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Sample records for taqman real-time pcrs

  1. 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

  2. Real-time TaqMan polymerase chain reaction to quantify the effects ...

    African Journals Online (AJOL)

    TaqMan polymerase chain reaction was developed to quantify the number of Bifidobacterium. We used this assay to detect genomic DNA of Bifidobacterium in the intestinal tract digesta of piglets, including duodenum, jejunum, ileum, cecum and colon. Our results indicated that, developed new real-time quantitative PCR ...

  3. Comparison of nested-multiplex, Taqman & SYBR Green real-time PCR in diagnosis of amoebic liver abscess in a tertiary health care institute in India.

    Science.gov (United States)

    Dinoop, K P; Parija, Subhash Chandra; Mandal, Jharna; Swaminathan, R P; Narayanan, P

    2016-01-01

    Amoebiasis is a common parasitic infection caused by Entamoeba histolytica and amoebic liver abscess (ALA) is the most common extraintestinal manifestation of amoebiasis. The aim of this study was to standardise real-time PCR assays (Taqman and SYBR Green) to detect E. histolytica from liver abscess pus and stool samples and compare its results with nested-multiplex PCR. Liver abscess pus specimens were subjected to DNA extraction. The extracted DNA samples were subjected to amplification by nested-multiplex PCR, Taqman (18S rRNA) and SYBR Green real-time PCR (16S-like rRNA assays to detect E. histolytica/E. dispar/E. moshkovskii). The amplification products were further confirmed by DNA sequence analysis. Receiver operator characteristic (ROC) curve analysis was done for nested-multiplex and SYBR Green real-time PCR and the area under the curve was calculated for evaluating the accuracy of the tests to dignose ALA. In all, 17, 19 and 25 liver abscess samples were positive for E. histolytica by nested-multiplex PCR, SYBR Green and Taqman real-time PCR assays, respectively. Significant differences in detection of E. histolytica were noted in the real-time PCR assays evaluated ( Pnested-multiplex PCR, SYBR Green real-time PCR and Taqman real-time PCR evaluated showed a positivity rate of 34, 38 and 50 per cent, respectively. Based on ROC curve analysis (considering Taqman real-time PCR as the gold standard), it was observed that SYBR Green real-time PCR was better than conventional nested-multiplex PCR for the diagnosis of ALA. Taqman real-time PCR targeting the 18S rRNA had the highest positivity rate evaluated in this study. Both nested multiplex and SYBR Green real-time PCR assays utilized were evaluated to give accurate results. Real-time PCR assays can be used as the gold standard in rapid and reliable diagnosis, and appropriate management of amoebiasis, replacing the conventional molecular methods.

  4. Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructanstructans.

    Science.gov (United States)

    Muller, Laura K.; Lorch, Jeffrey M.; Lindner, Daniel L.; O'Connor, Michael; Gargas, Andrea; Blehert, David S.

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg of genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was further qualified by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific, and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research.

  5. Identification and quantification of genetically modified Moonshade carnation lines using conventional and TaqMan real-time polymerase chain reaction methods.

    Science.gov (United States)

    Li, Peng; Jia, Junwei; Bai, Lan; Pan, Aihu; Tang, Xueming

    2013-07-01

    Genetically modified carnation (Dianthus caryophyllus L.) Moonshade was approved for planting and commercialization in several countries from 2004. Developing methods for analyzing Moonshade is necessary for implementing genetically modified organism labeling regulations. In this study, the 5'-transgene integration sequence was isolated using thermal asymmetric interlaced (TAIL)-PCR. Based upon the 5'-transgene integration sequence, conventional and TaqMan real-time PCR assays were established. The relative limit of detection for the conventional PCR assay was 0.05 % for Moonshade using 100 ng total carnation genomic DNA, corresponding to approximately 79 copies of the carnation haploid genome, and the limits of detection and quantification of the TaqMan real-time PCR assay were estimated to be 51 and 254 copies of haploid carnation genomic DNA, respectively. These results are useful for identifying and quantifying Moonshade and its derivatives.

  6. TaqMan MGB probe fluorescence real-time quantitative PCR for rapid detection of Chinese Sacbrood virus.

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    Ma Mingxiao

    Full Text Available Sacbrood virus (SBV is a picorna-like virus that affects honey bees (Apis mellifera and results in the death of the larvae. Several procedures are available to detect Chinese SBV (CSBV in clinical samples, but not to estimate the level of CSBV infection. The aim of this study was develop an assay for rapid detection and quantification of this virus. Primers and probes were designed that were specific for CSBV structural protein genes. A TaqMan minor groove binder (MGB probe-based, fluorescence real-time quantitative PCR was established. The specificity, sensitivity and stability of the assay were assessed; specificity was high and there were no cross-reactivity with healthy larvae or other bee viruses. The assay was applied to detect CSBV in 37 clinical samples and its efficiency was compared with clinical diagnosis, electron microscopy observation, and conventional RT-PCR. The TaqMan MGB-based probe fluorescence real-time quantitative PCR for CSBV was more sensitive than other methods tested. This assay was a reliable, fast, and sensitive method that was used successfully to detect CSBV in clinical samples. The technology can provide a useful tool for rapid detection of CSBV. This study has established a useful protocol for CSBV testing, epidemiological investigation, and development of animal models.

  7. The potential of TaqMan Array Cards for detection of multiple biological agents by real-time PCR.

    Directory of Open Access Journals (Sweden)

    Phillip A Rachwal

    Full Text Available The TaqMan Array Card architecture, normally used for gene expression studies, was evaluated for its potential to detect multiple bacterial agents by real-time PCR. Ten PCR assays targeting five biological agents (Bacillus anthracis, Burkholderia mallei, Burkholderia pseudomallei, Francisella tularensis, and Yersinia pestis were incorporated onto Array Cards. A comparison of PCR performance of each PCR in Array Card and singleplex format was conducted using DNA extracted from pure bacterial cultures. When 100 fg of agent DNA was added to Array Card channels the following levels of agent detection (where at least one agent PCR replicate returned a positive result were observed: Y. pestis 100%, B. mallei & F. tularensis 93%; B. anthracis 71%; B. pseudomallei 43%. For B. mallei & pseudomallei detection the BPM2 PCR, which detects both species, outperformed PCR assays specific to each organism indicating identification of the respective species would not be reproducible at the 100 fg level. Near 100% levels of detection were observed when 100 fg of DNA was added to each PCR in singleplex format with singleplex PCRs also returning sporadic positives at the 10 fg per PCR level. Before evaluating the use of Array Cards for the testing of environmental and clinical sample types, with potential levels of background DNA and PCR inhibitors, users would therefore have to accept a 10-fold reduction in sensitivity of PCR assays on the Array Card format, in order to benefit for the capacity to test multiple samples for multiple agents. A two PCR per agent strategy would allow the testing of 7 samples for the presence of 11 biological agents or 3 samples for 23 biological agents per card (with negative control channels.

  8. 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.

  9. 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.

  10. Bat white-nose syndrome: A real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans

    Science.gov (United States)

    Laura K Muller; Jeffrey M. Lorch; Daniel L. Lindner; Michael O' Connor; Andrea Gargas; David S. Blehert

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The...

  11. A TaqMan Real-Time PCR Assay for Detection and Quantification of Sporisorium scitamineum in Sugarcane

    Directory of Open Access Journals (Sweden)

    Yachun Su

    2013-01-01

    Full Text Available Sporisorium scitamineum is a fungal smut pathogen epidemic in sugarcane producing areas. Early detection and proper identification of the smut are an essential requirement in its management practice. In this study, we developed a TaqMan real-time PCR assay using specific primers (bEQ-F/bEQ-R and a TaqMan probe (bEQ-P which were designed based on the bE (b East mating type gene (Genbank Accession no. U61290.1. This method was more sensitive (a detection limit of 10 ag pbE DNA and 0.8 ng sugarcane genomic DNA than that of conventional PCR (10 fg and 100 ng, resp.. Reliability was demonstrated through the positive detection of samples collected from artificially inoculated sugarcane plantlets (FN40. This assay was capable of detecting the smut pathogen at the initial stage (12 h of infection and suitable for inspection of sugarcane pathogen-free seed cane and seedlings. Furthermore, quantification of pathogen was verified in pathogen-challenged buds in different sugarcane genotypes, which suggested its feasibility for evaluation of smut resistance in different sugarcane genotypes. Taken together, this novel assay can be used as a diagnostic tool for sensitive, accurate, fast, and quantitative detection of the smut pathogen especially for asymptomatic seed cane or plants and evaluation of smut resistance of sugarcane genotypes.

  12. 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.

  13. Development of SYBR Green and TaqMan quantitative real-time PCR assays for hepatopancreatic parvovirus (HPV) infecting Penaeus monodon in India.

    Science.gov (United States)

    Yadav, Reena; Paria, Anutosh; Mankame, Smruti; Makesh, M; Chaudhari, Aparna; Rajendran, K V

    2015-12-01

    Hepatopancreatic parvovirus (HPV) infects Penaeus monodon and causes mortality in the larval stages. Further, it has been implicated in the growth retardation in cultured P. monodon. Though different geographical isolates of HPV show large sequence variations, a sensitive PCR assay specific to Indian isolate has not yet been reported. Here, we developed a sensitive SYBR Green-based and TaqMan real-time PCR for the detection and quantification of the virus. A 441-bp PCR amplicon was cloned in pTZ57 R/T vector and the plasmid copy number was estimated. A 10-fold serial dilution of the plasmid DNA from 1 × 10(9) copies to 1 copy was prepared and used as the standard. The primers were tested initially using the standard on a conventional PCR format to determine the linearity of detection. The standards were further tested on real-time PCR format using SYBR Green and TaqMan chemistry and standard curves were generated based on the Ct values from three well replicates for each dilution. The assays were found to be sensitive, specific and reproducible with a wide dynamic range (1 × 10(9) to 10 copies) with coefficient of regression (R(2)) > 0.99, calculated average slope -3.196 for SYBR Green assay whereas, for TaqMan assay it was >0.99 and -3.367, respectively. The intra- and inter-assay variance of the Ct values ranged from 0.26% to 0.94% and 0.12% to 0.81%, respectively, for SYBR Green assay, and the inter-assay variance of the Ct values for TaqMan assay ranged from 0.07% to 1.93%. The specificity of the assays was proved by testing other DNA viruses of shrimp such as WSSV, IHHNV and MBV. Standardized assays were further tested to detect and quantify HPV in the post-larvae of P. monodon. The result was further compared with conventional PCR to test the reproducibility of the test. The assay was also used to screen Litopeneaus vannamei, Macrobrachium rosenbergii and Scylla serrata for HPV. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. 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.

  15. 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....

  16. Detection of viable Salmonella in ice cream by TaqMan real-time polymerase chain reaction assay combining propidium monoazide

    Directory of Open Access Journals (Sweden)

    Yuexia Wang

    2015-09-01

    Full Text Available Real-time polymerase chain reaction (PCR allows rapid detection of Salmonella in frozen dairy products, but it might cause a false positive detection result because it might amplify DNA from dead target cells as well. In this study, Salmonella-free frozen ice cream was initially inoculated with heat-killed Salmonella Typhimurium cells and stored at −18°C. Bacterial DNA extracted from the sample was amplified using TaqMan probe-based real-time PCR targeting the invA gene. Our results indicated that DNA from the dead cells remained stable in frozen ice cream for at least 20 days, and could produce fluorescence signal for real-time PCR as well. To overcome this limitation, propidium monoazide (PMA was combined with real-time PCR. PMA treatment can effectively prevent PCR amplification from heat-killed Salmonella cells in frozen ice cream. The PMA real-time PCR assay can selectively detect viable Salmonella at as low as 103 CFU/mL. Combining 18 hours of pre-enrichment with the assay allows for the detection of viable Salmonella at 100 CFU/mL and avoiding the false-positive result of dead cells. The PMA real-time PCR assay provides an alternative specifically for detection of viable Salmonella in ice cream. However, when the PMA real-time PCR assay was evaluated in ice cream subjected to frozen storage, it obviously underestimated the contamination situation of viable Salmonella, which might lead to a false negative result. According to this result, the use of enrichment prior to PMA real-time PCR analysis remains as the more appropriate approach.

  17. Detection of viable Salmonella in ice cream by TaqMan real-time polymerase chain reaction assay combining propidium monoazide.

    Science.gov (United States)

    Wang, Yuexia; Yang, Ming; Liu, Shuchun; Chen, Wanyi; Suo, Biao

    2015-09-01

    Real-time polymerase chain reaction (PCR) allows rapid detection of Salmonella in frozen dairy products, but it might cause a false positive detection result because it might amplify DNA from dead target cells as well. In this study, Salmonella-free frozen ice cream was initially inoculated with heat-killed Salmonella Typhimurium cells and stored at -18°C. Bacterial DNA extracted from the sample was amplified using TaqMan probe-based real-time PCR targeting the invA gene. Our results indicated that DNA from the dead cells remained stable in frozen ice cream for at least 20 days, and could produce fluorescence signal for real-time PCR as well. To overcome this limitation, propidium monoazide (PMA) was combined with real-time PCR. PMA treatment can effectively prevent PCR amplification from heat-killed Salmonella cells in frozen ice cream. The PMA real-time PCR assay can selectively detect viable Salmonella at as low as 10 3  CFU/mL. Combining 18 hours of pre-enrichment with the assay allows for the detection of viable Salmonella at 10 0  CFU/mL and avoiding the false-positive result of dead cells. The PMA real-time PCR assay provides an alternative specifically for detection of viable Salmonella in ice cream. However, when the PMA real-time PCR assay was evaluated in ice cream subjected to frozen storage, it obviously underestimated the contamination situation of viable Salmonella, which might lead to a false negative result. According to this result, the use of enrichment prior to PMA real-time PCR analysis remains as the more appropriate approach. Copyright © 2015. Published by Elsevier B.V.

  18. Rapid detection of Enterovirus and Coxsackievirus A10 by a TaqMan based duplex one-step real time RT-PCR assay.

    Science.gov (United States)

    Chen, Jingfang; Zhang, Rusheng; Ou, Xinhua; Yao, Dong; Huang, Zheng; Li, Linzhi; Sun, Biancheng

    2017-06-01

    A TaqMan based duplex one-step real time RT-PCR (rRT-PCR) assay was developed for the rapid detection of Coxsackievirus A10 (CV-A10) and other enterovirus (EVs) in clinical samples. The assay was fully evaluated and found to be specific and sensitive. When applied in 115 clinical samples, a 100% diagnostic sensitivity in CV-A10 detection and 97.4% diagnostic sensitivity in other EVs were found. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Rapid detection and subtyping of European swine influenza viruses in porcine clinical samples by haemagglutinin- and neuraminidase-specific tetra- and triplex real-time RT-PCRs.

    Science.gov (United States)

    Henritzi, Dinah; Zhao, Na; Starick, Elke; Simon, Gaelle; Krog, Jesper S; Larsen, Lars Erik; Reid, Scott M; Brown, Ian H; Chiapponi, Chiara; Foni, Emanuela; Wacheck, Silke; Schmid, Peter; Beer, Martin; Hoffmann, Bernd; Harder, Timm C

    2016-11-01

    A diversifying pool of mammalian-adapted influenza A viruses (IAV) with largely unknown zoonotic potential is maintained in domestic swine populations worldwide. The most recent human influenza pandemic in 2009 was caused by a virus with genes originating from IAV isolated from swine. Swine influenza viruses (SIV) are widespread in European domestic pig populations and evolve dynamically. Knowledge regarding occurrence, spread and evolution of potentially zoonotic SIV in Europe is poorly understood. Efficient SIV surveillance programmes depend on sensitive and specific diagnostic methods which allow for cost-effective large-scale analysis. New SIV haemagglutinin (HA) and neuraminidase (NA) subtype- and lineage-specific multiplex real-time RT-PCRs (RT-qPCR) have been developed and validated with reference virus isolates and clinical samples. A diagnostic algorithm is proposed for the combined detection in clinical samples and subtyping of SIV strains currently circulating in Europe that is based on a generic, M-gene-specific influenza A virus RT-qPCR. In a second step, positive samples are examined by tetraplex HA- and triplex NA-specific RT-qPCRs to differentiate the porcine subtypes H1, H3, N1 and N2. Within the HA subtype H1, lineages "av" (European avian-derived), "hu" (European human-derived) and "pdm" (human pandemic A/H1N1, 2009) are distinguished by RT-qPCRs, and within the NA subtype N1, lineage "pdm" is differentiated. An RT-PCR amplicon Sanger sequencing method of small fragments of the HA and NA genes is also proposed to safeguard against failure of multiplex RT-qPCR subtyping. These new multiplex RT-qPCR assays provide adequate tools for sustained SIV monitoring programmes in Europe. © 2016 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

  20. Cross-platform comparison of SYBR® Green real-time PCR with TaqMan PCR, microarrays and other gene expression measurement technologies evaluated in the MicroArray Quality Control (MAQC study

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    Dial Stacey L

    2008-07-01

    Full Text Available Abstract Background The MicroArray Quality Control (MAQC project evaluated the inter- and intra-platform reproducibility of seven microarray platforms and three quantitative gene expression assays in profiling the expression of two commercially available Reference RNA samples (Nat Biotechnol 24:1115-22, 2006. The tested microarrays were the platforms from Affymetrix, Agilent Technologies, Applied Biosystems, GE Healthcare, Illumina, Eppendorf and the National Cancer Institute, and quantitative gene expression assays included TaqMan® Gene Expression PCR Assay, Standardized (Sta RT-PCR™ and QuantiGene®. The data showed great consistency in gene expression measurements across different microarray platforms, different technologies and test sites. However, SYBR® Green real-time PCR, another common technique utilized by half of all real-time PCR users for gene expression measurement, was not addressed in the MAQC study. In the present study, we compared the performance of SYBR Green PCR with TaqMan PCR, microarrays and other quantitative technologies using the same two Reference RNA samples as the MAQC project. We assessed SYBR Green real-time PCR using commercially available RT2 Profiler™ PCR Arrays from SuperArray, containing primer pairs that have been experimentally validated to ensure gene-specificity and high amplification efficiency. Results The SYBR Green PCR Arrays exhibit good reproducibility among different users, PCR instruments and test sites. In addition, the SYBR Green PCR Arrays have the highest concordance with TaqMan PCR, and a high level of concordance with other quantitative methods and microarrays that were evaluated in this study in terms of fold-change correlation and overlap of lists of differentially expressed genes. Conclusion These data demonstrate that SYBR Green real-time PCR delivers highly comparable results in gene expression measurement with TaqMan PCR and other high-density microarrays.

  1. TaqMan real-time PCR assays for single-nucleotide polymorphisms which identify Francisella tularensis and its subspecies and subpopulations.

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    Dawn N Birdsell

    Full Text Available Francisella tularensis, the etiologic agent of tularemia and a Class A Select Agent, is divided into three subspecies and multiple subpopulations that differ in virulence and geographic distribution. Given these differences, there is a need to rapidly and accurately determine if a strain is F. tularensis and, if it is, assign it to subspecies and subpopulation. We designed TaqMan real-time PCR genotyping assays using eleven single nucleotide polymorphisms (SNPs that were potentially specific to closely related groups within the genus Francisella, including numerous subpopulations within F. tularensis species. We performed extensive validation studies to test the specificity of these SNPs to particular populations by screening the assays across a set of 565 genetically and geographically diverse F. tularensis isolates and an additional 21 genetic near-neighbor (outgroup isolates. All eleven assays correctly determined the genetic groups of all 565 F. tularensis isolates. One assay differentiates F. tularensis, F. novicida, and F. hispaniensis from the more genetically distant F. philomiragia and Francisella-like endosymbionts. Another assay differentiates F. tularensis isolates from near neighbors. The remaining nine assays classify F. tularensis-confirmed isolates into F. tularensis subspecies and subpopulations. The genotyping accuracy of these nine assays diminished when tested on outgroup isolates (i.e. non F. tularensis, therefore a hierarchical approach of assay usage is recommended wherein the F. tularensis-specific assay is used before the nine downstream assays. Among F. tularensis isolates, all eleven assays were highly sensitive, consistently amplifying very low concentrations of DNA. Altogether, these eleven TaqMan real-time PCR assays represent a highly accurate, rapid, and sensitive means of identifying the species, subspecies, and subpopulation of any F. tularensis isolate if used in a step-wise hierarchical scheme. These assays

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

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    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.

  3. Results of the Abbott RealTime HIV-1 assay for specimens yielding "target not detected" results by the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test.

    Science.gov (United States)

    Babady, N Esther; Germer, Jeffrey J; Yao, Joseph D C

    2010-03-01

    No significantly discordant results were observed between the Abbott RealTime HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all nine U.S. geographic regions and previously yielding "target not detected" results by CTM.

  4. Rapid detection and subtyping of European swine influenza viruses in porcine clinical samples by haemagglutinin- and neuraminidase-specific tetra- and triplex real-time RT-PCRs

    DEFF Research Database (Denmark)

    Henritzi, Dinah; Zhao, Na; Starick, Elke

    2016-01-01

    diagnostic methods which allow for cost-effective large-scale analysis. Methods New SIV haemagglutinin (HA) and neuraminidase (NA) subtype- and lineage-specific multiplex real-time RT-PCRs (RT-qPCR) have been developed and validated with reference virus isolates and clinical samples. Results A diagnostic....... Swine influenza viruses (SIV) are widespread in European domestic pig populations and evolve dynamically. Knowledge regarding occurrence, spread and evolution of potentially zoonotic SIV in Europe is poorly understood. Objectives Efficient SIV surveillance programmes depend on sensitive and specific......Background A diversifying pool of mammalian-adapted influenza A viruses (IAV) with largely unknown zoonotic potential is maintained in domestic swine populations worldwide. The most recent human influenza pandemic in 2009 was caused by a virus with genes originating from IAV isolated from swine...

  5. 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.

  6. Results of the Abbott RealTime HIV-1 Assay for Specimens Yielding “Target Not Detected” Results by the Cobas AmpliPrep/Cobas TaqMan HIV-1 Test▿

    OpenAIRE

    Babady, N. Esther; Germer, Jeffrey J.; Yao, Joseph D. C.

    2009-01-01

    No significantly discordant results were observed between the Abbott RealTime HIV-1 assay and the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test (CTM) among 1,190 unique clinical plasma specimens obtained from laboratories located in 40 states representing all nine U.S. geographic regions and previously yielding “target not detected” results by CTM.

  7. 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.

  8. 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.

  9. Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process

    Directory of Open Access Journals (Sweden)

    Kohn Michael

    2007-10-01

    Full Text Available Abstract Background Since real time PCR was first developed, several approaches to estimating the initial quantity of template in an RT-PCR reaction have been tried. While initially only the early thermal cycles corresponding to exponential duplication were used, lately there has been an effort to use all of the cycles in a PCR. The efforts have included both fitting empirical sigmoid curves and more elaborate mechanistic models that explore the chemical reactions taking place during each cycle. The more elaborate mechanistic models require many more parameters than can be fit from a single amplification, while the empirical models provide little insight and are difficult to tailor to specific reactants. Results We directly estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR. The basic model includes the duplication of DNA with the digestion of Taqman probe and the re-annealing between previously synthesized DNA strands of opposite orientation. By modelling the amount of Taqman probe digested and matching that with the observed fluorescence, the conversion factor between the number of fluorescing dye molecules and observed fluorescent emission can be estimated, along with the absolute initial amount of amplicon and the rate parameter for re-annealing. The model is applied to several PCR reactions with known amounts of amplicon and is shown to work reasonably well. An expanded version of the model allows duplication of amplicon without release of fluorescent dye, by adding 1 more parameter to the model. The additional process is helpful in most cases where the initial primer concentration exceeds the initial probe concentration. Software for applying the algorithm to data may be downloaded at http://www.niehs.nih.gov/research/resources/software/pcranalyzer/ Conclusion We present proof of the principle that a mechanistically based model can be fit to observations

  10. Molecular detection and species-specific identification of medically important Aspergillus species by real-time PCR in experimental invasive pulmonary aspergillosis.

    Science.gov (United States)

    Walsh, Thomas J; Wissel, Mark C; Grantham, Kevin J; Petraitiene, Ruta; Petraitis, Vidmantas; Kasai, Miki; Francesconi, Andrea; Cotton, Margaret P; Hughes, Johanna E; Greene, Lora; Bacher, John D; Manna, Pradip; Salomoni, Martin; Kleiboeker, Steven B; Reddy, Sushruth K

    2011-12-01

    Diagnosis of invasive pulmonary aspergillosis (IPA) remains a major challenge to clinical microbiology laboratories. We developed rapid and sensitive quantitative PCR (qPCR) assays for genus- and species-specific identification of Aspergillus infections by use of TaqMan technology. In order to validate these assays and understand their potential diagnostic utility, we then performed a blinded study of bronchoalveolar lavage (BAL) fluid specimens from well-characterized models of IPA with the four medically important species. A set of real-time qPCR primers and probes was developed by utilizing unique ITS1 regions for genus- and species-specific detection of the four most common medically important Aspergillus species (Aspergillus fumigatus, A. flavus, A. niger, and A. terreus). Pan-Aspergillus and species-specific qPCRs with BAL fluid were more sensitive than culture for detection of IPA caused by A. fumigatus in untreated (P < 0.0007) and treated (P ≤ 0.008) animals, respectively. For infections caused by A. terreus and A. niger, culture and PCR amplification from BAL fluid yielded similar sensitivities for untreated and treated animals. Pan-Aspergillus PCR was more sensitive than culture for detection of A. flavus in treated animals (P = 0.002). BAL fluid pan-Aspergillus and species-specific PCRs were comparable in sensitivity to BAL fluid galactomannan (GM) assay. The copy numbers from the qPCR assays correlated with quantitative cultures to determine the pulmonary residual fungal burdens in lung tissue. Pan-Aspergillus and species-specific qPCR assays may improve the rapid and accurate identification of IPA in immunocompromised patients.

  11. 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.

  12. Quantitative Tetraplex Real-Time Polymerase Chain Reaction Assay with TaqMan Probes Discriminates Cattle, Buffalo, and Porcine Materials in Food Chain.

    Science.gov (United States)

    Hossain, M A Motalib; Ali, Md Eaqub; Sultana, Sharmin; Asing; Bonny, Sharmin Quazi; Kader, Md Abdul; Rahman, M Aminur

    2017-05-17

    Cattle, buffalo, and porcine materials are widely adulterated, and their quantification might safeguard health, religious, economic, and social sanctity. Recently, conventional polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (RFLP) assays have been documented but they are just suitable for identification, cannot quantify adulterations. We described here a quantitative tetraplex real-time PCR assay with TaqMan Probes to quantify contributions from cattle, buffalo, and porcine materials simultaneously. Amplicon-sizes were very short (106-, 90-, and 146-bp for cattle, buffalo, and porcine) because longer targets could be broken down, bringing serious ambiguity in molecular diagnostics. False negative detection was eliminated through an endogenous control (141-bp site of eukaryotic 18S rRNA). Analysis of 27 frankfurters and 27 meatballs reflected 84-115% target recovery at 0.1-10% adulterations. Finally, a test of 36 commercial products revealed 71% beef frankfurters, 100% meatballs, and 85% burgers contained buffalo adulteration, but no porcine was found in beef products.

  13. Sensitive and specific detection of potentially allergenic almond (Prunus dulcis) in complex food matrices by Taqman real-time polymerase chain reaction in comparison to commercially available protein-based enzyme-linked immunosorbent assay

    International Nuclear Information System (INIS)

    Roeder, Martin; Vieths, Stefan; Holzhauser, Thomas

    2011-01-01

    Currently, causative immunotherapies are lacking in food allergy. The only option to prevent allergic reactions in susceptible individuals is to strictly avoid the offending food. Thus, reliable labelling of allergenic constituents is of major importance, but can only be achieved if appropriate specific and sensitive detection techniques for foods with allergenic potential are available. Almond is an allergenic food that requires mandatory labelling on prepackaged foods and belongs to the genus Prunus. Species of this genus are phylogenetically closely related. We observed commercially available almond specific ELISA being highly cross-reactive with other foods of the Prunoideae family, resulting in a false-positive detection of up to 500,000 mg kg -1 almond. Previously published PCR methods were reported to be cross-reactive with false positive results >1200 mg kg -1 . We describe the development of a novel almond specific real-time PCR, based on mutated mismatch primers and sequence specific Taqman probe detection, in comparison with two quantitative commercially available ELISA. PCR sensitivity was investigated with chocolate, chocolate coating and cookies spiked between 5 and 100,000 mg kg -1 almond. In all matrices almond was reproducibly detected by real-time PCR at the lowest spike level of 5 mg kg -1 . Further, between 100 and 100,000 mg kg -1 spiked almond, the method featured good correlation between quantified copy numbers and the amount of spiked almond. Within this range a similar relation between detectable signal and amount of almond was observed for both PCR and ELISA. In contrast to ELISA the Taqman real-time PCR method was highly specific in 59 food items with negligible cross-reactivity for a very limited number of Prunoideae foods. The real-time PCR analysis of 24 retail samples was in concordance with ELISA results: 21% (n = 5) contained undeclared almond. This is the first completely disclosed real-time PCR method for a specific and

  14. 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...

  15. TaqMan real-time polymerase chain reaction for detection of Ophidiomyces ophiodiicola, the fungus associated with snake fungal disease.

    Science.gov (United States)

    Bohuski, Elizabeth; Lorch, Jeffrey M; Griffin, Kathryn M; Blehert, David S

    2015-04-15

    Fungal skin infections associated with Ophidiomyces ophiodiicola, a member of the Chrysosporium anamorph of Nannizziopsis vriesii (CANV) complex, have been linked to an increasing number of cases of snake fungal disease (SFD) in captive snakes around the world and in wild snake populations in eastern North America. The emergence of SFD in both captive and wild situations has led to an increased need for tools to better diagnose and study the disease. We developed two TaqMan real-time polymerase chain reaction (PCR) assays to rapidly detect O. ophiodiicola in clinical samples. One assay targets the internal transcribed spacer region (ITS) of the fungal genome while the other targets the more variable intergenic spacer region (IGS). The PCR assays were qualified using skin samples collected from 50 snakes for which O. ophiodiicola had been previously detected by culture, 20 snakes with gross skin lesions suggestive of SFD but which were culture-negative for O. ophiodiicola, and 16 snakes with no clinical signs of infection. Both assays performed equivalently and proved to be more sensitive than traditional culture methods, detecting O. ophiodiicola in 98% of the culture-positive samples and in 40% of the culture-negative snakes that had clinical signs of SFD. In addition, the assays did not cross-react with a panel of 28 fungal species that are closely related to O. ophiodiicola or that commonly occur on the skin of snakes. The assays did, however, indicate that some asymptomatic snakes (~6%) may harbor low levels of the fungus, and that PCR should be paired with histology when a definitive diagnosis is required. These assays represent the first published methods to detect O. ophiodiicola by real-time PCR. The ITS assay has great utility for assisting with SFD diagnoses whereas the IGS assay offers a valuable tool for research-based applications.

  16. Sensitive and specific detection of potentially allergenic almond (Prunus dulcis) in complex food matrices by Taqman real-time polymerase chain reaction in comparison to commercially available protein-based enzyme-linked immunosorbent assay

    Energy Technology Data Exchange (ETDEWEB)

    Roeder, Martin; Vieths, Stefan [Division of Allergology, Paul-Ehrlich-Institut, Paul-Ehrlich-Strasse 51-59, 63225 Langen (Germany); Holzhauser, Thomas, E-mail: holth@pei.de [Division of Allergology, Paul-Ehrlich-Institut, Paul-Ehrlich-Strasse 51-59, 63225 Langen (Germany)

    2011-01-24

    Currently, causative immunotherapies are lacking in food allergy. The only option to prevent allergic reactions in susceptible individuals is to strictly avoid the offending food. Thus, reliable labelling of allergenic constituents is of major importance, but can only be achieved if appropriate specific and sensitive detection techniques for foods with allergenic potential are available. Almond is an allergenic food that requires mandatory labelling on prepackaged foods and belongs to the genus Prunus. Species of this genus are phylogenetically closely related. We observed commercially available almond specific ELISA being highly cross-reactive with other foods of the Prunoideae family, resulting in a false-positive detection of up to 500,000 mg kg{sup -1} almond. Previously published PCR methods were reported to be cross-reactive with false positive results >1200 mg kg{sup -1}. We describe the development of a novel almond specific real-time PCR, based on mutated mismatch primers and sequence specific Taqman probe detection, in comparison with two quantitative commercially available ELISA. PCR sensitivity was investigated with chocolate, chocolate coating and cookies spiked between 5 and 100,000 mg kg{sup -1} almond. In all matrices almond was reproducibly detected by real-time PCR at the lowest spike level of 5 mg kg{sup -1}. Further, between 100 and 100,000 mg kg{sup -1} spiked almond, the method featured good correlation between quantified copy numbers and the amount of spiked almond. Within this range a similar relation between detectable signal and amount of almond was observed for both PCR and ELISA. In contrast to ELISA the Taqman real-time PCR method was highly specific in 59 food items with negligible cross-reactivity for a very limited number of Prunoideae foods. The real-time PCR analysis of 24 retail samples was in concordance with ELISA results: 21% (n = 5) contained undeclared almond. This is the first completely disclosed real-time PCR method for a

  17. Quantitation of Marek's disease and chicken anemia viruses in organs of experimentally infected chickens and commercial chickens by multiplex real-time PCR.

    Science.gov (United States)

    Davidson, Irit; Raibshtein, I; Al-Touri, A

    2013-06-01

    The worldwide distribution of chicken anemia virus (CAV) and Marek's disease virus (MDV) is well documented. In addition to their economic significance in single- or dual-virus infections, the two viruses can often accompany various other pathogens and affect poultry health either directly, by causing tumors, anemia, and delayed growth, or indirectly, by aggravating other diseases, as a result of their immunosuppressive effects. After a decade of employing the molecular diagnosis of those viruses, which replaced conventional virus isolation, we present the development of a real-time multiplex PCR for the simultaneous detection of both viruses. The real-time PCRs for MDV and for CAV alone are more sensitive than the respective end-point PCRs. In addition, the multiplex real-time shows a similar sensitivity when compared to the single real-time PCR for each virus. The newly developed real-time multiplex PCR is of importance in terms of the diagnosis and detection of low copies of each virus, MDV and CAV in single- and in multiple-virus infections, and its applicability will be further evaluated.

  18. Real-time PCR for type-specific identification of herpes simplex in clinical samples: evaluation of type-specific results in the context of CNS diseases.

    Science.gov (United States)

    Meylan, Sylvain; Robert, Daniel; Estrade, Christine; Grimbuehler, Valérie; Péter, Olivier; Meylan, Pascal R; Sahli, Roland

    2008-02-01

    HSV-1 and HSV-2 cause CNS infections of dissimilar clinico-pathological characteristics with prognostic and therapeutic implications. To validate a type-specific real-time PCR that uses MGB/LNA Taqman probes and to review the virologico-clinical data of 25 eligible patients with non-neonatal CNS infections. This real-time PCR was evaluated against conventional PCR (26 CSF and 20 quality controls), and LightCycler assay (51 mucocutaneous, 8 CSF and 32 quality controls) and culture/immunofluorescence (75 mucocutaneous) to assess typing with independent methods. Taqman real-time PCR detected 240 HSV genomes per ml CSF, a level appropriate for the management of patients, and provided unambiguous typing for the 104 positive (62 HSV-1 and 42 HSV-2) out the 160 independent clinical samples tested. HSV type diagnosed by Taqman real-time PCR predicted final diagnosis (meningitis versus encephalitis/meningoencephalitis, p<0.001) in 24/25 patients at time of presentation, in contrast to clinical evaluation. Our real-time PCR, as a sensitive and specific means for type-specific HSV diagnosis, provided rapid prognostic information for patient management.

  19. Sensitive and specific detection of potentially allergenic almond (Prunus dulcis) in complex food matrices by Taqman(®) real-time polymerase chain reaction in comparison to commercially available protein-based enzyme-linked immunosorbent assay.

    Science.gov (United States)

    Röder, Martin; Vieths, Stefan; Holzhauser, Thomas

    2011-01-24

    Currently, causative immunotherapies are lacking in food allergy. The only option to prevent allergic reactions in susceptible individuals is to strictly avoid the offending food. Thus, reliable labelling of allergenic constituents is of major importance, but can only be achieved if appropriate specific and sensitive detection techniques for foods with allergenic potential are available. Almond is an allergenic food that requires mandatory labelling on prepackaged foods and belongs to the genus Prunus. Species of this genus are phylogenetically closely related. We observed commercially available almond specific ELISA being highly cross-reactive with other foods of the Prunoideae family, resulting in a false-positive detection of up to 500,000 mg kg(-1) almond. Previously published PCR methods were reported to be cross-reactive with false positive results >1200 mg kg(-1). We describe the development of a novel almond specific real-time PCR, based on mutated mismatch primers and sequence specific Taqman(®) probe detection, in comparison with two quantitative commercially available ELISA. PCR sensitivity was investigated with chocolate, chocolate coating and cookies spiked between 5 and 100,000 mg kg(-1) almond. In all matrices almond was reproducibly detected by real-time PCR at the lowest spike level of 5 mg kg(-1). Further, between 100 and 100,000 mg kg(-1) spiked almond, the method featured good correlation between quantified copy numbers and the amount of spiked almond. Within this range a similar relation between detectable signal and amount of almond was observed for both PCR and ELISA. In contrast to ELISA the Taqman(®) real-time PCR method was highly specific in 59 food items with negligible cross-reactivity for a very limited number of Prunoideae foods. The real-time PCR analysis of 24 retail samples was in concordance with ELISA results: 21% (n=5) contained undeclared almond. This is the first completely disclosed real-time PCR method for a specific and

  20. Lineage-Specific Real-Time RT-PCR for Yellow Fever Virus Outbreak Surveillance, Brazil.

    Science.gov (United States)

    Fischer, Carlo; Torres, Maria C; Patel, Pranav; Moreira-Soto, Andres; Gould, Ernest A; Charrel, Rémi N; de Lamballerie, Xavier; Nogueira, Rita Maria Ribeiro; Sequeira, Patricia C; Rodrigues, Cintia D S; Kümmerer, Beate M; Drosten, Christian; Landt, Olfert; Bispo de Filippis, Ana Maria; Drexler, Jan Felix

    2017-11-01

    The current yellow fever outbreak in Brazil prompted widespread yellow fever virus (YFV) vaccination campaigns, imposing a responsibility to distinguish between vaccine- and wild-type YFV-associated disease. We developed novel multiplex real-time reverse transcription PCRs that differentiate between vaccine and American wild-type YFV. We validated these highly specific and sensitive assays in an outbreak setting.

  1. Lineage-Specific Real-Time RT-PCR for Yellow Fever Virus Outbreak Surveillance, Brazil

    OpenAIRE

    Fischer, Carlo; Torres, Maria C.; Patel, Pranav; Moreira-Soto, Andres; Gould, Ernest A.; Charrel, Rémi N.; de Lamballerie, Xavier; Nogueira, Rita Maria Ribeiro; Sequeira, Patricia C.; Rodrigues, Cintia D.S.; Kümmerer, Beate M.; Drosten, Christian; Landt, Olfert; Bispo de Filippis, Ana Maria; Drexler, Jan Felix

    2017-01-01

    The current yellow fever outbreak in Brazil prompted widespread yellow fever virus (YFV) vaccination campaigns, imposing a responsibility to distinguish between vaccine- and wild-type YFV-associated disease. We developed novel multiplex real-time reverse transcription PCRs that differentiate between vaccine and American wild-type YFV. We validated these highly specific and sensitive assays in an outbreak setting.

  2. 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.

  3. Real-time PCR assays for hepatitis B virus DNA quantification may require two different targets.

    Science.gov (United States)

    Liu, Chao; Chang, Le; Jia, Tingting; Guo, Fei; Zhang, Lu; Ji, Huimin; Zhao, Junpeng; Wang, Lunan

    2017-05-12

    Quantification Hepatitis B virus (HBV) DNA plays a critical role in the management of chronic HBV infections. However, HBV is a DNA virus with high levels of genetic variation, and drug-resistant mutations have emerged with the use of antiviral drugs. If a mutation caused a sequence mismatched in the primer or probe of a commercial DNA quantification kit, this would lead to an underestimation of the viral load of the sample. The aim of this study was to determine whether commercial kits, which use only one pair of primers and a single probe, accurately quantify the HBV DNA levels and to develop an improved duplex real-time PCR assay. We developed a new duplex real-time PCR assay that used two pairs of primers and two probes based on the conserved S and C regions of the HBV genome. We performed HBV DNA quantitative detection of HBV samples and compared the results of our duplex real-time PCR assays with the COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. The target region of the discordant sample was amplified, sequenced, and validated using plasmid. The results of the duplex real-time PCR were in good accordance with the commercial COBAS TaqMan HBV Test version 2 and Daan real-time PCR assays. We showed that two samples from Chinese HBV infections underestimated viral loads when quantified by the Roche kit because of a mismatch between the viral sequence and the reverse primer of the Roche kit. The HBV DNA levels of six samples were undervalued by duplex real-time PCR assays of the C region because of mutations in the primer of C region. We developed a new duplex real-time PCR assay, and the results of this assay were similar to the results of commercial kits. The HBV DNA level could be undervalued when using the COBAS TaqMan HBV Test version 2 for Chinese HBV infections owing to a mismatch with the primer/probe. A duplex real-time PCR assay based on the S and C regions could solve this problem to some extent.

  4. Clinical Value of Treponema pallidum Real-Time PCR for Diagnosis of Syphilis

    NARCIS (Netherlands)

    Heymans, R.; van der Helm, J. J.; de Vries, H. J. C.; Fennema, H. S. A.; Coutinho, R. A.; Bruisten, S. M.

    2010-01-01

    The diagnosis of syphilis can be complicated when it is based on diverse clinical manifestations, dark-field microscopy, and serology. In the present study, therefore, we examined the additional clinical value of a Treponema pallidum real-time TaqMan PCR for the detection of primary and secondary

  5. Real-time PCR based on SYBR-Green I fluorescence: An alternative to the TaqMan assay for a relative quantification of gene rearrangements, gene amplifications and micro gene deletions

    Directory of Open Access Journals (Sweden)

    Puisieux Alain

    2003-10-01

    Full Text Available Abstract Background Real-time PCR is increasingly being adopted for RNA quantification and genetic analysis. At present the most popular real-time PCR assay is based on the hybridisation of a dual-labelled probe to the PCR product, and the development of a signal by loss of fluorescence quenching as PCR degrades the probe. Though this so-called 'TaqMan' approach has proved easy to optimise in practice, the dual-labelled probes are relatively expensive. Results We have designed a new assay based on SYBR-Green I binding that is quick, reliable, easily optimised and compares well with the published assay. Here we demonstrate its general applicability by measuring copy number in three different genetic contexts; the quantification of a gene rearrangement (T-cell receptor excision circles (TREC in peripheral blood mononuclear cells; the detection and quantification of GLI, MYC-C and MYC-N gene amplification in cell lines and cancer biopsies; and detection of deletions in the OPA1 gene in dominant optic atrophy. Conclusion Our assay has important clinical applications, providing accurate diagnostic results in less time, from less biopsy material and at less cost than assays currently employed such as FISH or Southern blotting.

  6. Development of a Taqman real-time PCR assay for rapid detection and quantification of Vibrio tapetis in extrapallial fluids of clams

    Directory of Open Access Journals (Sweden)

    Adeline Bidault

    2015-12-01

    Full Text Available The Gram-negative bacterium Vibrio tapetis is known as the causative agent of Brown Ring Disease (BRD in the Manila clam Venerupis (=Ruditapes philippinarum. This bivalve is the second most important species produced in aquaculture and has a high commercial value. In spite of the development of several molecular methods, no survey has been yet achieved to rapidly quantify the bacterium in the clam. In this study, we developed a Taqman real-time PCR assay targeting virB4 gene for accurate and quantitative identification of V. tapetis strains pathogenic to clams. Sensitivity and reproducibility of the method were assessed using either filtered sea water or extrapallial fluids of clam injected with the CECT4600T V. tapetis strain. Quantification curves of V. tapetis strain seeded in filtered seawater (FSW or extrapallial fluids (EF samples were equivalent showing reliable qPCR efficacies. With this protocol, we were able to specifically detect V. tapetis strains down to 1.125 101 bacteria per mL of EF or FSW, taking into account the dilution factor used for appropriate template DNA preparation. This qPCR assay allowed us to monitor V. tapetis load both experimentally or naturally infected Manila clams. This technique will be particularly useful for monitoring the kinetics of massive infections by V. tapetis and for designing appropriate control measures for aquaculture purposes.

  7. Multiplex Real-Time PCR Assay Using TaqMan Probes for the Identification of Trypanosoma cruzi DTUs in Biological and Clinical Samples

    Science.gov (United States)

    Cura, Carolina I.; Duffy, Tomas; Lucero, Raúl H.; Bisio, Margarita; Péneau, Julie; Jimenez-Coello, Matilde; Calabuig, Eva; Gimenez, María J.; Valencia Ayala, Edward; Kjos, Sonia A.; Santalla, José; Mahaney, Susan M.; Cayo, Nelly M.; Nagel, Claudia; Barcán, Laura; Málaga Machaca, Edith S.; Acosta Viana, Karla Y.; Brutus, Laurent; Ocampo, Susana B.; Aznar, Christine; Cuba Cuba, Cesar A.; Gürtler, Ricardo E.; Ramsey, Janine M.; Ribeiro, Isabela; VandeBerg, John L.; Yadon, Zaida E.; Osuna, Antonio; Schijman, Alejandro G.

    2015-01-01

    Background Trypanosoma cruzi has been classified into six Discrete Typing Units (DTUs), designated as TcI–TcVI. In order to effectively use this standardized nomenclature, a reproducible genotyping strategy is imperative. Several typing schemes have been developed with variable levels of complexity, selectivity and analytical sensitivity. Most of them can be only applied to cultured stocks. In this context, we aimed to develop a multiplex Real-Time PCR method to identify the six T. cruzi DTUs using TaqMan probes (MTq-PCR). Methods/Principal Findings The MTq-PCR has been evaluated in 39 cultured stocks and 307 biological samples from vectors, reservoirs and patients from different geographical regions and transmission cycles in comparison with a multi-locus conventional PCR algorithm. The MTq-PCR was inclusive for laboratory stocks and natural isolates and sensitive for direct typing of different biological samples from vectors, reservoirs and patients with acute, congenital infection or Chagas reactivation. The first round SL-IR MTq-PCR detected 1 fg DNA/reaction tube of TcI, TcII and TcIII and 1 pg DNA/reaction tube of TcIV, TcV and TcVI reference strains. The MTq-PCR was able to characterize DTUs in 83% of triatomine and 96% of reservoir samples that had been typed by conventional PCR methods. Regarding clinical samples, 100% of those derived from acute infected patients, 62.5% from congenitally infected children and 50% from patients with clinical reactivation could be genotyped. Sensitivity for direct typing of blood samples from chronic Chagas disease patients (32.8% from asymptomatic and 22.2% from symptomatic patients) and mixed infections was lower than that of the conventional PCR algorithm. Conclusions/Significance Typing is resolved after a single or a second round of Real-Time PCR, depending on the DTU. This format reduces carryover contamination and is amenable to quantification, automation and kit production. PMID:25993316

  8. 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

  9. 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.

  10. Diagnostic efficacy of a real time-PCR assay for Chlamydia trachomatis infection in infertile women in north India

    Directory of Open Access Journals (Sweden)

    Benu Dhawan

    2014-01-01

    Full Text Available Background & objectives: Little is known about the prevalence of Chlamydia trachomatis infection in Indian women with infertility. To improve the diagnosis of C. trachomatis infection in developing countries, there is an urgent need to establish cost-effective molecular test with high sensitivity and specificity. This study was conducted to determine the diagnostic utility of a real time-PCR assay for detention of C. trachomatis infection in infertile women attending an infertility clinic in north India. The in house real time-PCR assay was also compared with a commercial real-time PCR based detection system. Methods: Endocervical swabs, collected from 200 infertile women were tested for C. trachomatis by three different PCR assays viz. in-house real time-PCR targeting the cryptic plasmid using published primers, along with omp1 gene and cryptic plasmid based conventional PCR assays. Specimens were also subjected to direct fluorescence assay (DFA and enzyme immunoassay (EIA Performance of in-house real time-PCR was compared with that of COBAS Taqman C. trachomatis Test, version 2.0 on all in-house real time-PCR positive sample and 30 consecutive negative samples. Results: C. trachomatis infection was found in 13.5 per cent (27/200 infertile women by in-house real time-PCR, 11.5 per cent (23/200 by cryptic plasmid and/or omp1 gene based conventional PCR, 9 per cent (18/200 by DFA and 6.5 per cent (7/200 by EIA. The in-house real time-PCR exhibited a sensitivity and specificity of 100 per cent, considering COBAS Taqman CT Test as the gold standard. The negative and positive predictive values of the in-house real time-PCR were 100 per cent. The in-house real time-PCR could detect as low as 10 copies of C. trachomatis DNA per reaction. Interpretation & conclusions: In-house real time-PCR targeting the cryptic plasmid of C. trachomatis exhibited an excellent sensitivity and specificity similar to that of COBAS Taqman CT Test, v2.0 for detection of C

  11. EVALUATION OF A RAPID, QUANTITATIVE REAL-TIME PCR METHOD FOR ENUMERATION OF PATHOGENIC CANDIDA CELLS IN WATER

    Science.gov (United States)

    Quantitative Real-Time PCR (QRT-PCR) technology, incorporating fluorigenic 5' nuclease (TaqMan?) chemistry, was developed for the specific detection and quantification of six pathogenic species of Candida (C. albicans, C. tropicalis, C. krusei, C. parapsilosis, C. glabrata and C....

  12. 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.

  13. Use of a Real-Time PCR TaqMan Assay for Rapid Identification and Differentiation of Burkholderia pseudomallei and Burkholderia mallei

    OpenAIRE

    U'Ren, Jana M.; Van Ert, Matthew N.; Schupp, James M.; Easterday, W. Ryan; Simonson, Tatum S.; Okinaka, Richard T.; Pearson, Talima; Keim, Paul

    2005-01-01

    A TaqMan allelic-discrimination assay designed around a synonymous single-nucleotide polymorphism was used to genotype Burkholderia pseudomallei and Burkholderia mallei isolates. The assay rapidly identifies and discriminates between these two highly pathogenic bacteria and does not cross-react with genetic near neighbors, such as Burkholderia thailandensis and Burkholderia cepacia.

  14. Detection and Quantification of Methyl tert-Butyl Ether-Degrading Strain PM1 by Real-Time TaqMan PCR

    OpenAIRE

    Hristova, Krassimira R.; Lutenegger, Christian M.; Scow, Kate M.

    2001-01-01

    The fuel oxygenate methyl tert-butyl ether (MTBE), a widely distributed groundwater contaminant, shows potential for treatment by in situ bioremediation. The bacterial strain PM1 rapidly mineralizes and grows on MTBE in laboratory cultures and can degrade the contaminant when inoculated into groundwater or soil microcosms. We applied the TaqMan quantitative PCR method to detect and quantify strain PM1 in laboratory and field samples. Specific primers and probes were designed for the 16S ribos...

  15. On-Site Molecular Detection of Soil-Borne Phytopathogens Using a Portable Real-Time PCR System.

    Science.gov (United States)

    DeShields, Joseph B; Bomberger, Rachel A; Woodhall, James W; Wheeler, David L; Moroz, Natalia; Johnson, Dennis A; Tanaka, Kiwamu

    2018-02-23

    On-site diagnosis of plant diseases can be a useful tool for growers for timely decisions enabling the earlier implementation of disease management strategies that reduce the impact of the disease. Presently in many diagnostic laboratories, the polymerase chain reaction (PCR), particularly real-time PCR, is considered the most sensitive and accurate method for plant pathogen detection. However, laboratory-based PCRs typically require expensive laboratory equipment and skilled personnel. In this study, soil-borne pathogens of potato are used to demonstrate the potential for on-site molecular detection. This was achieved using a rapid and simple protocol comprising of magnetic bead-based nucleic acid extraction, portable real-time PCR (fluorogenic probe-based assay). The portable real-time PCR approach compared favorably with a laboratory-based system, detecting as few as 100 copies of DNA from Spongospora subterranea. The portable real-time PCR method developed here can serve as an alternative to laboratory-based approaches and a useful on-site tool for pathogen diagnosis.

  16. Multiplex real-time PCR assays for the identification of the potato cyst and tobacco cyst nematodes

    Science.gov (United States)

    TaqMan primer-probe sets were developed for the detection and identification of potato cyst nematodes (PCN) Globodera pallida and G. rostochiensis using two-tube, multiplex real-time PCR. One tube contained a primer-probe set specific for G. pallida (pale cyst nematode) multiplexed with another prim...

  17. The L2b real-time PCR targeting the pmpH gene of Chlamydia trachomatis used for the diagnosis of lymphogranuloma venereum is not specific to L2b strains.

    Science.gov (United States)

    Touati, A; Peuchant, O; Hénin, N; Bébéar, C; de Barbeyrac, B

    2016-06-01

    The French Reference Centre for chlamydiae uses two real-time PCRs targeting the pmpH gene of Chlamydia trachomatis to differentiate between L strains and variant L2b, responsible for a lymphogranuloma venereum outbreak in Europe. We compared the results obtained for 122 L2b C. trachomatis-positive specimens, using the two real-time PCRs, with the sequencing of the ompA gene. Only 91 specimens were confirmed as L2b. Our results demonstrate that the lymphogranuloma venereum outbreak is no longer dominated by the variant L2b, and that many L-positive specimens were misidentified as L2b with the method used, which raises the question of its specificity. Copyright © 2016 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  18. Detection and differentiation of Cryptosporidium by real-time polymerase chain reaction in stool samples from patients in Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    Roberta Flávia Ribeiro Rolando

    2012-06-01

    Full Text Available This study reports the first genetic characterisation of Cryptosporidium isolates in Brazil using real-time polymerase chain reaction (RT-PCR. A total of 1,197 faecal specimens from children and 10 specimens from human immunodeficiency virus-infected patients were collected between 1999-2010 and screened using microscopy. Forty-eight Cryptosporidium oocyst-positive isolates were identified and analysed using a generic TaqMan assay targeting the 18S rRNA to detect Cryptosporidium species and two other TaqMan assays to identify Cryptosporidium hominis and Cryptosporidium parvum. The 18S rRNA assay detected Cryptosporidium species in all 48 of the stool specimens. The C. parvum TaqMan assay correctly identified five/48 stool samples, while 37/48 stool specimens were correctly amplified in the C. hominis TaqMan assay. The results obtained in this study support previous findings showing that C. hominis infections are more prevalent than C. parvum infections in Brazil and they demonstrate that the TaqMan RT-PCR procedure is a simple, fast and valuable tool for the detection and differentiation of Cryptosporidium species.

  19. 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...

  20. Evaluation of an Improved U.S. Food and Drug Administration Method for the Detection of Cyclospora cayetanensis in Produce Using Real-Time PCR.

    Science.gov (United States)

    Murphy, Helen R; Lee, Seulgi; da Silva, Alexandre J

    2017-07-01

    Cyclospora cayetanensis is a protozoan parasite that causes human diarrheal disease associated with the consumption of fresh produce or water contaminated with C. cayetanensis oocysts. In the United States, foodborne outbreaks of cyclosporiasis have been linked to various types of imported fresh produce, including cilantro and raspberries. An improved method was developed for identification of C. cayetanensis in produce at the U.S. Food and Drug Administration. The method relies on a 0.1% Alconox produce wash solution for efficient recovery of oocysts, a commercial kit for DNA template preparation, and an optimized TaqMan real-time PCR assay with an internal amplification control for molecular detection of the parasite. A single laboratory validation study was performed to assess the method's performance and compare the optimized TaqMan real-time PCR assay and a reference nested PCR assay by examining 128 samples. The samples consisted of 25 g of cilantro or 50 g of raspberries seeded with 0, 5, 10, or 200 C. cayetanensis oocysts. Detection rates for cilantro seeded with 5 and 10 oocysts were 50.0 and 87.5%, respectively, with the real-time PCR assay and 43.7 and 94.8%, respectively, with the nested PCR assay. Detection rates for raspberries seeded with 5 and 10 oocysts were 25.0 and 75.0%, respectively, with the real-time PCR assay and 18.8 and 68.8%, respectively, with the nested PCR assay. All unseeded samples were negative, and all samples seeded with 200 oocysts were positive. Detection rates using the two PCR methods were statistically similar, but the real-time PCR assay is less laborious and less prone to amplicon contamination and allows monitoring of amplification and analysis of results, making it more attractive to diagnostic testing laboratories. The improved sample preparation steps and the TaqMan real-time PCR assay provide a robust, streamlined, and rapid analytical procedure for surveillance, outbreak response, and regulatory testing of foods for

  1. Development and first evaluation of a novel multiplex real-time PCR on whole blood samples for rapid pathogen identification in critically ill patients with sepsis.

    Science.gov (United States)

    van de Groep, Kirsten; Bos, Martine P; Savelkoul, Paul H M; Rubenjan, Anna; Gazenbeek, Christel; Melchers, Willem J G; van der Poll, Tom; Juffermans, Nicole P; Ong, David S Y; Bonten, Marc J M; Cremer, Olaf L

    2018-04-26

    Molecular tests may enable early adjustment of antimicrobial therapy and be complementary to blood culture (BC) which has imperfect sensitivity in critically ill patients. We evaluated a novel multiplex real-time PCR assay to diagnose bloodstream pathogens directly in whole blood samples (BSI-PCR). BSI-PCR included 11 species- and four genus-specific PCRs, a molecular Gram-stain PCR, and two antibiotic resistance markers. We collected 5 mL blood from critically ill patients simultaneously with clinically indicated BC. Microbial DNA was isolated using the Polaris method followed by automated DNA extraction. Sensitivity and specificity were calculated using BC as reference. BSI-PCR was evaluated in 347 BC-positive samples (representing up to 50 instances of each pathogen covered by the test) and 200 BC-negative samples. Bacterial species-specific PCR sensitivities ranged from 65 to 100%. Sensitivity was 26% for the Gram-positive PCR, 32% for the Gram-negative PCR, and ranged 0 to 7% for yeast PCRs. Yeast detection was improved to 40% in a smaller set-up. There was no overall association between BSI-PCR sensitivity and time-to-positivity of BC (which was highly variable), yet Ct-values were lower for true-positive versus false-positive PCR results. False-positive results were observed in 84 (4%) of the 2200 species-specific PCRs in 200 culture-negative samples, and ranged from 0 to 6% for generic PCRs. Sensitivity of BSI-PCR was promising for individual bacterial pathogens, but still insufficient for yeasts and generic PCRs. Further development of BSI-PCR will focus on improving sensitivity by increasing input volumes and on subsequent implementation as a bedside test.

  2. Performance evaluation of cobas HBV real-time PCR assay on Roche cobas 4800 System in comparison with COBAS AmpliPrep/COBAS TaqMan HBV Test.

    Science.gov (United States)

    Kim, Hanah; Hur, Mina; Bae, Eunsin; Lee, Kyung-A; Lee, Woo-In

    2018-02-19

    Hepatitis B virus (HBV) nucleic acid amplification testing (NAAT) is important for the diagnosis and management of HBV infection. We evaluated the analytical performance of the cobas HBV NAAT (Roche Diagnostics GmbH, Mannheim, Germany) on the cobas 4800 System in comparison with COBAS AmpliPrep/COBAS TaqMan HBV Test (CAP/CTM HBV). Precision was evaluated using three levels of cobas HBV/HCV/HIV-1 Control Kit, and linearity was evaluated across the anticipated measuring range (10.0-1.0×109 IU/mL) at seven levels using clinical samples. Detection capability, including limit of blank (LOB), limit of detection (LOD) and limit of quantitation (LOQ), was verified using the 4th WHO International Standard for HBV DNA for NAT (NIBSC code: 10/266). Correlation between the two systems was compared using 205 clinical samples (102 sera and 103 EDTA plasma). Repeatability and total imprecision (coefficient of variation) ranged from 0.5% to 3.8% and from 0.5% to 3.5%, respectively. Linearity (coefficient of determination, R2) was 0.999. LOB, LOD and LOQ were all acceptable within the observed proportion rate (85%). Correlation was very high between the two systems in both serum and plasma samples (correlation coefficient [r]=0.995). The new cobas HBV real-time PCR assay on the cobas 4800 System showed reliable analytical performances.

  3. Analytical Validation of Quantitative Real-Time PCR Methods for Quantification of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients.

    Science.gov (United States)

    Ramírez, Juan Carlos; Cura, Carolina Inés; da Cruz Moreira, Otacilio; Lages-Silva, Eliane; Juiz, Natalia; Velázquez, Elsa; Ramírez, Juan David; Alberti, Anahí; Pavia, Paula; Flores-Chávez, María Delmans; Muñoz-Calderón, Arturo; Pérez-Morales, Deyanira; Santalla, José; Marcos da Matta Guedes, Paulo; Peneau, Julie; Marcet, Paula; Padilla, Carlos; Cruz-Robles, David; Valencia, Edward; Crisante, Gladys Elena; Greif, Gonzalo; Zulantay, Inés; Costales, Jaime Alfredo; Alvarez-Martínez, Miriam; Martínez, Norma Edith; Villarroel, Rodrigo; Villarroel, Sandro; Sánchez, Zunilda; Bisio, Margarita; Parrado, Rudy; Maria da Cunha Galvão, Lúcia; Jácome da Câmara, Antonia Cláudia; Espinoza, Bertha; Alarcón de Noya, Belkisyole; Puerta, Concepción; Riarte, Adelina; Diosque, Patricio; Sosa-Estani, Sergio; Guhl, Felipe; Ribeiro, Isabela; Aznar, Christine; Britto, Constança; Yadón, Zaida Estela; Schijman, Alejandro G

    2015-09-01

    An international study was performed by 26 experienced PCR laboratories from 14 countries to assess the performance of duplex quantitative real-time PCR (qPCR) strategies on the basis of TaqMan probes for detection and quantification of parasitic loads in peripheral blood samples from Chagas disease patients. Two methods were studied: Satellite DNA (SatDNA) qPCR and kinetoplastid DNA (kDNA) qPCR. Both methods included an internal amplification control. Reportable range, analytical sensitivity, limits of detection and quantification, and precision were estimated according to international guidelines. In addition, inclusivity and exclusivity were estimated with DNA from stocks representing the different Trypanosoma cruzi discrete typing units and Trypanosoma rangeli and Leishmania spp. Both methods were challenged against 156 blood samples provided by the participant laboratories, including samples from acute and chronic patients with varied clinical findings, infected by oral route or vectorial transmission. kDNA qPCR showed better analytical sensitivity than SatDNA qPCR with limits of detection of 0.23 and 0.70 parasite equivalents/mL, respectively. Analyses of clinical samples revealed a high concordance in terms of sensitivity and parasitic loads determined by both SatDNA and kDNA qPCRs. This effort is a major step toward international validation of qPCR methods for the quantification of T. cruzi DNA in human blood samples, aiming to provide an accurate surrogate biomarker for diagnosis and treatment monitoring for patients with Chagas disease. Copyright © 2015 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  4. 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.

  5. Development of Real-Time PCR Methods for the Detection of Bacterial Meningitis Pathogens without DNA Extraction.

    Directory of Open Access Journals (Sweden)

    Jeni Vuong

    Full Text Available Neisseria meningitidis (Nm, Haemophilus influenzae (Hi, and Streptococcus pneumoniae (Sp are the lead causes of bacterial meningitis. Detection of these pathogens from clinical specimens using traditional real-time PCR (rt-PCR requires DNA extraction to remove the PCR inhibitors prior to testing, which is time consuming and labor intensive. In this study, five species-specific (Nm-sodC and -ctrA, Hi-hpd#1 and -hpd#3 and Sp-lytA and six serogroup-specific rt-PCR tests (A, B, C, W, X, Y targeting Nm capsular genes were evaluated in the two direct rt-PCR methods using PerfeCTa and 5x Omni that do not require DNA extraction. The sensitivity and specify of the two direct rt-PCR methods were compared to TaqMan traditional rt-PCR, the current standard rt-PCR method for the detection of meningitis pathogens. The LLD for all 11 rt-PCR tests ranged from 6,227 to 272,229 CFU/ml for TaqMan, 1,824-135,982 for 5x Omni, and 168-6,836 CFU/ml for PerfeCTa. The diagnostic sensitivity using TaqMan ranged from 89.2%-99.6%, except for NmB-csb, which was 69.7%. For 5x Omni, the sensitivity varied from 67.1% to 99.8%, with three tests below 90%. The sensitivity of these tests using PerfeCTa varied from 89.4% to 99.8%. The specificity ranges of the 11 tests were 98.0-99.9%, 97.5-99.9%, and 92.9-99.9% for TaqMan, 5x Omni, and PerfeCTa, respectively. PerfeCTa direct rt-PCR demonstrated similar or better sensitivity compared to 5x Omni direct rt-PCR or TaqMan traditional rt-PCR. Since the direct rt-PCR method does not require DNA extraction, it reduces the time and cost for processing CSF specimens, increases testing throughput, decreases the risk of cross-contamination, and conserves precious CSF. The direct rt-PCR method will be beneficial to laboratories with high testing volume.

  6. 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

  7. Partial validation of a TaqMan real-time quantitative PCR for the detection of ranaviruses

    DEFF Research Database (Denmark)

    Stilwell, Natalie K.; Whittington, Richard J.; Hick, Paul M.

    2018-01-01

    Ranaviruses are globally emerging pathogens negatively impacting wild and cultured fish, amphibians, and reptiles. Although conventional and diagnostic real-time PCR (qPCR) assays have been developed to detect ranaviruses, these assays often have not been tested against the known diversity of ran...

  8. 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.

  9. Development of a real-time clinical decision support system upon the Web MVC-based architecture for prostate cancer treatment.

    Science.gov (United States)

    Lin, Hsueh-Chun; Wu, Hsi-Chin; Chang, Chih-Hung; Li, Tsai-Chung; Liang, Wen-Miin; Wang, Jong-Yi Wang

    2011-03-08

    A real-time clinical decision support system (RTCDSS) with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs) and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC) architecture, by which the system can easily be adapted to different diseases and applications. We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital information system and be easily applied in other chronic diseases.

  10. Real-time quantitative PCR for retrovirus-like particle quantification in CHO cell culture.

    Science.gov (United States)

    de Wit, C; Fautz, C; Xu, Y

    2000-09-01

    Chinese hamster ovary (CHO) cells have been widely used to manufacture recombinant proteins intended for human therapeutic uses. Retrovirus-like particles, which are apparently defective and non-infectious, have been detected in all CHO cells by electron microscopy (EM). To assure viral safety of CHO cell-derived biologicals, quantification of retrovirus-like particles in production cell culture and demonstration of sufficient elimination of such retrovirus-like particles by the down-stream purification process are required for product market registration worldwide. EM, with a detection limit of 1x10(6) particles/ml, is the standard retrovirus-like particle quantification method. The whole process, which requires a large amount of sample (3-6 litres), is labour intensive, time consuming, expensive, and subject to significant assay variability. In this paper, a novel real-time quantitative PCR assay (TaqMan assay) has been developed for the quantification of retrovirus-like particles. Each retrovirus particle contains two copies of the viral genomic particle RNA (pRNA) molecule. Therefore, quantification of retrovirus particles can be achieved by quantifying the pRNA copy number, i.e. every two copies of retroviral pRNA is equivalent to one retrovirus-like particle. The TaqMan assay takes advantage of the 5'-->3' exonuclease activity of Taq DNA polymerase and utilizes the PRISM 7700 Sequence Detection System of PE Applied Biosystems (Foster City, CA, U.S.A.) for automated pRNA quantification through a dual-labelled fluorogenic probe. The TaqMan quantification technique is highly comparable to the EM analysis. In addition, it offers significant advantages over the EM analysis, such as a higher sensitivity of less than 600 particles/ml, greater accuracy and reliability, higher sample throughput, more flexibility and lower cost. Therefore, the TaqMan assay should be used as a substitute for EM analysis for retrovirus-like particle quantification in CHO cell

  11. Specific and straightforward molecular investigation of β-thalassemia mutations in the Malaysian Malays and Chinese using direct TaqMan genotyping assays.

    Science.gov (United States)

    Kho, S L; Chua, K H; George, E; Tan, J A M A

    2013-07-15

    Beta-thalassemia is a life-threatening inherited blood disorder. Rapid characterization of β-globin gene mutations is necessary because of the high frequency of Malaysian β-thalassemia carriers. A combination real-time polymerase chain reaction genotyping assay using TaqMan probes was developed to confirm β-globin gene mutations. In this study, primers and probes were designed to specifically identify 8 common β-thalassemia mutations in the Malaysian Malay and Chinese ethnic groups using the Primer Express software. "Blind tests" using DNA samples from healthy individuals and β-thalassemia patients with different genotypes were performed to determine the specificity and sensitivity of this newly designed assay. Our results showed 100% sensitivity and specificity for this novel assay. In conclusion, the TaqMan genotyping assay is a straightforward assay that allows detection of β-globin gene mutations in less than 40 min. The simplicity and reproducibility of the TaqMan genotyping assay permit its use in laboratories as a rapid and cost-effective diagnostic tool for confirmation of common β-thalassemia mutations in Malaysia.

  12. Development of a real-time clinical decision support system upon the web mvc-based architecture for prostate cancer treatment

    Directory of Open Access Journals (Sweden)

    Liang Wen-Miin

    2011-03-01

    Full Text Available Abstract Background A real-time clinical decision support system (RTCDSS with interactive diagrams enables clinicians to instantly and efficiently track patients' clinical records (PCRs and improve their quality of clinical care. We propose a RTCDSS to process online clinical informatics from multiple databases for clinical decision making in the treatment of prostate cancer based on Web Model-View-Controller (MVC architecture, by which the system can easily be adapted to different diseases and applications. Methods We designed a framework upon the Web MVC-based architecture in which the reusable and extractable models can be conveniently adapted to other hospital information systems and which allows for efficient database integration. Then, we determined the clinical variables of the prostate cancer treatment based on participating clinicians' opinions and developed a computational model to determine the pretreatment parameters. Furthermore, the components of the RTCDSS integrated PCRs and decision factors for real-time analysis to provide evidence-based diagrams upon the clinician-oriented interface for visualization of treatment guidance and health risk assessment. Results The resulting system can improve quality of clinical treatment by allowing clinicians to concurrently analyze and evaluate the clinical markers of prostate cancer patients with instantaneous clinical data and evidence-based diagrams which can automatically identify pretreatment parameters. Moreover, the proposed RTCDSS can aid interactions between patients and clinicians. Conclusions Our proposed framework supports online clinical informatics, evaluates treatment risks, offers interactive guidance, and provides real-time reference for decision making in the treatment of prostate cancer. The developed clinician-oriented interface can assist clinicians in conveniently presenting evidence-based information to patients and can be readily adapted to an existing hospital

  13. Clinical evaluation of β-tubulin real-time PCR for rapid diagnosis of dermatophytosis, a comparison with mycological methods.

    Science.gov (United States)

    Motamedi, Marjan; Mirhendi, Hossein; Zomorodian, Kamiar; Khodadadi, Hossein; Kharazi, Mahboobeh; Ghasemi, Zeinab; Shidfar, Mohammad Reza; Makimura, Koichi

    2017-10-01

    Following our previous report on evaluation of the beta tubulin real-time PCR for detection of dermatophytosis, this study aimed to compare the real-time PCR assay with conventional methods for the clinical assessment of its diagnostic performance. Samples from a total of 853 patients with suspected dermatophyte lesions were subjected to direct examination (all samples), culture (499 samples) and real-time PCR (all samples). Fungal DNA was extracted directly from clinical samples using a conical steel bullet, followed by purification with a commercial kit and subjected to the Taq-Man probe-based real-time PCR. The study showed that among the 499 specimens for which all three methods were used, 156 (31.2%), 128 (25.6%) and 205 (41.0%) were found to be positive by direct microscopy, culture and real-time PCR respectively. Real-time PCR significantly increased the detection rate of dermatophytes compared with microscopy (288 vs 229) with 87% concordance between the two methods. The sensitivity, specificity, positive predictive value, and negative predictive value of the real-time PCR was 87.5%, 85%, 66.5% and 95.2% respectively. Although real-time PCR performed better on skin than on nail samples, it should not yet fully replace conventional diagnosis. © 2017 Blackwell Verlag GmbH.

  14. Evaluation of a Multiplex Real-Time Reverse Transcriptase PCR Assay for Detection and Differentiation of Influenza Viruses A and B during the 2001-2002 Influenza Season in Israel

    Science.gov (United States)

    Hindiyeh, Musa; Levy, Virginia; Azar, Roberto; Varsano, Noemi; Regev, Liora; Shalev, Yael; Grossman, Zehava; Mendelson, Ella

    2005-01-01

    The ability to rapidly diagnose influenza virus infections is of the utmost importance in the evaluation of patients with upper respiratory tract infections. It is also important for the influenza surveillance activities performed by national influenza centers. In the present study we modified a multiplex real-time reverse transcriptase PCR (RT-PCR) assay (which uses TaqMan chemistry) and evaluated it for its ability to detect and concomitantly differentiate influenza viruses A and B in 370 patient samples collected during the 2001-2002 influenza season in Israel. The performance of the TaqMan assay was compared to those of a multiplex one-step RT-PCR with gel detection, a shell vial immunofluorescence assay, and virus isolation in tissue culture. The TaqMan assay had an excellent sensitivity for the detection of influenza viruses compared to that of tissue culture. The overall sensitivity and specificity of the TaqMan assay compared to the results of culture were 98.4 and 85.5%, respectively. The sensitivity and specificity of the TaqMan assay for the detection of influenza virus A alone were 100 and 91.1%, respectively. On the other hand, the sensitivity and specificity for the detection of influenza virus B alone were 95.7 and 98.7%, respectively. The rapid turnaround time for the performance of the TaqMan assay (4.5 h) and the relatively low direct cost encourage the routine use of this assay in place of tissue culture. We conclude that the multiplex TaqMan assay is highly suitable for the rapid diagnosis of influenza virus infections both in well-established molecular biology laboratories and in reference clinical laboratories. PMID:15695650

  15. 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.

  16. A Laboratory-Developed TaqMan Array Card for Simultaneous Detection of 19 Enteropathogens

    Science.gov (United States)

    Liu, Jie; Gratz, Jean; Amour, Caroline; Kibiki, Gibson; Becker, Stephen; Janaki, Lalitha; Verweij, Jaco J.; Taniuchi, Mami; Sobuz, Shihab U.; Haque, Rashidul; Haverstick, Doris M.

    2013-01-01

    The TaqMan Array Card (TAC) system is a 384-well singleplex real-time PCR format that has been used to detect multiple infection targets. Here we developed an enteric TaqMan Array Card to detect 19 enteropathogens, including viruses (adenovirus, astrovirus, norovirus GII, rotavirus, and sapovirus), bacteria (Campylobacter jejuni/C. coli, Clostridium difficile, Salmonella, Vibrio cholerae, diarrheagenic Escherichia coli strains including enteroaggregative E. coli [EAEC], enterotoxigenic E. coli [ETEC], enteropathogenic E. coli [EPEC], and Shiga-toxigenic E. coli [STEC]), Shigella/enteroinvasive E. coli (EIEC), protozoa (Cryptosporidium, Giardia lamblia, and Entamoeba histolytica), and helminths (Ascaris lumbricoides and Trichuris trichiura), as well as two extrinsic controls to monitor extraction and amplification efficiency (the bacteriophage MS2 and phocine herpesvirus). Primers and probes were newly designed or adapted from published sources and spotted onto microfluidic cards. Fecal samples were spiked with extrinsic controls, and DNA and RNA were extracted using the QiaAmp Stool DNA minikit and the QuickGene RNA Tissue kit, respectively, and then mixed with Ag-Path-ID One Step real-time reverse transcription-PCR (RT-PCR) reagents and loaded into cards. PCR efficiencies were between 90% and 105%, with linearities of 0.988 to 1. The limit of detection of the assays in the TAC was within a 10-fold difference from the cognate assays performed on plates. Precision testing demonstrated a coefficient of variation of below 5% within a run and 14% between runs. Accuracy was evaluated for 109 selected clinical specimens and revealed an average sensitivity and specificity of 85% and 77%, respectively, compared with conventional methods (including microscopy, culture, and immunoassay) and 98% and 96%, respectively, compared with our laboratory-developed PCR-Luminex assays. This TAC allows fast, accurate, and quantitative detection of a broad spectrum of enteropathogens and

  17. Clinical evaluation of a quantitative real time polymerase chain reaction assay for diagnosis of primary Epstein-Barr virus infection in children.

    Science.gov (United States)

    Pitetti, Raymond D; Laus, Stella; Wadowsky, Robert M

    2003-08-01

    Epstein-Barr virus (EBV) infectious mononucleosis is often diagnosed based on characteristic clinical features and either a positive heterophil antibody test or serology, both of which can be unreliable in young children. Real time quantitative PCR assays that measure EBV DNA load in serum or plasma are highly sensitive in young children, but serum and plasma contain inhibitors of PCR which must be removed by DNA extraction techniques. A real time TaqMan PCR assay was designed and evaluated for simultaneously measuring EBV DNA load and validating the removal of PCR inhibitors from serum samples. A serum sample was available from patients classified serologically as primary EBV infection (n = 28), EBV-seronegative (n = 25) and EBV-seropositive (n = 26). Patients were classified as having EBV infectious mononucleosis if they had specified clinical findings and > or =10% atypical lymphocytes in peripheral blood or had a positive Monospot test result. DNA was purified by a spin column method and tested in PCR reactions with primers for EBV DNA polymerase gene and internal control targets. Amplification of the two PCR products was measured in real time with separate TaqMan DNA probes labeled with various fluorescent reporters. The mean age of study patients was 9 years, 4 months. Twenty-one (75%) of the patients in the primary EBV infection group, one (4%) of the seronegatives and none of the seropositives had detectable EBV DNA. Within the primary infection group, those with detectable virus were more likely than those without detectable virus to have evidence of lymphadenopathy (14 of 16 vs.1 of 5; P = 0.011), higher mean atypical (11.7 vs.0.9%; P = 0.002) and absolute atypical (1.5 vs.0.1 x 109/l; P = 0.004) lymphocyte count, higher mean absolute lymphocyte count (4.7 vs.2.3 x 109/l; P = 0.026) and higher mean aspartate aminotransferase value (119.8 vs.37.3 IU/l; P = 0.036). Ten patients, all in the primary infection group, had EBV infectious mononucleosis, and all

  18. 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.

  19. Single reaction, real time RT-PCR detection of all known avian and human metapneumoviruses.

    Science.gov (United States)

    Lemaitre, E; Allée, C; Vabret, A; Eterradossi, N; Brown, P A

    2018-01-01

    Current molecular methods for the detection of avian and human metapneumovirus (AMPV, HMPV) are specifically targeted towards each virus species or individual subgroups of these. Here a broad range SYBR Green I real time RT-PCR was developed which amplified a highly conserved fragment of sequence in the N open reading frame. This method was sufficiently efficient and specific in detecting all MPVs. Its validation according to the NF U47-600 norm for the four AMPV subgroups estimated low limits of detection between 1000 and 10copies/μL, similar with detection levels described previously for real time RT-PCRs targeting specific subgroups. RNA viruses present a challenge for the design of durable molecular diagnostic test due to the rate of change in their genome sequences which can vary substantially in different areas and over time. The fact that the regions of sequence for primer hybridization in the described method have remained sufficiently conserved since the AMPV and HMPV diverged, should give the best chance of continued detection of current subgroups and of potential unknown or future emerging MPV strains. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Rapid quantification of semen hepatitis B virus DNA by real-time polymerase chain reaction

    Science.gov (United States)

    Qian, Wei-Ping; Tan, Yue-Qiu; Chen, Ying; Peng, Ying; Li, Zhi; Lu, Guang-Xiu; Lin, Marie C.; Kung, Hsiang-Fu; He, Ming-Ling; Shing, Li-Ka

    2005-01-01

    AIM: To examine the sensitivity and accuracy of real-time polymerase chain reaction (PCR) for the quantification of hepatitis B virus (HBV) DNA in semen. METHODS: Hepatitis B viral DNA was isolated from HBV carriers’ semen and sera using phenol extraction method and QIAamp DNA blood mini kit (Qiagen, Germany). HBV DNA was detected by conventional PCR and quantified by TaqMan technology-based real-time PCR (quantitative polymerase chain reaction (qPCR)). The detection threshold was 200 copies of HBV DNA for conventional PCR and 10 copies of HBV DNA for real time PCR per reaction. RESULTS: Both methods of phenol extraction and QIAamp DNA blood mini kit were suitable for isolating HBV DNA from semen. The value of the detection thresholds was 500 copies of HBV DNA per mL in the semen. The viral loads were 7.5 × 107 and 1.67 × 107 copies of HBV DNA per mL in two HBV infected patients’ sera, while 2.14 × 105 and 3.02 × 105 copies of HBV DNA per mL in the semen. CONCLUSION: Real-time PCR is a more sensitive and accurate method to detect and quantify HBV DNA in the semen. PMID:16149152

  1. 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.

  2. New approaches for the standardization and validation of a real-time qPCR assay using TaqMan probes for quantification of yellow fever virus on clinical samples with high quality parameters.

    Science.gov (United States)

    Fernandes-Monteiro, Alice G; Trindade, Gisela F; Yamamura, Anna M Y; Moreira, Otacilio C; de Paula, Vanessa S; Duarte, Ana Cláudia M; Britto, Constança; Lima, Sheila Maria B

    2015-01-01

    The development and production of viral vaccines, in general, involve several steps that need the monitoring of viral load throughout the entire process. Applying a 2-step quantitative reverse transcription real time PCR assay (RT-qPCR), viral load can be measured and monitored in a few hours. In this context, the development, standardization and validation of a RT-qPCR test to quickly and efficiently quantify yellow fever virus (YFV) in all stages of vaccine production are extremely important. To serve this purpose we used a plasmid construction containing the NS5 region from 17DD YFV to generate the standard curve and to evaluate parameters such as linearity, precision and specificity against other flavivirus. Furthermore, we defined the limits of detection as 25 copies/reaction, and quantification as 100 copies/reaction for the test. To ensure the quality of the method, reference controls were established in order to avoid false negative results. The qRT-PCR technique based on the use of TaqMan probes herein standardized proved to be effective for determining yellow fever viral load both in vivo and in vitro, thus becoming a very important tool to assure the quality control for vaccine production and evaluation of viremia after vaccination or YF disease.

  3. 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.

  4. Quantification of bovine leukemia virus proviral DNA using a low-cost real-time polymerase chain reaction.

    Science.gov (United States)

    Petersen, M I; Alvarez, I; Trono, K G; Jaworski, J P

    2018-04-11

    The detection of bovine leukemia virus (BLV) proviral DNA is an important tool to address whether an animal is infected with BLV. Compared with serological assays, real-time PCR accounts for greater sensitivity and can serve as a confirmatory test for the clarification of inconclusive or discordant serological test results. However, the high cost related to real-time PCR assays has limited their systematic inclusion in BLV surveillance and eradication programs. The aim of the present study was to validate a low-cost quantitative real-time PCR. Interestingly, by using SYBR Green detection dye, we were able to reduce the cost of a single reaction by a factor of 5 compared with most common assays based on the use of fluorogenic probes (i.e., TaqMan technology). This approach allowed a highly sensitive and specific detection and quantification of BLV proviral DNA from purified peripheral blood leukocytes and a milk matrix. Due to its simplicity and low cost, our in-house BLV SYBR quantitative real-time PCR might be used either as a screening or as a confirmatory test in BLV control programs. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  5. Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus.

    Science.gov (United States)

    Mari, Viviana; Losurdo, Michele; Lucente, Maria Stella; Lorusso, Eleonora; Elia, Gabriella; Martella, Vito; Patruno, Giovanni; Buonavoglia, Domenico; Decaro, Nicola

    2016-03-01

    HoBi-like pestiviruses are emerging pestiviruses that infect cattle causing clinical forms overlapping to those induced by bovine viral diarrhea virus (BVDV) 1 and 2. As a consequence of their widespread distribution reported in recent years, molecular tools for rapid discrimination among pestiviruses infecting cattle are needed. The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. The assay was found to be sensitive, specific and repeatable, ensuring detection of as few as 10(0)-10(1) viral RNA copies. No cross-reactions between different pestiviral species were observed even in samples artificially contaminated with more than one pestivirus. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. 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.

  7. Incidence of pulmonary aspergillosis and correlation of conventional diagnostic methods with nested PCR and real-time PCR assay using BAL fluid in intensive care unit patients.

    Science.gov (United States)

    Zarrinfar, Hossein; Makimura, Koichi; Satoh, Kazuo; Khodadadi, Hossein; Mirhendi, Hossein

    2013-05-01

    Although the incidence of invasive aspergillosis in the intensive care unit (ICU) is scarce, it has emerged as major problems in critically ill patients. In this study, the incidence of pulmonary aspergillosis (PA) in ICU patients has evaluated and direct microscopy and culture has compared with nested polymerase chain reaction (PCR) and real-time PCR for detection of Aspergillus fumigatus and A. flavus in bronchoalveolar lavage (BAL) samples of the patients. Thirty BAL samples obtained from ICU patients during a 16-month period were subjected to direct examinations on 20% potassium hydroxide (KOH) and culture on two culture media. Nested PCR targeting internal transcribed spacer ribosomal DNA and TaqMan real-time PCR assay targeting β-tubulin gene were used for the detection of A. fumigatus and A. flavus. Of 30 patients, 60% were men and 40% were women. The diagnosis of invasive PA was probable in 1 (3%), possible in 11 (37%), and not IPA in 18 (60%). Nine samples were positive in nested PCR including seven samples by A. flavus and two by A. fumigatus specific primers. The lowest amount of DNA that TaqMan real-time PCR could detect was ≥40 copy numbers. Only one of the samples had a positive result of A. flavus real-time PCR with Ct value of 37.5. Although a significant number of specimens were positive in nested PCR, results of this study showed that establishment of a correlation between the conventional methods with nested PCR and real-time PCR needs more data confirmed by a prospective study with a larger sample group. © 2013 Wiley Periodicals, Inc.

  8. Rapid Detection of Chlamydia trachomatis and Typing of the Lymphogranuloma venereum associated L-Serovars by TaqMan PCR

    Directory of Open Access Journals (Sweden)

    Henrich Birgit

    2008-04-01

    Full Text Available Abstract Background Infection due to Chlamydia trachomatis is the most common sexually transmitted bacterial disease of global health significance, and especially the L-serovars causing lymphogranuloma venereum are increasingly being found in Europe in men who have sex with men. Results The design and evaluation of a rapid, multiplex, real-time PCR targeting the major outer membrane protein (omp-1 -gene and a L-serovar-specific region of the polymorphic protein H (pmp-H -gene for the detection of Chlamydia trachomatis is reported here. The PCR takes place as a single reaction with an internal control. For L1-, L2- and L3-serovar differentiation a second set of real-time PCRs was evaluated based on the amplification of serovar-specific omp-1-regions. The detection limit of each real-time PCR, multiplexed or not, was 50 genome copies per reaction with an efficiency ranging from 90,5–95,2%. In a retrospective analysis of 50 ocular, rectal and urogenital specimens formerly tested to be positive for C. trachomatis we identified six L2-serovars in rectal specimens of HIV-positive men, one in a double-infection with L3, and one L2 in a urethral specimen of an HIV-negative male. Conclusion This unique real-time PCR is specific and convenient for the rapid routine-diagnostic detection of lymphogranuloma venereum-associated L-serovars and enables the subsequent differentiation of L1, L2 and L3 for epidemiologic studies.

  9. Rapid Detection of Chlamydia trachomatis and Typing of the Lymphogranuloma venereum associated L-Serovars by TaqMan PCR

    Science.gov (United States)

    Schaeffer, Anke; Henrich, Birgit

    2008-01-01

    Background Infection due to Chlamydia trachomatis is the most common sexually transmitted bacterial disease of global health significance, and especially the L-serovars causing lymphogranuloma venereum are increasingly being found in Europe in men who have sex with men. Results The design and evaluation of a rapid, multiplex, real-time PCR targeting the major outer membrane protein (omp-1) -gene and a L-serovar-specific region of the polymorphic protein H (pmp-H) -gene for the detection of Chlamydia trachomatis is reported here. The PCR takes place as a single reaction with an internal control. For L1-, L2- and L3-serovar differentiation a second set of real-time PCRs was evaluated based on the amplification of serovar-specific omp-1-regions. The detection limit of each real-time PCR, multiplexed or not, was 50 genome copies per reaction with an efficiency ranging from 90,5–95,2%. In a retrospective analysis of 50 ocular, rectal and urogenital specimens formerly tested to be positive for C. trachomatis we identified six L2-serovars in rectal specimens of HIV-positive men, one in a double-infection with L3, and one L2 in a urethral specimen of an HIV-negative male. Conclusion This unique real-time PCR is specific and convenient for the rapid routine-diagnostic detection of lymphogranuloma venereum-associated L-serovars and enables the subsequent differentiation of L1, L2 and L3 for epidemiologic studies. PMID:18447917

  10. 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.

  11. 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.

  12. 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.

  13. [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.

  14. Comparison of nine DNA extraction methods for the diagnosis of bovine tuberculosis by real time PCR

    Directory of Open Access Journals (Sweden)

    André Moura

    2016-07-01

    Full Text Available ABSTRACT: Bovine tuberculosis is an infectious disease with a high impact on the cattle industry, particularly in developing countries. PCR is a very sensitive method for detection of infectious agents, but the sensitivity of molecular diagnosis is largely dependent on the efficiency of the DNA extraction methods. The objective of this study was to evaluate DNA extraction methods for direct detection of Mycobacterium bovis in bovine tissue. Nine commercial kits for DNA extraction were evaluated when combined with two real time PCRs. The DNeasy Blood & Tissue Kit from QIAGEN showed better performance and sensitivity followed by the DNA Mini Kit RBC and FTA Elute Micro Card. Results suggested that, even when the analytical sensitivity of the qPCR is very high, the extraction method can influence the diagnostic sensitivity.

  15. Novel Molecular Beacon Probe-Based Real-Time RT-PCR Assay for Diagnosis of Crimean-Congo Hemorrhagic Fever Encountered in India

    Directory of Open Access Journals (Sweden)

    Aman Kamboj

    2014-01-01

    Full Text Available Crimean-Congo hemorrhagic fever (CCHF is an emerging zoonotic disease in India and requires immediate detection of infection both for preventing further transmission and for controlling the infection. The present study describes development, optimization, and evaluation of a novel molecular beacon-based real-time RT-PCR assay for rapid, sensitive, and specific diagnosis of Crimean-Congo hemorrhagic fever virus (CCHFV. The developed assay was found to be a better alternative to the reported TaqMan assay for routine diagnosis of CCHF.

  16. 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.

  17. Evaluation of the analytical performance of the new Abbott RealTime RT-PCRs for the quantitative detection of HCV and HIV-1 RNA

    NARCIS (Netherlands)

    Schutten, Martin; Fries, E; Burghoorn-Maas, C; Niesters, H G M

    2007-01-01

    BACKGROUND: Despite FDA approval and CE marking of commercial tests, manufacturer independent testing of technical aspects is important. OBJECTIVES: To evaluate the analytical performance of the new Abbott RealTime HCV and HIV-1 viral load tests. STUDY DESIGN: Sensitivity, specificity and

  18. Multiplex real-time PCR assay for detection of Escherichia coli O157:H7 and screening for non-O157 Shiga toxin-producing E. coli.

    Science.gov (United States)

    Li, Baoguang; Liu, Huanli; Wang, Weimin

    2017-11-09

    Shiga toxin-producing Escherichia coli (STEC), including E. coli O157:H7, are responsible for numerous foodborne outbreaks annually worldwide. E. coli O157:H7, as well as pathogenic non-O157:H7 STECs, can cause life-threating complications, such as bloody diarrhea (hemolytic colitis) and hemolytic-uremic syndrome (HUS). Previously, we developed a real-time PCR assay to detect E. coli O157:H7 in foods by targeting a unique putative fimbriae protein Z3276. To extend the detection spectrum of the assay, we report a multiplex real-time PCR assay to specifically detect E. coli O157:H7 and screen for non-O157 STEC by targeting Z3276 and Shiga toxin genes (stx1 and stx2). Also, an internal amplification control (IAC) was incorporated into the assay to monitor the amplification efficiency. The multiplex real-time PCR assay was developed using the Life Technology ABI 7500 System platform and the standard chemistry. The optimal amplification mixture of the assay contains 12.5 μl of 2 × Universal Master Mix (Life Technology), 200 nM forward and reverse primers, appropriate concentrations of four probes [(Z3276 (80 nM), stx1 (80 nM), stx2 (20 nM), and IAC (40 nM)], 2 μl of template DNA, and water (to make up to 25 μl in total volume). The amplification conditions of the assay were set as follows: activation of TaqMan at 95 °C for 10 min, then 40 cycles of denaturation at 95 °C for 10 s and annealing/extension at 60 °C for 60 s. The multiplex assay was optimized for amplification conditions. The limit of detection (LOD) for the multiplex assay was determined to be 200 fg of bacterial DNA, which is equivalent to 40 CFU per reaction which is similar to the LOD generated in single targeted PCRs. Inclusivity and exclusivity determinants were performed with 196 bacterial strains. All E. coli O157:H7 (n = 135) were detected as positive and all STEC strains (n = 33) were positive for stx1, or stx2, or stx1 and stx2 (Table 1). No cross reactivity was detected with Salmonella

  19. Smallpox and pan-orthopox virus detection by real-time 3'-minor groove binder TaqMan assays on the roche LightCycler and the Cepheid smart Cycler platforms.

    Science.gov (United States)

    Kulesh, David A; Baker, Robert O; Loveless, Bonnie M; Norwood, David; Zwiers, Susan H; Mucker, Eric; Hartmann, Chris; Herrera, Rafael; Miller, David; Christensen, Deanna; Wasieloski, Leonard P; Huggins, John; Jahrling, Peter B

    2004-02-01

    We designed, optimized, and extensively tested several sensitive and specific real-time PCR assays for rapid detection of both smallpox and pan-orthopox virus DNAs. The assays are based on TaqMan 3'-minor groove binder chemistry and were performed on both the rapid-cycling Roche LightCycler and the Cepheid Smart Cycler platforms. The hemagglutinin (HA) J7R, B9R, and B10R genes were used as targets for the variola virus-specific assays, and the HA and DNA polymerase-E9L genes were used as targets for the pan-orthopox virus assays. The five orthopox virus assays were tested against a panel of orthopox virus DNAs (both genomic and cloned) at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID). The results indicated that each assay was capable of detecting both the appropriate cloned gene and genomic DNA. The assays showed no cross-reactivity to the 78 DNAs in the USAMRIID bacterial cross-reactivity panel. The limit of detection (LOD) of each assay was determined to be between 12 and 25 copies of target DNA. The assays were also run against a blind panel of DNAs at the Centers for Disease Control and Prevention (CDC) on both the LightCycler and the Smart Cycler. The panel consisted of eight different variola virus isolates, five non-variola virus orthopox virus isolates, two varicella-zoster virus isolates, and one herpes simplex virus isolate. Each sample was tested in triplicate at 2.5 ng, 25 pg, 250 fg, and 2.5 fg, which represent 1.24 x 10(7), 1.24 x 10(5), 1.24 x 10(3), and 1.24 x 10(1) genome equivalents, respectively. The results indicated that each of the five assays was 100% specific (no false positives) when tested against both the USAMRIID panels and the CDC blind panel. With the CDC blind panel, the LightCycler was capable of detecting 96.2% of the orthopox virus DNAs and 93.8% of the variola virus DNAs. The Smart Cycler was capable of detecting 92.3% of the orthopox virus DNAs and between 75 and 93.8% of the variola virus DNAs

  20. 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...

  1. Simultaneous detection of five different DNA targets by real-time Taqman PCR using the Roche LightCycler480: Application in viral molecular diagnostics

    NARCIS (Netherlands)

    Molenkamp, Richard; van der Ham, Alwin; Schinkel, Janke; Beld, Marcel

    2007-01-01

    One of the most interesting aspects of real-time PCR based on the detection of fluorophoric labeled oligonucleotides is the possibility of being able to detect conveniently multiple targets in the same PCR reaction. Recently, Roche Diagnostics launched a real-time PCR platform, the LightCycler480

  2. 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.

  3. 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

  4. 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

  5. Methods for Real-Time PCR-Based Diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus Infections in an Opened Molecular Diagnostic Platform.

    Science.gov (United States)

    Opota, Onya; Brouillet, René; Greub, Gilbert; Jaton, Katia

    2017-01-01

    The advances in molecular biology of the last decades have dramatically improved the field of diagnostic bacteriology. In particular, PCR-based technologies have impacted the diagnosis of infections caused by obligate intracellular bacteria such as pathogens from the Chlamydiacae family. Here, we describe a real-time PCR-based method using the Taqman technology for the diagnosis of Chlamydia pneumoniae, Chlamydia psittaci, and Chlamydia abortus infection. The method presented here can be applied to various clinical samples and can be adapted on opened molecular diagnostic platforms.

  6. 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.

  7. 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.

  8. Smallpox and pan-Orthopox Virus Detection by Real-Time 3′-Minor Groove Binder TaqMan Assays on the Roche LightCycler and the Cepheid Smart Cycler Platforms

    Science.gov (United States)

    Kulesh, David A.; Baker, Robert O.; Loveless, Bonnie M.; Norwood, David; Zwiers, Susan H.; Mucker, Eric; Hartmann, Chris; Herrera, Rafael; Miller, David; Christensen, Deanna; Wasieloski, Leonard P.; Huggins, John; Jahrling, Peter B.

    2004-01-01

    We designed, optimized, and extensively tested several sensitive and specific real-time PCR assays for rapid detection of both smallpox and pan-orthopox virus DNAs. The assays are based on TaqMan 3′-minor groove binder chemistry and were performed on both the rapid-cycling Roche LightCycler and the Cepheid Smart Cycler platforms. The hemagglutinin (HA) J7R, B9R, and B10R genes were used as targets for the variola virus-specific assays, and the HA and DNA polymerase-E9L genes were used as targets for the pan-orthopox virus assays. The five orthopox virus assays were tested against a panel of orthopox virus DNAs (both genomic and cloned) at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID). The results indicated that each assay was capable of detecting both the appropriate cloned gene and genomic DNA. The assays showed no cross-reactivity to the 78 DNAs in the USAMRIID bacterial cross-reactivity panel. The limit of detection (LOD) of each assay was determined to be between 12 and 25 copies of target DNA. The assays were also run against a blind panel of DNAs at the Centers for Disease Control and Prevention (CDC) on both the LightCycler and the Smart Cycler. The panel consisted of eight different variola virus isolates, five non-variola virus orthopox virus isolates, two varicella-zoster virus isolates, and one herpes simplex virus isolate. Each sample was tested in triplicate at 2.5 ng, 25 pg, 250 fg, and 2.5 fg, which represent 1.24 × 107, 1.24 × 105, 1.24 × 103, and 1.24 × 101 genome equivalents, respectively. The results indicated that each of the five assays was 100% specific (no false positives) when tested against both the USAMRIID panels and the CDC blind panel. With the CDC blind panel, the LightCycler was capable of detecting 96.2% of the orthopox virus DNAs and 93.8% of the variola virus DNAs. The Smart Cycler was capable of detecting 92.3% of the orthopox virus DNAs and between 75 and 93.8% of the variola virus DNAs. However

  9. A sensitive, reproducible, and economic real-time reverse transcription PCR detecting avian metapneumovirus subtypes A and B.

    Science.gov (United States)

    Franzo, G; Drigo, M; Lupini, C; Catelli, E; Laconi, A; Listorti, V; Bonci, M; Naylor, C J; Martini, M; Cecchinato, M

    2014-06-01

    Use of real-time PCR is increasing in the diagnosis of infectious disease due to its sensitivity, specificity, and speed of detection. These characteristics make it particularly suited for the diagnosis of viral infections, like avian metapneumovirus (AMPV), for which effective control benefits from continuously updated knowledge of the epidemiological situation. Other real-time reverse transcription (RT)-PCRs have been published based on highly specific fluorescent dye-labeled probes, but they have high initial cost, complex validation, and a marked susceptibility to the genetic variability of their target sequence. With this in mind, we developed and validated a SYBR Green I-based quantitative RT-PCR for the detection of the two most prevalent AMPV subtypes (i.e., subtypes A and B). The assay demonstrated an analytical sensitivity comparable with that of a previously published real-time RT-PCR and the ability to detect RNA equivalent to approximately 0.5 infectious doses for both A and B subtypes. The high efficiency and linearity between viral titer and crossing point displayed for both subtypes make it suited for viral quantification. Optimization of reaction conditions and the implementation of melting curve analysis guaranteed the high specificity of the assay. The stable melting temperature difference between the two subtypes indicated the possibility of subtyping through melting temperature analysis. These characteristics make our assay a sensitive, specific, and rapid tool, enabling contemporaneous detection, quantification, and discrimination of AMPV subtype A and B.

  10. ABO Blood Group Genotyping by Real-time PCR in Kazakh Population

    Directory of Open Access Journals (Sweden)

    Pavel Tarlykov

    2014-12-01

    Full Text Available Introduction. ABO blood group genotyping is a new technology in hematology that helps prevent adverse transfusion reactions in patients. Identification of antigens on the surface of red blood cells is based on serology; however, genotyping employs a different strategy and is aimed directly at genes that determine the surface proteins. ABO blood group genotyping by real-time PCR has several crucial advantages over other PCR-based techniques, such as high rapidity and reliability of analysis. The purpose of this study was to examine nucleotide substitutions differences by blood types using a PCR-based method on Kazakh blood donors.Methods. The study was approved by the Ethics Committee of the National Center for Biotechnology. Venous blood samples from 369 healthy Kazakh blood donors, whose blood types had been determined by serological methods, were collected after obtaining informed consent. The phenotypes of the samples included blood group A (n = 99, B (n = 93, O (n = 132, and AB (n = 45. Genomic DNA was extracted using a salting-out method. PCR products of ABO gene were sequenced on an ABI 3730xl DNA analyzer (Applied Biosystems. The resulting nucleotide sequences were compared and aligned against reference sequence NM_020469.2. Real-time PCR analysis was performed on CFX96 Touch™ Real-Time PCR Detection System (BioRad.Results. Direct sequencing of ABO gene in 369 samples revealed that the vast majority of nucleotide substitutions that change the ABO phenotype were limited to exons 6 and 7 of the ABO gene at positions 261, 467, 657, 796, 803, 930 and 1,060. However, genotyping of only three of them (261, 796 and 803 resulted in identification of major ABO genotypes in the Kazakh population. As a result, TaqMan probe based real-time PCR assay for the specific detection of genotypes 261, 796 and 803 was developed. The assay did not take into account several other mutations that may affect the determination of blood group, because they have a

  11. 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.

  12. Characterization of Phytophthora nicotianae isolates in southeast Spain and their detection and quantification through a real-time TaqMan PCR.

    Science.gov (United States)

    Blaya, Josefa; Lacasa, Carmen; Lacasa, Alfredo; Martínez, Victoriano; Santísima-Trinidad, Ana B; Pascual, Jose A; Ros, Margarita

    2015-04-01

    The soil-borne pathogens Phytophthora nicotianae and P. capsici are the causal agents of root and stem rot of many plant species. Although P. capsici was considered the causal agent in one of the main pepper production areas of Spain to date, evidence of the presence of P. nicotianae was found. We aimed to survey the presence of P. nicotianae and study the variability in its populations in this area in order to improve the management of Tristeza disease. A new specific primer and a TaqMan probe were designed based on the internal transcribed spacer regions of ribosomal DNA to detect and quantify P. nicotianae. Both morphological and molecular analysis showed its presence and confirmed it to be the causal agent of the Phytophthora disease symptoms in the studied area. The genetic characterization among P. nicotianae populations showed a low variability of genetic diversity among the isolates. Only isolates of the A2 mating type were detected. Not only is a specific and early detection of P. nicotianae essential but also the study of genetic variability among isolates for the appropriate management of the disease, above all, in producing areas with favorable conditions for the advance of the disease. © 2014 Society of Chemical Industry.

  13. Development of a TaqMan Array Card for Acute-Febrile-Illness Outbreak Investigation and Surveillance of Emerging Pathogens, Including Ebola Virus.

    Science.gov (United States)

    Liu, Jie; Ochieng, Caroline; Wiersma, Steve; Ströher, Ute; Towner, Jonathan S; Whitmer, Shannon; Nichol, Stuart T; Moore, Christopher C; Kersh, Gilbert J; Kato, Cecilia; Sexton, Christopher; Petersen, Jeannine; Massung, Robert; Hercik, Christine; Crump, John A; Kibiki, Gibson; Maro, Athanasia; Mujaga, Buliga; Gratz, Jean; Jacob, Shevin T; Banura, Patrick; Scheld, W Michael; Juma, Bonventure; Onyango, Clayton O; Montgomery, Joel M; Houpt, Eric; Fields, Barry

    2016-01-01

    Acute febrile illness (AFI) is associated with substantial morbidity and mortality worldwide, yet an etiologic agent is often not identified. Convalescent-phase serology is impractical, blood culture is slow, and many pathogens are fastidious or impossible to cultivate. We developed a real-time PCR-based TaqMan array card (TAC) that can test six to eight samples within 2.5 h from sample to results and can simultaneously detect 26 AFI-associated organisms, including 15 viruses (chikungunya, Crimean-Congo hemorrhagic fever [CCHF] virus, dengue, Ebola virus, Bundibugyo virus, Sudan virus, hantaviruses [Hantaan and Seoul], hepatitis E, Marburg, Nipah virus, o'nyong-nyong virus, Rift Valley fever virus, West Nile virus, and yellow fever virus), 8 bacteria (Bartonella spp., Brucella spp., Coxiella burnetii, Leptospira spp., Rickettsia spp., Salmonella enterica and Salmonella enterica serovar Typhi, and Yersinia pestis), and 3 protozoa (Leishmania spp., Plasmodium spp., and Trypanosoma brucei). Two extrinsic controls (phocine herpesvirus 1 and bacteriophage MS2) were included to ensure extraction and amplification efficiency. Analytical validation was performed on spiked specimens for linearity, intra-assay precision, interassay precision, limit of detection, and specificity. The performance of the card on clinical specimens was evaluated with 1,050 blood samples by comparison to the individual real-time PCR assays, and the TAC exhibited an overall 88% (278/315; 95% confidence interval [CI], 84% to 92%) sensitivity and a 99% (5,261/5,326, 98% to 99%) specificity. This TaqMan array card can be used in field settings as a rapid screen for outbreak investigation or for the surveillance of pathogens, including Ebola virus. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  14. Real-time PCR genotyping assay for canine progressive rod-cone degeneration and mutant allele frequency in Toy Poodles, Chihuahuas and Miniature Dachshunds in Japan

    OpenAIRE

    KOHYAMA, Moeko; TADA, Naomi; MITSUI, Hiroko; TOMIOKA, Hitomi; TSUTSUI, Toshihiko; YABUKI, Akira; RAHMAN, Mohammad Mahbubur; KUSHIDA, Kazuya; MIZUKAMI, Keijiro; YAMATO, Osamu

    2015-01-01

    Canine progressive rod-cone degeneration (PRCD) is a middle- to late-onset, autosomal recessive, inherited retinal disorder caused by a substitution (c.5G>A) in the canine PRCD gene that has been identified in 29 or more purebred dogs. In the present study, a TaqMan probe-based real-time PCR assay was developed and evaluated for rapid genotyping and large-scale screening of the mutation. Furthermore, a genotyping survey was carried out in a population of the three most popular breeds in Japan...

  15. 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.

  16. Real-Time PCR Detection of Dogwood Anthracnose Fungus in Historical Herbarium Specimens from Asia.

    Science.gov (United States)

    Miller, Stephen; Masuya, Hayato; Zhang, Jian; Walsh, Emily; Zhang, Ning

    2016-01-01

    Cornus species (dogwoods) are popular ornamental trees and important understory plants in natural forests of northern hemisphere. Dogwood anthracnose, one of the major diseases affecting the native North American Cornus species, such as C. florida, is caused by the fungal pathogen Discula destructiva. The origin of this fungus is not known, but it is hypothesized that it was imported to North America with its host plants from Asia. In this study, a TaqMan real-time PCR assay was used to detect D. destructiva in dried herbarium and fresh Cornus samples. Several herbarium specimens from Japan and China were detected positive for D. destructiva, some of which were collected before the first report of the dogwood anthracnose in North America. Our findings further support that D. destructiva was introduced to North America from Asia where the fungus likely does not cause severe disease.

  17. Use of Multiplex Real-Time PCR To Diagnose Scrub Typhus.

    Science.gov (United States)

    Tantibhedhyangkul, Wiwit; Wongsawat, Ekkarat; Silpasakorn, Saowaluk; Waywa, Duangdao; Saenyasiri, Nuttawut; Suesuay, Jintapa; Thipmontree, Wilawan; Suputtamongkol, Yupin

    2017-05-01

    Scrub typhus, caused by Orientia tsutsugamushi , is a common cause of acute undifferentiated febrile illness in the Asia-Pacific region. However, its nonspecific clinical manifestation often prevents early diagnosis. We propose the use of PCR and serologic tests as diagnostic tools. Here, we developed a multiplex real-time PCR assay using hydrolysis (TaqMan) probes targeting O. tsutsugamushi 47-kDa, groEL , and human interferon beta (IFN-β gene) genes to improve early diagnosis of scrub typhus. The amplification efficiency was higher than 94%, and the lower detection limit was 10 copies per reaction. We used a human gene as an internal DNA quality and quantity control. To determine the sensitivity of this PCR assay, we selected patients with confirmed scrub typhus who exhibited a clear 4-fold increase in the level of IgG and/or IgM. The PCR assay result was positive in 45 of 52 patients, indicating a sensitivity of 86.5% (95% confidence interval [CI]: 74.2 to 94.4). The PCR assessment was negative for all 136 non-scrub typhus patients, indicating a specificity of 100% (95% CI: 97.3 to 100). In addition, this test helped diagnose patients with inconclusive immunofluorescence assay (IFA) results and using single blood samples. In conclusion, the real-time PCR assay proposed here is sensitive and specific in diagnosing scrub typhus. Combining PCR and serologic tests will improve the diagnosis of scrub typhus among patients presenting with acute febrile illness. Copyright © 2017 American Society for Microbiology.

  18. Market analysis of food products for detection of allergenic walnut (Juglans regia) and pecan (Carya illinoinensis) by real-time PCR.

    Science.gov (United States)

    López-Calleja, Inés María; de la Cruz, Silvia; González, Isabel; García, Teresa; Martín, Rosario

    2015-06-15

    Two real-time polymerase chain reaction (PCR)-based assays for detection of walnut (Juglans regia) and pecan (Carya illinoinensis) traces in a wide range of processed foods are described here. The method consists on a real-time PCR assay targeting the ITS1 region, using a nuclease (TaqMan) probe labeled with FAM and BBQ. The method was positive for walnut and pecan respectively, and negative for all other heterologous plants and animals tested. Using a series of model samples with defined raw walnut in wheat flour and heat-treated walnut in wheat flour with a range of concentrations of 0.1-100,000 mg kg(-1), a practical detection limit of 0.1 mg kg(-1) of walnut content was estimated. Identical binary mixtures were done for pecan, reaching the same limit of detection of 0.1 mg kg(-1). The assay was successfully trialed on a total of 232 commercial foodstuffs. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Simultaneous detection of Acidovorax avenae subsp. citrulli and Didymella bryoniae in cucurbit seedlots using magnetic capture hybridization and real-time polymerase chain reaction.

    Science.gov (United States)

    Ha, Y; Fessehaie, A; Ling, K S; Wechter, W P; Keinath, A P; Walcott, R R

    2009-06-01

    To improve the simultaneous detection of two pathogens in cucurbit seed, a combination of magnetic capture hybridization (MCH) and multiplex real-time polymerase chain reaction (PCR) was developed. Single-stranded DNA hybridization capture probes targeting DNA of Acidovorax avenae subsp. citrulli, causal agent of bacterial fruit blotch, and Didymella bryoniae, causal agent of gummy stem blight, were covalently attached to magnetic particles and used to selectively concentrate template DNA from cucurbit seed samples. Sequestered template DNAs were subsequently amplified by multiplex real-time PCR using pathogen-specific TaqMan PCR assays. The MCH multiplex real-time PCR assay displayed a detection threshold of A. avenae subsp. citrulli at 10 CFU/ml and D. bryoniae at 10(5) conidia/ml in mixtures of pure cultures of the two pathogens, which was 10-fold more sensitive than the direct real-time PCR assays for the two pathogens separately. Although the direct real-time PCR assay displayed a detection threshold for A. avenae subsp. citrulli DNA of 100 fg/microl in 25% (1/4 samples) of the samples assayed, MCH real-time PCR demonstrated 100% detection frequency (4/4 samples) at the same DNA concentration. MCH did not improve detection sensitivity for D. bryoniae relative to direct real-time PCR using conidial suspensions or seed washes from D. bryoniae-infested cucurbit seed. However, MCH real-time PCR facilitated detection of both target pathogens in watermelon and melon seed samples (n = 5,000 seeds/sample) in which 0.02% of the seed were infested with A. avenae subsp. citrulli and 0.02% were infested with D. bryoniae.

  20. 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.

  1. 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 .

  2. Development of real-time PCR assay for genetic identification of the mottled skate, Beringraja pulchra.

    Science.gov (United States)

    Hwang, In Kwan; Lee, Hae Young; Kim, Min-Hee; Jo, Hyun-Su; Choi, Dong-Ho; Kang, Pil-Won; Lee, Yang-Han; Cho, Nam-Soo; Park, Ki-Won; Chae, Ho Zoon

    2015-10-01

    The mottled skate, Beringraja pulchra is one of the commercially important fishes in the market today. However, B. pulchra identification methods have not been well developed. The current study reports a novel real-time PCR method based on TaqMan technology developed for the genetic identification of B. pulchra. The mitochondrial cytochrome oxidase subunit 1 (COI) nucleotide sequences of 29 B. pulchra, 157 skates and rays reported in GenBank DNA database were comparatively analyzed and the COI sequences specific to B. pulchra was identified. Based on this information, a system of specific primers and Minor Groove Binding (MGB) TaqMan probe were designed. The assay successfully discriminated in 29 specimens of B. pulchra and 27 commercial samples with unknown species identity. For B. pulchra DNA, an average Threshold Cycle (Ct) value of 19.1±0.1 was obtained. Among 27 commercial samples, two samples showed average Ct values 19.1±0.0 and 26.7±0.1, respectively and were confirmed to be B. pulchra based on sequencing. The other samples tested showed undetectable or extremely weak signals for the target fragment, which was also consistent with the sequencing results. These results reveal that the method developed is a rapid and efficient tool to identify B. pulchra and might prevent fraud or mislabeling during the distribution of B. pulchra products. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  3. Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

    Science.gov (United States)

    Chase, D.M.; Elliott, D.G.; Pascho, R.J.

    2006-01-01

    Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

  4. Development of a highly sensitive real-time nested RT-PCR assay in a single closed tube for detection of enterovirus 71 in hand, foot, and mouth disease.

    Science.gov (United States)

    Niu, Peihua; Qi, Shunxiang; Yu, Benzhang; Zhang, Chen; Wang, Ji; Li, Qi; Ma, Xuejun

    2016-11-01

    Enterovirus 71 (EV71) is one of the major causative agents of outbreaks of hand, foot, and mouth disease (HFMD). A commercial TaqMan probe-based real-time PCR assay has been widely used for the differential detection of EV71 despite its relatively high cost and failure to detect samples with a low viral load (Ct value > 35). In this study, a highly sensitive real-time nested RT-PCR (RTN RT-PCR) assay in a single closed tube for detection of EV71 in HFMD was developed. The sensitivity and specificity of this assay were evaluated using a reference EV71 stock and a panel of controls consisting of coxsackievirus A16 (CVA16) and common respiratory viruses, respectively. The clinical performance of this assay was evaluated and compared with those of a commercial TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional two-step nested RT-PCR assay. The limit of detection for the RTN RT-PCR assay was 0.01 TCID50/ml, with a Ct value of 38.3, which was the same as that of the traditional two-step nested RT-PCR assay and approximately tenfold lower than that of the qRT-PCR assay. When testing the reference strain EV71, this assay showed favorable detection reproducibility and no obvious cross-reactivity. The testing results of 100 clinical throat swabs from HFMD-suspected patients revealed that 41 samples were positive for EV71 by both RTN RT-PCR and traditional two-step nested RT-PCR assays, whereas only 29 were EV71 positive by qRT-PCR assay.

  5. TaqMan Real-Time Polymerase Chain Reaction and ...

    African Journals Online (AJOL)

    ISSN: 1596-5996 (print); 1596-9827 (electronic) ... Alcohol in humans is oxidized to acetaldehyde, which in turn is oxidized to .... cool to room temperature (15 - 25 oC) for at least. 5 min, and .... logical candidate gene for alcohol dependence. A.

  6. Improving clinical laboratory efficiency: a time-motion evaluation of the Abbott m2000 RealTime and Roche COBAS AmpliPrep/COBAS TaqMan PCR systems for the simultaneous quantitation of HIV-1 RNA and HCV RNA.

    Science.gov (United States)

    Amendola, Alessandra; Coen, Sabrina; Belladonna, Stefano; Pulvirenti, F Renato; Clemens, John M; Capobianchi, M Rosaria

    2011-08-01

    Diagnostic laboratories need automation that facilitates efficient processing and workflow management to meet today's challenges for expanding services and reducing cost, yet maintaining the highest levels of quality. Processing efficiency of two commercially available automated systems for quantifying HIV-1 and HCV RNA, Abbott m2000 system and Roche COBAS Ampliprep/COBAS TaqMan 96 (docked) systems (CAP/CTM), was evaluated in a mid/high throughput workflow laboratory using a representative daily workload of 24 HCV and 72 HIV samples. Three test scenarios were evaluated: A) one run with four batches on the CAP/CTM system, B) two runs on the Abbott m2000 and C) one run using the Abbott m2000 maxCycle feature (maxCycle) for co-processing these assays. Cycle times for processing, throughput and hands-on time were evaluated. Overall processing cycle time was 10.3, 9.1 and 7.6 h for Scenarios A), B) and C), respectively. Total hands-on time for each scenario was, in order, 100.0 (A), 90.3 (B) and 61.4 min (C). The interface of an automated analyzer to the laboratory workflow, notably system set up for samples and reagents and clean up functions, are as important as the automation capability of the analyzer for the overall impact to processing efficiency and operator hands-on time.

  7. 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.

  8. 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).

  9. Development of a taqman-based real-time PCR assay for the rapid and specific detection of novel duck- origin goose parvovirus.

    Science.gov (United States)

    Wang, Jianchang; Wang, Jinfeng; Cui, Yuan; Nan, Huizhu; Yuan, Wanzhe

    2017-08-01

    A real-time PCR assay was developed for specific detection of novel duck-origin goose parvovirus (N-GPV), the etiological agent of duck beak atrophy and dwarfism syndrome (BADS). The detection limit of the assay was 10 2 copies. The assay was useful in the prevention and control of BADS. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Efficiency of semi-automated fluorescent multiplex PCRs with 11 microsatellite markers for genetic studies of deer populations.

    Science.gov (United States)

    Bonnet, A; Thévenon, S; Maudet, F; Maillard, J C

    2002-10-01

    Thirty bovine and eight ovine microsatellite primer pairs were tested on four tropical deer species: Eld's and Swamp deer (highly threatened) and Rusa and Vietnamese Sika deer (economically important). Thirty markers gave an amplified product in all four species (78.9%). The number of polymorphic microsatellite markers varied among the species from 14 in Eld's deer (47%) to 20 in Swamp deer (67%). Among them, 11 microsatellite loci were multiplexed in three polymerase chain reactions (PCRs) and labelled with three different fluorochromes that can be loaded in one gel-lane. To test the efficiency of the multiplex, primary genetic studies (mean number of alleles, expected heterozygosities and Fis values) were carried out on four deer populations. Parentage exclusion probability and probability of identity were computed and discussed on a Swamp deer population. These multiplexes PCRs were also tested on several other deer species and subspecies. The aim of this study is to establish a tool useful for genetic studies of population structure and diversity in four tropical deer species which with few modifications can be applied to other species of the genus Cervus.

  11. 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...

  12. Application of quantitative real-time PCR compared to filtration methods for the enumeration of Escherichia coli in surface waters within Vietnam.

    Science.gov (United States)

    Vital, Pierangeli G; Van Ha, Nguyen Thi; Tuyet, Le Thi Hong; Widmer, Kenneth W

    2017-02-01

    Surface water samples in Vietnam were collected from the Saigon River, rural and suburban canals, and urban runoff canals in Ho Chi Minh City, Vietnam, and were processed to enumerate Escherichia coli. Quantification was done through membrane filtration and quantitative real-time polymerase chain reaction (PCR). Mean log colony-forming unit (CFU)/100 ml E. coli counts in the dry season for river/suburban canals and urban canals were log 2.8 and 3.7, respectively, using a membrane filtration method, while using Taqman quantitative real-time PCR they were log 2.4 and 2.8 for river/suburban canals and urban canals, respectively. For the wet season, data determined by the membrane filtration method in river/suburban canals and urban canals samples had mean counts of log 3.7 and 4.1, respectively. While mean log CFU/100 ml counts in the wet season using quantitative PCR were log 3 and 2, respectively. Additionally, the urban canal samples were significantly lower than those determined by conventional culture methods for the wet season. These results show that while quantitative real-time PCR can be used to determine levels of fecal indicator bacteria in surface waters, there are some limitations to its application and it may be impacted by sources of runoff based on surveyed samples.

  13. One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples

    Science.gov (United States)

    Mijatovic-Rustempasic, Slavica; Esona, Mathew D.; Tam, Ka Ian; Quaye, Osbourne; Bowen, Michael D.

    2016-01-01

    Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8–100% sensitivity, 99.7–100% specificity, 85–95% efficiency and a limit of detection of 4–60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81–92% efficiency and limit of detection of 150–600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8

  14. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S; Jaing, C

    2012-03-27

    The goal of this project is to develop forensic genotyping assays for select agent viruses, addressing a significant capability gap for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the Taqman signature development for South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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)

  20. 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....

  1. 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.)

  2. Development and validation of a real-time PCR for Chlamydia suis diagnosis in swine and humans.

    Directory of Open Access Journals (Sweden)

    Kristien De Puysseleyr

    Full Text Available Pigs are the natural host for Chlamydia suis, a pathogen which is phylogenetically highly related to the human pathogen C. trachomatis. Chlamydia suis infections are generally treated with tetracyclines. In 1998, tetracyline resistant C. suis strains emerged on U.S. pig farms and they are currently present in the Belgian, Cypriote, German, Israeli, Italian and Swiss pig industry. Infections with tetracycline resistant C. suis strains are mainly associated with severe reproductive failure leading to marked economical loss. We developed a sensitive and specific TaqMan probe-based C. suis real-time PCR for examining clinical samples of both pigs and humans. The analytical sensitivity of the real-time PCR is 10 rDNA copies/reaction without cross-amplifying DNA of other Chlamydia species. The PCR was successfully validated using conjunctival, pharyngeal and stool samples of slaughterhouse employees, as well as porcine samples from two farms with evidence of reproductive failure and one farm without clinical disease. Chlamydia suis was only detected in diseased pigs and in the eyes of humans. Positive humans had no clinical complaints. PCR results were confirmed by culture in McCoy cells. In addition, Chlamydia suis isolates were also examined by the tet(C PCR, designed for demonstrating the tetracycline resistance gene tet(C. The tet(C gene was only present in porcine C. suis isolates.

  3. Detection of Mycobacterium tuberculosis Complex in Paraffin-Embedded Tissues by the New Automated Abbott RealTime MTB Assay.

    Science.gov (United States)

    Fu, Yung-Chieh; Liao, I-Chuang; Chen, Hung-Mo; Yan, Jing-Jou

    2016-07-01

    The Abbott RealTime MTB assay, launched in June 2014, has been shown to have a competitive performance in the detection of the Mycobacterium tuberculosis (MTB) complex in respiratory specimens. The present study was conducted to investigate the usefulness of the Abbott MTB Realtime assay in the detection of MTB in formalin-fixed paraffin-embedded (FFPE) tissues. A total of 96 FFPE specimens obtained from microbiologically proven MTB cases (N=60) and nontuberculous Mycobacterium cases (N=36) were analyzed. The performance of the Abbott MTB Realtime assay was compared with that of the Roche Cobas TaqMan MTB assay. The overall sensitivity and specificity of the Abbott assay were 63.3% and 97.2%, respectively, compared with 11.7% and 100% for the Cobas assay. The detection rate of the Abbott assay was much higher among 37 acid-fast-positive specimens than among 23 acid-fast-negative specimens (89.3% versus 21.7%, respectively). The detection rate of the assay was higher among 29 resection specimens than among 31 small biopsy specimens (86.2% versus 41.9%, respectively). Our results suggest that the Abbott RealTime MTB assay can be used to differentiate MTB from nontuberculous mycobacterial infections in acid-fast-positive FFPE tissues. © 2016 by the Association of Clinical Scientists, Inc.

  4. Process algebra with timing : real time and discrete time

    NARCIS (Netherlands)

    Baeten, J.C.M.; Middelburg, C.A.; Bergstra, J.A.; Ponse, A.J.; Smolka, S.A.

    2001-01-01

    We present real time and discrete time versions of ACP with absolute timing and relative timing. The starting-point is a new real time version with absolute timing, called ACPsat, featuring urgent actions and a delay operator. The discrete time versions are conservative extensions of the discrete

  5. Process algebra with timing: Real time and discrete time

    NARCIS (Netherlands)

    Baeten, J.C.M.; Middelburg, C.A.

    1999-01-01

    We present real time and discrete time versions of ACP with absolute timing and relative timing. The startingpoint is a new real time version with absolute timing, called ACPsat , featuring urgent actions and a delay operator. The discrete time versions are conservative extensions of the discrete

  6. An OPTIMIZE study retrospective analysis for management of telaprevir-treated hepatitis C virus (HCV)-infected patients by use of the Abbott RealTime HCV RNA assay.

    Science.gov (United States)

    Sarrazin, Christoph; Dierynck, Inge; Cloherty, Gavin; Ghys, Anne; Janssen, Katrien; Luo, Donghan; Witek, James; Buti, Maria; Picchio, Gaston; De Meyer, Sandra

    2015-04-01

    Protease inhibitor (PI)-based response-guided triple therapies for hepatitis C virus (HCV) infection are still widely used. Noncirrhotic treatment-naive and prior relapser patients receiving telaprevir-based treatment are eligible for shorter, 24-week total therapy if HCV RNA is undetectable at both weeks 4 and 12. In this study, the concordance in HCV RNA assessments between the Roche High Pure System/Cobas TaqMan and Abbott RealTime HCV RNA assays and the impacts of different HCV RNA cutoffs on treatment outcome were evaluated. A total of 2,629 samples from 663 HCV genotype 1 patients receiving telaprevir/pegylated interferon/ribavirin in OPTIMIZE were analyzed using the High Pure System and reanalyzed using Abbott RealTime (limits of detection, 15.1 IU/ml versus 8.3 IU/ml; limits of quantification, 25 IU/ml versus 12 IU/ml, respectively). Overall, good concordance was observed between the assays. Using undetectable HCV RNA at week 4, 34% of the patients would be eligible for shorter treatment duration with Abbott RealTime versus 72% with the High Pure System. However, using Abbott RealTime, a similar proportion (74%) would be eligible. Of the patients receiving 24-week total therapy, 87% achieved a sustained virologic response with undetectable HCV RNA by the High Pure System or Abbott RealTime; however, 92% of the patients with undetectable HCV RNA by Abbott RealTime achieved a sustained virologic response. Using undetectable HCV RNA as the cutoff, the more sensitive Abbott RealTime assay would identify fewer patients eligible for shorter treatment than the High Pure System. Our data confirm the Abbott RealTime assay, to determine eligibility for shortened PI-based HCV treatment. (The study was registered with ClinicalTrials.gov under registration no. NCT01241760.). Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  7. Real-time radiography

    International Nuclear Information System (INIS)

    Bossi, R.H.; Oien, C.T.

    1981-01-01

    Real-time radiography is used for imaging both dynamic events and static objects. Fluorescent screens play an important role in converting radiation to light, which is then observed directly or intensified and detected. The radiographic parameters for real-time radiography are similar to conventional film radiography with special emphasis on statistics and magnification. Direct-viewing fluoroscopy uses the human eye as a detector of fluorescent screen light or the light from an intensifier. Remote-viewing systems replace the human observer with a television camera. The remote-viewing systems have many advantages over the direct-viewing conditions such as safety, image enhancement, and the capability to produce permanent records. This report reviews real-time imaging system parameters and components

  8. Real-time vision systems

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, R.; Hernandez, J.E.; Lu, Shin-yee [Lawrence Livermore National Lab., CA (United States)

    1994-11-15

    Many industrial and defence applications require an ability to make instantaneous decisions based on sensor input of a time varying process. Such systems are referred to as `real-time systems` because they process and act on data as it occurs in time. When a vision sensor is used in a real-time system, the processing demands can be quite substantial, with typical data rates of 10-20 million samples per second. A real-time Machine Vision Laboratory (MVL) was established in FY94 to extend our years of experience in developing computer vision algorithms to include the development and implementation of real-time vision systems. The laboratory is equipped with a variety of hardware components, including Datacube image acquisition and processing boards, a Sun workstation, and several different types of CCD cameras, including monochrome and color area cameras and analog and digital line-scan cameras. The equipment is reconfigurable for prototyping different applications. This facility has been used to support several programs at LLNL, including O Division`s Peacemaker and Deadeye Projects as well as the CRADA with the U.S. Textile Industry, CAFE (Computer Aided Fabric Inspection). To date, we have successfully demonstrated several real-time applications: bullet tracking, stereo tracking and ranging, and web inspection. This work has been documented in the ongoing development of a real-time software library.

  9. A real-time, quantitative PCR protocol for assessing the relative parasitemia of Leucocytozoon in waterfowl

    Science.gov (United States)

    Smith, Matthew M.; Schmutz, Joel A.; Apelgren, Chloe; Ramey, Andy M.

    2015-01-01

    Microscopic examination of blood smears can be effective at diagnosing and quantifying hematozoa infections. However, this method requires highly trained observers, is time consuming, and may be inaccurate for detection of infections at low levels of parasitemia. To develop a molecular methodology for identifying and quantifying Leucocytozoon parasite infection in wild waterfowl (Anseriformes), we designed a real-time, quantitative PCR protocol to amplify Leucocytozoon mitochondrial DNA using TaqMan fluorogenic probes and validated our methodology using blood samples collected from waterfowl in interior Alaska during late summer and autumn (n = 105). By comparing our qPCR results to those derived from a widely used nested PCR protocol, we determined that our assay showed high levels of sensitivity (91%) and specificity (100%) in detecting Leucocytozoon DNA from host blood samples. Additionally, results of a linear regression revealed significant correlation between the raw measure of parasitemia produced by our qPCR assay (Ct values) and numbers of parasites observed on blood smears (R2 = 0.694, P = 0.003), indicating that our assay can reliably determine the relative parasitemia levels among samples. This methodology provides a powerful new tool for studies assessing effects of haemosporidian infection in wild avian species.

  10. 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.

  11. Memory controllers for real-time embedded systems predictable and composable real-time systems

    CERN Document Server

    Akesson, Benny

    2012-01-01

      Verification of real-time requirements in systems-on-chip becomes more complex as more applications are integrated. Predictable and composable systems can manage the increasing complexity using formal verification and simulation.  This book explains the concepts of predictability and composability and shows how to apply them to the design and analysis of a memory controller, which is a key component in any real-time system. This book is generally intended for readers interested in Systems-on-Chips with real-time applications.   It is especially well-suited for readers looking to use SDRAM memories in systems with hard or firm real-time requirements. There is a strong focus on real-time concepts, such as predictability and composability, as well as a brief discussion about memory controller architectures for high-performance computing. Readers will learn step-by-step how to go from an unpredictable SDRAM memory, offering highly variable bandwidth and latency, to a predictable and composable shared memory...

  12. 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

  13. Quantification of ochratoxin A-producing molds in food products by SYBR Green and TaqMan real-time PCR methods

    DEFF Research Database (Denmark)

    Rodríguez, Alicia; Rodríguez, Mar; Luque, M. Isabel

    2011-01-01

    , usually reported in food products, were used as references. All strains were tested for OTA production by mycellar electrokinetic capillary electrophoresis (MECE) and high-pressure liquid chromatography-mass spectrometry (HPLC-MS). The ability of the optimized qPCR protocols to quantify OTA......Ochratoxin A (OTA) is a mycotoxin synthesized by a variety of different fungi, most of them from the genera Penicillium and Aspergillus. Early detection and quantification of OTA producing species is crucial to improve food safety. In the present work, two protocols of real-time qPCR based on SYBR......-producing molds was evaluated in different artificially inoculated foods. A good linear correlation was obtained over the range 1 x 104 to 10 conidia/g per reaction for all qPCR assays in the different food matrices (cooked and cured products and fruits). The detection limit in all inoculated foods ranged between...

  14. Detection, quantitation and identification of enteroviruses from surface waters and sponge tissue from the Florida Keys using real-time RT-PCR

    Science.gov (United States)

    Donaldson, K.A.; Griffin, Dale W.; Paul, J.H.

    2002-01-01

    A method was developed for the quantitative detection of pathogenic human enteroviruses from surface waters in the Florida Keys using Taqman (R) one-step Reverse transcription (RT)-PCR with the Model 7700 ABI Prism (R) Sequence Detection System. Viruses were directly extracted from unconcentrated grab samples of seawater, from seawater concentrated by vortex flow filtration using a 100kD filter and from sponge tissue. Total RNA was extracted from the samples, purified and concentrated using spin-column chromatography. A 192-196 base pair portion of the 5??? untranscribed region was amplified from these extracts. Enterovirus concentrations were estimated using real-time RT-PCR technology. Nine of 15 sample sites or 60% were positive for the presence of pathogenic human enteroviruses. Considering only near-shore sites, 69% were positive with viral concentrations ranging from 9.3viruses/ml to 83viruses/g of sponge tissue (uncorrected for extraction efficiency). Certain amplicons were selected for cloning and sequencing for identification. Three strains of waterborne enteroviruses were identified as Coxsackievirus A9, Coxsackievirus A16, and Poliovirus Sabin type 1. Time and cost efficiency of this one-step real-time RT-PCR methodology makes this an ideal technique to detect, quantitate and identify pathogenic enteroviruses in recreational waters. Copyright ?? 2002 Elsevier Science Ltd.

  15. Performance of the new automated Abbott RealTime MTB assay for rapid detection of Mycobacterium tuberculosis complex in respiratory specimens.

    Science.gov (United States)

    Chen, J H K; She, K K K; Kwong, T-C; Wong, O-Y; Siu, G K H; Leung, C-C; Chang, K-C; Tam, C-M; Ho, P-L; Cheng, V C C; Yuen, K-Y; Yam, W-C

    2015-09-01

    The automated high-throughput Abbott RealTime MTB real-time PCR assay has been recently launched for Mycobacterium tuberculosis complex (MTBC) clinical diagnosis. This study would like to evaluate its performance. We first compared its diagnostic performance with the Roche Cobas TaqMan MTB assay on 214 clinical respiratory specimens. Prospective analysis of a total 520 specimens was then performed to further evaluate the Abbott assay. The Abbott assay showed a lower limit of detection at 22.5 AFB/ml, which was more sensitive than the Cobas assay (167.5 AFB/ml). The two assays demonstrated a significant difference in diagnostic performance (McNemar's test; P = 0.0034), in which the Abbott assay presented significantly higher area under curve (AUC) than the Cobas assay (1.000 vs 0.880; P = 0.0002). The Abbott assay demonstrated extremely low PCR inhibition on clinical respiratory specimens. The automated Abbott assay required only very short manual handling time (0.5 h), which could help to improve the laboratory management. In the prospective analysis, the overall estimates for sensitivity and specificity of the Abbott assay were both 100 % among smear-positive specimens, whereas the smear-negative specimens were 96.7 and 96.1 %, respectively. No cross-reactivity with non-tuberculosis mycobacterial species was observed. The superiority in sensitivity of the Abbott assay for detecting MTBC in smear-negative specimens could further minimize the risk in MTBC false-negative detection. The new Abbott RealTime MTB assay has good diagnostic performance which can be a useful diagnostic tool for rapid MTBC detection in clinical laboratories.

  16. Essays in real-time forecasting

    OpenAIRE

    Liebermann, Joelle

    2012-01-01

    This thesis contains three essays in the field of real-time econometrics, and more particularlyforecasting.The issue of using data as available in real-time to forecasters, policymakers or financialmarkets is an important one which has only recently been taken on board in the empiricalliterature. Data available and used in real-time are preliminary and differ from ex-postrevised data, and given that data revisions may be quite substantial, the use of latestavailable instead of real-time can s...

  17. Standardization and application of real-time polymerase chain reaction for rapid detection of bluetongue virus

    Directory of Open Access Journals (Sweden)

    I. Karthika Lakshmi

    2018-04-01

    Full Text Available Aim: The present study was designed to standardize real-time polymerase chain reaction (PCR for detecting the bluetongue virus from blood samples of sheep collected during outbreaks of bluetongue disease in the year 2014 in Andhra Pradesh and Telangana states of India. Materials and Methods: A 10-fold serial dilution of Plasmid PUC59 with bluetongue virus (BTV NS3 insert was used to plot the standard curve. BHK-21 and KC cells were used for in vitro propagation of virus BTV-9 at a TCID50/ml of 105 ml and RNA was isolated by the Trizol method. Both reverse transcription -PCR and real-time PCR using TaqMan probe were carried out with RNA extracted from virus-spiked culture medium and blood to compare the sensitivity by means of finding out the limit of detection (LoD. The results were verified by inoculating the detected and undetected dilutions onto cell cultures with further cytological (cytopathic effect and molecular confirmation (by BTV-NS1 group-specific PCR. The standardized technique was then applied to field samples (blood for detecting BTV. Results: The slope of the standard curve obtained was -3.23, and the efficiency was 103%. The LoD with RT-PCR was 8.269Ex103 number of copies of plasmid, whereas it was 13 with real-time PCR for plasmid dilutions. Similarly, LoD was determined for virus-spiked culture medium, and blood with both the types of PCR and the values were 103 TCID 50/ml and 104 TCID 50/ml with RT-PCR and 10° TCID 50/ml and 102 TCID 50/ml with real-time PCR, respectively. The standardized technique was applied to blood samples collected from BTV suspected animals; 10 among 20 samples were found positive with Cq values ranging from 27 to 39. The Cq value exhibiting samples were further processed in cell cultures and were confirmed to be BT positive. Likewise, Cq undetected samples on processing in cell cultures turned out to be BTV negative. Conclusion: Real-time PCR was found to be a very sensitive as well as reliable method

  18. A quantitative PCR (TaqMan assay for pathogenic Leptospira spp

    Directory of Open Access Journals (Sweden)

    Symonds Meegan L

    2002-07-01

    Full Text Available Abstract Background Leptospirosis is an emerging infectious disease. The differential diagnosis of leptospirosis is difficult due to the varied and often "flu like" symptoms which may result in a missed or delayed diagnosis. There are over 230 known serovars in the genus Leptospira. Confirmatory serological diagnosis of leptospirosis is usually made using the microscopic agglutination test (MAT which relies on the use of live cultures as the source of antigen, often performed using a panel of antigens representative of local serovars. Other techniques, such as the enzyme linked immunosorbent assay (ELISA and slide agglutination test (SAT, can detect different classes of antibody but may be subject to false positive reactions and require confirmation of these results by the MAT. Methods The polymerase chain reaction (PCR has been used to detect a large number of microorganisms, including those of clinical significance. The sensitivity of PCR often precludes the need for isolation and culture, thus making it ideal for the rapid detection of organisms involved in acute infections. We employed real-time (quantitative PCR using TaqMan chemistry to detect leptospires in clinical and environmental samples. Results and Conclusions The PCR assay can be applied to either blood or urine samples and does not rely on the isolation and culture of the organism. Capability exists for automation and high throughput testing in a clinical laboratory. It is specific for Leptospira and may discriminate pathogenic and non-pathogenic species. The limit of detection is as low as two cells.

  19. 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.

  20. Ovation Prime Real-Time

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Ovation Prime Real-Time (OPRT) product is a real-time forecast and nowcast model of auroral power and is an operational implementation of the work by Newell et...

  1. Diagnostic accuracy of two multiplex real-time polymerase chain reaction assays for the diagnosis of meningitis in children in a resource-limited setting.

    Directory of Open Access Journals (Sweden)

    Jermaine Khumalo

    Full Text Available Accurate etiological diagnosis of meningitis is important, but difficult in resource-limited settings due to prior administration of antibiotics and lack of viral diagnostics. We aimed to develop and validate 2 real-time multiplex PCR (RT-PCR assays for the detection of common causes of community-acquired bacterial and viral meningitis in South African children.We developed 2 multiplex RT- PCRs for detection of S. pneumoniae, N. meningitidis, H. influenzae, enteroviruses, mumps virus and herpes simplex virus. We tested residual CSF samples from children presenting to a local paediatric hospital over a one-year period, whose CSF showed an abnormal cell count. Results were compared with routine diagnostic tests and the final discharge diagnosis. We calculated accuracy of the bacterial RT-PCR assay compared to CSF culture and using World Health Organisation definitions of laboratory-confirmed bacterial meningitis.From 292 samples, bacterial DNA was detected in 12 (4.1% and viral nucleic acids in 94 (32%. Compared to CSF culture, the sensitivity and specificity of the bacterial RT-PCR was 100% and 97.2% with complete agreement in organism identification. None of the cases positive by viral RT-PCR had a bacterial cause confirmed on CSF culture. Only 9/90 (10% of patients diagnosed clinically as bacterial meningitis or partially treated bacterial meningitis tested positive with the bacterial RT-PCR.In this population the use of 2 multiplex RT-PCRs targeting 6 common pathogens gave promising results. If introduced into routine diagnostic testing, these multiplex RT-PCR assays would supplement other diagnostic tests, and have the potential to limit unnecessary antibiotic therapy and hospitalisation.

  2. A novel photoinduced electron transfer (PET) primer technique for rapid real-time PCR detection of Cryptosporidium spp

    Energy Technology Data Exchange (ETDEWEB)

    Jothikumar, N., E-mail: jin2@cdc.gov; Hill, Vincent R.

    2013-06-28

    Highlights: •Uses a single-labeled fluorescent primer for real-time PCR. •The detection sensitivity of PET PCR was comparable to TaqMan PCR. •Melt curve analysis can be performed to confirm target amplicon production. •Conventional PCR primers can be converted to PET PCR primers. -- Abstract: We report the development of a fluorescently labeled oligonucleotide primer that can be used to monitor real-time PCR. The primer has two parts, the 3′-end of the primer is complimentary to the target and a universal 17-mer stem loop at the 5′-end forms a hairpin structure. A fluorescent dye is attached to 5′-end of either the forward or reverse primer. The presence of guanosine residues at the first and second position of the 3′ dangling end effectively quenches the fluorescence due to the photo electron transfer (PET) mechanism. During the synthesis of nucleic acid, the hairpin structure is linearized and the fluorescence of the incorporated primer increases several-fold due to release of the fluorescently labeled tail and the absence of guanosine quenching. As amplicons are synthesized during nucleic acid amplification, the fluorescence increase in the reaction mixture can be measured with commercially available real-time PCR instruments. In addition, a melting procedure can be performed to denature the double-stranded amplicons, thereby generating fluorescence peaks that can differentiate primer dimers and other non-specific amplicons if formed during the reaction. We demonstrated the application of PET-PCR for the rapid detection and quantification of Cryptosporidium parvum DNA. Comparison with a previously published TaqMan® assay demonstrated that the two real-time PCR assays exhibited similar sensitivity for a dynamic range of detection of 6000–0.6 oocysts per reaction. PET PCR primers are simple to design and less-expensive than dual-labeled probe PCR methods, and should be of interest for use by laboratories operating in resource

  3. A novel photoinduced electron transfer (PET) primer technique for rapid real-time PCR detection of Cryptosporidium spp

    International Nuclear Information System (INIS)

    Jothikumar, N.; Hill, Vincent R.

    2013-01-01

    Highlights: •Uses a single-labeled fluorescent primer for real-time PCR. •The detection sensitivity of PET PCR was comparable to TaqMan PCR. •Melt curve analysis can be performed to confirm target amplicon production. •Conventional PCR primers can be converted to PET PCR primers. -- Abstract: We report the development of a fluorescently labeled oligonucleotide primer that can be used to monitor real-time PCR. The primer has two parts, the 3′-end of the primer is complimentary to the target and a universal 17-mer stem loop at the 5′-end forms a hairpin structure. A fluorescent dye is attached to 5′-end of either the forward or reverse primer. The presence of guanosine residues at the first and second position of the 3′ dangling end effectively quenches the fluorescence due to the photo electron transfer (PET) mechanism. During the synthesis of nucleic acid, the hairpin structure is linearized and the fluorescence of the incorporated primer increases several-fold due to release of the fluorescently labeled tail and the absence of guanosine quenching. As amplicons are synthesized during nucleic acid amplification, the fluorescence increase in the reaction mixture can be measured with commercially available real-time PCR instruments. In addition, a melting procedure can be performed to denature the double-stranded amplicons, thereby generating fluorescence peaks that can differentiate primer dimers and other non-specific amplicons if formed during the reaction. We demonstrated the application of PET-PCR for the rapid detection and quantification of Cryptosporidium parvum DNA. Comparison with a previously published TaqMan® assay demonstrated that the two real-time PCR assays exhibited similar sensitivity for a dynamic range of detection of 6000–0.6 oocysts per reaction. PET PCR primers are simple to design and less-expensive than dual-labeled probe PCR methods, and should be of interest for use by laboratories operating in resource

  4. VERSE - Virtual Equivalent Real-time Simulation

    Science.gov (United States)

    Zheng, Yang; Martin, Bryan J.; Villaume, Nathaniel

    2005-01-01

    Distributed real-time simulations provide important timing validation and hardware in the- loop results for the spacecraft flight software development cycle. Occasionally, the need for higher fidelity modeling and more comprehensive debugging capabilities - combined with a limited amount of computational resources - calls for a non real-time simulation environment that mimics the real-time environment. By creating a non real-time environment that accommodates simulations and flight software designed for a multi-CPU real-time system, we can save development time, cut mission costs, and reduce the likelihood of errors. This paper presents such a solution: Virtual Equivalent Real-time Simulation Environment (VERSE). VERSE turns the real-time operating system RTAI (Real-time Application Interface) into an event driven simulator that runs in virtual real time. Designed to keep the original RTAI architecture as intact as possible, and therefore inheriting RTAI's many capabilities, VERSE was implemented with remarkably little change to the RTAI source code. This small footprint together with use of the same API allows users to easily run the same application in both real-time and virtual time environments. VERSE has been used to build a workstation testbed for NASA's Space Interferometry Mission (SIM PlanetQuest) instrument flight software. With its flexible simulation controls and inexpensive setup and replication costs, VERSE will become an invaluable tool in future mission development.

  5. Synthesis of O-serogroup specific positive controls and real-time PCR standards for nine clinically relevant non-O157 STECs.

    Science.gov (United States)

    Conrad, Cheyenne C; Gilroyed, Brandon H; McAllister, Tim A; Reuter, Tim

    2012-10-01

    Non-O157 Shiga toxin producing Escherichia coli (STEC) are gaining recognition as human pathogens, but no standardized method exists to identify them. Sequence analysis revealed that STEC can be classified on the base of variable O antigen regions into different O serotypes. Polymerase chain reaction is a powerful technique for thorough screening and complex diagnosis for these pathogens, but requires a positive control to verify qualitative and/or quantitative DNA-fragment amplification. Due to the pathogenic nature of STEC, controls are not readily available and cell culturing of STEC reference strains requires biosafety conditions of level 2 or higher. In order to bypass this limitation, controls of stacked O-type specific DNA-fragments coding for primer recognition sites were designed to screen for nine STEC serotypes frequently associated with human infection. The synthetic controls were amplified by PCR, cloned into a plasmid vector and transferred into bacteria host cells. Plasmids amplified by bacterial expression were purified, serially diluted and tested as standards for real-time PCR using SYBR Green and TaqMan assays. Utility of synthetic DNA controls was demonstrated in conventional and real-time PCR assays and validated with DNA from natural STEC strains. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. ISTTOK real-time architecture

    Energy Technology Data Exchange (ETDEWEB)

    Carvalho, Ivo S., E-mail: ivoc@ipfn.ist.utl.pt; Duarte, Paulo; Fernandes, Horácio; Valcárcel, Daniel F.; Carvalho, Pedro J.; Silva, Carlos; Duarte, André S.; Neto, André; Sousa, Jorge; Batista, António J.N.; Hekkert, Tiago; Carvalho, Bernardo B.

    2014-03-15

    Highlights: • All real-time diagnostics and actuators were integrated in the same control platform. • A 100 μs control cycle was achieved under the MARTe framework. • Time-windows based control with several event-driven control strategies implemented. • AC discharges with exception handling on iron core flux saturation. • An HTML discharge configuration was developed for configuring the MARTe system. - Abstract: The ISTTOK tokamak was upgraded with a plasma control system based on the Advanced Telecommunications Computing Architecture (ATCA) standard. This control system was designed to improve the discharge stability and to extend the operational space to the alternate plasma current (AC) discharges as part of the ISTTOK scientific program. In order to accomplish these objectives all ISTTOK diagnostics and actuators relevant for real-time operation were integrated in the control system. The control system was programmed in C++ over the Multi-threaded Application Real-Time executor (MARTe) which provides, among other features, a real-time scheduler, an interrupt handler, an intercommunications interface between code blocks and a clearly bounded interface with the external devices. As a complement to the MARTe framework, the BaseLib2 library provides the foundations for the data, code introspection and also a Hypertext Transfer Protocol (HTTP) server service. Taking advantage of the modular nature of MARTe, the algorithms of each diagnostic data processing, discharge timing, context switch, control and actuators output reference generation, run on well-defined blocks of code named Generic Application Module (GAM). This approach allows reusability of the code, simplified simulation, replacement or editing without changing the remaining GAMs. The ISTTOK control system GAMs run sequentially each 100 μs cycle on an Intel{sup ®} Q8200 4-core processor running at 2.33 GHz located in the ATCA crate. Two boards (inside the ATCA crate) with 32 analog

  7. ISTTOK real-time architecture

    International Nuclear Information System (INIS)

    Carvalho, Ivo S.; Duarte, Paulo; Fernandes, Horácio; Valcárcel, Daniel F.; Carvalho, Pedro J.; Silva, Carlos; Duarte, André S.; Neto, André; Sousa, Jorge; Batista, António J.N.; Hekkert, Tiago; Carvalho, Bernardo B.

    2014-01-01

    Highlights: • All real-time diagnostics and actuators were integrated in the same control platform. • A 100 μs control cycle was achieved under the MARTe framework. • Time-windows based control with several event-driven control strategies implemented. • AC discharges with exception handling on iron core flux saturation. • An HTML discharge configuration was developed for configuring the MARTe system. - Abstract: The ISTTOK tokamak was upgraded with a plasma control system based on the Advanced Telecommunications Computing Architecture (ATCA) standard. This control system was designed to improve the discharge stability and to extend the operational space to the alternate plasma current (AC) discharges as part of the ISTTOK scientific program. In order to accomplish these objectives all ISTTOK diagnostics and actuators relevant for real-time operation were integrated in the control system. The control system was programmed in C++ over the Multi-threaded Application Real-Time executor (MARTe) which provides, among other features, a real-time scheduler, an interrupt handler, an intercommunications interface between code blocks and a clearly bounded interface with the external devices. As a complement to the MARTe framework, the BaseLib2 library provides the foundations for the data, code introspection and also a Hypertext Transfer Protocol (HTTP) server service. Taking advantage of the modular nature of MARTe, the algorithms of each diagnostic data processing, discharge timing, context switch, control and actuators output reference generation, run on well-defined blocks of code named Generic Application Module (GAM). This approach allows reusability of the code, simplified simulation, replacement or editing without changing the remaining GAMs. The ISTTOK control system GAMs run sequentially each 100 μs cycle on an Intel ® Q8200 4-core processor running at 2.33 GHz located in the ATCA crate. Two boards (inside the ATCA crate) with 32 analog

  8. Real-time polymerase chain reaction-based approach for quantification of the pat gene in the T25 Zea mays event.

    Science.gov (United States)

    Weighardt, Florian; Barbati, Cristina; Paoletti, Claudia; Querci, Maddalena; Kay, Simon; De Beuckeleer, Marc; Van den Eede, Guy

    2004-01-01

    In Europe, a growing interest for reliable techniques for the quantification of genetically modified component(s) of food matrixes is arising from the need to comply with the European legislative framework on novel food products. Real-time polymerase chain reaction (PCR) is currently the most powerful technique for the quantification of specific nucleic acid sequences. Several real-time PCR methodologies based on different molecular principles have been developed for this purpose. The most frequently used approach in the field of genetically modified organism (GMO) quantification in food or feed samples is based on the 5'-3'-exonuclease activity of Taq DNA polymerase on specific degradation probes (TaqMan principle). A novel approach was developed for the establishment of a TaqMan quantification system assessing GMO contents around the 1% threshold stipulated under European Union (EU) legislation for the labeling of food products. The Zea mays T25 elite event was chosen as a model for the development of the novel GMO quantification approach. The most innovative aspect of the system is represented by the use of sequences cloned in plasmids as reference standards. In the field of GMO quantification, plasmids are an easy to use, cheap, and reliable alternative to Certified Reference Materials (CRMs), which are only available for a few of the GMOs authorized in Europe, have a relatively high production cost, and require further processing to be suitable for analysis. Strengths and weaknesses of the use of novel plasmid-based standards are addressed in detail. In addition, the quantification system was designed to avoid the use of a reference gene (e.g., a single copy, species-specific gene) as normalizer, i.e., to perform a GMO quantification based on an absolute instead of a relative measurement. In fact, experimental evidences show that the use of reference genes adds variability to the measurement system because a second independent real-time PCR-based measurement

  9. Ring trial 2016 for Bluetongue virus detection by real-time RT-PCR in France.

    Science.gov (United States)

    Sailleau, Corinne; Viarouge, Cyril; Breard, Emmanuel; Vitour, Damien; Zientara, Stephan

    2017-05-01

    Since the unexpected emergence of BTV-8 in Northern Europe and the incursion of BTV-8 and 1 in France in 2006-2007, molecular diagnosis has considerably evolved. Several real-time RT-PCR (rtRT-PCR) methods have been developed and published, and are currently being used in many countries across Europe for BTV detection and typing. In France, the national reference laboratory (NRL) for orbiviruses develops and validates 'ready-to-use' kits with private companies for viral RNA detection. The regional laboratories network that was set up to deal with a heavy demand for analyses has used these available kits. From 2007, ring tests were organized to monitor the performance of the French laboratories. This study presents the results of 63 regional laboratories in the ring trial organized in 2016. Blood samples were sent to the laboratories. Participants were asked to use the rtRT-PCR methods in place in their laboratory, for detection of all BTV serotypes and specifically BTV-8. The French regional laboratories are able to detect and genotype BTV in affected animals. Despite the use of several methods (i.e. RNA extraction and different commercial rtRT-PCRs), the network is homogeneous. The ring trial demonstrated that the French regional veterinary laboratories have reliable and robust BTV diagnostic tools for BTV genome detection.

  10. 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.

  11. 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.

  12. Detection of exogenous gene doping of IGF-I by a real-time quantitative PCR assay.

    Science.gov (United States)

    Zhang, Jin-Ju; Xu, Jing-Feng; Shen, Yong-Wei; Ma, Shi-Jiao; Zhang, Ting-Ting; Meng, Qing-Lin; Lan, Wen-Jun; Zhang, Chun; Liu, Xiao-Mei

    2017-07-01

    Gene doping can be easily concealed since its product is similar to endogenous protein, making its effective detection very challenging. In this study, we selected insulin-like growth factor I (IGF-I) exogenous gene for gene doping detection. First, the synthetic IGF-I gene was subcloned to recombinant adeno-associated virus (rAAV) plasmid to produce recombinant rAAV2/IGF-I-GFP vectors. Second, in an animal model, rAAV2/IGF-I-GFP vectors were injected into the thigh muscle tissue of mice, and then muscle and blood specimens were sampled at different time points for total DNA isolation. Finally, real-time quantitative PCR was employed to detect the exogenous gene doping of IGF-I. In view of the characteristics of endogenous IGF-I gene sequences, a TaqMan probe was designed at the junction of exons 2 and 3 of IGF-I gene to distinguish it from the exogenous IGF-I gene. In addition, an internal reference control plasmid and its probe were used in PCR to rule out false-positive results through comparison of their threshold cycle (Ct) values. Thus, an accurate exogenous IGF-I gene detection approach was developed in this study. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

  13. Real-time PCR detection of Paenibacillus spp. in raw milk to predict shelf life performance of pasteurized fluid milk products.

    Science.gov (United States)

    Ranieri, Matthew L; Ivy, Reid A; Mitchell, W Robert; Call, Emma; Masiello, Stephanie N; Wiedmann, Martin; Boor, Kathryn J

    2012-08-01

    Psychrotolerant sporeformers, specifically Paenibacillus spp., are important spoilage bacteria for pasteurized, refrigerated foods such as fluid milk. While Paenibacillus spp. have been isolated from farm environments, raw milk, processing plant environments, and pasteurized fluid milk, no information on the number of Paenibacillus spp. that need to be present in raw milk to cause pasteurized milk spoilage was available. A real-time PCR assay targeting the 16S rRNA gene was designed to detect Paenibacillus spp. in fluid milk and to discriminate between Paenibacillus and other closely related spore-forming bacteria. Specificity was confirmed using 16 Paenibacillus and 17 Bacillus isolates. All 16 Paenibacillus isolates were detected with a mean cycle threshold (C(T)) of 19.14 ± 0.54. While 14/17 Bacillus isolates showed no signal (C(T) > 40), 3 Bacillus isolates showed very weak positive signals (C(T) = 38.66 ± 0.65). The assay provided a detection limit of approximately 3.25 × 10(1) CFU/ml using total genomic DNA extracted from raw milk samples inoculated with Paenibacillus. Application of the TaqMan PCR to colony lysates obtained from heat-treated and enriched raw milk provided fast and accurate detection of Paenibacillus. Heat-treated milk samples where Paenibacillus (≥1 CFU/ml) was detected by this colony TaqMan PCR showed high bacterial counts (>4.30 log CFU/ml) after refrigerated storage (6°C) for 21 days. We thus developed a tool for rapid detection of Paenibacillus that has the potential to identify raw milk with microbial spoilage potential as a pasteurized product.

  14. Diagnosis of bacteremia in pediatric oncologic patients by in-house real-time PCR.

    Science.gov (United States)

    Quiles, Milene Gonçalves; Menezes, Liana Carballo; Bauab, Karen de Castro; Gumpl, Elke Kreuscher; Rocchetti, Talita Trevizani; Palomo, Flavia Silva; Carlesse, Fabianne; Pignatari, Antonio Carlos Campos

    2015-07-23

    Infections are the major cause of morbidity and mortality in children with cancer. Gaining a favorable prognosis for these patients depends on selecting the appropriate therapy, which in turn depends on rapid and accurate microbiological diagnosis. This study employed real-time PCR (qPCR) to identify the main pathogens causing bloodstream infection (BSI) in patients treated at the Pediatric Oncology Institute IOP-GRAACC-UNIFESP-Brazil. Antimicrobial resistance genes were also investigated using this methodology. A total of 248 samples from BACTEC® blood culture bottles and 99 whole-blood samples collected in tubes containing EDTA K2 Gel were isolated from 137 patients. All samples were screened by specific Gram probes for multiplex qPCR. Seventeen sequences were evaluated using gender-specific TaqMan probes and the resistance genes bla SHV, bla TEM, bla CTX, bla KPC, bla IMP, bla SPM, bla VIM, vanA, vanB and mecA were detected using the SYBR Green method. Positive qPCR results were obtained in 112 of the blood culture bottles (112/124), and 90 % agreement was observed between phenotypic and molecular microbial detection methods. For bacterial and fungal identification, the performance test showed: sensitivity 87 %; specificity 91 %; NPV 90 %; PPV 89 % and accuracy of 89 % when compared with the phenotypic method. The mecA gene was detected in 37 samples, extended-spectrum β-lactamases were detected in six samples and metallo-β-lactamase coding genes in four samples, with 60 % concordance between the two methods. The qPCR on whole blood detected eight samples possessing the mecA gene and one sample harboring the vanB gene. The bla KPC, bla VIM, bla IMP and bla SHV genes were not detected in this study. Real-time PCR is a useful tool in the early identification of pathogens and antimicrobial resistance genes from bloodstream infections of pediatric oncologic patients.

  15. Improved Method for the Detection and Quantification of Naegleria fowleri in Water and Sediment Using Immunomagnetic Separation and Real-Time PCR

    Directory of Open Access Journals (Sweden)

    Bonnie J. Mull

    2013-01-01

    Full Text Available Primary amebic meningoencephalitis (PAM is a rare and typically fatal infection caused by the thermophilic free-living ameba, Naegleria fowleri. In 2010, the first confirmed case of PAM acquired in Minnesota highlighted the need for improved detection and quantification methods in order to study the changing ecology of N. fowleri and to evaluate potential risk factors for increased exposure. An immunomagnetic separation (IMS procedure and real-time PCR TaqMan assay were developed to recover and quantify N. fowleri in water and sediment samples. When one liter of lake water was seeded with N. fowleri strain CDC:V212, the method had an average recovery of 46% and detection limit of 14 amebas per liter of water. The method was then applied to sediment and water samples with unknown N. fowleri concentrations, resulting in positive direct detections by real-time PCR in 3 out of 16 samples and confirmation of N. fowleri culture in 6 of 16 samples. This study has resulted in a new method for detection and quantification of N. fowleri in water and sediment that should be a useful tool to facilitate studies of the physical, chemical, and biological factors associated with the presence and dynamics of N. fowleri in environmental systems.

  16. A real-time architecture for time-aware agents.

    Science.gov (United States)

    Prouskas, Konstantinos-Vassileios; Pitt, Jeremy V

    2004-06-01

    This paper describes the specification and implementation of a new three-layer time-aware agent architecture. This architecture is designed for applications and environments where societies of humans and agents play equally active roles, but interact and operate in completely different time frames. The architecture consists of three layers: the April real-time run-time (ART) layer, the time aware layer (TAL), and the application agents layer (AAL). The ART layer forms the underlying real-time agent platform. An original online, real-time, dynamic priority-based scheduling algorithm is described for scheduling the computation time of agent processes, and it is shown that the algorithm's O(n) complexity and scalable performance are sufficient for application in real-time domains. The TAL layer forms an abstraction layer through which human and agent interactions are temporally unified, that is, handled in a common way irrespective of their temporal representation and scale. A novel O(n2) interaction scheduling algorithm is described for predicting and guaranteeing interactions' initiation and completion times. The time-aware predicting component of a workflow management system is also presented as an instance of the AAL layer. The described time-aware architecture addresses two key challenges in enabling agents to be effectively configured and applied in environments where humans and agents play equally active roles. It provides flexibility and adaptability in its real-time mechanisms while placing them under direct agent control, and it temporally unifies human and agent interactions.

  17. 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.

  18. Towards Real-Time Argumentation

    Directory of Open Access Journals (Sweden)

    Vicente JULIÁN

    2016-07-01

    Full Text Available In this paper, we deal with the problem of real-time coordination with the more general approach of reaching real-time agreements in MAS. Concretely, this work proposes a real-time argumentation framework in an attempt to provide agents with the ability of engaging in argumentative dialogues and come with a solution for their underlying agreement process within a bounded period of time. The framework has been implemented and evaluated in the domain of a customer support application. Concretely, we consider a society of agents that act on behalf of a group of technicians that must solve problems in a Technology Management Centre (TMC within a bounded time. This centre controls every process implicated in the provision of technological and customer support services to private or public organisations by means of a call centre. The contract signed between the TCM and the customer establishes penalties if the specified time is exceeded.

  19. PCR em tempo real para diagnóstico da leucose enzoótica bovina Enzootic bovine leukosis real time PCR

    Directory of Open Access Journals (Sweden)

    Natanael Lamas Dias

    2012-08-01

    Full Text Available O objetivo deste trabalho foi realizar a validação de uma reação em cadeia da polimerase em tempo real com o sistema Plexor® (qPCR para o diagnóstico da Leucose Enzoótica Bovina (LEB, por meio da comparação com testes de diagnóstico recomendados pela Organização Mundial de Saúde Animal (OIE. A qPCR foi comparada com duas outras técnicas: a PCR nested (nPCR e a imunodifusão em gel de ágar (IDGA. Das 82 amostras analisadas pela qPCR e nPCR, 79 apresentaram resultados concordantes, sendo a concordância, classificada pelo Índice Kappa, como alta. Entre as PCRs e a IDGA, o número de resultados concordantes foi de 71 e 69, respectivamente, para qPCR e nPCR, sendo a concordância classificada como considerável. A qPCR apresentou altos valores de sensibilidade e especificidade. Os valores preditivos da qPCR observados demonstraram a alta capacidade de classificação dos casos positivos e negativos. A qPCR não foi capaz de detectar três amostras positivas e tem custo ligeiramente superior que a nPCR. Entretanto, a qPCR é uma técnica mais rápida, menos susceptível a contaminações, tem alta sensibilidade, não utiliza e não gera resíduos carcinogênicos. Concluímos que a qPCR pode substituir a nPCR recomendada pela OIE no diagnóstico de rotina em áreas em que a LEB é endêmica, como no Brasil.The goal of this research was to validate a Plexor® real time Polymerase Chain Reaction (qPCR for Enzootic Bovine Leukosis (EBL diagnosis by comparison with methods recommend by the World Animal Health Organization (OIE. The qPCR was compared with two other techniques: the nested PCR (nPCR and to the agar gel immunodiffusion (AGID. Of 82 qPCR and nPCR analysed samples, 79 presented concordant results, being the concordance classified by Kappa Index as high. Between the PCRs and AGID, the number of concordant results was 71 and 69, out of 82, to qPCR and nPCR, respectively, being the concordance classified as considerable, in both

  20. Simultaneous detection of three pome fruit tree viruses by one-step multiplex quantitative RT-PCR.

    Science.gov (United States)

    Malandraki, Ioanna; Beris, Despoina; Isaioglou, Ioannis; Olmos, Antonio; Varveri, Christina; Vassilakos, Nikon

    2017-01-01

    A one-step multiplex real-time reverse transcription polymerase chain reaction (RT-qPCR) based on TaqMan probes was developed for the simultaneous detection of Apple mosaic virus (ApMV), Apple stem pitting virus (ASPV) and Apple stem grooving virus (ASGV) in total RNA of pome trees extracted with a CTAB method. The sensitivity of the method was established using in vitro synthesized viral transcripts serially diluted in RNA from healthy, virus-tested (negative) pome trees. The three viruses were simultaneously detected up to a 10-4 dilution of total RNA from a naturally triple-infected apple tree prepared in total RNA of healthy apple tissue. The newly developed RT-qPCR assay was at least one hundred times more sensitive than conventional single RT-PCRs. The assay was validated with 36 field samples for which nine triple and 11 double infections were detected. All viruses were detected simultaneously in composite samples at least up to the ratio of 1:150 triple-infected to healthy pear tissue, suggesting the assay has the capacity to examine rapidly a large number of samples in pome tree certification programs and surveys for virus presence.

  1. Real-time PCR in virology.

    Science.gov (United States)

    Mackay, Ian M; Arden, Katherine E; Nitsche, Andreas

    2002-03-15

    The use of the polymerase chain reaction (PCR) in molecular diagnostics has increased to the point where it is now accepted as the gold standard for detecting nucleic acids from a number of origins and it has become an essential tool in the research laboratory. Real-time PCR has engendered wider acceptance of the PCR due to its improved rapidity, sensitivity, reproducibility and the reduced risk of carry-over contamination. There are currently five main chemistries used for the detection of PCR product during real-time PCR. These are the DNA binding fluorophores, the 5' endonuclease, adjacent linear and hairpin oligoprobes and the self-fluorescing amplicons, which are described in detail. We also discuss factors that have restricted the development of multiplex real-time PCR as well as the role of real-time PCR in quantitating nucleic acids. Both amplification hardware and the fluorogenic detection chemistries have evolved rapidly as the understanding of real-time PCR has developed and this review aims to update the scientist on the current state of the art. We describe the background, advantages and limitations of real-time PCR and we review the literature as it applies to virus detection in the routine and research laboratory in order to focus on one of the many areas in which the application of real-time PCR has provided significant methodological benefits and improved patient outcomes. However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease.

  2. Real time programming environment for Windows

    Energy Technology Data Exchange (ETDEWEB)

    LaBelle, D.R. [LaBelle (Dennis R.), Clifton Park, NY (United States)

    1998-04-01

    This document provides a description of the Real Time Programming Environment (RTProE). RTProE tools allow a programmer to create soft real time projects under general, multi-purpose operating systems. The basic features necessary for real time applications are provided by RTProE, leaving the programmer free to concentrate efforts on his specific project. The current version supports Microsoft Windows{trademark} 95 and NT. The tasks of real time synchronization and communication with other programs are handled by RTProE. RTProE includes a generic method for connecting a graphical user interface (GUI) to allow real time control and interaction with the programmer`s product. Topics covered in this paper include real time performance issues, portability, details of shared memory management, code scheduling, application control, Operating System specific concerns and the use of Computer Aided Software Engineering (CASE) tools. The development of RTProE is an important step in the expansion of the real time programming community. The financial costs associated with using the system are minimal. All source code for RTProE has been made publicly available. Any person with access to a personal computer, Windows 95 or NT, and C or FORTRAN compilers can quickly enter the world of real time modeling and simulation.

  3. An In-Home Digital Network Architecture for Real-Time and Non-Real-Time Communication

    NARCIS (Netherlands)

    Scholten, Johan; Jansen, P.G.; Hanssen, F.T.Y.; Hattink, Tjalling

    2002-01-01

    This paper describes an in-home digital network architecture that supports both real-time and non-real-time communication. The architecture deploys a distributed token mechanism to schedule communication streams and to offer guaranteed quality-ofservice. Essentially, the token mechanism prevents

  4. MARTe: A Multiplatform Real-Time Framework

    Science.gov (United States)

    Neto, André C.; Sartori, Filippo; Piccolo, Fabio; Vitelli, Riccardo; De Tommasi, Gianmaria; Zabeo, Luca; Barbalace, Antonio; Fernandes, Horacio; Valcarcel, Daniel F.; Batista, Antonio J. N.

    2010-04-01

    Development of real-time applications is usually associated with nonportable code targeted at specific real-time operating systems. The boundary between hardware drivers, system services, and user code is commonly not well defined, making the development in the target host significantly difficult. The Multithreaded Application Real-Time executor (MARTe) is a framework built over a multiplatform library that allows the execution of the same code in different operating systems. The framework provides the high-level interfaces with hardware, external configuration programs, and user interfaces, assuring at the same time hard real-time performances. End-users of the framework are required to define and implement algorithms inside a well-defined block of software, named Generic Application Module (GAM), that is executed by the real-time scheduler. Each GAM is reconfigurable with a set of predefined configuration meta-parameters and interchanges information using a set of data pipes that are provided as inputs and required as output. Using these connections, different GAMs can be chained either in series or parallel. GAMs can be developed and debugged in a non-real-time system and, only once the robustness of the code and correctness of the algorithm are verified, deployed to the real-time system. The software also supplies a large set of utilities that greatly ease the interaction and debugging of a running system. Among the most useful are a highly efficient real-time logger, HTTP introspection of real-time objects, and HTTP remote configuration. MARTe is currently being used to successfully drive the plasma vertical stabilization controller on the largest magnetic confinement fusion device in the world, with a control loop cycle of 50 ?s and a jitter under 1 ?s. In this particular project, MARTe is used with the Real-Time Application Interface (RTAI)/Linux operating system exploiting the new ?86 multicore processors technology.

  5. Real-Time and Real-Fast Performance of General-Purpose and Real-Time Operating Systems in Multithreaded Physical Simulation of Complex Mechanical Systems

    Directory of Open Access Journals (Sweden)

    Carlos Garre

    2014-01-01

    Full Text Available Physical simulation is a valuable tool in many fields of engineering for the tasks of design, prototyping, and testing. General-purpose operating systems (GPOS are designed for real-fast tasks, such as offline simulation of complex physical models that should finish as soon as possible. Interfacing hardware at a given rate (as in a hardware-in-the-loop test requires instead maximizing time determinism, for which real-time operating systems (RTOS are designed. In this paper, real-fast and real-time performance of RTOS and GPOS are compared when simulating models of high complexity with large time steps. This type of applications is usually present in the automotive industry and requires a good trade-off between real-fast and real-time performance. The performance of an RTOS and a GPOS is compared by running a tire model scalable on the number of degrees-of-freedom and parallel threads. The benchmark shows that the GPOS present better performance in real-fast runs but worse in real-time due to nonexplicit task switches and to the latency associated with interprocess communication (IPC and task switch.

  6. GNSS global real-time augmentation positioning: Real-time precise satellite clock estimation, prototype system construction and performance analysis

    Science.gov (United States)

    Chen, Liang; Zhao, Qile; Hu, Zhigang; Jiang, Xinyuan; Geng, Changjiang; Ge, Maorong; Shi, Chuang

    2018-01-01

    Lots of ambiguities in un-differenced (UD) model lead to lower calculation efficiency, which isn't appropriate for the high-frequency real-time GNSS clock estimation, like 1 Hz. Mixed differenced model fusing UD pseudo-range and epoch-differenced (ED) phase observations has been introduced into real-time clock estimation. In this contribution, we extend the mixed differenced model for realizing multi-GNSS real-time clock high-frequency updating and a rigorous comparison and analysis on same conditions are performed to achieve the best real-time clock estimation performance taking the efficiency, accuracy, consistency and reliability into consideration. Based on the multi-GNSS real-time data streams provided by multi-GNSS Experiment (MGEX) and Wuhan University, GPS + BeiDou + Galileo global real-time augmentation positioning prototype system is designed and constructed, including real-time precise orbit determination, real-time precise clock estimation, real-time Precise Point Positioning (RT-PPP) and real-time Standard Point Positioning (RT-SPP). The statistical analysis of the 6 h-predicted real-time orbits shows that the root mean square (RMS) in radial direction is about 1-5 cm for GPS, Beidou MEO and Galileo satellites and about 10 cm for Beidou GEO and IGSO satellites. Using the mixed differenced estimation model, the prototype system can realize high-efficient real-time satellite absolute clock estimation with no constant clock-bias and can be used for high-frequency augmentation message updating (such as 1 Hz). The real-time augmentation message signal-in-space ranging error (SISRE), a comprehensive accuracy of orbit and clock and effecting the users' actual positioning performance, is introduced to evaluate and analyze the performance of GPS + BeiDou + Galileo global real-time augmentation positioning system. The statistical analysis of real-time augmentation message SISRE is about 4-7 cm for GPS, whlile 10 cm for Beidou IGSO/MEO, Galileo and about 30 cm

  7. Scalable Real-Time Negotiation Toolkit

    National Research Council Canada - National Science Library

    Lesser, Victor

    2004-01-01

    ... to implement an adaptive distributed sensor network. These activities involved the development of a distributed soft, real-time heuristic resource allocation protocol, the development of a domain-independent soft, real time agent architecture...

  8. Model Checking Real-Time Systems

    DEFF Research Database (Denmark)

    Bouyer, Patricia; Fahrenberg, Uli; Larsen, Kim Guldstrand

    2018-01-01

    This chapter surveys timed automata as a formalism for model checking real-time systems. We begin with introducing the model, as an extension of finite-state automata with real-valued variables for measuring time. We then present the main model-checking results in this framework, and give a hint...

  9. Modular specification of real-time systems

    DEFF Research Database (Denmark)

    Inal, Recep

    1994-01-01

    Duration Calculus, a real-time interval logic, has been embedded in the Z specification language to provide a notation for real-time systems that combines the modularisation and abstraction facilities of Z with a logic suitable for reasoning about real-time properties. In this article the notation...

  10. Hard Real-Time Networking on Firewire

    NARCIS (Netherlands)

    Zhang, Yuchen; Orlic, Bojan; Visser, Peter; Broenink, Jan

    2005-01-01

    This paper investigates the possibility of using standard, low-cost, widely used FireWire as a new generation fieldbus medium for real-time distributed control applications. A real-time software subsys- tem, RT-FireWire was designed that can, in combination with Linux-based real-time operating

  11. Multiprocessor scheduling for real-time systems

    CERN Document Server

    Baruah, Sanjoy; Buttazzo, Giorgio

    2015-01-01

    This book provides a comprehensive overview of both theoretical and pragmatic aspects of resource-allocation and scheduling in multiprocessor and multicore hard-real-time systems.  The authors derive new, abstract models of real-time tasks that capture accurately the salient features of real application systems that are to be implemented on multiprocessor platforms, and identify rules for mapping application systems onto the most appropriate models.  New run-time multiprocessor scheduling algorithms are presented, which are demonstrably better than those currently used, both in terms of run-time efficiency and tractability of off-line analysis.  Readers will benefit from a new design and analysis framework for multiprocessor real-time systems, which will translate into a significantly enhanced ability to provide formally verified, safety-critical real-time systems at a significantly lower cost.

  12. Rapid method for controlling the correct labeling of products containing common octopus (Octopus vulgaris) and main substitute species (Eledone cirrhosa and Dosidicus gigas) by fast real-time PCR.

    Science.gov (United States)

    Espiñeira, Montserrat; Vieites, Juan M

    2012-12-15

    The TaqMan real-time PCR has the highest potential for automation, therefore representing the currently most suitable method for screening, allowing the detection of fraudulent or unintentional mislabeling of species. This work describes the development of a real-time polymerase chain reaction (RT-PCR) system for the detection and identification of common octopus (Octopus vulgaris) and main substitute species (Eledone cirrhosa and Dosidicus gigas). This technique is notable for the combination of simplicity, speed, sensitivity and specificity in an homogeneous assay. The method can be applied to all kinds of products; fresh, frozen and processed, including those undergoing intensive processes of transformation. This methodology was validated to check how the degree of food processing affects the method and the detection of each species. Moreover, it was applied to 34 commercial samples to evaluate the labeling of products made from them. The methodology herein developed is useful to check the fulfillment of labeling regulations for seafood products and to verify traceability in commercial trade and for fisheries control. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Prototyping real-time systems

    OpenAIRE

    Clynch, Gary

    1994-01-01

    The traditional software development paradigm, the waterfall life cycle model, is defective when used for developing real-time systems. This thesis puts forward an executable prototyping approach for the development of real-time systems. A prototyping system is proposed which uses ESML (Extended Systems Modelling Language) as a prototype specification language. The prototyping system advocates the translation of non-executable ESML specifications into executable LOOPN (Language of Object ...

  14. Development of a Rickettsia bellii-Specific TaqMan Assay Targeting the Citrate Synthase Gene.

    Science.gov (United States)

    Hecht, Joy A; Allerdice, Michelle E J; Krawczak, Felipe S; Labruna, Marcelo B; Paddock, Christopher D; Karpathy, Sandor E

    2016-11-01

    Rickettsia bellii is a rickettsial species of unknown pathogenicity that infects argasid and ixodid ticks throughout the Americas. Many molecular assays used to detect spotted fever group (SFG) Rickettsia species do not detect R. bellii, so that infection with this bacterium may be concealed in tick populations when assays are used that screen specifically for SFG rickettsiae. We describe the development and validation of a R. bellii-specific, quantitative, real-time PCR TaqMan assay that targets a segment of the citrate synthase (gltA) gene. The specificity of this assay was validated against a panel of DNA samples that included 26 species of Rickettsia, Orientia, Ehrlichia, Anaplasma, and Bartonella, five samples of tick and human DNA, and DNA from 20 isolates of R. bellii, including 11 from North America and nine from South America. A R. bellii control plasmid was constructed, and serial dilutions of the plasmid were used to determine the limit of detection of the assay to be one copy per 4 µl of template DNA. This assay can be used to better determine the role of R. bellii in the epidemiology of tick-borne rickettsioses in the Western Hemisphere. Published by Oxford University Press on behalf of Entomological Society of America 2016. This work is written by US Government employees and is in the public domain in the US.

  15. A novel synthetic quantification standard including virus and internal report targets: application for the detection and quantification of emerging begomoviruses on tomato.

    Science.gov (United States)

    Péréfarres, Frédéric; Hoareau, Murielle; Chiroleu, Frédéric; Reynaud, Bernard; Dintinger, Jacques; Lett, Jean-Michel

    2011-08-05

    Begomovirus is a genus of phytopathogenic single-stranded DNA viruses, transmitted by the whitefly Bemisia tabaci. This genus includes emerging and economically significant viruses such as those associated with Tomato Yellow Leaf Curl Disease, for which diagnostic tools are needed to prevent dispersion and new introductions. Five real-time PCRs with an internal tomato reporter gene were developed for accurate detection and quantification of monopartite begomoviruses, including two strains of the Tomato yellow leaf curl virus (TYLCV; Mld and IL strains), the Tomato leaf curl Comoros virus-like viruses (ToLCKMV-like viruses) and the two molecules of the bipartite Potato yellow mosaic virus. These diagnostic tools have a unique standard quantification, comprising the targeted viral and internal report amplicons. These duplex real-time PCRs were applied to artificially inoculated plants to monitor and compare their viral development. Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 10(9) to 2 × 10(3) copies of genomic viral DNA/μL for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 10(8) to 2 × 10(3) copies of genomic viral DNA/μL for PYMV-A and ToLCKMV-like viruses. These real-time PCRs were applied to artificially inoculated plants and viral loads were compared at 10, 20 and 30 days post-inoculation. Different patterns of viral accumulation were observed between the bipartite and the monopartite begomoviruses. Interestingly, PYMV accumulated more viral DNA at each date for both genomic components compared to all the monopartite viruses. Also, PYMV reached its highest viral load at 10 dpi contrary to the other viruses (20 dpi). The accumulation kinetics of the two strains of emergent TYLCV differed from the ToLCKMV-like viruses in the higher quantities of viral DNA produced in the early phase of the infection and in the shorter time to reach this peak viral load. To detect and quantify a wide range of begomoviruses, five duplex

  16. A novel synthetic quantification standard including virus and internal report targets: application for the detection and quantification of emerging begomoviruses on tomato

    Directory of Open Access Journals (Sweden)

    Lett Jean-Michel

    2011-08-01

    Full Text Available Abstract Background Begomovirus is a genus of phytopathogenic single-stranded DNA viruses, transmitted by the whitefly Bemisia tabaci. This genus includes emerging and economically significant viruses such as those associated with Tomato Yellow Leaf Curl Disease, for which diagnostic tools are needed to prevent dispersion and new introductions. Five real-time PCRs with an internal tomato reporter gene were developed for accurate detection and quantification of monopartite begomoviruses, including two strains of the Tomato yellow leaf curl virus (TYLCV; Mld and IL strains, the Tomato leaf curl Comoros virus-like viruses (ToLCKMV-like viruses and the two molecules of the bipartite Potato yellow mosaic virus. These diagnostic tools have a unique standard quantification, comprising the targeted viral and internal report amplicons. These duplex real-time PCRs were applied to artificially inoculated plants to monitor and compare their viral development. Results Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 109 to 2 × 103 copies of genomic viral DNA/μL for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 108 to 2 × 103 copies of genomic viral DNA/μL for PYMV-A and ToLCKMV-like viruses. These real-time PCRs were applied to artificially inoculated plants and viral loads were compared at 10, 20 and 30 days post-inoculation. Different patterns of viral accumulation were observed between the bipartite and the monopartite begomoviruses. Interestingly, PYMV accumulated more viral DNA at each date for both genomic components compared to all the monopartite viruses. Also, PYMV reached its highest viral load at 10 dpi contrary to the other viruses (20 dpi. The accumulation kinetics of the two strains of emergent TYLCV differed from the ToLCKMV-like viruses in the higher quantities of viral DNA produced in the early phase of the infection and in the shorter time to reach this peak viral load. Conclusions To detect and

  17. Software Design Methods for Real-Time Systems

    Science.gov (United States)

    1989-12-01

    This module describes the concepts and methods used in the software design of real time systems . It outlines the characteristics of real time systems , describes...the role of software design in real time system development, surveys and compares some software design methods for real - time systems , and

  18. 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...

  19. 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...

  20. Distributed, Embedded and Real-time Java Systems

    CERN Document Server

    Wellings, Andy

    2012-01-01

    Research on real-time Java technology has been prolific over the past decade, leading to a large number of corresponding hardware and software solutions, and frameworks for distributed and embedded real-time Java systems.  This book is aimed primarily at researchers in real-time embedded systems, particularly those who wish to understand the current state of the art in using Java in this domain.  Much of the work in real-time distributed, embedded and real-time Java has focused on the Real-time Specification for Java (RTSJ) as the underlying base technology, and consequently many of the Chapters in this book address issues with, or solve problems using, this framework. Describes innovative techniques in: scheduling, memory management, quality of service and communication systems supporting real-time Java applications; Includes coverage of multiprocessor embedded systems and parallel programming; Discusses state-of-the-art resource management for embedded systems, including Java’s real-time garbage collect...

  1. T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory

    Science.gov (United States)

    Monnier, Stéphanie; Cox, David G; Albion, Tim; Canzian, Federico

    2005-01-01

    Background Single Nucleotide Polymorphism (SNP) genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS) need tools to organize the data flow. Results We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. Conclusion We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS. PMID:16221298

  2. Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays.

    Science.gov (United States)

    Harvey, John J; Chester, Stephanie; Burke, Stephen A; Ansbro, Marisela; Aden, Tricia; Gose, Remedios; Sciulli, Rebecca; Bai, Jing; DesJardin, Lucy; Benfer, Jeffrey L; Hall, Joshua; Smole, Sandra; Doan, Kimberly; Popowich, Michael D; St George, Kirsten; Quinlan, Tammy; Halse, Tanya A; Li, Zhen; Pérez-Osorio, Ailyn C; Glover, William A; Russell, Denny; Reisdorf, Erik; Whyte, Thomas; Whitaker, Brett; Hatcher, Cynthia; Srinivasan, Velusamy; Tatti, Kathleen; Tondella, Maria Lucia; Wang, Xin; Winchell, Jonas M; Mayer, Leonard W; Jernigan, Daniel; Mawle, Alison C

    2016-02-01

    In this study, a multicenter evaluation of the Life Technologies TaqMan(®) Array Card (TAC) with 21 custom viral and bacterial respiratory assays was performed on the Applied Biosystems ViiA™ 7 Real-Time PCR System. The goal of the study was to demonstrate the analytical performance of this platform when compared to identical individual pathogen specific laboratory developed tests (LDTs) designed at the Centers for Disease Control and Prevention (CDC), equivalent LDTs provided by state public health laboratories, or to three different commercial multi-respiratory panels. CDC and Association of Public Health Laboratories (APHL) LDTs had similar analytical sensitivities for viral pathogens, while several of the bacterial pathogen APHL LDTs demonstrated sensitivities one log higher than the corresponding CDC LDT. When compared to CDC LDTs, TAC assays were generally one to two logs less sensitive depending on the site performing the analysis. Finally, TAC assays were generally more sensitive than their counterparts in three different commercial multi-respiratory panels. TAC technology allows users to spot customized assays and design TAC layout, simplify assay setup, conserve specimen, dramatically reduce contamination potential, and as demonstrated in this study, analyze multiple samples in parallel with good reproducibility between instruments and operators. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Research of real-time communication software

    Science.gov (United States)

    Li, Maotang; Guo, Jingbo; Liu, Yuzhong; Li, Jiahong

    2003-11-01

    Real-time communication has been playing an increasingly important role in our work, life and ocean monitor. With the rapid progress of computer and communication technique as well as the miniaturization of communication system, it is needed to develop the adaptable and reliable real-time communication software in the ocean monitor system. This paper involves the real-time communication software research based on the point-to-point satellite intercommunication system. The object-oriented design method is adopted, which can transmit and receive video data and audio data as well as engineering data by satellite channel. In the real-time communication software, some software modules are developed, which can realize the point-to-point satellite intercommunication in the ocean monitor system. There are three advantages for the real-time communication software. One is that the real-time communication software increases the reliability of the point-to-point satellite intercommunication system working. Second is that some optional parameters are intercalated, which greatly increases the flexibility of the system working. Third is that some hardware is substituted by the real-time communication software, which not only decrease the expense of the system and promotes the miniaturization of communication system, but also aggrandizes the agility of the system.

  4. Integration of MDSplus in real-time systems

    International Nuclear Information System (INIS)

    Luchetta, A.; Manduchi, G.; Taliercio, C.

    2006-01-01

    RFX-mod makes extensive usage of real-time systems for feedback control and uses MDSplus to interface them to the main Data Acquisition system. For this purpose, the core of MDSplus has been ported to VxWorks, the operating system used for real-time control in RFX. Using this approach, it is possible to integrate real-time systems, but MDSplus is used only for non-real-time tasks, i.e. those tasks which are executed before and after the pulse and whose performance does not affect the system time constraints. More extensive use of MDSplus in real-time systems is foreseen, and a real-time layer for MDSplus is under development, which will provide access to memory-mapped pulse files, shared by the tasks running on the same CPU. Real-time communication will also be integrated in the MDSplus core to provide support for distributed memory-mapped pulse files

  5. Dense time discretization technique for verification of real time systems

    International Nuclear Information System (INIS)

    Makackas, Dalius; Miseviciene, Regina

    2016-01-01

    Verifying the real-time system there are two different models to control the time: discrete and dense time based models. This paper argues a novel verification technique, which calculates discrete time intervals from dense time in order to create all the system states that can be reached from the initial system state. The technique is designed for real-time systems specified by a piece-linear aggregate approach. Key words: real-time system, dense time, verification, model checking, piece-linear aggregate

  6. Storm real-time processing cookbook

    CERN Document Server

    Anderson, Quinton

    2013-01-01

    A Cookbook with plenty of practical recipes for different uses of Storm.If you are a Java developer with basic knowledge of real-time processing and would like to learn Storm to process unbounded streams of data in real time, then this book is for you.

  7. Mixed - mode Operating System for Real - time Performance

    Directory of Open Access Journals (Sweden)

    Hasan M. M.

    2017-11-01

    Full Text Available The purpose of the mixed-mode system research is to handle devices with the accuracy of real-time systems and at the same time, having all the benefits and facilities of a matured Graphic User Interface(GUIoperating system which is typicallynon-real-time. This mixed-mode operating system comprising of a real-time portion and a non-real-time portion was studied and implemented to identify the feasibilities and performances in practical applications (in the context of scheduled the real-time events. In this research an i8751 microcontroller-based hardware was used to measure the performance of the system in real-time-only as well as non-real-time-only configurations. The real-time portion is an 486DX-40 IBM PC system running under DOS-based real-time kernel and the non-real-time portion is a Pentium IIIbased system running under Windows NT. It was found that mixed-mode systems performed as good as a typical real-time system and in fact, gave many additional benefits such as simplified/modular programming and load tolerance.

  8. T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory

    Directory of Open Access Journals (Sweden)

    Albion Tim

    2005-10-01

    Full Text Available Abstract Background Single Nucleotide Polymorphism (SNP genotyping is a major activity in biomedical research. The Taqman technology is one of the most commonly used approaches. It produces large amounts of data that are difficult to process by hand. Laboratories not equipped with a Laboratory Information Management System (LIMS need tools to organize the data flow. Results We propose a package of Visual Basic programs focused on sample management and on the parsing of input and output TaqMan files. The code is written in Visual Basic, embedded in the Microsoft Office package, and it allows anyone to have access to those tools, without any programming skills and with basic computer requirements. Conclusion We have created useful tools focused on management of TaqMan genotyping data, a critical issue in genotyping laboratories whithout a more sophisticated and expensive system, such as a LIMS.

  9. Real-Time Polymerase Chain Reaction Detection of Trichomonas vaginalis from vaginal swabs: Validation of a Diagnostic Method and Preliminary Epidemiological Application

    Directory of Open Access Journals (Sweden)

    Carlo Mengoli

    2009-06-01

    Full Text Available Background Trichomonas vaginalis is the most common nonviral sexually trasmitted diseases (STDs agent. For females, the diagnostic gold standard is the culture of vaginal swab, which is labour-exacting.The direct microscopic examination of vaginal secretions is the most used approach, but its sensitivity depends on the skill of the observer. Objectives We evaluated an original real-time TaqMan-based Polymerase Chain Reaction (PCR technique.The scope of the study was to confirm the effectiveness of the molecular approach in a clinical context and to explore its relevance to an epidemiological investigation. Study Design a ß-tubulin gene was chosen as target sequence.The assay was designed to exploit the quantitative potential of the TaqMan procedure.The population sample was 583 adult females presenting at the Service from January 2005 to December 2005.Three vaginal swabs were collected from each patient, one for wet mount microscopy, one for broth culture, and one for the molecular assay. Results The prevalence was 3.3% (culture, 3.1% (microscopy, 3.8% (PCR.An excess risk was detected in the immigrant population (risk ratio by PCR = 28. Conclusions The molecular approach was the most accurate way to detect the protozoon.The real-time PCR is convenient in a busy laboratory, provided the necessary equipment is available, and it is suitable for epidemiological investigation.

  10. Identification of field caught Anopheles gambiae s.s. and Anopheles arabiensis by TaqMan single nucleotide polymorphism genotyping

    Directory of Open Access Journals (Sweden)

    Bayoh Nabie M

    2007-02-01

    Full Text Available Abstract Background Identification of Anopheles gambiae s.s. and Anopheles arabiensis from field-collected Anopheles gambiae s.l. is often necessary in basic and applied research, and in operational control programmes. The currently accepted method involves use of standard polymerase chain reaction amplification of ribosomal DNA (rDNA from the 3' 28S to 5' intergenic spacer region of the genome, and visual confirmation of amplicons of predicted size on agarose gels, after electrophoresis. This report describes development and evaluation of an automated, quantitative PCR method based upon TaqMan™ single nucleotide polymorphism (SNP genotyping. Methods Standard PCR, and TaqMan SNP genotyping with newly designed primers and fluorophore-labeled probes hybridizing to sequences of complementary rDNA specific for either An. gambiae s.s. or An. arabiensis, were conducted in three experiments involving field-collected An. gambiae s.l. from western Kenya, and defined laboratory strains. DNA extraction was from a single leg, sonicated for five minutes in buffer in wells of 96-well PCR plates. Results TaqMan SNP genotyping showed a reaction success rate, sensitivity, and species specificity comparable to that of standard PCR. In an extensive field study, only 29 of 3,041 (0.95% were determined to be hybrids by TaqMan (i.e., having rDNA sequences from both species, however, all but one were An. arabiensis by standard PCR, suggesting an acceptably low (ca. 1% error rate for TaqMan genotyping in mistakenly identifying species hybrids. Conclusion TaqMan SNP genotyping proved to be a sensitive and rapid method for identification of An. gambiae s.l. and An. arabiensis, with a high success rate, specific results, and congruence with the standard PCR method.

  11. Research in Distributed Real-Time Systems

    Science.gov (United States)

    Mukkamala, R.

    1997-01-01

    This document summarizes the progress we have made on our study of issues concerning the schedulability of real-time systems. Our study has produced several results in the scalability issues of distributed real-time systems. In particular, we have used our techniques to resolve schedulability issues in distributed systems with end-to-end requirements. During the next year (1997-98), we propose to extend the current work to address the modeling and workload characterization issues in distributed real-time systems. In particular, we propose to investigate the effect of different workload models and component models on the design and the subsequent performance of distributed real-time systems.

  12. Real-time data access layer for MDSplus

    International Nuclear Information System (INIS)

    Manduchi, G.; Luchetta, A.; Taliercio, C.; Fredian, T.; Stillerman, J.

    2008-01-01

    Recent extensions to MDSplus allow data handling in long discharges and provide a real-time data access and communication layer. The real-time data access layer is an additional component of MDSplus: it is possible to use the traditional MDSplus API during normal operation, and to select a subset of data items to be used in real time. Real-time notification is provided by a communication layer using a publish-subscribe pattern. The notification covers processes sharing the same data items even running on different machines, thus allowing the implementation of distributed control systems. The real-time data access layer has been developed for Windows, Linux, and VxWorks; it is currently being ported to Linux RTAI. In order to quantify the fingerprint of the presented system, the performance of the real-time access layer approach is compared with that of an ad hoc, manually optimized program in a sample real-time application

  13. A Real-Time Systems Symposium Preprint.

    Science.gov (United States)

    1983-09-01

    Real - Time Systems Symposium Preprint Interim Tech...estimate of the occurence of the error. Unclassii ledSECUqITY CLASSIF’ICA T" NO MI*IA If’ inDI /’rrd erter for~~ble. ’Corrputnqg A REAL - TIME SYSTEMS SYMPOSIUM...ABSTRACT This technical report contains a preprint of a paper accepted for presentation at the REAL - TIME SYSTEMS SYMPOSIUM, Arlington,

  14. Benefits of real-time gas management

    International Nuclear Information System (INIS)

    Nolty, R.; Dolezalek, D. Jr.

    1994-01-01

    In today's competitive gas gathering, processing, storage and transportation business environment, the requirements to do business are continually changing. These changes arise from government regulations such as the amendments to the Clean Air Act concerning the environment and FERC Order 636 concerning business practices. Other changes are due to advances in technology such as electronic flow measurement (EFM) and real-time communications capabilities within the gas industry. Gas gathering, processing, storage and transportation companies must be flexible in adapting to these changes to remain competitive. These dynamic requirements can be met with an open, real-time gas management computer information system. Such a system provides flexible services with a variety of software applications. Allocations, nominations management and gas dispatching are examples of applications that are provided on a real-time basis. By providing real-time services, the gas management system enables operations personnel to make timely adjustments within the current accounting period. Benefits realized from implementing a real-time gas management system include reduced unaccountable gas, reduced imbalance penalties, reduced regulatory violations, improved facility operations and better service to customers. These benefits give a company the competitive edge. This article discusses the applications provided, the benefits from implementing a real-time gas management system, and the definition of such a system

  15. Making real-time reactive systems reliable

    Science.gov (United States)

    Marzullo, Keith; Wood, Mark

    1990-01-01

    A reactive system is characterized by a control program that interacts with an environment (or controlled program). The control program monitors the environment and reacts to significant events by sending commands to the environment. This structure is quite general. Not only are most embedded real time systems reactive systems, but so are monitoring and debugging systems and distributed application management systems. Since reactive systems are usually long running and may control physical equipment, fault tolerance is vital. The research tries to understand the principal issues of fault tolerance in real time reactive systems and to build tools that allow a programmer to design reliable, real time reactive systems. In order to make real time reactive systems reliable, several issues must be addressed: (1) How can a control program be built to tolerate failures of sensors and actuators. To achieve this, a methodology was developed for transforming a control program that references physical value into one that tolerates sensors that can fail and can return inaccurate values; (2) How can the real time reactive system be built to tolerate failures of the control program. Towards this goal, whether the techniques presented can be extended to real time reactive systems is investigated; and (3) How can the environment be specified in a way that is useful for writing a control program. Towards this goal, whether a system with real time constraints can be expressed as an equivalent system without such constraints is also investigated.

  16. Space Weather and Real-Time Monitoring

    Directory of Open Access Journals (Sweden)

    S Watari

    2009-04-01

    Full Text Available Recent advance of information and communications technology enables to collect a large amount of ground-based and space-based observation data in real-time. The real-time data realize nowcast of space weather. This paper reports a history of space weather by the International Space Environment Service (ISES in association with the International Geophysical Year (IGY and importance of real-time monitoring in space weather.

  17. Research Directions in Real-Time Systems.

    Science.gov (United States)

    1996-09-01

    This report summarizes a survey of published research in real time systems . Material is presented that provides an overview of the topic, focusing on...communications protocols and scheduling techniques. It is noted that real - time systems deserve special attention separate from other areas because of...formal tools for design and analysis of real - time systems . The early work on applications as well as notable theoretical advances are summarized

  18. Real-Time MENTAT programming language and architecture

    Science.gov (United States)

    Grimshaw, Andrew S.; Silberman, Ami; Liu, Jane W. S.

    1989-01-01

    Real-time MENTAT, a programming environment designed to simplify the task of programming real-time applications in distributed and parallel environments, is described. It is based on the same data-driven computation model and object-oriented programming paradigm as MENTAT. It provides an easy-to-use mechanism to exploit parallelism, language constructs for the expression and enforcement of timing constraints, and run-time support for scheduling and exciting real-time programs. The real-time MENTAT programming language is an extended C++. The extensions are added to facilitate automatic detection of data flow and generation of data flow graphs, to express the timing constraints of individual granules of computation, and to provide scheduling directives for the runtime system. A high-level view of the real-time MENTAT system architecture and programming language constructs is provided.

  19. 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.

  20. Run-time middleware to support real-time system scenarios

    NARCIS (Netherlands)

    Goossens, K.; Koedam, M.; Sinha, S.; Nelson, A.; Geilen, M.

    2015-01-01

    Systems on Chip (SOC) are powerful multiprocessor systems capable of running multiple independent applications, often with both real-time and non-real-time requirements. Scenarios exist at two levels: first, combinations of independent applications, and second, different states of a single

  1. Advanced real-time manipulation of video streams

    CERN Document Server

    Herling, Jan

    2014-01-01

    Diminished Reality is a new fascinating technology that removes real-world content from live video streams. This sensational live video manipulation actually removes real objects and generates a coherent video stream in real-time. Viewers cannot detect modified content. Existing approaches are restricted to moving objects and static or almost static cameras and do not allow real-time manipulation of video content. Jan Herling presents a new and innovative approach for real-time object removal with arbitrary camera movements.

  2. Archtecture of distributed real-time systems

    OpenAIRE

    Wing Leung, Cheuk

    2013-01-01

    CRAFTERS (Constraint and Application Driven Framework for Tailoring Embedded Real-time System) project aims to address the problem of uncertainty and heterogeneity in a distributed system by providing seamless, portable connectivity and middleware. This thesis contributes to the project by investigating the techniques that can be used in a distributed real-time embedded system. The conclusion is that, there is a list of specifications to be meet in order to provide a transparent and real-time...

  3. The real-time price elasticity of electricity

    NARCIS (Netherlands)

    Lijesen, M.G.

    2007-01-01

    The real-time price elasticity of electricity contains important information on the demand response of consumers to the volatility of peak prices. Despite the importance, empirical estimates of the real-time elasticity are hardly available. This paper provides a quantification of the real-time

  4. Implementing Run-Time Evaluation of Distributed Timing Constraints in a Real-Time Environment

    DEFF Research Database (Denmark)

    Kristensen, C. H.; Drejer, N.

    1994-01-01

    In this paper we describe a solution to the problem of implementing run-time evaluation of timing constraints in distributed real-time environments......In this paper we describe a solution to the problem of implementing run-time evaluation of timing constraints in distributed real-time environments...

  5. Rapid Identification and Quantification of Aureococcus anophagefferens by qPCR Method (Taqman) in the Qinhuangdao Coastal Area: A Region for Recurrent Brown Tide Breakout in China.

    Science.gov (United States)

    Wang, Li-Ping; Lei, Kun

    2016-12-01

    Since 2009, Aureococcus anophagefferens has caused brown tide to occur recurrently in Qinhuangdao coastal area, China. Because the algal cells of A. anophagefferens are so tiny (~3 µm) that it is very hard to identify exactly under a microscope for natural water samples, it is very urgent to develop a method for efficient and continuous monitoring. Here specific primers and Taqman probe are designed to develop a real-time quantitative PCR (qPCR) method for identification and quantification continually. The algal community and cell abundance of A. anophagefferens in the study area (E 119°20'-119°50' and N 39°30'-39°50') from April to October in 2013 are detected by pyrosequencing, and are used to validate the specification and precision of qPCR method for natural samples. Both pyrosequencing and qPCR shows that the targeted cells are present only in May, June and July, and the cell abundance are July > June > May. Although there are various algal species including dinoflagellata, diatom, Cryptomonadales, Chrysophyceae and Chlorophyta living in the natural seawater simultaneously, no disturbance happens to qPCR method. This qPCR method could detect as few as 10 targeted cells, indicating it is able to detect the algal cells at pre-bloom levels. Therefore, qPCR with Taqman probe provides a powerful and sensitive method to monitor the brown tide continually in Qinhuangdao coastal area, China. The results provide a necessary technology support for forecasting the brown tide initiation, in China.

  6. REAL TIME SYSTEM OPERATIONS 2006-2007

    Energy Technology Data Exchange (ETDEWEB)

    Eto, Joseph H.; Parashar, Manu; Lewis, Nancy Jo

    2008-08-15

    The Real Time System Operations (RTSO) 2006-2007 project focused on two parallel technical tasks: (1) Real-Time Applications of Phasors for Monitoring, Alarming and Control; and (2) Real-Time Voltage Security Assessment (RTVSA) Prototype Tool. The overall goal of the phasor applications project was to accelerate adoption and foster greater use of new, more accurate, time-synchronized phasor measurements by conducting research and prototyping applications on California ISO's phasor platform - Real-Time Dynamics Monitoring System (RTDMS) -- that provide previously unavailable information on the dynamic stability of the grid. Feasibility assessment studies were conducted on potential application of this technology for small-signal stability monitoring, validating/improving existing stability nomograms, conducting frequency response analysis, and obtaining real-time sensitivity information on key metrics to assess grid stress. Based on study findings, prototype applications for real-time visualization and alarming, small-signal stability monitoring, measurement based sensitivity analysis and frequency response assessment were developed, factory- and field-tested at the California ISO and at BPA. The goal of the RTVSA project was to provide California ISO with a prototype voltage security assessment tool that runs in real time within California ISO?s new reliability and congestion management system. CERTS conducted a technical assessment of appropriate algorithms, developed a prototype incorporating state-of-art algorithms (such as the continuation power flow, direct method, boundary orbiting method, and hyperplanes) into a framework most suitable for an operations environment. Based on study findings, a functional specification was prepared, which the California ISO has since used to procure a production-quality tool that is now a part of a suite of advanced computational tools that is used by California ISO for reliability and congestion management.

  7. A study of real-time content marketing : formulating real-time content marketing based on content, search and social media

    OpenAIRE

    Nguyen, Thi Kim Duyen

    2015-01-01

    The primary objective of this research is to understand profoundly the new concept of content marketing – real-time content marketing on the aspect of the digital marketing experts. Particularly, the research will focus on the real-time content marketing theories and how to build real-time content marketing strategy based on content, search and social media. It also finds out how marketers measure and keep track of conversion rates of their real-time content marketing plan. Practically, th...

  8. Novel approach for CES1 genotyping

    DEFF Research Database (Denmark)

    Bjerre, Ditte; Berg Rasmussen, Henrik

    2018-01-01

    AIM: Development of a specific procedure for genotyping of CES1A1 (CES1) and CES1A2, a hybrid of CES1A1 and the pseudogene CES1P1. MATERIALS & METHODS: The number of CES1A1 and CES1A2 copies and that of CES1P1 were determined using real-time PCR. Long range PCRs followed by secondary PCRs allowed...

  9. Application of XML in real-time data warehouse

    Science.gov (United States)

    Zhao, Yanhong; Wang, Beizhan; Liu, Lizhao; Ye, Su

    2009-07-01

    At present, XML is one of the most widely-used technologies of data-describing and data-exchanging, and the needs for real-time data make real-time data warehouse a popular area in the research of data warehouse. What effects can we have if we apply XML technology to the research of real-time data warehouse? XML technology solves many technologic problems which are impossible to be addressed in traditional real-time data warehouse, and realize the integration of OLAP (On-line Analytical Processing) and OLTP (Online transaction processing) environment. Then real-time data warehouse can truly be called "real time".

  10. Mixed - mode Operating System for Real - time Performance

    OpenAIRE

    Hasan M. M.; Sultana S.; Foo C.K.

    2017-01-01

    The purpose of the mixed-mode system research is to handle devices with the accuracy of real-time systems and at the same time, having all the benefits and facilities of a matured Graphic User Interface(GUI)operating system which is typicallynon-real-time. This mixed-mode operating system comprising of a real-time portion and a non-real-time portion was studied and implemented to identify the feasibilities and performances in practical applications (in the context of scheduled the real-time e...

  11. Mixed-mode Operating System for Real-time Performance

    Directory of Open Access Journals (Sweden)

    M.M. Hasan

    2017-11-01

    Full Text Available The purpose of the mixed-mode system research is to handle devices with the accuracy of real-time systems and at the same time, having all the benefits and facilities of a matured Graphic User Interface (GUI operating system which is typically nonreal-time. This mixed-mode operating system comprising of a real-time portion and a non-real-time portion was studied and implemented to identify the feasibilities and performances in practical applications (in the context of scheduled the real-time events. In this research an i8751 microcontroller-based hardware was used to measure the performance of the system in real-time-only as well as non-real-time-only configurations. The real-time portion is an 486DX-40 IBM PC system running under DOS-based realtime kernel and the non-real-time portion is a Pentium III based system running under Windows NT. It was found that mixed-mode systems performed as good as a typical realtime system and in fact, gave many additional benefits such as simplified/modular programming and load tolerance.

  12. Testing of real-time-software

    International Nuclear Information System (INIS)

    Friesland, G.; Ovenhausen, H.

    1975-05-01

    The situation in the area of testing real-time-software is unsatisfactory. During the first phase of the project PROMOTE (prozessorientiertes Modul- und Gesamttestsystem) an analysis of the momentary situation took place, results of which are summarized in the following study about some user interviews and an analysis of relevant literature. 22 users (industry, software-houses, hardware-manufacturers, and institutes) have been interviewed. Discussions were held about reliability of real-time software with special interest to error avoidance, testing, and debugging. Main aims of the analysis of the literature were elaboration of standard terms, comparison of existing test methods and -systems, and the definition of boundaries to related areas. During the further steps of this project some means and techniques will be worked out to systematically test real-time software. (orig.) [de

  13. Validation and Assessment of Multi-GNSS Real-Time Precise Point Positioning in Simulated Kinematic Mode Using IGS Real-Time Service

    Directory of Open Access Journals (Sweden)

    Liang Wang

    2018-02-01

    Full Text Available Precise Point Positioning (PPP is a popular technology for precise applications based on the Global Navigation Satellite System (GNSS. Multi-GNSS combined PPP has become a hot topic in recent years with the development of multiple GNSSs. Meanwhile, with the operation of the real-time service (RTS of the International GNSS Service (IGS agency that provides satellite orbit and clock corrections to broadcast ephemeris, it is possible to obtain the real-time precise products of satellite orbits and clocks and to conduct real-time PPP. In this contribution, the real-time multi-GNSS orbit and clock corrections of the CLK93 product are applied for real-time multi-GNSS PPP processing, and its orbit and clock qualities are investigated, first with a seven-day experiment by comparing them with the final multi-GNSS precise product ‘GBM’ from GFZ. Then, an experiment involving real-time PPP processing for three stations in the Multi-GNSS Experiment (MGEX network with a testing period of two weeks is conducted in order to evaluate the convergence performance of real-time PPP in a simulated kinematic mode. The experimental result shows that real-time PPP can achieve a convergence performance of less than 15 min for an accuracy level of 20 cm. Finally, the real-time data streams from 12 globally distributed IGS/MGEX stations for one month are used to assess and validate the positioning accuracy of real-time multi-GNSS PPP. The results show that the simulated kinematic positioning accuracy achieved by real-time PPP on different stations is about 3.0 to 4.0 cm for the horizontal direction and 5.0 to 7.0 cm for the three-dimensional (3D direction.

  14. Development and evaluation of Taqman assays for the differentiation of Dickeya (sub)species

    NARCIS (Netherlands)

    Wolf, van der J.M.; Haas, de B.H.; Hoof, van R.A.; Haan, de E.G.; Bovenkamp, van den G.W.

    2014-01-01

    TaqMan assays were developed for the detection of seven Dickeya species, namely D. dianthicola, D. dadantii, D. paradisiaca, D. chrysanthemi, D. zeae, D. dieffenbachiae and D. solani. Sequences of the gene coding for dnaX were used for the design of primers and probes. In studies with axenic

  15. Quantitation of O6-methylguanine-DNA methyltransferase gene messenger RNA in gliomas by means of real-time RT-PCR and clinical response to nitrosoureas.

    Science.gov (United States)

    Tanaka, Satoshi; Oka, Hidehiro; Fujii, Kiyotaka; Watanabe, Kaoru; Nagao, Kumi; Kakimoto, Atsushi

    2005-09-01

    1. O6-methylguanine-DNA methyltransferase (MGMT) mRNA was measured in 50 malignant gliomas that had received 1-(4-amino-2-methyl-5-pyrimidynyl) methyl-3-(2-chloroethyl)-3-nitrosourea hydrochloride (ACNU) after the resection of the tumor by real-time reverse transcription-polymerase chain reaction (RT-PCR) using TaqMan probe. 2. The mean absolute value of MGMTmRNA normalized to the level of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) for 50 tumors was 1.29 x 10(4)+/- 1.28 x 10(4) copy/microg RNA (mean +/- SD). The amount of MGMTmRNA less than 6 x 10(3) copy/microg RNA was the most significant factor in predicting the initial effect of treatment with ACNU by multi-variant regression analysis (p = 0.0157). 3. These results suggest that quantitation of MGMTmRNA is the excellent method for predicting for the effect of ACNU in glioma therapy.

  16. The FERMI-Elettra distributed real-time framework

    International Nuclear Information System (INIS)

    Pivetta, L.; Gaio, G.; Passuello, R.; Scalamera, G.

    2012-01-01

    FERMI-Elettra is a Free Electron Laser (FEL) based on a 1.5 GeV linac. The pulsed operation of the accelerator and the necessity to characterize and control each electron bunch requires synchronous acquisition of the beam diagnostics together with the ability to drive actuators in real-time at the linac repetition rate. The Adeos/Xenomai real-time extensions have been adopted in order to add real-time capabilities to the Linux based control system computers running the Tango software. A software communication protocol based on Gigabit Ethernet and known as Network Reflective Memory (NRM) has been developed to implement a shared memory across the whole control system, allowing computers to communicate in real-time. The NRM architecture, the real-time performance and the integration in the control system are described. (authors)

  17. Real-time video quality monitoring

    Science.gov (United States)

    Liu, Tao; Narvekar, Niranjan; Wang, Beibei; Ding, Ran; Zou, Dekun; Cash, Glenn; Bhagavathy, Sitaram; Bloom, Jeffrey

    2011-12-01

    The ITU-T Recommendation G.1070 is a standardized opinion model for video telephony applications that uses video bitrate, frame rate, and packet-loss rate to measure the video quality. However, this model was original designed as an offline quality planning tool. It cannot be directly used for quality monitoring since the above three input parameters are not readily available within a network or at the decoder. And there is a great room for the performance improvement of this quality metric. In this article, we present a real-time video quality monitoring solution based on this Recommendation. We first propose a scheme to efficiently estimate the three parameters from video bitstreams, so that it can be used as a real-time video quality monitoring tool. Furthermore, an enhanced algorithm based on the G.1070 model that provides more accurate quality prediction is proposed. Finally, to use this metric in real-world applications, we present an example emerging application of real-time quality measurement to the management of transmitted videos, especially those delivered to mobile devices.

  18. Real-time PCR quantification of human complement C4A and C4B genes

    Directory of Open Access Journals (Sweden)

    Fust George

    2006-01-01

    Full Text Available Abstract Background The fourth component of human complement (C4, an essential factor of the innate immunity, is represented as two isoforms (C4A and C4B in the genome. Although these genes differ only in 5 nucleotides, the encoded C4A and C4B proteins are functionally different. Based on phenotypic determination, unbalanced production of C4A and C4B is associated with several diseases, such as systemic lupus erythematosus, type 1 diabetes, several autoimmune diseases, moreover with higher morbidity and mortality of myocardial infarction and increased susceptibility for bacterial infections. Despite of this major clinical relevance, only low throughput, time and labor intensive methods have been used so far for the quantification of C4A and C4B genes. Results A novel quantitative real-time PCR (qPCR technique was developed for rapid and accurate quantification of the C4A and C4B genes applying a duplex, TaqMan based methodology. The reliable, single-step analysis provides the determination of the copy number of the C4A and C4B genes applying a wide range of DNA template concentration (0.3–300 ng genomic DNA. The developed qPCR was applied to determine C4A and C4B gene dosages in a healthy Hungarian population (N = 118. The obtained data were compared to the results of an earlier study of the same population. Moreover a set of 33 samples were analyzed by two independent methods. No significant difference was observed between the gene dosages determined by the employed techniques demonstrating the reliability of the novel qPCR methodology. A Microsoft Excel worksheet and a DOS executable are also provided for simple and automated evaluation of the measured data. Conclusion This report describes a novel real-time PCR method for single-step quantification of C4A and C4B genes. The developed technique could facilitate studies investigating disease association of different C4 isotypes.

  19. Heterogeneous Embedded Real-Time Systems Environment

    Science.gov (United States)

    2003-12-01

    AFRL-IF-RS-TR-2003-290 Final Technical Report December 2003 HETEROGENEOUS EMBEDDED REAL - TIME SYSTEMS ENVIRONMENT Integrated...HETEROGENEOUS EMBEDDED REAL - TIME SYSTEMS ENVIRONMENT 6. AUTHOR(S) Cosmo Castellano and James Graham 5. FUNDING NUMBERS C - F30602-97-C-0259

  20. Temporal Proof Methodologies for Real-Time Systems,

    Science.gov (United States)

    1990-09-01

    real time systems that communicate either through shared variables or by message passing and real time issues such as time-outs, process priorities (interrupts) and process scheduling. The authors exhibit two styles for the specification of real - time systems . While the first approach uses bounded versions of temporal operators the second approach allows explicit references to time through a special clock variable. Corresponding to two styles of specification the authors present and compare two fundamentally different proof

  1. Real-time communication protocols: an overview

    NARCIS (Netherlands)

    Hanssen, F.T.Y.; Jansen, P.G.

    2003-01-01

    This paper describes several existing data link layer protocols that provide real-time capabilities on wired networks, focusing on token-ring and Carrier Sense Multiple Access based networks. Existing modifications to provide better real-time capabilities and performance are also described. Finally

  2. Self-Organization in Embedded Real-Time Systems

    CERN Document Server

    Brinkschulte, Uwe; Rettberg, Achim

    2013-01-01

    This book describes the emerging field of self-organizing, multicore, distributed and real-time embedded systems.  Self-organization of both hardware and software can be a key technique to handle the growing complexity of modern computing systems. Distributed systems running hundreds of tasks on dozens of processors, each equipped with multiple cores, requires self-organization principles to ensure efficient and reliable operation. This book addresses various, so-called Self-X features such as self-configuration, self-optimization, self-adaptation, self-healing and self-protection. Presents open components for embedded real-time adaptive and self-organizing applications; Describes innovative techniques in: scheduling, memory management, quality of service, communications supporting organic real-time applications; Covers multi-/many-core embedded systems supporting real-time adaptive systems and power-aware, adaptive hardware and software systems; Includes case studies of open embedded real-time self-organizi...

  3. Development of a pan-Simbu real-time reverse transcriptase PCR for the detection of Simbu serogroup viruses and comparison with SBV diagnostic PCR systems.

    Science.gov (United States)

    Fischer, Melina; Schirrmeier, Horst; Wernike, Kerstin; Wegelt, Anne; Beer, Martin; Hoffmann, Bernd

    2013-11-05

    Schmallenberg virus (SBV), a novel orthobunyavirus of the Simbu serogroup, was first identified in October 2011 in dairy cattle in Germany, where it caused fever, diarrhea and a drop in milk yield. Since then, SBV additionally has been detected in adult sheep and goats. Although symptoms of acute infection were not observed, infection during a vulnerable phase of pregnancy caused congenital malformations and stillbirths. In view of the current situation and the possible emergence of further Simbu serogroup members, a pan-Simbu real-time reverse transcriptase (RT) PCR system for the reliable detection of Simbu serogroup viruses should be developed. In this study a pan-Simbu real-time RT-PCR system was established and compared to several SBV real-time RT-PCR assays. All PCR-systems were tested using a panel of different Simbu serogroup viruses as well as several field samples from diseased cattle, sheep and goats originating from all over Germany. Several pan-Simbu real-time RT-PCR products were sequenced via Sanger sequencing. Furthermore, in silico analyses were performed to investigate suitability for the detection of further orthobunyaviruses. All tested members of the Simbu serogroup (n = 14) as well as most of the field samples were successfully detected by the pan-Simbu real-time RT-PCR system. The comparison of this intercalating dye assay with different TaqMan probe-based assays developed for SBV diagnostics confirmed the functionality of the pan-Simbu assay for screening purposes. However, the SBV-TaqMan-assay SBV-S3 delivered the highest analytical sensitivity of less than ten copies per reaction for duplex systems including an internal control. In addition, for confirmation of SBV-genome detection the highly specific SBV-M1 assay was established. The pan-Simbu real-time RT-PCR system was able to detect all tested members of the Simbu serogroup, most of the SBV field samples as well as three tested Bunyamwera serogroup viruses with a suitable

  4. Real-time systems scheduling fundamentals

    CERN Document Server

    Chetto, Maryline

    2014-01-01

    Real-time systems are used in a wide range of applications, including control, sensing, multimedia, etc.  Scheduling is a central problem for these computing/communication systems since responsible of software execution in a timely manner. This book provides state of knowledge in this domain with special emphasis on the key results obtained within the last decade. This book addresses foundations as well as the latest advances and findings in Real-Time Scheduling, giving all references to important papers. But nevertheless the chapters will be short and not overloaded with confusing details.

  5. Real-time specifications

    DEFF Research Database (Denmark)

    David, A.; Larsen, K.G.; Legay, A.

    2015-01-01

    A specification theory combines notions of specifications and implementations with a satisfaction relation, a refinement relation, and a set of operators supporting stepwise design. We develop a specification framework for real-time systems using Timed I/O Automata as the specification formalism......, with the semantics expressed in terms of Timed I/O Transition Systems. We provide constructs for refinement, consistency checking, logical and structural composition, and quotient of specifications-all indispensable ingredients of a compositional design methodology. The theory is implemented in the new tool Ecdar...

  6. Comparison of allelic discrimination by dHPLC, HRM, and TaqMan in the detection of BRAF mutation V600E.

    Science.gov (United States)

    Carbonell, Pablo; Turpin, María C; Torres-Moreno, Daniel; Molina-Martínez, Irene; García-Solano, José; Perez-Guillermo, Miguel; Conesa-Zamora, Pablo

    2011-09-01

    The V600E mutation in the BRAF oncogene is associated with colorectal carcinomas, with mismatch-repair deficiency and, recently, with nonresponse to epidermal growth factor receptor inhibitor therapy. The use of reliable techniques for its detection is important. The aim of our study was to compare the performance characteristics in V600E detection of denaturing high-performance liquid chromatography (dHPLC) and high-resolution melting (HRM) with TaqMan allelic discrimination as well as direct-sequencing methods in a series of 195 colorectal paraffin-embedded specimens up to the age of 15 years. The effectiveness for obtaining results on mutation status was best using TaqMan (96.9%), followed by dHPLC (93.3%), HRM (88.7%), and sequencing (88.2%). In general, TaqMan was best for analyzing older tissues, whereas sequencing was the least efficient. Heterozygotic V600E was detected in 11.6%, 9.9%, 11.6%, and 9.9% of tissues using TaqMan, dHPLC, HRM, and sequencing, respectively. Result concordances between dHPLC and TaqMan or sequencing were excellent (κ = 0.9411 and κ = 0.8988, respectively); for HRM, the concordances were good (κ = 0.7973 and κ = 0.7488, respectively). By using DNA dilutions from tumor tissue, a minimum of 10% of V600E harboring cancer content was required for the analysis by dHPLC and HRM. dHPLC could detect four non-V600E mutations, whereas HRM detected one. Our results indicate that dHPLC and HRM are techniques that can be reliably used for the detection of the BRAFV600E mutation in archival paraffin-embedded tissues. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  7. On Real-Time Systems Using Local Area Networks.

    Science.gov (United States)

    1987-07-01

    87-35 July, 1987 CS-TR-1892 On Real - Time Systems Using Local Area Networks*I VShem-Tov Levi Department of Computer Science Satish K. Tripathit...1892 On Real - Time Systems Using Local Area Networks* Shem-Tov Levi Department of Computer Science Satish K. Tripathit Department of Computer Science...constraints and the clock systems that feed the time to real - time systems . A model for real-time system based on LAN communication is presented in

  8. Approaching near real-time biosensing: microfluidic microsphere based biosensor for real-time analyte detection.

    Science.gov (United States)

    Cohen, Noa; Sabhachandani, Pooja; Golberg, Alexander; Konry, Tania

    2015-04-15

    In this study we describe a simple lab-on-a-chip (LOC) biosensor approach utilizing well mixed microfluidic device and a microsphere-based assay capable of performing near real-time diagnostics of clinically relevant analytes such cytokines and antibodies. We were able to overcome the adsorption kinetics reaction rate-limiting mechanism, which is diffusion-controlled in standard immunoassays, by introducing the microsphere-based assay into well-mixed yet simple microfluidic device with turbulent flow profiles in the reaction regions. The integrated microsphere-based LOC device performs dynamic detection of the analyte in minimal amount of biological specimen by continuously sampling micro-liter volumes of sample per minute to detect dynamic changes in target analyte concentration. Furthermore we developed a mathematical model for the well-mixed reaction to describe the near real time detection mechanism observed in the developed LOC method. To demonstrate the specificity and sensitivity of the developed real time monitoring LOC approach, we applied the device for clinically relevant analytes: Tumor Necrosis Factor (TNF)-α cytokine and its clinically used inhibitor, anti-TNF-α antibody. Based on the reported results herein, the developed LOC device provides continuous sensitive and specific near real-time monitoring method for analytes such as cytokines and antibodies, reduces reagent volumes by nearly three orders of magnitude as well as eliminates the washing steps required by standard immunoassays. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Mixed-mode Operating System for Real-time Performance

    OpenAIRE

    M.M. Hasan; S. Sultana; C.K. Foo

    2017-01-01

    The purpose of the mixed-mode system research is to handle devices with the accuracy of real-time systems and at the same time, having all the benefits and facilities of a matured Graphic User Interface (GUI) operating system which is typically nonreal-time. This mixed-mode operating system comprising of a real-time portion and a non-real-time portion was studied and implemented to identify the feasibilities and performances in practical applications (in the context of scheduled the real-time...

  10. Linux real-time framework for fusion devices

    Energy Technology Data Exchange (ETDEWEB)

    Neto, Andre [Associacao Euratom-IST, Instituto de Plasmas e Fusao Nuclear, Av. Rovisco Pais, 1049-001 Lisboa (Portugal)], E-mail: andre.neto@cfn.ist.utl.pt; Sartori, Filippo; Piccolo, Fabio [Euratom-UKAEA, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Barbalace, Antonio [Euratom-ENEA Association, Consorzio RFX, 35127 Padova (Italy); Vitelli, Riccardo [Dipartimento di Informatica, Sistemi e Produzione, Universita di Roma, Tor Vergata, Via del Politecnico 1-00133, Roma (Italy); Fernandes, Horacio [Associacao Euratom-IST, Instituto de Plasmas e Fusao Nuclear, Av. Rovisco Pais, 1049-001 Lisboa (Portugal)

    2009-06-15

    A new framework for the development and execution of real-time codes is currently being developed and commissioned at JET. The foundations of the system are Linux, the Real Time Application Interface (RTAI) and a wise exploitation of the new i386 multi-core processors technology. The driving motivation was the need to find a real-time operating system for the i386 platform able to satisfy JET Vertical Stabilisation Enhancement project requirements: 50 {mu}s cycle time. Even if the initial choice was the VxWorks operating system, it was decided to explore an open source alternative, mostly because of the costs involved in the commercial product. The work started with the definition of a precise set of requirements and milestones to achieve: Linux distribution and kernel versions to be used for the real-time operating system; complete characterization of the Linux/RTAI real-time capabilities; exploitation of the multi-core technology; implementation of all the required and missing features; commissioning of the system. Latency and jitter measurements were compared for Linux and RTAI in both user and kernel-space. The best results were attained using the RTAI kernel solution where the time to reschedule a real-time task after an external interrupt is of 2.35 {+-} 0.35 {mu}s. In order to run the real-time codes in the kernel-space, a solution to provide user-space functionalities to the kernel modules had to be designed. This novel work provided the most common functions from the standard C library and transparent interaction with files and sockets to the kernel real-time modules. Kernel C++ support was also tested, further developed and integrated in the framework. The work has produced very convincing results so far: complete isolation of the processors assigned to real-time from the Linux non real-time activities, high level of stability over several days of benchmarking operations and values well below 3 {mu}s for task rescheduling after external interrupt. From

  11. Linux real-time framework for fusion devices

    International Nuclear Information System (INIS)

    Neto, Andre; Sartori, Filippo; Piccolo, Fabio; Barbalace, Antonio; Vitelli, Riccardo; Fernandes, Horacio

    2009-01-01

    A new framework for the development and execution of real-time codes is currently being developed and commissioned at JET. The foundations of the system are Linux, the Real Time Application Interface (RTAI) and a wise exploitation of the new i386 multi-core processors technology. The driving motivation was the need to find a real-time operating system for the i386 platform able to satisfy JET Vertical Stabilisation Enhancement project requirements: 50 μs cycle time. Even if the initial choice was the VxWorks operating system, it was decided to explore an open source alternative, mostly because of the costs involved in the commercial product. The work started with the definition of a precise set of requirements and milestones to achieve: Linux distribution and kernel versions to be used for the real-time operating system; complete characterization of the Linux/RTAI real-time capabilities; exploitation of the multi-core technology; implementation of all the required and missing features; commissioning of the system. Latency and jitter measurements were compared for Linux and RTAI in both user and kernel-space. The best results were attained using the RTAI kernel solution where the time to reschedule a real-time task after an external interrupt is of 2.35 ± 0.35 μs. In order to run the real-time codes in the kernel-space, a solution to provide user-space functionalities to the kernel modules had to be designed. This novel work provided the most common functions from the standard C library and transparent interaction with files and sockets to the kernel real-time modules. Kernel C++ support was also tested, further developed and integrated in the framework. The work has produced very convincing results so far: complete isolation of the processors assigned to real-time from the Linux non real-time activities, high level of stability over several days of benchmarking operations and values well below 3 μs for task rescheduling after external interrupt. From being the

  12. Static Schedulers for Embedded Real-Time Systems

    Science.gov (United States)

    1989-12-01

    Because of the need for having efficient scheduling algorithms in large scale real time systems , software engineers put a lot of effort on developing...provide static schedulers for he Embedded Real Time Systems with single processor using Ada programming language. The independent nonpreemptable...support the Computer Aided Rapid Prototyping for Embedded Real Time Systems so that we determine whether the system, as designed, meets the required

  13. Real-time motional Stark effect in jet

    International Nuclear Information System (INIS)

    Alves, D.; Stephen, A.; Hawkes, N.; Dalley, S.; Goodyear, A.; Felton, R.; Joffrin, E.; Fernandes, H.

    2004-01-01

    The increasing importance of real-time measurements and control systems in JET experiments, regarding e.g. Internal Transport Barrier (ITB) and q-profile control, has motivated the development of a real-time motional Stark effect (MSE) system. The MSE diagnostic allows the measurement of local magnetic fields in different locations along the neutral beam path providing, therefore, local measurement of the current and q-profiles. Recently in JET, an upgrade of the MSE diagnostic has been implemented, incorporating a totally new system which allows the use of this diagnostic as a real-time control tool as well as an extended data source for off-line analysis. This paper will briefly describe the technical features of the real-time diagnostic with main focus on the system architecture, which consists of a VME crate hosting three PowerPC processor boards and a fast ADC, all connected via Front Panel Data Port (FPDP). The DSP algorithm implements a lockin-amplifier required to demodulate the JET MSE signals. Some applications for the system will be covered such as: feeding the real-time equilibrium reconstruction code (EQUINOX) and allowing the full coverage analysis of the Neutral Beam time window. A brief comparison between the real-time MSE analysis and the off-line analysis will also be presented

  14. Scala for Real-Time Systems?

    DEFF Research Database (Denmark)

    Schoeberl, Martin

    2015-01-01

    Java served well as a general-purpose language. However, during its two decades of constant change it has gotten some weight and legacy in the language syntax and the libraries. Furthermore, Java's success for real-time systems is mediocre. Scala is a modern object-oriented and functional language...... with interesting new features. Although a new language, it executes on a Java virtual machine, reusing that technology. This paper explores Scala as language for future real-time systems....

  15. Towards exascale real-time RFI mitigation

    NARCIS (Netherlands)

    van Nieuwpoort, R.V.

    2016-01-01

    We describe the design and implementation of an extremely scalable real-time RFI mitigation method, based on the offline AOFlagger. All algorithms scale linearly in the number of samples. We describe how we implemented the flagger in the LOFAR real-time pipeline, on both CPUs and GPUs. Additionally,

  16. Time-Optimal Real-Time Test Case Generation using UPPAAL

    DEFF Research Database (Denmark)

    Hessel, Anders; Larsen, Kim Guldstrand; Nielsen, Brian

    2004-01-01

    Testing is the primary software validation technique used by industry today, but remains ad hoc, error prone, and very expensive. A promising improvement is to automatically generate test cases from formal models of the system under test. We demonstrate how to automatically generate real...... test purposes or generated automatically from various coverage criteria of the model.......-time conformance test cases from timed automata specifications. Specifically we demonstrate how to fficiently generate real-time test cases with optimal execution time i.e test cases that are the fastest possible to execute. Our technique allows time optimal test cases to be generated using manually formulated...

  17. Performance evaluation of near-real-time accounting systems

    International Nuclear Information System (INIS)

    Anon.

    1981-01-01

    Examples are given illustrating the application of near-real-time accounting concepts and principles to actual nuclear facilities. Experience with prototypical systems at the AGNS reprocessing plant and the Los Alamos plutonium facility is described using examples of actual data to illustrate the performance and effectiveness of near-real-time systems. The purpose of the session is to enable participants to: (1) identify the major components of near-real-time accounting systems; (2) describe qualitatively the advantages, limitations, and performance of such systems in real nuclear facilities; (3) identify process and facility design characteristics that affect the performance of near-real-time systems; and (4) describe qualitatively the steps necessary to implement a near-real-time accounting and control system in a nuclear facility

  18. Distributed Issues for Ada Real-Time Systems

    Science.gov (United States)

    1990-07-23

    NUMBERS Distributed Issues for Ada Real - Time Systems MDA 903-87- C- 0056 S. AUTHOR(S) Thomas E. Griest 7. PERFORMING ORGANiZATION NAME(S) AND ADORESS(ES) 8...considerations. I Adding to the problem of distributed real - time systems is the issue of maintaining a common sense of time among all of the processors...because -omeone is waiting for the final output of a very large set of computations. However in real - time systems , consistent meeting of short-term

  19. Design Specifications for Adaptive Real-Time Systems

    Science.gov (United States)

    1991-12-01

    TICfl \\ E CT E Design Specifications for JAN’\\ 1992 Adaptive Real - Time Systems fl Randall W. Lichota U, Alice H. Muntz - December 1991 \\ \\\\/ 0 / r...268-2056 Technical Report CMU/SEI-91-TR-20 ESD-91-TR-20 December 1991 Design Specifications for Adaptive Real - Time Systems Randall W. Lichota Hughes...Design Specifications for Adaptive Real - Time Systems Abstract: The design specification method described in this report treats a software

  20. Design Recovery Technology for Real-Time Systems.

    Science.gov (United States)

    1995-10-01

    RL-TR-95-208 Final Technical Report October 1995 DESIGN RECOVERY TECHNOLOGY FOR REAL TIME SYSTEMS The MITRE Corporation Lester J. Holtzblatt...92 - Jan 95 4. TTTLE AND SUBTITLE DESIGN RECOVERY TECHNOLOGY FOR REAL - TIME SYSTEMS 6. AUTHOR(S) Lester J. Holtzblatt, Richard Piazza, and Susan...behavior of real - time systems in general, our initial efforts have centered on recovering this information from one system in particular, the Modular

  1. Comparison of multiplex RT-PCR and real-time HybProbe assay for serotyping of dengue virus using reference strains and clinical samples from India

    Directory of Open Access Journals (Sweden)

    Anita Chakravarti

    2016-01-01

    Full Text Available Background: Dengue virus serotyping is crucial from clinical management and epidemiological point of view. Aims: To compare efficacy of two molecular detection and typing methods, namely, multiplex reverse transcription polymerase chain reaction (RT-PCR and real-time Hybprobe assay using a panel of known dilution of four reference Dengue virus strains and a panel of sera collected from clinically suspected dengue patients. Settings: This study was conducted at a tertiary-care teaching hospital in Delhi, India. Materials and Methods: Dengue serotype specific virus strains were used as prototypes for serotyping assays. Viral load was quantified by quantitative real time reverse transcription polymerase chain reaction (qRT-PCR. Acute phase serum samples were collected from 79 patients with clinically suspected Dengue fever on their first day of presentation during September-October 2012. Viral RNA from serum and cell culture supernatant was extracted. Reverse transcription was carried out. Quantitative detection of DENV RNA from reference strain culture supernatants and each of the 79 patient samples by real-time PCR was performed using light cycler Taqman master mix kit. Serotyping was done by multiplex RT-PCR assay and Hybprobe assay. Results: The multiplex RT-PCR assay, though found to be 100% specific, couldn't serotype either patient or reference strains with viral load less than 1000 RNA copies/ml. The Hybprobe assay was found to have 100% specificity and had a lower limit of serotype detection of merely 3.54 RNA copies/ml. Conclusions: HybProbe assay has an important role especially in situations where serotyping is to be performed in clinical samples with low viral load.

  2. [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.

  3. Real-time communication for distributed plasma control systems

    Energy Technology Data Exchange (ETDEWEB)

    Luchetta, A. [Consorzio RFX, Associazione Euratom-ENEA sulla Fusione, Corso Stati Uniti 4, Padova 35127 (Italy)], E-mail: adriano.luchetta@igi.cnr.it; Barbalace, A.; Manduchi, G.; Soppelsa, A.; Taliercio, C. [Consorzio RFX, Associazione Euratom-ENEA sulla Fusione, Corso Stati Uniti 4, Padova 35127 (Italy)

    2008-04-15

    Real-time control applications will benefit in the near future from the enhanced performance provided by multi-core processor architectures. Nevertheless real-time communication will continue to be critical in distributed plasma control systems where the plant under control typically is distributed over a wide area. At RFX-mod real-time communication is crucial for hard real-time plasma control, due to the distributed architecture of the system, which consists of several VMEbus stations. The system runs under VxWorks and uses Gigabit Ethernet for sub-millisecond real-time communication. To optimize communication in the system, a set of detailed measurements has been carried out on the target platforms (Motorola MVME5100 and MVME5500) using either the VxWorks User Datagram Protocol (UDP) stack or raw communication based on the data link layer. Measurements have been carried out also under Linux, using its UDP stack or, in alternative, RTnet, an open source hard real-time network protocol stack. RTnet runs under Xenomai or RTAI, two popular real-time extensions based on the Linux kernel. The paper reports on the measurements carried out and compares the results, showing that the performance obtained by using open source code is suitable for sub-millisecond real-time communication in plasma control.

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

    Science.gov (United States)

    Nagy, Alexander; Černíková, Lenka; Vitásková, Eliška; Křivda, Vlastimil; Dán, Ádám; Dirbáková, Zuzana; Jiřincová, Helena; Procházka, Bohumír; Sedlák, Kamil; Havlíčková, Martina

    2016-01-01

    In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence. PMID:27031831

  5. A European multicientre study on the comparison of HBV viral loads between VERIS HBV assay and Roche COBAS® TAQMAN® HBV test, Abbott RealTime HBV assay, Siemens VERSANT HBV assay, and Qiagen artus HBV RG kit.

    Science.gov (United States)

    Braun, Patrick; Delgado, Rafael; Drago, Monica; Fanti, Diana; Fleury, Hervé; Izopet, Jacques; Lombardi, Alessandra; Marcos, MaAngeles; Sauné, Karine; O'Shea, Siobhan; Pérez-Rivilla, Alfredo; Ramble, John; Trimoulet, Pascale; Vila, Jordi; Whittaker, Duncan; Artus, Alain; Rhodes, Daniel

    2017-10-01

    Hepatitis B viral load testing is essential to treatment and monitoring decisions in patients with chronic Hepatitis B. Beckman Coulter has developed the VERIS HBV Assay (Veris) for use on the fully automated DxN VERIS Molecular Diagnostics System. 1 OBJECTIVES: To evaluate the clinical performance of the Veris HBV Assay at multiple EU laboratories STUDY DESIGN: Method comparison was performed with a total of 344 plasma specimens from HBV infected patients tested with Veris and COBAS ® TaqMan ® HBV Test (Cobas), 207 specimens tested with Veris and RealTime HBV Assay (RealTime), 86 specimens tested with Veris and VERSANT ® HBV Assay (Versant), and 74 specimens tested with Veris and artus ® HBV RG PCR kit (artus). Bland-Altman analysis showed average bias of -0.46 log 10 IU/mL between Veris and Cobas, -0.46 log 10 IU/mL between Veris and RealTime, -0.36 log 10 IU/mL between Veris and Versant, and -0.12 log 10 IU/mL between Veris and artus. Bias was consistent across the assay range. Patient monitoring results using Veris demonstrated similar viral load trends over time to Cobas, RealTime, and artus. The VERIS HBV Assay demonstrated comparable clinical performance, with varying degrees of negative bias, compared to other currently marketed assays for HBV DNA monitoring. This negative bias should be taken into consideration if switching monitoring methods to Veris. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Real-time quasi-3D tomographic reconstruction

    Science.gov (United States)

    Buurlage, Jan-Willem; Kohr, Holger; Palenstijn, Willem Jan; Joost Batenburg, K.

    2018-06-01

    Developments in acquisition technology and a growing need for time-resolved experiments pose great computational challenges in tomography. In addition, access to reconstructions in real time is a highly demanded feature but has so far been out of reach. We show that by exploiting the mathematical properties of filtered backprojection-type methods, having access to real-time reconstructions of arbitrarily oriented slices becomes feasible. Furthermore, we present , software for visualization and on-demand reconstruction of slices. A user of can interactively shift and rotate slices in a GUI, while the software updates the slice in real time. For certain use cases, the possibility to study arbitrarily oriented slices in real time directly from the measured data provides sufficient visual and quantitative insight. Two such applications are discussed in this article.

  7. An algorithm for learning real-time automata

    NARCIS (Netherlands)

    Verwer, S.E.; De Weerdt, M.M.; Witteveen, C.

    2007-01-01

    We describe an algorithm for learning simple timed automata, known as real-time automata. The transitions of real-time automata can have a temporal constraint on the time of occurrence of the current symbol relative to the previous symbol. The learning algorithm is similar to the redblue fringe

  8. De toekomst van Real Time Intelligence

    NARCIS (Netherlands)

    Broek, J. van den; Berg, C.H. van den

    2013-01-01

    Al direct vanaf de start van de Nationale Politie is gewerkt aan het opzetten van tien real-time intelligence centra in Nederland. Van daaruit worden 24 uur per dag en zeven dagen in de week agenten op straat actief ondersteund met real-time informatie bij de melding waar ze op af gaan. In de visie

  9. Real-Time Parameter Identification

    Data.gov (United States)

    National Aeronautics and Space Administration — Armstrong researchers have implemented in the control room a technique for estimating in real time the aerodynamic parameters that describe the stability and control...

  10. Real time process algebra with time-dependent conditions

    NARCIS (Netherlands)

    Baeten, J.C.M.; Middelburg, C.A.

    We extend the main real time version of ACP presented in [6] with conditionals in which the condition depends on time. This extension facilitates flexible dependence of proccess behaviour on initialization time. We show that the conditions concerned generalize the conditions introduced earlier

  11. Compiling models into real-time systems

    International Nuclear Information System (INIS)

    Dormoy, J.L.; Cherriaux, F.; Ancelin, J.

    1992-08-01

    This paper presents an architecture for building real-time systems from models, and model-compiling techniques. This has been applied for building a real-time model-based monitoring system for nuclear plants, called KSE, which is currently being used in two plants in France. We describe how we used various artificial intelligence techniques for building it: a model-based approach, a logical model of its operation, a declarative implementation of these models, and original knowledge-compiling techniques for automatically generating the real-time expert system from those models. Some of those techniques have just been borrowed from the literature, but we had to modify or invent other techniques which simply did not exist. We also discuss two important problems, which are often underestimated in the artificial intelligence literature: size, and errors. Our architecture, which could be used in other applications, combines the advantages of the model-based approach with the efficiency requirements of real-time applications, while in general model-based approaches present serious drawbacks on this point

  12. Compiling models into real-time systems

    International Nuclear Information System (INIS)

    Dormoy, J.L.; Cherriaux, F.; Ancelin, J.

    1992-08-01

    This paper presents an architecture for building real-time systems from models, and model-compiling techniques. This has been applied for building a real-time model-base monitoring system for nuclear plants, called KSE, which is currently being used in two plants in France. We describe how we used various artificial intelligence techniques for building it: a model-based approach, a logical model of its operation, a declarative implementation of these models, and original knowledge-compiling techniques for automatically generating the real-time expert system from those models. Some of those techniques have just been borrowed from the literature, but we had to modify or invent other techniques which simply did not exist. We also discuss two important problems, which are often underestimated in the artificial intelligence literature: size, and errors. Our architecture, which could be used in other applications, combines the advantages of the model-based approach with the efficiency requirements of real-time applications, while in general model-based approaches present serious drawbacks on this point

  13. Real Time Linux - The RTOS for Astronomy?

    Science.gov (United States)

    Daly, P. N.

    The BoF was attended by about 30 participants and a free CD of real time Linux-based upon RedHat 5.2-was available. There was a detailed presentation on the nature of real time Linux and the variants for hard real time: New Mexico Tech's RTL and DIAPM's RTAI. Comparison tables between standard Linux and real time Linux responses to time interval generation and interrupt response latency were presented (see elsewhere in these proceedings). The present recommendations are to use RTL for UP machines running the 2.0.x kernels and RTAI for SMP machines running the 2.2.x kernel. Support, both academically and commercially, is available. Some known limitations were presented and the solutions reported e.g., debugging and hardware support. The features of RTAI (scheduler, fifos, shared memory, semaphores, message queues and RPCs) were described. Typical performance statistics were presented: Pentium-based oneshot tasks running > 30kHz, 486-based oneshot tasks running at ~ 10 kHz, periodic timer tasks running in excess of 90 kHz with average zero jitter peaking to ~ 13 mus (UP) and ~ 30 mus (SMP). Some detail on kernel module programming, including coding examples, were presented showing a typical data acquisition system generating simulated (random) data writing to a shared memory buffer and a fifo buffer to communicate between real time Linux and user space. All coding examples were complete and tested under RTAI v0.6 and the 2.2.12 kernel. Finally, arguments were raised in support of real time Linux: it's open source, free under GPL, enables rapid prototyping, has good support and the ability to have a fully functioning workstation capable of co-existing hard real time performance. The counter weight-the negatives-of lack of platforms (x86 and PowerPC only at present), lack of board support, promiscuous root access and the danger of ignorance of real time programming issues were also discussed. See ftp://orion.tuc.noao.edu/pub/pnd/rtlbof.tgz for the StarOffice overheads

  14. The real-time price elasticity of electricity

    International Nuclear Information System (INIS)

    Lijesen, Mark G.

    2007-01-01

    The real-time price elasticity of electricity contains important information on the demand response of consumers to the volatility of peak prices. Despite the importance, empirical estimates of the real-time elasticity are hardly available. This paper provides a quantification of the real-time relationship between total peak demand and spot market prices. We find a low value for the real-time price elasticity, which may partly be explained from the fact that not all users observe the spot market price. If we correct for this phenomenon, we find the elasticity to be fairly low for consumers currently active in the spot market. If this conclusion applies to all users, this would imply a limited scope for government intervention in supply security issues. (Author)

  15. A Programmable Microkernel for Real-Time Systems

    Science.gov (United States)

    2003-06-01

    A Programmable Microkernel for Real - Time Systems Christoph M. Kirsch Thomas A. Henzinger Marco A.A. Sanvido Report No. UCB/CSD-3-1250 June 2003...TITLE AND SUBTITLE A Programmable Microkernel for Real - Time Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 A Programmable Microkernel for Real - Time Systems ∗ Christoph M

  16. Real-time object-oriented programming: studies and proposals

    International Nuclear Information System (INIS)

    Fouquier, Gilles

    1996-01-01

    This thesis contributes to the introduction of real-time features in object-oriented programming. Object-oriented programming favours modularity and reusability. Therefore, its application to real-time introduces many theoretical and conceptual problems. To deal with these problems, a new real-time object-oriented programming model is presented. This model is based on the active object model which allows concurrence and maintains the encapsulation property. The real-time aspect is treated by replacing the concept of task by the concept of method processing and by associating a real-time constraint to each message (priority or deadline). The set of all the running methods is scheduled. This model, called ATOME, contains several sub-models to deal with the usual concurrence control integrating their priority and deadline processing. The classical HPF and EDF scheduling avoid priority or deadline inversion. This model and its variants are new proposals to program real-time applications in the object-oriented way, therefore easing reusability and code writing. The feasibility of this approach is demonstrated by extending and existing active object-based language to real-time, in using the rules defined in the ATOME model. (author) [fr

  17. Real-time simulation of large-scale floods

    Science.gov (United States)

    Liu, Q.; Qin, Y.; Li, G. D.; Liu, Z.; Cheng, D. J.; Zhao, Y. H.

    2016-08-01

    According to the complex real-time water situation, the real-time simulation of large-scale floods is very important for flood prevention practice. Model robustness and running efficiency are two critical factors in successful real-time flood simulation. This paper proposed a robust, two-dimensional, shallow water model based on the unstructured Godunov- type finite volume method. A robust wet/dry front method is used to enhance the numerical stability. An adaptive method is proposed to improve the running efficiency. The proposed model is used for large-scale flood simulation on real topography. Results compared to those of MIKE21 show the strong performance of the proposed model.

  18. Mechatronic modeling of real-time wheel-rail contact

    CERN Document Server

    Bosso, Nicola; Gugliotta, Antonio; Somà, Aurelio

    2013-01-01

    Real-time simulations of the behaviour of a rail vehicle require realistic solutions of the wheel-rail contact problem which can work in a real-time mode. Examples of such solutions for the online mode have been well known and are implemented within standard and commercial tools for the simulation codes for rail vehicle dynamics. This book is the result of the research activities carried out by the Railway Technology Lab of the Department of Mechanical and Aerospace Engineering at Politecnico di Torino. This book presents work on the project for the development of a real-time wheel-rail contact model and provides the simulation results obtained with dSpace real-time hardware. Besides this, the implementation of the contact model for the development of a real-time model for the complex mechatronic system of a scaled test rig is presented in this book and may be useful for the further validation of the real-time contact model with experiments on a full scale test rig.

  19. Internet-accessible real-time weather information system

    Digital Repository Service at National Institute of Oceanography (India)

    Desai, R.G.P.; Joseph, A.; Desa, E.; Mehra, P.; Desa, E.; Gouveia, A.D.

    An internet-accessible real-time weather information system has been developed. This system provides real-time accessibility to weather information from a multitude of spatially distributed weather stations. The Internet connectivity also offers...

  20. Automated real-time software development

    Science.gov (United States)

    Jones, Denise R.; Walker, Carrie K.; Turkovich, John J.

    1993-01-01

    A Computer-Aided Software Engineering (CASE) system has been developed at the Charles Stark Draper Laboratory (CSDL) under the direction of the NASA Langley Research Center. The CSDL CASE tool provides an automated method of generating source code and hard copy documentation from functional application engineering specifications. The goal is to significantly reduce the cost of developing and maintaining real-time scientific and engineering software while increasing system reliability. This paper describes CSDL CASE and discusses demonstrations that used the tool to automatically generate real-time application code.

  1. Geomagnetic Observatory Data for Real-Time Applications

    Science.gov (United States)

    Love, J. J.; Finn, C. A.; Rigler, E. J.; Kelbert, A.; Bedrosian, P.

    2015-12-01

    The global network of magnetic observatories represents a unique collective asset for the scientific community. Historically, magnetic observatories have supported global magnetic-field mapping projects and fundamental research of the Earth's interior and surrounding space environment. More recently, real-time data streams from magnetic observatories have become an important contributor to multi-sensor, operational monitoring of evolving space weather conditions, especially during magnetic storms. In this context, the U.S. Geological Survey (1) provides real-time observatory data to allied space weather monitoring projects, including those of NOAA, the U.S. Air Force, NASA, several international agencies, and private industry, (2) collaborates with Schlumberger to provide real-time geomagnetic data needed for directional drilling for oil and gas in Alaska, (3) develops products for real-time evaluation of hazards for the electric-power grid industry that are associated with the storm-time induction of geoelectric fields in the Earth's conducting lithosphere. In order to implement strategic priorities established by the USGS Natural Hazards Mission Area and the National Science and Technology Council, and with a focus on developing new real-time products, the USGS is (1) leveraging data management protocols already developed by the USGS Earthquake Program, (2) developing algorithms for mapping geomagnetic activity, a collaboration with NASA and NOAA, (3) supporting magnetotelluric surveys and developing Earth conductivity models, a collaboration with Oregon State University and the NSF's EarthScope Program, (4) studying the use of geomagnetic activity maps and Earth conductivity models for real-time estimation of geoelectric fields, (5) initiating geoelectric monitoring at several observatories, (6) validating real-time estimation algorithms against historical geomagnetic and geoelectric data. The success of these long-term projects is subject to funding constraints

  2. Real-time earthquake data feasible

    Science.gov (United States)

    Bush, Susan

    Scientists agree that early warning devices and monitoring of both Hurricane Hugo and the Mt. Pinatubo volcanic eruption saved thousands of lives. What would it take to develop this sort of early warning and monitoring system for earthquake activity?Not all that much, claims a panel assigned to study the feasibility, costs, and technology needed to establish a real-time earthquake monitoring (RTEM) system. The panel, drafted by the National Academy of Science's Committee on Seismology, has presented its findings in Real-Time Earthquake Monitoring. The recently released report states that “present technology is entirely capable of recording and processing data so as to provide real-time information, enabling people to mitigate somewhat the earthquake disaster.” RTEM systems would consist of two parts—an early warning system that would give a few seconds warning before severe shaking, and immediate postquake information within minutes of the quake that would give actual measurements of the magnitude. At this time, however, this type of warning system has not been addressed at the national level for the United States and is not included in the National Earthquake Hazard Reduction Program, according to the report.

  3. Verifying real-time systems against scenario-based requirements

    DEFF Research Database (Denmark)

    Larsen, Kim Guldstrand; Li, Shuhao; Nielsen, Brian

    2009-01-01

    We propose an approach to automatic verification of real-time systems against scenario-based requirements. A real-time system is modeled as a network of Timed Automata (TA), and a scenario-based requirement is specified as a Live Sequence Chart (LSC). We define a trace-based semantics for a kernel...... subset of the LSC language. By equivalently translating an LSC chart into an observer TA and then non-intrusively composing this observer with the original system model, the problem of verifying a real-time system against a scenario-based requirement reduces to a classical real-time model checking...

  4. 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.))

  5. Temporal Specification and Verification of Real-Time Systems.

    Science.gov (United States)

    1991-08-30

    of concrete real - time systems can be modeled adequately. Specification: We present two conservative extensions of temporal logic that allow for the...logic. We present both model-checking algorithms for the automatic verification of finite-state real - time systems and proof methods for the deductive verification of real - time systems .

  6. ClockWork: a Real-Time Feasibility Analysis Tool

    NARCIS (Netherlands)

    Jansen, P.G.; Hanssen, F.T.Y.; Mullender, Sape J.

    ClockWork shows that we can improve the flexibility and efficiency of real-time kernels. We do this by proposing methods for scheduling based on so-called Real-Time Transactions. ClockWork uses Real-Time Transactions which allow scheduling decisions to be taken by the system. A programmer does not

  7. Failure analysis of real-time systems

    International Nuclear Information System (INIS)

    Jalashgar, A.; Stoelen, K.

    1998-01-01

    This paper highlights essential aspects of real-time software systems that are strongly related to the failures and their course of propagation. The significant influence of means-oriented and goal-oriented system views in the description, understanding and analysing of those aspects is elaborated. The importance of performing failure analysis prior to reliability analysis of real-time systems is equally addressed. Problems of software reliability growth models taking the properties of such systems into account are discussed. Finally, the paper presents a preliminary study of a goal-oriented approach to model the static and dynamic characteristics of real-time systems, so that the corresponding analysis can be based on a more descriptive and informative picture of failures, their effects and the possibility of their occurrence. (author)

  8. Can Real-Time Data Also Be Climate Quality?

    Science.gov (United States)

    Brewer, M.; Wentz, F. J.

    2015-12-01

    GMI, AMSR-2 and WindSat herald a new era of highly accurate and timely microwave data products. Traditionally, there has been a large divide between real-time and re-analysis data products. What if these completely separate processing systems could be merged? Through advanced modeling and physically based algorithms, Remote Sensing Systems (RSS) has narrowed the gap between real-time and research-quality. Satellite microwave ocean products have proven useful for a wide array of timely Earth science applications. Through cloud SST capabilities have enormously benefited tropical cyclone forecasting and day to day fisheries management, to name a few. Oceanic wind vectors enhance operational safety of shipping and recreational boating. Atmospheric rivers are of import to many human endeavors, as are cloud cover and knowledge of precipitation events. Some activities benefit from both climate and real-time operational data used in conjunction. RSS has been consistently improving microwave Earth Science Data Records (ESDRs) for several decades, while making near real-time data publicly available for semi-operational use. These data streams have often been produced in 2 stages: near real-time, followed by research quality final files. Over the years, we have seen this time delay shrink from months or weeks to mere hours. As well, we have seen the quality of near real-time data improve to the point where the distinction starts to blur. We continue to work towards better and faster RFI filtering, adaptive algorithms and improved real-time validation statistics for earlier detection of problems. Can it be possible to produce climate quality data in real-time, and what would the advantages be? We will try to answer these questions…

  9. Academic Training: Real Time Process Control - Lecture series

    CERN Multimedia

    Françoise Benz

    2004-01-01

    ACADEMIC TRAINING LECTURE REGULAR PROGRAMME 7, 8 and 9 June From 11:00 hrs to 12:00 hrs - Main Auditorium bldg. 500 Real Time Process Control T. Riesco / CERN-TS What exactly is meant by Real-time? There are several definitions of real-time, most of them contradictory. Unfortunately the topic is controversial, and there does not seem to be 100% agreement over the terminology. Real-time applications are becoming increasingly important in our daily lives and can be found in diverse environments such as the automatic braking system on an automobile, a lottery ticket system, or robotic environmental samplers on a space station. These lectures will introduce concepts and theory like basic concepts timing constraints, task scheduling, periodic server mechanisms, hard and soft real-time.ENSEIGNEMENT ACADEMIQUE ACADEMIC TRAINING Françoise Benz 73127 academic.training@cern.ch

  10. 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.

  11. Reviewing real-time performance of nuclear reactor safety systems

    International Nuclear Information System (INIS)

    Preckshot, G.G.

    1993-08-01

    The purpose of this paper is to recommend regulatory guidance for reviewers examining real-time performance of computer-based safety systems used in nuclear power plants. Three areas of guidance are covered in this report. The first area covers how to determine if, when, and what prototypes should be required of developers to make a convincing demonstration that specific problems have been solved or that performance goals have been met. The second area has recommendations for timing analyses that will prove that the real-time system will meet its safety-imposed deadlines. The third area has description of means for assessing expected or actual real-time performance before, during, and after development is completed. To ensure that the delivered real-time software product meets performance goals, the paper recommends certain types of code-execution and communications scheduling. Technical background is provided in the appendix on methods of timing analysis, scheduling real-time computations, prototyping, real-time software development approaches, modeling and measurement, and real-time operating systems

  12. Reviewing real-time performance of nuclear reactor safety systems

    Energy Technology Data Exchange (ETDEWEB)

    Preckshot, G.G. [Lawrence Livermore National Lab., CA (United States)

    1993-08-01

    The purpose of this paper is to recommend regulatory guidance for reviewers examining real-time performance of computer-based safety systems used in nuclear power plants. Three areas of guidance are covered in this report. The first area covers how to determine if, when, and what prototypes should be required of developers to make a convincing demonstration that specific problems have been solved or that performance goals have been met. The second area has recommendations for timing analyses that will prove that the real-time system will meet its safety-imposed deadlines. The third area has description of means for assessing expected or actual real-time performance before, during, and after development is completed. To ensure that the delivered real-time software product meets performance goals, the paper recommends certain types of code-execution and communications scheduling. Technical background is provided in the appendix on methods of timing analysis, scheduling real-time computations, prototyping, real-time software development approaches, modeling and measurement, and real-time operating systems.

  13. Connecting real-time data to algorithms and databases: EarthCube's Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS)

    Science.gov (United States)

    Daniels, M. D.; Graves, S. J.; Kerkez, B.; Chandrasekar, V.; Vernon, F.; Martin, C. L.; Maskey, M.; Keiser, K.; Dye, M. J.

    2015-12-01

    The Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS) project was funded under the National Science Foundation's EarthCube initiative. CHORDS addresses the ever-increasing importance of real-time scientific data in the geosciences, particularly in mission critical scenarios, where informed decisions must be made rapidly. Access to constant streams of real-time data also allow many new transient phenomena in space-time to be observed, however, much of these streaming data are either completely inaccessible or only available to proprietary in-house tools or displays. Small research teams do not have the resources to develop tools for the broad dissemination of their unique real-time data and require an easy to use, scalable, cloud-based solution to facilitate this access. CHORDS will make these diverse streams of real-time data available to the broader geosciences community. This talk will highlight a recently developed CHORDS portal tools and processing systems which address some of the gaps in handling real-time data, particularly in the provisioning of data from the "long-tail" scientific community through a simple interface that is deployed in the cloud, is scalable and is able to be customized by research teams. A running portal, with operational data feeds from across the nation, will be presented. The processing within the CHORDS system will expose these real-time streams via standard services from the Open Geospatial Consortium (OGC) in a way that is simple and transparent to the data provider, while maximizing the usage of these investments. The ingestion of high velocity, high volume and diverse data has allowed the project to explore a NoSQL database implementation. Broad use of the CHORDS framework by geoscientists will help to facilitate adaptive experimentation, model assimilation and real-time hypothesis testing.

  14. Investigations on the frequency of norovirus contamination of ready-to-eat food items in Istanbul, Turkey, by using real-time reverse transcription PCR.

    Science.gov (United States)

    Yilmaz, Aysun; Bostan, Kamil; Altan, Eda; Muratoglu, Karlo; Turan, Nuri; Tan, Derya; Helps, Christopher; Yilmaz, Huseyin

    2011-05-01

    Investigation of norovirus (NoV) contamination of food items is important because many outbreaks occur after consumption of contaminated shellfish, vegetables, fruits, and water. The frequency of NoV contamination in food items has not previously been investigated in Turkey. The aim of this study was to investigate the frequency of human NoV genogroups (G) I and II in ready-to-eat tomatoes, parsley, green onion, lettuce, mixed salads, and cracked wheat balls. RNA was extracted with the RNeasy Mini Kit, and a real-time reverse transcription (RT) PCR assay was performed using primers specific for NoV GI and GII. Among the 525 samples analyzed, NoV GII was detected in 1 green onion sample and 1 tomato sample by both SYBR Green and TaqMan real-time RT-PCR assays; no GI virus was detected. The Enterobactericaeae and Escherichia coli levels in the NoV-positive green onion were 6.56 and 1.28 log CFU/g, and those in the tomato were 5.55 and 1.30 log CFU/g, respectively. No significant difference in the bacterial levels was found between the NoV-positive and NoV-negative samples. This study is the first in which NoV GII was found in ready-to-eat food collected from Istanbul, Turkey; thus, these foods may be considered a risk to human health. Epidemiological studies and measures to prevent NoV infection should be considered.

  15. Virtual timers in hierarchical real-time systems

    NARCIS (Netherlands)

    Heuvel, van den M.M.H.P.; Holenderski, M.J.; Cools, W.A.; Bril, R.J.; Lukkien, J.J.; Zhu, D.

    2009-01-01

    Hierarchical scheduling frameworks (HSFs) provide means for composing complex real-time systems from welldefined subsystems. This paper describes an approach to provide hierarchically scheduled real-time applications with virtual event timers, motivated by the need for integrating priority

  16. Real-time video compressing under DSP/BIOS

    Science.gov (United States)

    Chen, Qiu-ping; Li, Gui-ju

    2009-10-01

    This paper presents real-time MPEG-4 Simple Profile video compressing based on the DSP processor. The programming framework of video compressing is constructed using TMS320C6416 Microprocessor, TDS510 simulator and PC. It uses embedded real-time operating system DSP/BIOS and the API functions to build periodic function, tasks and interruptions etcs. Realize real-time video compressing. To the questions of data transferring among the system. Based on the architecture of the C64x DSP, utilized double buffer switched and EDMA data transfer controller to transit data from external memory to internal, and realize data transition and processing at the same time; the architecture level optimizations are used to improve software pipeline. The system used DSP/BIOS to realize multi-thread scheduling. The whole system realizes high speed transition of a great deal of data. Experimental results show the encoder can realize real-time encoding of 768*576, 25 frame/s video images.

  17. Real-time ISEE data system

    Science.gov (United States)

    Tsurutani, B. T.; Baker, D. N.

    1979-01-01

    A real-time ISEE data system directed toward predicting geomagnetic substorms and storms is discussed. Such a system may allow up to 60+ minutes advance warning of magnetospheric substorms and up to 30 minute warnings of geomagnetic storms (and other disturbances) induced by high-speed streams and solar flares. The proposed system utilizes existing capabilities of several agencies (NASA, NOAA, USAF), and thereby minimizes costs. This same concept may be applicable to data from other spacecraft, and other NASA centers; thus, each individual experimenter can receive quick-look data in real time at his or her base institution.

  18. A distributed agent architecture for real-time knowledge-based systems: Real-time expert systems project, phase 1

    Science.gov (United States)

    Lee, S. Daniel

    1990-01-01

    We propose a distributed agent architecture (DAA) that can support a variety of paradigms based on both traditional real-time computing and artificial intelligence. DAA consists of distributed agents that are classified into two categories: reactive and cognitive. Reactive agents can be implemented directly in Ada to meet hard real-time requirements and be deployed on on-board embedded processors. A traditional real-time computing methodology under consideration is the rate monotonic theory that can guarantee schedulability based on analytical methods. AI techniques under consideration for reactive agents are approximate or anytime reasoning that can be implemented using Bayesian belief networks as in Guardian. Cognitive agents are traditional expert systems that can be implemented in ART-Ada to meet soft real-time requirements. During the initial design of cognitive agents, it is critical to consider the migration path that would allow initial deployment on ground-based workstations with eventual deployment on on-board processors. ART-Ada technology enables this migration while Lisp-based technologies make it difficult if not impossible. In addition to reactive and cognitive agents, a meta-level agent would be needed to coordinate multiple agents and to provide meta-level control.

  19. A Process For Performance Evaluation Of Real-Time Systems

    Directory of Open Access Journals (Sweden)

    Andrew J. Kornecki

    2003-12-01

    Full Text Available Real-time developers and engineers must not only meet the system functional requirements, but also the stringent timing requirements. One of the critical decisions leading to meeting these timing requirements is the selection of an operating system under which the software will be developed and run. Although there is ample documentation on real-time systems performance and evaluation, little can be found that combines such information into an efficient process for use by developers. As the software industry moves towards clearly defined processes, creation of appropriate guidelines describing a process for performance evaluation of real-time system would greatly benefit real-time developers. This technology transition research focuses on developing such a process. PROPERT (PROcess for Performance Evaluation of Real Time systems - the process described in this paper - is based upon established techniques for evaluating real-time systems. It organizes already existing real-time performance criteria and assessment techniques in a manner consistent with a well-formed process, based on the Personal Software Process concepts.

  20. 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

  1. Real-time holographic endoscopy

    Science.gov (United States)

    Smigielski, Paul; Albe, Felix; Dischli, Bernard

    1992-08-01

    Some new experiments concerning holographic endoscopy are presented. The quantitative measurements of deformations of objects are obtained by the double-exposure and double- reference beam method, using either a cw-laser or a pulsed laser. Qualitative experiments using an argon laser with time-average holographic endoscopy are also presented. A video film on real-time endoscopic holographic interferometry was recorded with the help of a frequency-doubled YAG-laser working at 25 Hz for the first time.

  2. Real-time computational photon-counting LiDAR

    Science.gov (United States)

    Edgar, Matthew; Johnson, Steven; Phillips, David; Padgett, Miles

    2018-03-01

    The availability of compact, low-cost, and high-speed MEMS-based spatial light modulators has generated widespread interest in alternative sampling strategies for imaging systems utilizing single-pixel detectors. The development of compressed sensing schemes for real-time computational imaging may have promising commercial applications for high-performance detectors, where the availability of focal plane arrays is expensive or otherwise limited. We discuss the research and development of a prototype light detection and ranging (LiDAR) system via direct time of flight, which utilizes a single high-sensitivity photon-counting detector and fast-timing electronics to recover millimeter accuracy three-dimensional images in real time. The development of low-cost real time computational LiDAR systems could have importance for applications in security, defense, and autonomous vehicles.

  3. Real time magnetic resonance guided endomyocardial local delivery

    Science.gov (United States)

    Corti, R; Badimon, J; Mizsei, G; Macaluso, F; Lee, M; Licato, P; Viles-Gonzalez, J F; Fuster, V; Sherman, W

    2005-01-01

    Objective: To investigate the feasibility of targeting various areas of left ventricle myocardium under real time magnetic resonance (MR) imaging with a customised injection catheter equipped with a miniaturised coil. Design: A needle injection catheter with a mounted resonant solenoid circuit (coil) at its tip was designed and constructed. A 1.5 T MR scanner with customised real time sequence combined with in-room scan running capabilities was used. With this system, various myocardial areas within the left ventricle were targeted and injected with a gadolinium-diethylenetriaminepentaacetic acid (DTPA) and Indian ink mixture. Results: Real time sequencing at 10 frames/s allowed clear visualisation of the moving catheter and its transit through the aorta into the ventricle, as well as targeting of all ventricle wall segments without further image enhancement techniques. All injections were visualised by real time MR imaging and verified by gross pathology. Conclusion: The tracking device allowed real time in vivo visualisation of catheters in the aorta and left ventricle as well as precise targeting of myocardial areas. The use of this real time catheter tracking may enable precise and adequate delivery of agents for tissue regeneration. PMID:15710717

  4. Analytical characteristics and comparative evaluation of Aptima HCV quant Dx assay with the Abbott RealTime HCV assay and Roche COBAS AmpliPrep/COBAS TaqMan HCV quantitative test v2.0.

    Science.gov (United States)

    Worlock, A; Blair, D; Hunsicker, M; Le-Nguyen, T; Motta, C; Nguyen, C; Papachristou, E; Pham, J; Williams, A; Vi, M; Vinluan, B; Hatzakis, A

    2017-04-04

    The Aptima HCV Quant Dx assay (Aptima assay) is a fully automated quantitative assay on the Panther® system. This assay is intended for confirmation of diagnosis and monitoring of HCV RNA in plasma and serum specimens. The purpose of the testing described in this paper was to evaluate the performance of the Aptima assay. The analytical sensitivity, analytical specificity, precision, and linearity of the Aptima assay were assessed. The performance of the Aptima assay was compared to two commercially available HCV assays; the Abbott RealTime HCV assay (Abbott assay, Abbott Labs Illinois, USA) and the Roche COBAS Ampliprep/COBAS Taqman HCV Quantitative Test v2.0 (Roche Assay, Roche Molecular Systems, Pleasanton CA, USA). The 95% Lower Limit of Detection (LoD) of the assay was determined from dilutions of the 2nd HCV WHO International Standard (NIBSC 96/798 genotype 1) and HCV positive clinical specimens in HCV negative human plasma and serum. Probit analysis was performed to generate the 95% predicted detection limits. The Lower Limit of Quantitation (LLoQ) was established for each genotype by diluting clinical specimens and the 2nd HCV WHO International Standard (NIBSC 96/798 genotype 1) in HCV negative human plasma and serum. Specificity was determined using 200 fresh and 536 frozen HCV RNA negative clinical specimens including 370 plasma specimens and 366 serum specimens. Linearity for genotypes 1 to 6 was established by diluting armored RNA or HCV positive clinical specimens in HCV negative serum or plasma from 8.08 log IU/mL to below 1 log IU/mL. Precision was tested using a 10 member panel made by diluting HCV positive clinical specimens or spiking armored RNA into HCV negative plasma and serum. A method comparison was conducted against the Abbott assay using 1058 clinical specimens and against the Roche assay using 608 clinical specimens from HCV infected patients. In addition, agreement between the Roche assay and the Aptima assay using specimens with low

  5. Prototyping Real-Time Control in the SPS

    CERN Document Server

    Andersson, J; Jensen, L; Jones, R; Lamont, M; Wenninger, J; Wijnands, Thijs; CERN. Geneva. AB Department

    2003-01-01

    Real-time control of beam related parameters will be required in the LHC. In order to gain experience of the issues involved in implementing distributed real-time control over large distances, a prototype local orbit feedback system is being developed in the SPS. This will use 6 pickups, each equipped with the full LHC acquisition electronics chain and linked to a real-time communication and feedback system. This reports summarises the .rst tests performed with this system in October 2002, where the data from four pickups was successfully acquired and displayed at 10 Hz in the control room.

  6. Formal methods for dependable real-time systems

    Science.gov (United States)

    Rushby, John

    1993-01-01

    The motivation for using formal methods to specify and reason about real time properties is outlined and approaches that were proposed and used are sketched. The formal verifications of clock synchronization algorithms are concluded as showing that mechanically supported reasoning about complex real time behavior is feasible. However, there was significant increase in the effectiveness of verification systems since those verifications were performed, at it is to be expected that verifications of comparable difficulty will become fairly routine. The current challenge lies in developing perspicuous and economical approaches to the formalization and specification of real time properties.

  7. Real time detecting system for turning force

    Energy Technology Data Exchange (ETDEWEB)

    Xiaobin, Yue [China Academy of Engineering Physics, Mianyang (China). Inst. of Machinery Manufacturing Technology

    2001-07-01

    How to get the real-time value of forces dropped on the tool in the course of processing by piezoelectric sensors is introduced. First, the analog signals of the cutting force were achieved by these sensors, amplified and transferred into digital signals by A/D transferring card. Then real-time software reads the information, put it into its own coordinate, drew the curve of forces, displayed it on the screen by the real time and saved it for the technicians to analyze the situation of the tool. So the cutting parameter can be optimized to improve surface quality of the pieces.

  8. 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.

  9. Real-time systems scheduling 2 focuses

    CERN Document Server

    Chetto, Maryline

    2014-01-01

    Real-time systems are used in a wide range of applications, including control, sensing, multimedia, etc. Scheduling is a central problem for these computing/communication systems since it is responsible for software execution in a timely manner. This book, the second of two volumes on the subject, brings together knowledge on specific topics and discusses the recent advances for some of them.  It addresses foundations as well as the latest advances and findings in real-time scheduling, giving comprehensive references to important papers, but the chapters are short and not overloaded with co

  10. Real-time Avatar Animation from a Single Image.

    Science.gov (United States)

    Saragih, Jason M; Lucey, Simon; Cohn, Jeffrey F

    2011-01-01

    A real time facial puppetry system is presented. Compared with existing systems, the proposed method requires no special hardware, runs in real time (23 frames-per-second), and requires only a single image of the avatar and user. The user's facial expression is captured through a real-time 3D non-rigid tracking system. Expression transfer is achieved by combining a generic expression model with synthetically generated examples that better capture person specific characteristics. Performance of the system is evaluated on avatars of real people as well as masks and cartoon characters.

  11. An Analysis of Input/Output Paradigms for Real-Time Systems

    Science.gov (United States)

    1990-07-01

    timing and concurrency aspects of real - time systems . This paper illustrates how to build a mathematical model of the schedulability of a real-time...various design alternatives. The primary characteristic that distinguishes real-time system from non- real - time systems is the importance of time. The

  12. Spying on real-time computers to improve performance

    International Nuclear Information System (INIS)

    Taff, L.M.

    1975-01-01

    The sampled program-counter histogram, an established technique for shortening the execution times of programs, is described for a real-time computer. The use of a real-time clock allows particularly easy implementation. (Auth.)

  13. Genotyping of Hepatitis C virus isolated from hepatitis patients in Southeast of Iran by taqman realtime PCR

    International Nuclear Information System (INIS)

    Farivar, T.N.; Johari, P.

    2011-01-01

    Objectives: To check TaqMan Realtime PCR in detecting genotypes of hepatitis C virus in Iran. Methods: From July 2007 to April 2009, HCV genotyping was done on 52 patients who were referred to Research Centre for infectious Disease and Tropical Medicine, in Bou-Ali Hospital, Zahedan University of Medical Sciences. All these patients had proven hepatitis C infection. Results: Out of 52 anti HCV positive samples, 28(53.84%) had genotype 1, 2 cases (3.88 %) had genotype 2 , 12 (23.08 %) had genotype 3 and 7 (13.4 %) had genotype 4 . Mixed infection with genotypes 1 and 3 was seen in 3 cases (5.77 %). Conclusion: TaqMan probes for detecting genotyping of HCV were successful in picking genotyping of HCV infection especially those with mixed genotypes. (author)

  14. PERTS: A Prototyping Environment for Real-Time Systems

    Science.gov (United States)

    Liu, Jane W. S.; Lin, Kwei-Jay; Liu, C. L.

    1993-01-01

    PERTS is a prototyping environment for real-time systems. It is being built incrementally and will contain basic building blocks of operating systems for time-critical applications, tools, and performance models for the analysis, evaluation and measurement of real-time systems and a simulation/emulation environment. It is designed to support the use and evaluation of new design approaches, experimentations with alternative system building blocks, and the analysis and performance profiling of prototype real-time systems.

  15. Real-time multiple image manipulations

    International Nuclear Information System (INIS)

    Arenson, J.S.; Shalev, S.; Legris, J.; Goertzen, Y.

    1984-01-01

    There are many situations in which it is desired to manipulate two or more images under real-time operator control. The authors have investigated a number of such cases in order to determine their value and applicability in clinical medicine and laboratory research. Several examples are presented in detail. The DICOM-8 video image computer system was used due to its capability of storing two 512 x 512 x 8 bit images and operating on them, and/or an incoming video frame, with any of a number of real time operations including addition, subtraction, inversion, averaging, logical AND, NAND, OR, NOR, NOT, XOR and XNOR, as well as combinations of these. Some applications involve manipulations of or among the stored images. In others, a stored image is used as a mask or template for positioning or adjusting a second image to be grabbed via a video camera. The accuracy of radiotherapy treatment is verified by comparing port films with the original radiographic planning film, which is previously digitized and stored. Moving the port film on the light box while viewing the real-time subtraction image allows for adjustments of zoom, translation and rotation, together with contrast and edge enhancement

  16. Real-time position reconstruction with hippocampal place cells.

    Science.gov (United States)

    Guger, Christoph; Gener, Thomas; Pennartz, Cyriel M A; Brotons-Mas, Jorge R; Edlinger, Günter; Bermúdez I Badia, S; Verschure, Paul; Schaffelhofer, Stefan; Sanchez-Vives, Maria V

    2011-01-01

    Brain-computer interfaces (BCI) are using the electroencephalogram, the electrocorticogram and trains of action potentials as inputs to analyze brain activity for communication purposes and/or the control of external devices. Thus far it is not known whether a BCI system can be developed that utilizes the states of brain structures that are situated well below the cortical surface, such as the hippocampus. In order to address this question we used the activity of hippocampal place cells (PCs) to predict the position of an rodent in real-time. First, spike activity was recorded from the hippocampus during foraging and analyzed off-line to optimize the spike sorting and position reconstruction algorithm of rats. Then the spike activity was recorded and analyzed in real-time. The rat was running in a box of 80 cm × 80 cm and its locomotor movement was captured with a video tracking system. Data were acquired to calculate the rat's trajectories and to identify place fields. Then a Bayesian classifier was trained to predict the position of the rat given its neural activity. This information was used in subsequent trials to predict the rat's position in real-time. The real-time experiments were successfully performed and yielded an error between 12.2 and 17.4% using 5-6 neurons. It must be noted here that the encoding step was done with data recorded before the real-time experiment and comparable accuracies between off-line (mean error of 15.9% for three rats) and real-time experiments (mean error of 14.7%) were achieved. The experiment shows proof of principle that position reconstruction can be done in real-time, that PCs were stable and spike sorting was robust enough to generalize from the training run to the real-time reconstruction phase of the experiment. Real-time reconstruction may be used for a variety of purposes, including creating behavioral-neuronal feedback loops or for implementing neuroprosthetic control.

  17. The IPERMOB System for Effective Real-Time Road Travel Time Measurement and Prediction

    OpenAIRE

    Martelli, Francesca; Renda, Maria Elena; Santi, Paolo

    2010-01-01

    Accurate, real-time measurement and estimation of road travel time is considered a central problem in the design of advanced Intelligent Transportation Systems. In particular, whether eective, real-time collection of travel time measurements in a urban area is possible is, to the best of our knowledge, still an open problem. In this paper, we introduce the IPERMOB system for efficient, real-time collection of travel time measurements in urban areas through vehicular networks. We demonstrate t...

  18. Games and Scenarios for Real-Time System Validation

    DEFF Research Database (Denmark)

    Li, Shuhao

    This thesis presents research on the validation of real-time embedded software systems in the context of model-based development. The thesis proposes scenario-based and game-theoretic approaches to system analysis, verification, synthesis and testing to address the challenges that arise from....... By linking our prototype translators with existing model checker Uppaal and game solver Uppaal-Tiga, we show that these methods contribute to the interaction correctness and timeliness of early system designs. The thesis also shows that testing a real-time reactive system can be viewed as playing a timed...... communicating real-time systems can be modeled and specified with LSC. By translating LSC to timed automata (TAs), we reduce scenario-based model consistency checking and property verification to CTL real-time model checking problems, and reduce scenario-based synthesis to a timed game solving problem...

  19. Real time refractive index measurement by ESPI

    International Nuclear Information System (INIS)

    Torroba, R.; Joenathan, C.

    1991-01-01

    In this paper a method to measure refractive index variations in real time is reported. A technique to introduce reference fringes in real time is discussed. Both the theoretical and experimental results are presented and an example with phase shifting is given. (author). 8 refs, 5 figs

  20. The Synthesis of Intelligent Real-Time Systems

    Science.gov (United States)

    1990-11-09

    Synthesis of Intelligent Real - Time Systems . The purpose of the effort was to develop and extend theories and techniques that facilitate the design and...implementation of intelligent real - time systems . In particular, Teleos has extended situated-automata theory to apply to situations in which the system has

  1. Real-time software for the COMPASS tokamak plasma control

    International Nuclear Information System (INIS)

    Valcarcel, D.F.; Duarte, A.S.; Neto, A.; Carvalho, I.S.; Carvalho, B.B.; Fernandes, H.; Sousa, J.; Sartori, F.; Janky, F.; Cahyna, P.; Hron, M.; Panek, R.

    2010-01-01

    The COMPASS tokamak has started its operation recently in Prague and to meet the necessary operation parameters its real-time system, for data processing and control, must be designed for both flexibility and performance, allowing the easy integration of code from several developers and to guarantee the desired time cycle. For this purpose an Advanced Telecommunications Computing Architecture based real-time system has been deployed with a solution built on a multi-core x86 processor. It makes use of two software components: the BaseLib2 and the MARTe (Multithreaded Application Real-Time executor) real-time frameworks. The BaseLib2 framework is a generic real-time library with optimized objects for the implementation of real-time algorithms. This allowed to build a library of modules that process the acquired data and execute control algorithms. MARTe executes these modules in kernel space Real-Time Application Interface allowing to attain the required cycle time and a jitter of less than 1.5 μs. MARTe configuration and data storage are accomplished through a Java hardware client that connects to the FireSignal control and data acquisition software. This article details the implementation of the real-time system for the COMPASS tokamak, in particular the organization of the control code, the design and implementation of the communications with the actuators and how MARTe integrates with the FireSignal software.

  2. Real-time software for the COMPASS tokamak plasma control

    Energy Technology Data Exchange (ETDEWEB)

    Valcarcel, D.F., E-mail: danielv@ipfn.ist.utl.p [Associacao EURATOM/IST, Instituto de Plasmas e Fusao Nuclear - Laboratorio Associado, Instituto Superior Tecnico, P-1049-001 Lisboa (Portugal); Duarte, A.S.; Neto, A.; Carvalho, I.S.; Carvalho, B.B.; Fernandes, H.; Sousa, J. [Associacao EURATOM/IST, Instituto de Plasmas e Fusao Nuclear - Laboratorio Associado, Instituto Superior Tecnico, P-1049-001 Lisboa (Portugal); Sartori, F. [Euratom-UKAEA, Culham Science Centre, Abingdon, OX14 3DB Oxon (United Kingdom); Janky, F.; Cahyna, P.; Hron, M.; Panek, R. [Institute of Plasma Physics AS CR, v.v.i., Association EURATOM/IPP.CR, Za Slovankou 3, 182 00 Prague (Czech Republic)

    2010-07-15

    The COMPASS tokamak has started its operation recently in Prague and to meet the necessary operation parameters its real-time system, for data processing and control, must be designed for both flexibility and performance, allowing the easy integration of code from several developers and to guarantee the desired time cycle. For this purpose an Advanced Telecommunications Computing Architecture based real-time system has been deployed with a solution built on a multi-core x86 processor. It makes use of two software components: the BaseLib2 and the MARTe (Multithreaded Application Real-Time executor) real-time frameworks. The BaseLib2 framework is a generic real-time library with optimized objects for the implementation of real-time algorithms. This allowed to build a library of modules that process the acquired data and execute control algorithms. MARTe executes these modules in kernel space Real-Time Application Interface allowing to attain the required cycle time and a jitter of less than 1.5 {mu}s. MARTe configuration and data storage are accomplished through a Java hardware client that connects to the FireSignal control and data acquisition software. This article details the implementation of the real-time system for the COMPASS tokamak, in particular the organization of the control code, the design and implementation of the communications with the actuators and how MARTe integrates with the FireSignal software.

  3. Real-Time Optimization and Control of Next-Generation Distribution

    Science.gov (United States)

    -Generation Distribution Infrastructure Real-Time Optimization and Control of Next-Generation Distribution developing a system-theoretic distribution network management framework that unifies real-time voltage and Infrastructure | Grid Modernization | NREL Real-Time Optimization and Control of Next

  4. Real time psychrometric data collection

    International Nuclear Information System (INIS)

    McDaniel, K.H.

    1996-01-01

    Eight Mine Weather Stations (MWS) installed at the Waste Isolation Pilot Plant (WIPP) to monitor the underground ventilation system are helping to simulate real-time ventilation scenarios. Seasonal weather extremes can result in variations of Natural Ventilation Pressure (NVP) which can significantly effect the ventilation system. The eight MWS(s) (which previously collected and stored temperature, barometric pressure and relative humidity data for subsequent NVP calculations) were upgraded to provide continuous real-time data to the site wide Central monitoring System. This data can now be utilized by the ventilation engineer to create realtime ventilation simulations and trends which assist in the prediction and mitigation of NVP and psychrometric related events

  5. Accumulated lipids rather than the rigid cell walls impede the extraction of genetic materials for effective colony PCRs in Chlorella vulgaris

    Science.gov (United States)

    2013-01-01

    Background Failure of colony PCRs in green microalga Chlorella vulgaris is typically attributed to the difficulty in disrupting its notoriously rigid cell walls for releasing the genetic materials and therefore the development of an effective colony PCR procedure in C. vulgaris presents a challenge. Results Here we identified that colony PCR results were significantly affected by the accumulated lipids rather than the rigid cell walls of C. vulgaris. The higher lipids accumulated in C. vulgaris negatively affects the effective amplification by DNA polymerase. Based on these findings, we established a simple and extremely effective colony PCR procedure in C. vulgaris. By simply pipetting/votexing the pellets of C. vulgaris in 10 ul of either TE (10 mM Tris/1 mM EDTA) or 0.2% SDS buffer at room temperature, followed by the addition of 10 ul of either hexane or Phenol:Chloroform:Isoamyl Alcohol in the same PCR tube for extraction. The resulting aqueous phase was readily PCR-amplified as genomic DNA templates as demonstrated by successful amplification of the nuclear 18S rRNA and the chloroplast rbcL gene. This colony PCR protocol is effective and robust in C. vulgaris and also demonstrates its effectiveness in other Chlorella species. Conclusions The accumulated lipids rather than the rigid cell walls of C. vulgaris significantly impede the extraction of genetic materials and subsequently the effective colony PCRs. The finding has the potential to aid the isolation of high-quality total RNAs and mRNAs for transcriptomic studies in addition to the genomic DNA isolation in Chlorella. PMID:24219401

  6. 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.

  7. Real-time reactor coolant system pressure/temperature limit system

    International Nuclear Information System (INIS)

    Newton, D.G.; Schemmel, R.R.; Van Scooter, W.E. Jr.

    1991-01-01

    This patent describes an system, used in controlling the operating of a nuclear reactor coolant system, which automatically calculates and displays allowable reactor coolant system pressure/temperature limits within the nuclear reactor coolant system based upon real-time inputs. It comprises: means for producing signals representative of real-time operating parameters of the nuclear reactor cooling system; means for developing pressure and temperature limits relating the real-time operating parameters of the nuclear reactor coolant system, for normal and emergency operation thereof; means for processing the signals representative of real-time operating parameters of the nuclear reactor coolant system to perform calculations of a best estimate of signals, check manual inputs against permissible valves and test data acquisition hardware for validity and over/under range; and means for comparing the representative signals with limits for the real-time operating parameters to produce a signal for a real-time display of the pressure and temperature limits and of the real-time operating parameters use an operator in controlling the operation of the nuclear reactor coolant system

  8. Route around real time

    International Nuclear Information System (INIS)

    Terrier, Francois

    1996-01-01

    The greater and greater autonomy and complexity asked to the control and command systems lead to work on introducing techniques such as Artificial Intelligence or concurrent object programming in industrial applications. However, while the critical feature of these systems impose to control the dynamics of the proposed solutions, their complexity often imposes a high adaptability to a partially modelled environment. The studies presented start from low level control and command systems to more complex applications at higher levels, such as 'supervision systems'. Techniques such as temporal reasoning and uncertainty management are proposed for the first studies, while the second are tackled with programming techniques based on the real time object paradigm. The outcomes of this itinerary crystallize on the ACCORD project which targets to manage - on the whole life cycle of a real time application - these two problematics, sometimes antagonistic: control of the dynamics and adaptivity. (author) [fr

  9. Recent achievements in real-time computational seismology in Taiwan

    Science.gov (United States)

    Lee, S.; Liang, W.; Huang, B.

    2012-12-01

    Real-time computational seismology is currently possible to be achieved which needs highly connection between seismic database and high performance computing. We have developed a real-time moment tensor monitoring system (RMT) by using continuous BATS records and moment tensor inversion (CMT) technique. The real-time online earthquake simulation service is also ready to open for researchers and public earthquake science education (ROS). Combine RMT with ROS, the earthquake report based on computational seismology can provide within 5 minutes after an earthquake occurred (RMT obtains point source information ROS completes a 3D simulation real-time now. For more information, welcome to visit real-time computational seismology earthquake report webpage (RCS).

  10. A Real-Time PCR Assay Based on 5.8S rRNA Gene (5.8S rDNA) for Rapid Detection of Candida from Whole Blood Samples.

    Science.gov (United States)

    Guo, Yi; Yang, Jing-Xian; Liang, Guo-Wei

    2016-06-01

    The prevalence of Candida in bloodstream infections (BSIs) has increased. To date, the identification of Candida in BSIs still mainly relies on blood culture and serological tests, but they have various limitations. Therefore, a real-time PCR assay for the detection of Candida from whole blood is presented. The unique primers/probe system was designed on 5.8S rRNA gene (5.8S rDNA) of Candida genus. The analytical sensitivity was determined by numbers of positive PCRs in 12 repetitions. At the concentration of 10(1) CFU/ml blood, positive PCR rates of 100 % were obtained for C. albicans, C. parapsilosis, C. tropicalis, and C. krusei. The detection rate for C. glabrata was 75 % at 10(1) CFU/ml blood. The reaction specificity was 100 % when evaluating the assay using DNA samples from clinical isolates and human blood. The maximum CVs of intra-assay and inter-assay for the detection limit were 1.22 and 2.22 %, respectively. To assess the clinical applicability, 328 blood samples from 82 patients were prospectively tested and real-time PCR results were compared with results from blood culture. Diagnostic sensitivity of the PCR was 100 % using as gold standard blood culture, and specificity was 98.4 %. Our data suggest that the developed assay can be used in clinical laboratories as an accurate and rapid screening test for the Candida from whole blood. Although further evaluation is warranted, our assay holds promise for earlier diagnosis of candidemia.

  11. Method evaluation of Fusarium DNA extraction from mycelia and wheat for down-stream real-time PCR quantification and correlation to mycotoxin levels.

    Science.gov (United States)

    Fredlund, Elisabeth; Gidlund, Ann; Olsen, Monica; Börjesson, Thomas; Spliid, Niels Henrik Hytte; Simonsson, Magnus

    2008-04-01

    Identification of Fusarium species by traditional methods requires specific skill and experience and there is an increased interest for new molecular methods for identification and quantification of Fusarium from food and feed samples. Real-time PCR with probe technology (Taqman) can be used for the identification and quantification of several species of Fusarium from cereal grain samples. There are several critical steps that need to be considered when establishing a real-time PCR-based method for DNA quantification, including extraction of DNA from the samples. In this study, several DNA extraction methods were evaluated, including the DNeasy Plant Mini Spin Columns (Qiagen), the Bio robot EZ1 (Qiagen) with the DNeasy Blood and Tissue Kit (Qiagen), and the Fast-DNA Spin Kit for Soil (Qbiogene). Parameters such as DNA quality and stability, PCR inhibitors, and PCR efficiency were investigated. Our results showed that all methods gave good PCR efficiency (above 90%) and DNA stability whereas the DNeasy Plant Mini Spin Columns in combination with sonication gave the best results with respect to Fusarium DNA yield. The modified DNeasy Plant Mini Spin protocol was used to analyse 31 wheat samples for the presence of F. graminearum and F. culmorum. The DNA level of F. graminearum could be correlated to the level of DON (r(2) = 0.9) and ZEN (r(2) = 0.6) whereas no correlation was found between F. culmorum and DON/ZEA. This shows that F. graminearum and not F. culmorum, was the main producer of DON in Swedish wheat during 2006.

  12. Proceedings of the Real-Time Systems Engineering Workshop

    Science.gov (United States)

    2001-08-01

    real - time systems engineering. The workshop was held as part of the SEI Symposium in...Washington, DC, during September 2000. The objective of the workshop was to identify key issues and obtain feedback from attendees concerning real - time systems engineering...and interoperability. This report summarizes the workshop in terms of foundation, management, and technical topics, and it contains a discussion related to developing a community of interest for real - time systems

  13. Validation of RNAi by real time PCR

    DEFF Research Database (Denmark)

    Josefsen, Knud; Lee, Ying Chiu

    2011-01-01

    Real time PCR is the analytic tool of choice for quantification of gene expression, while RNAi is concerned with downregulation of gene expression. Together, they constitute a powerful approach in any loss of function studies of selective genes. We illustrate here the use of real time PCR to verify...

  14. Evaluation of a TaqMan Array Card for Detection of Central Nervous System Infections.

    Science.gov (United States)

    Onyango, Clayton O; Loparev, Vladimir; Lidechi, Shirley; Bhullar, Vinod; Schmid, D Scott; Radford, Kay; Lo, Michael K; Rota, Paul; Johnson, Barbara W; Munoz, Jorge; Oneko, Martina; Burton, Deron; Black, Carolyn M; Neatherlin, John; Montgomery, Joel M; Fields, Barry

    2017-07-01

    Infections of the central nervous system (CNS) are often acute, with significant morbidity and mortality. Routine diagnosis of such infections is limited in developing countries and requires modern equipment in advanced laboratories that may be unavailable to a number of patients in sub-Saharan Africa. We developed a TaqMan array card (TAC) that detects multiple pathogens simultaneously from cerebrospinal fluid. The 21-pathogen CNS multiple-pathogen TAC (CNS-TAC) assay includes two parasites ( Balamuthia mandrillaris and Acanthamoeba ), six bacterial pathogens ( Streptococcus pneumonia e, Haemophilus influenzae , Neisseria meningitidis , Mycoplasma pneumoniae , Mycobacterium tuberculosis , and Bartonella ), and 13 viruses (parechovirus, dengue virus, Nipah virus, varicella-zoster virus, mumps virus, measles virus, lyssavirus, herpes simplex viruses 1 and 2, Epstein-Barr virus, enterovirus, cytomegalovirus, and chikungunya virus). The card also includes human RNase P as a nucleic acid extraction control and an internal manufacturer control, GAPDH (glyceraldehyde-3-phosphate dehydrogenase). This CNS-TAC assay can test up to eight samples for all 21 agents within 2.5 h following nucleic acid extraction. The assay was validated for linearity, limit of detection, sensitivity, and specificity by using either live viruses (dengue, mumps, and measles viruses) or nucleic acid material (Nipah and chikungunya viruses). Of 120 samples tested by individual real-time PCR, 35 were positive for eight different targets, whereas the CNS-TAC assay detected 37 positive samples across nine different targets. The CNS-TAC assays showed 85.6% sensitivity and 96.7% specificity. Therefore, the CNS-TAC assay may be useful for outbreak investigation and surveillance of suspected neurological disease. Copyright © 2017 American Society for Microbiology.

  15. Performance evaluation of the new Roche cobas AmpliPrep/cobas TaqMan HCV test, version 2.0, for detection and quantification of hepatitis C virus RNA

    NARCIS (Netherlands)

    S.D. Pas (Suzan); R. Molenkamp (Richard); J. Schinkel (Janke); S. Rebers; C. Copra (Cederick); S. Seven-Deniz; D. Thamke (Diana); R.J. de Knegt (Robert); B.L. Haagmans (Bart); M. Schutten (Martin)

    2013-01-01

    textabstractTo evaluate the analytical performance and explore the clinical applicability of the new Roche cobas AmpliPrep/cobas TaqMan HCV test, v2.0 (CAP/CTM v2.0), a platform comparison was performed on panels and diagnostic samples with the Roche cobas AmpliPrep/cobas TaqMan HCV test (CAP/CTM

  16. SignalR real time application development

    CERN Document Server

    Ingebrigtsen, Einar

    2013-01-01

    This step-by-step guide gives you practical advice, tips, and tricks that will have you writing real-time apps quickly and easily.If you are a .NET developer who wants to be at the cutting edge of development, then this book is for you. Real-time application development is made simple in this guide, so as long as you have basic knowledge of .NET, a copy of Visual Studio, and NuGet installed, you are ready to go.

  17. 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)

  18. Limited Preemptive Scheduling in Real-time Systems

    OpenAIRE

    Thekkilakattil, Abhilash

    2016-01-01

    Preemptive and non-preemptive scheduling paradigms typically introduce undesirable side effects when scheduling real-time tasks, mainly in the form of preemption overheads and blocking, that potentially compromise timeliness guarantees. The high preemption overheads in preemptive real-time scheduling may imply high resource utilization, often requiring significant over-provisioning, e.g., pessimistic Worst Case Execution Time (WCET) approximations. Non-preemptive scheduling, on the other hand...

  19. 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

  20. Coordinating Transit Transfers in Real Time

    Science.gov (United States)

    2016-05-06

    Transfers are a major source of travel time variability for transit passengers. Coordinating transfers between transit routes in real time can reduce passenger waiting times and travel time variability, but these benefits need to be contrasted with t...

  1. Timing organization of a real-time multicore processor

    DEFF Research Database (Denmark)

    Schoeberl, Martin; Sparsø, Jens

    2017-01-01

    Real-time systems need a time-predictable computing platform. Computation, communication, and access to shared resources needs to be time-predictable. We use time division multiplexing to statically schedule all computation and communication resources, such as access to main memory or message...... passing over a network-on-chip. We use time-driven communication over an asynchronous network-on-chip to enable time division multiplexing even in a globally asynchronous, locally synchronous multicore architecture. Using time division multiplexing at all levels of the architecture yields in a time...

  2. Real-time logo detection and tracking in video

    Science.gov (United States)

    George, M.; Kehtarnavaz, N.; Rahman, M.; Carlsohn, M.

    2010-05-01

    This paper presents a real-time implementation of a logo detection and tracking algorithm in video. The motivation of this work stems from applications on smart phones that require the detection of logos in real-time. For example, one application involves detecting company logos so that customers can easily get special offers in real-time. This algorithm uses a hybrid approach by initially running the Scale Invariant Feature Transform (SIFT) algorithm on the first frame in order to obtain the logo location and then by using an online calibration of color within the SIFT detected area in order to detect and track the logo in subsequent frames in a time efficient manner. The results obtained indicate that this hybrid approach allows robust logo detection and tracking to be achieved in real-time.

  3. A reliable information management for real-time systems

    International Nuclear Information System (INIS)

    Nishihara, Takuo; Tomita, Seiji

    1995-01-01

    In this paper, we propose a system configuration suitable for the hard realtime systems in which integrity and durability of information are important. On most hard real-time systems, where response time constraints are critical, the data which program access are volatile, and may be lost in case the systems are down. But for some real-time systems, the value-added intelligent network (IN) systems, e.g., integrity and durability of the stored data are very important. We propose a distributed system configuration for such hard real-time systems, comprised of service control modules and data management modules. The service control modules process transactions and responses based on deadline control, and the data management modules deal the stored data based on information recovery schemes well-restablished in fault real-time systems. (author)

  4. The Implementation of a Real-Time Polyphase Filter

    OpenAIRE

    Adámek, Karel; Novotný, Jan; Armour, Wes

    2014-01-01

    In this article we study the suitability of dierent computational accelerators for the task of real-time data processing. The algorithm used for comparison is the polyphase filter, a standard tool in signal processing and a well established algorithm. We measure performance in FLOPs and execution time, which is a critical factor for real-time systems. For our real-time studies we have chosen a data rate of 6.5GB/s, which is the estimated data rate for a single channel on the SKAs Low Frequenc...

  5. Improving Timeliness in Real-Time Secure Database Systems

    National Research Council Canada - National Science Library

    Son, Sang H; David, Rasikan; Thuraisingham, Bhavani

    2006-01-01

    .... In addition to real-time requirements, security is usually required in many applications. Multilevel security requirements introduce a new dimension to transaction processing in real-time database systems...

  6. Model-Checking Real-Time Control Programs

    DEFF Research Database (Denmark)

    Iversen, T. K.; Kristoffersen, K. J.; Larsen, Kim Guldstrand

    2000-01-01

    In this paper, we present a method for automatic verification of real-time control programs running on LEGO(R) RCX(TM) bricks using the verification tool UPPALL. The control programs, consisting of a number of tasks running concurrently, are automatically translated into the mixed automata model...... of UPPAAL. The fixed scheduling algorithm used by the LEGO(R) RCX(TM) processor is modeled in UPPALL, and supply of similar (sufficient) timed automata models for the environment allows analysis of the overall real-time system using the tools of UPPALL. To illustrate our technique for sorting LEGO(R) bricks...

  7. Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS)

    Science.gov (United States)

    Daniels, M. D.; Graves, S. J.; Vernon, F.; Kerkez, B.; Chandra, C. V.; Keiser, K.; Martin, C.

    2014-12-01

    Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS) Access, utilization and management of real-time data continue to be challenging for decision makers, as well as researchers in several scientific fields. This presentation will highlight infrastructure aimed at addressing some of the gaps in handling real-time data, particularly in increasing accessibility of these data to the scientific community through cloud services. The Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS) system addresses the ever-increasing importance of real-time scientific data, particularly in mission critical scenarios, where informed decisions must be made rapidly. Advances in the distribution of real-time data are leading many new transient phenomena in space-time to be observed, however real-time decision-making is infeasible in many cases that require streaming scientific data as these data are locked down and sent only to proprietary in-house tools or displays. This lack of accessibility to the broader scientific community prohibits algorithm development and workflows initiated by these data streams. As part of NSF's EarthCube initiative, CHORDS proposes to make real-time data available to the academic community via cloud services. The CHORDS infrastructure will enhance the role of real-time data within the geosciences, specifically expanding the potential of streaming data sources in enabling adaptive experimentation and real-time hypothesis testing. Adherence to community data and metadata standards will promote the integration of CHORDS real-time data with existing standards-compliant analysis, visualization and modeling tools.

  8. Time-critical multirate scheduling using contemporary real-time operating system services

    Science.gov (United States)

    Eckhardt, D. E., Jr.

    1983-01-01

    Although real-time operating systems provide many of the task control services necessary to process time-critical applications (i.e., applications with fixed, invariant deadlines), it may still be necessary to provide a scheduling algorithm at a level above the operating system in order to coordinate a set of synchronized, time-critical tasks executing at different cyclic rates. The scheduling requirements for such applications and develops scheduling algorithms using services provided by contemporary real-time operating systems.

  9. Development of duplex real-time PCR for the detection of WSSV and PstDV1 in cultivated shrimp.

    Science.gov (United States)

    Leal, Carlos A G; Carvalho, Alex F; Leite, Rômulo C; Figueiredo, Henrique C P

    2014-07-05

    The White spot syndrome virus (WSSV) and Penaeus stylirostris penstyldensovirus 1 (previously named Infectious hypodermal and hematopoietic necrosis virus-IHHNV) are two of the most important viral pathogens of penaeid shrimp. Different methods have been applied for diagnosis of these viruses, including Real-time PCR (qPCR) assays. A duplex qPCR method allows the simultaneous detection of two viruses in the same sample, which is more cost-effective than assaying for each virus separately. Currently, an assay for the simultaneous detection of the WSSV and the PstDV1 in shrimp is unavailable. The aim of this study was to develop and standardize a duplex qPCR assay for the simultaneous detection of the WSSV and the PstDV1 in clinical samples of diseased L. vannamei. In addition, to evaluate the performance of two qPCR master mixes with regard to the clinical sensitivity of the qPCR assay, as well as, different methods for qPCR results evaluation. The duplex qPCR assay for detecting WSSV and PstDV1 in clinical samples was successfully standardized. No difference in the amplification of the standard curves was observed between the duplex and singleplex assays. Specificities and sensitivities similar to those of the singleplex assays were obtained using the optimized duplex qPCR. The analytical sensitivities of duplex qPCR were two copies of WSSV control plasmid and 20 copies of PstDV1 control plasmid. The standardized duplex qPCR confirmed the presence of viral DNA in 28 from 43 samples tested. There was no difference for WSSV detection using the two kits and the distinct methods for qPCR results evaluation. High clinical sensitivity for PstDV1 was obtained with TaqMan Universal Master Mix associated with relative threshold evaluation. Three cases of simultaneous infection by the WSSV and the PstDV1 were identified with duplex qPCR. The standardized duplex qPCR was shown to be a robust, highly sensitive, and feasible diagnostic tool for the simultaneous detection of the

  10. 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.

  11. Real-time sonography in obstetrics.

    Science.gov (United States)

    Anderson, S G

    1978-03-01

    Three hundred fifty real-time scans were performed on pregnant women for various indications. Placental localization was satisfactorily obtained in 173 of 174 studies. Estimates of fetal gestation from directly measured biparietal diameter were +/-2 weeks of actual gestation in 153 of 172 (88.9%) measurements. The presence or absence of fetal motion and cardiac activity established a diagnosis of fetal viability or fetal death in 32 patients after the first trimester. Accurate diagnosis was made in 52 of 57 patients with threatened abortions, and two of these errors occurred in scans performed before completion of the eighth postmenstrual week. Because of the ability to demonstrate fetal motion, real-time sonography should have many applications in obstetrics.

  12. Real-time ISEE data system

    International Nuclear Information System (INIS)

    Tsurutani, B.T.; Baker, D.N.

    1979-01-01

    Prediction of geomagnetic substorms and storms would be of great scientific and commercial interest. A real-time ISEE data system directed toward this purpose is discussed in detail. Such a system may allow up to 60+ minutes advance warning of magnetospheric substorms and up to 30 minute warnings of geomagnetic storms (and other disturbances) induced by high-speed streams and solar flares. The proposed system utilizes existing capabilities of several agencies (NASA, NOAA, USAF), and thereby minimizes costs. This same concept may be applicable to data from other spacecraft, and other NASA centers; thus, each individual experimenter can receive quick-look data in real time at his or her base institution. 6 figures, 1 table

  13. Automated Real-Time Clearance Analyzer (ARCA), Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The Automated Real-Time Clearance Analyzer (ARCA) addresses the future safety need for Real-Time System-Wide Safety Assurance (RSSA) in aviation and progressively...

  14. Real-time interactive treatment planning

    International Nuclear Information System (INIS)

    Otto, Karl

    2014-01-01

    The goal of this work is to develop an interactive treatment planning platform that permits real-time manipulation of dose distributions including DVHs and other dose metrics. The hypothesis underlying the approach proposed here is that the process of evaluating potential dose distribution options and deciding on the best clinical trade-offs may be separated from the derivation of the actual delivery parameters used for the patient’s treatment. For this purpose a novel algorithm for deriving an Achievable Dose Estimate (ADE) was developed. The ADE algorithm is computationally efficient so as to update dose distributions in effectively real-time while accurately incorporating the limits of what can be achieved in practice. The resulting system is a software environment for interactive real-time manipulation of dose that permits the clinician to rapidly develop a fully customized 3D dose distribution. Graphical navigation of dose distributions is achieved by a sophisticated method of identifying contributing fluence elements, modifying those elements and re-computing the entire dose distribution. 3D dose distributions are calculated in ∼2–20 ms. Including graphics processing overhead, clinicians may visually interact with the dose distribution (e.g. ‘drag’ a DVH) and display updates of the dose distribution at a rate of more than 20 times per second. Preliminary testing on various sites shows that interactive planning may be completed in ∼1–5 min, depending on the complexity of the case (number of targets and OARs). Final DVHs are derived through a separate plan optimization step using a conventional VMAT planning system and were shown to be achievable within 2% and 4% in high and low dose regions respectively. With real-time interactive planning trade-offs between Target(s) and OARs may be evaluated efficiently providing a better understanding of the dosimetric options available to each patient in static or adaptive RT. (paper)

  15. Real-time statistical quality control and ARM

    International Nuclear Information System (INIS)

    Blough, D.K.

    1992-05-01

    An important component of the Atmospheric Radiation Measurement (ARM) Program is real-time quality control of data obtained from meteorological instruments. It is the goal of the ARM program to enhance the predictive capabilities of global circulation models by incorporating in them more detailed information on the radiative characteristics of the earth's atmosphere. To this end, a number of Cloud and Radiation Testbeds (CART's) will be built at various locations worldwide. Each CART will consist of an array of instruments designed to collect radiative data. The large amount of data obtained from these instruments necessitates real-time processing in order to flag outliers and possible instrument malfunction. The Bayesian dynamic linear model (DLM) proves to be an effective way of monitoring the time series data which each instrument generates. It provides a flexible yet powerful approach to detecting in real-time sudden shifts in a non-stationary multivariate time series. An application of these techniques to data arising from a remote sensing instrument to be used in the CART is provided. Using real data from a wind profiler, the ability of the DLM to detect outliers is studied. 5 refs

  16. Explaining How to Play Real-Time Strategy Games

    Science.gov (United States)

    Metoyer, Ronald; Stumpf, Simone; Neumann, Christoph; Dodge, Jonathan; Cao, Jill; Schnabel, Aaron

    Real-time strategy games share many aspects with real situations in domains such as battle planning, air traffic control, and emergency response team management which makes them appealing test-beds for Artificial Intelligence (AI) and machine learning. End user annotations could help to provide supplemental information for learning algorithms, especially when training data is sparse. This paper presents a formative study to uncover how experienced users explain game play in real-time strategy games. We report the results of our analysis of explanations and discuss their characteristics that could support the design of systems for use by experienced real-time strategy game users in specifying or annotating strategy-oriented behavior.

  17. Correspondence between imaginary-time and real-time finite-temperature field theory

    International Nuclear Information System (INIS)

    Kobes, R.

    1990-01-01

    It is known that one-particle-irreducible graphs found using the imaginary-time formalism of finite-temperature field theory differ in general with those of the real-time formalism. Here it is shown that within the real-time formalism one can consider a sum of graphs, motivated by causality arguments, which at least in a number of simple examples agree with the corresponding analytically continued imaginary-time result. The occurrence of multiple statistical factors in this sum of graphs is discussed

  18. Refactoring Real-Time Java Profiles

    DEFF Research Database (Denmark)

    Søndergaard, Hans; Thomsen, Bent; Ravn, Anders Peter

    2011-01-01

    Just like other software, Java profiles benefits from refactoring when they have been used and have evolved for some time. This paper presents a refactoring of the Real-Time Specification for Java (RTSJ) and the Safety Critical Java (SCJ) profile (JSR-302). It highlights core concepts and makes...

  19. Criticality: static profiling for real-time programs

    DEFF Research Database (Denmark)

    Brandner, Florian; Hepp, Stefan; Jordan, Alexander

    2014-01-01

    With the increasing performance demand in real-time systems it becomes more and more important to provide feedback to programmers and software development tools on the performance-relevant code parts of a real-time program. So far, this information was limited to an estimation of the worst....... Experiments using well-established real-time benchmark programs show an interesting distribution of the criticality values, revealing considerable amounts of highly critical as well as uncritical code. The metric thus provides ideal information to programmers and software development tools to optimize...... view covering the entire code base, tools in the spirit of program profiling are required. This work proposes an efficient approach to compute worst-case timing information for all code parts of a program using a complementary metric, called criticality. Every statement of a program is assigned...

  20. Compilation and synthesis for real-time embedded controllers

    DEFF Research Database (Denmark)

    Fränzle, Martin; Müller-Olm, Markus

    1999-01-01

    This article provides an overview over two constructive approaches to provably correct hard real-time code generation where hard real-time code is generated from abstract requirements rather than verified against the timing requirements a posteriori. The first, more pragmatic approach is concerne......-time systems at a very high level of abstraction....

  1. Real-time advanced nuclear reactor core model

    International Nuclear Information System (INIS)

    Koclas, J.; Friedman, F.; Paquette, C.; Vivier, P.

    1990-01-01

    The paper describes a multi-nodal advanced nuclear reactor core model. The model is based on application of modern equivalence theory to the solution of neutron diffusion equation in real time employing the finite differences method. The use of equivalence theory allows the application of the finite differences method to cores divided into hundreds of nodes, as opposed to the much finer divisions (in the order of ten thousands of nodes) where the unmodified method is currently applied. As a result the model can be used for modelling of the core kinetics for real time full scope training simulators. Results of benchmarks, validate the basic assumptions of the model and its applicability to real-time simulation. (orig./HP)

  2. Hardware locks for a real-time Java chip multiprocessor

    DEFF Research Database (Denmark)

    Strøm, Torur Biskopstø; Puffitsch, Wolfgang; Schoeberl, Martin

    2016-01-01

    A software locking mechanism commonly protects shared resources for multithreaded applications. This mechanism can, especially in chip-multiprocessor systems, result in a large synchronization overhead. For real-time systems in particular, this overhead increases the worst-case execution time....... This improvement can allow a larger number of real-time tasks to be reliably scheduled on a multiprocessor real-time platform....

  3. Hard Real-Time Linux for Off-The-Shelf Multicore Architectures

    OpenAIRE

    Radder, Dirk

    2015-01-01

    This document describes the research results that were obtained from the development of a real-time extension for the Linux operating system. The paper describes a full extension of the kernel, which enables hard real-time performance on a 64-bit x86 architecture. In the first part of this study, real-time systems are categorized and concepts of real-time operating systems are introduced to the reader. In addition, numerous well-known real-time operating systems are considered. QNX Neutrino, ...

  4. Processor tradeoffs in distributed real-time systems

    Science.gov (United States)

    Krishna, C. M.; Shin, Kang G.; Bhandari, Inderpal S.

    1987-01-01

    The problem of the optimization of the design of real-time distributed systems is examined with reference to a class of computer architectures similar to the continuously reconfigurable multiprocessor flight control system structure, CM2FCS. Particular attention is given to the impact of processor replacement and the burn-in time on the probability of dynamic failure and mean cost. The solution is obtained numerically and interpreted in the context of real-time applications.

  5. Developments in architecture for real-time data systems

    International Nuclear Information System (INIS)

    Heath, R.L.; Myers, W.R.

    1975-01-01

    Real-time data systems typically operate at two levels: a fast-response instrument-oriented level for data acquisition and control, and a slow human-oriented level for interaction and computation. Traditional minicomputer data systems support real-time applications by implementation of background/foreground software. Recent developments in computer technology including microprocessors enable the functional organization of hardware in distributed or hierarchical form to provide new system structures for real-time requirements. Examples of systems with distributed architecture will be discussed in detail

  6. Identification of pyrG Used as an Endogenous Reference Gene in Qualitative and Real-Time Quantitative PCR Detection of Pleurotus ostreatus.

    Science.gov (United States)

    Zheng, Shi; Shan, Luying; Zhuang, Yongliang; Shang, Ying

    2018-03-01

    As a well-known edible fungus rich in nutrients, Pleurotus ostreatus has been used as an alternative to expensive wild edible fungi. Specifically, the fact that using P. ostreatus instead of other expensive wild edible fungi has damaged the rights and interests of consumers. Among the existing methods for detection of food adulteration, the amplification of endogenous reference gene is the most accurate method. However, an ideal endogenous reference gene for P. ostreatus has yet to be developed. In this study, a DNA extraction method for P. ostreatus was optimized, and pyrG was selected as a species-specific gene through sequence alignment. This gene was subsequently subjected to qualitative and quantitative Polymerase Chain Reaction (PCR) assays with 3 different P. ostreatus varieties and 7 other species. A low detection limit of 5 pg/μL was obtained by TaqMan quantitative PCR, and no pyrG amplification product was observed in the 7 other species. No allelic variation was detected in P. ostreatus varieties. These experiments confirmed that pyrG was an ideal endogenous reference gene for the qualitative and real-time quantitative PCR detection of P. ostreatus. This method was also suitable for the examination of processed P. ostreatus samples and determination of adulteration in wild mushrooms. The pyrG gene was chosen as an ideal endogenous reference gene for the qualitative and real-time quantitative PCR detection of P. ostreatus, and the detection limit was 5 pg/μL for the quantification. This method is used not only for raw materials but also for processed P. ostreatus products and other processed mushroom foods. © 2018 Institute of Food Technologists®.

  7. Specification and Automated Verification of Real-Time Behaviour

    DEFF Research Database (Denmark)

    Kristensen, C.H.; Andersen, J.H.; Skou, A.

    1995-01-01

    In this paper we sketch a method for specification and automatic verification of real-time software properties.......In this paper we sketch a method for specification and automatic verification of real-time software properties....

  8. Specification and Automated Verification of Real-Time Behaviour

    DEFF Research Database (Denmark)

    Andersen, J.H.; Kristensen, C.H.; Skou, A.

    1996-01-01

    In this paper we sketch a method for specification and automatic verification of real-time software properties.......In this paper we sketch a method for specification and automatic verification of real-time software properties....

  9. Survey of real-time processing systems for big data

    DEFF Research Database (Denmark)

    Liu, Xiufeng; Lftikhar, Nadeem; Xie, Xike

    2014-01-01

    In recent years, real-time processing and analytics systems for big data–in the context of Business Intelligence (BI)–have received a growing attention. The traditional BI platforms that perform regular updates on daily, weekly or monthly basis are no longer adequate to satisfy the fast......-changing business environments. However, due to the nature of big data, it has become a challenge to achieve the real-time capability using the traditional technologies. The recent distributed computing technology, MapReduce, provides off-the-shelf high scalability that can significantly shorten the processing time...... for big data; Its open-source implementation such as Hadoop has become the de-facto standard for processing big data, however, Hadoop has the limitation of supporting real-time updates. The improvements in Hadoop for the real-time capability, and the other alternative real-time frameworks have been...

  10. Timing system solution for MedAustron; Real-time event and data distribution network

    International Nuclear Information System (INIS)

    Stefanic, R.; Tavcar, R.; Dedic, J.; Gutleber, J.; Moser, R.

    2012-01-01

    MedAustron is an ion beam research and therapy centre under construction in Wiener Neustadt, Austria. The facility features a synchrotron particle accelerator for light ions. The timing system for this class of accelerators has been developed in close collaboration between MedAustron and Cosylab. Mitigating economical and technological risks, we have chosen a proven, widely used Micro Research Finland (MRF) timing equipment and redesigned its FPGA firmware, extending its high-logic services above transport layer, as required by machine specifics. We obtained a generic real-time broadcast network for coordinating actions of a compact, pulse-to-pulse modulation based particle accelerator. High-level services include support for virtual accelerators and a rich selection of event response mechanisms. The system uses a combination of a real-time link for downstream events and a non-real-time link for upstream messaging and non time-critical communication. It comes with National Instruments LabVIEW-based software support, ready to be integrated into PXIe based front-end controllers. This article explains the high level logic services provided by the real-time link, describes the non-real-time interfaces and presents the software configuration mechanisms. (authors)

  11. Real-time variables dictionary (RTVD), and expert system for development of real-time applications in nuclear power plants

    International Nuclear Information System (INIS)

    Senra Martinez, A.; Schirru, R.; Dutra Thome Filho, Z.

    1990-01-01

    It is presented in this paper a computerized methodology based on a data dictionary managed by an expert system called Real-Time Variables Dictionary (RTVD). This system is very usefull for development of real-time applications in nuclear power plants. It is described in details the RTVD functions and its implantation in a VAX 8600 computer. It is also pointed out the concepts of artificial intelligence used in teh RTVD

  12. Rt-Space: A Real-Time Stochastically-Provisioned Adaptive Container Environment

    Science.gov (United States)

    2017-08-04

    Real-Time Systems (ECRTS) Conference Location: Toulouse, France Paper Title: Multiprocessor Real-Time Locking Protocols for Replicated Resources...Conference Location: Lille, France Paper Title: A Contention-Sensitive Fine-Grained Locking Protocol for Multiprocessor Real-Time Systems Publication...On the Soft Real-Time Optimality of Global EDF on Multiprocessors: From Identical to Uniform Heterogeneous Publication Type: Conference Paper or

  13. Real-Time Engagement Area Development Program (READ-Pro)

    National Research Council Canada - National Science Library

    Burger, Joseph

    2002-01-01

    The Real Time Engagement Area Development Program (READ-Pro) is a PC-based prototype system which provides company-level commanders with real-time operational analysis tools to develop ENGAGEMENT AREAS(EA) for direct fire (DF) systems...

  14. MAC-Level Communication Time Modeling and Analysis for Real-Time WSNs

    Directory of Open Access Journals (Sweden)

    STANGACIU, V.

    2016-02-01

    Full Text Available Low-level communication protocols and their timing behavior are essential to developing wireless sensor networks (WSNs able to provide the support and operating guarantees required by many current real-time applications. Nevertheless, this aspect still remains an issue in the state-of-the-art. In this paper we provide a detailed analysis of a recently proposed MAC-level communication timing model and demonstrate its usability in designing real-time protocols. The results of a large set of measurements are also presented and discussed here, in direct relation to the main time parameters of the analyzed model.

  15. 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)

  16. Competitive On-Line Scheduling for Overloaded Real-Time Systems

    Science.gov (United States)

    1993-09-01

    Real - Time Systems by Gilad Koren a dissertation submitted in partial fulfillment of the requirements...Overloaded Real - Time Systems 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK...1.1 Introduction : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : : 2 1.1.1 Real - Time Systems : : : : : : : : : : : : : : : : : : : : : : : : : : : :

  17. Real-time operating system timing jitter and its impact on motor control

    Science.gov (United States)

    Proctor, Frederick M.; Shackleford, William P.

    2001-12-01

    General-purpose microprocessors are increasingly being used for control applications due to their widespread availability and software support for non-control functions like networking and operator interfaces. Two classes of real-time operating systems (RTOS) exist for these systems. The traditional RTOS serves as the sole operating system, and provides all OS services. Examples include ETS, LynxOS, QNX, Windows CE and VxWorks. RTOS extensions add real-time scheduling capabilities to non-real-time OSes, and provide minimal services needed for the time-critical portions of an application. Examples include RTAI and RTL for Linux, and HyperKernel, OnTime and RTX for Windows NT. Timing jitter is an issue in these systems, due to hardware effects such as bus locking, caches and pipelines, and software effects from mutual exclusion resource locks, non-preemtible critical sections, disabled interrupts, and multiple code paths in the scheduler. Jitter is typically on the order of a microsecond to a few tens of microseconds for hard real-time operating systems, and ranges from milliseconds to seconds in the worst case for soft real-time operating systems. The question of its significance on the performance of a controller arises. Naturally, the smaller the scheduling period required for a control task, the more significant is the impact of timing jitter. Aside from this intuitive relationship is the greater significance of timing on open-loop control, such as for stepper motors, than for closed-loop control, such as for servo motors. Techniques for measuring timing jitter are discussed, and comparisons between various platforms are presented. Techniques to reduce jitter or mitigate its effects are presented. The impact of jitter on stepper motor control is analyzed.

  18. Real-time subway information for improving transit ridership.

    Science.gov (United States)

    2016-08-01

    In recent years, the standardization of transit schedule information has yielded a dramatic increase in the accessibility of computerized transit schedules and given rise to real-time service schedules. Two such real-time service schedules are the Ge...

  19. Feedback as Real-Time Constructions

    Science.gov (United States)

    Keiding, Tina Bering; Qvortrup, Ane

    2014-01-01

    This article offers a re-description of feedback and the significance of time in feedback constructions based on systems theory. It describes feedback as internal, real-time constructions in a learning system. From this perspective, feedback is neither immediate nor delayed, but occurs in the very moment it takes place. This article argues for a…

  20. Building Real-Time Collaborative Applications with a Federated Architecture

    Directory of Open Access Journals (Sweden)

    Pablo Ojanguren-Menendez

    2015-12-01

    Full Text Available Real-time collaboration is being offered by multiple libraries and APIs (Google Drive Real-time API, Microsoft Real-Time Communications API, TogetherJS, ShareJS, rapidly becoming a mainstream option for webservices developers. However, they are offered as centralised services running in a single server, regardless if they are free/open source or proprietary software. After re-engineering Apache Wave (former Google Wave, we can now provide the first decentralised and federated free/open source alternative. The new API allows to develop new real-time collaborative web applications in both JavaScript and Java environments.

  1. "Internet of Things" Real-Time Free Flap Monitoring.

    Science.gov (United States)

    Kim, Sang Hun; Shin, Ho Seong; Lee, Sang Hwan

    2018-01-01

    Free flaps are a common treatment option for head and neck reconstruction in plastic reconstructive surgery, and monitoring of the free flap is the most important factor for flap survival. In this study, the authors performed real-time free flap monitoring based on an implanted Doppler system and "internet of things" (IoT)/wireless Wi-Fi, which is a convenient, accurate, and efficient approach for surgeons to monitor a free flap. Implanted Doppler signals were checked continuously until the patient was discharged by the surgeon and residents using their own cellular phone or personal computer. If the surgeon decided that a revision procedure or exploration was required, the authors checked the consumed time (positive signal-to-operating room time) from the first notification when the flap's status was questioned to the determination for revision surgery according to a chart review. To compare the efficacy of real-time monitoring, the authors paired the same number of free flaps performed by the same surgeon and monitored the flaps using conventional methods such as a physical examination. The total survival rate was greater in the real-time monitoring group (94.7% versus 89.5%). The average time for the real-time monitoring group was shorter than that for the conventional group (65 minutes versus 86 minutes). Based on this study, real-time free flap monitoring using IoT technology is a method that surgeon and reconstruction team can monitor simultaneously at any time in any situation.

  2. An integrated technique for developing real-time systems

    NARCIS (Netherlands)

    Hooman, J.J.M.; Vain, J.

    1995-01-01

    The integration of conceptual modeling techniques, formal specification, and compositional verification is considered for real time systems within the knowledge engineering context. We define constructive transformations from a conceptual meta model to a real time specification language and give

  3. SLStudio: Open-source framework for real-time structured light

    DEFF Research Database (Denmark)

    Wilm, Jakob; Olesen, Oline Vinter; Larsen, Rasmus

    2014-01-01

    that this software makes real-time 3D scene capture more widely accessible and serves as a foundation for new structured light scanners operating in real-time, e.g. 20 depth images per second and more. The use cases for such scanners are plentyfull, however due to the computational constraints, all public......An open-source framework for real-time structured light is presented. It is called “SLStudio”, and enables real-time capture of metric depth images. The framework is modular, and extensible to support new algorithms for scene encoding/decoding, triangulation, and aquisition hardware. It is the aim...... implementations so far are limited to offline processing. With “SLStudio”, we are making a platform available which enables researchers from many different fields to build application specific real time 3D scanners. The software is hosted at http://compute.dtu.dk/~jakw/slstudio....

  4. Real Time Processing

    CERN Multimedia

    CERN. Geneva; ANDERSON, Dustin James; DOGLIONI, Caterina

    2015-01-01

    The LHC provides experiments with an unprecedented amount of data. Experimental collaborations need to meet storage and computing requirements for the analysis of this data: this is often a limiting factor in the physics program that would be achievable if the whole dataset could be analysed. In this talk, I will describe the strategies adopted by the LHCb, CMS and ATLAS collaborations to overcome these limitations and make the most of LHC data: data parking, data scouting, and real-time analysis.

  5. Real-time safety risk assessment based on a real-time location system for hydropower construction sites.

    Science.gov (United States)

    Jiang, Hanchen; Lin, Peng; Fan, Qixiang; Qiang, Maoshan

    2014-01-01

    The concern for workers' safety in construction industry is reflected in many studies focusing on static safety risk identification and assessment. However, studies on real-time safety risk assessment aimed at reducing uncertainty and supporting quick response are rare. A method for real-time safety risk assessment (RTSRA) to implement a dynamic evaluation of worker safety states on construction site has been proposed in this paper. The method provides construction managers who are in charge of safety with more abundant information to reduce the uncertainty of the site. A quantitative calculation formula, integrating the influence of static and dynamic hazards and that of safety supervisors, is established to link the safety risk of workers with the locations of on-site assets. By employing the hidden Markov model (HMM), the RTSRA provides a mechanism for processing location data provided by the real-time location system (RTLS) and analyzing the probability distributions of different states in terms of false positives and negatives. Simulation analysis demonstrated the logic of the proposed method and how it works. Application case shows that the proposed RTSRA is both feasible and effective in managing construction project safety concerns.

  6. Improving the molecular diagnosis of Chlamydia psittaci and Chlamydia abortus infection with a species-specific duplex real-time PCR.

    Science.gov (United States)

    Opota, Onya; Jaton, Katia; Branley, James; Vanrompay, Daisy; Erard, Veronique; Borel, Nicole; Longbottom, David; Greub, Gilbert

    2015-10-01

    Chlamydia psittaci and Chlamydia abortus are closely related intracellular bacteria exhibiting different tissue tropism that may cause severe but distinct infection in humans. C. psittaci causes psittacosis, a respiratory zoonotic infection transmitted by birds. C. abortus is an abortigenic agent in small ruminants, which can also colonize the human placenta and lead to foetal death and miscarriage. Infections caused by C. psittaci and C. abortus are underestimated mainly due to diagnosis difficulties resulting from their strict intracellular growth. We developed a duplex real-time PCR to detect and distinguish these two bacteria in clinical samples. The first PCR (PCR1) targeted a sequence of the 16S-23S rRNA operon allowing the detection of both C. psittaci and C. abortus. The second PCR (PCR2) targeted the coding DNA sequence CPSIT_0607 unique to C. psittaci. The two PCRs showed 100 % detection for ≥ 10 DNA copies per reaction (1000 copies ml(- 1)). Using a set of 120 samples, including bacterial reference strains, clinical specimens and infected cell culture material, we monitored 100 % sensitivity and 100 % specificity for the detection of C. psittaci and C. abortus for PCR1. When PCR1 was positive, PCR2 could discriminate C. psittaci from C. abortus with a positive predictive value of 100 % and a negative predictive value of 88 %. In conclusion, this new duplex PCR represents a low-cost and time-saving method with high-throughput potential, expected to improve the routine diagnosis of psittacosis and pregnancy complication in large-scale screening programs and also during outbreaks.

  7. 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...

  8. Real time gamma-ray signature identifier

    Science.gov (United States)

    Rowland, Mark [Alamo, CA; Gosnell, Tom B [Moraga, CA; Ham, Cheryl [Livermore, CA; Perkins, Dwight [Livermore, CA; Wong, James [Dublin, CA

    2012-05-15

    A real time gamma-ray signature/source identification method and system using principal components analysis (PCA) for transforming and substantially reducing one or more comprehensive spectral libraries of nuclear materials types and configurations into a corresponding concise representation/signature(s) representing and indexing each individual predetermined spectrum in principal component (PC) space, wherein an unknown gamma-ray signature may be compared against the representative signature to find a match or at least characterize the unknown signature from among all the entries in the library with a single regression or simple projection into the PC space, so as to substantially reduce processing time and computing resources and enable real-time characterization and/or identification.

  9. Real-Time Business Intelligence for the Utilities Industry

    Directory of Open Access Journals (Sweden)

    Janina POPEANGA

    2012-12-01

    Full Text Available In today’s competitive environment with rapid innovation in smart metering and smart grids, there is an increased need for real-time business intelligence (RTBI in the utilities industry. Giving the fact that this industry is an environment where decisions are time sensitive, RTBI solutions will help utilities improve customer experiences and operational efficiencies. The focus of this paper is on the importance of real-time business intelligence (RTBI in the utilities industry, outlining our vision of real-time business intelligence for this industry. Besides the analysis in this area, the article presents as a case study the Oracle Business Intelligence solution for utilities.

  10. Real-time laser holographic interferometry for aerodynamics

    International Nuclear Information System (INIS)

    Lee, G.

    1987-01-01

    Recent developments in thermoplastic recording holograms and advancements in automated image digitalization and analysis make real-time laser holographic interferometry feasible for two-dimensional flows such as airfoil flows. Typical airfoil measurements would include airfoil pressure distributions, wake and boundary layer profiles, and flow field density contours. This paper addresses some of the problems and requirements of a real-time laser holographic interferometer. 13 references

  11. Coordinated scheduling for dynamic real-time systems

    Science.gov (United States)

    Natarajan, Swaminathan; Zhao, Wei

    1994-01-01

    In this project, we addressed issues in coordinated scheduling for dynamic real-time systems. In particular, we concentrated on design and implementation of a new distributed real-time system called R-Shell. The design objective of R-Shell is to provide computing support for space programs that have large, complex, fault-tolerant distributed real-time applications. In R-shell, the approach is based on the concept of scheduling agents, which reside in the application run-time environment, and are customized to provide just those resource management functions which are needed by the specific application. With this approach, we avoid the need for a sophisticated OS which provides a variety of generalized functionality, while still not burdening application programmers with heavy responsibility for resource management. In this report, we discuss the R-Shell approach, summarize the achievement of the project, and describe a preliminary prototype of R-Shell system.

  12. A real-time photogrammetry system based on embedded architecture

    Directory of Open Access Journals (Sweden)

    S. Y. Zheng

    2014-06-01

    Full Text Available In order to meet the demand of real-time spatial data processing and improve the online processing capability of photogrammetric system, a kind of real-time photogrammetry method is proposed in this paper. According to the proposed method, system based on embedded architecture is then designed: using FPGA, ARM+DSP and other embedded computing technology to build specialized hardware operating environment, transplanting and optimizing the existing photogrammetric algorithm to the embedded system, and finally real-time photogrammetric data processing is realized. At last, aerial photogrammetric experiment shows that the method can achieve high-speed and stable on-line processing of photogrammetric data. And the experiment also verifies the feasibility of the proposed real-time photogrammetric system based on embedded architecture. It is the first time to realize real-time aerial photogrammetric system, which can improve the online processing efficiency of photogrammetry to a higher level and broaden the application field of photogrammetry.

  13. Real-Time Tropospheric Delay Estimation using IGS Products

    Science.gov (United States)

    Stürze, Andrea; Liu, Sha; Söhne, Wolfgang

    2014-05-01

    The Federal Agency for Cartography and Geodesy (BKG) routinely provides zenith tropospheric delay (ZTD) parameter for the assimilation in numerical weather models since more than 10 years. Up to now the results flowing into the EUREF Permanent Network (EPN) or E-GVAP (EUMETNET EIG GNSS water vapour programme) analysis are based on batch processing of GPS+GLONASS observations in differential network mode. For the recently started COST Action ES1206 about "Advanced Global Navigation Satellite Systems tropospheric products for monitoring severe weather events and climate" (GNSS4SWEC), however, rapid updates in the analysis of the atmospheric state for nowcasting applications require changing the processing strategy towards real-time. In the RTCM SC104 (Radio Technical Commission for Maritime Services, Special Committee 104) a format combining the advantages of Precise Point Positioning (PPP) and Real-Time Kinematic (RTK) is under development. The so-called State Space Representation approach is defining corrections, which will be transferred in real-time to the user e.g. via NTRIP (Network Transport of RTCM via Internet Protocol). Meanwhile messages for precise orbits, satellite clocks and code biases compatible to the basic PPP mode using IGS products are defined. Consequently, the IGS Real-Time Service (RTS) was launched in 2013 in order to extend the well-known precise orbit and clock products by a real-time component. Further messages e.g. with respect to ionosphere or phase biases are foreseen. Depending on the level of refinement, so different accuracies up to the RTK level shall be reachable. In co-operation of BKG and the Technical University of Darmstadt the real-time software GEMon (GREF EUREF Monitoring) is under development. GEMon is able to process GPS and GLONASS observation and RTS product data streams in PPP mode. Furthermore, several state-of-the-art troposphere models, for example based on numerical weather prediction data, are implemented. Hence, it

  14. Reduced computational cost in the calculation of worst case response time for real time systems

    OpenAIRE

    Urriza, José M.; Schorb, Lucas; Orozco, Javier D.; Cayssials, Ricardo

    2009-01-01

    Modern Real Time Operating Systems require reducing computational costs even though the microprocessors become more powerful each day. It is usual that Real Time Operating Systems for embedded systems have advance features to administrate the resources of the applications that they support. In order to guarantee either the schedulability of the system or the schedulability of a new task in a dynamic Real Time System, it is necessary to know the Worst Case Response Time of the Real Time tasks ...

  15. Real-time measurement and control at Jet. Experiment Control

    International Nuclear Information System (INIS)

    Felton, R.; Zabeo, L.; Sartori, F.; Piccolo, F.; Farthing, J.; Budd, T.; Dorling, S.; McCullen, P.; Harling, J.; Dalley, S.; Goodyear, A.; Stephen, A.; Card, P.; Bright, M.; Lucock, R.; Jones, E.; Griph, S.; Hogben, C.; Beldishevski, M.; Buckley, M.; Davis, J.; Young, I.; Hemming, O.; Wheatley, M.; Heesterman, P.; Lloyd, G.; Walters, M.; Bridge, R.; Leggate, H.; Howell, D.; Zastrow, K.D.; Giroud, C.; Coffey, I.; Hawkes, N.; Stamp, M.; Barnsley, R.; Edlington, T.; Guenther, K.; Gowers, C.; Popovichef, S.; Huber, A.; Ingesson, C.; Joffrin, E.; Mazon, D.; Moreau, D.; Murari, A.; Riva, M.; Barana, O.; Bolzonella, T.; Valisa, M.; Innocente, P.; Zerbini, M.; Bosak, K.; Blum, J.; Vitale, E.; Crisanti, F.; La Luna, E. de; Sanchez, J.

    2004-01-01

    Over the past few ears, the preparation of ITER-relevant plasma scenarios has been the main focus experimental activity on tokamaks. The development of integrated, simultaneous, real-time controls of plasma shape, current, pressure, temperature, radiation, neutron profiles, and also impurities, ELMs (edge localized modes) and MHD are now seen to be essential for further development of quasi-steady state conditions with feedback, or the stabilisation of transient phenomena with event-driven actions. For this thrust, the EFDA JET Real Time Project has developed a set of real-time plasma measurements, experiment control, and communication facilities. The Plasma Diagnostics used for real-time experiments are Far Infra Red interferometry, polarimetry, visible, UV and X-ray spectroscopy, LIDAR, bolometry, neutron and magnetics. Further analysis systems produce integrated results such as temperature profiles on geometry derived from MHD equilibrium solutions. The Actuators include toroidal, poloidal and divertor coils, gas and pellet fuelling, neutral beam injection, radiofrequency (ICRH) waves and microwaves (LH). The Heating/Fuelling Operators can either define a power or gas request waveform or select the real-time instantaneous power/gas request from the Real Time Experiment Central Control (RTCC) system. The Real Time Experiment Control system provides both a high-level, control-programming environment and interlocks with the actuators. A MATLAB facility is being developed for the development of more complex controllers. The plasma measurement, controller and plant control systems communicate in ATM network. The EFDA Real Time project is essential groundwork for future reactors such as ITER. It involves many staff from several institutions. The facility is now frequently used in experiments. (authors)

  16. Intelligent data management for real-time spacecraft monitoring

    Science.gov (United States)

    Schwuttke, Ursula M.; Gasser, Les; Abramson, Bruce

    1992-01-01

    Real-time AI systems have begun to address the challenge of restructuring problem solving to meet real-time constraints by making key trade-offs that pursue less than optimal strategies with minimal impact on system goals. Several approaches for adapting to dynamic changes in system operating conditions are known. However, simultaneously adapting system decision criteria in a principled way has been difficult. Towards this end, a general technique for dynamically making such trade-offs using a combination of decision theory and domain knowledge has been developed. Multi-attribute utility theory (MAUT), a decision theoretic approach for making one-time decisions is discussed and dynamic trade-off evaluation is described as a knowledge-based extension of MAUT that is suitable for highly dynamic real-time environments, and provides an example of dynamic trade-off evaluation applied to a specific data management trade-off in a real-world spacecraft monitoring application.

  17. Real-time earthquake monitoring: Early warning and rapid response

    Science.gov (United States)

    1991-01-01

    A panel was established to investigate the subject of real-time earthquake monitoring (RTEM) and suggest recommendations on the feasibility of using a real-time earthquake warning system to mitigate earthquake damage in regions of the United States. The findings of the investigation and the related recommendations are described in this report. A brief review of existing real-time seismic systems is presented with particular emphasis given to the current California seismic networks. Specific applications of a real-time monitoring system are discussed along with issues related to system deployment and technical feasibility. In addition, several non-technical considerations are addressed including cost-benefit analysis, public perceptions, safety, and liability.

  18. True Time API Link (real time arrival info)

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — This link will take you to the site where you can create an account to access Port Authority's real time arrival information. To request access to Port Authority's...

  19. Experiments with the Sun Java Real-Time System -- Part 2

    National Research Council Canada - National Science Library

    Auguston, Mikhail; Cook, Thomas S; Drusinsky, Doron; Michael, James B; Otani, Thomas W; Shing, Man-Tak

    2007-01-01

    In the authors' first report on the Sun Java Real-Time System (RTS), they concluded that it is preferable to use real-time Java threads that use heap memory rather than no-heap real-time threads (NHRTTs...

  20. An approach to a real-time distribution system

    Science.gov (United States)

    Kittle, Frank P., Jr.; Paddock, Eddie J.; Pocklington, Tony; Wang, Lui

    1990-01-01

    The requirements of a real-time data distribution system are to provide fast, reliable delivery of data from source to destination with little or no impact to the data source. In this particular case, the data sources are inside an operational environment, the Mission Control Center (MCC), and any workstation receiving data directly from the operational computer must conform to the software standards of the MCC. In order to supply data to development workstations outside of the MCC, it is necessary to use gateway computers that prevent unauthorized data transfer back to the operational computers. Many software programs produced on the development workstations are targeted for real-time operation. Therefore, these programs must migrate from the development workstation to the operational workstation. It is yet another requirement for the Data Distribution System to ensure smooth transition of the data interfaces for the application developers. A standard data interface model has already been set up for the operational environment, so the interface between the distribution system and the application software was developed to match that model as closely as possible. The system as a whole therefore allows the rapid development of real-time applications without impacting the data sources. In summary, this approach to a real-time data distribution system provides development users outside of the MCC with an interface to MCC real-time data sources. In addition, the data interface was developed with a flexible and portable software design. This design allows for the smooth transition of new real-time applications to the MCC operational environment.

  1. FTA real-time transit information assessment : white paper on literature review of real-time transit information systems.

    Science.gov (United States)

    Real-time transit information systems are key technology applications within the transit industry designed to provide better customer service by disseminating timely and accurate information. Riders use this information to make various decisions abou...

  2. Facial Expression Emotion Detection for Real-Time Embedded Systems

    Directory of Open Access Journals (Sweden)

    Saeed Turabzadeh

    2018-01-01

    Full Text Available Recently, real-time facial expression recognition has attracted more and more research. In this study, an automatic facial expression real-time system was built and tested. Firstly, the system and model were designed and tested on a MATLAB environment followed by a MATLAB Simulink environment that is capable of recognizing continuous facial expressions in real-time with a rate of 1 frame per second and that is implemented on a desktop PC. They have been evaluated in a public dataset, and the experimental results were promising. The dataset and labels used in this study were made from videos, which were recorded twice from five participants while watching a video. Secondly, in order to implement in real-time at a faster frame rate, the facial expression recognition system was built on the field-programmable gate array (FPGA. The camera sensor used in this work was a Digilent VmodCAM — stereo camera module. The model was built on the Atlys™ Spartan-6 FPGA development board. It can continuously perform emotional state recognition in real-time at a frame rate of 30. A graphical user interface was designed to display the participant’s video in real-time and two-dimensional predict labels of the emotion at the same time.

  3. 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 ...

  4. Boat, wake, and wave real-time simulation

    Science.gov (United States)

    Świerkowski, Leszek; Gouthas, Efthimios; Christie, Chad L.; Williams, Owen M.

    2009-05-01

    We describe the extension of our real-time scene generation software VIRSuite to include the dynamic simulation of small boats and their wakes within an ocean environment. Extensive use has been made of the programmabilty available in the current generation of GPUs. We have demonstrated that real-time simulation is feasible, even including such complexities as dynamical calculation of the boat motion, wake generation and calculation of an FFTgenerated sea state.

  5. Ten years of R&D and full automation in molecular diagnosis.

    Science.gov (United States)

    Greub, Gilbert; Sahli, Roland; Brouillet, René; Jaton, Katia

    2016-01-01

    A 10-year experience of our automated molecular diagnostic platform that carries out 91 different real-time PCR is described. Progresses and future perspectives in molecular diagnostic microbiology are reviewed: why automation is important; how our platform was implemented; how homemade PCRs were developed; the advantages/disadvantages of homemade PCRs, including the critical aspects of troubleshooting and the need to further reduce the turnaround time for specific samples, at least for defined clinical settings such as emergencies. The future of molecular diagnosis depends on automation, and in a novel perspective, it is time now to fully acknowledge the true contribution of molecular diagnostic and to reconsider the indication for PCR, by also using these tests as first-line assays.

  6. A Distributed Computing Network for Real-Time Systems.

    Science.gov (United States)

    1980-11-03

    7 ) AU2 o NAVA TUNDEWATER SY$TEMS CENTER NEWPORT RI F/G 9/2 UIS RIBUT E 0 COMPUTIN G N LTWORK FOR REAL - TIME SYSTEMS .(U) UASSIFIED NOV Al 6 1...MORAIS - UT 92 dLEVEL c A Distributed Computing Network for Real - Time Systems . 11 𔃺-1 Gordon E/Morson I7 y tm- ,r - t "en t As J 2 -p .. - 7 I’ cNaval...NUMBER TD 5932 / N 4. TITLE mand SubotI. S. TYPE OF REPORT & PERIOD COVERED A DISTRIBUTED COMPUTING NETWORK FOR REAL - TIME SYSTEMS 6. PERFORMING ORG

  7. Optimization of Partitioned Architectures to Support Soft Real-Time Applications

    DEFF Research Database (Denmark)

    Tamas-Selicean, Domitian; Pop, Paul

    2014-01-01

    In this paper we propose a new Tabu Search-based design optimization strategy for mixed-criticality systems implementing hard and soft real-time applications on the same platform. Our proposed strategy determined an implementation such that all hard real-time applications are schedulable and the ......In this paper we propose a new Tabu Search-based design optimization strategy for mixed-criticality systems implementing hard and soft real-time applications on the same platform. Our proposed strategy determined an implementation such that all hard real-time applications are schedulable...... and the quality of service of the soft real-time tasks is maximized. We have evaluated our strategy using an aerospace case study....

  8. LHCb's Time-Real Alignment in RunII

    CERN Multimedia

    Batozskaya, Varvara

    2015-01-01

    LHCb has introduced a novel real-time detector alignment and calibration strategy for LHC Run 2. Data collected at the start of the fill will be processed in a few minutes and used to update the alignment, while the calibration constants will be evaluated for each run. This procedure will improve the quality of the online alignment. Critically, this new real-time alignment and calibration procedure allows identical constants to be used in the online and offline reconstruction, thus improving the correlation between triggered and offline selected events. This offers the opportunity to optimise the event selection in the trigger by applying stronger constraints. The required computing time constraints are met thanks to a new dedicated framework using the multi-core farm infrastructure for the trigger. The motivation for a real-time alignment and calibration of the LHCb detector is discussed from both the operational and physics performance points of view. Specific challenges of this novel configur...

  9. Real-time PCR in detection and quantitation of Leishmania donovani for the diagnosis of Visceral Leishmaniasis patients and the monitoring of their response to treatment

    Science.gov (United States)

    Ghosh, Prakash; Khan, Md. Anik Ashfaq; Duthie, Malcolm S.; Vallur, Aarthy C.; Picone, Alessandro; Howard, Randall F.; Reed, Steven G.

    2017-01-01

    Sustained elimination of Visceral Leishmaniasis (VL) requires the reduction and control of parasite reservoirs to minimize the transmission of Leishmania donovani infection. A simple, reproducible and definitive diagnostic procedure is therefore indispensable for the early and accurate detection of parasites in VL, Relapsed VL (RVL) and Post Kala-azar Dermal Leishmaniasis (PKDL) patients, all of whom are potential reservoirs of Leishmania parasites. To overcome the limitations of current diagnostic approaches, a novel quantitative real-time polymerase chain reaction (qPCR) method based on Taqman chemistry was devised for the detection and quantification of L. donovani in blood and skin. The diagnostic efficacy was evaluated using archived peripheral blood buffy coat DNA from 40 VL, 40 PKDL, 10 RVL, 20 cured VL, and 40 cured PKDL along with 10 tuberculosis (TB) cases and 80 healthy endemic controls. Results were compared to those obtained using a Leishmania-specific nested PCR (Ln-PCR). The real time PCR assay was 100% (95% CI, 91.19–100%) sensitive in detecting parasite genomes in VL and RVL samples and 85.0% (95% CI, 70.16–94.29%) sensitive for PKDL samples. In contrast, the sensitivity of Ln-PCR was 77.5% (95% CI, 61.55–89.16%) for VL samples, 100% (95%CI, 69.15–100%) for RVL samples, and 52.5% (95% CI, 36.13–68.49%) for PKDL samples. There was significant discordance between the two methods with the overall sensitivity of the qPCR assay being considerably higher than Ln-PCR. None of the assay detected L. donovani DNA in buffy coats from cured VL cases, and reduced infectious burdens were demonstrated in cured PKDL cases who remained positive in 7.5% (3/40) and 2.5% (1/40) cases by real-time PCR and Ln-PCR, respectively. Both assays were 100% (95% CI, 95.98–100) specific with no positive signals in either endemic healthy control or TB samples. The real time PCR assay we developed offers a molecular tool for accurate detection of circulating L

  10. Towards real-time regional earthquake simulation I: real-time moment tensor monitoring (RMT) for regional events in Taiwan

    Science.gov (United States)

    Lee, Shiann-Jong; Liang, Wen-Tzong; Cheng, Hui-Wen; Tu, Feng-Shan; Ma, Kuo-Fong; Tsuruoka, Hiroshi; Kawakatsu, Hitoshi; Huang, Bor-Shouh; Liu, Chun-Chi

    2014-01-01

    We have developed a real-time moment tensor monitoring system (RMT) which takes advantage of a grid-based moment tensor inversion technique and real-time broad-band seismic recordings to automatically monitor earthquake activities in the vicinity of Taiwan. The centroid moment tensor (CMT) inversion technique and a grid search scheme are applied to obtain the information of earthquake source parameters, including the event origin time, hypocentral location, moment magnitude and focal mechanism. All of these source parameters can be determined simultaneously within 117 s after the occurrence of an earthquake. The monitoring area involves the entire Taiwan Island and the offshore region, which covers the area of 119.3°E to 123.0°E and 21.0°N to 26.0°N, with a depth from 6 to 136 km. A 3-D grid system is implemented in the monitoring area with a uniform horizontal interval of 0.1° and a vertical interval of 10 km. The inversion procedure is based on a 1-D Green's function database calculated by the frequency-wavenumber (fk) method. We compare our results with the Central Weather Bureau (CWB) catalogue data for earthquakes occurred between 2010 and 2012. The average differences between event origin time and hypocentral location are less than 2 s and 10 km, respectively. The focal mechanisms determined by RMT are also comparable with the Broadband Array in Taiwan for Seismology (BATS) CMT solutions. These results indicate that the RMT system is realizable and efficient to monitor local seismic activities. In addition, the time needed to obtain all the point source parameters is reduced substantially compared to routine earthquake reports. By connecting RMT with a real-time online earthquake simulation (ROS) system, all the source parameters will be forwarded to the ROS to make the real-time earthquake simulation feasible. The RMT has operated offline (2010-2011) and online (since January 2012 to present) at the Institute of Earth Sciences (IES), Academia Sinica

  11. Real-Time Pore Pressure Detection: Indicators and Improved Methods

    Directory of Open Access Journals (Sweden)

    Jincai Zhang

    2017-01-01

    Full Text Available High uncertainties may exist in the predrill pore pressure prediction in new prospects and deepwater subsalt wells; therefore, real-time pore pressure detection is highly needed to reduce drilling risks. The methods for pore pressure detection (the resistivity, sonic, and corrected d-exponent methods are improved using the depth-dependent normal compaction equations to adapt to the requirements of the real-time monitoring. A new method is proposed to calculate pore pressure from the connection gas or elevated background gas, which can be used for real-time pore pressure detection. The pore pressure detection using the logging-while-drilling, measurement-while-drilling, and mud logging data is also implemented and evaluated. Abnormal pore pressure indicators from the well logs, mud logs, and wellbore instability events are identified and analyzed to interpret abnormal pore pressures for guiding real-time drilling decisions. The principles for identifying abnormal pressure indicators are proposed to improve real-time pore pressure monitoring.

  12. Real-time photorealistic stereoscopic rendering of fire

    Science.gov (United States)

    Rose, Benjamin M.; McAllister, David F.

    2007-02-01

    We propose a method for real-time photorealistic stereo rendering of the natural phenomenon of fire. Applications include the use of virtual reality in fire fighting, military training, and entertainment. Rendering fire in real-time presents a challenge because of the transparency and non-static fluid-like behavior of fire. It is well known that, in general, methods that are effective for monoscopic rendering are not necessarily easily extended to stereo rendering because monoscopic methods often do not provide the depth information necessary to produce the parallax required for binocular disparity in stereoscopic rendering. We investigate the existing techniques used for monoscopic rendering of fire and discuss their suitability for extension to real-time stereo rendering. Methods include the use of precomputed textures, dynamic generation of textures, and rendering models resulting from the approximation of solutions of fluid dynamics equations through the use of ray-tracing algorithms. We have found that in order to attain real-time frame rates, our method based on billboarding is effective. Slicing is used to simulate depth. Texture mapping or 2D images are mapped onto polygons and alpha blending is used to treat transparency. We can use video recordings or prerendered high-quality images of fire as textures to attain photorealistic stereo.

  13. Development and validation of a real-time PCR assay for specific and sensitive detection of canid herpesvirus 1.

    Science.gov (United States)

    Decaro, Nicola; Amorisco, Francesca; Desario, Costantina; Lorusso, Eleonora; Camero, Michele; Bellacicco, Anna Lucia; Sciarretta, Rossana; Lucente, Maria Stella; Martella, Vito; Buonavoglia, Canio

    2010-10-01

    A TaqMan-based real-time PCR assay targeting the glycoprotein B-encoding gene was developed for diagnosis of canid herpesvirus 1 (CHV-1) infection. The established assay was highly specific, since no cross-reactions were observed with other canine DNA viruses, including canine parvovirus type 2, canine minute virus, or canine adenovirus types 1 and 2. The detection limit was 10(1) and 1.20 x 10(1) DNA copies per 10 microl(-1) of template for standard DNA and a CHV-1-positive kidney sample, respectively: about 1-log higher than a gel-based PCR assay targeting the thymidine kinase gene. The assay was also reproducible, as shown by satisfactory low intra-assay and inter-assay coefficients of variation. CHV-1 isolates of different geographical origins were recognised by the TaqMan assay. Tissues and clinical samples collected from three pups which died of CHV-1 neonatal infection were also tested, displaying a wide distribution of CHV-l DNA in their organs. Unlike other CHV-1-specific diagnostic methods, this quantitative assay permits simultaneous detection and quantitation of CHV-1 DNA in a wide range of canine tissues and body fluids, thus providing a useful tool for confirmation of a clinical diagnosis, for the study of viral pathogenesis and for evaluation of the efficacy of vaccines and antiviral drugs. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  14. OMPS Near Real-time Products Available Through NASA LANCE (Land Atmosphere Near Real-time Capability for EOS)

    Science.gov (United States)

    Warnock, A.; Durbin, P. B.; Cechini, M. F.; Masuoka, E.

    2017-12-01

    Near real-time (NRT) images from the NASA Ozone Mapping and Profiler Suite (OMPS) for sulfur dioxide, total column ozone and aerosol index products are now available through NASA's online Land Atmosphere Near real-time Capability for EOS (LANCE) system. Color palettes, image dimensions and data ranges have been aligned with the corresponding OMI products, allowing for direct comparison of OMPS NRT images with OMI NRT images already available in NASA Worldview. The images are delivered to LANCE within hours of satellite observation. LANCE NRT imagery can be interactively viewed through Worldview and the Global Imagery Browse Services (GIBS).

  15. Real-time radiography at the NECTAR facility

    International Nuclear Information System (INIS)

    Buecherl, T.; Lierse von Gostomski, Ch.

    2011-01-01

    A feasibility study has shown that real-time radiography using fission neutrons is possible at the NECTAR facility, when using an improved detection system for fast variations (Buecherl et al., 2009 ). Continuing this study, real-time measurements of slowly varying processes like the water uptake in medium sized trunks (diameter about 12 cm) and of slow periodic processes (e.g. a slowly rotating iron disk) are investigated successfully using the existing detection system.

  16. Real-time radiography at the NECTAR facility

    Science.gov (United States)

    Bücherl, T.; Lierse von Gostomski, Ch.

    2011-09-01

    A feasibility study has shown that real-time radiography using fission neutrons is possible at the NECTAR facility, when using an improved detection system for fast variations (Bücherl et al., 2009 [1]). Continuing this study, real-time measurements of slowly varying processes like the water uptake in medium sized trunks (diameter about 12 cm) and of slow periodic processes (e.g. a slowly rotating iron disk) are investigated successfully using the existing detection system.

  17. Real-time radiography at the NECTAR facility

    Energy Technology Data Exchange (ETDEWEB)

    Buecherl, T., E-mail: thomas.buecherl@radiochemie.de [Lehrstuhl fuer Radiochemie (RCM), Technische Universitaet Muenchen (TUM), Walther-Meissner-Str. 3, 85748 Garching (Germany); Lierse von Gostomski, Ch. [Lehrstuhl fuer Radiochemie (RCM), Technische Universitaet Muenchen (TUM), Walther-Meissner-Str. 3, 85748 Garching (Germany)

    2011-09-21

    A feasibility study has shown that real-time radiography using fission neutrons is possible at the NECTAR facility, when using an improved detection system for fast variations (Buecherl et al., 2009 ). Continuing this study, real-time measurements of slowly varying processes like the water uptake in medium sized trunks (diameter about 12 cm) and of slow periodic processes (e.g. a slowly rotating iron disk) are investigated successfully using the existing detection system.

  18. Research of real-time performance based on VxWorks embedded system

    International Nuclear Information System (INIS)

    Liu Daming; Li Haiming

    2011-01-01

    In the research of mechanism and heating efficiency of Ion Cyclotron Range of Frequency (ICRF) heating, data acquisition system with high real-time performance needed. By the means of system logic analyzer, SPY and other relevant software on VxWorks embedded operating system for real-time testing gives real-time data of the system. Real-time level to achieve balances used time and processor idle time, real-time data acquisition, and minimize the interference of external to the system, ensure the system work in its own set of scheduling trajectory. Interrupt switching time and task context switching time meet the system requirements. (authors)

  19. Real time ray tracing of skeletal implicit surfaces

    DEFF Research Database (Denmark)

    Rouiller, Olivier; Bærentzen, Jakob Andreas

    Modeling and rendering in real time is usually done via rasterization of polygonal meshes. We present a method to model with skeletal implicit surfaces and an algorithm to ray trace these surfaces in real time in the GPU. Our skeletal representation of the surfaces allows to create smooth models...

  20. Multiresource allocation and scheduling for periodic soft real-time applications

    Science.gov (United States)

    Gopalan, Kartik; Chiueh, Tzi-cker

    2001-12-01

    Real-time applications that utilize multiple system resources, such as CPU, disks, and network links, require coordinated scheduling of these resources in order to meet their end-to-end performance requirements. Most state-of-the-art operating systems support independent resource allocation and deadline-driven scheduling but lack coordination among multiple heterogeneous resources. This paper describes the design and implementation of an Integrated Real-time Resource Scheduler (IRS) that performs coordinated allocation and scheduling of multiple heterogeneous resources on the same machine for periodic soft real-time application. The principal feature of IRS is a heuristic multi-resource allocation algorithm that reserves multiple resources for real-time applications in a manner that can maximize the number of applications admitted into the system in the long run. At run-time, a global scheduler dispatches the tasks of the soft real-time application to individual resource schedulers according to the precedence constraints between tasks. The individual resource schedulers, which could be any deadline based schedulers, can make scheduling decisions locally and yet collectively satisfy a real-time application's performance requirements. The tightness of overall timing guarantees is ultimately determined by the properties of individual resource schedulers. However, IRS maximizes overall system resource utilization efficiency by coordinating deadline assignment across multiple tasks in a soft real-time application.

  1. Robust Real-Time Tracking for Visual Surveillance

    Directory of Open Access Journals (Sweden)

    Aguilera Josep

    2007-01-01

    Full Text Available This paper describes a real-time multi-camera surveillance system that can be applied to a range of application domains. This integrated system is designed to observe crowded scenes and has mechanisms to improve tracking of objects that are in close proximity. The four component modules described in this paper are (i motion detection using a layered background model, (ii object tracking based on local appearance, (iii hierarchical object recognition, and (iv fused multisensor object tracking using multiple features and geometric constraints. This integrated approach to complex scene tracking is validated against a number of representative real-world scenarios to show that robust, real-time analysis can be performed.

  2. Real-Time Forecasting Revisited: Letting the Data Decide

    OpenAIRE

    Jackson Kitchen; John Kitchen

    2013-01-01

    Real-time GDP forecasting, also often known as “nowcasting,” produces estimates for current-quarter real GDP growth, typically based on a centered value from a set of estimates from incoming indicators. These real-time measures are usually intended to be data-based and to not be based on forecaster judgment or add factors. Even so, estimation methodologies in this research area—and prior versions of the system we use—typically have been constrained by using various “fixed” relationships, such...

  3. Expert systems for real-time monitoring and fault diagnosis

    Science.gov (United States)

    Edwards, S. J.; Caglayan, A. K.

    1989-01-01

    Methods for building real-time onboard expert systems were investigated, and the use of expert systems technology was demonstrated in improving the performance of current real-time onboard monitoring and fault diagnosis applications. The potential applications of the proposed research include an expert system environment allowing the integration of expert systems into conventional time-critical application solutions, a grammar for describing the discrete event behavior of monitoring and fault diagnosis systems, and their applications to new real-time hardware fault diagnosis and monitoring systems for aircraft.

  4. Large holographic displays for real-time applications

    Science.gov (United States)

    Schwerdtner, A.; Häussler, R.; Leister, N.

    2008-02-01

    Holography is generally accepted as the ultimate approach to display three-dimensional scenes or objects. Principally, the reconstruction of an object from a perfect hologram would appear indistinguishable from viewing the corresponding real-world object. Up to now two main obstacles have prevented large-screen Computer-Generated Holograms (CGH) from achieving a satisfactory laboratory prototype not to mention a marketable one. The reason is a small cell pitch CGH resulting in a huge number of hologram cells and a very high computational load for encoding the CGH. These seemingly inevitable technological hurdles for a long time have not been cleared limiting the use of holography to special applications, such as optical filtering, interference, beam forming, digital holography for capturing the 3-D shape of objects, and others. SeeReal Technologies has developed a new approach for real-time capable CGH using the socalled Tracked Viewing Windows technology to overcome these problems. The paper will show that today's state of the art reconfigurable Spatial Light Modulators (SLM), especially today's feasible LCD panels are suited for reconstructing large 3-D scenes which can be observed from large viewing angles. For this to achieve the original holographic concept of containing information from the entire scene in each part of the CGH has been abandoned. This substantially reduces the hologram resolution and thus the computational load by several orders of magnitude making thus real-time computation possible. A monochrome real-time prototype measuring 20 inches has been built and demonstrated at last year's SID conference and exhibition 2007 and at several other events.

  5. The Raptor Real-Time Processing Architecture

    Science.gov (United States)

    Galassi, M.; Starr, D.; Wozniak, P.; Brozdin, K.

    The primary goal of Raptor is ambitious: to identify interesting optical transients from very wide field of view telescopes in real time, and then to quickly point the higher resolution Raptor ``fovea'' cameras and spectrometer to the location of the optical transient. The most interesting of Raptor's many applications is the real-time search for orphan optical counterparts of Gamma Ray Bursts. The sequence of steps (data acquisition, basic calibration, source extraction, astrometry, relative photometry, the smarts of transient identification and elimination of false positives, telescope pointing feedback, etc.) is implemented with a ``component'' approach. All basic elements of the pipeline functionality have been written from scratch or adapted (as in the case of SExtractor for source extraction) to form a consistent modern API operating on memory resident images and source lists. The result is a pipeline which meets our real-time requirements and which can easily operate as a monolithic or distributed processing system. Finally, the Raptor architecture is entirely based on free software (sometimes referred to as ``open source'' software). In this paper we also discuss the interplay between various free software technologies in this type of astronomical problem.

  6. Real-Time Operating System/360

    Science.gov (United States)

    Hoffman, R. L.; Kopp, R. S.; Mueller, H. H.; Pollan, W. D.; Van Sant, B. W.; Weiler, P. W.

    1969-01-01

    RTOS has a cost savings advantage for real-time applications, such as those with random inputs requiring a flexible data routing facility, display systems simplified by a device independent interface language, and complex applications needing added storage protection and data queuing.

  7. Real Time Fire Reconnaissance Satellite Monitoring System Failure Model

    Science.gov (United States)

    Nino Prieto, Omar Ariosto; Colmenares Guillen, Luis Enrique

    2013-09-01

    In this paper the Real Time Fire Reconnaissance Satellite Monitoring System is presented. This architecture is a legacy of the Detection System for Real-Time Physical Variables which is undergoing a patent process in Mexico. The methodologies for this design are the Structured Analysis for Real Time (SA- RT) [8], and the software is carried out by LACATRE (Langage d'aide à la Conception d'Application multitâche Temps Réel) [9,10] Real Time formal language. The system failures model is analyzed and the proposal is based on the formal language for the design of critical systems and Risk Assessment; AltaRica. This formal architecture uses satellites as input sensors and it was adapted from the original model which is a design pattern for physical variation detection in Real Time. The original design, whose task is to monitor events such as natural disasters and health related applications, or actual sickness monitoring and prevention, as the Real Time Diabetes Monitoring System, among others. Some related work has been presented on the Mexican Space Agency (AEM) Creation and Consultation Forums (2010-2011), and throughout the International Mexican Aerospace Science and Technology Society (SOMECYTA) international congress held in San Luis Potosí, México (2012). This Architecture will allow a Real Time Fire Satellite Monitoring, which will reduce the damage and danger caused by fires which consumes the forests and tropical forests of Mexico. This new proposal, permits having a new system that impacts on disaster prevention, by combining national and international technologies and cooperation for the benefit of humankind.

  8. Real time equilibrium reconstruction for tokamak discharge control

    International Nuclear Information System (INIS)

    Ferron, J.R.; Walker, M.L.; Lao, L.L.; St John, H.E.; Humphreys, D.A.; Leuer, J.A.

    1998-01-01

    A practical method for performing a tokamak equilibrium reconstruction in real time for arbitrary time varying discharge shapes and current profiles is described. An approximate solution to the Grad-Shafranov equilibrium relation is found which best fits the diagnostic measurements. Thus, a solution for the spatial distribution of poloidal flux and toroidal current density is available in real time that is consistent with plasma force balance, allowing accurate evaluation of parameters such as discharge shape and safety factor profile. The equilibrium solutions are produced at a rate sufficient for discharge control. This equilibrium reconstruction algorithm has been implemented on the digital plasma control system for the DIII-D tokamak. The first application of real time equilibrium reconstruction to discharge shape control is described. (author)

  9. Issues Involved in Developing Ada Real-Time Systems

    Science.gov (United States)

    1989-02-15

    expensive modifications to the compiler or Ada runtime system to fit a particular application. Whether we can solve the problems of programming real - time systems in...lock in solutions to problems that are not yet well understood in standards as rigorous as the Ada language. Moreover, real - time systems typically have

  10. Real-time disk scheduling in a mixed-media file system

    NARCIS (Netherlands)

    Bosch, H.G.P.; Mullender, Sape J.

    2000-01-01

    This paper presents our real-time disk scheduler called the Delta L scheduler, which optimizes unscheduled best-effort disk requests by giving priority to best-effort disk requests while meeting real-time request deadlines. Our scheduler tries to execute real-time disk requests as much as possible

  11. Real-time PCR genotyping assay for canine progressive rod-cone degeneration and mutant allele frequency in Toy Poodles, Chihuahuas and Miniature Dachshunds in Japan.

    Science.gov (United States)

    Kohyama, Moeko; Tada, Naomi; Mitsui, Hiroko; Tomioka, Hitomi; Tsutsui, Toshihiko; Yabuki, Akira; Rahman, Mohammad Mahbubur; Kushida, Kazuya; Mizukami, Keijiro; Yamato, Osamu

    2016-03-01

    Canine progressive rod-cone degeneration (PRCD) is a middle- to late-onset, autosomal recessive, inherited retinal disorder caused by a substitution (c.5G>A) in the canine PRCD gene that has been identified in 29 or more purebred dogs. In the present study, a TaqMan probe-based real-time PCR assay was developed and evaluated for rapid genotyping and large-scale screening of the mutation. Furthermore, a genotyping survey was carried out in a population of the three most popular breeds in Japan (Toy Poodles, Chihuahuas and Miniature Dachshunds) to determine the current mutant allele frequency. The assay separated all the genotypes of canine PRCD rapidly, indicating its suitability for large-scale surveys. The results of the survey showed that the mutant allele frequency in Toy Poodles was high enough (approximately 0.09) to allow the establishment of measures for the prevention and control of this disorder in breeding kennels. The mutant allele was detected in Chihuahuas for the first time, but the frequency was lower (approximately 0.02) than that in Toy Poodles. The mutant allele was not detected in Miniature Dachshunds. This assay will allow the selective breeding of dogs from the two most popular breeds (Toy Poodle and Chihuahua) in Japan and effective prevention or control of the disorder.

  12. Real time urbanism

    Directory of Open Access Journals (Sweden)

    Ana Ruiz Varona

    2012-12-01

    Full Text Available Nowadays, given the technological revolution of the society of information, the administrative management of the cities faces a new problem not as related to the projection of the urban space as to the capacity of controlling and measuring the process of direct and centralized production of the cities by part of some non-homogeneous social multitudes, in a hyper-accelerated time towards instantaneity. Against libertarian apologies of the new “participative urbanisms”, the article puts forward a discourse that shows the lost associated to the new problem of temporal instantaneity. In this regard we claim new process of mediation that allow administrations and urbanist monitoring the production of the city. To that end, a previous and necessary step will be the redefinition of the role of a new real time urbanist.

  13. Real-Time Imaging System for the OpenPET

    Science.gov (United States)

    Tashima, Hideaki; Yoshida, Eiji; Kinouchi, Shoko; Nishikido, Fumihiko; Inadama, Naoko; Murayama, Hideo; Suga, Mikio; Haneishi, Hideaki; Yamaya, Taiga

    2012-02-01

    The OpenPET and its real-time imaging capability have great potential for real-time tumor tracking in medical procedures such as biopsy and radiation therapy. For the real-time imaging system, we intend to use the one-pass list-mode dynamic row-action maximum likelihood algorithm (DRAMA) and implement it using general-purpose computing on graphics processing units (GPGPU) techniques. However, it is difficult to make consistent reconstructions in real-time because the amount of list-mode data acquired in PET scans may be large depending on the level of radioactivity, and the reconstruction speed depends on the amount of the list-mode data. In this study, we developed a system to control the data used in the reconstruction step while retaining quantitative performance. In the proposed system, the data transfer control system limits the event counts to be used in the reconstruction step according to the reconstruction speed, and the reconstructed images are properly intensified by using the ratio of the used counts to the total counts. We implemented the system on a small OpenPET prototype system and evaluated the performance in terms of the real-time tracking ability by displaying reconstructed images in which the intensity was compensated. The intensity of the displayed images correlated properly with the original count rate and a frame rate of 2 frames per second was achieved with average delay time of 2.1 s.

  14. Effects of computing time delay on real-time control systems

    Science.gov (United States)

    Shin, Kang G.; Cui, Xianzhong

    1988-01-01

    The reliability of a real-time digital control system depends not only on the reliability of the hardware and software used, but also on the speed in executing control algorithms. The latter is due to the negative effects of computing time delay on control system performance. For a given sampling interval, the effects of computing time delay are classified into the delay problem and the loss problem. Analysis of these two problems is presented as a means of evaluating real-time control systems. As an example, both the self-tuning predicted (STP) control and Proportional-Integral-Derivative (PID) control are applied to the problem of tracking robot trajectories, and their respective effects of computing time delay on control performance are comparatively evaluated. For this example, the STP (PID) controller is shown to outperform the PID (STP) controller in coping with the delay (loss) problem.

  15. A New Generation of Real-Time Systems in the JET Tokamak

    Science.gov (United States)

    Alves, Diogo; Neto, Andre C.; Valcarcel, Daniel F.; Felton, Robert; Lopez, Juan M.; Barbalace, Antonio; Boncagni, Luca; Card, Peter; De Tommasi, Gianmaria; Goodyear, Alex; Jachmich, Stefan; Lomas, Peter J.; Maviglia, Francesco; McCullen, Paul; Murari, Andrea; Rainford, Mark; Reux, Cedric; Rimini, Fernanda; Sartori, Filippo; Stephen, Adam V.; Vega, Jesus; Vitelli, Riccardo; Zabeo, Luca; Zastrow, Klaus-Dieter

    2014-04-01

    Recently, a new recipe for developing and deploying real-time systems has become increasingly adopted in the JET tokamak. Powered by the advent of x86 multi-core technology and the reliability of JET's well established Real-Time Data Network (RTDN) to handle all real-time I/O, an official Linux vanilla kernel has been demonstrated to be able to provide real-time performance to user-space applications that are required to meet stringent timing constraints. In particular, a careful rearrangement of the Interrupt ReQuests' (IRQs) affinities together with the kernel's CPU isolation mechanism allows one to obtain either soft or hard real-time behavior depending on the synchronization mechanism adopted. Finally, the Multithreaded Application Real-Time executor (MARTe) framework is used for building applications particularly optimised for exploring multi-core architectures. In the past year, four new systems based on this philosophy have been installed and are now part of JET's routine operation. The focus of the present work is on the configuration aspects that enable these new systems' real-time capability. Details are given about the common real-time configuration of these systems, followed by a brief description of each system together with results regarding their real-time performance. A cycle time jitter analysis of a user-space MARTe based application synchronizing over a network is also presented. The goal is to compare its deterministic performance while running on a vanilla and on a Messaging Real time Grid (MRG) Linux kernel.

  16. Real Time Structured Light and Applications

    DEFF Research Database (Denmark)

    Wilm, Jakob

    Structured light scanning is a versatile method for 3D shape acquisition. While much faster than most competing measurement techniques, most high-end structured light scans still take in the order of seconds to complete. Low-cost sensors such as Microsoft Kinect and time of flight cameras have made......, increased processing power, and methods presented in this thesis, it is possible to perform structured light scans in real time with 20 depth measurements per second. This offers new opportunities for studying dynamic scenes, quality control, human-computer interaction and more. This thesis discusses...... several aspects of real time structured light systems and presents contributions within calibration, scene coding and motion correction aspects. The problem of reliable and fast calibration of such systems is addressed with a novel calibration scheme utilising radial basis functions [Contribution B...

  17. Real-Time Scheduling for Preventing Information Leakage with Preemption Overheads

    Directory of Open Access Journals (Sweden)

    BAEK, H.

    2017-05-01

    Full Text Available Real-time systems (RTS are characterized by tasks executing in a timely manner to meet its deadlines as a real-time constraint. Most studies of RTS have focused on these criteria as primary design points. However, recent increases in security threats to various real-time systems have shown that enhanced security support must be included as an important design point, retro-fitting such support to existing systems as necessary. In this paper, we propose a new pre-flush technique referred to as flush task reservation for FP scheduling (FTR-FP to conditionally sanitize the state of resources shared by real-time tasks by invoking a flush task (FT in order to mitigate information leakage/corruption of real-time systems. FTR-FP extends existing works exploiting FTs to be applicable more general scheduling algorithms and security model. We also propose modifications to existing real-time scheduling algorithms to implement a pre-flush technique as a security constraint, and analysis technique to verify schedulability of the real-time scheduling. For better analytic capability, our analysis technique provides a count of the precise number of preemptions that a task experiences offline. Our evaluation results demonstrate that our proposed schedulability analysis improves the performance of existing scheduling algorithms in terms of schedulability and preemption cost.

  18. 76 FR 42536 - Real-Time System Management Information Program

    Science.gov (United States)

    2011-07-19

    ...-Time System Management Information Program AGENCY: Federal Highway Administration (FHWA), DOT. ACTION... Real-Time System Management Information Program and general information about current and planned... establishing requirements for the Real-Time System Management Information Program on November 8, 2010, at 75 FR...

  19. 75 FR 68418 - Real-Time System Management Information Program

    Science.gov (United States)

    2010-11-08

    ...-Time System Management Information Program AGENCY: Federal Highway Administration (FHWA), DOT. ACTION...) to establish a Real-Time System Management Information Program that provides, in all States, the... traveler information. The purposes of the Real-Time System Management Information Program are to: (1...

  20. Data processing system for real-time control

    International Nuclear Information System (INIS)

    Oasa, K.; Mochizuki, O.; Toyokawa, R.; Yahiro, K.

    1983-01-01

    Real-time control, for large Tokamak JT-60, requires various data processings between diagnostic devices to control system. These processings require to high speed performance so that it aims at giving information necessary for feedback control during discharges. Then, the architecture of this system has hierachical structure of processors. These processors are connected each other by the CAMAC modules and the optical communication network, which is the 5 M bytes/second CAMAC serial highway. This system has two kinds of intelligences for this purpose. One is ACM-PU pairs in some torus hall crates which has a microcomputerized auxiliary controller and a preprocessing unit. Other is real-time processor which has a minicomputer and preprocessing unit. Most of the real-time processing, for example Abel inversion are characteristic to the diagnostic devices. Such a processing is carried out by an ACM-PU pair in the crate dedicated to the diagnostic device. Some processings, however, are also necessary which compute secondary parameters as functions of primary parameters. A typical example is Zeff, which is a function of Te, Ne and bremsstrahluny intensity. The real-time processor is equipped for such secondary processings and transfer the results. Preprocessing unit -PU- attached to ACM and real-time processor contains a signal processor, which executes in parallel such function as move, add and multiply during one micro-instruction cycle of 200 nsec. According to the progress of the experiment, more high speed processing are required, so the authors developed the PU-X module that contains multi signal processors. After a shot, inter-shot-processor which consists of general-purpose computers, gathers data into the database, then analyze them, and improve these processes to more effective

  1. Real-Time Disk Scheduling in a Mixed-Media File System

    NARCIS (Netherlands)

    Bosch, H.G.P.; Mullender, Sape J.

    2000-01-01

    This paper presents our real-time disk scheduler called the L scheduler, which optimizes unscheduled best-effort disk requests by giving priority to best-effort disk requests while meeting real-time request deadlines. Our scheduler tries to execute real-time disk requests as much as possible in the

  2. Partial strands synthesizing leads to inevitable aborting and complicated products in consecutive polymerase chain reactions (PCRs)

    Institute of Scientific and Technical Information of China (English)

    LUO Rui; ZHANG DaMing

    2007-01-01

    Various abnormal phenomena have been observed during PCR so far. The present study performed a series of consecutive PCRs (including many rounds of re-amplification continuously) and found that the abortion of re-amplification was inevitable as long as a variety of complicated product appeared.The aborting stages varied, according to the lengths of targets. Longer targets reached the abortion earlier than the shorter ones, marked by appearance of the complex that was immobile in electrophoresis. Denatured gel-electrophoresis revealed that the complex was mainly made up of shorter or partially synthesized strands, together with small amounts of full-length ones. Able to be digested by S1 nuclease but unable by restriction endonucleases (REs), the complex was proved to consist of both single regions and double-helix regions that kept the complex stable thermodynamically. Simulations gave evidence that partial strands, even at lower concentration, could disturb re-amplification effectively and lead to the abortion of re-amplifications finally. It was pointed out that the partial strands formed chiefly via polymerase's infidelity, and hence the solution to lighten the abnormality was also proposed.

  3. Recurrent high level parvovirus B19/genotype 2 viremia in a renal transplant recipient analyzed by real-time PCR for simultaneous detection of genotypes 1 to 3.

    Science.gov (United States)

    Liefeldt, Lutz; Plentz, Annelie; Klempa, Boris; Kershaw, Olivia; Endres, Anne-Sophie; Raab, Ulla; Neumayer, Hans-H; Meisel, Helga; Modrow, Susanne

    2005-01-01

    Organ transplant recipients infected with parvovirus B19 frequently develop persistent viremia associated with chronic anemia and pure red cell aplasia. In this study, a male renal transplant recipient who had been infected with parvovirus B19/genotype 2 after renal transplantation at the age of 34 years is described. The patient was repeatedly treated with high dose intravenous immunoglobulin (IVIG) that resulted in the resolvement of symptoms but not in virus eradication. During an observation period of 33 months after transplantation three phases associated with high parvovirus B19 viremia were observed. Both the first and the second viremic phases were combined with severe anemia. Parvovirus B19 specific IgM-antibodies were initially detected at the beginning of the second phase in continually rising concentrations. Initially eradication of the virus by immunoglobulin therapy was reported after the first viremic phase [Liefeldt et al. (2002): Nephrol Dial Transplant 17:1840-1842]. Retrospectively this statement has to be corrected. It was based on the use of a qualitative PCR assay specific for parvovirus B19 genotype 1 associated with reduced sensitivity for detection of genotype 2. After sequence analysis of the viral DNA and adjustment of a real-time PCR assay (TaqMan) for quantitative detection of all three B19 virus genotypes analysis of consecutive serum samples allowed the demonstration of long lasting phases with reduced viral loads following IVIG-treatment. These results demonstrate that IVIG treatment of parvovirus B19-triggered anemia in transplant recipients offers an opportunity to resolve symptoms, but does not guarantee eradication of the virus. Since reactivation of parvovirus B19 infection can result in high virus load associated with the recurrence of symptoms repeated screening for viral DNA is recommended using the TaqMan system established for quantitative detection of all three genotypes of parvovirus B19. Copyright 2005 Wiley-Liss, Inc.

  4. Real-time centre detection of an OLED structure

    NARCIS (Netherlands)

    Pieters, R.S.; Jonker, P.P.; Nijmeijer, H.

    2009-01-01

    The research presented in this paper focuses on real-time image processing for visual servoing, i.e. the positioning of a x-y table by using a camera only instead of encoders. A camera image stream plus real-time image processing determines the position in the next iteration of the table controller.

  5. Real-Time Center Detection of an OLED Structure

    NARCIS (Netherlands)

    Pieters, R.S.; Jonker, P.P.; Nijmeijer, H.; Blanc-Talon, J.; Philips, W.; Popescu, D.; Scheunders, P.

    2009-01-01

    The research presented in this paper focuses on real-time image processing for visual servoing, i.e. the positioning of a x-y table by using a camera only instead of encoders. A camera image stream plus real-time image processing determines the position in the next iteration of the table controller.

  6. X-real-time executive (X-RTE) an ultra-high reliable real-time executive for safety critical systems

    International Nuclear Information System (INIS)

    Suresh Babu, R.M.

    1995-01-01

    With growing number of application of computers in safety critical systems of nuclear plants there has been a need to assure high quality and reliability of the software used in these systems. One way to assure software quality is to use qualified software components. Since the safety systems and control systems are real-time systems there is a need for a real-time supervisory software to guarantee temporal response of the system. This report describes one such software package, called X-Real-Time Executive (or X-RTE), which was developed in Reactor Control Division, BARC. The report describes all the capabilities and unique features of X-RTE and compares it with a commercially available operating system. The features of X-RTE include pre-emptive scheduling, process synchronization, inter-process communication, multi-processor support, temporal support, debug facility, high portability, high reliability, high quality, and extensive documentation. Examples have been used very liberally to illustrate the underlying concepts. Besides, the report provides a brief description about the methods used, during the software development, to assure high quality and reliability of X-RTE. (author). refs., 11 figs., tabs

  7. Real time freeway incident detection.

    Science.gov (United States)

    2014-04-01

    The US Department of Transportation (US-DOT) estimates that over half of all congestion : events are caused by highway incidents rather than by rush-hour traffic in big cities. Real-time : incident detection on freeways is an important part of any mo...

  8. Cost Analysis for Real-time Java Scoped-memory Areas

    Directory of Open Access Journals (Sweden)

    Delvin Defoe

    2007-08-01

    Full Text Available Java has recently joined C and C++ as a development platform for real-time and embedded applications. Java's garbage collection, while generally a useful feature, can be problematic for these applications: garbage collection occurs at unpredictable times and its latency is typically unbounded. This can compromise necessary real-time guarantees. To overcome these limitations, the Real-Time for Java Expert Group (RTJEG proposed the Real-Time Specification for Java (RTSJ, which introduced new memory models and new threads to utilize those models. One such memory model uses scoped-memory areas, which work best in the context of a NoHeapRealtimeThread (NHRT. Although much work has been done with scoped-memory areas and NHRTs, there is no system-independent analysis of their costs. In this article we present an asymptotic analysis for RTSJ scoped-memory areas and NHRTs.

  9. Synchronization and fault-masking in redundant real-time systems

    Science.gov (United States)

    Krishna, C. M.; Shin, K. G.; Butler, R. W.

    1983-01-01

    A real time computer may fail because of massive component failures or not responding quickly enough to satisfy real time requirements. An increase in redundancy - a conventional means of improving reliability - can improve the former but can - in some cases - degrade the latter considerably due to the overhead associated with redundancy management, namely the time delay resulting from synchronization and voting/interactive consistency techniques. The implications of synchronization and voting/interactive consistency algorithms in N-modular clusters on reliability are considered. All these studies were carried out in the context of real time applications. As a demonstrative example, we have analyzed results from experiments conducted at the NASA Airlab on the Software Implemented Fault Tolerance (SIFT) computer. This analysis has indeed indicated that in most real time applications, it is better to employ hardware synchronization instead of software synchronization and not allow reconfiguration.

  10. High-speed real-time OFDM transmission based on FPGA

    Science.gov (United States)

    Xiao, Xin; Li, Fan; Yu, Jianjun

    2016-02-01

    In this paper, we review our recent research progresses on real-time orthogonal frequency division multiplexing (OFDM) transmission based on FPGA. We successfully demonstrated four-channel wavelength-division multiplexing (WDM) 256.51Gb/s 16-ary quadrature amplitude modulation (16QAM)-OFDM signal transmission system for short-reach optical amplifier free inter-connection with real-time reception. Four optical carriers are modulated by four different 16QAM-OFDM signals via 10G-class direct modulation lasers (DMLs). We achieved highest capacity real-time reception optical OFDM signal transmission over 2.4-km SMF with the bit-error ratio (BER) under soft-decision forward error correction (SD-FEC) limitation of 2.4×10-2. In order to achieve higher spectrum efficiency (SE), we demonstrate 4-channel high level QAM-OFDM transmission over 20-km SMF-28 with real-time reception. 58.72-Gb/s 256QAM-OFDM and 56.4-Gb/s 128QAM-OFDM signal transmission within 25-GHz grid is achieved with the BER under 2.4×10-2 and real-time reception.

  11. Upgrade of the COMPASS tokamak real-time control system

    Energy Technology Data Exchange (ETDEWEB)

    Janky, F., E-mail: filip.janky.work@gmail.com [Institute of Plasma Physics, AS CR, v.v.i., Association EURATOM/IPP.CR, Za Slovankou 3, 18200 Prague (Czech Republic); Charles University in Prague, Faculty of Mathematics and Physics, V Holesovickach 2, 18000 Prague (Czech Republic); Havlicek, J. [Institute of Plasma Physics, AS CR, v.v.i., Association EURATOM/IPP.CR, Za Slovankou 3, 18200 Prague (Czech Republic); Charles University in Prague, Faculty of Mathematics and Physics, V Holesovickach 2, 18000 Prague (Czech Republic); Batista, A.J.N. [Associação EURATOM/IST, Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001 Lisboa (Portugal); Kudlacek, O.; Seidl, J. [Institute of Plasma Physics, AS CR, v.v.i., Association EURATOM/IPP.CR, Za Slovankou 3, 18200 Prague (Czech Republic); Neto, A.C. [Associação EURATOM/IST, Instituto de Plasmas e Fusão Nuclear, Instituto Superior Técnico, Universidade Técnica de Lisboa, 1049-001 Lisboa (Portugal); Pipek, J.; Hron, M. [Institute of Plasma Physics, AS CR, v.v.i., Association EURATOM/IPP.CR, Za Slovankou 3, 18200 Prague (Czech Republic); Mikulin, O. [Institute of Plasma Physics, AS CR, v.v.i., Association EURATOM/IPP.CR, Za Slovankou 3, 18200 Prague (Czech Republic); Czech Technical University, Faculty of Nuclear Sciences and Physical Engineering, V Holesovickach 2, 18000 Prague (Czech Republic); and others

    2014-03-15

    Highlights: • An upgrade of the COMPASS real-time system has been made to generally improve the plasma performance. • Stability of discharges in SNT configuration has been increased. • Plasma flat-top phase length has been extended. • Central solenoid protection has been developed. • Plasma position estimation has been improved. - Abstract: The COMPASS plasma control system is based on the MARTe real-time framework. Thanks to MARTe modularity and flexibility new algorithms have been developed for plasma diagnostic (plasma position calculation), control (shaping field control), and protection systems (central solenoid protection). Moreover, the MARTe framework itself was modified to broaden the communication capabilities via Aurora. This paper presents the recent upgrades and improvements made to the COMPASS real-time plasma control system, focusing on the issues related to precision of the real-time calculations, and discussing the improvements in terms of discharge parameters and stability. In particular, the new real-time system has given the possibility to analyze and to minimize the transport delays of each control loop.

  12. Testing Real-Time Systems Using UPPAAL

    DEFF Research Database (Denmark)

    Hessel, Anders; Larsen, Kim Guldstrand; Mikucionis, Marius

    2008-01-01

    This chapter presents principles and techniques for model-based black-box conformance testing of real-time systems using the Uppaal model-checking tool-suite. The basis for testing is given as a network of concurrent timed automata specified by the test engineer. Relativized input...

  13. The tracing of mycobacteria in drinking water supply systems by culture, conventional, and real time PCRs

    Czech Academy of Sciences Publication Activity Database

    Klanicová, B.; Seďa, Jaromír; Slaná, I.; Slaný, M.; Pavlík, I.

    2013-01-01

    Roč. 67, č. 6 (2013), s. 725-731 ISSN 0343-8651 Institutional support: RVO:60077344 Keywords : avium subsp paratuberculosis * nontuberculous mycobacteria * potable water * survival * intracellulare Subject RIV: EE - Microbiology, Virology Impact factor: 1.359, year: 2013

  14. NSTX-U Advances in Real-Time C++11 on Linux

    Science.gov (United States)

    Erickson, Keith G.

    2015-08-01

    Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11 standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) will serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.

  15. NSTX-U Advances in Real-Time C++11 on Linux

    International Nuclear Information System (INIS)

    Erickson, Keith G.

    2015-01-01

    Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) will serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation's real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds

  16. RealCalc : a real time Java calculation tool. Application to HVSR estimation

    Science.gov (United States)

    Hloupis, G.; Vallianatos, F.

    2009-04-01

    Java computation platform is not a newcomer in the seismology field. It is mainly used for applications regarding collecting, requesting, spreading and visualizing seismological data because it is productive, safe and has low maintenance costs. Although it has very attractive characteristics for the engineers, Java didn't used frequently in real time applications where prediction and reliability required as a reaction to real world events. The main reasons for this are the absence of priority support (such as priority ceiling or priority inversion) and the use of an automated memory management (called garbage collector). To overcome these problems a number of extensions have been proposed with the Real Time Specification for Java (RTSJ) being the most promising and used one. In the current study we used the RTSJ to build an application that receives data continuously and provides estimations in real time. The application consists of four main modules: incoming data, preprocessing, estimation and publication. As an application example we present real time HVSR estimation. Microtremors recordings are collected continuously from the incoming data module. The preprocessing module consists of a window selector tool based on wavelets which is applied on the incoming data stream in order derive the most stationary parts. The estimation module provides all the necessary calculations according to user specifications. Finally the publication module except the results presentation it also calculates attributes and relevant statistics for each site (temporal variations, HVSR stability). Acknowledgements This work is partially supported by the Greek General Secretariat of Research and Technology in the frame of Crete Regional Project 2000- 2006 (M1.2): "TALOS: An integrated system of seismic hazard monitoring and management in the front of the Hellenic Arc", CRETE PEP7 (KP_7).

  17. Real-time hybrid simulation using the convolution integral method

    International Nuclear Information System (INIS)

    Kim, Sung Jig; Christenson, Richard E; Wojtkiewicz, Steven F; Johnson, Erik A

    2011-01-01

    This paper proposes a real-time hybrid simulation method that will allow complex systems to be tested within the hybrid test framework by employing the convolution integral (CI) method. The proposed CI method is potentially transformative for real-time hybrid simulation. The CI method can allow real-time hybrid simulation to be conducted regardless of the size and complexity of the numerical model and for numerical stability to be ensured in the presence of high frequency responses in the simulation. This paper presents the general theory behind the proposed CI method and provides experimental verification of the proposed method by comparing the CI method to the current integration time-stepping (ITS) method. Real-time hybrid simulation is conducted in the Advanced Hazard Mitigation Laboratory at the University of Connecticut. A seismically excited two-story shear frame building with a magneto-rheological (MR) fluid damper is selected as the test structure to experimentally validate the proposed method. The building structure is numerically modeled and simulated, while the MR damper is physically tested. Real-time hybrid simulation using the proposed CI method is shown to provide accurate results

  18. Managing high-bandwidth real-time data storage

    Energy Technology Data Exchange (ETDEWEB)

    Bigelow, David D. [Los Alamos National Laboratory; Brandt, Scott A [Los Alamos National Laboratory; Bent, John M [Los Alamos National Laboratory; Chen, Hsing-Bung [Los Alamos National Laboratory

    2009-09-23

    There exist certain systems which generate real-time data at high bandwidth, but do not necessarily require the long-term retention of that data in normal conditions. In some cases, the data may not actually be useful, and in others, there may be too much data to permanently retain in long-term storage whether it is useful or not. However, certain portions of the data may be identified as being vitally important from time to time, and must therefore be retained for further analysis or permanent storage without interrupting the ongoing collection of new data. We have developed a system, Mahanaxar, intended to address this problem. It provides quality of service guarantees for incoming real-time data streams and simultaneous access to already-recorded data on a best-effort basis utilizing any spare bandwidth. It has built in mechanisms for reliability and indexing, can scale upwards to meet increasing bandwidth requirements, and handles both small and large data elements equally well. We will show that a prototype version of this system provides better performance than a flat file (traditional filesystem) based version, particularly with regard to quality of service guarantees and hard real-time requirements.

  19. Measurement of Epstein-Barr virus DNA loads in whole blood and plasma by TaqMan PCR and in peripheral blood lymphocytes by competitive PCR.

    Science.gov (United States)

    Wadowsky, Robert M; Laus, Stella; Green, Michael; Webber, Steven A; Rowe, David

    2003-11-01

    Epstein-Barr virus (EBV) DNA load values were measured in samples of whole blood (n = 60) and plasma (n = 59) by TaqMan PCR and in samples of peripheral blood lymphocytes (PBLs) (n = 60) by competitive PCR (cPCR). The samples were obtained from 44 transplant recipients. The whole-blood and PBL loads correlated highly (r(2) > 0.900), whereas the plasma and PBL loads correlated poorly (r(2) = 0.512). Testing of whole blood by TaqMan PCR is an acceptable alternative to testing of PBLs by cPCR for quantifying EBV DNA load.

  20. Hardware Approach for Real Time Machine Stereo Vision

    Directory of Open Access Journals (Sweden)

    Michael Tornow

    2006-02-01

    Full Text Available Image processing is an effective tool for the analysis of optical sensor information for driver assistance systems and controlling of autonomous robots. Algorithms for image processing are often very complex and costly in terms of computation. In robotics and driver assistance systems, real-time processing is necessary. Signal processing algorithms must often be drastically modified so they can be implemented in the hardware. This task is especially difficult for continuous real-time processing at high speeds. This article describes a hardware-software co-design for a multi-object position sensor based on a stereophotogrammetric measuring method. In order to cover a large measuring area, an optimized algorithm based on an image pyramid is implemented in an FPGA as a parallel hardware solution for depth map calculation. Object recognition and tracking are then executed in real-time in a processor with help of software. For this task a statistical cluster method is used. Stabilization of the tracking is realized through use of a Kalman filter. Keywords: stereophotogrammetry, hardware-software co-design, FPGA, 3-d image analysis, real-time, clustering and tracking.

  1. SMR-CL, A Real-time Control Language for Mobile Robots

    DEFF Research Database (Denmark)

    Andersen, Nils Axel; Ravn, Ole

    2004-01-01

    The paper describes requirements and implementation of a tactical control lan¬guage for mobile robots. Emphasis is given to the real-time issues of the language especially the isolation of the hard real-time and the soft real-time layers of the mobile robot control system. The language may be used...

  2. 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.)

  3. Real-Time Head Pose Estimation on Mobile Platforms

    Directory of Open Access Journals (Sweden)

    Jianfeng Ren

    2010-06-01

    Full Text Available Many computer vision applications such as augmented reality require head pose estimation. As far as the real-time implementation of head pose estimation on relatively resource limited mobile platforms is concerned, it is required to satisfy real-time constraints while maintaining reasonable head pose estimation accuracy. The introduced head pose estimation approach in this paper is an attempt to meet this objective. The approach consists of the following components: Viola-Jones face detection, color-based face tracking using an online calibration procedure, and head pose estimation using Hu moment features and Fisher linear discriminant. Experimental results running on an actual mobile device are reported exhibiting both the real- time and accuracy aspects of the developed approach.

  4. Software engineering aspects of real-time programming concepts

    Science.gov (United States)

    Schoitsch, Erwin

    1986-08-01

    Real-time programming is a discipline of great importance not only in process control, but also in fields like communication, office automation, interactive databases, interactive graphics and operating systems development. General concepts of concurrent programming and constructs for process-synchronization are discussed in detail. Tasking and synchronization concepts, methods of process communication, interrupt and timeout handling in systems based on semaphores, signals, conditional critical regions or on real-time languages like Concurrent PASCAL, MODULA, CHILL and ADA are explained and compared with each other. The second part deals with structuring and modularization of technical processes to build reliable and maintainable real time systems. Software-quality and software engineering aspects are considered throughout the paper.

  5. Exploring Earthquakes in Real-Time

    Science.gov (United States)

    Bravo, T. K.; Kafka, A. L.; Coleman, B.; Taber, J. J.

    2013-12-01

    Earthquakes capture the attention of students and inspire them to explore the Earth. Adding the ability to view and explore recordings of significant and newsworthy earthquakes in real-time makes the subject even more compelling. To address this opportunity, the Incorporated Research Institutions for Seismology (IRIS), in collaboration with Moravian College, developed ';jAmaSeis', a cross-platform application that enables students to access real-time earthquake waveform data. Students can watch as the seismic waves are recorded on their computer, and can be among the first to analyze the data from an earthquake. jAmaSeis facilitates student centered investigations of seismological concepts using either a low-cost educational seismograph or streamed data from other educational seismographs or from any seismic station that sends data to the IRIS Data Management System. After an earthquake, students can analyze the seismograms to determine characteristics of earthquakes such as time of occurrence, distance from the epicenter to the station, magnitude, and location. The software has been designed to provide graphical clues to guide students in the analysis and assist in their interpretations. Since jAmaSeis can simultaneously record up to three stations from anywhere on the planet, there are numerous opportunities for student driven investigations. For example, students can explore differences in the seismograms from different distances from an earthquake and compare waveforms from different azimuthal directions. Students can simultaneously monitor seismicity at a tectonic plate boundary and in the middle of the plate regardless of their school location. This can help students discover for themselves the ideas underlying seismic wave propagation, regional earthquake hazards, magnitude-frequency relationships, and the details of plate tectonics. The real-time nature of the data keeps the investigations dynamic, and offers students countless opportunities to explore.

  6. Real-time electricity pricing mechanism in China based on system dynamics

    International Nuclear Information System (INIS)

    He, Yongxiu; Zhang, Jixiang

    2015-01-01

    Highlights: • The system dynamics is used to research the real-time electricity pricing mechanism. • Four kinds of the real-time electricity pricing models are carried out and simulated. • It analysed the electricity price, the user satisfaction and the social benefits under the different models. • Market pricing is the trend of the real-time electricity pricing mechanism. • Initial development path of the real-time price mechanism for China is designed between 2015 and 2030. - Abstract: As an important means of demand-side response, the reasonable formulation of the electricity price mechanism will have an important impact on the balance between the supply and demand of electric power. With the introduction of Chinese intelligence apparatus and the rapid development of smart grids, real-time electricity pricing, as the frontier electricity pricing mechanism in the smart grid, will have great significance on the promotion of energy conservation and the improvement of the total social surplus. From the perspective of system dynamics, this paper studies different real-time electricity pricing mechanisms based on load structure, cost structure and bidding and analyses the situation of user satisfaction and the total social surplus under different pricing mechanisms. Finally, through the comparative analysis of examples under different real-time pricing scenarios, this paper aims to explore and design the future dynamic real-time electricity pricing mechanism in China, predicts the dynamic real-time pricing level and provides a reference for real-time electricity price promotion in the future

  7. Quo vadis? : persuasive computing using real time queue information

    NARCIS (Netherlands)

    Meys, Wouter; Groen, Maarten

    2014-01-01

    By presenting tourists with real-time information an increase in efficiency and satisfaction of their day planning can be achieved. At the same time, real-time information services can offer the municipality the opportunity to spread the tourists throughout the city centre. An important factor for

  8. Scenario-based verification of real-time systems using UPPAAL

    DEFF Research Database (Denmark)

    Li, Shuhao; Belaguer, Sandie; David, Alexandre

    2010-01-01

    Abstract This paper proposes two approaches to tool-supported automatic verification of dense real-time systems against scenario-based requirements, where a system is modeled as a network of timed automata (TAs) or as a set of driving live sequence charts (LSCs), and a requirement is specified...... as a separate monitored LSC chart. We make timed extensions to a kernel subset of the LSC language and define a trace-based semantics. By translating a monitored LSC chart to a behavior-equivalent observer TA and then non-intrusively composing this observer with the original TA modeled real-time system......, the problem of scenario-based verification reduces to a computation tree logic (CTL) real-time model checking problem. In case the real time system is modeled as a set of driving LSC charts, we translate these driving charts and the monitored chart into a behavior-equivalent network of TAs by using a “one...

  9. A curriculum for real-time computer and control systems engineering

    Science.gov (United States)

    Halang, Wolfgang A.

    1990-01-01

    An outline of a syllabus for the education of real-time-systems engineers is given. This comprises the treatment of basic concepts, real-time software engineering, and programming in high-level real-time languages, real-time operating systems with special emphasis on such topics as task scheduling, hardware architectures, and especially distributed automation structures, process interfacing, system reliability and fault-tolerance, and integrated project development support systems. Accompanying course material and laboratory work are outlined, and suggestions for establishing a laboratory with advanced, but low-cost, hardware and software are provided. How the curriculum can be extended into a second semester is discussed, and areas for possible graduate research are listed. The suitable selection of a high-level real-time language and supporting operating system for teaching purposes is considered.

  10. High performance real-time flight simulation at NASA Langley

    Science.gov (United States)

    Cleveland, Jeff I., II

    1994-01-01

    In order to meet the stringent time-critical requirements for real-time man-in-the-loop flight simulation, computer processing operations must be deterministic and be completed in as short a time as possible. This includes simulation mathematical model computational and data input/output to the simulators. In 1986, in response to increased demands for flight simulation performance, personnel at NASA's Langley Research Center (LaRC), working with the contractor, developed extensions to a standard input/output system to provide for high bandwidth, low latency data acquisition and distribution. The Computer Automated Measurement and Control technology (IEEE standard 595) was extended to meet the performance requirements for real-time simulation. This technology extension increased the effective bandwidth by a factor of ten and increased the performance of modules necessary for simulator communications. This technology is being used by more than 80 leading technological developers in the United States, Canada, and Europe. Included among the commercial applications of this technology are nuclear process control, power grid analysis, process monitoring, real-time simulation, and radar data acquisition. Personnel at LaRC have completed the development of the use of supercomputers for simulation mathematical model computational to support real-time flight simulation. This includes the development of a real-time operating system and the development of specialized software and hardware for the CAMAC simulator network. This work, coupled with the use of an open systems software architecture, has advanced the state of the art in real time flight simulation. The data acquisition technology innovation and experience with recent developments in this technology are described.

  11. Real-time water quality monitoring and providing water quality ...

    Science.gov (United States)

    EPA and the U.S. Geological Survey (USGS) have initiated the “Village Blue” research project to provide real-time water quality monitoring data to the Baltimore community and increase public awareness about local water quality in Baltimore Harbor and the Chesapeake Bay. The Village Blue demonstration project complements work that a number of state and local organizations are doing to make Baltimore Harbor “swimmable and fishable” 2 by 2020. Village Blue is designed to build upon EPA’s “Village Green” project which provides real-time air quality information to communities in six locations across the country. The presentation, “Real-time water quality monitoring and providing water quality information to the Baltimore Community”, summarizes the Village Blue real-time water quality monitoring project being developed for the Baltimore Harbor.

  12. Real Time Radiation Monitoring Using Nanotechnology

    Science.gov (United States)

    Li, Jing (Inventor); Hanratty, James J. (Inventor); Wilkins, Richard T. (Inventor); Lu, Yijiang (Inventor)

    2016-01-01

    System and method for monitoring receipt and estimating flux value, in real time, of incident radiation, using two or more nanostructures (NSs) and associated terminals to provide closed electrical paths and to measure one or more electrical property change values .DELTA.EPV, associated with irradiated NSs, during a sequence of irradiation time intervals. Effects of irradiation, without healing and with healing, of the NSs, are separately modeled for first order and second order healing. Change values.DELTA.EPV are related to flux, to cumulative dose received by NSs, and to radiation and healing effectivity parameters and/or.mu., associated with the NS material and to the flux. Flux and/or dose are estimated in real time, based on EPV change values, using measured .DELTA.EPV values. Threshold dose for specified changes of biological origin (usually undesired) can be estimated. Effects of time-dependent radiation flux are analyzed in pre-healing and healing regimes.

  13. The Case For Prediction-based Best-effort Real-time Systems.

    Science.gov (United States)

    1999-01-01

    Real - time Systems Peter A. Dinda Loukas Kallivokas January...DISTRIBUTION STATEMENT A Approved for Public Release Distribution Unlimited DTIG QUALBR DISSECTED X The Case For Prediction-based Best-effort Real - time Systems Peter...Mellon University Pittsburgh, PA 15213 A version of this paper appeared in the Seventh Workshop on Parallel and Distributed Real - Time Systems

  14. A Stack Cache for Real-Time Systems

    DEFF Research Database (Denmark)

    Schoeberl, Martin; Nielsen, Carsten

    2016-01-01

    Real-time systems need time-predictable computing platforms to allowfor static analysis of the worst-case execution time. Caches are important for good performance, but data caches arehard to analyze for the worst-case execution time. Stack allocated data has different properties related...

  15. Applying MDA to SDR for Space to Model Real-time Issues

    Science.gov (United States)

    Blaser, Tammy M.

    2007-01-01

    NASA space communications systems have the challenge of designing SDRs with highly-constrained Size, Weight and Power (SWaP) resources. A study is being conducted to assess the effectiveness of applying the MDA Platform-Independent Model (PIM) and one or more Platform-Specific Models (PSM) specifically to address NASA space domain real-time issues. This paper will summarize our experiences with applying MDA to SDR for Space to model real-time issues. Real-time issues to be examined, measured, and analyzed are: meeting waveform timing requirements and efficiently applying Real-time Operating System (RTOS) scheduling algorithms, applying safety control measures, and SWaP verification. Real-time waveform algorithms benchmarked with the worst case environment conditions under the heaviest workload will drive the SDR for Space real-time PSM design.

  16. A European multicientre study on the comparison of HIV-1 viral loads between VERIS HIV-1 Assay and Roche COBAS® TAQMAN® HIV-1 test, Abbott RealTime HIV-1 Assay, and Siemens VERSANT HIV-1 Assay.

    Science.gov (United States)

    Braun, Patrick; Delgado, Rafael; Drago, Monica; Fanti, Diana; Fleury, Hervé; Hofmann, Jörg; Izopet, Jacques; Kühn, Sebastian; Lombardi, Alessandra; Mancon, Alessandro; Marcos, Mª Angeles; Mileto, Davide; Sauné, Karine; O'Shea, Siobhan; Pérez-Rivilla, Alfredo; Ramble, John; Trimoulet, Pascale; Vila, Jordi; Whittaker, Duncan; Artus, Alain; Rhodes, Daniel

    2017-07-01

    Viral load monitoring is essential for patients under treatment for HIV. Beckman Coulter has developed the VERIS HIV-1 Assay for use on the novel, automated DxN VERIS Molecular Diagnostics System. ¥ OBJECTIVES: Evaluation of the clinical performance of the new quantitative VERIS HIV-1 Assay at multiple EU laboratories. Method comparison with the VERIS HIV-1 Assay was performed with 415 specimens at 5 sites tested with COBAS ® AmpliPrep/COBAS ® TaqMan ® HIV-1 Test, v2.0, 169 specimens at 3 sites tested with RealTime HIV-1 Assay, and 202 specimens from 2 sites tested with VERSANT HIV-1 Assay. Patient monitoring sample results from 4 sites were also compared. Bland-Altman analysis showed the average bias between VERIS HIV-1 Assay and COBAS HIV-1 Test, RealTime HIV-1 Assay, and VERSANT HIV-1 Assay to be 0.28, 0.39, and 0.61 log 10 cp/mL, respectively. Bias at low end levels below 1000cp/mL showed predicted bias to be <0.3 log 10 cp/mL for VERIS HIV-1 Assay versus COBAS HIV-1 Test and RealTime HIV-1 Assay, and <0.5 log 10 cp/mL versus VERSANT HIV-1 Assay. Analysis on 174 specimens tested with the 0.175mL volume VERIS HIV-1 Assay and COBAS HIV-1 Test showed average bias of 0.39 log 10 cp/mL. Patient monitoring results using VERIS HIV-1 Assay demonstrated similar viral load trends over time to all comparators. The VERIS HIV-1 Assay for use on the DxN VERIS System demonstrated comparable clinical performance to COBAS ® HIV-1 Test, RealTime HIV-1 Assay, and VERSANT HIV-1 Assay. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Advanced real-time multi-display educational system (ARMES): An innovative real-time audiovisual mentoring tool for complex robotic surgery.

    Science.gov (United States)

    Lee, Joong Ho; Tanaka, Eiji; Woo, Yanghee; Ali, Güner; Son, Taeil; Kim, Hyoung-Il; Hyung, Woo Jin

    2017-12-01

    The recent scientific and technologic advances have profoundly affected the training of surgeons worldwide. We describe a novel intraoperative real-time training module, the Advanced Robotic Multi-display Educational System (ARMES). We created a real-time training module, which can provide a standardized step by step guidance to robotic distal subtotal gastrectomy with D2 lymphadenectomy procedures, ARMES. The short video clips of 20 key steps in the standardized procedure for robotic gastrectomy were created and integrated with TilePro™ software to delivery on da Vinci Surgical Systems (Intuitive Surgical, Sunnyvale, CA). We successfully performed the robotic distal subtotal gastrectomy with D2 lymphadenectomy for patient with gastric cancer employing this new teaching method without any transfer errors or system failures. Using this technique, the total operative time was 197 min and blood loss was 50 mL and there were no intra- or post-operative complications. Our innovative real-time mentoring module, ARMES, enables standardized, systematic guidance during surgical procedures. © 2017 Wiley Periodicals, Inc.

  18. Simultaneous detection and quantification of Phytophthora nicotianae and P. cactorum, and distribution analyses in strawberry greenhouses by duplex real-time PCR.

    Science.gov (United States)

    Li, Mingzhu; Inada, Minoru; Watanabe, Hideki; Suga, Haruhisa; Kageyama, Koji

    2013-01-01

    Phytophthora nicotianae and P. cactorum cause Phytophthora rot of strawberry. A duplex real-time PCR technique for simultaneous detection and quantification of the two pathogens was developed. Species-specific primers for P. nicotianae and P. cactorum were designed based on the internal transcribed spacer regions (ITS) of rDNA and the ras-related protein gene Ypt1, respectively. TaqMan probes were labeled with FAM for P. nicotianae and HEX for P. cactorum. Specificities were demonstrated using 52 isolates, including various soil-borne pathogens. Sensitivities for P. nicotianae and P. cactorum DNAs were 10 fg and 1 pg, respectively. The technique was applied to naturally infested soil and root samples; the two pathogens were detected and the target DNA concentrations were quantified. Significant correlations of DNA quantities in roots and the surrounding soils were found. The minimum soil DNA concentration predicting the development of disease symptoms was estimated as 20 pg (g soil)(-1). In three strawberry greenhouses examined, the target DNA concentrations ranged from 1 to 1,655 pg (g soil)(-1) for P. nicotianae and from 13 to 233 pg (g soil)(-1) for P. cactorum. The method proved fast and reliable, and provides a useful tool to monitor P. nicotianae and P. cactorum in plants or soils.

  19. Integrating Real-time Earthquakes into Natural Hazard Courses

    Science.gov (United States)

    Furlong, K. P.; Benz, H. M.; Whitlock, J. S.; Bittenbinder, A. N.; Bogaert, B. B.

    2001-12-01

    Natural hazard courses are playing an increasingly important role in college and university earth science curricula. Students' intrinsic curiosity about the subject and the potential to make the course relevant to the interests of both science and non-science students make natural hazards courses popular additions to a department's offerings. However, one vital aspect of "real-life" natural hazard management that has not translated well into the classroom is the real-time nature of both events and response. The lack of a way to entrain students into the event/response mode has made implementing such real-time activities into classroom activities problematic. Although a variety of web sites provide near real-time postings of natural hazards, students essentially learn of the event after the fact. This is particularly true for earthquakes and other events with few precursors. As a result, the "time factor" and personal responsibility associated with natural hazard response is lost to the students. We have integrated the real-time aspects of earthquake response into two natural hazard courses at Penn State (a 'general education' course for non-science majors, and an upper-level course for science majors) by implementing a modification of the USGS Earthworm system. The Earthworm Database Management System (E-DBMS) catalogs current global seismic activity. It provides earthquake professionals with real-time email/cell phone alerts of global seismic activity and access to the data for review/revision purposes. We have modified this system so that real-time response can be used to address specific scientific, policy, and social questions in our classes. As a prototype of using the E-DBMS in courses, we have established an Earthworm server at Penn State. This server receives national and global seismic network data and, in turn, transmits the tailored alerts to "on-duty" students (e-mail, pager/cell phone notification). These students are responsible to react to the alarm

  20. Advances in Real-Time Systems

    CERN Document Server

    Chakraborty, Samarjit

    2012-01-01

    This volume contains the lectures given in honor to Georg Farber as tribute to his contributions in the area of real-time and embedded systems. The chapters of many leading scientists cover a wide range of aspects, like robot or automotive vision systems or medical aspects.

  1. Resource-Parameterized Timing Analysis of Real-Time Systems

    DEFF Research Database (Denmark)

    Kim, Jin Hyun; Legay, Axel; Larsen, Kim Guldstrand

    2015-01-01

    on a specic platform. For the same reason, a configuration of platforms cannot be independent from applications in most cases. This paper proposes a new analysis framework of real-time systems where an application and a platform can be analyzed in a fully independent way such that not only the application...

  2. Developing infrared array controller with software real time operating system

    Science.gov (United States)

    Sako, Shigeyuki; Miyata, Takashi; Nakamura, Tomohiko; Motohara, Kentaro; Uchimoto, Yuka Katsuno; Onaka, Takashi; Kataza, Hirokazu

    2008-07-01

    Real-time capabilities are required for a controller of a large format array to reduce a dead-time attributed by readout and data transfer. The real-time processing has been achieved by dedicated processors including DSP, CPLD, and FPGA devices. However, the dedicated processors have problems with memory resources, inflexibility, and high cost. Meanwhile, a recent PC has sufficient resources of CPUs and memories to control the infrared array and to process a large amount of frame data in real-time. In this study, we have developed an infrared array controller with a software real-time operating system (RTOS) instead of the dedicated processors. A Linux PC equipped with a RTAI extension and a dual-core CPU is used as a main computer, and one of the CPU cores is allocated to the real-time processing. A digital I/O board with DMA functions is used for an I/O interface. The signal-processing cores are integrated in the OS kernel as a real-time driver module, which is composed of two virtual devices of the clock processor and the frame processor tasks. The array controller with the RTOS realizes complicated operations easily, flexibly, and at a low cost.

  3. Replacing OSE with Real Time capable Linux

    OpenAIRE

    Boman, Simon; Rutgersson, Olof

    2009-01-01

    For many years OSE has been a common used operating system, with real time extensions enhancements, in embed-ded systems. But in the last decades, Linux has grown and became a competitor to common operating systems and, in recent years, even as an operating system with real time extensions. With this in mind, ÅF was interested in replacing the quite expensive OSE with some distribution of the open source based Linux on a PowerPC MPC8360. Therefore, our purpose with thesis is to implement Linu...

  4. Real time processor for array speckle interferometry

    Science.gov (United States)

    Chin, Gordon; Florez, Jose; Borelli, Renan; Fong, Wai; Miko, Joseph; Trujillo, Carlos

    1989-02-01

    The authors are constructing a real-time processor to acquire image frames, perform array flat-fielding, execute a 64 x 64 element two-dimensional complex FFT (fast Fourier transform) and average the power spectrum, all within the 25 ms coherence time for speckles at near-IR (infrared) wavelength. The processor will be a compact unit controlled by a PC with real-time display and data storage capability. This will provide the ability to optimize observations and obtain results on the telescope rather than waiting several weeks before the data can be analyzed and viewed with offline methods. The image acquisition and processing, design criteria, and processor architecture are described.

  5. Real-Time Multi-Directional Equipment Site

    Data.gov (United States)

    Federal Laboratory Consortium — As part of the George E. Brown, Jr. Network for Earthquake Engineering Simulation (NEES) Program, Lehigh University has established the Real-Time Multi-Directional...

  6. Multivariate performance reliability prediction in real-time

    International Nuclear Information System (INIS)

    Lu, S.; Lu, H.; Kolarik, W.J.

    2001-01-01

    This paper presents a technique for predicting system performance reliability in real-time considering multiple failure modes. The technique includes on-line multivariate monitoring and forecasting of selected performance measures and conditional performance reliability estimates. The performance measures across time are treated as a multivariate time series. A state-space approach is used to model the multivariate time series. Recursive forecasting is performed by adopting Kalman filtering. The predicted mean vectors and covariance matrix of performance measures are used for the assessment of system survival/reliability with respect to the conditional performance reliability. The technique and modeling protocol discussed in this paper provide a means to forecast and evaluate the performance of an individual system in a dynamic environment in real-time. The paper also presents an example to demonstrate the technique

  7. Improved Real-time Denoising Method Based on Lifting Wavelet Transform

    Directory of Open Access Journals (Sweden)

    Liu Zhaohua

    2014-06-01

    Full Text Available Signal denoising can not only enhance the signal to noise ratio (SNR but also reduce the effect of noise. In order to satisfy the requirements of real-time signal denoising, an improved semisoft shrinkage real-time denoising method based on lifting wavelet transform was proposed. The moving data window technology realizes the real-time wavelet denoising, which employs wavelet transform based on lifting scheme to reduce computational complexity. Also hyperbolic threshold function and recursive threshold computing can ensure the dynamic characteristics of the system, in addition, it can improve the real-time calculating efficiency as well. The simulation results show that the semisoft shrinkage real-time denoising method has quite a good performance in comparison to the traditional methods, namely soft-thresholding and hard-thresholding. Therefore, this method can solve more practical engineering problems.

  8. Towards Real Time Simulation of Ship-Ship Interaction

    DEFF Research Database (Denmark)

    Lindberg, Ole; Bingham, Harry B.; Engsig-Karup, Allan Peter

    2012-01-01

    We present recent and preliminary work directed towards the development of a simplified, physics-based model for improved simulation of ship-ship interaction that can be used for both analysis and real-time computing (i.e. with real-time constraints due to visualization). The goal is to implement...... accurate (realistic) and much faster ship-wave and ship-ship simulations than are currently possible. The coupling of simulation with visualization should improve the visual experience such that it can be perceived as more realistic in training. Today the state-of-art in real-time ship-ship interaction...... is for efficiency reasons and time-constraints in visualization based on model experiments in towing tanks and precomputed force tables. We anticipate that the fast, and highly parallel, algorithm described by Engsig-Karup et al. [2011] for execution on affordable modern high-throughput Graphics Processing Units...

  9. Real-time motion-adaptive-optimization (MAO) in TomoTherapy

    Energy Technology Data Exchange (ETDEWEB)

    Lu Weiguo; Chen Mingli; Ruchala, Kenneth J; Chen Quan; Olivera, Gustavo H [TomoTherapy Inc., 1240 Deming Way, Madison, WI (United States); Langen, Katja M; Kupelian, Patrick A [MD Anderson Cancer Center-Orlando, Orlando, FL (United States)], E-mail: wlu@tomotherapy.com

    2009-07-21

    IMRT delivery follows a planned leaf sequence, which is optimized before treatment delivery. However, it is hard to model real-time variations, such as respiration, in the planning procedure. In this paper, we propose a negative feedback system of IMRT delivery that incorporates real-time optimization to account for intra-fraction motion. Specifically, we developed a feasible workflow of real-time motion-adaptive-optimization (MAO) for TomoTherapy delivery. TomoTherapy delivery is characterized by thousands of projections with a fast projection rate and ultra-fast binary leaf motion. The technique of MAO-guided delivery calculates (i) the motion-encoded dose that has been delivered up to any given projection during the delivery and (ii) the future dose that will be delivered based on the estimated motion probability and future fluence map. These two pieces of information are then used to optimize the leaf open time of the upcoming projection right before its delivery. It consists of several real-time procedures, including 'motion detection and prediction', 'delivered dose accumulation', 'future dose estimation' and 'projection optimization'. Real-time MAO requires that all procedures are executed in time less than the duration of a projection. We implemented and tested this technique using a TomoTherapy (registered) research system. The MAO calculation took about 100 ms per projection. We calculated and compared MAO-guided delivery with two other types of delivery, motion-without-compensation delivery (MD) and static delivery (SD), using simulated 1D cases, real TomoTherapy plans and the motion traces from clinical lung and prostate patients. The results showed that the proposed technique effectively compensated for motion errors of all test cases. Dose distributions and DVHs of MAO-guided delivery approached those of SD, for regular and irregular respiration with a peak-to-peak amplitude of 3 cm, and for medium and large

  10. Real-time motion-adaptive-optimization (MAO) in TomoTherapy

    International Nuclear Information System (INIS)

    Lu Weiguo; Chen Mingli; Ruchala, Kenneth J; Chen Quan; Olivera, Gustavo H; Langen, Katja M; Kupelian, Patrick A

    2009-01-01

    IMRT delivery follows a planned leaf sequence, which is optimized before treatment delivery. However, it is hard to model real-time variations, such as respiration, in the planning procedure. In this paper, we propose a negative feedback system of IMRT delivery that incorporates real-time optimization to account for intra-fraction motion. Specifically, we developed a feasible workflow of real-time motion-adaptive-optimization (MAO) for TomoTherapy delivery. TomoTherapy delivery is characterized by thousands of projections with a fast projection rate and ultra-fast binary leaf motion. The technique of MAO-guided delivery calculates (i) the motion-encoded dose that has been delivered up to any given projection during the delivery and (ii) the future dose that will be delivered based on the estimated motion probability and future fluence map. These two pieces of information are then used to optimize the leaf open time of the upcoming projection right before its delivery. It consists of several real-time procedures, including 'motion detection and prediction', 'delivered dose accumulation', 'future dose estimation' and 'projection optimization'. Real-time MAO requires that all procedures are executed in time less than the duration of a projection. We implemented and tested this technique using a TomoTherapy (registered) research system. The MAO calculation took about 100 ms per projection. We calculated and compared MAO-guided delivery with two other types of delivery, motion-without-compensation delivery (MD) and static delivery (SD), using simulated 1D cases, real TomoTherapy plans and the motion traces from clinical lung and prostate patients. The results showed that the proposed technique effectively compensated for motion errors of all test cases. Dose distributions and DVHs of MAO-guided delivery approached those of SD, for regular and irregular respiration with a peak-to-peak amplitude of 3 cm, and for medium and large prostate motions. The results conceptually

  11. Real-Time Operating Systems for Multicore Embedded Systems

    OpenAIRE

    Tomiyama, Hiroyuki; Honda, Shinya; Takada, Hiroaki

    2008-01-01

    Multicore systems-on-chip have become popular inthe design of embedded systems in order to simultaneously achieve high performance and low power consumption. On the software side, real-time operating systems are necessary in orderto handle growing complexity of embedded software. This paper describes requirements, design principles and implementation techniques for real-time operating systems to be used inasymmetric multicore systems.

  12. Documentation Driven Development for Complex Real-Time Systems

    Science.gov (United States)

    2004-12-01

    This paper presents a novel approach for development of complex real - time systems , called the documentation-driven development (DDD) approach. This... time systems . DDD will also support automated software generation based on a computational model and some relevant techniques. DDD includes two main...stakeholders to be easily involved in development processes and, therefore, significantly improve the agility of software development for complex real

  13. Real-time transfer and display of radiography image

    International Nuclear Information System (INIS)

    Liu Ximing; Wu Zhifang; Miao Jicheng

    2000-01-01

    The information process network of cobalt-60 container inspection system is a local area network based on PC. The system requires reliable transfer of radiography image between collection station and process station and the real-time display of radiography image on process station. Due to the very high data acquisition rate, in order to realize the real-time transfer and display of radiography image, 100 M Ethernet technology and network process communication technology are adopted in the system. Windows Sockets is the most common process communication technology up to now. Several kinds of process communication way under Windows Sockets technology are compared and tested. Finally the author realized 1 Mbyte/s' inerrant image transfer and real-time display with blocked datagram transfer technology

  14. Pseudo real-time imaging systems with nonredundant pinhole arrays

    International Nuclear Information System (INIS)

    Han, K.S.; Berzins, G.J.; Roach, W.H.

    1976-01-01

    Coded aperture techniques, because of their efficiency and three-dimensional information content, represent potentially powerful tools for LMFBR safety experiment diagnostics. These techniques should be even more powerful if the data can be interpreted in real time or in pseudo real time. For example, to satisfy the stated goals for LMFBR diagnostics (1-ms time resolution and 1-mm spatial resolution), it is conceivable that several hundred frames of coded data would be recorded. To unscramble all of this information into reconstructed images could be a laborious, time-consuming task. A way to circumvent the tedium is with the use of the described hybrid digital/analog real-time imaging system. Some intermediate results are described briefly

  15. Real-time control using open source RTOS

    Science.gov (United States)

    Irwin, Philip C.; Johnson, Richard L., Jr.

    2002-12-01

    Complex telescope systems such as interferometers tend to rely heavily on hard real-time operating systems (RTOS). It has been standard practice at NASA's Jet Propulsion Laboratory (JPL) and many other institutions to use costly commercial RTOSs and hardware. After developing a real-time toolkit for VxWorks on the PowerPC platform (dubbed RTC), the interferometry group at JPL is porting this code to the real-time Application Interface (RTAI), an open source RTOS that is essentially an extension to the Linux kernel. This port has the potential to reduce software and hardware costs for future projects, while increasing the level of performance. The goals of this paper are to briefly describe the RTC toolkit, highlight the successes and pitfalls of porting the toolkit from VxWorks to Linux-RTAI, and to discuss future enhancements that will be implemented as a direct result of this port. The first port of any body of code is always the most difficult since it uncovers the OS-specific calls and forces "red flags" into those portions of the code. For this reason, It has also been a huge benefit that the project chose a generic, platform independent OS extension, ACE, and its CORBA counterpart, TAO. This port of RTC will pave the way for conversions to other environments, the most interesting of which is a non-real-time simulation environment, currently being considered by the Space Interferometry Mission (SIM) and the Terrestrial Planet Finder (TPF) Projects.

  16. Real-time speech gisting for ATC applications

    Science.gov (United States)

    Dunkelberger, Kirk A.

    1995-06-01

    Command and control within the ATC environment remains primarily voice-based. Hence, automatic real time, speaker independent, continuous speech recognition (CSR) has many obvious applications and implied benefits to the ATC community: automated target tagging, aircraft compliance monitoring, controller training, automatic alarm disabling, display management, and many others. However, while current state-of-the-art CSR systems provide upwards of 98% word accuracy in laboratory environments, recent low-intrusion experiments in the ATCT environments demonstrated less than 70% word accuracy in spite of significant investments in recognizer tuning. Acoustic channel irregularities and controller/pilot grammar verities impact current CSR algorithms at their weakest points. It will be shown herein, however, that real time context- and environment-sensitive gisting can provide key command phrase recognition rates of greater than 95% using the same low-intrusion approach. The combination of real time inexact syntactic pattern recognition techniques and a tight integration of CSR, gisting, and ATC database accessor system components is the key to these high phase recognition rates. A system concept for real time gisting in the ATC context is presented herein. After establishing an application context, discussion presents a minimal CSR technology context then focuses on the gisting mechanism, desirable interfaces into the ATCT database environment, and data and control flow within the prototype system. Results of recent tests for a subset of the functionality are presented together with suggestions for further research.

  17. Real time animation of space plasma phenomena

    International Nuclear Information System (INIS)

    Jordan, K.F.; Greenstadt, E.W.

    1987-01-01

    In pursuit of real time animation of computer simulated space plasma phenomena, the code was rewritten for the Massively Parallel Processor (MPP). The program creates a dynamic representation of the global bowshock which is based on actual spacecraft data and designed for three dimensional graphic output. This output consists of time slice sequences which make up the frames of the animation. With the MPP, 16384, 512 or 4 frames can be calculated simultaneously depending upon which characteristic is being computed. The run time was greatly reduced which promotes the rapid sequence of images and makes real time animation a foreseeable goal. The addition of more complex phenomenology in the constructed computer images is now possible and work proceeds to generate these images

  18. Formal Verification and Implementation of Real-Time Applications

    Directory of Open Access Journals (Sweden)

    Liviu Haţegan

    2009-12-01

    Full Text Available This paper presents a method for the formal description, verification and automatic source code generation of embedded real-time multitasking applications, based on a model consisting of networks of timed automata. The model describes a real-time operating system kernel and application tasks, taking into consideration both non-preemptive and preemptive scheduling. The timing properties of theproposed model can be verified using a modelchecking tool. We also provide a solution for C source code generation based on the application’s model. For this purpose a unified resource access interface was implemented.

  19. Real-time embedded systems design principles and engineering practices

    CERN Document Server

    Fan, Xiaocong

    2015-01-01

    This book integrates new ideas and topics from real time systems, embedded systems, and software engineering to give a complete picture of the whole process of developing software for real-time embedded applications. You will not only gain a thorough understanding of concepts related to microprocessors, interrupts, and system boot process, appreciating the importance of real-time modeling and scheduling, but you will also learn software engineering practices such as model documentation, model analysis, design patterns, and standard conformance. This book is split into four parts to help you

  20. Real-time Testing of Operating Systems on Raspberry Pi

    OpenAIRE

    Murstad, Amund

    2016-01-01

    A subset of operating systems are called ``real time'' operating systems. While a general operating system like Windows or OSX can make no guarantee when a process gets to run, a real time one has the ability to do so. They are used for systems where the quality of the results from the operating system is not only defined by their correctness, but also by when they arrive. These kinds of systems are called Real-time Systems and can be divided into soft, hard and firm. If a deadline is missed ...