered when applying it in practice. This article reviews the principle of qPCR quantification and its applications to microbial ecology studies in various wastewater treatment environments. Here we also address several limitations of qPCR-based approaches that can affect the validity of quantification data: template nucleic acid quality, nucleic acid extraction efficiency, specificity of group-specific primers and probes, amplification of nonviable DNA, gene copy number variation, and limited number of sequences in the database. Even with such limitations, qPCR is reportedly among the best methods for quantitatively investigating environmental microbial communities. The application of qPCR is and will continue to be increasingly common in studies of wastewater treatment systems. To obtain reliable analyses, however, the limitations that have often been overlooked must be carefully considered when interpreting the results. Copyright © 2013 Elsevier Inc. All rights reserved.

Detection, quantification and genotyping of Herpes Simplex Virus in cervicovaginal secretions by real-time PCR: a cross sectional survey

Directory of Open Access Journals (Sweden)

Natividad-Sancho Angels

2005-08-01

Full Text Available Abstract Background Herpes Simplex Virus (HSV Genital Ulcer Disease (GUD is an important public health problem, whose interaction with HIV results in mutually enhancing epidemics. Conventional methods for detecting HSV tend to be slow and insensitive. We designed a rapid PCR-based assay to quantify and type HSV in cervicovaginal lavage (CVL fluid of subjects attending a Genito-Urinary Medicine (GUM clinic. Vaginal swabs, CVL fluid and venous blood were collected. Quantitative detection of HSV was conducted using real time PCR with HSV specific primers and SYBR Green I. Fluorogenic TaqMan Minor Groove Binder (MGB probes designed around a single base mismatch in the HSV DNA polymerase I gene were used to type HSV in a separate reaction. The Kalon test was used to detect anti-HSV-2 IgG antibodies in serum. Testing for HIV, other Sexually Transmitted Infections (STI and related infections was based on standard clinical and laboratory methods. Results Seventy consecutive GUM clinic attendees were studied. Twenty-seven subjects (39% had detectable HSV DNA in CVL fluid; HSV-2 alone was detected in 19 (70% subjects, HSV-1 alone was detected in 4 (15% subjects and both HSV types were detected in 4 (15% subjects. Eleven out of 27 subjects (41% with anti-HSV-2 IgG had detectable HSV-2 DNA in CVL fluid. Seven subjects (10% were HIV-positive. Three of seven (43% HIV-infected subjects and two of five subjects with GUD (40% were secreting HSV-2. None of the subjects in whom HSV-1 was detected had GUD. Conclusion Quantitative real-time PCR and Taqman MGB probes specific for HSV-1 or -2 were used to develop an assay for quantification and typing of HSV. The majority of subjects in which HSV was detected had low levels of CVL fluid HSV, with no detectable HSV-2 antibodies and were asymptomatic.

The design of a real-time distributed system

International Nuclear Information System (INIS)

Hertzberger, L.O.; Tuynman, F.; Mullender, S.J.; Poletiek, G.; Vermeulen, J.C.; Renesse, R. van; Tanenbaum, A.S.

1986-01-01

In modern physics experiments an increasing number and variety of programmable processors is used. As a consequence, a software environment is needed that provides an integrated approach to development, testing and use of real-time distributed software. This contribution is based on work being done in the AMOEBA Distributed Operating System Project and the FADOS Real-Time Distributed Operating System Project. A short description of both systems is presented as an example of how basic real-time operating system services can be organized. AMOEBA is the result of fundamental research in the field of distributed operating systems, while FADOS has been designed for applications as encountered in experimental high-energy physics. (Auth.)

Development of an event-specific hydrolysis probe quantitative real-time polymerase chain reaction assay for Embrapa 5.1 genetically modified common bean (Phaseolus vulgaris).

Science.gov (United States)

Treml, Diana; Venturelli, Gustavo L; Brod, Fábio C A; Faria, Josias C; Arisi, Ana C M

2014-12-10

A genetically modified (GM) common bean event, namely Embrapa 5.1, resistant to the bean golden mosaic virus (BGMV), was approved for commercialization in Brazil. Brazilian regulation for genetically modified organism (GMO) labeling requires that any food containing more than 1% GMO be labeled. The event-specific polymerase chain reaction (PCR) method has been the primary trend for GMO identification and quantitation because of its high specificity based on the flanking sequence. This work reports the development of an event-specific assay, named FGM, for Embrapa 5.1 detection and quantitation by use of SYBR Green or hydrolysis probe. The FGM assay specificity was tested for Embrapa 2.3 event (a noncommercial GM common bean also resistant to BGMV), 46 non-GM common bean varieties, and other crop species including maize, GM maize, soybean, and GM soybean. The FGM assay showed high specificity to detect the Embrapa 5.1 event. Standard curves for the FGM assay presented a mean efficiency of 95% and a limit of detection (LOD) of 100 genome copies in the presence of background DNA. The primers and probe developed are suitable for the detection and quantitation of Embrapa 5.1.

Invariance of the solid-liquid interfacial energy in electrowetting probed via capillary condensation.

Science.gov (United States)

Gupta, Rohini; Olivier, Gloria K; Frechette, Joelle

2010-07-20

Capillary condensation is employed to probe the solid-liquid interfacial energy in electrowetting on dielectric. The height of an annular water meniscus formed via capillary condensation inside the surface force apparatus is measured as a function of the potential applied across the meniscus and the dielectric stack where the meniscus is formed. According to the Kelvin equation, a decrease in the solid-liquid interfacial energy at constant temperature and relative humidity should lead to an increase in the meniscus height. Our experimental results on nanometer-sized meniscus are in agreement with the work of Mugele [J. Phys.: Condens. Matter 2007, 19, 375112] and unequivocally demonstrate that the real contact angle (or the solid-liquid interfacial energy) remains unaltered in electrowetting on dielectric.

Real-time PCR of the mammalian hydroxymethylbilane synthase (HMBS gene for analysis of flea (Ctenocephalides felis feeding patterns on dogs

Directory of Open Access Journals (Sweden)

Wang Chengming

2012-01-01

Full Text Available Abstract Background Precise data on quantitative kinetics of blood feeding of fleas, particularly immediately after contact with the host, are essential for understanding dynamics of flea-borne disease transmission and for evaluating flea control strategies. Standard methods used are inadequate for studies that simulate early events after real-life flea access to the host. Methods Here, we developed a novel quantitative polymerase chain reaction targeting mammalian DNA within fleas to quantify blood consumption with high sensitivity and specificity. We used primers and fluorescent probes that amplify the hydroxymethylbilane synthase (HMBS gene, an evolutionary divergent gene that is unlikely to be detected in insects by mammalian-specific primers and probes. To validate this assay, fleas were placed on dogs, allowed to distribute in the hair, and removed at specific time points with single-use combs. Fleas were then immediately homogenized by vigorous shaking with ceramic beads in guanidinium-based DNA preservation buffer for DNA extraction. Results The specificity of this assay was ascertained by amplification of canine, feline and equine blood with differential product melting temperatures (Tm, and lack of amplification of bovine and porcine blood and of adult fleas reared from larvae fed with bovine blood. Sensitivity of the assay was established by limiting dilution and detection of single copies of HMBS DNA equivalent to 0.043 nL blood. Application of the assay indicated that after 15 minutes on a dog, male and female fleas had ingested low, but similar amounts of approximately 1.1. nL blood. Saturation uptake of 118 and 100 nL blood per flea was found at 30 and 60 min on the dog, respectively. Conclusions The HMBS PCR method developed here offers the advantages of both exquisite sensitivity and specificity that make it superior to other approaches for quantification of blood ingested by fleas. The capability to detect minute quantities of

Real-world comparison of two molecular methods for detection of respiratory viruses

Directory of Open Access Journals (Sweden)

Miller E Kathryn

2011-06-01

Full Text Available Abstract Background Molecular polymerase chain reaction (PCR based assays are increasingly used to diagnose viral respiratory infections and conduct epidemiology studies. Molecular assays have generally been evaluated by comparing them to conventional direct fluorescent antibody (DFA or viral culture techniques, with few published direct comparisons between molecular methods or between institutions. We sought to perform a real-world comparison of two molecular respiratory viral diagnostic methods between two experienced respiratory virus research laboratories. Methods We tested nasal and throat swab specimens obtained from 225 infants with respiratory illness for 11 common respiratory viruses using both a multiplex assay (Respiratory MultiCode-PLx Assay [RMA] and individual real-time RT-PCR (RT-rtPCR. Results Both assays detected viruses in more than 70% of specimens, but there was discordance. The RMA assay detected significantly more human metapneumovirus (HMPV and respiratory syncytial virus (RSV, while RT-rtPCR detected significantly more influenza A. We speculated that primer differences accounted for these discrepancies and redesigned the primers and probes for influenza A in the RMA assay, and for HMPV and RSV in the RT-rtPCR assay. The tests were then repeated and again compared. The new primers led to improved detection of HMPV and RSV by RT-rtPCR assay, but the RMA assay remained similar in terms of influenza detection. Conclusions Given the absence of a gold standard, clinical and research laboratories should regularly correlate the results of molecular assays with other PCR based assays, other laboratories, and with standard virologic methods to ensure consistency and accuracy.

MethPrimer: designing primers for methylation PCRs.

Science.gov (United States)

Li, Long-Cheng; Dahiya, Rajvir

2002-11-01

DNA methylation is an epigenetic mechanism of gene regulation. Bisulfite- conversion-based PCR methods, such as bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP), remain the most commonly used techniques for methylation mapping. Existing primer design programs developed for standard PCR cannot handle primer design for bisulfite-conversion-based PCRs due to changes in DNA sequence context caused by bisulfite treatment and many special constraints both on the primers and the region to be amplified for such experiments. Therefore, the present study was designed to develop a program for such applications. MethPrimer, based on Primer 3, is a program for designing PCR primers for methylation mapping. It first takes a DNA sequence as its input and searches the sequence for potential CpG islands. Primers are then picked around the predicted CpG islands or around regions specified by users. MethPrimer can design primers for BSP and MSP. Results of primer selection are delivered through a web browser in text and in graphic view.

Development of a multiplex qPCR in real time for quantification and differential diagnosis of Salmonella Gallinarum and Salmonella Pullorum.

Science.gov (United States)

Rubio, Marcela da Silva; Penha Filho, Rafael Antonio Casarin; Almeida, Adriana Maria de; Berchieri, Angelo

2017-12-01

Currently there are 2659 Salmonella serovars. The host-specific biovars Salmonella Pullorum and Salmonella Gallinarum cause systemic infections in food-producing and wild birds. Fast diagnosis is crucial to control the dissemination in avian environments. The present work describes the development of a multiplex qPCR in real time using a low-cost DNA dye (SYBr Green) to identify and quantify these biovars. Primers were chosen based on genomic regions of difference (RoD) and optimized to control dimers. Primers pSGP detect both host-specific biovars but not other serovars and pSG and pSP differentiate biovars. Three amplicons showed different melting temperatures (Tm), allowing differentiation. The pSGP amplicon (97 bp) showed Tm of 78°C for both biovars. The pSG amplicon (273 bp) showed a Tm of 86.2°C for S. Gallinarum and pSP amplicon (260 bp) dissociated at 84.8°C for S. Pullorum identification. The multiplex qPCR in real time showed high sensitivity and was capable of quantifying 10 8 -10 1 CFU of these biovars.

Real-Time Congestion Management in Distribution Networks by Flexible Demand Swap

DEFF Research Database (Denmark)

Huang, Shaojun; Wu, Qiuwei

2017-01-01

In addition to the day-ahead congestion management in distribution networks, the real-time congestion management is very important because many unforeseen events can occur at the real operation time, e.g. loss of generation of distributed energy resources (DERs) or inaccurate forecast of energy...... pumps (HPs) for real time congestion management. The swap method can maintain the power balance of the system and avoid the imbalance cost of activating the flexibility service. An algorithm for forming swaps through optimal power flow (OPF) and mixed integer linear programming (MILP) is proposed...... consumption or production. Flexibility service from demand will be a good option to solve the real-time congestions if the cost of activating the flexibility service is fully addressed. This paper proposes a new method, namely “swap”, to employ the flexibility service from electric vehicles (EVs) and heat...

First discussion for fostering the photovoltaic energy in Mexico; Primer coloquio para el fomento de la energia fotovoltaica en Mexico

Energy Technology Data Exchange (ETDEWEB)

NONE

2007-06-15

The varied spheres (political, environmental, economic, scientific and social) day by day are looking for the key issues, which are going to make them to preserve or disappear either in the present or in the future. Therefore, it was carried out the first conversation in the State of Zacatecas, Mexico. Here there were shown different advances related to the renewable energies by those spheres. Generally speaking, it was in this event where there were gather together private and government organs in order to present every issue related to the use and to the promotion of the renewable energies. By these means, it was probed that the renewable energies are: the current market, the groundbreaking technology, the best option friendly-environment, the panacea for the society and for the improvement of the economy of many countries both developing countries and developed countries. The renewable energy topic is seen from different point of views. [Spanish] Las diferentes esferas que rigen el dia a dia; es decir, la politica, el medio ambiente, la economia, las ciencias y la sociedad, siempre estan en busca de cuestiones que las hagan crecer y evolucionar para asi seguir ocupando un espacio no solo en el presente sino tambien en el futuro. En esta ocasion fue en el primer coloquio, realizado en el Estado de Zacatecas, Mexico, donde dichas esferas se reunieron con el fin de mostrar sus diversos avances acerca de las energias fotovoltaicas. En otras palabras, fue en este coloquio donde se reunieron organos privados y gubernamentales con el fin de mostrar todo lo relacionado con el uso y la promocion de las energias renovables. Comprobando que las energias renovables son tanto: el mercado de hoy, la tecnologia de punta, la mejor opcion ambiental, la panacea para la sociedad y para la mejora de la economia de muchos paises en vias de desarrollo y de primer mundo. En estas ponencias no solo se habla de las energias renovables desde un aspecto cientifico, sino tambien financiero

A sensitive detection method for MPLW515L or MPLW515K mutation in chronic myeloproliferative disorders with locked nucleic acid-modified probes and real-time polymerase chain reaction.

OpenAIRE

Alessandro, Pancrazzi; Paola, Guglielmelli; Vanessa, Ponziani; Gaetano, Bergamaschi; Alberto, Bosi; Giovanni, Barosi; Alessandro M, Vannucchi

2008-01-01

Acquired mutations in the juxtamembrane region of MPL (W515K or W515L), the receptor for thrombopoietin, have been described in patients with primary myelofibrosis or essential thrombocythemia, which are chronic myeloproliferative disorders. We have developed a real-time polymerase chain reaction assay for the detection and quantification of MPL mutations that is based on locked nucleic acid fluorescent probes. Mutational analysis was performed using DNA from granulocytes. Reference curves we...

A data acquisition system for real-time magnetic equilibrium reconstruction on ASDEX Upgrade and its application to NTM stabilization experiments

Energy Technology Data Exchange (ETDEWEB)

Giannone, L., E-mail: Louis.Giannone@ipp.mpg.de [Max Planck Institute for Plasma Physics, EURATOM Association, 85748 Garching (Germany); Reich, M.; Maraschek, M.; Poli, E.; Rapson, C.; Barrera, L.; McDermott, R.; Mlynek, A. [Max Planck Institute for Plasma Physics, EURATOM Association, 85748 Garching (Germany); Ruan, Q. [National Instruments, Austin, TX 78759-3504 (United States); Treutterer, W. [Max Planck Institute for Plasma Physics, EURATOM Association, 85748 Garching (Germany); Wenzel, L. [National Instruments, Austin, TX 78759-3504 (United States); Bock, A.; Conway, G.; Fischer, R.; Fuchs, J.C.; Lackner, K. [Max Planck Institute for Plasma Physics, EURATOM Association, 85748 Garching (Germany); McCarthy, P.J. [Department of Physics, University College Cork, Association EURATOM-DCU, Cork (Ireland); Preuss, R. [Max Planck Institute for Plasma Physics, EURATOM Association, 85748 Garching (Germany); Rampp, M. [Computing Centre (RZG) of the Max Planck Society and the Max Planck Institute for Plasma Physics, 85748 Garching (Germany); Schuhbeck, K.H. [Max Planck Institute for Plasma Physics, EURATOM Association, 85748 Garching (Germany); and others

2013-12-15

Highlights: • Calculation of real-time tokamak magnetic equilibrium with constraints from magnetic probes. • Parallel equilibrium calculation including the Motional Stark Effect diagnostic as additional constraints. • Feedback control of mirror for pre-emptive ECCD stabilization of neo-classical tearing modes. • Probe calibration by individual poloidal field coil currents. • Optimized parameters for poloidal field coil location, integrator gains and the location and orientation of magnetic probes. -- Abstract: The pre-emptive stabilization of a neoclassical tearing mode, NTM, requires the calculation of the tokamak magnetic equilibrium in real-time. A launcher mirror is positioned to deposit electron cyclotron current drive on the rational surface where the NTM should appear. A real-time Grad–Shafranov solver using constraints from magnetic probe, flux loop and Motional Stark Effect measurements has been developed to locate these rational surfaces and deliver this information to the mirror controller in real-time. A novel algorithm significantly reduces the number of operations required in the first and second step of the solver. Contour integrals are carried out to calculate the q profile as a function of normalized radius and the rational surfaces are found by spline interpolation. A cycle time of 0.6 ms for calculating two tokamak equilibria in parallel using four current basis functions with magnetic constraints only and using six current basis functions with magnetic and MSE constraints has been achieved. Using these tools, pre-emptive stabilization of a m/n = 3/2 NTM mode in ASDEX Upgrade could be demonstrated.

Real Time Emulation of Dynamic Tariff for Congestion Management in Distribution Networks

DEFF Research Database (Denmark)

Rasmussen, Theis Bo; Wu, Qiuwei; Huang, Shaojun

2016-01-01

This paper presents the real time evaluation of the dynamic tariff (DT) method for alleviating congestion in a distribution networks with high penetration of distributed energy resources (DERs). The DT method is implemented in a real time digital testing platform that emulates a real distribution...

The ability of T2/B4 primers to detect Leishmania infantum among ...

African Journals Online (AJOL)

SERVER

2008-04-03

Apr 3, 2008 ... Reverse Primer (5`-CCT CTC TTT TTT CNC TGT GC-3`). (Schönian et al., 1996),. B. Forward Primer (RV1) (5`-GTG GGG GAG GGG CGT TCT-3`) and Reverse Primer (RV2) (5`-ATT TTA CAC CAA CCC CCA GTT-. 3`) (Lachaud et al., 2002; Reale et al., 1999),. C. Forward Primer (T2) (5`-CGG CTT CGC ...

Evaluating effectiveness of real-time advanced traveler information systems using a small test vehicle fleet

Science.gov (United States)

1997-01-01

ADVANCE was an in-vehicle advanced traveler information system (ATIS) providing route guidance in real time that operated in the northwestern portion and northwest suburbs of Chicago, Illinois. It used probe vehicles to generate dynamically travel ti...

Energy Resources Intelligent Management using on line real-time simulation: A decision support tool for sustainable manufacturing

International Nuclear Information System (INIS)

Cassettari, Lucia; Bendato, Ilaria; Mosca, Marco; Mosca, Roberto

2017-01-01

Highlights: • A new way to manage the self production of energy from RES in manufacturing industry. • Optimization in terms of both energy costs and environmental impact (CO_2 emissions). • The use of on-line real-time Discrete Event Simulation to manage the stochasticity. • The energy production plan is dynamically suited to weather and manufacturing needs. • The test case presented highlights the effectiveness of the proposed methodology. - Abstract: At a historic time when the eco-sustainability of industrial manufacturing is considered one of the cornerstones of relations between people and the environment, the use of energy from Renewable Energy Sources (RES) has become a fundamental element of this new vision. After years of vain attempts to hammer out an agreement to significantly reduce CO_2 emissions produced by the burning of fossil fuels, a binding global accord was finally reached (Paris December 2015 - New York April 2016). As we know, however, some of the most commonly-used RES, such as solar or wind, present the problem of discontinuity in energy production due to the variability of weather and climatic conditions. For this reason, the authors thought it appropriate to study a new methodology capable of marrying industrial users’ instantaneous need for energy with the production capacity of Renewable Energy Sources, supplemented, when necessary, by energy created through self-production and possibly acquired from third-party suppliers. All of this in order to minimize CO_2 emissions and company energy costs. Given the massive presence of stochastic and sometimes aleatory elements, for the proposed energy management model we have used both Monte Carlo simulation and on-line real-time Discrete Event Simulation (DES), as well as appropriate predictive algorithms. A test conducted on a tannery located in southern Italy, equipped with a 700 KWp photovoltaic installation, showed extremely interesting results, both economically and

Real-Time Wavelet-Based Coordinated Control of Hybrid Energy Storage Systems for Denoising and Flattening Wind Power Output

Directory of Open Access Journals (Sweden)

Tran Thai Trung

2014-10-01

Full Text Available Since the penetration level of wind energy is continuously increasing, the negative impact caused by the fluctuation of wind power output needs to be carefully managed. This paper proposes a novel real-time coordinated control algorithm based on a wavelet transform to mitigate both short-term and long-term fluctuations by using a hybrid energy storage system (HESS. The short-term fluctuation is eliminated by using an electric double-layer capacitor (EDLC, while the wind-HESS system output is kept constant during each 10-min period by a Ni-MH battery (NB. State-of-charge (SOC control strategies for both EDLC and NB are proposed to maintain the SOC level of storage within safe operating limits. A ramp rate limitation (RRL requirement is also considered in the proposed algorithm. The effectiveness of the proposed algorithm has been tested by using real time simulation. The simulation model of the wind-HESS system is developed in the real-time digital simulator (RTDS/RSCAD environment. The proposed algorithm is also implemented as a user defined model of the RSCAD. The simulation results demonstrate that the HESS with the proposed control algorithm can indeed assist in dealing with the variation of wind power generation. Moreover, the proposed method shows better performance in smoothing out the fluctuation and managing the SOC of battery and EDLC than the simple moving average (SMA based method.

Assessing the benefits of residential demand response in a real time distribution energy market

International Nuclear Information System (INIS)

Siano, Pierluigi; Sarno, Debora

2016-01-01

Highlights: • A new probabilistic methodology, integrating DR in a distribution energy market is proposed. • The method can alleviate distribution network congestions. • This method based on D-LMPs allows cost savings for end-user customers. • Innovative thermal and shiftable loads Real Time control algorithms are also presented. - Abstract: In the field of electricity distribution networks and with the advent of smart grids and microgrids, the use of Distribution Locational Marginal Price (D-LMPs) in a Real Time (RT) distribution market managed by a Distribution System Operator (DSO) is discussed in presence of empowered residential end-users that are able to bid for energy by a demand aggregator while following Demand Response (DR) initiatives. Each customer is provided by a transactive controller, which reads the locational market signals and answers with a bid taking into account the user preferences about some appliances involved in DR activities and controlled by smart plugs-in. In particular, Heating Ventilation and Air Conditioning (HVAC) appliances and shiftable loads are controlled so that their consumption profile can be modified according to the price of energy. In order to assess the effectiveness of the proposed method in terms of energy and cost saving, an innovative probabilistic methodology for evaluating the impact of residential DR choices considering uncertainties related to load demand, user preferences, environmental conditions, house thermal behavior and wholesale market trends has been proposed. The uncertainties related to the stochastic variations of the variables involved are modeled by using the Monte Carlo Simulation (MCS) method. The combination of MCS and RT distribution market simulation based on D-LMPs are used to assess the operation and impact of the DR method over one month. Simulations results on an 84-buses distribution network confirmed that the proposed method allows saving costs for residential end-users and making

Real-time control of electron density in a capacitively coupled plasma

International Nuclear Information System (INIS)

Keville, Bernard; Gaman, Cezar; Turner, Miles M.; Zhang Yang; Daniels, Stephen; Holohan, Anthony M.

2013-01-01

Reactive ion etching (RIE) is sensitive to changes in chamber conditions, such as wall seasoning, which have a deleterious effect on process reproducibility. The application of real time, closed loop control to RIE may reduce this sensitivity and facilitate production with tighter tolerances. The real-time, closed loop control of plasma density with RF power in a capacitively coupled argon plasma using a hairpin resonance probe as a sensor is described. Elementary control analysis shows that an integral controller provides stable and effective set point tracking and disturbance attenuation. The trade off between performance and robustness may be quantified in terms of one parameter, namely the position of the closed loop pole. Experimental results are presented, which are consistent with the theoretical analysis.

Real-time in vivo luminescence dosimetry in radiotherapy and mammography using Al{sub 2}O{sub 3}:C

Energy Technology Data Exchange (ETDEWEB)

Aznar, M.C.

2005-06-15

New treatment and clinical imaging techniques have created a need for accurate and practical in vivo dosimeters in radiation medicine. This work describes the development of a new optical-fiber radiation dosimeter system, based on radioluminescence (RL) and optically stimulated luminescence (OSL) from carbon-doped aluminium oxide (Al2O3:C), for applications in radiotherapy and mammography. This system offers several features, such as a small detector, high sensitivity, real-time read-out, and the ability to measure both dose rate and absorbed dose. Measurement protocols and algorithms for the correction of responses were developed to enable a reliable absorbed dose assessment from the RL and OSL signals. At radiotherapy energies, the variation of the signal with beam parameters was smaller than 1% (1 SD). Treatment-like experiments in phantoms, and in vivo measurements during complex patient treatments (such as intensity-modulated radiation therapy) indicate that the RL/OSL dosimetry system can reliably measure the absorbed dose within 2%. The real-time RL signal also enables an individual dose assessment from each field. The RL/OSL dosimetry system was also used during mammography examinations. In such conditions, the reproducibility of the measurements showed to be around 3%. In vivo measurements on three patients showed that the presence of the RL/OSL probes did not degrade the diagnostic quality of the radiograph and that the system could be used to measure exit doses (i.e., absorbed doses on the inferior surface of the breast). A Monte Carlo study proved that the energy dependence of the RL/OSL system at these low energies could be reduced by optimizing the design of the probes. It is concluded that the new RL/OSL dosimetry system shows considerable potential for applications in both radiotherapy and mammography. (au)

Real-time shadows

CERN Document Server

Eisemann, Elmar; Assarsson, Ulf; Wimmer, Michael

2011-01-01

Important elements of games, movies, and other computer-generated content, shadows are crucial for enhancing realism and providing important visual cues. In recent years, there have been notable improvements in visual quality and speed, making high-quality realistic real-time shadows a reachable goal. Real-Time Shadows is a comprehensive guide to the theory and practice of real-time shadow techniques. It covers a large variety of different effects, including hard, soft, volumetric, and semi-transparent shadows.The book explains the basics as well as many advanced aspects related to the domain

Internally controlled, generic real-time PCR for quantification and multiplex real-time PCR with serotype-specific probes for serotyping of dengue virus infections

NARCIS (Netherlands)

Menting, Sandra; Thai, Khoa T. D.; Nga, Tran T. T.; Phuong, Hoang L.; Klatser, Paul; Wolthers, Katja C.; Binh, Tran Q.; de Vries, Peter J.; Beld, Marcel

2011-01-01

Dengue has become a global public health problem and a sensitive diagnostic test for early phase detection can be life saving. An internally controlled, generic real-time PCR was developed and validated by testing serial dilutions of a DENV positive control RNA in the presence of a fixed amount of

Dependable Real-Time Systems

Science.gov (United States)

1991-09-30

0196 or 413 545-0720 PI E-mail Address: krithi@nirvan.cs.umass.edu, stankovic(ocs.umass.edu Grant or Contract Title: Dependable Real - Time Systems Grant...Dependable Real - Time Systems " Grant or Contract Number: N00014-85-k-0398 L " Reporting Period: 1 Oct 87 - 30 Sep 91 , 2. Summary of Accomplishments ’ 2.1 Our...in developing a sound approach to scheduling tasks in complex real - time systems , (2) developed a real-time operating system kernel, a preliminary

Energy Tracking in Classrooms - A Real Time Experiment with Grade 5 Students

Science.gov (United States)

Lam, H. M.; Ho, F.

2015-12-01

ISF Academy, a K-G12 school in Hong Kong with over 1500 students and currently spanning 3 buildings, is retrofitting the school with an energy tracking system in three phases. The first phase during the fall of 2015 will include retrofitting eight Grade 5 classrooms. This new program will show the daily energy usage data from these classrooms. The Grade 5 students receive feedback on their energy use in real time as they compete over two months in their homeroom classes to lower their electrical use, and subsequently their carbon footprint. This competition style initiative will teach the 180 Grade 5 students about their energy usage in a fun and informative manner. ISF Academy has over 400 air-conditioners and we have already determined that the air conditioners are the largest single use of energy in the school. The energy tracking system installed and maintained by from Global Design Corporation utilizes uniquely identified current detectors attached to circuit breakers, to monitor electrical use of individual circuits. These detectors will also monitor the energy used for classroom lighting, fans and plugs, as well as the air conditioners. The system has been installed and the Grade 5 classrooms averaged between 40 kWh and 120 kWh of usage in May 2015. This data will be used as the baseline for the competition. Further analysis can also be done with the data, such as calculating the carbon emissions reduction throughout the school year, providing possible class learning activities and also aiding in future energy use and carbon footprint predictions. The data collected will help refine phase 2 and 3 of the installation, expanding the system to more buildings and also giving insight to the rollout of the system to the whole school when the systems are fully in place.

Development of real-time low energy electron calorimeter

International Nuclear Information System (INIS)

Noriah Mod Ali; Smith, F.A.

1999-01-01

A low energy electron beam calorimeter with a thin film window has been fabricated to facilitate a reliable method of dose assessment for electron beam energies down to 200 keV. The system was designed to incorporate a data-logger in order that it could be used on the self-shielded 200 keV facility at MINT. In use, the calorimeter started logging temperature a short time before it passed under the beam and it continued taking data until well after the end of the irradiation. Data could be retrieved at any time after the calorimeter had emerged from the irradiator

Quantitative real-time PCR technique for the identification of E. coli residual DNA in streptokinase recombinant product.

Science.gov (United States)

Fazelahi, Mansoureh; Kia, Vahid; Kaghazian, Hooman; Paryan, Mahdi

2017-11-26

Recombinant streptokinase is a biopharmaceutical which is usually produced in E. coli. Residual DNA as a contamination and risk factor may remain in the product. It is necessary to control the production procedure to exclude any possible contamination. The aim of the present study was to develop a highly specific and sensitive quantitative real-time PCR-based method to determine the amount of E. coli DNA in recombinant streptokinase. A specific primers and a probe was designed to detect all strains of E. coli. To determine the specificity, in addition to using NCBI BLASTn, 28 samples including human, bacterial, and viral genomes were used. The results confirmed that the assay detects no genomic DNA but E. coli's and the specificity was determined to be 100%. To determine the sensitivity and limit of detection of the assay, a 10-fold serial dilution (10 1 to 10 7 copies/µL) was tested in triplicate. The sensitivity of the test was determined to be 101 copies/µL or 35 fg/µL. Inter-assay and intra-assay were determined to be 0.86 and 1.69%, respectively. Based on the results, this assay can be used as an accurate method to evaluate the contamination of recombinant streptokinase in E. coli.

Strategies for the inclusion of an internal amplification control in conventional and real time PCR detection of Campylobacter spp. in chicken fecal samples

DEFF Research Database (Denmark)

Lund, Marianne; Madsen, Mogens

2006-01-01

To illustrate important issues in optimization of a PCR assay with an internal control four different primer combinations for conventional PCR, two non-competitive and two competitive set-ups for real time PCR were used for detection of Campylobacter spp. in chicken faecal samples....... In the conventional PCR assays the internal control was genomic DNA from Yersinia ruckeri, which is not found in chicken faeces. This internal control was also used in one of the set LIPS in real time PCR. In the three other set-ups different DNA fragments of 109 bp length prepared from two oligos of each 66 bp...... by a simple extension reaction was used. All assays were optimized to avoid loss of target sensitivity due to the presence of the internal control by adjusting the amount of internal control primers in the duplex assays and the amount of internal control in all assays. Furthermore. the assays were tested...

LabVIEW Real-Time

CERN Multimedia

CERN. Geneva; Flockhart, Ronald Bruce; Seppey, P

2003-01-01

With LabVIEW Real-Time, you can choose from a variety of RT Series hardware. Add a real-time data acquisition component into a larger measurement and automation system or create a single stand-alone real-time solution with data acquisition, signal conditioning, motion control, RS-232, GPIB instrumentation, and Ethernet connectivity. With the various hardware options, you can create a system to meet your precise needs today, while the modularity of the system means you can add to the solution as your system requirements grow. If you are interested in Reliable and Deterministic systems for Measurement and Automation, you will profit from this seminar. Agenda: Real-Time Overview LabVIEW RT Hardware Platforms - Linux on PXI Programming with LabVIEW RT Real-Time Operating Systems concepts Timing Applications Data Transfer

Immunity-based optimal estimation approach for a new real time group elevator dynamic control application for energy and time saving.

Science.gov (United States)

Baygin, Mehmet; Karakose, Mehmet

2013-01-01

Nowadays, the increasing use of group elevator control systems owing to increasing building heights makes the development of high-performance algorithms necessary in terms of time and energy saving. Although there are many studies in the literature about this topic, they are still not effective enough because they are not able to evaluate all features of system. In this paper, a new approach of immune system-based optimal estimate is studied for dynamic control of group elevator systems. The method is mainly based on estimation of optimal way by optimizing all calls with genetic, immune system and DNA computing algorithms, and it is evaluated with a fuzzy system. The system has a dynamic feature in terms of the situation of calls and the option of the most appropriate algorithm, and it also adaptively works in terms of parameters such as the number of floors and cabins. This new approach which provides both time and energy saving was carried out in real time. The experimental results comparatively demonstrate the effects of method. With dynamic and adaptive control approach in this study carried out, a significant progress on group elevator control systems has been achieved in terms of time and energy efficiency according to traditional methods.

Immunity-Based Optimal Estimation Approach for a New Real Time Group Elevator Dynamic Control Application for Energy and Time Saving

Directory of Open Access Journals (Sweden)

Mehmet Baygin

2013-01-01

Full Text Available Nowadays, the increasing use of group elevator control systems owing to increasing building heights makes the development of high-performance algorithms necessary in terms of time and energy saving. Although there are many studies in the literature about this topic, they are still not effective enough because they are not able to evaluate all features of system. In this paper, a new approach of immune system-based optimal estimate is studied for dynamic control of group elevator systems. The method is mainly based on estimation of optimal way by optimizing all calls with genetic, immune system and DNA computing algorithms, and it is evaluated with a fuzzy system. The system has a dynamic feature in terms of the situation of calls and the option of the most appropriate algorithm, and it also adaptively works in terms of parameters such as the number of floors and cabins. This new approach which provides both time and energy saving was carried out in real time. The experimental results comparatively demonstrate the effects of method. With dynamic and adaptive control approach in this study carried out, a significant progress on group elevator control systems has been achieved in terms of time and energy efficiency according to traditional methods.

Concepts of real time and semi-real time material control

International Nuclear Information System (INIS)

Lovett, J.E.

1975-01-01

After a brief consideration of the traditional material balance accounting on an MBA basis, this paper explores the basic concepts of real time and semi-real time material control, together with some of the major problems to be solved. Three types of short-term material control are discussed: storage, batch processing, and continuous processing. (DLC)

Real Time Systems

DEFF Research Database (Denmark)

Christensen, Knud Smed

2000-01-01

Describes fundamentals of parallel programming and a kernel for that. Describes methods for modelling and checking parallel problems. Real time problems.......Describes fundamentals of parallel programming and a kernel for that. Describes methods for modelling and checking parallel problems. Real time problems....

Amide I SFG Spectral Line Width Probes the Lipid-Peptide and Peptide-Peptide Interactions at Cell Membrane In Situ and in Real Time.

Science.gov (United States)

Zhang, Baixiong; Tan, Junjun; Li, Chuanzhao; Zhang, Jiahui; Ye, Shuji

2018-06-13

The balance of lipid-peptide and peptide-peptide interactions at cell membrane is essential to a large variety of cellular processes. In this study, we have experimentally demonstrated for the first time that sum frequency generation vibrational spectroscopy can be used to probe the peptide-peptide and lipid-peptide interactions in cell membrane in situ and in real time by determination of the line width of amide I band of protein backbone. Using a "benchmark" model of α-helical WALP23, it is found that the dominated lipid-peptide interaction causes a narrow line width of the amide I band, whereas the peptide-peptide interaction can markedly broaden the line width. When WALP23 molecules insert into the lipid bilayer, a quite narrow line width of the amide I band is observed because of the lipid-peptide interaction. In contrast, when the peptide lies down on the bilayer surface, the line width of amide I band becomes very broad owing to the peptide-peptide interaction. In terms of the real-time change in the line width, the transition from peptide-peptide interaction to lipid-peptide interaction is monitored during the insertion of WALP23 into 1,2-dipalmitoyl- sn-glycero-3-phospho-(1'- rac-glycerol) (DPPG) lipid bilayer. The dephasing time of a pure α-helical WALP23 in 1-palmitoyl-2-oleoyl- sn-glycero-3-phospho-(1'- rac-glycerol) and DPPG bilayer is determined to be 2.2 and 0.64 ps, respectively. The peptide-peptide interaction can largely accelerate the dephasing time.

Real time expert systems

International Nuclear Information System (INIS)

Asami, Tohru; Hashimoto, Kazuo; Yamamoto, Seiichi

1992-01-01

Recently, aiming at the application to the plant control for nuclear reactors and traffic and communication control, the research and the practical use of the expert system suitable to real time processing have become conspicuous. In this report, the condition for the required function to control the object that dynamically changes within a limited time is presented, and the technical difference between the real time expert system developed so as to satisfy it and the expert system of conventional type is explained with the actual examples and from theoretical aspect. The expert system of conventional type has the technical base in the problem-solving equipment originating in STRIPS. The real time expert system is applied to the fields accompanied by surveillance and control, to which conventional expert system is hard to be applied. The requirement for the real time expert system, the example of the real time expert system, and as the techniques of realizing real time processing, the realization of interruption processing, dispersion processing, and the mechanism of maintaining the consistency of knowledge are explained. (K.I.)

Real Time Pricing and the Real Live Firm

Energy Technology Data Exchange (ETDEWEB)

Moezzi, Mithra; Goldman, Charles; Sezgen, Osman; Bharvirkar, Ranjit; Hopper, Nicole

2004-05-26

Energy economists have long argued the benefits of real time pricing (RTP) of electricity. Their basis for modeling customers response to short-term fluctuations in electricity prices are based on theories of rational firm behavior, where management strives to minimize operating costs and optimize profit, and labor, capital and energy are potential substitutes in the firm's production function. How well do private firms and public sector institutions operating conditions, knowledge structures, decision-making practices, and external relationships comport with these assumptions and how might this impact price response? We discuss these issues on the basis of interviews with 29 large (over 2 MW) industrial, commercial, and institutional customers in the Niagara Mohawk Power Corporation service territory that have faced day-ahead electricity market prices since 1998. We look at stories interviewees told about why and how they respond to RTP, why some customers report that they can't, and why even if they can, they don't. Some firms respond as theorized, and we describe their load curtailment strategies. About half of our interviewees reported that they were unable to either shift or forego electricity consumption even when prices are high ($0.50/kWh). Reasons customers gave for why they weren't price-responsive include implicit value placed on reliability, pricing structures, lack of flexibility in adjusting production inputs, just-in-time practices, perceived barriers to onsite generation, and insufficient time. We draw these observations into a framework that could help refine economic theory of dynamic pricing by providing real-world descriptions of how firms behave and why.

Development and Validation of a TaqMan Real-Time PCR Assay for the Specific Detection and Quantification of Fusarium fujikuroi in Rice Plants and Seeds.

Science.gov (United States)

Carneiro, Greice Amaral; Matić, Slavica; Ortu, Giuseppe; Garibaldi, Angelo; Spadaro, Davide; Gullino, Maria Lodovica

2017-07-01

Bakanae disease, which is caused by the seedborne pathogen Fusarium fujikuroi, is found throughout the world on rice. A TaqMan real-time PCR has been developed on the TEF 1-α gene to detect F. fujikuroi in different rice tissues. Three primer/probe sets were tested. The selected set produced an amplicon of 84 bp and was specific for F. fujikuroi with respect to eight Fusarium species of rice and six other rice common pathogens. The assay was validated for specificity, selectivity, sensitivity, repeatability, and reproducibility. The detection limit was set at 27.5 fg of DNA, which is approximately equivalent to one haploid genome of F. fujikuroi. The developed TaqMan real-time assay was able to efficiently detect and quantify F. fujikuroi from rice culms, leaves, roots, and seeds. At 1 week post-germination (wpg), the pathogen was more diffused in the green tissues, while at 3 wpg it was uniformly spread also in the roots. The highest concentration of F. fujikuroi was measured in the M6 cultivar, which showed around 1,450 fungal cells/g. The assay was sufficiently sensitive to detect a few genomic equivalents in the rice seeds, corresponding to 9.89 F. fujikuroi cells/g. The assay permitted bakanae disease to be detected in asymptomatic tissues at the early rice development stages.

Dynamics of Vaginal Bacterial Communities in Women Developing Bacterial Vaginosis, Candidiasis, or No Infection, Analyzed by PCR-Denaturing Gradient Gel Electrophoresis and Real-Time PCR▿

Science.gov (United States)

Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G. G.; Brigidi, Patrizia

2007-01-01

The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA. PMID:17644631

Dynamics of vaginal bacterial communities in women developing bacterial vaginosis, candidiasis, or no infection, analyzed by PCR-denaturing gradient gel electrophoresis and real-time PCR.

Science.gov (United States)

Vitali, Beatrice; Pugliese, Ciro; Biagi, Elena; Candela, Marco; Turroni, Silvia; Bellen, Gert; Donders, Gilbert G G; Brigidi, Patrizia

2007-09-01

The microbial flora of the vagina plays a major role in preventing genital infections, including bacterial vaginosis (BV) and candidiasis (CA). An integrated approach based on PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and real-time PCR was used to study the structure and dynamics of bacterial communities in vaginal fluids of healthy women and patients developing BV and CA. Universal eubacterial primers and Lactobacillus genus-specific primers, both targeted at 16S rRNA genes, were used in DGGE and real-time PCR analysis, respectively. The DGGE profiles revealed that the vaginal flora was dominated by Lactobacillus species under healthy conditions, whereas several potentially pathogenic bacteria were present in the flora of women with BV. Lactobacilli were the predominant bacterial population in the vagina for patients affected by CA, but changes in the composition of Lactobacillus species were observed. Real-time PCR analysis allowed the quantitative estimation of variations in lactobacilli associated with BV and CA diseases. A statistically significant decrease in the relative abundance of lactobacilli was found in vaginal fluids of patients with BV compared to the relative abundance of lactobacilli in the vaginal fluids of healthy women and patients with CA.

Development of real-time PCR for detection and quantitation of Streptococcus parauberis.

Science.gov (United States)

Nguyen, T L; Lim, Y J; Kim, D-H; Austin, B

2016-01-01

Streptococcus parauberis is an increasing threat to aquaculture of olive flounder, Paralichthys olivaceus Temminck & Schlegel, in South Korea. We developed a real-time polymerase chain reaction (PCR) method using the TaqMan probe assay to detect and quantify S. parauberis by targeting the gyrB gene sequences, which are effective for molecular analysis of the genus Streptococcus. Our real-time PCR assay is capable of detecting 10 fg of genomic DNA per reaction. The intra- and interassay coefficient of variation (CV) values ranged from 0.42-1.95%, demonstrating that the assay has good reproducibility. There was not any cross-reactivity to Streptococcus iniae or to other streptococcal/lactococcal fish pathogens, such as S. agalactiae and Lactococcus garvieae, indicating that the assay is highly specific to S. parauberis. The results of the real-time PCR assay corresponded well to those of conventional culture assays for S. parauberis from inoculated tissue homogenates (r = 0.957; P < 0.05). Hence, this sensitive and specific real-time PCR is a valuable tool for diagnostic quantitation of S. parauberis in clinical samples. © 2014 John Wiley & Sons Ltd.

Use of real-time qPCR to quantify members of the unculturable heterotrophic bacterial community in a deep sea marine sponge, Vetulina sp.

Science.gov (United States)

Cassler, M; Peterson, C L; Ledger, A; Pomponi, S A; Wright, A E; Winegar, R; McCarthy, P J; Lopez, J V

2008-04-01

In this report, real-time quantitative PCR (TaqMan qPCR) of the small subunit (SSU) 16S-like rRNA molecule, a universal phylogenetic marker, was used to quantify the relative abundance of individual bacterial members of a diverse, yet mostly unculturable, microbial community from a marine sponge. Molecular phylogenetic analyses of bacterial communities derived from Caribbean Lithistid sponges have shown a wide diversity of microbes that included at least six major subdivisions; however, very little overlap was observed between the culturable and unculturable microbial communities. Based on sequence data of three culture-independent Lithistid-derived representative bacteria, we designed probe/primer sets for TaqMan qPCR to quantitatively characterize selected microbial residents in a Lithistid sponge, Vetulina, metagenome. TaqMan assays included specificity testing, DNA limit of detection analysis, and quantification of specific microbial rRNA sequences such as Nitrospira-like microbes and Actinobacteria up to 172 million copies per microgram per Lithistid sponge metagenome. By contrast, qPCR amplification with probes designed for common previously cultured sponge-associated bacteria in the genera Rheinheimera and Marinomonas and a representative of the CFB group resulted in only minimal detection of the Rheiheimera in total DNA extracted from the sponge. These data verify that a large portion of the microbial community within Lithistid sponges may consist of currently unculturable microorganisms.

The accuracy of using the lytA-gene to distinguish Streptococcus pneumoniae from related species

DEFF Research Database (Denmark)

Greve, Thomas; Møller, Jens Kjølseth

2012-01-01

with primers and probes. The remaining 11 S. pneumoniae strains could be placed in a different cluster, which also contained the five S. mitis and two S. pseudopneumoniae strains. All strains had no match with primers and probes. The S. pneumoniae strains in the second cluster were all characterised by being....... The real-time PCR targeting the lytA-gene thus constitutes a sensitive and specific assay that distinguishes S. pneumoniae from its close relatives in the Mitis group....

VizPrimer: a web server for visualized PCR primer design based on known gene structure.

Science.gov (United States)

Zhou, Yang; Qu, Wubin; Lu, Yiming; Zhang, Yanchun; Wang, Xiaolei; Zhao, Dongsheng; Yang, Yi; Zhang, Chenggang

2011-12-15

The visualization of gene structure plays an important role in polymerase chain reaction (PCR) primer design, especially for eukaryotic genes with a number of splice variants that users need to distinguish between via PCR. Here, we describe a visualized web server for primer design named VizPrimer. It utilizes the new information technology (IT) tools, HTML5 to display gene structure and JavaScript to interact with the users. In VizPrimer, the users can focus their attention on the gene structure and primer design strategy, without wasting time calculating the exon positions of splice variants or manually configuring complicated parameters. In addition, VizPrimer is also suitable for the design of PCR primers for amplifying open reading frames and detecting single nucleotide polymorphisms (SNPs). VizPrimer is freely available at http://biocompute.bmi.ac.cn/CZlab/VizPrimer/. The web server supported browsers: Chrome (≥5.0), Firefox (≥3.0), Safari (≥4.0) and Opera (≥10.0). zhangcg@bmi.ac.cn; yangyi528@vip.sina.com.

Specific and sensitive diagnosis of syphilis using a real-time PCR for Treponema pallidum

NARCIS (Netherlands)

Koek, A. G.; Bruisten, S. M.; Dierdorp, M.; van Dam, A. P.; Templeton, K.

2006-01-01

A real-time PCR assay with a Taqman probe was developed that targeted the polA gene of Treponema pallidum. The test was validated using an analytical panel (n = 140) and a clinical panel of genital samples (n = 112) from patients attending a sexually transmitted infections clinic. High sensitivities

Real Time Seismic Prediction while Drilling

Science.gov (United States)

Schilling, F. R.; Bohlen, T.; Edelmann, T.; Kassel, A.; Heim, A.; Gehring, M.; Lüth, S.; Giese, R.; Jaksch, K.; Rechlin, A.; Kopf, M.; Stahlmann, J.; Gattermann, J.; Bruns, B.

2009-12-01

Efficient and safe drilling is a prerequisite to enhance the mobility of people and goods, to improve the traffic as well as utility infrastructure of growing megacities, and to ensure the growing energy demand while building geothermal and in hydroelectric power plants. Construction within the underground is often building within the unknown. An enhanced risk potential for people and the underground building may arise if drilling enters fracture zones, karsts, brittle rocks, mixed solid and soft rocks, caves, or anthropogenic obstacles. Knowing about the material behavior ahead of the drilling allows reducing the risk during drilling and construction operation. In drilling operations direct observations from boreholes can be complemented with geophysical investigations. In this presentation we focus on “real time” seismic prediction while drilling which is seen as a prerequisite while using geophysical methods in modern drilling operations. In solid rocks P- and S-wave velocity, refraction and reflection as well as seismic wave attenuation can be used for the interpretation of structures ahead of the drilling. An Integrated Seismic Imaging System (ISIS) for exploration ahead of a construction is used, where a pneumatic hammer or a magnetostrictive vibration source generate repetitive signals behind the tunneling machine. Tube waves are generated which travel along the tunnel to the working face. There the tube waves are converted to mainly S- but also P-Waves which interact with the formation ahead of the heading face. The reflected or refracted waves travel back to the working front are converted back to tube waves and recorded using three-component geophones which are fit into the tips of anchor rods. In near real time, the ISIS software allows for an integrated 3D imaging and interpretation of the observed data, geological and geotechnical parameters. Fracture zones, heterogeneities, and variations in the rock properties can be revealed during the drilling

Real-Time Business Intelligence in the MIRABEL Smart Grid System

DEFF Research Database (Denmark)

Fischer, Ulrike; Kaulakiene, Dalia; Khalefa, Mohamed

2012-01-01

of energy related data, and must be able to react rapidly (but intelligently) when conditions change, leading to substantial real-time business intelligence challenges. This paper discusses these challenges and presents data management solutions in the European smart grid project MIRABEL. These solutions......) data. Experimental studies show that the proposed solutions support important real-time business intelligence tasks in a smart grid system....

Real-time monitoring and operational control of drinking-water systems

CERN Document Server

Ocampo-Martínez, Carlos; Pérez, Ramon; Cembrano, Gabriela; Quevedo, Joseba; Escobet, Teresa

2017-01-01

This book presents a set of approaches for the real-time monitoring and control of drinking-water networks based on advanced information and communication technologies. It shows the reader how to achieve significant improvements in efficiency in terms of water use, energy consumption, water loss minimization, and water quality guarantees. The methods and approaches presented are illustrated and have been applied using real-life pilot demonstrations based on the drinking-water network in Barcelona, Spain. The proposed approaches and tools cover: • decision-making support for real-time optimal control of water transport networks, explaining how stochastic model predictive control algorithms that take explicit account of uncertainties associated with energy prices and real demand allow the main flow and pressure actuators—pumping stations and pressure regulation valves—and intermediate storage tanks to be operated to meet demand using the most sustainable types of source and with minimum electricity costs;...

A real-time RT-PCR method to detect viable Giardia lamblia cysts in environmental waters.

Science.gov (United States)

Baque, Robert H; Gilliam, Amy O; Robles, Liza D; Jakubowski, Walter; Slifko, Theresa R

2011-05-01

Currently, USEPA Method 1623 is the standard assay used for simultaneous detection of Giardia cysts and Cryptosporidium oocysts in various water matrices. However, the method is unable to distinguish between species, genotype, or to assess viability. Therefore, the objective of the present study was to address the shortcomings of USEPA Method 1623 by developing a novel molecular-based method that can assess viability of Giardia cysts in environmental waters and identify genotypes that pose a human health threat (assemblage groups A and B). Primers and TaqMan(®) probes were designed to target the beta-giardin gene in order to discriminate among species and assemblages. Viability was determined by detection of de-novo mRNA synthesis after heat induction. The beta-giardin primer/probe sets were able to detect and differentiate between Giardia lamblia assemblages A and B, and did not detect Giardia muris (mouse species) or G. lamblia assemblages C, D, E and F (non-human), with the exception of Probe A which did detect G. lamblia assemblage F DNA. Additionally, DNA or cDNA of other waterborne organisms were not detected, suggesting that the method is specific to Giardia assemblages. Assay applicability was demonstrated by detection of viable G. lamblia cysts in spiked (assemblage B) and unspiked (assemblage A and B) reclaimed water samples. Copyright © 2011 Elsevier Ltd. All rights reserved.

Multiplex, rapid and sensitive isothermal detection of nucleic-acid sequence by endonuclease restriction-mediated real-time multiple cross displacement amplification

Directory of Open Access Journals (Sweden)

Yi eWang

2016-05-01

Full Text Available We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA, which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5’ end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labelled at the 5’ end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5’ end short sequences and their complementary sequences, which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 minutes, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

Multiplex, Rapid, and Sensitive Isothermal Detection of Nucleic-Acid Sequence by Endonuclease Restriction-Mediated Real-Time Multiple Cross Displacement Amplification.

Science.gov (United States)

Wang, Yi; Wang, Yan; Zhang, Lu; Liu, Dongxin; Luo, Lijuan; Li, Hua; Cao, Xiaolong; Liu, Kai; Xu, Jianguo; Ye, Changyun

2016-01-01

We have devised a novel isothermal amplification technology, termed endonuclease restriction-mediated real-time multiple cross displacement amplification (ET-MCDA), which facilitated multiplex, rapid, specific and sensitive detection of nucleic-acid sequences at a constant temperature. The ET-MCDA integrated multiple cross displacement amplification strategy, restriction endonuclease cleavage and real-time fluorescence detection technique. In the ET-MCDA system, the functional cross primer E-CP1 or E-CP2 was constructed by adding a short sequence at the 5' end of CP1 or CP2, respectively, and the new E-CP1 or E-CP2 primer was labeled at the 5' end with a fluorophore and in the middle with a dark quencher. The restriction endonuclease Nb.BsrDI specifically recognized the short sequence and digested the newly synthesized double-stranded terminal sequences (5' end short sequences and their complementary sequences), which released the quenching, resulting on a gain of fluorescence signal. Thus, the ET-MCDA allowed real-time detection of single or multiple targets in only a single reaction, and the positive results were observed in as short as 12 min, detecting down to 3.125 fg of genomic DNA per tube. Moreover, the analytical specificity and the practical application of the ET-MCDA were also successfully evaluated in this study. Here, we provided the details on the novel ET-MCDA technique and expounded the basic ET-MCDA amplification mechanism.

NASA SMART Probe: Breast Cancer Application

Science.gov (United States)

Mah, Robert W.; Norvig, Peter (Technical Monitor)