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Sample records for strip assay genotype

  1. Lateral flow strip assay

    Science.gov (United States)

    Miles, Robin R [Danville, CA; Benett, William J [Livermore, CA; Coleman, Matthew A [Oakland, CA; Pearson, Francesca S [Livermore, CA; Nasarabadi, Shanavaz L [Livermore, CA

    2011-03-08

    A lateral flow strip assay apparatus comprising a housing; a lateral flow strip in the housing, the lateral flow strip having a receiving portion; a sample collection unit; and a reagent reservoir. Saliva and/or buccal cells are collected from an individual using the sample collection unit. The sample collection unit is immersed in the reagent reservoir. The tip of the lateral flow strip is immersed in the reservoir and the reagent/sample mixture wicks up into the lateral flow strip to perform the assay.

  2. Genotyping of hepatitis C virus-comparison of three assays.

    Science.gov (United States)

    Haushofer, Alexander C; Berg, Jörg; Hauer, René; Trubert-Exinger, Doris; Stekel, Herbert G; Kessler, Harald H

    2003-08-01

    Genotyping of hepatitis C virus (HCV) is clinically relevant to epidemiology, prognosis, and therapeutical management of HCV infection. Accuracy and specificity of three assays for HCV genotyping/subtyping were determined. The TruGene HCV 5'NC Genotyping Kit (TruGene), which is a direct sequencing test and two assays based on reversed hybridization, Inno-LiPA HCV II assay and ViennaLab HCV Strip Assay, were compared. Amplification products generated by the Cobas Amplicor HCV Test were used. A total of 100 consecutive HCV RNA positive samples derived from patients with chronic hepatitis C were examined for their genotypes/subtypes by the three assays. Identification of genotypes and subtypes by the TruGene assay as reference test for the Inno-LiPA HCV II assay and the ViennaLab HCV Strip Assay or Inno-LiPA HCV II assay as reference test for the TruGene and the ViennaLab HCV Strip Assay showed similar results for overall accuracies (TruGene as reference test for Inno-LiPA HCV II and ViennaLab HCV Strip Assay, genotypes/subtypes: 100%/95.5% and 97%/92%; Inno-LiPA HCV II as reference test for TruGene and ViennaLab HCV Strip Assay, genotypes/subtypes: 99%/85.9% and 97%/87.9%) and specificities (TruGene as reference test for Inno-LiPA HCV II and ViennaLab HCV Strip Assay, genotypes/subtypes: 100%/97.8% and 99%/97.7%; Inno-LiPA HCV II as reference test for TruGene and ViennaLab HCV Strip Assay, genotypes/subtypes: 100%/99.4% and 99.7%/98%). The three assays were found to be reliable for the detection and discrimination of all HCV genotypes common in Europe and in North America and to be suitable for the routine diagnostic laboratory.

  3. Quantifiable Lateral Flow Assay Test Strips

    Science.gov (United States)

    2003-01-01

    As easy to read as a home pregnancy test, three Quantifiable Lateral Flow Assay (QLFA) strips used to test water for E. coli show different results. The brightly glowing control line on the far right of each strip indicates that all three tests ran successfully. But the glowing test line on the middle left and bottom strips reveal their samples were contaminated with E. coli bacteria at two different concentrations. The color intensity correlates with concentration of contamination.

  4. Colloidal gold probe based rapid immunochromatographic strip assay for cortisol

    Energy Technology Data Exchange (ETDEWEB)

    Nara, Seema, E-mail: seemanara@mnnit.ac.in [Department of Applied Mechanics (Biotechnology), Motilal Nehru National Institute of Technology, Allahabad 211004 (India); Department of Reproductive Biomedicine, National Institute of Health and Family Welfare, Munirka, New Delhi 110067 (India); Center for BioMedical Engineering, Indian Institute of Technology, New Delhi 110016 (India); Tripathi, Vinay [Department of Reproductive Biomedicine, National Institute of Health and Family Welfare, Munirka, New Delhi 110067 (India); Center for BioMedical Engineering, Indian Institute of Technology, New Delhi 110016 (India); Singh, Harpal [Center for BioMedical Engineering, Indian Institute of Technology, New Delhi 110016 (India); Shrivastav, Tulsidas G. [Department of Reproductive Biomedicine, National Institute of Health and Family Welfare, Munirka, New Delhi 110067 (India)

    2010-12-03

    A rapid and semi-quantitative immunochromatographic strip (ICS) test for cortisol analysis in serum was developed. The test strip was based on a competitive assay format. Colloidal gold nanoparticles were synthesized and coupled with cortisol-3-carboxymethyloxime-adipic acid dihydrazide-bovine serum albumin (F-3-CMO-ADH-BSA) antigen to directly compete with cortisol in human serum samples. F-3-CMO-ADH-BSA-gold label and uncoupled colloidal gold nanoparticles were appropriately characterized using UV-vis spectroscopy, transmission electron microscopy and atomic force microscopy. Anticortisol antibody raised against F-3-CMO-BSA immunogen in New Zealand white rabbits was coated on the NC membrane as test line. Anti-BSA antibody was used as control line. The lower detection limit of the ICS test was 30 ng mL{sup -1} with visual detection and was completed in 10 min. About 30 human serum samples were also analyzed by the developed strip test and their range of cortisol concentration was established. The developed ICS test is rapid, economic and user friendly.

  5. Most common genotypes and risk factors for HCV in Gaza strip: a cross sectional study

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    Abu-Jadallah Salah Y

    2009-07-01

    Full Text Available Abstract Background The present work aims at determining HCV genotypes in patients with chronic HCV infection, in Gaza strip, Palestine. The most common risk factors for HCV transmission were also evaluated in conjunction with the genotyping data. Results The study shows that there are only two major genotypes of HCV in Gaza Strip: Genotype 1 (subtypes 1a and 1b collectively contribute to 28.3% of the cases, and genotype 4 (subtypes 4a and 4c/d collectively contribute to 64.1% of the cases. Mixed infection with the two genotypes was also present among 7.6% of the cases. In this study a statistically significant relationship was established between the distribution of these genotypes and the patients' living place, traveling history, history of blood transfusion and history of surgical operations. Conclusion The present study is the first to link HCV genotyping in Gaza strip with its possible roots of transmission. Traveling to endemic countries, especially Egypt; blood transfusion and surgical operations are major roots of HCV infection in Gaza strip. The results indicate that iatrogenic and nosocomial procedures may be responsible for the majority of HCV infections in Gaza strip.

  6. Performance comparison of the versant HCV genotype 2.0 assay (LiPA) and the abbott realtime HCV genotype II assay for detecting hepatitis C virus genotype 6.

    Science.gov (United States)

    Yang, Ruifeng; Cong, Xu; Du, Shaocai; Fei, Ran; Rao, Huiying; Wei, Lai

    2014-10-01

    The Versant HCV genotype 2.0 assay (line probe assay [LiPA] 2.0), based on reverse hybridization, and the Abbott Realtime HCV genotype II assay (Realtime II), based on genotype-specific real-time PCR, have been widely used to analyze hepatitis C virus (HCV) genotypes. However, their performances for detecting HCV genotype 6 infections have not been well studied. Here, we analyzed genotype 6 in 63 samples from the China HCV Genotyping Study that were originally identified as genotype 6 using the LiPA 2.0. The genotyping results were confirmed by nonstructural 5B (NS5B) or core sequence phylogenetic analysis. A total of 57 samples were confirmed to be genotype 6 (51 genotype 6a, 5 genotype 6n, and 1 genotype 6e). Four samples identified as a mixture of genotypes 6 and 4 by the LiPA 2.0 were confirmed to be genotype 3b. The remaining two samples classified as genotype 6 by the LiPA 2.0 were confirmed to be genotype 1b, which were intergenotypic recombinants and excluded from further comparison. In 57 genotype 6 samples detected using the Realtime II version 2.00 assay, 47 genotype 6a samples were identified as genotype 6, one 6e sample was misclassified as genotype 1, and four 6a and five 6n samples yielded indeterminate results. Nine nucleotide profiles in the 5' untranslated region affected the performances of both assays. Therefore, our analysis shows that both assays have limitations in identifying HCV genotype 6. The LiPA 2.0 cannot distinguish some 3b samples from genotype 6 samples. The Realtime II assay fails to identify some 6a and all non-6a subtypes, and it misclassifies genotype 6e as genotype 1. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

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

    Science.gov (United States)

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

    2018-01-11

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

  8. The KRAS Strip Assay for detection of KRAS mutation in Egyptian patients with colorectal cancer (CRC): A pilot study

    International Nuclear Information System (INIS)

    Abd El Kader, Y.; Safwat, E.; Kassem, H.A.; Kassem, N.M.; Emera, G.

    2013-01-01

    Background: Epidermal growth factor receptor (EGFR) and its downstream factors KRAS and BRAF are mutated in several types of cancer, affecting the clinical response to EGFR inhibitors. Mutations in the EGFR kinase domain predict sensitivity to the tyrosine kinase inhibitors gefltinib and erlotinib in lung adenocarcinoma, while activating point mutations in KRAS and BRAF confer resistance to the anti-EGFR monoclonal antibody cetuximab in colorectal cancer. The development of new generation methods for systematic mutation screening of these genes will allow more appropriate therapeutic choices. Purpose: Detection of KRAS mutation in Egyptian colorectal cancer (CRC) patients by the KRAS Strip Assay. Methods: Examination of 20 colorectal cancer (CRC) patients is done to detect KRAS mutations by KRAS Strip Assay. For the Strip Assay, a mutant-enriched PCR was followed by hybridization to KRAS-specific probes bound to a nitrocellulose strip. Results: Among 20 patients, KRAS mutations were identified in 80% of patients by the KRAS Strip Assay. Conclusions: Our preliminary results suggest that KRAS Strip Assay is an alternative to protocols currently in use for KRAS mutation detection

  9. Immunochromatographic strip assay for detection of bioactive Ganoderma triterpenoid, ganoderic acid A in Ganoderma lingzhi.

    Science.gov (United States)

    Sakamoto, Seiichi; Kikkawa, Nao; Kohno, Toshitaka; Shimizu, Kuniyoshi; Tanaka, Hiroyuki; Morimoto, Satoshi

    2016-10-01

    Ganoderic acid A (GAA) is one of the major Ganoderma triterpenes produced by medicinal mushroom belonging to the genus Ganoderma (Ganodermataceae). Due to its interesting pharmacological activities, Ganoderma species have been traditionally used in China for the treatment of various diseases. Herein, we developed a colloidal gold-based immunochromatographic strip assay (ICA) for the rapid detection of GAA using highly specific monoclonal antibody against GAA (MAb 12A) conjugated with gold nanoparticles. Using the developed ICA, the detection of GAA can be completed within 15min after dipping the test strip into an analyte solution with the limit of detection (LOD) for GAA of ~500ng/mL. In addition, this system makes it possible to perform a semi-quantitative analysis of GAA in Ganoderma lingzhi, where high reliability was evaluated by enzyme-linked immunosorbent assay (ELISA). The newly developed ICA can potentially be applied to the standardization of Ganoderma using GAA as an index because GAA is major triterpenoid present much in the mushroom. Copyright © 2016. Published by Elsevier B.V.

  10. Pathogenic assays of acanthamoeba belonging to the t4 genotype.

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    Hamed Mirjalali

    2013-12-01

    Full Text Available Acanthamoeba genus is introduced as opportunistic and cosmopolitan parasite. Monkey and wistar rat are appropriate models for experimental study on Acanthamoeba infection. In this study Acanthamoeba spp. were isolated from hot spring (HS, windows dust (WD and a corneal sample of keratitis patient (KP and their pathogenicity surveyed by in vitro and in vivo tests.Isolates of Acanthamoeba were cultivated axenically for 12 months in PYG medium. Overall, 30 wistar rats, in 6 equal groups were used for developing experimental Acanthamoeba keratitis (AK and Granulomatous Amoebic Encephalitis (GAE. The Keratitis and Granulomatous Encephalitis experiments were performed by intrastromal and intranasal inoculation of Acanthamoeba cysts, respectively. Pathogenicity of the three isolates was also evaluated by in vitro test using osmotolerance and temperature tolerance assays. Identification of genotypes were performed by PCR technique and sequencing.None of the isolates could perform AK and GAE in wistar rats, although all isolates were described as T4 genotype. Isolates obtained from KP and WD could grow only in 30 °C, but not in 37 °C and 40 °C. On the other hand, HS isolate grew in 30 °C and 37 °C but not in 40 °C. Moreover, all of isolate grew in 0.5 M mannitol but not in 1 M and 1.5 M.T4 isolates with a long-term axenic culture and different factors related to host and parasite may play role in pathogenicity of these free-living amoebae.

  11. Evaluation of a reverse-hybridization StripAssay for the detection of genetic polymorphisms leading to acenocoumarol sensitivity.

    Science.gov (United States)

    Gialeraki, Argyri; Markatos, Christos; Grouzi, Elisabeth; Merkouri, Efrosyni; Travlou, Anthi; Politou, Marianna

    2010-04-01

    Acenocoumarol is mainly catabolized by CYP2C9 isoform of cytochrome P450 (CYP) liver complex and exerts its anticoagulant effect through the inhibition of Vitamin K Epoxide Reductase (VKOR). The most important genetic polymorphisms which lead to an impaired enzymatic activity and therefore predispose to acenocoumarol sensitivity, are considered to be CYP2C9*2 (Arg144Cys), CYP2C9*3 (Ile359Leu) and VKORC1-1639G>A, respectively. In this study we compared the results of the PGXThrombo StripAssay kit (ViennaLab Diagnostics,Vienna, Austria) with direct DNA sequencing and in house Restriction Fragment Length Polymorphisms (RFLP) for the detection of the aforementioned Single Nucleotide Polymorphisms (SNPs). The reverse hybridization StripAssay was found to be equally effective with RFLP and direct DNA sequencing for the detection of CYP2C9*2 and CYP2C9*3 polymorphisms, respectively. The comparison of the RFLP reference method with the reverse hybridization StripAssay for the detection of VKORC1-1639 G>A polymorphism showed that the reverse hybridization StripAsssay might misclassify some A/A homozygotes as heterozygotes. Optimization of the hybridization procedures may eliminate the extra low signal band observed in some samples at the reverse hybridization StripAssay and improve its diagnostic value.

  12. 21 CFR 866.3950 - In vitro human immunodeficiency virus (HIV) drug resistance genotype assay.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false In vitro human immunodeficiency virus (HIV) drug... Serological Reagents § 866.3950 In vitro human immunodeficiency virus (HIV) drug resistance genotype assay. (a) Identification. The in vitro HIV drug resistance genotype assay is a device that consists of nucleic acid reagent...

  13. Temperature Switch PCR (TSP: Robust assay design for reliable amplification and genotyping of SNPs

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    Mather Diane E

    2009-12-01

    Full Text Available Abstract Background Many research and diagnostic applications rely upon the assay of individual single nucleotide polymorphisms (SNPs. Thus, methods to improve the speed and efficiency for single-marker SNP genotyping are highly desirable. Here, we describe the method of temperature-switch PCR (TSP, a biphasic four-primer PCR system with a universal primer design that permits amplification of the target locus in the first phase of thermal cycling before switching to the detection of the alleles. TSP can simplify assay design for a range of commonly used single-marker SNP genotyping methods, and reduce the requirement for individual assay optimization and operator expertise in the deployment of SNP assays. Results We demonstrate the utility of TSP for the rapid construction of robust and convenient endpoint SNP genotyping assays based on allele-specific PCR and high resolution melt analysis by generating a total of 11,232 data points. The TSP assays were performed under standardised reaction conditions, requiring minimal optimization of individual assays. High genotyping accuracy was verified by 100% concordance of TSP genotypes in a blinded study with an independent genotyping method. Conclusion Theoretically, TSP can be directly incorporated into the design of assays for most current single-marker SNP genotyping methods. TSP provides several technological advances for single-marker SNP genotyping including simplified assay design and development, increased assay specificity and genotyping accuracy, and opportunities for assay automation. By reducing the requirement for operator expertise, TSP provides opportunities to deploy a wider range of single-marker SNP genotyping methods in the laboratory. TSP has broad applications and can be deployed in any animal and plant species.

  14. [Hepatitis C virus genotyping: comparison of the Abbott RealTime HCV Genotype II assay and NS5B sequencing].

    Science.gov (United States)

    Vaghefi, P; Marchadier, E; Dussaix, E; Roque-Afonso, A-M

    2010-04-01

    Hepatitis C virus genotyping is needed for treatment decision and monitoring. The results of a genotyping assay based on real-time PCR and TaqMan chemistry were compared with the results of NS5B region sequencing. One hundred and two sera (genotypes 1-6) were tested. Amplification and detection of viral RNA were performed with the Abbott RealTime HCV Genotype II assay targeting 5'non-coded region (5'NC) for the identification of genotypes 1 to 6 and NS5B, for 1a and 1b subtypes detection. Sequencing of 5'NC fragment was used to resolve discrepant results. No indeterminate results were obtained. Concordance with NS5B sequencing was 93% (95 on 102), 96% at the genotype level (98 on 102) and 93% for genotype 1 subtyping (40 on 43). Discordant genotyping results were a 2f subtype identified as 5, a 6a typed as 1, a 3a identified as a 1-3 co-infection and a 4r identified as a 1-4 co-infection. Discordant subtyping results were 2 1b subtypes only typed as 1 and a 1e identified as 1a. Abbott RealTime HCV Genotype II assay is a rapid, automated and simple to interpret method for HCV genotyping. It allows the detection of possible mixed infections which might have a negative impact on therapeutic response. However, the discrepant results found in this small series underline the need for assay optimization. Copyright 2009 Elsevier Masson SAS. All rights reserved.

  15. Accuracy of a commercially available assay for HCV genotyping and subtyping in the clinical practice.

    Science.gov (United States)

    González, Victoria; Gomes-Fernandes, Meissiner; Bascuñana, Elisabet; Casanovas, Sònia; Saludes, Verónica; Jordana-Lluch, Elena; Matas, Lurdes; Ausina, Vicenç; Martró, Elisa

    2013-09-01

    Hepatitis C virus (HCV) genotyping is mandatory for tailoring dose and duration of pegylated interferon-α plus ribavirin treatment and for deciding on triple therapy eligibility. Additionally, subtyping may play a role in helping to select future treatment regimens that include directly-acting antivirals. However, commercial assays for HCV genotyping fail to identify the genotype/subtype in some cases. Our aims were (i) to determine the success rate of the commercial genotyping assay Abbott RealTime HCV Genotype II at identifying the genotype and the HCV-1 subtype; and (ii) to phylogenetically characterise the obtained indeterminate results. HCV genotyping results obtained between 2009 and 2012 in a Spanish reference hospital were reviewed. A total of 896 people were genotyped with the Abbott RealTime HCV Genotype II assay. Specimens with an indeterminate result were retrospectively genotyped using the reference method based on the phylogenetic analysis of HCV NS5B sequences. Using the commercially available assay, an indeterminate HCV genotype result was obtained in 20 of 896 patients (2.2%); these corresponded to genotypes 3a, 3k and 4d. Importantly, 8.6% of all cases where genotype 3 was detected were indeterminate. In addition, the HCV-1 subtype was not assigned in 29 of 533 cases (5.4%). The implementation in the clinical microbiology laboratory of the reference method for HCV genotyping allows indeterminate genotype/subtype results to be interpreted and may lead to the identification of previously uncharacterised subtypes. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Acetylcholinesterase Inhibitors Assay Using Colorimetric pH Sensitive Strips and Image Analysis by a Smartphone

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    Adam Kostelnik

    2017-01-01

    Full Text Available Smartphones are widely spread and their usage does not require any trained personnel. Recently, smartphones were successfully used in analytical chemistry as a simple detection tool in some applications. This paper focuses on immobilization of acetylcholinesterase (AChE onto commercially available pH strips with stabilization in the gelatin membrane. AChE degrades acetylcholine into choline and acetic acid which causes color change of acid-base indicator. Smartphone served as a tool for measurement of indicator color change from red to orange while inhibitors blocked this process. AChE inhibitors were measured with limits of detection, 149 nM and 22.3 nM for galanthamine and donepezil, respectively. Organic solvents were measured for method interferences. Measurement procedure was performed on 3D printed holder and digital photography was evaluated using red-green-blue (RGB channels. The invented assay was validated to the standard Ellman’s test and verified on murine plasma samples spiked with inhibitors. We consider that the assay is fully suitable for practical performance.

  17. Colloidal Gold Probe-Based Immunochromatographic Strip Assay for the Rapid Detection of Microbial Transglutaminase in Frozen Surimi

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    Daming Fan

    2016-01-01

    Full Text Available Adding microbial transglutaminase (MTGase to frozen surimi to enable the surimi to be sold as a higher-grade product at a higher price defrauds surimi product manufacturers and undercuts legitimate industry prices. Therefore, it is important to develop an accurate method of detecting the presence of MTGase in surimi. In this study, an immunochromatographic strip assay with a colloidal gold antibody probe was successfully developed and used to rapidly and qualitatively detect MTGase in surimi samples. The results were obtained in less than 10 min. The limit for the qualitative detection of MTGase using the immunochromatographic strip assay was identified as 1.0 μg/mL. The results of the immunochromatographic strip analysis of frozen surimi samples were verified by comparison with the results of a sandwich enzyme-linked immunosorbent assay. The colloidal gold probe-based immunochromatographic strip assay was thus found to be a rapid, economical, and user friendly method of detecting MTGase in surimi.

  18. Colloidal gold-based immunochromatographic strip assay for the rapid detection of three natural estrogens in milk.

    Science.gov (United States)

    Wang, Zhongxing; Guo, Lingling; Liu, Liqiang; Kuang, Hua; Xu, Chuanlai

    2018-09-01

    In this study, we developed highly sensitive and specific monoclonal antibodies (mAbs) against estrone (E 1 ), 17β-estradiol (17β-E 2 ), and estriol (E 3 ). The half-maximal inhibitory concentration values of anti-E 1 , anti-17β-E 2 , and anti-E 3 mAbs were 0.46, 0.36, and 0.39 ng/mL, respectively, based on competitive enzyme-linked immunosorbent assay (ic-ELISA) results. A rapid colloidal gold-based immunoassay strip assay was developed for the determination of E 1, 17β-E 2 , and E 3 residues in milk samples. The assay had a visual cut-off value of 5 ng/mL, and required 10 min to assess with the naked eye. The results obtained from the immunochromatographic strip assay were consistent with those obtained from ic-ELISA and gas chromatography-mass spectrometry. The immunochromatographic strip assay is useful and rapid for the detection of E 1 , 17β-E 2 , and E 3 in milk. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. The need for a sequencing-based assay to supplement the Abbott m2000 RealTime HCV Genotype II assay: a 1 year analysis.

    Science.gov (United States)

    Benedet, Marlin; Adachi, Dena; Wong, Anita; Wong, Sallene; Pabbaraju, Kanti; Tellier, Raymond; Tang, Julian W

    2014-07-01

    Hepatitis C (HCV) genotyping is important for treatment planning. The Abbott m2000 RealTime HCV Genotype II assay is a PCR-based assay targeting specific regions of the 5'NCR gene for genotypes 1-6, and the NS5b gene for subgenotypes 1a/1b. However, not all genotypes can be resolved, with results being reported as: 'indeterminate', 'mixed', 'genotype X reactivity with Y', or just the major genotype 1 alone. To assess the supplementary testing required for these unresolved HCV genotypes, these samples were tested further using an in-house core/E1 sequencing assay. The resulting genotypes/subgenotypes were assigned using phylogenetic analysis with reference HCV genotype sequences. Additional testing was conducted using the INNO-LiPA HCV II assay for truly mixed genotypes. Out of 1052 samples tested, 89 (8.5%) underwent further sequencing to determine the HCV genotype: 16 that were 'indeterminate' on the m2000, were mostly genotype 2s and 3s by sequencing; 12 that were 'mixed', were mostly one of the genotypes reported in the mixture; 7 that were 'X reactivity with Y', were usually genotype X; 54 that gave just a major genotype 1 result were mostly 1a, with some 6 and 1b, and a few 1c. For three truly mixed genotypes, additional testing using the VERSANT(®) HCV Genotype Assay (LiPA) 2.0, showed two mixed 1 and 3, and one indistinguishable 6c-6l genotypes. The Abbott m2000 RealTime HCV Genotype II assay can resolve most (∼90%) HCV genotypes. However in 9-10% of cases, to fully resolve the genotype, additional testing is required. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Development of a TaqMan assay for the six major genotypes of hepatitis C virus: Comparison with commercial assays

    DEFF Research Database (Denmark)

    Engle, Ronald E; Russell, Rodney S; Purcell, Robert H

    2008-01-01

    A quantitative real-time PCR assay was developed that detects genomic RNA from reference strains representing the six major genotypes of hepatitis C virus (HCV) with equal sensitivity and accurately measured HCV RNA in JFH1 HCV-infected Huh7.5 cells. The method is indirectly calibrated to the first...... international (WHO 96/790) HCV standard preparation and has a linear dynamic range of 10(2.6)-10(6.5) IU/ml. In addition, the inter- and intra-assay precision were approximately 3% CV and HCV RNA Nucleic Acid Technology kits...... (Versant HCV RNA 3.0 b-DNA and Amplicor HCV Monitor), that also employ the WHO standard, allowed validation of the TaqMan assay against all major HCV genotypes. Both commercial methods detected HCV RNA over a wide dynamic range, but showed a consistent difference of about 0.3 log10 when evaluating samples...

  1. A complete molecular biology assay for hepatitis C virus detection, quantification and genotyping

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    Yara Silva Casanova

    2014-06-01

    Full Text Available Introduction Molecular biology procedures to detect, genotype and quantify hepatitis C virus (HCV RNA in clinical samples have been extensively described. Routine commercial methods for each specific purpose (detection, quantification and genotyping are also available, all of which are typically based on polymerase chain reaction (PCR targeting the HCV 5′ untranslated region (5′UTR. This study was performed to develop and validate a complete serial laboratory assay that combines real-time nested reverse transcription-polymerase chain reaction (RT-PCR and restriction fragment length polymorphism (RFLP techniques for the complete molecular analysis of HCV (detection, genotyping and viral load in clinical samples. Methods Published HCV sequences were compared to select specific primers, probe and restriction enzyme sites. An original real-time nested RT-PCR-RFLP assay was then developed and validated to detect, genotype and quantify HCV in plasma samples. Results The real-time nested RT-PCR data were linear and reproducible for HCV analysis in clinical samples. High correlations (> 0.97 were observed between samples with different viral loads and the corresponding read cycle (Ct - Cycle threshold, and this part of the assay had a wide dynamic range of analysis. Additionally, HCV genotypes 1, 2 and 3 were successfully distinguished using the RFLP method. Conclusions A complete serial molecular assay was developed and validated for HCV detection, quantification and genotyping.

  2. SNaPaer: a practical single nucleotide polymorphism multiplex assay for genotyping of Pseudomonas aeruginosa.

    Science.gov (United States)

    Eusebio, Nadia; Pinheiro, Tiago; Amorim, Adelina A; Gamboa, Fernanda; Saraiva, Lucília; Gusmão, Leonor; Amorim, António; Araujo, Ricardo

    2013-01-01

    Multilocus sequence typing (MLST) represents the gold standard genotyping method in studies concerning microbial population structure, being particularly helpful in the detection of clonal relatedness. However, its applicability on large-scale genotyping is limited due to the high cost and time spent on the task. The selection of the most informative nucleotide positions simplifies genomic characterization of bacteria. A simple and informative multiplex, SNaPaer assay, was developed and genotyping of Pseudomonas aeruginosa was obtained after a single reaction of multiplex PCR amplification and mini-sequencing. This cost-effective technique allowed the analysis of a Portuguese set of isolates (n = 111) collected from three distinct hospitals and the genotyping data could be obtained in less than six hours. Point mutations were shown to be the most frequent event responsible for diversification of the Portuguese population sample. The Portuguese isolates corroborated the epidemic hypothesis for P. aeruginosa population. SNaPaer genotyping assay provided a discriminatory power of 0.9993 for P. aeruginosa, by testing in silico several hundreds of MLST profiles available online. The newly proposed assay targets less than 0.01% of the total MLST length and guarantees reproducibility, unambiguous analysis and the possibility of comparing and transferring data between different laboratories. The plasticity of the method still supports the addition of extra molecular markers targeting specific purposes/populations. SNaPaer can be of great value to clinical laboratories by facilitating routine genotyping of P. aeruginosa.

  3. Rapid, quantitative and sensitive immunochromatographic assay based on stripping voltammetric detection of a metal ion label

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Fang; Wang, Kaihua; Lin, Yuehe

    2005-10-10

    A novel, sensitive immunochromatographic electrochemical biosensor (IEB) which combines an immunochromatographic strip technique with an electrochemical detection technique is demonstrated. The IEB takes advantages of the speed and low-cost of the conventional immunochromatographic test kits and high-sensitivity of stripping voltammetry. Bismuth ions (Bi3+) have been coupled with the antibody through the bifunctional chelating agent diethylenetriamine pentaacetic acid (DTPA). After immunoreactions, Bi3+ was released and quantified by anodic stripping voltammetry at a built-in single-use screen-printed electrode. As an example for the applications of such novel device, the detection of human chorionic gonadotronphin (HCG) in a specimen was performed. This biosensor provides a more user-friendly, rapid, clinically accurate, and less expensive immunoassay for such analysis in specimens than currently available test kits.

  4. A multicenter evaluation of the Abbott RealTime HCV genotype II assay

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    Marco Ciotti

    2009-12-01

    Full Text Available Viral genotype is an important determinant of the therapeutical outcome of the chronic hepatitis C and is useful in clinical practice to determine the duration of treatment1.While the viral type shows a clear association with therapeutic success, there is currently no evidence to that effect for HCV subtype, whose value is thus confined to epidemiological studies.The Abbott RealTime HCV Genotype II assay, through the use of Minor Groove Binder probes (MGB is able to distinguish genotypes 1 to 6 (target 5’-UTR region and subtypes 1a and 1b (NS5B region. In four different Italian centers a comparison between the Abbott RealTime HCV Genotype II assay and the Versant HCV Genotype 2.0 (LIPA has been performed.A total of 143 non selected samples with the request of HCV genotyping have been analysed. 141/143 samples (98.6% have provided reportable results with both tests (2 indeterminates with LIPA. Concordance at the type level was 96.5% (136/141. Considering the 136 concordant samples, the distribution was as follows: type 1 = 61 (44.9%, 2 = 36 (26.5%, 3 = 21 (15.4%, 4 = 17 (12.5% 5 = 1 (0.7%. Both assays assigned subtype in 56/61 (91.8% samples of genotype 1 (3 and 2 samples only provided the type for LIPA and Abbott, respectively and 50/56 (89.3% had concordant subtype. It is worth to note that 4 of the 5 samples with discordant subtype Abbott 1a/LiPA 1b came from the only center that used for LIPA the 5-UTR amplicon, loosing the benefit of the core region which has been introduced in the version 2 of the test to improve the accuracy in distinguishing between 1a and 1b.There was only one discordant sample at type level (Abbott 4, LIPA 1b which after sequencing and phylogenetic analysis was resolved as type 4. Four mixed infections were detected, 3 with the Abbott test (two 1a+4 and one 1b+3 and 1 with the LIPA test (1a+3. In all cases the comparison test showed a single genotype 1 infection. The new Abbott RealTime HCV Genotype II assay showed a

  5. High accuracy genotyping directly from genomic DNA using a rolling circle amplification based assay

    Directory of Open Access Journals (Sweden)

    Du Yuefen

    2003-05-01

    Full Text Available Abstract Background Rolling circle amplification of ligated probes is a simple and sensitive means for genotyping directly from genomic DNA. SNPs and mutations are interrogated with open circle probes (OCP that can be circularized by DNA ligase when the probe matches the genotype. An amplified detection signal is generated by exponential rolling circle amplification (ERCA of the circularized probe. The low cost and scalability of ligation/ERCA genotyping makes it ideally suited for automated, high throughput methods. Results A retrospective study using human genomic DNA samples of known genotype was performed for four different clinically relevant mutations: Factor V Leiden, Factor II prothrombin, and two hemochromatosis mutations, C282Y and H63D. Greater than 99% accuracy was obtained genotyping genomic DNA samples from hundreds of different individuals. The combined process of ligation/ERCA was performed in a single tube and produced fluorescent signal directly from genomic DNA in less than an hour. In each assay, the probes for both normal and mutant alleles were combined in a single reaction. Multiple ERCA primers combined with a quenched-peptide nucleic acid (Q-PNA fluorescent detection system greatly accellerated the appearance of signal. Probes designed with hairpin structures reduced misamplification. Genotyping accuracy was identical from either purified genomic DNA or genomic DNA generated using whole genome amplification (WGA. Fluorescent signal output was measured in real time and as an end point. Conclusions Combining the optimal elements for ligation/ERCA genotyping has resulted in a highly accurate single tube assay for genotyping directly from genomic DNA samples. Accuracy exceeded 99 % for four probe sets targeting clinically relevant mutations. No genotypes were called incorrectly using either genomic DNA or whole genome amplified sample.

  6. Evaluation of GenoType NTM-DR Assay for Identification of Mycobacterium chimaera.

    Science.gov (United States)

    Mok, Simone; Rogers, Thomas R; Fitzgibbon, Margaret

    2017-06-01

    Identification of species within the Mycobacterium avium complex (MAC) is difficult, and most current diagnostic laboratory tests cannot distinguish between species included in the complex. Differentiation of species within the MAC is important, as Mycobacterium chimaera has recently emerged as a major cause of invasive cardiovascular infections following open heart surgery. A new commercial diagnostic assay, GenoType NTM-DR ver. 1.0, is intended to differentiate between three species within the MAC, namely, Mycobacterium avium , Mycobacterium intracellulare , and Mycobacterium chimaera In this study, we investigated an archival collection of 173 MAC isolates using 16S rRNA and 16S-23S internal transcribed spacer (ITS) gene sequencing, and GenoType NTM-DR was evaluated for identifying M. chimaera and other species belonging to the MAC. Species identification of 157/173 (91%) isolates with the GenoType NTM-DR assay was in agreement with 16S rRNA and 16S-23S ITS gene sequencing results. Misidentification occurred with 16 isolates which belonged to four species included in the MAC that are rarely encountered in clinical specimens. Despite some limitations of this assay, GenoType NTM-DR had 100% specificity for identifying M. chimaera This novel assay will enable diagnostic laboratories to differentiate species belonging to the Mycobacterium avium complex and to accurately identify M. chimaera It can produce rapid results and is also more cost efficient than gene sequencing methods. Copyright © 2017 American Society for Microbiology.

  7. Use of Genotype MTBDRplus Assay for Diagnosis of Multidrug-Resistant Tuberculosis in Nepal

    Directory of Open Access Journals (Sweden)

    Elina Maharjan

    2017-01-01

    Full Text Available The main aims of this study were to study the patterns of mutations in rpoB, katG, and inhA genes in Mycobacterium tuberculosis strains isolated from patients from Nepal and to evaluate the performance of genotype MTBDRplus assay, taking conventional drug susceptibility testing as gold standard for diagnosis of MDR-TB. A total of 69 Mycobacterium tuberculosis strains isolated from 73 smear positive sputum samples from patients suspected of suffering from multidrug-resistant tuberculosis were used in our study. The drug susceptibility pattern of Mycobacterium tuberculosis isolated from these sputum specimens was determined by using genotype MTBDRplus assay taking conventional drug susceptibility testing as reference. The sensitivity and specificity of the genotype MTBDRplus assay for the detection of MDR-TB were found to be 88.7% and 100%, respectively. 88.7% of the rifampicin resistant isolates had mutations in rpoB gene. Similarly, 79.7% and 9.4% of isoniazid resistant isolates had mutations in katG and inhA genes, respectively. Genotype MTBDRplus assay was found to be very rapid and highly sensitive and specific method for diagnosis of MDR-TB and will be very helpful for early diagnosis of MDR-TB in high tuberculosis burden countries.

  8. Evaluation of the Genotype® MTBDRplus assay as a tool for drug resistance surveys

    NARCIS (Netherlands)

    Rigouts, L.; Hoza, A. S.; de Rijk, P.; Torrea, G.; Chonde, T. M.; Basra, D.; Zignol, M.; van Leth, F.; Egwaga, S. M.; van Deun, A.

    2011-01-01

    A national tuberculosis (TB) drug resistance survey in Tanzania. To compare the performance of the Genotype® MTBDRplus line-probe assay (LPA) on smear-positive sputum specimens with conventional culture and isoniazid (INH) plus rifampicin (RMP) drug susceptibility testing (DST). Mycobacterium

  9. Immunochromatographic strip assay for the rapid and sensitive detection of Salmonella Typhimurium in artificially contaminated tomato samples.

    Science.gov (United States)

    Shukla, Shruti; Leem, Hyerim; Lee, Jong-Suk; Kim, Myunghee

    2014-06-01

    This study was designed to confirm the applicability of a liposome-based immunochromatographic assay for the rapid detection of Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella Typhimurium) in artificially contaminated tomato samples. To determine the detection limit and pre-enrichment incubation time (10, 12, and 18 h pre-enrichment in 1% buffered peptone water), the tests were performed with different cell numbers of Salmonella Typhimurium (3 × 10(0), 3 × 10(1), 3 × 10(2), and 3 × 10(3) CFU·mL(-1)) inoculated into 25 g of crushed tomato samples. The assay was able to detect as few as 30 Salmonella Typhimurium cells per 25 g of tomato samples (1.2 cells·g(-1)) after 12 h pre-enrichment incubation. Moreover, when the developed assay was compared with traditional morphological and biochemical culture-based methods as well as colloidal gold nanoparticle-based commercial test strips, the developed assay yielded positive results for the detection of Salmonella Typhimurium within a shorter period time. These findings confirm that the developed assay may have practical application for the sensitive detection of Salmonella Typhimurium in various food samples, including raw vegetables, with a relatively low detection limit and shorter analysis time.

  10. Development and Evaluation of Three Real-Time PCR Assays for Genotyping and Source Tracking Cryptosporidium spp. in Water

    Science.gov (United States)

    Li, Na; Neumann, Norman F.; Ruecker, Norma; Alderisio, Kerri A.; Sturbaum, Gregory D.; Villegas, Eric N.; Chalmers, Rachel; Monis, Paul; Feng, Yaoyu

    2015-01-01

    The occurrence of Cryptosporidium oocysts in drinking source water can present a serious public health risk. To rapidly and effectively assess the source and human-infective potential of Cryptosporidium oocysts in water, sensitive detection and correct identification of oocysts to the species level (genotyping) are essential. In this study, we developed three real-time PCR genotyping assays, two targeting the small-subunit (SSU) rRNA gene (18S-LC1 and 18S-LC2 assays) and one targeting the 90-kDa heat shock protein (hsp90) gene (hsp90 assay), and evaluated the sensitivity and Cryptosporidium species detection range of these assays. Using fluorescence resonance energy transfer probes and melt curve analysis, the 18S-LC1 and hsp90 assays could differentiate common human-pathogenic species (C. parvum, C. hominis, and C. meleagridis), while the 18S-LC2 assay was able to differentiate nonpathogenic species (such as C. andersoni) from human-pathogenic ones commonly found in source water. In sensitivity evaluations, the 18S-LC2 and hsp90 genotyping assays could detect as few as 1 Cryptosporidium oocyst per sample. Thus, the 18S-LC2 and hsp90 genotyping assays might be used in environmental monitoring, whereas the 18S-LC1 genotyping assay could be useful for genotyping Cryptosporidium spp. in clinical specimens or wastewater samples. PMID:26092455

  11. Simultaneous detection of dual biomarkers from humans exposed to organophosphorus pesticides by combination of immunochromatographic test strip and ellman assay.

    Science.gov (United States)

    Yang, Mingming; Zhao, Yuting; Wang, Limin; Paulsen, Michael; Simpson, Christopher D; Liu, Fengquan; Du, Dan; Lin, Yuehe

    2018-05-01

    A novel sandwich immunoassay based immunochromatographic test strip (ICTS) has been developed for simultaneously measuring both butyrylcholinesterase (BChE) activity and the total amount of BChE (including inhibited and active enzyme) from 70 μLpost-exposure human plasma sample. The principle of this method is based on the BChE monoclonal antibody (MAb) capable of acting as both capture antibody and detection antibody. The BChE MAb which was immobilized on the test line was able to recognize both organophosphorus BChE adducts (OP-BChE) and BChE and provided equal binding affinity, permitting detection of the total enzyme amount in post-exposure human plasma samples. The formed immunocomplexes on the test line can further be excised from the test-strip for subsequent off-line measurement of BChE activity using the Ellman assay. Therefore, dual biomarkers of BChE activity and phosphorylation (OP-BChE) will be obtained simultaneously. The whole sandwich-immunoassay was performed on one ICTS, greatly reducing analytical time. The ICTS sensor showed excellent linear responses for assaying total amount of BChE and active BChE ranging from 0.22 to 3.58nM and 0.22-7.17nM, respectively. Both the signal detection limits are 0.10nM. We validated the practical application of the proposed method to measure 124 human plasma samples from orchard workers and cotton farmers with long-term exposure to organophosphorus pesticides (OPs). The results were in highly agreement with LC/MS/MS which verified our method is extremely accurate. Combining the portability and rapidity of test strip and the compatibility of BChE MAb as both capture antibody and detection antibody, the developed method provides a baseline-free, low-cost and rapid tool for in-field monitoring of OP exposures. Copyright © 2018 Elsevier B.V. All rights reserved.

  12. Development and characterization of a high density SNP genotyping assay for cattle.

    Directory of Open Access Journals (Sweden)

    Lakshmi K Matukumalli

    Full Text Available The success of genome-wide association (GWA studies for the detection of sequence variation affecting complex traits in human has spurred interest in the use of large-scale high-density single nucleotide polymorphism (SNP genotyping for the identification of quantitative trait loci (QTL and for marker-assisted selection in model and agricultural species. A cost-effective and efficient approach for the development of a custom genotyping assay interrogating 54,001 SNP loci to support GWA applications in cattle is described. A novel algorithm for achieving a compressed inter-marker interval distribution proved remarkably successful, with median interval of 37 kb and maximum predicted gap of <350 kb. The assay was tested on a panel of 576 animals from 21 cattle breeds and six outgroup species and revealed that from 39,765 to 46,492 SNP are polymorphic within individual breeds (average minor allele frequency (MAF ranging from 0.24 to 0.27. The assay also identified 79 putative copy number variants in cattle. Utility for GWA was demonstrated by localizing known variation for coat color and the presence/absence of horns to their correct genomic locations. The combination of SNP selection and the novel spacing algorithm allows an efficient approach for the development of high-density genotyping platforms in species having full or even moderate quality draft sequence. Aspects of the approach can be exploited in species which lack an available genome sequence. The BovineSNP50 assay described here is commercially available from Illumina and provides a robust platform for mapping disease genes and QTL in cattle.

  13. Differentiation of N-acetyltransferase 2 (NAT2 rapid and intermediate acetylator based on genotype and urinary assay

    Directory of Open Access Journals (Sweden)

    Rika Yuliwulandari

    2017-10-01

    Full Text Available Background Determination of the acetylator type of NAT2 generally can be predicted based on genotype data from the NAT2 database. However, in some reported studies, it does not show 100 per cent concordance with the phenotype based on urinary assay. The assay generally only differentiates the rapid and slow acetylator but does not consider the intermediate one. Aims We conducted this study to define the phenotype of NAT2 based on both genotyping and urinary assay and to determine the concordance rate between both methods in rapid and intermediate acetylator groups. Methods NAT2 genotyping was done using the PCR-direct sequencing in a total of 30 healthy subjects. However, for the NAT2 phenotypes we only selected 19 healthy subjects that carry rapid or intermediate acetylator genotype, without involving slow acetylator phenotype. The assay was done by measuring the ratios of urinary caffeine metabolites following controlled diet exposure. Results Both data obtained from genotyping and urinary assay showed 2 samples that belonged to the rapid acetylator and 17 samples that belonged to the intermediate acetylator. The mean metabolic ratio of the rapid acetylator group showed a higher level (0.5 than the intermediate group (0.28. The predicted acetylation status of NAT2 SNPs from genotyping was matched with the phenotype which was determined by urinary analysis. Conclusion Our result showed a 100 per cent concordance of NAT2 phenotype based on the genotyping and urinary assay. Based on this study we suggest that NAT2 phenotype based on genotyping method is simpler and faster, rather than using the urinary assay that is more laborious and costly.

  14. Simplified PCR protocols for INNO-LiPA HBV Genotyping and INNO-LiPA HBV PreCore assays

    NARCIS (Netherlands)

    Qutub, Mohammed O.; Germer, Jeffrey J.; Rebers, Sjoerd P. H.; Mandrekar, Jayawant N.; Beld, Marcel G. H. M.; Yao, Joseph D. C.

    2006-01-01

    INNO-LiPA HBV Genotyping (LiPA HBV GT) and INNO-LiPA HBV PreCore (LiPA HBV PC) are commercially available assays for hepatitis B virus (HBV) characterization. These assays are labor-intensive and may be prone to exogenous DNA contamination due to their use of nested PCR amplification procedures and

  15. Genotyping performance assessment of whole genome amplified DNA with respect to multiplexing level of assay and its period of storage.

    Directory of Open Access Journals (Sweden)

    Daniel W H Ho

    Full Text Available Whole genome amplification can faithfully amplify genomic DNA (gDNA with minimal bias and substantial genome coverage. Whole genome amplified DNA (wgaDNA has been tested to be workable for high-throughput genotyping arrays. However, issues about whether wgaDNA would decrease genotyping performance at increasing multiplexing levels and whether the storage period of wgaDNA would reduce genotyping performance have not been examined. Using the Sequenom MassARRAY iPLEX Gold assays, we investigated 174 single nucleotide polymorphisms for 3 groups of matched samples: group 1 of 20 gDNA samples, group 2 of 20 freshly prepared wgaDNA samples, and group 3 of 20 stored wgaDNA samples that had been kept frozen at -70°C for 18 months. MassARRAY is a medium-throughput genotyping platform with reaction chemistry different from those of high-throughput genotyping arrays. The results showed that genotyping performance (efficiency and accuracy of freshly prepared wgaDNA was similar to that of gDNA at various multiplexing levels (17-plex, 21-plex, 28-plex and 36-plex of the MassARRAY assays. However, compared with gDNA or freshly prepared wgaDNA, stored wgaDNA was found to give diminished genotyping performance (efficiency and accuracy due to potentially inferior quality. Consequently, no matter whether gDNA or wgaDNA was used, better genotyping efficiency would tend to have better genotyping accuracy.

  16. Hepatitis C Virus Genie: A Web 2.0 Interpretation and Analytics Platform for the Versant Hepatitis C Virus Genotype Line Probe Assay Version 2.0.

    Science.gov (United States)

    Dussaq, Alex M; Soni, Abha; Willey, Christopher; Park, Seung L; Harada, Shuko

    2017-01-01

    Hepatitis C virus (HCV) genotyping at our institution is performed using the Versant HCV genotype 2.0 Line Probe Assay (LiPA). The last steps of this procedure are manual, laborious, and error-prone process that involves the comparison of the banding pattern on a test strip to a physical reference table. We developed a web-based HCV genotype interpretation platform that utilizes a scanned image to generate the genotypes, thus minimizing interpretation time and reducing error. HCV Genie 2 utilizes a database of banding patterns in conjuncture with image analysis algorithms to determine the genotype for any number of scanned LiPA strips. HCV Genie 2 is built with client-side JavaScript; allowing the program to run in the user' browser rather than on an unknown server, essentially eliminating data and patient privacy concerns. HCV Genie 2 was tested over 2 months and proved identical to human expert interpretation for 148 samples (>1000 bands identified). Manual intervention was required only for two faint bands and one false-positive band; this was done utilizing the built-in-user interface. Utilizing the original method, the trained laboratory technician interpretation time for 16 samples was 13.8 (±0.96) min as compared to 5.0 (±1.09) min with HCV Genie 2, a 63.8% decrease. In addition to the time savings, the new method provides an additional validation step, which decreases the potential for errors. Our institution has moved exclusively to utilize the new techniques and tools described here. Both experienced technicians and the molecular pathologists at our institution prefer the workflow using HCV Genie. It is easier for the technicians to prepare and document, and the pathologists are more rapidly able to review and confirm results. The use of this tool will lead to increase the quality of patient care delivered through this test methodology by decreasing the potential for error. The algorithms developed here can be ported to similar band identification

  17. Hepatitis C virus Genie: A web 2.0 interpretation and analytics platform for the Versant Hepatitis C virus genotype Line Probe Assay version 2.0

    Directory of Open Access Journals (Sweden)

    Alex M Dussaq

    2017-01-01

    Full Text Available Context: Hepatitis C virus (HCV genotyping at our institution is performed using the Versant HCV genotype 2.0 Line Probe Assay (LiPA. The last steps of this procedure are manual, laborious, and error-prone process that involves the comparison of the banding pattern on a test strip to a physical reference table. Aim: We developed a web-based HCV genotype interpretation platform that utilizes a scanned image to generate the genotypes, thus minimizing interpretation time and reducing error. Subjects and Methods: HCV Genie 2 utilizes a database of banding patterns in conjuncture with image analysis algorithms to determine the genotype for any number of scanned LiPA strips. HCV Genie 2 is built with client-side JavaScript; allowing the program to run in the user' browser rather than on an unknown server, essentially eliminating data and patient privacy concerns. Results: HCV Genie 2 was tested over 2 months and proved identical to human expert interpretation for 148 samples (>1000 bands identified. Manual intervention was required only for two faint bands and one false-positive band; this was done utilizing the built-in-user interface. Utilizing the original method, the trained laboratory technician interpretation time for 16 samples was 13.8 (±0.96 min as compared to 5.0 (±1.09 min with HCV Genie 2, a 63.8% decrease. In addition to the time savings, the new method provides an additional validation step, which decreases the potential for errors. Conclusions: Our institution has moved exclusively to utilize the new techniques and tools described here. Both experienced technicians and the molecular pathologists at our institution prefer the workflow using HCV Genie. It is easier for the technicians to prepare and document, and the pathologists are more rapidly able to review and confirm results. The use of this tool will lead to increase the quality of patient care delivered through this test methodology by decreasing the potential for error. The

  18. Evaluation of the Abbott realtime HCV genotype II RUO (GT II) assay with reference to 5'UTR, core and NS5B sequencing.

    Science.gov (United States)

    Mallory, Melanie A; Lucic, Danijela X; Sears, Mitchell T; Cloherty, Gavin A; Hillyard, David R

    2014-05-01

    HCV genotyping is a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen. To evaluate the concordance between the Abbott GT II assay and genotyping by sequencing subregions of the HCV 5'UTR, core and NS5B. The Abbott assay was used to genotype 127 routine patient specimens and 35 patient specimens with unusual subtypes and mixed infection. Abbott results were compared to genotyping by 5'UTR, core and NS5B sequencing. Sequences were genotyped using the NCBI non-redundant database and the online genotyping tool COMET. Among routine specimens, core/NS5B sequencing identified 93 genotype 1s, 13 genotype 2s, 15 genotype 3s, three genotype 4s, two genotype 6s and one recombinant specimen. Genotype calls by 5'UTR, core, NS5B sequencing and the Abbott assay were 97.6% concordant. Core/NS5B sequencing identified two discrepant samples as genotype 6 (subtypes 6l and 6u) while Abbott and 5'UTR sequencing identified these samples as genotype 1 with no subtype. The Abbott assay subtyped 91.4% of genotype 1 specimens. Among the 35 rare specimens, the Abbott assay inaccurately genotyped 3k, 6e, 6o, 6q and one genotype 4 variant; gave indeterminate results for 3g, 3h, 4r, 6m, 6n, and 6q specimens; and agreed with core/NS5B sequencing for mixed specimens. The Abbott assay is an automated HCV genotyping method with improved accuracy over 5'UTR sequencing. Samples identified by the Abbott assay as genotype 1 with no subtype may be rare subtypes of other genotypes and thus require confirmation by another method. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

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

    2012-01-01

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

  20. A new lateral flow strip assay (LFSA) using a pair of aptamers for the detection of Vaspin.

    Science.gov (United States)

    Ahmad Raston, Nurul Hanun; Nguyen, Van-Thuan; Gu, Man Bock

    2017-07-15

    A new lateral flow strip assay (LFSA) using a pair of aptamers has been designed and successfully developed using a pair of aptamers-functionalized with gold nanoparticles (AuNPs). This new LFSA biosensor system utilizes a cognate aptamer duo binding to vaspin, a target protein, at the two different binding sites, and exhibited a sensitive and highly selective response to vaspin. A sandwich-type format in LFSA was developed based on biotin-labeled primary V1 aptamer immobilized on streptavidin coated membrane as a capturing probe and secondary V49 aptamer conjugated with AuNPs as a signaling probe. Using this LFSA, vaspin could be visibly observed within the detectable concentrations of vaspin up to 5nM in both buffer and serum conditions. The sensitivity of this LFSA developed in this study was ranged from 0.137 to 25nM in buffer and from 0.105 to 25nM in spiked human serum, respectively. The limit of detection (LOD) of this LFSA was found to be 0.137nM and 0.105nM in buffer and spiked human serum condition, respectively. Therefore, this study has shown successful development of a simple yet effective LFSA for vaspin detection, and this development is not only limited to this target, but also other targets with a pair of aptamers available, without any special and laborious instrumentations. This system will be particularly useful as a screening tool for rapid on-site detection of any targets with a pair of aptamers generated. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. A genotypic HIV-1 proviral DNA coreceptor tropism assay: characterization in viremic subjects

    Science.gov (United States)

    2014-01-01

    Background HIV-1 coreceptor tropism testing is used to evaluate eligibility for CCR5 antagonist therapy. However, HIV-1 RNA-based tests are not suitable for virologically suppressed patients, therefore the use of proviral DNA tropism testing has been investigated. We describe a novel proviral DNA-based genotypic tropism assay and compare its performance to that of a sensitive HIV-1 RNA-based genotypic test. Methods Tropism was determined using HIV-1 plasma RNA and proviral DNA from 42 paired samples from patients with plasma viral loads ≥1000 HIV-1 RNA copies/mL. Proviral DNA sample types included whole blood, separated peripheral blood mononuclear cells resuspended in phosphate-buffered saline and peripheral blood mononuclear cells resuspended in spun plasma. The HIV-1 envelope V3 region was PCR-amplified, sequenced in triplicate, and analyzed for tropism with the geno2pheno algorithm using a 10% false-positive rate (FPR). Results Amplicons were obtained from proviral DNA and plasma RNA in 41/42 samples. Tropism predictions were highly concordant (93%–98%) between proviral DNA and plasma RNA, regardless of the proviral DNA isolation method. Non-R5 proviral DNA results were obtained for 100% of patients with detectable non-R5 plasma HIV-1 RNA results. Geno2pheno FPRs for proviral DNA and plasma RNA were highly correlated (Spearman rho = 0.86). Conclusions Our findings demonstrate that proviral DNA tropism determinations from whole blood or peripheral blood mononuclear cells were highly concordant with plasma HIV-1 RNA tropism determinations. This assay may be useful for screening virologically suppressed patients for CCR5-antagonist eligibility and for research purposes. PMID:24904682

  2. Comparison of analytical and clinical performance of CLART HPV2 genotyping assay to Linear Array and Hybrid Capture 2

    DEFF Research Database (Denmark)

    Ejegod, Ditte Møller; Rebolj, Matejka; Bonde, Jesper

    2015-01-01

    prone to inter-observer variability. The reading of test results on the CLART HPV2 genotyping assay is, on the other hand, automated. The aim of our study was to directly compare the detection of HPV genotypes and high-grade cervical intraepithelial neoplasia (CIN) by CLART, Linear Array (LA...... to the Danish nation-wide Pathology Data Bank. For comparison of CLART and LA in terms of genotype detection, we calculated κ-coefficients, and proportions of overall and positive agreement. For comparison of CIN detection between CLART, LA, and HC2, we calculated the relative sensitivity and specificity...

  3. Evaluation of genotype MTBDRplus VER 2.0 line probe assay for the detection of MDR-TB in smear positive and negative sputum samples.

    Science.gov (United States)

    Meaza, Abyot; Kebede, Abebaw; Yaregal, Zelalem; Dagne, Zekarias; Moga, Shewki; Yenew, Bazezew; Diriba, Getu; Molalign, Helina; Tadesse, Mengistu; Adisse, Desalegn; Getahun, Muluwork; Desta, Kassu

    2017-04-17

    Multi drug resistant tuberculosis (MDR-TB) poses formidable challenges to TB control due to its complex diagnostic and treatment challenges and often associated with a high rate of mortality. Accurate and rapid detection of MDR-TB is critical for timely initiation of treatment. Line Probe Assay (LPA) is a qualitative in vitro diagnostic test based on DNA-STRIP technology for the identification of the M. tuberculosis complex and its resistance to rifampicin (RMP) and/or isoniazid (INH). Hain Lifescience, GmbH, Germany has improved the sensitivity of Genotype MTBDRplus VER 2.0 LPA for the detection of MDR-TB; with the possibility of applying the tool in smear negative sputum samples. A cross sectional study was conducted on 274 presumptive MDR-TB patients referred to the National TB Reference Laboratory (NTRL), Ethiopian Public Health Institute (EPHI) who submitted sputum samples for laboratory diagnosis of drug resistant-TB testing. Seventy-two smear and culture positive samples processed in smear positive direct LPA category and 197 smear negative sputum samples were processed for direct LPA. Among the smear negative samples 145 (73.6%) were culture negative and 26 (13.2%) were culture positive. All specimens were processed using NALC-NaOH method and ZN smear microscopy done from sediments. Genotype MTBDRplus VER 2.0 done from processed sputum sediments and the result was compared against the reference, BACTEC MGIT 960 culture and DST. Sensitivity, specificity, PPV and NPV of Genotype MTBDRplus VER 2.0 assay was determined and P-value TB from direct smear positive sputum samples. The sensitivity, specificity, PPV and NPV of Genotype MTBDR plus VER 2.0 LPA were 77.8, 97.2, 82.4 and 97.2%, respectively, for the detection of M. tuberculosis from direct smear negative sputum samples. Fourteen (53.8%) samples had valid results with LPA among the 26 smear negative culture positive samples. The remaining 8 (30.8%) and 4 (15.4%) were invalid and negative with LPA

  4. A two-step real-time PCR assay for quantitation and genotyping of human parvovirus 4.

    Science.gov (United States)

    Väisänen, E; Lahtinen, A; Eis-Hübinger, A M; Lappalainen, M; Hedman, K; Söderlund-Venermo, M

    2014-01-01

    Human parvovirus 4 (PARV4) of the family Parvoviridae was discovered in a plasma sample of a patient with an undiagnosed acute infection in 2005. Currently, three PARV4 genotypes have been identified, however, with an unknown clinical significance. Interestingly, these genotypes seem to differ in epidemiology. In Northern Europe, USA and Asia, genotypes 1 and 2 have been found to occur mainly in persons with a history of injecting drug use or other parenteral exposure. In contrast, genotype 3 appears to be endemic in sub-Saharan Africa, where it infects children and adults without such risk behaviour. In this study, a novel straightforward and cost-efficient molecular assay for both quantitation and genotyping of PARV4 DNA was developed. The two-step method first applies a single-probe pan-PARV4 qPCR for screening and quantitation of this relatively rare virus, and subsequently, only the positive samples undergo a real-time PCR-based multi-probe genotyping. The new qPCR-GT method is highly sensitive and specific regardless of the genotype, and thus being suitable for studying the clinical impact and occurrence of the different PARV4 genotypes. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Possible incorrect genotyping of heterozygous factor V Leiden and Prothrombin 20210 gene mutations by the GeneXpert assay.

    Science.gov (United States)

    Marturano, Alessandro; Bury, Loredana; Gresele, Paolo

    2014-08-05

    The GeneXpert analyzer is a hands-off system for the detection of Factor V Leiden and of Prothrombin G20210A (GPRO) gene thrombophilic mutations. Although the system is efficient and easy to use, we report the rare possibility of incorrect genotyping. 1648 samples were evaluated using the GeneXpert HemosIL Factor II and Factor V assay: 1319 were freshly analyzed while 329 were frozen, thawed and diluted with saline prior to analysis to avoid clogging of the instrument syringe. Two samples, both heterozygous, one for the factor V Leiden and the other for the GPRO gene, were incorrectly genotyped as homozygous for the relative mutation. Inspection of the Ct values and amplification curves and genotyping with PCR revealed the correct genotype as heterozygous for factor V Leiden and GPRO mutation. The GeneXpert HemosIL Factor II and Factor V assay is an automated, fast genotyping assay requiring almost no sample manipulation, advantageous characteristics if compared with other PCR-based methods. However, an inattentive use of it can generate incorrect diagnosis. A careful handling of the sample, in particular correct dilution of frozen/thawed samples before analysis, and the inspection of the amplification curves and Ct values are required to avoid artifacts. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Multiplex ligation-dependent probe amplification (MLPA) assay for blood group genotyping, copy number quantification, and analysis of RH variants

    NARCIS (Netherlands)

    Veldhuisen, Barbera; van der Schoot, C. E.; de Haas, Masja

    2015-01-01

    The blood group multiplex ligation-dependent probe amplification (MLPA) is a comprehensive assay, developed for genotyping the majority of clinically relevant blood group antigens in both patients and donors. The MLPA is an easy method to apply and only requires a thermal cycler and capillary

  7. CONFIRMATIONAL IDENTIFICATION OF ESCHERICHIA COLI, A COMPARISON OF GENOTYPIC AND PHENOTYPIC ASSAYS FOR GLUTAMATE DECARBOXYLASE AND B-D-GLUCURONIDASE

    Science.gov (United States)

    Genotypic and phenotypic assays for glutamate decarboxylase (GAD) and B-D-glucuronidase (GUD) were compared for their abilities to detect various strains of Escherichia coli and to discriminate among other bacterial species. Test strains included nonpathogenic E.coli, three major...

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

    Directory of Open Access Journals (Sweden)

    Dawn N Birdsell

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

  9. Human papillomavirus detection with genotyping by the cobas and Aptima assays: Significant differences in HPV 16 detection?

    Science.gov (United States)

    Chorny, Joseph A; Frye, Teresa C; Fisher, Beth L; Remmers, Carol L

    2018-03-23

    The primary high-risk human papillomavirus (hrHPV) assays in the United States are the cobas (Roche) and the Aptima (Hologic). The cobas assay detects hrHPV by DNA analysis while the Aptima detects messenger RNA (mRNA) oncogenic transcripts. As the Aptima assay identifies oncogenic expression, it should have a lower rate of hrHPV and genotype detection. The Kaiser Permanente Regional Reference Laboratory in Denver, Colorado changed its hrHPV assay from the cobas to the Aptima assay. The rates of hrHPV detection and genotyping were compared over successive six-month periods. The overall hrHPV detection rates by the two platforms were similar (9.5% versus 9.1%) and not statistically different. For genotyping, the HPV 16 rate by the cobas was 1.6% and by the Aptima it was 1.1%. These differences were statistically different with the Aptima detecting nearly one-third less HPV 16 infections. With the HPV 18 and HPV 18/45, there was a slightly higher detection rate of HPV 18/45 by the Aptima platform (0.5% versus 0.9%) and this was statistically significant. While HPV 16 represents a low percentage of hrHPV infections, it was detected significantly less by the Aptima assay compared to the cobas assay. This has been previously reported, although not highlighted. Given the test methodologies, one would expect the Aptima to detect less HPV 16. This difference appears to be mainly due to a significantly increased number of non-oncogenic HPV 16 infections detected by the cobas test as there were no differences in HPV 16 detection rates in the high-grade squamous intraepithelial lesions indicating that the two tests have similar sensitivities for oncogenic HPV 16. © 2018 Wiley Periodicals, Inc.

  10. Synthesis of carboxyl-capped and bright YVO4:Eu,Bi nanoparticles and their applications in immunochromatographic test strip assay

    International Nuclear Information System (INIS)

    Luo, Min; Sun, Tian-Ying; Wang, Jia-Hong; Yang, Peng; Gan, Liang; Liang, Li-Lei; Yu, Xue-Feng; Gong, Xing-Hou

    2013-01-01

    Graphical abstract: - Highlights: • The morphology and properties of YVO 4 :Eu,Bi nanoparticles were investigated. • YVO 4 :Eu,Bi were coupled with IgG for bioprobes due to their good properties. • YVO 4 :Eu,Bi were applied to immunochromatographic test strip assay. - Abstract: Carboxyl-capped YVO 4 :Eu,Bi nanoparticles with average diameter of ∼10 nm were synthesized via a copolymer of phosphono and carboxylic acid mediated hydrothermal method. Under a 350 nm ultraviolet light excitation, the YVO 4 :Eu,Bi NPs exhibit sharp and bright red emission peaked at 615 nm and with highest quantum yield of ∼43%. Furthermore, the nanoparticles show good water/buffer stability and feasible bioconjugation benefiting from the carboxylic groups on their surface. Based on these kind optical and surface properties of the YVO 4 :Eu,Bi nanoparticles, an immunochromatographic test strip assay for quantitative determination of human IgG was achieved. This protocol can be extended to other rare-earth nanoparticles with the purpose of developing bioprobes for desired applications

  11. Evaluation of the Abbott RealTime HCV genotype II plus RUO (PLUS) assay with reference to core and NS5B sequencing.

    Science.gov (United States)

    Mallory, Melanie A; Lucic, Danijela; Ebbert, Mark T W; Cloherty, Gavin A; Toolsie, Dan; Hillyard, David R

    2017-05-01

    HCV genotyping remains a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen. Current commercial genotyping assays may have difficulty identifying 1a, 1b and genotype 6. To evaluate the concordance for identifying 1a, 1b, and genotype 6 between two methods: the PLUS assay and core/NS5B sequencing. This study included 236 plasma and serum samples previously genotyped by core/NS5B sequencing. Of these, 25 samples were also previously tested by the Abbott RealTime HCV GT II Research Use Only (RUO) assay and yielded ambiguous results. The remaining 211 samples were routine genotype 1 (n=169) and genotype 6 (n=42). Genotypes obtained from sequence data were determined using a laboratory-developed HCV sequence analysis tool and the NCBI non-redundant database. Agreement between the PLUS assay and core/NS5B sequencing for genotype 1 samples was 95.8% (162/169), with 96% (127/132) and 95% (35/37) agreement for 1a and 1b samples respectively. PLUS results agreed with core/NS5B sequencing for 83% (35/42) of unselected genotype 6 samples, with the remaining seven "not detected" by the PLUS assay. Among the 25 samples with ambiguous GT II results, 15 were concordant by PLUS and core/NS5B sequencing, nine were not detected by PLUS, and one sample had an internal control failure. The PLUS assay is an automated method that identifies 1a, 1b and genotype 6 with good agreement with gold-standard core/NS5B sequencing and can aid in the resolution of certain genotype samples with ambiguous GT II results. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Development of a colloidal gold immunochromatographic strip assay for simple and fast detection of human α-lactalbumin in genetically modified cow milk.

    Science.gov (United States)

    Tao, Chenyu; Zhang, Qingde; Feng, Na; Shi, Deshi; Liu, Bang

    2016-03-01

    The qualitative and quantitative declaration of food ingredients is important to consumers, especially for genetically modified food as it experiences a rapid increase in sales. In this study, we designed an accurate and rapid detection system using colloidal gold immunochromatographic strip assay (GICA) methods to detect genetically modified cow milk. First, we prepared 2 monoclonal antibodies for human α-lactalbumin (α-LA) and measured their antibody titers; the one with the higher titer was used for further experiments. Then, we found the optimal pH value and protein amount of GICA for detection of pure milk samples. The developed strips successfully detected genetically modified cow milk and non-modified cow milk. To determine the sensitivity of GICA, a quantitative ELISA system was used to determine the exact amount of α-LA, and then genetically modified milk was diluted at different rates to test the sensitivity of GICA; the sensitivity was 10 μg/mL. Our results demonstrated that the applied method was effective to detect human α-LA in cow milk. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  13. Development of a real-time RT-PCR and Reverse Line probe Hybridisation assay for the routine detection and genotyping of Noroviruses in Ireland.

    LENUS (Irish Health Repository)

    Menton, John F

    2007-01-01

    BACKGROUND: Noroviruses are the most common cause of non-bacterial gastroenteritis. Improved detection methods have seen a large increase in the number of human NoV genotypes in the last ten years. The objective of this study was to develop a fast method to detect, quantify and genotype positive NoV samples from Irish hospitals. RESULTS: A real-time RT-PCR assay and a Reverse Line Blot Hybridisation assay were developed based on the ORF1-ORF2 region. The sensitivity and reactivity of the two assays used was validated using a reference stool panel containing 14 NoV genotypes. The assays were then used to investigate two outbreaks of gastroenteritis in two Irish hospitals. 56 samples were screened for NoV using a real-time RT-PCR assay and 26 samples were found to be positive. Genotyping of these positive samples found that all positives belonged to the GII\\/4 variant of NoV. CONCLUSION: The combination of the Real-time assay and the reverse line blot hybridisation assay provided a fast and accurate method to investigate a NoV associated outbreak. It was concluded that the predominant genotype circulating in these Irish hospitals was GII\\/4 which has been associated with the majority of NoV outbreaks worldwide. The assays developed in this study are useful tools for investigating NoV infection.

  14. Comprehensive genotyping for 18 blood group systems using a multiplex ligation-dependent probe amplification assay shows a high degree of accuracy

    NARCIS (Netherlands)

    Haer-Wigman, Lonneke; Ji, Yanli; Lodén, Martin; de Haas, Masja; van der Schoot, C. Ellen; Veldhuisen, Barbera

    2013-01-01

    In recent years genotyping methods have been implemented in blood banks as alternative to comprehensive serologic typing. We evaluated a newly developed assay for convenient and comprehensive genotyping of blood group alleles based on multiplex ligation-dependent probe amplification (MLPA)

  15. Genotype-specific Taqman® assays for the detection and rapid characterisation of European strains of viral haemorrhagic septicaemia virus.

    Science.gov (United States)

    Bland, Fiona; Snow, Michael; Garver, Kyle A; Matejusova, Iveta

    2013-02-01

    Viral haemorrhagic septicaemia virus (VHSV) is the agent of a disease that causes mortality events in marine and freshwater fish. It is one of the most important pathogens in European rainbow trout (Oncorhynchus mykiss) aquaculture. Four major genotypes of the virus are recognised reflecting different geographic and host ranges. Genotyping of VHS isolates is important for disease management enabling monitoring of disease spread into new geographical regions or susceptible species. This study sought to develop molecular tools for rapid and efficient classification of European VHSV genotypes. Specificity of genotype-specific real-time reverse transcription polymerase chain reaction (RT-qPCR) assays targeting the viral nucleoprotein (N) gene was tested using 66 viral isolates. All designed Taqman(®) RT-qPCR assays were genotype specific, displayed a high sensitivity and together constituted a diagnostic method for the rapid discrimination of European VHSV genotypes. Practical diagnostic applications of such assays demonstrated in this study include: (1) rapid genotype determination of isolates; and (2) identification of mixed-genotype isolates originating from pooled samples in areas where genotype distribution is known to overlap. However, the most important application will be supporting international VHSV surveillance programmes through the provision of a rapid specific and sensitive isolate characterisation method. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

  16. Differential Detection of Human Papillomavirus Genotypes and Cervical Intraepithelial Neoplasia by Four Commercial Assays

    DEFF Research Database (Denmark)

    Rebolj, Matejka; Bonde, Jesper; Preisler, Sarah

    2016-01-01

    Laboratories can nowadays choose from >100 Human Papillomavirus (HPV) assays for cervical screening. Our previous analysis based on the data from the Danish Horizon study, however, showed that four widely used assays, Hybrid Capture 2 (HC2), cobas, CLART and APTIMA, frequently do not detect the s...

  17. Performance of commonly used genotypic assays and comparison with phenotypic assays of HIV-1 coreceptor tropism in acutely HIV-1-infected patients.

    Science.gov (United States)

    Ceresola, Elisa Rita; Nozza, Silvia; Sampaolo, Michela; Pignataro, Angela Rosa; Saita, Diego; Ferrarese, Roberto; Ripa, Marco; Deng, Wenjie; Mullins, James I; Boeri, Enzo; Tambussi, Giuseppe; Toniolo, Antonio; Lazzarin, Adriano; Clementi, Massimo; Canducci, Filippo

    2015-05-01

    Although founder viruses in primary HIV-1 infections (PHIs) typically use the CCR5 coreceptor (R5-tropic), 3%-19% of subjects also harbour CXCR4-using viruses (X4-tropic), making tropism determination before CCR5 antagonist usage mandatory. Genotypic methods can be used to accurately determine HIV-1 tropism in chronically infected patients. We compared the results of genotypic methods [geno2pheno, PSSMx4r5 including a novel nucleotide-input version (ntPSSM) and distant segments (ds)Kernel] to predict coreceptor usage in a cohort of 67 PHIs. Specimens with discrepant results were phenotypically tested after cloning the V3 gene region into proviral backbones. Recombinant viruses were used to infect U87 indicator cell lines bearing CD4 and either CCR5 or CXCR4. Geno2pheno10%, PSSMx4r5 and (ds)Kernel gave identical predictions in 85% of cases. Geno2pheno10% predicted the presence of CXCR4 viruses in 18% of patients. Two patients were predicted to carry X4-tropic viruses by all algorithms and X4-tropic viruses were detected in at least one of the recombinant AD8 or NL4-3 backbone-based assays. Ten samples resulted in discordant predictions with at least one algorithm. Full concordance between tropism prediction by using population sequencing and phenotypic assays was observed only with ntPSSM. Geno2pheno prediction and the phenotypic assay gave the same results in a minority of 'discordant' patients. Compared with both PSSMx4r5 versions, (ds)Kernel and our phenotypic assay, geno2pheno10% overestimated the frequency of X4-tropic viruses (18% versus 3%). ntPSSM was able to detect one additional X4 virus compared with (ds)Kernel that was confirmed with the phenotypic assay. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  18. Developmental validation of mitochondrial DNA genotyping assays for adept matrilineal inference of biogeographic ancestry at a continental level.

    Science.gov (United States)

    Chaitanya, Lakshmi; van Oven, Mannis; Weiler, Natalie; Harteveld, Joyce; Wirken, Laura; Sijen, Titia; de Knijff, Peter; Kayser, Manfred

    2014-07-01

    Mitochondrial DNA (mtDNA) can be used for matrilineal biogeographic ancestry prediction and can thus provide investigative leads towards identifying unknown suspects, when conventional autosomal short tandem repeat (STR) profiling fails to provide a match. Recently, six multiplex genotyping assays targeting 62 ancestry-informative mitochondrial single nucleotide polymorphisms (mt-SNPs) were developed. This hierarchical system of assays allows detection of the major haplogroups present in Africa, America, Western Eurasia, Eastern Eurasia, Australia and Oceania, thus revealing the broad geographic region of matrilineal origin of a DNA donor. Here, we provide a forensic developmental validation study of five multiplex assays targeting all the 62 ancestry-informative mt-SNPs following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. We demonstrate that the assays are highly sensitive; being able to produce full profiles at input DNA amounts of as little as 1pg. The assays were shown to be highly robust and efficient in providing information from degraded samples and from simulated casework samples of different substrates such as blood, semen, hair, saliva and trace DNA samples. Reproducible results were successfully achieved from concordance testing across three independent laboratories depicting the ease and reliability of these assays. Overall, our results demonstrate the suitability of these five mt-SNP assays for application to forensic casework and other purposes aiming to establish an individual's matrilineal genetic ancestry. With this validated tool, it is now possible to determine the matrilineal biogeographic origin of unknown individuals on the level of continental resolution from forensic DNA samples to provide investigative leads in criminal and missing person cases where autosomal STR profiling is uninformative. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  19. Use of an allele-specific polymerase chain reaction assay to genotype pyrethroid resistant strains of Boophilus microplus (Acari: Ixodidae).

    Science.gov (United States)

    Guerrero, F D; Davey, R B; Miller, R J

    2001-01-01

    A polymerase chain reaction-based assay was developed to detect the presence of a pyrethroid resistance-associated amino acid substitution in Boophilus microplus (Canestrini). The assay uses a simple method for the extraction of genomic DNA from individual larvae and genotypes individuals for the presence of a Phe-->Ile amino acid substitution in the S6 transmembrane segment of domain III of the para-like sodium channel, clearly distinguishing heterozygotes from homozygotes. High frequencies for this amino acid substitution were found in the Corrales and San Felipe strains, which have target site insensitivity mechanisms for pyrethroid resistance. The Caporal resistant strain contained lower yet substantial numbers of amino acid-substituted alleles. Low amino acid substitution frequencies were found in the susceptible reference Gonzales strain and the Coatzacoalcos strain, which has metabolic esterase-mediated pyrethroid resistance. The amino acid substitution was not found in six other strains that were susceptible to pyrethroids.

  20. Development of a high-resolution melting genotyping assay for the angiotensin I converting enzyme insertion/deletion polymorphism and establishment of genotype-specific reference intervals in a Danish population.

    Science.gov (United States)

    Nissen, Peter H; Campbell, Nina Buntzen; Højskov, Carsten S; Fløe, Andreas; Hoffmann, Hans Jürgen; Hilberg, Ole; Ladefoged, Søren A; Møller, Holger J

    2015-01-01

    The serum-angiotensin I converting enzyme (s-ACE) activity is influenced by a genetic insertion/deletion (I/D) polymorphism in the ACE gene, and the resulting large interindividual variation in s-ACE limits the use of normal reference intervals in the evaluation of sarcoidosis. In this study, we developed a new method for genotyping the I/D polymorphism in ACE and established genotype-specific reference intervals in order to improve the diagnostic accuracy and the value for treatment of sarcoidosis. The new genotyping assay is based on high-resolution melting (HRM) using LCGreen + and was used to genotype 400 healthy Danish individuals. The assay was compared to a real-time polymerase chain reaction (RT-PCR) assay in a validation set of 86 samples. Enzyme activity in serum was measured using the Infinity™ ACE Liquid Stable Reagent from Thermo adapted for the ABX Pentra analyzer. There was full concordance between genotyping assays. The three genotypes II, ID and DD were present with a frequency of 0.23, 0.51 and 0.26. The distribution of s-ACE values in the total population was non-Gaussian (non-parametric 95% reference interval 12.0-60.0 U/L). The median activities of the genotypes differed significantly (Preference intervals for the subpopulations were determined to 6.3-38.5, 14.0-56.0 and 23.3-71.2 U/L for II, ID and DD, respectively. We have developed a simple and robust method for ACE genotyping and determined genotype-specific reference intervals for s-ACE concentrations in the Danish population. The new reference intervals may increase the value of s-ACE measurements. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  1. Evaluation of an Immunochromatographic Strip (Xenostrip –Tv Test for Diagnosis of Vaginal Trichomoniasis Compared with Wet Mount and PCR Assay

    Directory of Open Access Journals (Sweden)

    MH Feiz-Haddad

    2008-09-01

    Full Text Available "nBackground: Trichomoniasis, caused by Trichomonas vaginalis, is one of the most common sexually transmitted infections in the world. Diagnosis of T. vaginalis is performed by different methods, including wet mount, culture, serological methods and PCR, which required laboratory equipments and expert laboratory personnel. The aim of this study was evaluation of immunochromatographic strip test (Xenostrip-Tv for diagnosis of vaginal trichomoniasis compared with wet mount and PCR assay."nMethods: In this prospective study vaginal swabs were obtained from 100 women with genital complaints demanding a speculum examination, referred to Imam Khomeini and Amir Kabir hospitals in Ahwaz, Khuzestan Province. Samples were first examined by wet mount and Xenostrip-Tv. PCR assay was performed in the next step using TVK3 and TVK7 primers initially. The positive samples were then confirmed by the second PCR assay using TVA5-1 and TVA6 primers."nResults: PCR with TVA5-1 and TVA6 primers was determined as gold standard. The wet mount as well as Xenostrip-Tv sensitivity and specificity were 73.3% and 100%, respectively in comparison with gold standard. The sensitivity and specificity of PCR with primers TVK3 and TVK7 were also determined as 100% and 96.6%, respectively. The infection rates were 14% for wet mount and Xenostrip-Tv, 21% for PCR with primers TVK3 plus TVK7 and 19% with the gold standard PCR using TVA5-1 and TVA6 primers."nConclusion: Xenostrip- Tv could be used for diagnosis of vaginal trichomoniasis in regions with no laboratory diagnostic facilities.

  2. Evaluation of the cobas® GT hepatitis C virus genotyping assay in G1-6 viruses including low viral loads and LiPA failures.

    Science.gov (United States)

    Némoz, Benjamin; Roger, Léa; Leroy, Vincent; Poveda, Jean-Dominique; Morand, Patrice; Larrat, Sylvie

    2018-01-01

    Direct-acting antiviral (DAA) drug performances depend on the viral genotype. So international recommendations give typing of the virus a prerequisite for treatment choice and patient management. Commercially available HCV genotyping kits are scarce and this analysis is often in-house using tedious PCRs and Sanger sequencing, leading to a lack of standardization. A newly commercialized HCV genotyping assay based on real-time PCR has been developed by Roche Diagnostics (Mannheim, Germany). We compared this new assay with our in-house PCRs -sequencing technique on 101 regular samples and 81 LiPA failures or low viral load samples. No genotype or 1a/1b subtype mismatch was observed. Two samples were misidentified at the subtype level without clinical impact. Three genotype 1b and two genotype 1a samples with low viral load could not be subtyped. Nevertheless, 13 (13%) samples from the regular panel and 35 (43%) from the more difficult-to-type panels failed to give results on first pass with the Roche kit. Failures were mostly associated with genotype 3 subtype a, with genotype 4 subtype non-a, or with viral loads <200 IU/mL (p = 0.0061). The workflow allowed a non-specialized technician to obtain results in less than 4 hours whereas 2 to 3 days and experienced staff were required with the in-house assay. In conclusion, the Roche cobas® HCV GT kit is easy and rapid to use and provides reliable results. The high rate of uninterpretable results particularly for low viral load samples and less frequent genotypes, and the absence of subtyping for non-genotype 1 could require sending complex samples to a specialized laboratory.

  3. Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.

    Directory of Open Access Journals (Sweden)

    Zhiyong Zhou

    Full Text Available Commercially available HIV-1 drug resistance (HIVDR genotyping assays are expensive and have limitations in detecting non-B subtypes and circulating recombinant forms that are co-circulating in resource-limited settings (RLS. This study aimed to optimize a low cost and broadly sensitive in-house assay in detecting HIVDR mutations in the protease (PR and reverse transcriptase (RT regions of pol gene. The overall plasma genotyping sensitivity was 95.8% (N = 96. Compared to the original in-house assay and two commercially available genotyping systems, TRUGENE® and ViroSeq®, the optimized in-house assay showed a nucleotide sequence concordance of 99.3%, 99.6% and 99.1%, respectively. The optimized in-house assay was more sensitive in detecting mixture bases than the original in-house (N = 87, P<0.001 and TRUGENE® and ViroSeq® assays. When the optimized in-house assay was applied to genotype samples collected for HIVDR surveys (N = 230, all 72 (100% plasma and 69 (95.8% of the matched dried blood spots (DBS in the Vietnam transmitted HIVDR survey were genotyped and nucleotide sequence concordance was 98.8%; Testing of treatment-experienced patient plasmas with viral load (VL ≥ and <3 log10 copies/ml from the Nigeria and Malawi surveys yielded 100% (N = 46 and 78.6% (N = 14 genotyping rates, respectively. Furthermore, all 18 matched DBS stored at room temperature from the Nigeria survey were genotyped. Phylogenetic analysis of the 236 sequences revealed that 43.6% were CRF01_AE, 25.9% subtype C, 13.1% CRF02_AG, 5.1% subtype G, 4.2% subtype B, 2.5% subtype A, 2.1% each subtype F and unclassifiable, 0.4% each CRF06_CPX, CRF07_BC and CRF09_CPX.The optimized in-house assay is broadly sensitive in genotyping HIV-1 group M viral strains and more sensitive than the original in-house, TRUGENE® and ViroSeq® in detecting mixed viral populations. The broad sensitivity and substantial reagent cost saving make this assay more accessible

  4. Optimization of a low cost and broadly sensitive genotyping assay for HIV-1 drug resistance surveillance and monitoring in resource-limited settings.

    Science.gov (United States)

    Zhou, Zhiyong; Wagar, Nick; DeVos, Joshua R; Rottinghaus, Erin; Diallo, Karidia; Nguyen, Duc B; Bassey, Orji; Ugbena, Richard; Wadonda-Kabondo, Nellie; McConnell, Michelle S; Zulu, Isaac; Chilima, Benson; Nkengasong, John; Yang, Chunfu

    2011-01-01

    Commercially available HIV-1 drug resistance (HIVDR) genotyping assays are expensive and have limitations in detecting non-B subtypes and circulating recombinant forms that are co-circulating in resource-limited settings (RLS). This study aimed to optimize a low cost and broadly sensitive in-house assay in detecting HIVDR mutations in the protease (PR) and reverse transcriptase (RT) regions of pol gene. The overall plasma genotyping sensitivity was 95.8% (N = 96). Compared to the original in-house assay and two commercially available genotyping systems, TRUGENE® and ViroSeq®, the optimized in-house assay showed a nucleotide sequence concordance of 99.3%, 99.6% and 99.1%, respectively. The optimized in-house assay was more sensitive in detecting mixture bases than the original in-house (N = 87, P<0.001) and TRUGENE® and ViroSeq® assays. When the optimized in-house assay was applied to genotype samples collected for HIVDR surveys (N = 230), all 72 (100%) plasma and 69 (95.8%) of the matched dried blood spots (DBS) in the Vietnam transmitted HIVDR survey were genotyped and nucleotide sequence concordance was 98.8%; Testing of treatment-experienced patient plasmas with viral load (VL) ≥ and <3 log10 copies/ml from the Nigeria and Malawi surveys yielded 100% (N = 46) and 78.6% (N = 14) genotyping rates, respectively. Furthermore, all 18 matched DBS stored at room temperature from the Nigeria survey were genotyped. Phylogenetic analysis of the 236 sequences revealed that 43.6% were CRF01_AE, 25.9% subtype C, 13.1% CRF02_AG, 5.1% subtype G, 4.2% subtype B, 2.5% subtype A, 2.1% each subtype F and unclassifiable, 0.4% each CRF06_CPX, CRF07_BC and CRF09_CPX. The optimized in-house assay is broadly sensitive in genotyping HIV-1 group M viral strains and more sensitive than the original in-house, TRUGENE® and ViroSeq® in detecting mixed viral populations. The broad sensitivity and substantial reagent cost saving make this assay more accessible for

  5. Genotyping of human parvovirus B19 in clinical samples from Brazil and Paraguay using heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing

    Directory of Open Access Journals (Sweden)

    Marcos César Lima de Mendonça

    2011-06-01

    Full Text Available Heteroduplex mobility assay, single-stranded conformation polymorphism and nucleotide sequencing were utilised to genotype human parvovirus B19 samples from Brazil and Paraguay. Ninety-seven serum samples were collected from individuals presenting with abortion or erythema infectiosum, arthropathies, severe anaemia and transient aplastic crisis; two additional skin samples were collected by biopsy. After the procedure, all clinical samples were classified as genotype 1.

  6. Performance of two Real-Time RT-PCR assays for quantitation of hepatitis C virus RNA: evaluation on HCV genotypes 1-4.

    Science.gov (United States)

    Elkady, Abeer; Tanaka, Yasuhito; Kurbanov, Fuat; Sugauchi, Fuminaka; Sugiyama, Masaya; Khan, Anis; Ali, Elsayed Mostafa; Mouhamed, Layla; Abou el-fetouh, Sahar; AbdEl-Hameed, AbdEl-Rahaman; Mizokami, Masashi

    2010-11-01

    Accuracy for monitoring of the concentration of hepatitis C virus (HCV) RNA represents a major challenge throughout the management of patients with chronic hepatitis C. To investigate the genotype-independent efficiency and the accuracy of two real-time detection reverse transcription-polymerase chain reaction (RT-PCR) assays; the Cobas Ampliprep/Cobas TaqMan (CAP/CTM); and the Abbott RealTime HCV (ART), a total of 184 samples with different HCV subtypes were examined; 1b (n=58), 2a (n=39), 2b (n=26), 3a (n=20), and 4 (n=41). A robust linear correlation was observed between the two assays applied to genotypes 1b, 2a, 2b, and 3a [the correlation coefficient (R) ranged from 0.99 to 0.98], but not to genotype 4 specimens (R=0.78). A significant difference in measurements of HCV RNA using CAP/CTM and ART in serum samples with genotypes 1b and 4 was observed (0.72, -0.53 log IU/ml, PHCV core antigen and HCV RNA values by either of the HCV RNA quantitation assays applied to all genotypes with exception of genotype 4, for which R was higher with ART (R=0.95) than with CAP/CTM (R=0.80). The lower limit of detection of CAP/CTM and ART were 41.4 and 28.5 IU/ml using the WHO standards, respectively. In conclusion, two RT-PCR assays had a high efficiency and accuracy for quantitation of HCV RNA of genotypes 2a, 2b, and 3a, but the mean values of HCV RNA differed for genotype 1b and 4. © 2010 Wiley-Liss, Inc.

  7. DETERMINATION OF VIRAL TROPISM BY GENOTYPING AND PHENOTYPING ASSAYS IN BRAZILIAN HIV-1-INFECTED PATIENTS

    Directory of Open Access Journals (Sweden)

    Liã Bárbara Arruda

    2014-07-01

    Full Text Available The clinical application of CCR5 antagonists involves first determining the coreceptor usage by the infecting viral strain. Bioinformatics programs that predict coreceptor usage could provide an alternative method to screen candidates for treatment with CCR5 antagonists, particularly in countries with limited financial resources. Thus, the present study aims to identify the best approach using bioinformatics tools for determining HIV-1 coreceptor usage in clinical practice. Proviral DNA sequences and Trofile results from 99 HIV-1-infected subjects under clinical monitoring were analyzed in this study. Based on the Trofile results, the viral variants present were 81.1% R5, 21.4% R5X4 and 1.8% X4. Determination of tropism using a Geno2pheno[coreceptor] analysis with a false positive rate of 10% gave the most suitable performance in this sampling: the R5 and X4 strains were found at frequencies of 78.5% and 28.4%, respectively, and there was 78.6% concordance between the phenotypic and genotypic results. Further studies are needed to clarify how genetic diversity amongst virus strains affects bioinformatics-driven approaches for determining tropism. Although this strategy could be useful for screening patients in developing countries, some limitations remain that restrict the wider application of coreceptor usage tests in clinical practice.

  8. A high resolution melting (HRM) technology-based assay for cost-efficient clinical detection and genotyping of herpes simplex virus (HSV)-1 and HSV-2.

    Science.gov (United States)

    Lieveld, M; Carregosa, A; Benoy, I; Redzic, N; Berth, M; Vanden Broeck, D

    2017-10-01

    Genital herpes can be caused by two very similar viruses, herpes simplex virus (HSV)-1 or HSV-2. These two HSV types cannot be distinguished clinically, but genotyping is recommended in the first-episodes of genital herpes to guide counselling and management. Quantitative polymerase chain reaction (qPCR) is the preferred diagnostic method for HSV typing. However, commercial qPCR methods use expensive fluorescent labeled probes for detection. Furthermore, most low-cost methods are not able to differentiate between HSV-1 and -2. The aim of this study was to develop a high resolution melting (HRM) technology-based assay for sensitive HSV-1 and HSV-2 detection and genotyping. Using a panel of 46 clinical specimens, the performance of the HRM assay was compared to two commercial HSV tests: the HRM assay detected HSV in all 23 positive samples, with no false positive results (100% concordance with HSV I/II Real-TM assay). Additionally, the HRM assay correctly genotyped both HSV types in a subset of these clinical samples, as determined by the Realstar HSV PCR Kit. The HSV HRM assay provides a cost-effective alternative method to conventional more expensive assays and can be used in routine clinical specimens, in cases where it is particularly necessary to detect and distinguish HSV-1 from -2. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Genotyping assay for differentiation of wild-type and vaccine viruses in subjects immunized with live attenuated influenza vaccine.

    Directory of Open Access Journals (Sweden)

    Victoria Matyushenko

    Full Text Available Live attenuated influenza vaccines (LAIVs are considered as safe and effective tool to control influenza in different age groups, especially in young children. An important part of the LAIV safety evaluation is the detection of vaccine virus replication in the nasopharynx of the vaccinees, with special attention to a potential virus transmission to the unvaccinated close contacts. Conducting LAIV clinical trials in some geographical regions with year-round circulation of influenza viruses warrants the development of robust and reliable tools for differentiating vaccine viruses from wild-type influenza viruses in nasal pharyngeal wash (NPW specimens of vaccinated subjects. Here we report the development of genotyping assay for the detection of wild-type and vaccine-type influenza virus genes in NPW specimens of young children immunized with Russian-backbone seasonal trivalent LAIV using Sanger sequencing from newly designed universal primers. The new primer set allowed amplification and sequencing of short fragments of viral genes in NPW specimens and appeared to be more sensitive than conventional real-time RT-PCR protocols routinely used for the detection and typing/subtyping of influenza virus in humans. Furthermore, the new assay is capable of defining the origin of wild-type influenza virus through BLAST search with the generated sequences of viral genes fragments.

  10. Identification of six New World Leishmania species through the implementation of a High-Resolution Melting (HRM) genotyping assay.

    Science.gov (United States)

    Hernández, Carolina; Alvarez, Catalina; González, Camila; Ayala, Martha Stella; León, Cielo Maritza; Ramírez, Juan David

    2014-11-14

    Leishmaniases are tropical zoonotic diseases, caused by parasites from the genus Leishmania. New World (NW) species are related to sylvatic cycles although urbanization processes have been reported in some South American Countries such as Colombia. This eco-epidemiological complexity imposes a challenge to the detection of circulating parasite species, not only related to human cases but also infecting vectors and reservoirs. Currently, no harmonized methods have been deployed to discriminate the NW Leishmania species. Herein, we conducted a systematic and mechanistic High-Resolution Melting (HRM) assay targeted to HSP70 and ITS1. Specific primers were designed that coupled with a HRM analyses permitted to discriminate six NW Leishmania species. In order to validate the herein described algorithm, we included 35 natural isolates obtained from human cases, insect vectors and mammals. Our genotyping assay allowed the correct assignment of the six NW Leishmania species (L. mexicana, L. infantum (chagasi), L. amazonensis, L. panamensis, L. guyanensis and L. braziliensis) based on reference strains. When the algorithm was applied to a set of well-characterized strains by means of PCR-RFLP, MLEE and monoclonal antibodies (MA) we observed a tailored concordance between the HRM and PCR-RFLP/MLEE/MA (KI = 1.0). Additionally, we tested the limit of detection for the HRM method showing that this is able to detect at least 10 equivalent-parasites per mL. This is a rapid and reliable method to conduct molecular epidemiology and host-parasite association studies in endemic areas.

  11. Lactase Non-Persistence Genotyping: Comparison of Two Real-Time PCR Assays and Assessment of Concomitant Fructose/Sorbitol Malabsorption Rates.

    Science.gov (United States)

    Enko, Dietmar; Pollheimer, Verena; Németh, Stefan; Pühringer, Helene; Stolba, Robert; Halwachs-Baumann, Gabriele; Kriegshäuser, Gernot

    2016-01-01

    Genetic testing is a standard technique for the diagnosis of primary adult-type hypolactasia, also referred to as lactase non-persistence. The aim of this study was to compare the lactase gene (LCT) C/T-13910 polymorphism genotyping results of two commercially available real-time (RT)-PCR assays in patients referred to our outpatient clinic for primary lactose malabsorption testing. Furthermore, concomitant conditions of fructose/sorbitol malabsorption were assessed. Samples obtained from 100 patients were tested in parallel using the LCT T-13910C ToolSet for Light Cycler (Roche, Rotkreuz, Switzerland) and the LCT-13910C>T RealFast Assay (ViennaLab Diagnostics GmbH, Vienna, Austria). Additionally, patients were also screened for the presence of fructose/sorbitol malabsorption by functional hydrogen (H2)/methane (CH4) breath testing (HMBT). Cohen's Kappa (κ) was used to calculate the agreement between the two genotyping methods. The exact Chi-Square test was performed to compare fructose/sorbitol HMBT with LCT genotyping results. Twenty-one (21.0%) patients had a LCT C/C-13910 genotype suggestive of lactase non-persistence, and 79 (79.0%) patients were identified with either a LCT T/C-13910 or T/T-13910 genotype (i.e., lactase persistence). In all genotype groups, concordance between the two RT-PCR assays was 100%. Cohen's κ demonstrated perfect observed agreement (p Fructose and sorbitol malabsorption was observed in 13/100 (13.0%) and 25/100 (25.0%) individuals, respectively. Both RT-PCR assays are robust and reliable LCT genotyping tools in a routine clinical setting. Concomitant fructose and/or sorbitol malabsorption should be considered in individuals with suspected lactase-non-persistence. However, standardization of clinical interpretation of laboratory HMBT results is required.

  12. A type-specific nested PCR assay established and applied for investigation of HBV genotype and subgenotype in Chinese patients with chronic HBV infection

    Directory of Open Access Journals (Sweden)

    Nie Jing-Jing

    2012-06-01

    Full Text Available Abstract Background Many studies have suggested that hepatitis B virus (HBV genotypes show not only geographical distribution and race specificity, but also are associated with disease progression and response to interferon treatment. The objective of this study was to develop a nested polymerase chain reaction (nPCR assay for genotypes A-D and subgenotypes B1, B2, C1 and C2 of hepatitis B virus (HBV and to investigate the distribution characteristics of HBV genotypes/subgenotype in China. Methods After redesigning the primers and optimizing the reaction conditions using common Taq polymerase, the sensitivity, specificity and reproducibility of the method were evaluated using plasmids and serum samples. In total, 642 serum samples from patients with chronic HBV infection were applied to investigate the distribution of HBV genotype and subgenotype in China. Results The genotype and subgenotype could be identified when the HBV DNA load of a sample was ≥102.3 IU/mL. For the 639 successfully genotyped samples, the sequencing results of 130 randomly selected samples (20.3%, 130/639 were consistent with those of the nPCR method. The present study showed that HBV genotype B (11.2%, 72/642, C (68.2%, 438/642 and D (7.2%, 46/642 were circulating in China, while genotype C was the dominant strain except for western region where genotype D was the prevalent strain. The main subgenotypes of genotypes B and C were B2 (87.5%, 63/72 and C2 (92.9%, 407/438, respectively. Conclusions The low-cost nPCR method would be a useful tool for clinical and epidemiological investigation in the regions where genotypes A-D are predominant.

  13. Elastic strips

    OpenAIRE

    Chubelaschwili, David; Pinkall, Ulrich

    2010-01-01

    Motivated by the problem of finding an explicit description of a developable narrow Moebius strip of minimal bending energy, which was first formulated by M. Sadowsky in 1930, we will develop the theory of elastic strips. Recently E.L. Starostin and G.H.M. van der Heijden found a numerical description for an elastic Moebius strip, but did not give an integrable solution. We derive two conservation laws, which describe the equilibrium equations of elastic strips. In applying these laws we find...

  14. Type-specific PCR assays for Babesia bovis msa-1 genotypes in Asia: Revisiting the genetic diversity in Sri Lanka, Mongolia, and Vietnam.

    Science.gov (United States)

    Liyanagunawardena, Nilukshi; Sivakumar, Thillaiampalam; Kothalawala, Hemal; Silva, Seekkuge Susil Priyantha; Battsetseg, Badgar; Lan, Dinh Thi Bich; Inoue, Noboru; Igarashi, Ikuo; Yokoyama, Naoaki

    2016-01-01

    Babesia bovis is the most virulent Babesia organism, resulting in a high mortality rate in cattle. The genetic diversity of B. bovis merozoite surface antigens (MSAs), such as MSA-1, MSA-2b, and MSA-2c, might be linked to altered immune profiles in the host animals. The present study aimed to develop type-specific PCR assays for Asian msa-1 genotypes, thereby re-analyzing the genetic diversity of msa-1 in Sri Lanka, Mongolia, and Vietnam. Specific primers were designed for nine Asian msa-1 genotypes, which had been detected based on the phylogeny constructed using msa-1 gene sequences retrieved from the GenBank database. Specificity of the type-specific PCR assays was confirmed using plasmids containing the inserts of msa-1 gene fragments that represent Asian genotypes. Furthermore, no amplicons were observed by these PCR assays when DNA samples of Babesia bigemina, Babesia ovata, Theileria annulata, Theileria orientalis, Trypanosoma evansi, Trypanosoma theileri, Anaplasma marginale, and Anaplasma bovis, and non-infected bovine blood were analyzed. In total, 109 B. bovis-positive blood DNA samples sourced from Sri Lanka (44 cattle), Mongolia (26 cattle), and Vietnam (23 cattle and 16 water buffaloes) were then screened by the type-specific PCR assays. The sequences derived from all of the PCR amplicons were phylogenetically analyzed. Out of 109 DNA samples, 23 (20 from cattle and 3 from water buffaloes) were positive for at least one genotype. In agreement with previous studies, five and four different genotypes were detected among the DNA samples from Sri Lanka and Vietnam, respectively. In contrast, four genotypes, including three novel genotypes, were detected from Mongolia. Five DNA samples were found to be co-infected with multiple genotypes. The sequences of the PCR amplicons clustered phylogenetically within the corresponding clades. These findings indicated that the type-specific PCR assays described herein are useful for the determination of genotypic

  15. Rapid genotyping assays for the 4-base pair deletion of canine MDR1/ABCB1 gene and low frequency of the mutant allele in Border Collie dogs.

    Science.gov (United States)

    Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

    2012-01-01

    P-glycoprotein, encoded by the MDR1 or ABCB1 gene, is an integral component of the blood-brain barrier as an efflux pump for xenobiotics crucial in limiting drug uptake into the central nervous system. Dogs homozygous for a 4-base pair deletion of the canine MDR1 gene show altered expression or function of P-glycoprotein, resulting in neurotoxicosis after administration of the substrate drugs. In the present study, the usefulness of microchip electrophoresis for genotyping assays detecting this deletion mutation was evaluated. Mutagenically separated polymerase chain reaction (MS-PCR) and real-time PCR assays were newly developed and evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies dogs in Japan to determine the allele frequency in this breed. Microchip electrophoresis showed advantages in detection sensitivity and time saving over other modes of electrophoresis. The MS-PCR assay clearly discriminated all genotypes. Real-time PCR assay was most suitable for a large-scale survey due to its high throughput and rapidity. The genotyping survey demonstrated that the carrier and mutant allele frequencies were 0.49% and 0.25%, respectively, suggesting that the mutant allele frequency in Border Collies is markedly low compared to that in the susceptible dog breeds such as rough and smooth Collies.

  16. Evaluation of three PCR assays for the identification of the sheep strain (genotype 1) of Echinococcus granulosus in canid feces and parasite tissues

    NARCIS (Netherlands)

    Boufana, Belgees S; Campos-Ponce, Maiza; Naidich, Ariel; Buishi, Imad; Lahmar, Selma; Zeyhle, Eberhard; Jenkins, David J; Combes, Benoit; Wen, Hao; Xiao, Ning; Nakao, Minoru; Ito, Akira; Qiu, Jiamin; Craig, Philip S

    2008-01-01

    The performance of 3 PCR assays for the identification of the G1 sheep genotype of Echinococcus granulosus was evaluated using tissue and canid fecal samples. The "Dinkel" and "Stefanić" primers were the most sensitive in detecting E. granulosus DNA in feces of necropsied dogs (73.7% and 100%,

  17. A closed-tube assay for genotyping of the 32-bp deletion polymorphism in the chemokine receptor 5 (CCR5) gene

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Werge, Thomas

    2007-01-01

    in the presence of Sybr Green I for allele discrimination. After having established robust conditions for the assay, we used it to genotype 590 unknown DNA samples. A blinded comparison with a procedure based upon agarose gel electrophoresis of amplified material revealed complete concordance between the two...

  18. The Usefulness of Defining Rapid Virological Response by a Very Sensitive Assay (TMA) during Treatment of HCV Genotype 2/3 Infection

    DEFF Research Database (Denmark)

    Dalgard, Olav; Martinot-Peignoux, Michelle; Verbaan, Hans

    2015-01-01

    The aim of this study was to determine in patients with HCV genotype 2 or 3 the performance at week 4 of two assays with different sensitivities for HCV RNA detection, for the prediction of SVR and stratification for treatment duration (14 and 24 weeks). Recruitment was from two trials comparing 14...... and 24 weeks treatment to patients with rapid virological response (RVR) (n = 550). RVR was originally defined as HCV RNA HCV-RNA was prospectively...... measured with COBAS Amplicor V2, Roche (CA) (lower detection limit 50 IU/ml) and retrospectively assessed with VERSANT HCV-RNA Qualitative Assay, Siemens (TMA) (lower limit detection 10 IU/ml). Genotype 3 was present in 80% and genotype 2 in 20%. A SVR was achieved in 82%. At week 4 HCV...

  19. A closed-tube assay for genotyping of the 32-bp deletion polymorphism in the chemokine receptor 5 (CCR5) gene

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Werge, Thomas

    2007-01-01

    We have developed a closed-tube assay for determination of the chemokine receptor type 5 (CCR5) 32-bp deletion allele, which protects against infections with HIV and modulates susceptibility to a variety of inflammatory diseases. This assay utilizes dissociation analysis of amplified products...... in the presence of Sybr Green I for allele discrimination. After having established robust conditions for the assay, we used it to genotype 590 unknown DNA samples. A blinded comparison with a procedure based upon agarose gel electrophoresis of amplified material revealed complete concordance between the two...

  20. Novel rapid genotyping assays for neuronal ceroid lipofuscinosis in Border Collie dogs and high frequency of the mutant allele in Japan.

    Science.gov (United States)

    Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Kawahara, Natsuko; Hayashi, Daisuke; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

    2011-11-01

    Neuronal ceroid lipofuscinosis (NCL) constitutes a group of recessively inherited lysosomal storage diseases that primarily affect neuronal cells. Such diseases share certain clinical and pathologic features in human beings and animals. Neuronal ceroid lipofuscinosis in Border Collie dogs was first detected in Australia in the 1980s, and the pathogenic mutation was shown to be a nonsense mutation (c.619C>T) in exon 4 in canine CLN5 gene. In the present study, novel rapid genotyping assays including polymerase chain reaction (PCR)-restriction fragment length polymorphism, PCR primer-induced restriction analysis, mutagenically separated PCR, and real-time PCR with TaqMan minor groove binder probes, were developed. The utility of microchip electrophoresis was also evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies in Japan using these assays to determine the current allele frequency in Japan, providing information to control and prevent this disease in the next stage. All assays developed in the current study are available to discriminate these genotypes, and microchip electrophoresis showed a timesaving advantage over agarose gel electrophoresis. Of all assays, real-time PCR was the most suitable for large-scale examination because of its high throughput. The genotyping survey demonstrated that the carrier frequency was 8.1%. This finding suggested that the mutant allele frequency of NCL in Border Collies is high enough in Japan that measures to control and prevent the disease would be warranted. The genotyping assays developed in the present study could contribute to the prevention of NCL in Border Collies.

  1. Amplification of the Gp41 gene for detection of mutations conferring resistance to HIV-1 fusion inhibitors on genotypic assay

    Science.gov (United States)

    Tanumihardja, J.; Bela, B.

    2017-08-01

    Fusion inhibitors have potential for future use in HIV control programs in Indonesia, so the capacity to test resistance to such drugs needs to be developed. Resistance-detection with a genotypic assay began with amplification of the target gene, gp41. Based on the sequence of the two most common HIV subtypes in Indonesia, AE and B, a primer pair was designed. Plasma samples containing both subtypes were extracted to obtain HIV RNA. Using PCR, the primer pair was used to produce the amplification product, the identity of which was checked based on length under electrophoresis. Eleven plasma samples were included in this study. One-step PCR using the primer pair was able to amplify gp41 from 54.5% of the samples, and an unspecific amplification product was seen in 1.1% of the samples. Amplification failed in 36.4% of the samples, which may be due to an inappropriate primer sequence. It was also found that the optimal annealing temperature for producing the single expected band was 57.2 °C. With one-step PCR, the designed primer pair amplified the HIV-1 gp41 gene from subtypes AE and B. However, further research should be done to determine the conditions that will increase the sensitivity and specificity of the amplification process.

  2. The New Aptima HBV Quant Real-Time TMA Assay Accurately Quantifies Hepatitis B Virus DNA from Genotypes A to F.

    Science.gov (United States)

    Chevaliez, Stéphane; Dauvillier, Claude; Dubernet, Fabienne; Poveda, Jean-Dominique; Laperche, Syria; Hézode, Christophe; Pawlotsky, Jean-Michel

    2017-04-01

    Sensitive and accurate hepatitis B virus (HBV) DNA detection and quantification are essential to diagnose HBV infection, establish the prognosis of HBV-related liver disease, and guide the decision to treat and monitor the virological response to antiviral treatment and the emergence of resistance. Currently available HBV DNA platforms and assays are generally designed for batching multiple specimens within an individual run and require at least one full day of work to complete the analyses. The aim of this study was to evaluate the ability of the newly developed, fully automated, one-step Aptima HBV Quant assay to accurately detect and quantify HBV DNA in a large series of patients infected with different HBV genotypes. The limit of detection of the assay was estimated to be 4.5 IU/ml. The specificity of the assay was 100%. Intra-assay and interassay coefficients of variation ranged from 0.29% to 5.07% and 4.90% to 6.85%, respectively. HBV DNA levels from patients infected with HBV genotypes A to F measured with the Aptima HBV Quant assay strongly correlated with those measured by two commercial real-time PCR comparators (Cobas AmpliPrep/Cobas TaqMan HBV test, version 2.0, and Abbott RealTi m e HBV test). In conclusion, the Aptima HBV Quant assay is sensitive, specific, and reproducible and accurately quantifies HBV DNA in plasma samples from patients with chronic HBV infections of all genotypes, including patients on antiviral treatment with nucleoside or nucleotide analogues. The Aptima HBV Quant assay can thus confidently be used to detect and quantify HBV DNA in both clinical trials with new anti-HBV drugs and clinical practice. Copyright © 2017 American Society for Microbiology.

  3. Comparison of the performance in detection of HPV infections between the high-risk HPV genotyping real time PCR and the PCR-reverse dot blot assays.

    Science.gov (United States)

    Zhang, Lahong; Dai, Yibei; Chen, Jiahuan; Hong, Liquan; Liu, Yuhua; Ke, Qiang; Chen, Yiwen; Cai, Chengsong; Liu, Xia; Chen, Zhaojun

    2018-01-01

    A new multiplex real-time PCR assay, the high-risk HPV genotyping real time PCR assay (HR HPV RT-PCR), has been developed to detect 15 high-risk HPV types with respective viral loads. In this report, a total of 684 cervical specimens from women diagnosed with vaginitis were assessed by the HR HPV RT-PCR and the PCR reaction and reverse dot blot (PCR-RDB) assays, using a PCR-sequencing method as a reference standard. A total coincidence of 97.7% between the HR HPV RT PCR and the PCR-RDB assays was determined with a Kappa value of 0.953. The HR HPV RT PCR assay had sensitivity, specificity, and concordance rates (accuracy) of 99.7%, 99.7%, and 99.7%, respectively, as confirmed by PCR-sequencing, while the PCR-RDB assay had respective rates of 98.8%, 97.1%, and 98.0%. The overall rate of HPV infection, determined by PCR-sequencing, in women diagnosed with vaginitis was 49.85%, including 36.26% of single infection and 13.6% of multiple infections. The most common infections among the 15 high-risk HPV types in women diagnosed with vaginitis were HPV-52, HPV-16, and HPV-58, with a total detection rate of 10.23%, 7.75%, and 5.85%, respectively. We conclude that the HR HPV RT PCR assay exhibits better clinical performance than the PCR-RDB assay, and is an ideal alternative method for HPV genotyping. In addition, the HR HPV RT PCR assay provides HPV DNA viral loads, and could serve as a quantitative marker in the diagnosis and treatment of single and multiple HPV infections. © 2017 Wiley Periodicals, Inc.

  4. The New Aptima HCV Quant Dx Real-time TMA Assay Accurately Quantifies Hepatitis C Virus Genotype 1-6 RNA.

    Science.gov (United States)

    Chevaliez, Stéphane; Dubernet, Fabienne; Dauvillier, Claude; Hézode, Christophe; Pawlotsky, Jean-Michel

    2017-06-01

    Sensitive and accurate hepatitis C virus (HCV) RNA detection and quantification is essential for the management of chronic hepatitis C therapy. Currently available platforms and assays are usually batched and require at least 5hours of work to complete the analyses. The aim of this study was to evaluate the ability of the newly developed Aptima HCV Quant Dx assay that eliminates the need for batch processing and automates all aspects of nucleic acid testing in a single step, to accurately detect and quantify HCV RNA in a large series of patients infected with different HCV genotypes. The limit of detection was estimated to be 2.3 IU/mL. The specificity of the assay was 98.6% (95% confidence interval: 96.1%-99.5%). Intra-assay and inter-assay coefficients of variation ranged from 0.09% to 5.61%, and 1.05% to 3.65%, respectively. The study of serum specimens from patients infected with HCV genotypes 1 to 6 showed a satisfactory relationship between HCV RNA levels measured by the Aptima HCV Quant Dx assay, and both real-time PCR comparators (Abbott RealTime HCV and Cobas AmpliPrep/Cobas TaqMan HCV Test, version 2.0, assays). the new Aptima HCV Quant Dx assay is rapid, sensitive, reasonably specific and reproducible and accurately quantifies HCV RNA in serum samples from patients with chronic HCV infection, including patients on antiviral treatment. The Aptima HCV Quant Dx assay can thus be confidently used to detect and quantify HCV RNA in both clinical trials with new anti-HCV drugs and clinical practice in Europe and the US. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. An ultra-sensitive monoclonal antibody-based fluorescent microsphere immunochromatographic test strip assay for detecting aflatoxin M1 in milk

    Science.gov (United States)

    A rapid lateral flow fluorescent microspheres immunochromatography test strip (FMs-ICTS) has been developed for the detection of aflatoxin M1 (AFM1) residues in milk. For this purpose, an ultra-sensitive anti-AFM1 monoclonal antibody (MAb) 1D3 was prepared and identified. The IC50 value of the MA...

  6. Genotyping of a tri-allelic polymorphism by a novel melting curve assay in MTHFD1L: an association study of nonsyndromic Cleft in Ireland

    LENUS (Irish Health Repository)

    Minguzzi, Stefano

    2012-04-20

    AbstractBackgroundPolymorphisms within the MTHFD1L gene were previously associated with risk of neural tube defects in Ireland. We sought to test the most significant MTHFD1L polymorphisms for an association with risk of cleft in an Irish cohort. This required the development of a new melting curve assay to genotype the technically challenging MTHFD1L triallelic deletion\\/insertion polymorphism (rs3832406).MethodsMelting curve analysis was used to genotype the MTHFD1L triallelic deletion\\/insertion polymorphism (rs3832406) and a Single Nucleotide Polymorphism rs17080476 in an Irish cohort consisting of 981 Irish case-parent trios and 1,008 controls. Tests for association with nonsyndromic cleft lip with or without cleft palate and cleft palate included case\\/control analysis, mother\\/control analysis and Transmission Disequilibrium Tests of case-parent trios.ResultsA successful melting curve genotyping assay was developed for the deletion\\/insertion polymorphism (rs3832406). The TDT analysis initially showed that the rs3832406 polymorphism was associated with isolated cleft lip with or without cleft palate. However, corrected p-values indicated that this association was not significant.ConclusionsMelting Curve Analysis can be employed to successfully genotype challenging polymorphisms such as the MTHFD1L triallelic deletion\\/insertion polymorphism (DIP) reported here (rs3832406) and is a viable alternative to capillary electrophoresis. Corrected p-values indicate no association between MTHFD1L and risk of cleft in an Irish cohort.

  7. A novel lateral flow assay based on GoldMag nanoparticles and its clinical applications for genotyping of MTHFR C677T polymorphisms

    Science.gov (United States)

    Hui, Wenli; Zhang, Sinong; Zhang, Chao; Wan, Yinsheng; Zhu, Juanli; Zhao, Gang; Wu, Songdi; Xi, Dujuan; Zhang, Qinlu; Li, Ningning; Cui, Yali

    2016-02-01

    Current techniques for single nucleotide polymorphism (SNP) detection require tedious experimental procedures and expensive and sophisticated instruments. In this study, a visual genotyping method has been successfully established via combining ARMS-PCR with gold magnetic nanoparticle (GoldMag)-based lateral flow assay (LFA) and applied to the genotyping of methylenetetrahydrofolate reductase (MTHFR) C677T. C677T substitution of the gene MTHFR leads to an increased risk of diseases. The genotyping result is easily achievable by visual observation within 5 minutes after loading of the PCR products onto the LFA device. The system is able to accurately assess a broad detection range of initial starting genomic DNA amounts from 5 ng to 1200 ng per test sample. The limit of detection reaches 5 ng. Furthermore, our PCR-LFA system was applied to clinical trials for screening 1721 individuals for the C677T genotypes. The concordance rate of the genotyping results detected by PCR-LFA was up to 99.6% when compared with the sequencing results. Collectively, our PCR-LFA has been proven to be rapid, accurate, sensitive, and inexpensive. This new method is highly applicable for C677T SNP screening in laboratories and clinical practices. More promisingly, it could also be extended to the detection of SNPs of other genes.

  8. Determining major genotypes of hepatitis C virus among transplant recipients by real-time polymerase chain reaction assay.

    Science.gov (United States)

    Feyznezhad, Roya; Behzadi, Mohammad Amin; Yaghobi, Ramin; Ziyaeyan, Mazyar

    2015-02-01

    Hepatitis C virus (HCV) infection still exists as a health concern among the transplant patients. Because of the severity of the disease, different responses to treatment, and side effects resulting from long therapeutic period, determination of genotypes and viral loads can help choose the best treatment protocols. This study aimed to determine the HCV genotypes and its distribution patterns among liver, kidney, and bone marrow recipient candidates across Iran, referred to Namazi Hospital, southern Iran. A total of 101 individuals, including 44 (43.6%) liver, 55 (54.5%) kidney, and 2 (2%) bone marrow recipient candidates, with ages ranging between 5 and 74 years (Mean ±SD: 46.53 ± 13.73 y) participated in this study. From those, whole blood sample were collected and anti-HCV antibodies, RNA detection, and genotyping were performed on plasma using commercial chromatographic immunoassay, TaqMan one-step real-time polymerase chain reaction (RT-PCR), and genotyping RT-PCR kits, respectively. The frequencies of anti-HCV antibodies, RNA, various genotypes, and the viral load were compared with respect to gender, age, and transplant recipient groups. Of 101 individuals, 47 (46.5%) were positive for anti-HCV antibodies and 34 (33.7%) for RNA with a significant difference (P < 0.05). RNA copy number ranged from 4.6 × 103 to 3.11 × 107 copies/mL, median: 2.92 × 106 copies/mL, with no statistical differences in all groups. Analyses revealed no significant differences between the frequencies of anti-HCV antibodies or RNA in different groups. The frequencies of the genotypes 1 (50%) and 3 (35.3%) were higher than those of the genotypes 2 (2.9%), 4 (2.9%), and undetermined one (8.8%). Genotype 1 was significantly more prevalent in liver transplant recipients, those older than 40 years, and male cases (P < 0.05). Considering the high frequency of genotypes 1 and 3 among the studied groups, it is suggested that before and after transplantation programs be improved to manage

  9. SNaPAfu: a novel single nucleotide polymorphism multiplex assay for aspergillus fumigatus direct detection, identification and genotyping in clinical specimens.

    Directory of Open Access Journals (Sweden)

    Rita Caramalho

    Full Text Available OBJECTIVE: Early diagnosis of invasive aspergillosis is essential for positive patient outcome. Likewise genotyping of fungal isolates is desirable for outbreak control in clinical setting. We designed a molecular assay that combines detection, identification, and genotyping of Aspergillus fumigatus in a single reaction. METHODS: To this aim we combined 20 markers in a multiplex reaction and the results were seen following mini-sequencing readings. Pure culture extracts were firstly tested. Thereafter, Aspergillus-DNA samples obtained from clinical specimens of patients with possible, probable, or proven aspergillosis according to European Organization for the Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG criteria. RESULTS: A new set of designed primers allowed multilocus sequence typing (MLST gene amplification in a single multiplex reaction. The newly proposed SNaPAfu assay had a specificity of 100%, a sensitivity of 89% and detection limit of 1 ITS copy/mL (∼0.5 fg genomic Aspergillus-DNA/mL. The marker A49_F was detected in 89% of clinical samples. The SNaPAfu assay was accurately performed on clinical specimens using only 1% of DNA extract (total volume 50 µL from 1 mL of used bronchoalveolar lavage. CONCLUSIONS: The first highly sensitive and specific, time- and cost-economic multiplex assay was implemented that allows detection, identification, and genotyping of A. fumigatus strains in a single amplification followed by mini-sequencing reaction. The new test is suitable to clinical routine and will improve patient management.

  10. Real-time PCR assays for detection of Brucella spp. and the identification of genotype ST27 in bottlenose dolphins (Tursiops truncatus).

    Science.gov (United States)

    Wu, Qingzhong; McFee, Wayne E; Goldstein, Tracey; Tiller, Rebekah V; Schwacke, Lori

    2014-05-01

    Rapid detection of Brucella spp. in marine mammals is challenging. Microbiologic culture is used for definitive diagnosis of brucellosis, but is time consuming, has low sensitivity and can be hazardous to laboratory personnel. Serological methods can aid in diagnosis, but may not differentiate prior exposure versus current active infection and may cross-react with unrelated Gram-negative bacteria. This study reports a real-time PCR assay for the detection of Brucella spp. and application to screen clinical samples from bottlenose dolphins stranded along the coast of South Carolina, USA. The assay was found to be 100% sensitive for the Brucella strains tested, and the limit of detection was 0.27fg of genomic DNA from Brucella ceti B1/94 per PCR volume. No amplification was detected for the non-Brucella pathogens tested. Brucella DNA was detected in 31% (55/178) of clinical samples tested. These studies indicate that the real-time PCR assay is highly sensitive and specific for the detection of Brucella spp. in bottlenose dolphins. We also developed a second real-time PCR assay for rapid identification of Brucella ST27, a genotype that is associated with human zoonotic infection. Positive results were obtained for Brucella strains which had been identified as ST27 by multilocus sequence typing. No amplification was found for other Brucella strains included in this study. ST27 was identified in 33% (18/54) of Brucella spp. DNA-positive clinical samples. To our knowledge, this is the first report on the use of a real-time PCR assay for identification of Brucella genotype ST27 in marine mammals. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Sensitive Deep-Sequencing-Based HIV-1 Genotyping Assay To Simultaneously Determine Susceptibility to Protease, Reverse Transcriptase, Integrase, and Maturation Inhibitors, as Well as HIV-1 Coreceptor Tropism

    Science.gov (United States)

    Gibson, Richard M.; Meyer, Ashley M.; Winner, Dane; Archer, John; Feyertag, Felix; Ruiz-Mateos, Ezequiel; Leal, Manuel; Robertson, David L.; Schmotzer, Christine L.

    2014-01-01

    With 29 individual antiretroviral drugs available from six classes that are approved for the treatment of HIV-1 infection, a combination of different phenotypic and genotypic tests is currently needed to monitor HIV-infected individuals. In this study, we developed a novel HIV-1 genotypic assay based on deep sequencing (DeepGen HIV) to simultaneously assess HIV-1 susceptibilities to all drugs targeting the three viral enzymes and to predict HIV-1 coreceptor tropism. Patient-derived gag-p2/NCp7/p1/p6/pol-PR/RT/IN- and env-C2V3 PCR products were sequenced using the Ion Torrent Personal Genome Machine. Reads spanning the 3′ end of the Gag, protease (PR), reverse transcriptase (RT), integrase (IN), and V3 regions were extracted, truncated, translated, and assembled for genotype and HIV-1 coreceptor tropism determination. DeepGen HIV consistently detected both minority drug-resistant viruses and non-R5 HIV-1 variants from clinical specimens with viral loads of ≥1,000 copies/ml and from B and non-B subtypes. Additional mutations associated with resistance to PR, RT, and IN inhibitors, previously undetected by standard (Sanger) population sequencing, were reliably identified at frequencies as low as 1%. DeepGen HIV results correlated with phenotypic (original Trofile, 92%; enhanced-sensitivity Trofile assay [ESTA], 80%; TROCAI, 81%; and VeriTrop, 80%) and genotypic (population sequencing/Geno2Pheno with a 10% false-positive rate [FPR], 84%) HIV-1 tropism test results. DeepGen HIV (83%) and Trofile (85%) showed similar concordances with the clinical response following an 8-day course of maraviroc monotherapy (MCT). In summary, this novel all-inclusive HIV-1 genotypic and coreceptor tropism assay, based on deep sequencing of the PR, RT, IN, and V3 regions, permits simultaneous multiplex detection of low-level drug-resistant and/or non-R5 viruses in up to 96 clinical samples. This comprehensive test, the first of its class, will be instrumental in the development of new

  12. Evaluation of Hepatitis C Virus Core Antigen Assays in Detecting Recombinant Viral Antigens of Various Genotypes

    Science.gov (United States)

    Saeed, Mohsan; Suzuki, Ryosuke; Kondo, Madoka; Aizaki, Hideki; Kato, Takanobu; Mizuochi, Toshiaki; Wakita, Takaji; Watanabe, Haruo; Suzuki, Tetsuro

    2009-01-01

    A single substitution within the hepatitis C virus core antigen sequence, A48T, which is observed in ∼30% of individuals infected with genotype 2a virus, reduces the sensitivity of a commonly used chemiluminescence enzyme immunoassay. Quantitation of the antigen is improved by using a distinct anticore antibody with a different epitope. PMID:19812276

  13. Effects of human PrPSc type and PRNP genotype in an in-vitro conversion assay.

    Science.gov (United States)

    Jones, Michael; Peden, Alexander H; Wight, Darren; Prowse, Christopher; Macgregor, Ian; Manson, Jean; Turner, Marc; Ironside, James W; Head, Mark W

    2008-12-03

    Prion protein type and codon 129 genotype are thought to be major determinants of susceptibility and phenotype in human prion diseases. Using an in-vitro system (protein misfolding cyclic amplification) we have attempted to model human prion protein conversion using the abnormal prion protein associated with each of the major sporadic Creutzfeldt-Jakob disease subtypes, in substrates containing the normal cellular form of the prion protein of each of the three possible human PRNP codon 129 polymorphic genotypes. The prion protein type is converted with fidelity in these amplification reactions, but the efficiency of conversion depends both on the methionine/valine polymorphic status of the sporadic Creutzfeldt-Jakob disease seed and substrate homogenate, and on the abnormal prion protein type.

  14. Transcriptome-Wide Single Nucleotide Polymorphisms (SNPs for Abalone (Haliotis midae: Validation and Application Using GoldenGate Medium-Throughput Genotyping Assays

    Directory of Open Access Journals (Sweden)

    Rouvay Roodt-Wilding

    2013-09-01

    Full Text Available Haliotis midae is one of the most valuable commercial abalone species in the world, but is highly vulnerable, due to exploitation, habitat destruction and predation. In order to preserve wild and cultured stocks, genetic management and improvement of the species has become crucial. Fundamental to this is the availability and employment of molecular markers, such as microsatellites and Single Nucleotide Polymorphisms (SNPs . Transcriptome sequences generated through sequencing-by-synthesis technology were utilized for the in vitro and in silico identification of 505 putative SNPs from a total of 316 selected contigs. A subset of 234 SNPs were further validated and characterized in wild and cultured abalone using two Illumina GoldenGate genotyping assays. Combined with VeraCode technology, this genotyping platform yielded a 65%−69% conversion rate (percentage polymorphic markers with a global genotyping success rate of 76%−85% and provided a viable means for validating SNP markers in a non-model species. The utility of 31 of the validated SNPs in population structure analysis was confirmed, while a large number of SNPs (174 were shown to be informative and are, thus, good candidates for linkage map construction. The non-synonymous SNPs (50 located in coding regions of genes that showed similarities with known proteins will also be useful for genetic applications, such as the marker-assisted selection of genes of relevance to abalone aquaculture.

  15. Comparison of Real-Time Multiplex Human Papillomavirus (HPV) PCR Assays with INNO-LiPA HPV Genotyping Extra Assay▿

    OpenAIRE

    Else, Elizabeth A.; Swoyer, Ryan; Zhang, Yuhua; Taddeo, Frank J.; Bryan, Janine T.; Lawson, John; Van Hyfte, Inez; Roberts, Christine C.

    2011-01-01

    Real-time type-specific multiplex human papillomavirus (HPV) PCR assays were developed to detect HPV DNA in samples collected for the efficacy determination of the quadrivalent HPV (type 6, 11, 16, and 18) L1 virus-like particle (VLP) vaccine (Gardasil). Additional multiplex (L1, E6, and E7 open reading frame [ORF]) or duplex (E6 and E7 ORF) HPV PCR assays were developed to detect high-risk HPV types, including HPV type 31 (HPV31), HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV56, HPV58, and H...

  16. Use of the glycophorin A somatic mutation assay for rapid, unambiguous identification of Fanconi anemia homozygotes regardless of GPA genotype.

    Science.gov (United States)

    Evdokimova, Viktoria N; McLoughlin, Reagan K; Wenger, Sharon L; Grant, Stephen G

    2005-05-15

    A 7-year-old girl was hospitalized with pancytopenia requiring blood transfusion. She and an older brother with suspicious symptoms were referred for laboratory testing to confirm a clinical diagnosis of Fanconi anemia (FA). Blood samples from these two children and one parent were examined with the GPA somatic mutation assay. The patient's total GPA somatic mutation frequency of 1.4 x 10(-4) was determined despite the confounding effects of her recent transfusion, and was greater than 10-fold higher than that of a population of pediatric controls, consistent with the known FA phenotype. Her brother was not informative for the standard GPA assay, which requires heterozygosity for the MN blood group, but was analyzed with a modified assay that measured only allele loss mutation. His mutation frequency, 6.8 x 10(-4) was also supportive of a diagnosis of FA. Both analyses also showed evidence of ongoing mutation through terminal erythroblast differentiation, a characteristic of patients with DNA repair syndromes which further confirmed the diagnoses. These conclusions were confirmed with traditional DEB-induced chromosome breakage studies. The quantitative and qualitative aspects of the GPA assay relevant for applying this test for FA diagnosis, and perhaps for carrier detection, are discussed. (c) 2005 Wiley-Liss, Inc., A Wiley Company.

  17. A method for genotyping elite breeding stocks of leaf chicory (Cichorium intybus L.) by assaying mapped microsatellite marker loci.

    Science.gov (United States)

    Ghedina, Andrea; Galla, Giulio; Cadalen, Thierry; Hilbert, Jean-Louis; Caenazzo, Silvano Tiozzo; Barcaccia, Gianni

    2015-12-30

    Leaf chicory (Cichorium intybus subsp. intybus var. foliosum L.) is a diploid plant species (2n = 18) of the Asteraceae family. The term "chicory" specifies at least two types of cultivated plants: a leafy vegetable, which is highly differentiated with respect to several cultural types, and a root crop, whose current industrial utilization primarily addresses the extraction of inulin or the production of a coffee substitute. The populations grown are generally represented by local varieties (i.e., landraces) with high variation and adaptation to the natural and anthropological environment where they originated, and have been yearly selected and multiplied by farmers. Currently, molecular genetics and biotechnology are widely utilized in marker-assisted breeding programs in this species. In particular, molecular markers are becoming essential tools for developing parental lines with traits of interest and for assessing the specific combining ability of these lines to breed F1 hybrids. The present research deals with the implementation of an efficient method for genotyping elite breeding stocks developed from old landraces of leaf chicory, Radicchio of Chioggia, which are locally dominant in the Veneto region, using 27 microsatellite (SSR) marker loci scattered throughout the linkage groups. Information on the genetic diversity across molecular markers and plant accessions was successfully assessed along with descriptive statistics over all marker loci and inbred lines. Our overall data support an efficient method for assessing a multi-locus genotype of plant individuals and lineages that is useful for the selection of new varieties and the certification of local products derived from Radicchio of Chioggia. This method proved to be useful for assessing the observed degree of homozygosity of the inbred lines as a measure of their genetic stability; plus it allowed an estimate of the specific combining ability (SCA) between maternal and paternal inbred lines on the

  18. Real-time PCR assays for hepatitis C virus RNA (genotype 1) is useful for evaluating virological response to the treatment with peginterferon-alpha2b and ribavirin.

    Science.gov (United States)

    Nakaya, Mika; Enomoto, Masaru; Fujii, Hideki; Kobayashi, Sawako; Iwai, Shuji; Morikawa, Hiroyasu; Tamori, Akihiro; Sakaguchi, Hiroki; Kawada, Norifumi

    2013-12-01

    The real-time PCR, such as Abbott RealTime assay, have replaced end-point PCR, such as Amplicor assays, for the measurement of HCV RNA. However, 'response-guided therapy' to use on-treatment response for tailoring the duration of treatment with peginterferon-alpha and ribavirin has not been fully evaluated for real-time PCR. 43 patients with HCV genotype 1 (24 who had complete early virological responses (cEVR) on Amplicor assay and received 48-week therapy, and 19 who had late virological responses (LVR) and received 72-week therapy) were recruited. Using a RealTime assay, we retrospectively measured HCV RNA in stored sera. In 10 samples obtained during therapy, HCV RNA was undetectable on the Amplicor assay, but detectable on the RealTime assay. Among patients with cEVR on the Amplicor assay, those with detectable HCV RNA on the RealTime assay at week 12 were less likely to have a sustained virological response (SVR) than those without (2/4 vs 17/20, p = 0.116). Among patients with LVR on the Amplicor assay, those with HCV RNA detectable on the RealTime assay at week 24 were significantly less likely to have SVR than those without (1/4 vs 12/15, p = 0.041). The RealTime assay may be useful for tailoring duration of treatment for the patient with HCV genotype 1.

  19. Evaluation of sensitivity and specificity of GenoType MTBDRplus line probe assay in rapid diagnosis of tuberculous pleural effusion

    OpenAIRE

    Irfan, Muhammad; Jabeen, Kauser; Shahzad, Hira; Zubairi, Ali Bin Sarwar; Hasan, Rumina

    2015-01-01

    Background: Pakistan has an annual tuberculosis (TB) incidence rate of 233 per 100,000 population and ranks sixth among the high TB burden countries worldwide. Tuberculous pleural effusion (TPE) occurs in up to 25% of TB patients. Owing to the pauci-bacillary nature of the pleural fluid, the diagnosis of TPE is a challenge. Objective: The aim of the present study is to evaluate the performance of MTBDRplus line probe assay in terms of its sensitivity and specificity for the rapid TB diagno...

  20. Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure.

    Science.gov (United States)

    Donaldson, Michael E; Rico, Yessica; Hueffer, Karsten; Rando, Halie M; Kukekova, Anna V; Kyle, Christopher J

    2018-01-01

    Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation

  1. Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

    DEFF Research Database (Denmark)

    Ramos, Antonio M; Crooijmans, Richard P M A; Nabeel, Nabeel A

    2009-01-01

    generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. Methodology/Principal Findings A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain......) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now...... commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion...

  2. Field evaluation of a broadly sensitive HIV-1 in-house genotyping assay for use with both plasma and dried blood spot specimens in a resource-limited country.

    Science.gov (United States)

    Inzaule, Seth; Yang, Chunfu; Kasembeli, Alex; Nafisa, Lillian; Okonji, Jully; Oyaro, Boaz; Lando, Richard; Mills, Lisa A; Laserson, Kayla; Thomas, Timothy; Nkengasong, John; Zeh, Clement

    2013-02-01

    HIV-1 drug resistance (HIVDR) assays are important tools in clinical management of HIV-infected patients on antiretroviral therapy (ART) and surveillance of drug-resistant variants at population levels. The high cost associated with commercial assays hinders their use in resource-limited settings. We adopted and validated a low-cost in-house assay using 68 matched plasma and dried blood spot (DBS) samples with a median viral load (VL) of 58,187 copies/ml, ranging from 253 to 3,264,850 against the commercial assay ViroSeq. Results indicated that the in-house assay not only had a higher plasma genotyping rate than did ViroSeq (94% versus 78%) but also was able to genotype 89.5% (51/57) of the matched DBS samples with VLs of ≥ 1,000 copies/ml. The sensitivity in detecting DR mutations by the in-house assay was 98.29% (95% confidence interval [CI], 97.86 to 98.72) on plasma and 96.54 (95% CI, 95.93 to 97.15) on DBS, and the specificity was 99.97% (95% CI, 99.91 to 100.00) for both sample types compared to ViroSeq. The minor DR mutation differences detected by the in-house assay against ViroSeq did not result in clinical significance. In addition, cost analysis showed that the in-house assay could reduce the genotyping cost by about 60% for both plasma and DBS compared to ViroSeq. This field condition evaluation highlights the potential utility of a cost-effective, subtype-independent, in-house genotyping assay using both plasma and DBS specimens for HIVDR clinical monitoring and population-based surveillance in resource-limited settings.

  3. Software for optimization of SNP and PCR-RFLP genotyping to discriminate many genomes with the fewest assays

    Directory of Open Access Journals (Sweden)

    Wagner Mark C

    2005-05-01

    Full Text Available Abstract Background Microbial forensics is important in tracking the source of a pathogen, whether the disease is a naturally occurring outbreak or part of a criminal investigation. Results A method and SPR Opt (SNP and PCR-RFLP Optimization software to perform a comprehensive, whole-genome analysis to forensically discriminate multiple sequences is presented. Tools for the optimization of forensic typing using Single Nucleotide Polymorphism (SNP and PCR-Restriction Fragment Length Polymorphism (PCR-RFLP analyses across multiple isolate sequences of a species are described. The PCR-RFLP analysis includes prediction and selection of optimal primers and restriction enzymes to enable maximum isolate discrimination based on sequence information. SPR Opt calculates all SNP or PCR-RFLP variations present in the sequences, groups them into haplotypes according to their co-segregation across those sequences, and performs combinatoric analyses to determine which sets of haplotypes provide maximal discrimination among all the input sequences. Those set combinations requiring that membership in the fewest haplotypes be queried (i.e. the fewest assays be performed are found. These analyses highlight variable regions based on existing sequence data. These markers may be heterogeneous among unsequenced isolates as well, and thus may be useful for characterizing the relationships among unsequenced as well as sequenced isolates. The predictions are multi-locus. Analyses of mumps and SARS viruses are summarized. Phylogenetic trees created based on SNPs, PCR-RFLPs, and full genomes are compared for SARS virus, illustrating that purported phylogenies based only on SNP or PCR-RFLP variations do not match those based on multiple sequence alignment of the full genomes. Conclusion This is the first software to optimize the selection of forensic markers to maximize information gained from the fewest assays, accepting whole or partial genome sequence data as input. As

  4. Cost analysis of residual viremia detected by two real-time PCR assays for response-guided (dual or triple therapy of HCV genotype 1 infection

    Directory of Open Access Journals (Sweden)

    Alessio Aghemo

    2016-12-01

    Full Text Available Cost analysis of residual viremia detected by two real-time PCR assays for response-guided (dual or triple therapy of HCV genotype 1 infectionIntroductionThe duration of interferon-based dual and triple therapies for HCV-G1 is determined by assessment of early viral kinetics. We conducted a cost analysis to determine the mean cost of dual or triple therapy treatment for a patient with HCV-G1, where the therapy duration (24 or 48 weeks is guided by HCV-RNA assay.MethodsHCV-RNA was assessed by two widely used real-time PCR-based assays, Cobas Ampliprep/Cobas TaqMan (CAP-CTM and Real-Time HCV (ART. As far as the dual therapy (PegINFα-2b and RBV is concerned, at week 12 of treatment 16.0% of patients (27/169 were eligible to receive a shorter duration of therapy (24 weeks according to CAP-CTM and 8.9% (15/169 according to ART: 26 patients achieved SVR (15.4% with CAP-CTM and 15 with ART (8.9%. With regard to triple therapy (TPV, PegINFα-2a and RBV, at week 12 of treatment 59.6% of patients (31/52 were eligible to receive a shorter duration of therapy (24 weeks according to CAP-CTM and 28.8% (15/52 according to ART: 30 patients achieved SVR (57.7% with CAP-CTM and 13 with ART (25.0%. The cost analysis was conducted from the perspective of the Italian National Health Service (NHS. Only drug (TPV, PegINFα-2a, PegINFα-2b and RBV and test (CAP-CTM and ART costs were taken into account. Ex-factory prices (included all discounts and national tariffs were used to calculate drug consumptions and tests, respectively. Costs were assessed in Euros 2015.ResultsWith regard to dual therapy, the overall mean treatment cost per patient with CAP-CTM (€9,572.77 was lower than with ART (€9,876.19. With regard to triple therapy, the overall mean treatment cost per patient was lower with CAP-CTM (€31,354.40 than with ART (€33,155.26.ConclusionsCAP-CTM HCV-RNA assay was cost-saving from the Italian NHS perspective compared with ART HCV-RNA assay in the dual

  5. TRI12 based quantitative real-time PCR assays reveal the distribution of trichothecene genotypes of F. graminearum and F. culmorum isolates in Danish small grain cereals

    DEFF Research Database (Denmark)

    Nielsen, L.K.; Jensen, Jens Due; Rodriguez, A.

    2012-01-01

    Quantitative real-time PCR assays, based on polymorphisms in the TRI12 gene of the trichothecene pathway, were developed to identify and quantify the trichothecene genotypes producing 3-acetyl-deoxynivalenol (3ADON), 15-acetyl-deoxynivalenol (15ADON) or nivalenol (NIV) in the Fusarium graminearum...

  6. Evaluation of sequencing of HCV core/E1, NS5A and NS5B as a genotype predictive tool in comparison with commercial assays targeting 5'UTR.

    Science.gov (United States)

    McCormick, Adele L; Macartney, Malcolm J; Abdi-Abshir, Ikran; Labbett, Wendy; Smith, Colette; Irish, Dianne; Webster, Daniel P; Haque, Tanzina

    2015-05-01

    Hepatitis C virus (HCV) genotyping is required for tailoring the dose and duration of antiviral therapy, predicting virological response rates, and selecting future treatment options. To establish whether baseline genotypes, performed by INNO-LiPA Version 1.0 (v1.0), before 2008, were valid for making treatment decisions now or whether genotypic determination should be repeated. Furthermore, to evaluate concordance between Abbott RealTime genotype II assay (RT) and genotyping by sequencing HCV C/E1, NS5A, NS5B. Genotyping by RT and sequencing was performed on paired historic and current specimens from 50 patients previously baseline genotyped using INNO-LiPA. Of 100 samples from 50 patients, ≥ 2 of HCV genomic target regions yielded a sequence that was suitable for genotyping, with 100% concordance, providing no evidence of recombination events. Genotype and subtype prediction based on RT and sequencing agreed in 62.8% historic and 72.7% current specimens, with a kappa coefficient score of 0.48 and 0.76, respectively. LiPA could not subtype 46% of HCV gt1 infections, and LiPA subgenotype was only in agreement with RT and sequencing in 28.6% cases, where matched baseline and historic specimens were available. Three patients were indeterminate by RT, and five patients with HCV gt1 infections could not be subtyped by RT. However, RT revealed mixed infections in five patients where sequencing detected only single HCV infection at 20% threshold. Genotyping by sequencing, exhibited excellent concordance, with moderate to good agreement with RT, and could resolve RT indeterminates and subtype HCV-gt1 infections not possible by LiPA. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Development of a rapid multiplex PCR assay to genotype Pasteurella multocida strains by use of the lipopolysaccharide outer core biosynthesis locus.

    Science.gov (United States)

    Harper, Marina; John, Marietta; Turni, Conny; Edmunds, Mark; St Michael, Frank; Adler, Ben; Blackall, P J; Cox, Andrew D; Boyce, John D

    2015-02-01

    Pasteurella multocida is a Gram-negative bacterial pathogen that is the causative agent of a wide range of diseases in many animal species, including humans. A widely used method for differentiation of P. multocida strains involves the Heddleston serotyping scheme. This scheme was developed in the early 1970s and classifies P. multocida strains into 16 somatic or lipopolysaccharide (LPS) serovars using an agar gel diffusion precipitin test. However, this gel diffusion assay is problematic, with difficulties reported in accuracy, reproducibility, and the sourcing of quality serovar-specific antisera. Using our knowledge of the genetics of LPS biosynthesis in P. multocida, we have developed a multiplex PCR (mPCR) that is able to differentiate strains based on the genetic organization of the LPS outer core biosynthesis loci. The accuracy of the LPS-mPCR was compared with classical Heddleston serotyping using LPS compositional data as the "gold standard." The LPS-mPCR correctly typed 57 of 58 isolates; Heddleston serotyping was able to correctly and unambiguously type only 20 of the 58 isolates. We conclude that our LPS-mPCR is a highly accurate LPS genotyping method that should replace the Heddleston serotyping scheme for the classification of P. multocida strains. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  8. A first genotyping assay of French cattle breeds based on a new allele of the extension gene encoding the melanocortin-1 receptor (Mc1r

    Directory of Open Access Journals (Sweden)

    Julien Raymond

    2000-09-01

    Full Text Available Abstract The seven transmembrane domain melanocortin-1 receptor (Mc1r encoded by the coat color extension gene (E plays a key role in the signaling pathway of melanin synthesis. Upon the binding of agonist (melanocortin hormone, α-MSH or antagonist (Agouti protein ligands, the melanosomal synthesis of eumelanin and/or phaeomelanin pigments is stimulated or inhibited, respectively. Different alleles of the extension gene were cloned from unrelated animals belonging to French cattle breeds and sequenced. The wild type E allele was mainly present in Normande cattle, the dominant ED allele in animals with black color (i.e. Holstein, whereas the recessive e allele was identified in homozygous animals exhibiting a more or less strong red coat color (Blonde d'Aquitaine, Charolaise, Limousine and Salers. A new allele, named E1, was found in either homozygous (E1/E1 or heterozygous (E1/E individuals in Aubrac and Gasconne breeds. This allele displayed a 4 amino acid duplication (12 nucleotides located within the third cytoplasmic loop of the receptor, a region known to interact with G proteins. A first genotyping assay of the main French cattle breeds is described based on these four extension alleles.

  9. Varicose vein stripping

    Science.gov (United States)

    ... stripping; Venous reflux - vein stripping; Venous ulcer - veins Patient Instructions Surgical wound care - open Varicose veins - what to ask your doctor Images Circulatory system References American Family Physician. Management of varicose veins. www.aafp.org/afp/2008/ ...

  10. Development of an endpoint genotyping assay to detect the Mycoplasma pneumoniae 23S rRNA gene and distinguish the existence of macrolide resistance-associated mutations at position 2063.

    Science.gov (United States)

    Suzuki, Yu; Seto, Junji; Shimotai, Yoshitaka; Ikeda, Tatsuya; Yahagi, Kazue; Mizuta, Katsumi; Matsuzaki, Yoko; Hongo, Seiji

    2016-12-01

    The prevalence of macrolide-resistant Mycoplasma pneumoniae harboring a mutation in the 23S rRNA gene is increasing, and rapid detection assays are needed for clinical management. We developed an endpoint genotyping assay to detect the M. pneumoniae 23S rRNA gene and determine the existence of macrolide resistance-associated mutations at position 2063 (A2063G, A2063T and A2063C mutations). This A2063B genotyping assay detected more than 50 copies/reaction of the M. pneumoniae gene in every nucleotide mutation at position 2063. Of 42 clinical specimens, 3 were positive without mutation, 6 were positive with the A2063G mutation, and 33 were negative. The results were confirmed using nested PCR with the sequencing of the M. pneumoniae 23S rRNA gene, and a high sensitivity (90%), specificity (100%), and coincidence ratio (kappa coefficient=0.93) were obtained. Therefore, the A2063B genotyping assay is useful for the rapid discrimination of macrolide resistance mutations at position 2063. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. The Strip Module

    DEFF Research Database (Denmark)

    Pedersen, Tommy

    1996-01-01

    When the behaviour of a ship in waves is to be predicted it is convenient to have a tool which includes different approaches to the problem.The aim of this project is to develop such a tool named the strip theory module. The strip theory module will consist of submodules dependent on the I....... At last a postprocessor will be included with facilities for statistical calculations and for plots and prints of the results.The project is divided into 7 tasks where the third is to be completed.This report has two aims. To give an introduction to the project of developing a strip theory module......-ship code available at the department. It will be structured as a general preprocessor mainly to determine the hydrodynamic mass and damping. A strip processor including three different theories: A linear frequency domain strip theory, a quadratic strip theory and a nonlinear time domain strip theory...

  12. A newly developed real-time PCR assay for detection and quantification of Fusarium oxysporum and its use in compatible and incompatible interactions with grafted melon genotypes.

    Science.gov (United States)

    Haegi, Anita; Catalano, Valentina; Luongo, Laura; Vitale, Salvatore; Scotton, Michele; Ficcadenti, Nadia; Belisario, Alessandra

    2013-08-01

    A reliable and species-specific real-time quantitative polymerase chain reaction (qPCR) assay was developed for detection of the complex soilborne anamorphic fungus Fusarium oxysporum. The new primer pair, designed on the translation elongation factor 1-α gene with an amplicon of 142 bp, was highly specific to F. oxysporum without cross reactions with other Fusarium spp. The protocol was applied to grafted melon plants for the detection and quantification of F. oxysporum f. sp. melonis, a devastating pathogen of this cucurbit. Grafting technologies are widely used in melon to confer resistance against new virulent races of F. oxysporum f. sp. melonis, while maintaining the properties of valuable commercial varieties. However, the effects on the vascular pathogen colonization have not been fully investigated. Analyses were performed on 'Charentais-T' (susceptible) and 'Nad-1' (resistant) melon cultivars, both used either as rootstock and scion, and inoculated with F. oxysporum f. sp. melonis race 1 and race 1,2. Pathogen development was compared using qPCR and isolations from stem tissues. Early asymptomatic melon infections were detected with a quantification limit of 1 pg of fungal DNA. The qPCR protocol clearly showed that fungal development was highly affected by host-pathogen interaction (compatible or incompatible) and time (days postinoculation). The principal significant effect (P ≤ 0.01) on fungal development was due to the melon genotype used as rootstock, and this effect had a significant interaction with time and F. oxysporum f. sp. melonis race. In particular, the amount of race 1,2 DNA was significantly higher compared with that estimated for race 1 in the incompatible interaction at 18 days postinoculation. The two fungal races were always present in both the rootstock and scion of grafted plants in either the compatible or incompatible interaction.

  13. Nucleic acid amplification of HIV-1 integrase sequence subtypes CRF01_AE and B for development of HIV anti-integrase drug resistance genotyping assay

    Science.gov (United States)

    Adlar, F. R.; Bela, B.

    2017-08-01

    To anticipate the potential use of anti-integrase drugs in Indonesia for treatment of HIV-1 infection, the development of a drug resistance genotyping assay for anti-integrase is crucial in identifying the genetic drug resistance profile of Indonesian HIV-1 strains. This experiment aimed to amplify a target region in the integrase gene of Indonesian HIV-1 subtypes CRF01_AE and B that contain genetic mutations known to confer resistance to anti-integrase drug. Eleven archived plasma samples from individuals living with HIV-1 were obtained from the Virology and Cancer Pathobiology Research Center for Health Service (VCPRC FKUI-RSCM) laboratory. One of the plasma samples contained HIV-1 subtype B, and the remaining plasma samples contained subtype CRF01_AE. The target regions for all samples were amplified through RT-PCR, with an annealing temperature of 55 °C, using the primer pair AE_POL 4086F and AE_POL 5232R that were designed by VCPRC FKUI-RSCM. The results of this experiment show that 18.2% (2/11) of the samples were successfully amplified using the one-step RT-PCR. While the primer pair was effective in amplifying the target region in the integrase gene sequence for subtype B (100%; 1/1), it had a low efficacy (10%, 1/10) for subtype CRF01_AE. In conclusion, the primer pair can be used to amplify the target region in Indonesian HIV-1 strain subtypes CRF01_AE and B. However, optimization of the PCR condition and an increased number of samples would help to determine an accurate representation of the efficacy of the primer pair.

  14. Comparison of Genotypic and Phenotypic HIV Type 1 Tropism Assay: Results from the Screening Samples of Cenicriviroc Study 202, a Randomized Phase II Trial in Treatment-Naive Subjects

    Science.gov (United States)

    Johnson, Erik P.; Siaw, Martin F.; Van Baelen, Ben; Ogden, Richard; Platt, Jamie L.; Pesano, Rick L.; Lefebvre, Eric

    2014-01-01

    Abstract Cenicriviroc is a once-daily oral CCR5/CCR2 antagonist in development for treatment of HIV infection. CVC Study 202 (652-2-202; NCT01338883) excluded treatment-naive subjects demonstrated to harbor non-R5 (CXCR4-tropic or dual-mixed) tropic HIV-1 by either genotypic or phenotypic tropism testing. Here we compare the results of genotypic and phenotypic tropism testing in Study 202. A total of 304 subjects screened had paired genotypic and phenotypic results. Genotypic tropism testing (GTT) incorporated triplicate population sequencing using the geno2pheno algorithm and the PSSM algorithm, followed by ultradeep sequencing (UDS) for samples with R5 results. All samples were further evaluated with a phenotypic test, the enhanced-sensitivity Trofile assay (ESTA). Concordance between GTT and ESTA was 80% and increased to 84% when only geno2pheno was used for triplicate population sequencing. GTT (geno2pheno) classified 18% of the samples as non-R5 compared to 16% by ESTA. Only one-third of samples with non-R5 results by either test were classified as non-R5 by both tests. Median CD4(+) cell counts were lower in patients with concordant non-R5 results by UDS and ESTA than in subjects with an R5 result by either assay (p=0.0004). UDS detected non-R5 virus in an additional 27/304 subjects (median 15% non-R5, interquartile range: 3.7–62%) with R5 results by ESTA. In conclusion, the geno2pheno algorithm improves concordance of GTT with a clinically validated phenotypic tropism assay as does the use of UDS. These findings provide support for recent guidelines indicating that genotypic tropism testing may be considered as an alternative to phenotypic testing. PMID:23875707

  15. Comparison of In-House Multiplex Real Time PCR, Diagcor GenoFlow HPV Array Test and INNO-LiPA HPV Genotyping Extra Assays with LCD- Array Kit for Human Papillomavirus Genotyping in Cervical Liquid Based Cytology Specimens and Genital Lesions in Tehran, Iran.

    Science.gov (United States)

    Sohrabi, Amir; Rahnamaye-Farzami, Marjan; Mirab-Samiee, Siamak; Mahdavi, Saeed; Babaei, Monireh

    2016-01-01

    Human papillomavirus is a major etiologic agent for some human common cancers. Cervical precancer and cancer is the most prevalent dysplasia by HPV genotypes. Various rapid and sensitive methods have been developed into readily HPV genotyping. In the present study, we compared the performance of Real Time PCR, GenoFlow HPV Array, and INNO-LiPA HPV Genotyping Extra Assays with LCD- Array. From 108 cervical samples, HPV was detected in 33 women (30.55%). Among detected HPV genotypes, HPV 6 and 11 were dominant genotypes. Comparing these methods revealed that for Real Time PCR, Genoflow, and INNO-LiPA in comparison with LCD Array, sensitivity and specificity were 94.2%, 93%; 76.7%, 93%; 64%, 96.5%, respectively. Overall, accuracy and precision of these methods were more than 80% and 90%, respectively. It seems that these methods are reliable and suitable for detection and genotyping of HPVs in cervical disorders and other dysplasia associated with human papillomaviruses.

  16. Anatomy Comic Strips

    Science.gov (United States)

    Park, Jin Seo; Kim, Dae Hyun; Chung, Min Suk

    2011-01-01

    Comics are powerful visual messages that convey immediate visceral meaning in ways that conventional texts often cannot. This article's authors created comic strips to teach anatomy more interestingly and effectively. Four-frame comic strips were conceptualized from a set of anatomy-related humorous stories gathered from the authors' collective…

  17. Science Comic Strips

    Science.gov (United States)

    Kim, Dae Hyun; Jang, Hae Gwon; Shin, Dong Sun; Kim, Sun-Ja; Yoo, Chang Young; Chung, Min Suk

    2012-01-01

    Science comic strips entitled Dr. Scifun were planned to promote science jobs and studies among professionals (scientists, graduate and undergraduate students) and children. To this end, the authors collected intriguing science stories as the basis of scenarios, and drew four-cut comic strips, first on paper and subsequently as computer files.…

  18. ALICE silicon strip module

    CERN Multimedia

    Maximilien Brice

    2006-01-01

    This small silicon detector strip will be inserted into the inner tracking system (ITS) on the ALICE detector at CERN. This detector relies on state-of-the-art particle tracking techniques. These double-sided silicon strip modules have been designed to be as lightweight and delicate as possible as the ITS will eventually contain five square metres of these devices.

  19. Test strip and method for its use

    International Nuclear Information System (INIS)

    1981-01-01

    A test strip device is described which is useful in performing binding assays involving antigens, antibodies, hormones, vitamins, metabolites or pharmacological agents. The device is capable of application to analytical methods in which a set of sequential test reactions is involved and in which a minute sample size may be used. This test strip is particularly useful in radioimmunoassays. The use of the device is illustrated in radioimmunoassays for 1) thyroxine in serum, 2) the triiodothyronine binding capacity of serum and 3) folic acid and its analogues in serum. (U.K.)

  20. Multiplex Detection and Genotyping of Point Mutations Involved in Charcot-Marie-Tooth Disease Using a Hairpin Microarray-Based Assay

    Directory of Open Access Journals (Sweden)

    Yasser Baaj

    2009-01-01

    Full Text Available We previously developed a highly specific method for detecting SNPs with a microarray-based system using stem-loop probes. In this paper we demonstrate that coupling a multiplexing procedure with our microarray method is possible for the simultaneous detection and genotyping of four point mutations, in three different genes, involved in Charcot-Marie-Tooth disease. DNA from healthy individuals and patients was amplified, labeled with Cy3 by multiplex PCR; and hybridized to microarrays. Spot signal intensities were 18 to 74 times greater for perfect matches than for mismatched target sequences differing by a single nucleotide (discrimination ratio for “homozygous” DNA from healthy individuals. “Heterozygous” mutant DNA samples gave signal intensity ratios close to 1 at the positions of the mutations as expected. Genotyping by this method was therefore reliable. This system now combines the principle of highly specific genotyping based on stem-loop structure probes with the advantages of multiplex analysis.

  1. Rapid Detection of Carbapenemase Production in Enterobacteriaceae by Use of a Modified Paper Strip Carba NP Method.

    Science.gov (United States)

    Ho, Pak-Leung; Wang, Ya; Wing-Sze Tse, Cindy; Fung, Kitty Sau-Chun; Cheng, Vincent Chi-Chung; Lee, Rodney; To, Wing-Kin; Lai, Raymond Wai-Man; Luk, Wei-Kwang; Que, Tak-Lun; Tsang, Dominic Ngai-Chong

    2018-01-01

    Rapid and accurate detection of carbapenemase-producing Enterobacteriaceae (CPE) is important for preventing their spread in health care settings. We compared the performance of the Carba NP (CNP) test using the CLSI tube method with that using a modified paper strip method for the detection of carbapenemases in 390 Enterobacteriaceae isolates. The isolates were identified by Hong Kong's carbapenem-resistant Enterobacteriaceae surveillance program in 2016 and comprised 213 CPE and 177 carbapenemase-negative Enterobacteriaceae isolates. Molecular genotype was used as the reference. The test results were read at different time points for the CLSI method (1 min, 5 min, 1 h, and 2 h) and strip method (1 min and 5 min). The strip CNP and CLSI CNP tests correctly detect carbapenemase production in 93% and 93% of KPC producers, 100% and 38% of IMI producers, 94% and 85% of IMP producers, 98% and 90% of NDM producers, and 29% and 12% of OXA producers, respectively. Overall, the strip method has superior sensitivity to the CLSI method (86% versus 75%, respectively; P methods was 100%. By the CLSI method, 27%, 14%, 29%, and 6% of the CPE isolates were positive at 1 min, 5 min, 1 h, and 2 h, respectively. In contrast, by the strip method, 76% of the CPE isolates were positive at 1 min, and an additional 10% were positive at 5 min. In conclusion, the Carba NP test by use of the modified strip method has a higher sensitivity and a shorter assay time than that those by use of the CLSI tube method. Copyright © 2017 American Society for Microbiology.

  2. Performance characteristics of the COBAS Ampliprep/COBAS TaqMan v2.0 and the Abbott RealTime hepatitis C assays - implications for response-guided therapy in genotype 1 infections.

    Science.gov (United States)

    Taylor, Ninon; Haschke-Becher, Elisabeth; Greil, Richard; Strasser, Michael; Oberkofler, Hannes

    2014-01-01

    With the advent of the protease inhibitors boceprevir and telaprevir a novel therapy approach for HCV genotype 1 infected subjects has become standard of care. Quantification of HCV viral load (VL) represents an important predictor of treatment response. Two different real-time PCR platforms, the COBAS Ampliprep/COBAS TaqMan v2.0 (CAP-CTM v2.0) and the Abbott RealTime (ART) HCV assay are most widely used. We performed a comparative evaluation of both systems focusing on genotype 1 HCV quantification using clinical specimens, the fourth WHO International Standard for HCV and the Paul Ehrlich National Standard, respectively. The HCV VL assays showed an excellent overall agreement in the clinical specimens studied (R(2)=0.912). Discrepant results were obtained at the low VL end. Four samples tested negative with CAP-CTM v2.0 but were detectable with ART and two samples were undetectable with ART but tested positive with CAP-CTM v2.0. The coefficient of variation in replicate measurements of both reference materials was higher for CAP-CTM v2.0 as compared with ART at the clinical decision point for boceprevir (≥100 IU/ml), but was similar for the two assays at the clinical decision point for telaprevir (≥1,000 IU/ml). The tendency for underestimation of the diluted standards was higher for ART than for CAP-CTM v2.0. Although both assays allowed accurate determination of VL levels in clinical samples, careful interpretation of results at the low VL end is essential. Furthermore, discontinuation of therapy based on single HCV RNA measurement should be carefully reconciled, unless the issue of assay variability has been addressed adequately.

  3. A closed-tube assay for genotyping of the 32-bp deletion polymorphism in the chemokine receptor 5 (CCR5) gene

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Werge, Thomas

    2007-01-01

    We have developed a closed-tube assay for determination of the chemokine receptor type 5 (CCR5) 32-bp deletion allele, which protects against infections with HIV and modulates susceptibility to a variety of inflammatory diseases. This assay utilizes dissociation analysis of amplified products...

  4. Study comparing human papillomavirus (HPV) real-time multiplex PCR and Hybrid Capture II INNO-LiPA v2 HPV genotyping PCR assays

    DEFF Research Database (Denmark)

    Iftner, Thomas; Germ, Liesje; Swoyer, Ryan

    2009-01-01

    (HCII-LiPA v2). SurePath residual samples were split into two aliquots. One aliquot was subjected to HCII testing followed by DNA extraction and LiPA v2 genotyping. The second aliquot was shipped to a second laboratory, where DNA was extracted and HPV multiplex PCR testing was performed. Comparisons...

  5. Development of highly reliable in silico SNP resource and genotyping assay from exome capture and sequencing: an example from black spruce (Picea mariana).

    Science.gov (United States)

    Pavy, Nathalie; Gagnon, France; Deschênes, Astrid; Boyle, Brian; Beaulieu, Jean; Bousquet, Jean

    2016-03-01

    Picea mariana is a widely distributed boreal conifer across Canada and the subject of advanced breeding programmes for which population genomics and genomic selection approaches are being developed. Targeted sequencing was achieved after capturing P. mariana exome with probes designed from the sequenced transcriptome of Picea glauca, a distant relative. A high capture efficiency of 75.9% was reached although spruce has a complex and large genome including gene sequences interspersed by some long introns. The results confirmed the relevance of using probes from congeneric species to perform successfully interspecific exome capture in the genus Picea. A bioinformatics pipeline was developed including stringent criteria that helped detect a set of 97,075 highly reliable in silico SNPs. These SNPs were distributed across 14,909 genes. Part of an Infinium iSelect array was used to estimate the rate of true positives by validating 4267 of the predicted in silico SNPs by genotyping trees from P. mariana populations. The true positive rate was 96.2% for in silico SNPs, compared to a genotyping success rate of 96.7% for a set 1115 P. mariana control SNPs recycled from previous genotyping arrays. These results indicate the high success rate of the genotyping array and the relevance of the selection criteria used to delineate the new P. mariana in silico SNP resource. Furthermore, in silico SNPs were generally of medium to high frequency in natural populations, thus providing high informative value for future population genomics applications. © 2015 John Wiley & Sons Ltd.

  6. Quantum strips on surfaces

    OpenAIRE

    Krejcirik, David

    2002-01-01

    Motivated by the theory of quantum waveguides, we investigate the spectrum of the Laplacian, subject to Dirichlet boundary conditions, in a curved strip of constant width that is defined as a tubular neighbourhood of an infinite curve in a two-dimensional Riemannian manifold. Under the assumption that the strip is asymptotically straight in a suitable sense, we localise the essential spectrum and find sufficient conditions which guarantee the existence of geometrically induced bound states. I...

  7. 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

  8. An Evaluation of Quantitative PCR Assays (TaqMan® and SYBR Green for the Detection of Babesia bigemina and Babesia bovis, and a Novel Fluorescent-ITS1-PCR Capillary Electrophoresis Method for Genotyping B. bovis Isolates

    Directory of Open Access Journals (Sweden)

    Bing Zhang

    2016-09-01

    Full Text Available Babesia spp. are tick-transmitted haemoparasites causing tick fever in cattle. In Australia, economic losses to the cattle industry from tick fever are estimated at AUD$26 Million per annum. If animals recover from these infections, they become immune carriers. Here we describe a novel multiplex TaqMan qPCR targeting cytochrome b genes for the identification of Babesia spp. The assay shows high sensitivity, specificity and reproducibility, and allows quantification of parasite DNA from Babesia bovis and B. bigemina compared to standard PCR assays. A previously published cytochrome b SYBR Green qPCR was also tested in this study, showing slightly higher sensitivity than the Taqman qPCRs but requires melting curve analysis post-PCR to confirm specificity. The SYBR Green assays were further evaluated using both diagnostic submissions and vaccinated cattle (at 7, 9, 11 and 14 days post-inoculation showed that B. bigemina can be detected more frequently than B. bovis. Due to fewer circulating parasites, B. bovis detection in carrier animals requires higher DNA input. Preliminary data for a novel fluorescent PCR genotyping based on the Internal Transcribed Spacer 1 region to detect vaccine and field alleles of B. bovis are described. This assay is capable of detecting vaccine and novel field isolate alleles in a single sample.

  9. Lateral flow assays

    NARCIS (Netherlands)

    Posthuma-Trumpie, G.A.; Amerongen, van A.

    2012-01-01

    A simple version of immunochemical-based methods is the Lateral Flow Assay (LFA). It is a dry chemistry technique (reagents are included); the fluid from the sample runs through a porous membrane (often nitrocellulose) by capillary force. Typically the membrane is cut as a strip of 0.5*5 cm. In most

  10. The Cobas AmpliPrep/Cobas TaqMan HCV Test, Version 2.0, Real-Time PCR Assay Accurately Quantifies Hepatitis C Virus Genotype 4 RNA

    OpenAIRE

    Chevaliez, Stéphane; Bouvier-Alias, Magali; Rodriguez, Christophe; Soulier, Alexandre; Poveda, Jean-Dominique; Pawlotsky, Jean-Michel

    2013-01-01

    Accurate hepatitis C virus (HCV) RNA quantification is mandatory for the management of chronic hepatitis C therapy. The first-generation Cobas AmpliPrep/Cobas TaqMan HCV test (CAP/CTM HCV) underestimated HCV RNA levels by >1-log10 international units/ml in a number of patients infected with HCV genotype 4 and occasionally failed to detect it. The aim of this study was to evaluate the ability of the Cobas AmpliPrep/Cobas TaqMan HCV test, version 2.0 (CAP/CTM HCV v2.0), to accurately quantify H...

  11. micro strip gas chamber

    CERN Multimedia

    1998-01-01

    About 16 000 Micro Strip Gas Chambers like this one will be used in the CMS tracking detector. They will measure the tracks of charged particles to a hundredth of a millimetre precision in the region near the collision point where the density of particles is very high. Each chamber is filled with a gas mixture of argon and dimethyl ether. Charged particles passing through ionise the gas, knocking out electrons which are collected on the aluminium strips visible under the microscope. Such detectors are being used in radiography. They give higher resolution imaging and reduce the required dose of radiation.

  12. ALICE Silicon Strip Detector

    CERN Multimedia

    Nooren, G

    2013-01-01

    The Silicon Strip Detector (SSD) constitutes the two outermost layers of the Inner Tracking System (ITS) of the ALICE Experiment. The SSD plays a crucial role in the tracking of the particles produced in the collisions connecting the tracks from the external detectors (Time Projection Chamber) to the ITS. The SSD also contributes to the particle identification through the measurement of their energy loss.

  13. Selective chemical stripping

    Science.gov (United States)

    Malavallon, Olivier

    1995-04-01

    At the end of the 80's, some of the large European airlines expressed a wish for paint systems with improved strippability on their aircraft, allowing the possibility to strip down to the primer without altering it, using 'mild' chemical strippers based on methylene chloride. These improvements were initially intended to reduce costs and stripping cycle times while facilitating rapid repainting, and this without the need to change the conventionally used industrial facilities. The level of in-service performance of these paint systems was to be the same as the previous ones. Requirements related to hygiene safety and the environment were added to these initial requirements. To meet customers' expectations, Aerospatiale, within the Airbus Industry GIE, formed a work group. This group was given the task of specifying, following up the elaboration and qualifying the paint systems allowing requirements to be met, in relation with the paint suppliers and the airlines. The analysis made in this report showed the interest of transferring as far upstream as possible (to paint conception level) most of the technical constraints related to stripping. Thus, the concept retained for the paint system, allowing selective chemical stripping, is a 3-coat system with characteristics as near as possible to the previously used paints.

  14. Development of a Genetic Map for Onion (Allium cepa L. Using Reference-Free Genotyping-by-Sequencing and SNP Assays

    Directory of Open Access Journals (Sweden)

    Jinkwan Jo

    2017-09-01

    Full Text Available Single nucleotide polymorphisms (SNPs play important roles as molecular markers in plant genomics and breeding studies. Although onion (Allium cepa L. is an important crop globally, relatively few molecular marker resources have been reported due to its large genome and high heterozygosity. Genotyping-by-sequencing (GBS offers a greater degree of complexity reduction followed by concurrent SNP discovery and genotyping for species with complex genomes. In this study, GBS was employed for SNP mining in onion, which currently lacks a reference genome. A segregating F2 population, derived from a cross between ‘NW-001’ and ‘NW-002,’ as well as multiple parental lines were used for GBS analysis. A total of 56.15 Gbp of raw sequence data were generated and 1,851,428 SNPs were identified from the de novo assembled contigs. Stringent filtering resulted in 10,091 high-fidelity SNP markers. Robust SNPs that satisfied the segregation ratio criteria and with even distribution in the mapping population were used to construct an onion genetic map. The final map contained eight linkage groups and spanned a genetic length of 1,383 centiMorgans (cM, with an average marker interval of 8.08 cM. These robust SNPs were further analyzed using the high-throughput Fluidigm platform for marker validation. This is the first study in onion to develop genome-wide SNPs using GBS. The resulting SNP markers and developed linkage map will be valuable tools for genetic mapping of important agronomic traits and marker-assisted selection in onion breeding programs.

  15. De novo SNP calling from RAD sequences for a mink (Neovison vison) specific genotyping assay

    DEFF Research Database (Denmark)

    Thirstrup, Janne Pia; Pujolar, José Martin; Larsen, Peter F

    mink from Brown and Black color types were obtained. A mean of 49,789,860.2 (± 9,813,587.2) raw reads of high quality per sample were sequenced. SNPs were called using the software pipeline Stacks. The populations program was used to estimate population structure and genetic divergence between the two...... color types. 1,576,944 catalog tags were generated with a 10X minimum depth of coverage. 224,095 candidate SNPs polymorphic for the two color types were called. Using strict filtering criteria in order to increase the success of assay design a total of 1,256 SNPs were finally identified....

  16. Photosensitive Strip RETHGEM

    CERN Document Server

    Peskov, Vladimir; Nappi, E.; Oliveira, R.; Paic, G.; Pietropaolo, F.; Picchi, P.

    2008-01-01

    An innovative photosensitive gaseous detector, consisting of a GEM like amplification structure with double layered electrodes (instead of commonly used metallic ones) coated with a CsI reflective photocathode, is described. In one of our latest designs, the inner electrode consists of a metallic grid and the outer one is made of resistive strips; the latter are manufactured by a screen printing technology on the top of the metallic strips grid The inner metallic grid is used for 2D position measurements whereas the resistive layer provides an efficient spark protected operation at high gains - close to the breakdown limit. Detectors with active areas of 10cm x10cm and 10cm x20cm were tested under various conditions including the operation in photosensitive gas mixtures containing ethylferrocene or TMAE vapors. The new technique could have many applications requiring robust and reliable large area detectors for UV visualization, as for example, in Cherenkov imaging devices.

  17. Alcohol Saliva Strip Test

    OpenAIRE

    Thokala, Madhusudhana Rao; Dorankula, Shyam Prasad Reddy; Muddana, Keertrthi; Velidandla, Surekha Reddy

    2014-01-01

    Alcohol is a factor in many categories of injury. Alcohol intoxication is frequently associated with injuries from falls, fires, drowning, overdoses, physical and sexual abusements, occupational accidents, traffic accidents and domestic violence. In many instances, for forensic purpose, it may be necessary to establish whether the patients have consumed alcohol that would have been the reason for the injury/accidents. Combining rapidity and reliability, alcohol saliva strip test (AST) has bee...

  18. Screening Chinese soybean genotypes for Agrobacterium-mediated genetic transformation suitability.

    Science.gov (United States)

    Song, Zhang-yue; Tian, Jing-luan; Fu, Wei-zhe; Li, Lin; Lu, Ling-hong; Zhou, Lian; Shan, Zhi-hui; Tang, Gui-xiang; Shou, Hui-xia

    2013-04-01

    The Agrobacterium-mediated transformation system is the most commonly used method in soybean transformation. Screening of soybean genotypes favorable for Agrobacterium-infection and tissue regeneration is the most important step to establish an efficient genetic transformation system. In this study, twenty soybean genotypes that originated from different soybean production regions in China were screened for transient infection, regeneration capacity, and stable transgenic efficiency. Three genotypes, Yuechun 04-5, Yuechun 03-3, and Tianlong 1, showed comparable stable transgenic efficiencies with that of the previously reported American genotypes Williams 82 and Jack in our experimental system. For the Tianlong 1, the average stable transformation efficiency is 4.59%, higher than that of control genotypes (Jack and Williams 82), which is enough for further genomic research and genetic engineering. While polymerase chain reaction (PCR), LibertyLink strips, and β-glucuronidase (GUS) staining assays were used to detect the insertion and expression of the transgene, leaves painted with 135 mg/L Basta could efficiently identify the transformants.

  19. Screening Chinese soybean genotypes for Agrobacterium-mediated genetic transformation suitability*

    Science.gov (United States)

    Song, Zhang-yue; Tian, Jing-luan; Fu, Wei-zhe; Li, Lin; Lu, Ling-hong; Zhou, Lian; Shan, Zhi-hui; Tang, Gui-xiang; Shou, Hui-xia

    2013-01-01

    The Agrobacterium-mediated transformation system is the most commonly used method in soybean transformation. Screening of soybean genotypes favorable for Agrobacterium-infection and tissue regeneration is the most important step to establish an efficient genetic transformation system. In this study, twenty soybean genotypes that originated from different soybean production regions in China were screened for transient infection, regeneration capacity, and stable transgenic efficiency. Three genotypes, Yuechun 04-5, Yuechun 03-3, and Tianlong 1, showed comparable stable transgenic efficiencies with that of the previously reported American genotypes Williams 82 and Jack in our experimental system. For the Tianlong 1, the average stable transformation efficiency is 4.59%, higher than that of control genotypes (Jack and Williams 82), which is enough for further genomic research and genetic engineering. While polymerase chain reaction (PCR), LibertyLink strips, and β-glucuronidase (GUS) staining assays were used to detect the insertion and expression of the transgene, leaves painted with 135 mg/L Basta could efficiently identify the transformants. PMID:23549846

  20. Spray Rolling Aluminum Strip

    Energy Technology Data Exchange (ETDEWEB)

    Lavernia, E.J.; Delplanque, J-P; McHugh, K.M.

    2006-05-10

    Spray forming is a competitive low-cost alternative to ingot metallurgy for manufacturing ferrous and non-ferrous alloy shapes. It produces materials with a reduced number of processing steps, while maintaining materials properties, with the possibility of near-net-shape manufacturing. However, there are several hurdles to large-scale commercial adoption of spray forming: 1) ensuring strip is consistently flat, 2) eliminating porosity, particularly at the deposit/substrate interface, and 3) improving material yield. Through this program, a new strip/sheet casting process, termed spray rolling, has been developed, which is an innovative manufacturing technique to produce aluminum net-shape products. Spray rolling combines the benefits of twin-roll casting and conventional spray forming, showing a promising potential to overcome the above hurdles associated with spray forming. Spray rolling requires less energy and generates less scrap than conventional processes and, consequently, enables the development of materials with lower environmental impacts in both processing and final products. Spray Rolling was developed as a collaborative project between the University of California-Davis, the Colorado School of Mines, the Idaho National Engineering and Environmental Laboratory, and an industry team. The following objectives of this project were achieved: (1) Demonstration of the feasibility of the spray rolling process at the bench-scale level and evaluation of the materials properties of spray rolled aluminum strip alloys; and (2) Demonstration of 2X scalability of the process and documentation of technical hurdles to further scale up and initiate technology transfer to industry for eventual commercialization of the process.

  1. Dynamic Underground Stripping Project

    International Nuclear Information System (INIS)

    Aines, R.; Newmark, R.; McConachie, W.; Udell, K.; Rice, D.; Ramirez, A.; Siegel, W.; Buettner, M.; Daily, W.; Krauter, P.; Folsom, E.; Boegel, A.J.; Bishop, D.; Udell, K.

    1992-01-01

    LLNL is collaborating with the UC Berkeley College of Engineering to develop and demonstrate a system of thermal remediation and underground imaging techniques for use in rapid cleanup of localized underground spills. Called ''Dynamic Stripping'' to reflect the rapid and controllable nature of the process, it will combine steam injection, direct electrical heating, and tomographic geophysical imaging in a cleanup of the LLNL gasoline spill. In the first 8 months of the project, a Clean Site engineering test was conducted to prove the field application of the techniques before moving the contaminated site in FY 92

  2. Electronic rumble strip

    Science.gov (United States)

    Stauffer, Donald R.; Lenz, James

    1997-02-01

    Single vehicle run-off-road accidents are responsible for significant numbers of injuries and fatalities, and significant property damage. This fact spurs interest in warning systems to alert drivers that vehicles are drifting towards the edge of the road, and that a run-off road accident is imminent. An early attempt at such a warning system is the use of machined grooves on the shoulder to create a rumble strip. Such a system only provides warning, however, as the vehicle actually leaves the traffic lane. More desirable is a system that warns in anticipation of such departure. Honeywell has under development a magnetic lateral guidance system that couples a sensitive magnetoresistive transducer with a magnetic traffic marking tape being developed by 3M. While this development was initially undertaken for use in automated highways, or for special tasks such as guiding snowplow owners, the system can provide an effective, all-weather warning system to provide alert of impending departure from the roadway. This electronic rumble strip is actually a simpler system than the baseline guidance system, and can monitor both distance from the traffic lane edge and the speed of approach to the edge with a low cost sensor.

  3. Readout of silicon strip detectors

    CERN Document Server

    Dabrowski, W

    2003-01-01

    Various architectural and technological options of readout electronics for silicon strip detectors in vertex and tracking applications are discussed briefly. The ABCD3T ASIC for the readout of silicon strip detectors in the ATLAS semiconductor tracker is presented. The architecture of the chip, some design issues and radiation effects are discussed.

  4. The CMS Silicon Strip Tracker

    CERN Document Server

    Azzurri, P

    2005-01-01

    With over 200 square meters of sensitive Silicon and almost 10 million readout channels, the Silicon Strip Tracker of the CMS experiment at the LHC will be the largest Silicon strip detector ever built. The design, construction and expected performance of the CMS Tracker is reviewed in the following.

  5. Bismuth-based electrochemical stripping analysis

    Science.gov (United States)

    Wang, Joseph

    2004-01-27

    Method and apparatus for trace metal detection and analysis using bismuth-coated electrodes and electrochemical stripping analysis. Both anodic stripping voltammetry and adsorptive stripping analysis may be employed.

  6. Persistência do plano experimental em ensaios de avaliação de germoplasma elite de feijão Experimental plan persistence in elite genotypes evaluation for beans assays

    Directory of Open Access Journals (Sweden)

    Lindolfo Storck

    2007-12-01

    Full Text Available A determinação do tamanho de parcela e do número de repetições é importante para a correta avaliação e diferenciação de genótipos. Assim, o planejamento de experimentos pode ser feito utilizando-se os resultados obtidos em ensaios já realizados. O objetivo deste trabalho foi verificar a repetibilidade do índice de heterogeneidade e do plano experimental, numa mesma área experimental com a cultura do feijão, durante sete anos (2000 a 2006. Quatorze ensaios de competição de germoplasma elite de feijão foram conduzidos em Santa Maria, RS, Brasil - em duas épocas de cultivo (safra e safrinha, com diferentes números de entradas (linhagens avançadas e cultivares, no delineamento experimental de blocos ao acaso, com três repetições. Para cada ensaio, foram estimados a média, o coeficiente de variação, o coeficiente de correlação intraclasse e o índice de heterogeneidade do rendimento de grãos de feijão. Também foram estimadas as diferenças verdadeiras entre duas médias de tratamentos pelo método de Hatheway para diferentes valores do índice de heterogeneidade, número de repetições e tamanho de parcela. A freqüência dos valores do índice de heterogeneidade entre 0,2 e 0,7 foi de 71%, evidenciando que o plano experimental, com base nos resultados de experimentos anteriores, tem validade em 71% dos casos. Não parece haver predominância de valores do índice de heterogeneidade em função da época de cultivo - safra ou safrinha, ou do tipo de experimento - VCU ou Cultivares, mostrando boa repetibilidade ou persistência no decorrer dos anos.The determination of the plot size and the repetition number is important to the correct evaluation and differentiation of genotypes. The experimental planning can be made using previous results in already conducted assays. The objective of this work is to verify the repeatability of the heterogeneity index and the experimental plan, in the same experimental area with beans

  7. Range gated strip proximity sensor

    Science.gov (United States)

    McEwan, T.E.

    1996-12-03

    A range gated strip proximity sensor uses one set of sensor electronics and a distributed antenna or strip which extends along the perimeter to be sensed. A micro-power RF transmitter is coupled to the first end of the strip and transmits a sequence of RF pulses on the strip to produce a sensor field along the strip. A receiver is coupled to the second end of the strip, and generates a field reference signal in response to the sequence of pulse on the line combined with received electromagnetic energy from reflections in the field. The sensor signals comprise pulses of radio frequency signals having a duration of less than 10 nanoseconds, and a pulse repetition rate on the order of 1 to 10 MegaHertz or less. The duration of the radio frequency pulses is adjusted to control the range of the sensor. An RF detector feeds a filter capacitor in response to received pulses on the strip line to produce a field reference signal representing the average amplitude of the received pulses. When a received pulse is mixed with a received echo, the mixing causes a fluctuation in the amplitude of the field reference signal, providing a range-limited Doppler type signature of a field disturbance. 6 figs.

  8. ATLAS Strips Upgrade

    CERN Document Server

    Miñano, Mercedes

    2009-01-01

    It is foreseen to increase the luminosity of the LHC at CERN around 2020 by about an order of magnitude (SLHC). The ATLAS experiment will require a new particle tracking system for SLHC operation in order to cope with the increase in background events by about one order of magnitude at the higher luminosity. , an all silicon detector with enhanced radiation hardness is being designed. A massive R&D programme, involving many particles physics groups and several leadings manufacturers of silicon detectors for particle physics, is underway to develop silicon sensors with sufficient radiation hardness. In this framework new sensor materials like p-type silicon and the 3D technology are investigated. In parallel, the SCT commissioning experience has taught us to look into alternative module concepts, in which higher levels of integration are combined with the modularity of the SCT approach. We will report on the status of the R&D projects on radiation hard silicon strip detectors for particle physics, link...

  9. ATLAS Strip Upgrade

    CERN Document Server

    Bernabeu, J; The ATLAS collaboration

    2012-01-01

    A phased upgrade of the Large Hadron Collider (LHC) at CERN is planned. The last upgrade phase (HL-LHC) is currently foreseen in 2022-2023. It aims to increase the integrated luminosity to about ten times the original LHC design luminosity. To cope with the harsh conditions in terms of particle rates and radiation dose expected during HL-LHC operation, the ATLAS collaboration is developing technologies for a complete tracker replacement. This new detector will need to provide extreme radiation hardness and a high granularity, within the tight constraints imposed by the existing detectors and their services. An all-silicon high-granularity tracking detector is proposed. An international R&D collaboration is working on the strip layers for this new tracker. A number of large area prototype planar detectors produced on p-type wafers have been designed and fabricated for use at HL-LHC. These prototype detectors and miniature test detectors have been irradiated to a set of fluences matched to HL-LHC expectatio...

  10. Characterization of galvannealed strip

    International Nuclear Information System (INIS)

    Moreas, G.; Hardy, Y.

    1999-01-01

    With the aim of enhancing coating quality control during galvannealing process, an online microscopic image acquisition sensor has been developed at CRM. In galvannealing process, the ζ phase surface density is a coating quality characteristic, and the on-line microscope, equipped with optics placed at 20 mm from the surface, grabs 250 μm x 190 μm images on which ζ crystals (approximate dimensions: 1 μm x 10 μm) can be clearly identified. On-line, the sensor is mounted in front of a roll where the strip has a stable position. The coating surface to sensor optics distance is continuously measured by an accurate triangulation sensor (1 μm repeatability) and is adjusted in such a way that, due to roll eccentricity, the image is focused at least twice per revolution. When focused, image of moving product is frozen by a short (10 ns) laser light pulse and is grabbed. The obtained image is then processed to extract ζ phase percentage and allows adjustment of process parameters to reach the desired coating characteristics. (author)

  11. Use of reverse transcription-real time polymerase chain reaction (real time RT-PCR) assays with Universal Probe Library (UPL) probes for the detection and genotyping of infectious pancreatic necrosis virus strains isolated in Chile.

    Science.gov (United States)

    Calleja, Felipe; Godoy, Marcos G; Cárcamo, Juan G; Bandín, Isabel; Yáñez, Alejandro J; Dopazo, Carlos P; Kibenge, Fred S; Avendaño-Herrera, Ruben

    2012-07-01

    Reverse transcription-real time polymerase chain reaction (real time RT-PCR) assay with Universal Probe Library (UPL) probes has been developed for the detection and genotyping of Chilean infectious pancreatic necrosis virus (IPNV) isolates from infected cell culture. Partial nucleotide sequences (1175 bp) of the VP2 coding region from a selection of 7 Chilean IPNV isolates showed that they clustered into two main groups strongly correlated with Genogroups 1 and 5 proposed by Blake et al. (2001), corresponding to types West Buxton (WB) and Spajarup (Sp), respectively. Based on the VP2 gene sequences of those 7 Chilean isolates and different reference IPNV strains, 2 sets of candidate primer/UPL probes (# 8 and # 117) were designed and evaluated with a total of 32 field isolates isolated from Atlantic salmon (Salmo salar), rainbow trout (Oncorhynchus mykiss) and Pacific salmon (Oncorhynchus kisutch) farms from 2006 to 2010 in Chile. The UPL probes clearly differentiated the same two major Genogroups that those recognized by sequencing analysis. Among the Chilean isolates examined, 18 yielded amplification with UPL probe # 8, and 14 with probe # 117, respectively corresponding to types Sp and WB, as demonstrated by typing by sequencing. Based on the findings reported below, it has been demonstrated that the combined real time RT-PCR protocol with UPLs approach was efficient in discriminating distinct Genogroups of IPNV cultured in fish cell lines and, therefore, recommended its use for detection and typing of IPN viruses. The study also confirmed the existence of two IPNV type strains in Chilean salmonid aquaculture. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Buffers and vegetative filter strips

    Science.gov (United States)

    Matthew J. Helmers; Thomas M. Isenhart; Michael G. Dosskey; Seth M. Dabney

    2008-01-01

    This chapter describes the use of buffers and vegetative filter strips relative to water quality. In particular, we primarily discuss the herbaceous components of the following NRCS Conservation Practice Standards.

  13. Upconversion fluorescent strip sensor for rapid determination of Vibrio anguillarum

    Science.gov (United States)

    Zhao, Peng; Wu, Yuanyuan; Zhu, Yihua; Yang, Xiaoling; Jiang, Xin; Xiao, Jingfan; Zhang, Yuanxing; Li, Chunzhong

    2014-03-01

    Here, we report a simple and ultrasensitive upconversion fluorescent strip sensor based on NaYF4:Yb,Er nanoparticles (NPs) and the lateral flow immunochromatographic assay (LFIA). Carboxyl-modified β-NaYF4:Yb,Er NPs were successfully synthesized by a facile one-pot solvothermal approach, upon further coupling with monoclonal antibody, the resultant UCNPs-antibody conjugates probes were used in LFIA and served as signal vehicles for the fluorescent reporters. V. anguillarum was used as a model analyte to demonstrate the use of this strip sensor. The limit of the detection for the fluorescent strip was determined as 102 CFU mL-1, which is 100 times lower than those displayed by enzyme-linked immunosorbent assays, while the time needed for the detection was only 15 min. Furthermore, no cross-reaction with other eight pathogens was found, indicating the good specificity of the strip. This developed LFIA would offer the potential as a useful tool for the quantification of pathogens analysis in the future.

  14. Towards a point-of-care strip test to diagnose sickle cell anemia.

    Directory of Open Access Journals (Sweden)

    Meaghan Bond

    Full Text Available A rapid test to identify patients with sickle cell disease could have important benefits in low-resource settings. Sickle cell anemia (SCA affects about 300,000 newborns each year, the majority of whom are born in sub-Saharan Africa. Low-cost therapies are available to treat SCA, but most countries in sub-Saharan Africa lack robust neonatal screening programs needed to identify patients in need of treatment. To address this need, we developed and evaluated a competitive lateral flow assay that identifies patients with SCA (genotype HbSS in 15 minutes using undiluted whole blood. A small volume of blood (0.5 μL- 3 μL is mixed with antibody-coated blue latex beads in a tube and applied to the strip. Strips are then placed in a well of running buffer and allowed to run for 10 minutes. Laboratory evaluation with samples containing different proportions of hemoglobin A (HbA and hemoglobin S (HbS indicated that the test should enable identification of SCA patients but not persons with sickle cell trait (SCT. We evaluated the test using 41 samples from individuals with SCA, SCT, and normal blood. With visual inspection or quantitative analysis, we found a 98% accuracy when differentiating SCA from normal and SCT samples as a group (90% sensitivity and 100% specificity for identifying SCA. This work demonstrates important steps towards making a lateral flow test for hemoglobinopathies more appropriate for point-of-care use; further work is needed before the test is appropriate for clinical use.

  15. Optical strip waveguide: an analysis.

    Science.gov (United States)

    Ogusu, K; Kawakami, S; Nishida, S

    1979-03-15

    An analysis of the strip waveguide is presented with special emphasis on reflection and transmission of a wave obliquely incident on the side of a strip. Mode conversion and the contribution of radiation modes are taken into account in the formulation. The numerical results of the mode conversion and attenuation constant of the fundamental leaky mode are presented and compared with the results of other authors. The numerical accuracy of our analysis is also checked by two different procedures. It is found that the radiation modes have considerable effects on the waveguide characteristics.

  16. Detection of Acanthamoeba on the ocular surface in a Spanish population using the Schirmer strip test: pathogenic potential, molecular classification and evaluation of the sensitivity to chlorhexidine and voriconazole of the isolated Acanthamoeba strains.

    Science.gov (United States)

    Rocha-Cabrera, Pedro; Reyes-Batlle, María; Martín-Navarro, Carmen María; Dorta-Gorrín, Alexis; López-Arencibia, Atteneri; Sifaoui, Ines; Martínez-Carretero, Enrique; Piñero, José E; Martín-Barrera, Fernando; Valladares, Basilio; Lorenzo-Morales, Jacob

    2015-08-01

    Pathogenic strains of Acanthamoeba are causative agents of a sight-threatening infection of the cornea known as Acanthamoeba keratitis, which is often associated with the misuse of contact lenses. However, there is still a question remaining to be answered, which is whether these micro-organisms are present on the ocular surface of healthy individuals. Therefore, the aim of this study was to determine the presence of Acanthamoeba on the ocular surface in healthy patients and also in those with other ocular surface infections. Sterile Schirmer test strips were used to collect samples from a group of patients who attended an ophthalmology consultation at the Hospital del Norte, Icod de los Vinos, Tenerife, Canary Islands. Most of the patients (46 individuals, 79.31  %) presented ocular surface pathologies such as blepharitis or conjunctivitis; the rest did not present any pathology. None of the patients included in the study wore contact lenses. The collected samples were cultured in 2  % non-nutrient agar plates and positive plates were then cultured in axenic conditions for further analyses. Molecular analysis classified all isolated strains as belonging to Acanthamoeba genotype tbl4, and osmotolerance and thermotolerance assays revealed that all strains were potentially pathogenic. Furthermore, all strains were assayed for sensitivity against voriconazole and chlorhexidine. Assays showed that both drugs were active against the tested strains. In conclusion, the Schirmer strip test is proposed as an effective tool for the detection of Acanthamoeba on the ocular surface.

  17. Buttock Lifting with Polypropylene Strips.

    Science.gov (United States)

    Ballivian Rico, José; Esteche, Atilio; Hanke, Carlos José Ramírez; Ribeiro, Ricardo Cavalcanti

    2016-04-01

    The purpose of this study was to evaluate the results of gluteal suspension with polypropylene strips. Ninety healthy female patients between the ages of 20 and 50 years (mean, 26 years), who wished to remodel their buttocks from December 2004 to February 2013 were studied retrospectively. All 90 patients were treated with 2 strips of polypropylene on each buttock using the following procedures: 27 (30 %) patients were suspended with polypropylene strips; 63 (70 %) patients were treated with tumescent liposuction in the sacral "V", lower back, supragluteal regions, and flanks to improve buttocks contour (aspirated volume of fat from 350 to 800 cc); 16 (18 %) patients underwent fat grafting in the subcutaneous and intramuscular layers (up to 300 cc in each buttock to increase volume); 5 (6 %) patients received implants to increase volume; and 4 (4.4 %) patients underwent removal and relocation of intramuscular gluteal implants to improve esthetics. Over an 8-year period, 90 female patients underwent gluteal suspension surgeries. Good esthetic results without complications were obtained in 75 of 90 (84 %) cases. Complications occurred in 15 of 90 (16.6 %) patients, including strip removal due to postoperative pain in 1 (1.1 %) patient, and seroma in both subgluteal sulci in 3 (3.3 %) patients. The results of this study performed in 90 patients over 8 years showed that the suspension with polypropylene strips performed as a single procedure or in combination with other cosmetic methods helps to enhance and lift ptosed gluteal and paragluteal areas. This journal requires that the authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266.

  18. Core Gene Expression and Association of Genotypes with Viral ...

    African Journals Online (AJOL)

    HP

    Purpose: To determine genotypic distribution, ribonucleic acid (RNA) RNA viral load and express core gene from Hepatitis C Virus (HCV) infected patients in Punjab, Pakistan. Methods: A total of 1690 HCV RNA positive patients were included in the study. HCV genotyping was tested by type-specific genotyping assay, viral ...

  19. Adsorptive stripping voltammetric methods for determination of aripiprazole

    Directory of Open Access Journals (Sweden)

    Derya Aşangil

    2012-06-01

    Full Text Available Anodic behavior of aripiprazole (ARP was studied using electrochemical methods. Charge transfer, diffusion and surface coverage coefficients of adsorbed molecules and the number of electrons transferred in electrode mechanisms were calculated for quasi-reversible and adsorption-controlled electrochemical oxidation of ARP at 1.15 V versus Ag/AgCl at pH 4.0 in Britton–Robinson buffer (BR on glassy carbon electrode. Voltammetric methods for direct determination of ARP in pharmaceutical dosage forms and biological samples were developed. Linearity range is found as from 11.4 μM (5.11 mg/L to 157 μM (70.41 mg/L without stripping mode and it is found as from 0.221 μM (0.10 mg/L to 13.6 μM (6.10 mg/L with stripping mode. Limit of detection (LOD was found to be 0.11 μM (0.05 mg/L in stripping voltammetry. Methods were successfully applied to assay the drug in tablets, human serum and human urine with good recoveries between 95.0% and 104.6% with relative standard deviation less than 10%. Keywords: Adsorptive stripping voltammetry, Aripiprazole, Electrochemical behavior, Human serum and urine, Pharmaceuticals

  20. Genotype 3 is the predominant hepatitis C genotype in a multi-ethnic Asian population in Malaysia.

    Science.gov (United States)

    Ho, Shiaw-Hooi; Ng, Kee-Peng; Kaur, Harvinder; Goh, Khean-Lee

    2015-06-01

    Genotypes of hepatitis C virus (HCV) are distributed differently across the world. There is a paucity of such data in a multi-ethnic Asian population like Malaysia. The objectives of this study were to determine the distribution of HCV genotypes between major ethnic groups and to ascertain their association with basic demographic variables like age and gender. This was a cross-sectional prospective study conducted from September 2007 to September 2013. Consecutive patients who were detected to have anti-HCV antibodies in the University of Malaya Medical Centre were included and tested for the presence of HCV RNA using Roche Cobas Amplicor Analyzer and HCV genotype using Roche single Linear Array HCV Genotyping strip. Five hundred and ninety-six subjects were found to have positive anti-HCV antibodies during this period of time. However, only 396 (66.4%) were HCV RNA positive and included in the final analysis. Our results showed that HCV genotype 3 was the predominant genotype with overall frequency of 61.9% followed by genotypes 1 (35.9%), 2 (1.8%) and 6 (0.5%). There was a slightly higher prevalence of HCV genotype 3 among the Malays when compared to the Chinese (P=0.043). No other statistical significant differences were observed in the distribution of HCV genotypes among the major ethnic groups. There was also no association between the predominant genotypes and basic demographic variables. In a multi-ethnic Asian society in Malaysia, genotype 3 is the predominant genotype among all the major ethnic groups with genotype 1 as the second commonest genotype. Both genotypes 2 and 6 are uncommon. Neither genotype 4 nor 5 was detected. There is no identification of HCV genotype according to ethnic origin, age and gender.

  1. Enzyme assays.

    Science.gov (United States)

    Brodelius, P E

    1991-02-01

    The past year or so has seen the development of new enzyme assays, as well as the improvement of existing ones. Assays are becoming more rapid and sensitive as a result of modifications such as amplification of the enzyme product(s). Recombinant DNA technology is now being recognized as a particularly useful tool in the search for improved assay systems.

  2. Collisional stripping of planetary crusts

    Science.gov (United States)

    Carter, Philip J.; Leinhardt, Zoë M.; Elliott, Tim; Stewart, Sarah T.; Walter, Michael J.

    2018-02-01

    Geochemical studies of planetary accretion and evolution have invoked various degrees of collisional erosion to explain differences in bulk composition between planets and chondrites. Here we undertake a full, dynamical evaluation of 'crustal stripping' during accretion and its key geochemical consequences. Crusts are expected to contain a significant fraction of planetary budgets of incompatible elements, which include the major heat producing nuclides. We present smoothed particle hydrodynamics simulations of collisions between differentiated rocky planetesimals and planetary embryos. We find that the crust is preferentially lost relative to the mantle during impacts, and we have developed a scaling law based on these simulations that approximates the mass of crust that remains in the largest remnant. Using this scaling law and a recent set of N-body simulations of terrestrial planet formation, we have estimated the maximum effect of crustal stripping on incompatible element abundances during the accretion of planetary embryos. We find that on average approximately one third of the initial crust is stripped from embryos as they accrete, which leads to a reduction of ∼20% in the budgets of the heat producing elements if the stripped crust does not reaccrete. Erosion of crusts can lead to non-chondritic ratios of incompatible elements, but the magnitude of this effect depends sensitively on the details of the crust-forming melting process on the planetesimals. The Lu/Hf system is fractionated for a wide range of crustal formation scenarios. Using eucrites (the products of planetesimal silicate melting, thought to represent the crust of Vesta) as a guide to the Lu/Hf of planetesimal crust partially lost during accretion, we predict the Earth could evolve to a superchondritic 176Hf/177Hf (3-5 parts per ten thousand) at present day. Such values are in keeping with compositional estimates of the bulk Earth. Stripping of planetary crusts during accretion can lead to

  3. Dynamic Underground Stripping Demonstration Project

    International Nuclear Information System (INIS)

    Aines, R.; Newmark, R.; McConachie, W.; Rice, D.; Ramirez, A.; Siegel, W.; Buettner, M.; Daily, W.; Krauter, P.; Folsom, E.; Boegel, A.J.; Bishop, D.; udel, K.

    1992-03-01

    LLNL is collaborating with the UC Berkeley College of Engineering to develop and demonstrate a system of thermal remediation and underground imaging techniques for use in rapid cleanup of localized underground spills. Called ''Dynamic Stripping'' to reflect the rapid and controllable nature of the process, it will combine steam injection, direct electrical heating, and tomographic geophysical imaging in a cleanup of the LLNL gasoline spill. In the first 8 months of the project, a Clean Site engineering test was conducted to prove the field application of the techniques before moving to the contaminated site in FY 92

  4. 3D silicon strip detectors

    Energy Technology Data Exchange (ETDEWEB)

    Parzefall, Ulrich [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany)], E-mail: ulrich.parzefall@physik.uni-freiburg.de; Bates, Richard [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Boscardin, Maurizio [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy); Dalla Betta, Gian-Franco [INFN and Universita' di Trento, via Sommarive 14, 38050 Povo di Trento (Italy); Eckert, Simon [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Eklund, Lars; Fleta, Celeste [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Jakobs, Karl; Kuehn, Susanne [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Lozano, Manuel [Instituto de Microelectronica de Barcelona, IMB-CNM, CSIC, Barcelona (Spain); Pahn, Gregor [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Parkes, Chris [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Pellegrini, Giulio [Instituto de Microelectronica de Barcelona, IMB-CNM, CSIC, Barcelona (Spain); Pennicard, David [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Piemonte, Claudio; Ronchin, Sabina [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy); Szumlak, Tomasz [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Zoboli, Andrea [INFN and Universita' di Trento, via Sommarive 14, 38050 Povo di Trento (Italy); Zorzi, Nicola [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy)

    2009-06-01

    While the Large Hadron Collider (LHC) at CERN has started operation in autumn 2008, plans for a luminosity upgrade to the Super-LHC (sLHC) have already been developed for several years. This projected luminosity increase by an order of magnitude gives rise to a challenging radiation environment for tracking detectors at the LHC experiments. Significant improvements in radiation hardness are required with respect to the LHC. Using a strawman layout for the new tracker of the ATLAS experiment as an example, silicon strip detectors (SSDs) with short strips of 2-3 cm length are foreseen to cover the region from 28 to 60 cm distance to the beam. These SSD will be exposed to radiation levels up to 10{sup 15}N{sub eq}/cm{sup 2}, which makes radiation resistance a major concern for the upgraded ATLAS tracker. Several approaches to increasing the radiation hardness of silicon detectors exist. In this article, it is proposed to combine the radiation hard 3D-design originally conceived for pixel-style applications with the benefits of the established planar technology for strip detectors by using SSDs that have regularly spaced doped columns extending into the silicon bulk under the detector strips. The first 3D SSDs to become available for testing were made in the Single Type Column (STC) design, a technological simplification of the original 3D design. With such 3D SSDs, a small number of prototype sLHC detector modules with LHC-speed front-end electronics as used in the semiconductor tracking systems of present LHC experiments were built. Modules were tested before and after irradiation to fluences of 10{sup 15}N{sub eq}/cm{sup 2}. The tests were performed with three systems: a highly focused IR-laser with 5{mu}m spot size to make position-resolved scans of the charge collection efficiency, an Sr{sup 90}{beta}-source set-up to measure the signal levels for a minimum ionizing particle (MIP), and a beam test with 180 GeV pions at CERN. This article gives a brief overview of

  5. Diffraction by a finite strip

    Science.gov (United States)

    Williams, M. H.

    1982-01-01

    A new approach is presented to diffraction problems involving plane strip barriers or slit apertures. These are problems that display the effects of multiple interacting edges. The approach taken here provides exact, compact solutions. The theory is introduced through a series of examples that are, in fact, the 'standard' problems of the subject, diffraction of a plane oblique wave by a slit, for example. In each case, the solutions are found to depend explicitly on a single 'special' function and its Fourier transform. These fundamental functions are described, with the emphasis placed on practical computational methods. The example problems are all couched in the language of acoustics.

  6. First detection and genotyping of Giardia intestinalis in stool samples collected from children in Ghazni Province, eastern Afghanistan and evaluation of the PCR assay in formalin-fixed specimens.

    Science.gov (United States)

    Lass, Anna; Karanis, Panagiotis; Korzeniewski, Krzysztof

    2017-08-01

    It is estimated that faecal-orally transmitted diseases are common in Afghanistan, as a consequence of poor hygienic standards of life and widespread contamination of water and food with both human and animal faeces. However, there is little information in the literature concerning infections caused by intestinal parasites in the Afghan population. In this study, we report the occurrence of Giardia intestinalis assemblages (A and B) in formalin-fixed stool samples collected from 245 Afghan schoolchildren living in Ghazni Province in eastern Afghanistan. Detection of the parasite's DNA and genotyping was performed using real-time PCR, specific to the β-giardin gene of G. intestinalis. Positive results were recorded in 52 (21.2%) samples. Genotyping was successful in 39 faecal samples and showed the predominance of assemblage B of G. intestinalis in this population (15 assemblage A and 24 assemblage B). Co-infection with both genotypes A and B was detected in four samples. Additionally, we evaluated the effect of 10% buffered formalin fixative on the detection of G. intestinalis DNA using real-time PCR and nested PCR characterised by different lengths of PCR products (74 and 479 bp, respectively). The human faeces containing the Giardia cysts were tested for 16 weeks. Amplification of G. intestinalis DNA with real-time PCR was possible up to 6 weeks of preservation of stool sample in formalin, compared to only 2 weeks with nested PCR. This suggests that real-time PCR is a more suitable tool in cases where stool samples have to be kept in formalin for longer periods of time.

  7. Mechanical behaviour of a creased thin strip

    OpenAIRE

    Liu, Jie; Xu, Shanqing; Wen, Guilin; Xie, Yi Min

    2018-01-01

    In this study the mechanical behaviour of a creased thin strip under opposite-sense bending was investigated. It was found that a simple crease, which led to the increase of the second moment of area, could significantly alter the overall mechanical behaviour of a thin strip, for example the peak moment could be increased by 100 times. The crease was treated as a cylindrical segment of a small radius. Parametric studies demonstrated that the geometry of the strip could stron...

  8. Ammonia stripping of biologically treated liquid manure.

    Science.gov (United States)

    Alitalo, Anni; Kyrö, Aleksis; Aura, Erkki

    2012-01-01

    A prerequisite for efficient ammonia removal in air stripping is that the pH of the liquid to be stripped is sufficiently high. Swine manure pH is usually around 7. At pH 7 (at 20°C), only 0.4% of ammonium is in ammonia form, and it is necessary to raise the pH of swine slurry to achieve efficient ammonia removal. Because manure has a very high buffering capacity, large amounts of chemicals are needed to change the slurry pH. The present study showed that efficient air stripping of manure can be achieved with a small amount of chemicals and without strong bases like NaOH. Slurry was subjected to aerobic biological treatment to raise pH before stripping. This facilitated 8 to 32% ammonia removal without chemical treatment. The slurry was further subjected to repeated cycles of stripping with MgO and Ca(OH)(2) additions after the first and second strippings, respectively, to raise slurry pH in between the stripping cycles. After three consecutive stripping cycles, 59 to 86% of the original ammonium had been removed. It was shown that the reduction in buffer capacity of the slurry was due to ammonia and carbonate removal during the stripping cycles. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  9. Optimizing the Stripping Procedure for LHCb

    CERN Document Server

    Richardson, Rachel

    2017-01-01

    The LHCb experiment faces a major challenge from the large amounts of data received while the LHC is running. The ability to sort this information in a useful manner is important for working groups to perform physics analyses. Both hardware and software triggers are used to decrease the data rate and then the stripping process is used to sort the data into streams and further into stripping lines. This project studies the hundreds of stripping lines to look for overlaps between them in order to make the stripping process more efficient.

  10. Potential profile in a conducting polymer strip

    DEFF Research Database (Denmark)

    Bay, Lasse; West, Keld; Vlachopoulos, Nikolaos

    2002-01-01

    Many conjugated polymers show an appreciable difference in volume between their oxidized and reduced forms. This property can be utilized in soft electrochemically driven actuators, "artificial muscles". Several geometries have been proposed for the conversion of the volume expansion into useful...... mechanical work. In a particularly simple geometry, the length change of polymer strips is exploited. The polymer strips are connected to the driving circuit at the end of the strip that is attached to the support of the device. The other end of the strip is connected to the load. The advantage of this set...

  11. Performance evaluation of the Abbott RealTime HCV Genotype II for hepatitis C virus genotyping.

    Science.gov (United States)

    Sohn, Yong-Hak; Ko, Sun-Young; Kim, Myeong Hee; Oh, Heung-Bum

    2010-04-01

    The Abbott RealTime hepatitis C virus (HCV) Genotype II (Abbott Molecular Inc.) for HCV genotyping, which uses real-time PCR technology, has recently been developed. Accuracy and sensitivity of detection were assessed using the HCV RNA PHW202 performance panel (SeraCare Life Sciences). Consistency with restriction fragment mass polymorphism (RFMP) data, cross-reactivity with other viruses, and the ability to detect minor strains in mixtures of genotypes 1 and 2 were evaluated using clinical samples. All performance panel viruses were correctly genotyped at levels of >500 IU/mL. Results were 100% concordant with RFMP genotypic data (66/66). However, 5% (3/66) of the samples examined displayed probable genotypic cross reactivity. No cross reactivity with other viruses was evident. Minor strains in the mixtures were not effectively distinguished, even at quantities higher than the detection limit. The Abbott RealTime HCV Genotype II assay was very accurate and yielded results consistent with RFMP data. Although the assay has the advantages of automation and short turnaround time, we suggest that further improvements are necessary before it is used routinely in clinical practice. Efforts are needed to decrease cross reactivity among genotypes and to improve the ability to detect minor genotypes in mixed infections.

  12. A real-time quantitative assay for hepatitis B DNA virus (HBV developed to detect all HBV genotypes Ensaio quantitativo em tempo real para o DNA do vírus da hepatite B (HBV desenvolvido para detectar todos os genótipos do HBV

    Directory of Open Access Journals (Sweden)

    Roberta Sitnik

    2010-06-01

    Full Text Available Hepatitis B virus (HBV is a major cause of chronic liver disease worldwide. Besides genotype, quantitative analysis of HBV infection is extensively used for monitoring disease progression and treatment. Affordable viral load monitoring is desirable in resource-limited settings and it has been already shown to be useful in developing countries for other viruses such as Hepatitis C virus (HCV and HIV. In this paper, we describe the validation of a real-time PCR assay for HBV DNA quantification with TaqMan chemistry and MGB probes. Primers and probes were designed using an alignment of sequences from all HBV genotypes in order to equally amplify all of them. The assay is internally controlled and was standardized with an international HBV panel. Its efficacy was evaluated comparing the results with two other methods: Versant HBV DNA Assay 3.0 (bDNA, Siemens, NY, USA and another real-time PCR from a reference laboratory. Intra-assay and inter-assay reproducibilities were determined and the mean of CV values obtained were 0.12 and 0.09, respectively. The assay was validated with a broad dynamic range and is efficient for amplifying all HBV genotypes, providing a good option to quantify HBV DNA as a routine procedure, with a cheap and reliable protocol.O vírus da Hepatite B (HBV é uma das principais causas de doença crônica do fígado no mundo. Além do genótipo, a análise quantitativa do HBV é amplamente utilizada para monitorar a progressão da doença e o tratamento. Em locais com recursos escassos, métodos baratos para o monitoramento da carga viral são desejáveis e, em países em desenvolvimento, sua utilidade já foi demonstrada para outros vírus, como o da Hepatite C e HIV. Neste trabalho, descrevemos a validação de um teste de PCR em Tempo Real para a quantificação do DNA do HBV utilizando sondas Taqman/MGB. Os oligos e sondas foram escolhidos usando um alinhamento contendo seqüências de todos os genótipos do HBV para

  13. The 'KATOD-1' strip readout ASIC for cathode strip chamber

    International Nuclear Information System (INIS)

    Golutvin, I.A.; Gorbunov, N.V.; Karzhavin, V.Yu.; Khabarov, V.S.; Movchan, S.A.; Smolin, D.A.; Dvornikov, O.V.; Shumejko, N.M.; Chekhovskij, V.A.

    2001-01-01

    The 'KATOD-1', a 16-channels readout ASIC, has been designed to perform tests of P3 and P4 full-scale prototypes of the cathode strip chamber for the ME1/1 forward muon station of the Compact Muon Solenoid (CMS) experiment. The ASIC channel consists of two charge-sensitive preamplifiers, a three-stage shaper with cancellation, and an output driver. The ASIC is instrumented with control of gain, in the range of (-4.2 : +5.0) mV/fC, and control of output pulse-shape. The equivalent input noise is equal to 2400 e with the slope of 12 e/pF for detector capacity up to 200 pF. The peaking time is 100 ns for the chamber signal. The ASIC has been produced by a microwave Bi-jFET technology

  14. Simultaneous determination of trace-levels of alloying zinc and copper by semi-mercury-free potentiometric stripping analysis with chemometric data treatment

    DEFF Research Database (Denmark)

    Andersen, Jens Enevold Thaulov; Hansen, Elo Harald

    1998-01-01

    Assays of copper and zinc in brass samples were performed by Semi-Mercury Free Potentiometric Stripping Analysis (S-MF PSA) using a thin-film mercury covered glassy-carbon working electrode and dissolved oxygen as oxidizing agent during the stripping step. The stripping peak transients were resol...... by factors in the range 2.104 - 5.105 which resulted in quantification of the copper and of zinc contents comparable to the specified values within 10%. On the basis of the chemometric treatment, an empirical expression is deduced relating the stripping time to the recorded potential....

  15. Development of Three PCR Assays for the Differentiation between Echinococcus shiquicus, E. granulosus (G1 genotype), and E. multilocularis DNA in the Co-Endemic Region of Qinghai-Tibet plateau, China

    Science.gov (United States)

    Boufana, Belgees; Umhang, Gérald; Qiu, Jiamin; Chen, Xingwang; Lahmar, Samia; Boué, Franck; Jenkins, David; Craig, Philip

    2013-01-01

    To investigate echinococcosis in co-endemic regions, three polymerase chain reaction (PCR) assays based on the amplification of a fragment within the NADH dehydrogenase subunit 1 (ND1) mitochondrial gene were optimized for the detection of Echinococcus shiquicus, Echinococcus granulosus G1, and Echinococcus multilocularis DNA derived from parasite tissue or canid fecal samples. Specificity using parasite tissue-derived DNA was found to be 100% except for E. shiquicus primers that faintly detected E. equinus DNA. Sensitivity of the three assays for DNA detection was between 2 and 10 pg. Ethanol precipitation of negative PCR fecal samples was used to eliminate false negatives and served to increase sensitivity as exemplified by an increase in detection from 0% to 89% of E. shiquicus coproDNA using necropsy-positive fox samples. PMID:23438764

  16. New strips of convergence for Dirichlet series

    OpenAIRE

    Defant, Andreas

    2010-01-01

    In this article we study the interplay of the theory of classical Dirichlet series in one complex variable with recent development on monomial expansions of holomorphic functions in infinitely many variables. For a given Dirichlet series we obtain new strips of convergence in the complex plane related to Bohr’s classical strips of uniform but non absolute convergence.

  17. Hardness of approximation for strip packing

    DEFF Research Database (Denmark)

    Adamaszek, Anna Maria; Kociumaka, Tomasz; Pilipczuk, Marcin

    2017-01-01

    Strip packing is a classical packing problem, where the goal is to pack a set of rectangular objects into a strip of a given width, while minimizing the total height of the packing. The problem has multiple applications, for example, in scheduling and stock-cutting, and has been studied extensive...

  18. Mechanical behaviour of a creased thin strip

    Directory of Open Access Journals (Sweden)

    J. Liu

    2018-02-01

    Full Text Available In this study the mechanical behaviour of a creased thin strip under opposite-sense bending was investigated. It was found that a simple crease, which led to the increase of the second moment of area, could significantly alter the overall mechanical behaviour of a thin strip, for example the peak moment could be increased by 100 times. The crease was treated as a cylindrical segment of a small radius. Parametric studies demonstrated that the geometry of the strip could strongly influence its flexural behaviour. We showed that the uniform thickness and the radius of the creased segment had the greatest and the least influence on the mechanical behaviour, respectively. We further revealed that material properties could dramatically affect the overall mechanical behaviour of the creased strip by gradually changing the material from being linear elastic to elastic-perfect plastic. After the formation of the fold, the moment of the two ends of the strip differed considerably when the elasto-plastic materials were used, especially for materials with smaller tangent modulus in the plastic range. The deformation patterns of the thin strips from the finite element simulations were verified by physical models made of thin metal strips. The findings from this study provide useful information for designing origami structures for engineering applications using creased thin strips.

  19. MWCNTs based high sensitive lateral flow strip biosensor for rapid determination of aqueous mercury ions.

    Science.gov (United States)

    Yao, Li; Teng, Jun; Zhu, Mengya; Zheng, Lei; Zhong, Youhao; Liu, Guodong; Xue, Feng; Chen, Wei

    2016-11-15

    Here, we describe a disposable multi-walled carbon nanotubes (MWCNTs) labeled nucleic acid lateral flow strip biosensor for rapid and sensitive detection of aqueous mercury ions (Hg(2+)). Unlike the conventional colloidal gold nanoparticle based strip biosensors, the carboxylated MWCNTs were selected as the labeling substrate because of its high specific surface area for immobilization of recognition probes, improved stability and enhanced detection sensitivity of the strip biosensor. Combining the sandwich-type of T-Hg(2+)-T recognition mechanism with the optical properties of MWCNTs on lateral flow strip, optical black bands were observed on the lateral flow strips. Parameters (such as membrane category, the MWCNTs concentration, the amount of MWCNT-DNA probe, and the volume of the test probe) that govern the sensitivity and reproducibility of the sensor were optimized. The response of the optimized biosensor was highly linear over the range of 0.05-1ppb target Hg(2+), and the detection threshold was estimated at 0.05 ppb within a 15-min assay time. The sensitivity was 10-fold higher than the conventional colloidal gold based strip biosensor. More importantly, the stability of the sensor was also greatly improved with the usage of MWCNTs as the labeling. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

  20. CMS Silicon Strip Tracker Performance

    CERN Document Server

    Agram, Jean-Laurent

    2012-01-01

    The CMS Silicon Strip Tracker (SST), consisting of 9.6 million readout channels from 15148 modules and covering an area of 198 square meters, needs to be precisely calibrated in order to correctly reconstruct the events recorded. Calibration constants are derived from different workflows, from promptly reconstructed events with particles as well as from commissioning events gathered just before the acquisition of physics runs. The performance of the SST has been carefully studied since the beginning of data taking: the noise of the detector, data integrity, signal-over-noise ratio, hit reconstruction efficiency and resolution have been all investigated with time and for different conditions. In this paper we describe the reconstruction strategies, the calibration procedures and the detector performance results from the latest CMS operation.

  1. Ultrasonic examination of JBK-75 strip material

    International Nuclear Information System (INIS)

    Cook, K.V.; Cunningham, R.A. Jr.; Lewis, J.C.; McClung, R.W.

    1982-12-01

    An ultrasonic inspection system was assembled to inspect the JBK-75 stainless steel sheath material (for the Large Coil Project) for the Westinghouse-Airco superconducting magnet program. The mechanical system provided for handling the 180-kg (400-lb) coils of strip material [1.6 mm thick by 78 mm wide by 90 to 120 m long (0.064 by 3.07 in. by 300 to 400 ft)], feeding the strip through the ultrasonic inspection and cleaning stations, and respooling the coils. We inspected 54 coils of strip for both longitudinal and laminar flaws. Simulated flaws were used to calibrate both inspections. Saw-cut notches [0.28 mm deep (0.011 in., about 17% of the strip thickness)] were used to calibrate the longitudinal flaw inspections; 1.59-mm-diam (0.063-in.) flat-bottom holes drilled halfway through a calibration strip were used to calibrate the laminar flaw tests

  2. Prototype Strip Barrel Modules for the ATLAS ITk Strip Detector

    CERN Document Server

    Sawyer, Craig; The ATLAS collaboration

    2017-01-01

    The module design for the Phase II Upgrade of the new ATLAS Inner Tracker (ITk) detector at the LHC employs integrated low mass assembly using single-sided flexible circuits with readout ASICs and a powering circuit incorporating control and monitoring of HV, LV and temperature on the module. Both readout and powering circuits are glued directly onto the silicon sensor surface resulting in a fully integrated, extremely low radiation length module which simultaneously reduces the material requirements of the local support structure by allowing a reduced width stave structure to be employed. Such a module concept has now been fully demonstrated using so-called ABC130 and HCC130 ASICs fabricated in 130nm CMOS technology to readout ATLAS12 n+-in-p silicon strip sensors. Low voltage powering for these demonstrator modules has been realised by utilising a DCDC powerboard based around the CERN FEAST ASIC. This powerboard incorporates an HV multiplexing switch based on a Panasonic GaN transistor. Control and monitori...

  3. Aeroelastic deformation of a perforated strip

    Science.gov (United States)

    Guttag, M.; Karimi, H. H.; Falcón, C.; Reis, P. M.

    2018-01-01

    We perform a combined experimental and numerical investigation into the static deformation of perforated elastic strips under uniform aerodynamic loading at high-Reynolds-number conditions. The static shape of the porous strips, clamped either horizontally or vertically, is quantified as they are deformed by wind loading, induced by a horizontal flow. The experimental profiles are compared to numerical simulations using a reduced model that takes into account the normal drag force on the deformed surface. For both configurations (vertical and horizontal clamping), we compute the drag coefficient of the strip, by fitting the experimental data to the model, and find that it decreases as a function of porosity. Surprisingly, we find that, for every value of porosity, the drag coefficients for the horizontal configuration are larger than those of the vertical configuration. For all data in both configurations, with the exception of the continuous strip clamped vertically, a linear relation is found between the porosity and drag. Making use of this linearity, we can rescale the drag coefficient in a way that it becomes constant as a function of the Cauchy number, which relates the force due to fluid loading on the elastic strip to its bending rigidity, independently of the material properties and porosity of the strip and the flow speed. Our findings on flexible strips are contrasted to previous work on rigid perforated plates. These results highlight some open questions regarding the usage of reduced models to describe the deformation of flexible structures subjected to aerodynamic loading.

  4. Corn and Soybeans in a Strip Intercropping System: Crop Growth Rates, Radiation Interception, and Grain Yield Components

    Directory of Open Access Journals (Sweden)

    Diego Verdelli

    2012-01-01

    Full Text Available Crop growth rates (CGR, radiation interception (IPAR, yields, and their components were determined in two crops monocultures (using one corn and two soybean genotypes and in intercropped “strips,” during three growing seasons. Corn yield in the strips significantly increased in the three seasons (13–16% as compared to that in the monocultures. This response was due to increased yield in corn plants of the border rows of the strips, which was highly correlated to an increased IPAR, allowing high CGR at critical crop stages. As a result, more dry matter was partitioned to grain and also an increased number of ears per plant were generated. Conversely, yields of soybeans in the strips were 2 to 11% lower than that in the monocultures, with variable significance depending on soybean cultivar and/or year. Grain number per unit area was the yield component most closely associated to yield variation in both crops. We believe that if yield components of this system are more closely identified, more appropriate genotypes will fit into strip intercropping, thus contributing to the spread of this technique and thus to the sustainability of actual massive monocultured agricultural systems.

  5. Hormone assay

    International Nuclear Information System (INIS)

    Eisentraut, A.M.

    1977-01-01

    An improved radioimmunoassay is described for measuring total triiodothyronine or total thyroxine levels in a sample of serum containing free endogenous thyroid hormone and endogenous thyroid hormone bound to thyroid hormone binding protein. The thyroid hormone is released from the protein by adding hydrochloric acid to the serum. The pH of the separated thyroid hormone and thyroid hormone binding protein is raised in the absence of a blocking agent without interference from the endogenous protein. 125 I-labelled thyroid hormone and thyroid hormone antibodies are added to the mixture, allowing the labelled and unlabelled thyroid hormone and the thyroid hormone antibody to bind competitively. This results in free thyroid hormone being separated from antibody bound thyroid hormone and thus the unknown quantity of thyroid hormone may be determined. A thyroid hormone test assay kit is described for this radioimmunoassay. It provides a 'single tube' assay which does not require blocking agents for endogenous protein interference nor an external solid phase sorption step for the separation of bound and free hormone after the competitive binding step; it also requires a minimum number of manipulative steps. Examples of the assay are given to illustrate the reproducibility, linearity and specificity of the assay. (UK)

  6. A video strip chart program

    International Nuclear Information System (INIS)

    Jones, N.L.

    1994-01-01

    A strip chart recorder has been utilized for trend analysis of the Oak Ridge National Laboratory EN tandem since 1987. At the EN, the author could not afford the nice eight channel thermal pen recorder that was used at the 25 URC. He had to suffice with two channel fiber tip or capillary pen type recorders retrieved from salvage and maintained with parts from other salvaged recorders. After cycling through several machines that eventually became completely unserviceable, a search for a new thermal recorder was begun. As much as he hates to write computer code, he decided to try his hand at getting an old data acquisition unit, that had been retrieved several years ago from salvage, to meet his needs. A BASIC language compiler was used because time was not available to learn a more advanced language. While attempting to increase acquisition and scroll speed on the 6 MHz 80286 that the code was first developed on, it became apparent that scrolling only the first small portion of the screen at high speed and then averaging that region and histogramming the average provided both the speed necessary for capturing fairly short duration events, and a trend record without use of back scrolling and disk storage routines. This turned out to be quite sufficient

  7. The Panda Strip Asic: Pasta

    Science.gov (United States)

    Lai, A.

    2018-01-01

    PASTA is the 64 channel front-end chip, designed in a 110 nm CMOS technology to read out the strip sensors of the Micro Vertex Detector (MVD) of the PANDA experiment. This chip provides high resolution timestamp and deposited charge information by means of the time-over-threshold technique. Its working principle is based on a predecessor, the TOFPET ASIC, that was designed for medical applications. A general restructuring of the architecture was needed, in order to meet the specific requirements imposed by the physics programme of PANDA, especially in terms of radiation tolerance, spatial constraints, and readout in absence of a first level hardware trigger. The first revision of PASTA is currently under evaluation at the Forschungszentrum Jülich, where a data acquisition system dedicated to the MVD prototypes has been developed. This paper describes the main aspect of the chip design, gives an overview of the data acquisition system used for the verification, and shows the first results regarding the performance of PASTA.

  8. Dynamic underground stripping demonstration project

    International Nuclear Information System (INIS)

    Newmark, R.L.

    1992-04-01

    LLNL is collaborating with the UC Berkeley College of Engineering to develop and demonstrate a system of thermal remediation techniques for rapid cleanup of localized underground spills. Called dynamic stripping to reflect the rapid and controllable nature of the process, it will combine steam injection, direct electrical heating, and tomographic geophysical imaging in a cleanup of the LLNL gasoline spill. In the first eight months of the project, a Clean Site engineering test was conducted to prove the field application of the techniques. Tests then began on the contaminated site in FY 1992. This report describes the work at the Clean Site, including design and performance criteria, test results, interpretations, and conclusions. We fielded 'a wide range of new designs and techniques, some successful and some not. In this document, we focus on results and performance, lessons learned, and design and operational changes recommended for work at the contaminated site. Each section focuses on a different aspect of the work and can be considered a self-contained contribution

  9. Specificity of the Linear Array HPV Genotyping Test for detecting human papillomavirus genotype 52 (HPV-52)

    OpenAIRE

    Kocjan, Boštjan; Poljak, Mario; Oštrbenk, Anja

    2015-01-01

    Introduction: HPV-52 is one of the most frequent human papillomavirus (HPV) genotypes causing significant cervical pathology. The most widely used HPV genotyping assay, the Roche Linear Array HPV Genotyping Test (Linear Array), is unable to identify HPV- 52 status in samples containing HPV-33, HPV-35, and/or HPV-58. Methods: Linear Array HPV-52 analytical specificity was established by testing 100 specimens reactive with the Linear Array HPV- 33/35/52/58 cross-reactive probe, but not with the...

  10. Prevalences, Genotypes, and Risk Factors for HIV Transmission in South America

    National Research Council Canada - National Science Library

    Montano, Silvia M; Sanchez, Jose L; Laguna-Torres, Alberto; Cuchi, Paloma; Avila, Maria M; Weissenbacher, Mercedes; Serra, Margarita; Russi, Jose Vinoles ;Jose C; Aguayo, Nicolas

    2005-01-01

    .... Enzyme-linked immunosorbent assay screening and Western blot confirmatory testing were performed, and env heteroduplex mobility assay genotyping and DNA sequencing were performed on a subset of HIV-positive subjects...

  11. Prevention of Stripping under Chip Seals

    Science.gov (United States)

    2017-10-01

    Eighteen chip-sealed roadways in eight cities and counties in Minnesota were evaluated both in the field (for condition surveys and density tests) and in the laboratory (for permeability, stripping, tensile-strength ratio, asphalt film thickness, and...

  12. Buffer Strips for Riparian Zone Management

    National Research Council Canada - National Science Library

    1991-01-01

    This study provides a review of technical literature concerning the width of riparian buffer strips needed to protect water quality and maintain other important values provided by riparian ecosystem...

  13. Temperature Profile of the Duracell Test Strip.

    Science.gov (United States)

    Viiri, Jouni; Kettunen, Lasse

    1996-01-01

    Presents the temperature profile of the Duracell Test Strip obtained using a Inframetrics 740 thermal imaging radiometer and ThermaGRAM95 software and compares this to the theoretical profile derived by Clark and Bonicamp. (JRH)

  14. Deuteron stripping reactions using dirac phenomenology

    Science.gov (United States)

    Hawk, E. A.; McNeil, J. A.

    2001-04-01

    In this work deuteron stripping reactions are studied using the distorted wave born approximation employing dirac phenomenological potentials. In 1982 Shepard and Rost performed zero-range dirac phenomenological stripping calculations and found a dramatic reduction in the predicted cross sections when compared with similar nonrelativistic calculations. We extend the earlier work by including full finite range effects as well as the deuteron's internal D-state. Results will be compared with traditional nonrelativistic approaches and experimental data at low energy.

  15. The charge collection in silicon strip detectors

    International Nuclear Information System (INIS)

    Boehringer, T.; Hubbeling, L.; Weilhammer, P.; Kemmer, J.; Koetz, U.; Riebesell, M.; Belau, E.; Klanner, R.; Lutz, G.; Neugebauer, E.; Seebrunner, H.J.; Wylie, A.

    1983-02-01

    The charge collection in silicon detectors has been studied, by measuring the response to high-energy particles of a 20μm pitch strip detector as a function of applied voltage and magnetic field. The results are well described by a simple model. The model is used to predict the spatial resolution of silicon strip detectors and to propose a detector with optimized spatial resolution. (orig.)

  16. Properties isotropy of magnesium alloy strip workpieces

    OpenAIRE

    Р. Кавалла; В. Ю. Бажин

    2016-01-01

    The paper discusses the issue of obtaining high quality cast workpieces of magnesium alloys produced by strip roll-casting. Producing strips of magnesium alloys by combining the processes of casting and rolling when liquid melt is fed continuously to fast rolls is quite promising and economic. In the process of sheet stamping considerable losses of metal occur on festoons formed due to anisotropy of properties of foil workpiece, as defined by the macro- and microstructure and modes of rolling...

  17. 33 CFR 157.128 - Stripping system.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 2 2010-07-01 2010-07-01 false Stripping system. 157.128 Section... Crude Oil Washing (COW) System on Tank Vessels Design, Equipment, and Installation § 157.128 Stripping system. (a) Each tank vessel having a COW system under § 157.10(e), § 157.10a(a)(2), or § 157.10c(b)(2...

  18. Quantitative comparison of 3 enamel-stripping devices in vitro: how precisely can we strip teeth?

    Science.gov (United States)

    Johner, Alexander Marc; Pandis, Nikolaos; Dudic, Alexander; Kiliaridis, Stavros

    2013-04-01

    In this in-vitro study, we aimed to investigate the predictability of the expected amount of stripping using 3 common stripping devices on premolars. One hundred eighty extracted premolars were mounted and aligned in silicone. Tooth mobility was tested with Periotest (Medizintechnik Gulden, Modautal, Germany) (8.3 ± 2.8 units). The selected methods for interproximal enamel reduction were hand-pulled strips (Horico, Hapf Ringleb & Company, Berlin, Germany), oscillating segmental disks (O-drive-OD 30; KaVo Dental, Biberach, Germany), and motor-driven abrasive strips (Orthofile; SDC Switzerland, Lugano-Grancia, Switzerland). With each device, the operator intended to strip 0.1, 0.2, 0.3, or 0.4 mm on the mesial side of 15 teeth. The teeth were scanned before and after stripping with a 3-dimensional laser scanner. Superposition and measurement of stripped enamel on the most mesial point of the tooth were conducted with Viewbox software (dHal Software, Kifissia, Greece). The Wilcoxon signed rank test and the Kruskal-Wallis test were applied; statistical significance was set at alpha ≤ 0.05. Large variations between the intended and the actual amounts of stripped enamel, and between stripping procedures, were observed. Significant differences were found at 0.1 mm of intended stripping (P ≤ 0.05) for the hand-pulled method and at 0.4 mm of intended stripping (P ≤ 0.001 to P = 0.05) for all methods. For all scenarios of enamel reduction, the actual amount of stripping was less than the predetermined and expected amount of stripping. The Kruskal-Wallis analysis showed no significant differences between the 3 methods. There were variations in the stripped amounts of enamel, and the stripping technique did not appear to be a significant predictor of the actual amount of enamel reduction. In most cases, actual stripping was less than the intended amount of enamel reduction. Copyright © 2013 American Association of Orthodontists. Published by Mosby, Inc. All rights

  19. [Hepatitis B virus genotypes and the response to lamivudine therapy].

    Science.gov (United States)

    Zalewska, Małgorzata; Domagała, Małgorzata; Simon, Krzysztof; Gładysz, Andrzej

    2005-12-01

    Hepatitis B virus (HBV) can be classified into eight major genotypes (A-H) that have mainly a geographic distribution. The HBV genotype may influence disease progression, HBeAg seroconversion rates, response to antiviral treatment. The aim of study was to analyze the distribution and frequency of genotypes in patients with chronic hepatitis B. Response to lamivudine 100 mg daily therapy was examined in respect to genotype. Sixty six patients (45 (68,2%) male, 21 (31,8%) female) with chronic hepatits B were enrolled. HBV genotypes were assigned before treatment with INNO-LiPA HBV Genotyping, Innogenetics, N. V., Ghent assay, which is a line probe test based on the reverse hybridization principle. In baseline and after 12 months of treatment serological markers of HBV infection, alanine aminotransferase (ALT) activities and HBV DNA serum levels were tested. Patients with chronic hepatitis B were infected predominantly with genotype A. HBV genotype distribution was: 78,8% for genotype A, 13,6% for genotype D, 1,5% for mixed infection with genotypes A and D. Distribution of genotypes A and D was asymmetrically regardless of sex, HBeAg status, ALT and HBV DNA levels. Four (6,1%) specimens had indeterminate A results by LiPA. There were no significant differences between patients with genotypes A and D regarding age and sex. There were also no significant differences between these two groups regarding rates of HBeAg and anti-HBe positivity, ALT activity and viral load. Twenty months of lamivudine (100 mg daily) therapy resulted in significant decreases in serum HBV DNA and ALT activities in patients with genotype A as well as with genotype D. After 12 months of treatment there were no statistical differences in HBeAg seroconversion rates, ALT activities, viral loads, frequency of HBeAg and anti-HBe between genotypes A and D.

  20. Immune chromatography: a quantitative radioimmunological assay

    International Nuclear Information System (INIS)

    Davis, J.W.; Demetriades, M.; Bowen, J.M.

    1984-01-01

    Immune chromatography, a radioimmunological binding assay, employs paper chromatography to separate immune complexes from free antigen and antibodies. During chromatography free antigen and antibodies become distributed throughout the paper, while immune complexes remain near the bottoms of the strips. The chromatographic differences can be made quantitative by using either iodinated antigens or antibodies. Under these conditions nanogram quantities of antigen can be detected or antibodies in sera diluted several 1000-fold. The immune chromatography assay can also be performed as an indirect assay, since the paper strips are cut from nitrocellulose paper. In this case the immune components are absorbed by the paper during chromatography. Antigen is then detected with an iodinated second antibody. The indirect immune chromatography assay is particularly useful for identifying different sera that react with the same antigen. Reaction with the first serum before chromatography reduces the amount of antigen available to the second serum following chromatography. In addition to characterizing the immune chromatography procedure, we discuss the possible applications of chromatography assays for the quantitation of other types of molecular binding interactions. (Auth.)

  1. Radioreceptor assays

    International Nuclear Information System (INIS)

    Lapka, R.

    1985-01-01

    Radioreceptor assay (RRA) is an analytical method using the specific interaction of some pharmaceuticals and endogenic substances (ligands) with specific receptors present in certin tissues of living organisms. RRA uses the principle of isotope dilution. The method is described in detail of the preparation of receptors, samples and radioligands, conditions of incubation, the separation of free and bound radioligand, and the mathematical evaluation of RRA. The sensitivity of RRA is measured in units to tens of pg. The specificity of RRA relates to a group of substances with similar pharmacological effect. RRA may be used for identifying neuroleptics, antidepressants, anxiolytics, ergot alkaloids, beta blockers, anticholinergic drugs, certain hormones and neuropeptides. (M.D.)

  2. Internal restriction sites: quality assurance aids in genotyping.

    Science.gov (United States)

    O'Rourke, Brendon A; Dennis, Julie A; Healy, Peter J

    2006-03-01

    Improvements to restriction fragment length polymorphism (RFLP)-based genotyping assays currently used for detection of mutations responsible for bovine ferrochelatase and myophosphorylase deficiencies, and equine hyperkalemic periodic paralysis (HYPP) are described. Reports of sporadic inhibition of restriction enzyme activity suggest a critical factor in RFLP-based genotyping assays should be assurance that restriction enzymes perform to specification with every sample. The RFLP genotyping assays that use either a mismatched recognition sequence in one or both of the oligonucleotides, or incorporate a second native site within the PCR amplicon, provide the mechanism by which efficiency of restriction enzymes can be assessed with every sample. The outcome is confirmation of the activity of the discriminating enzyme regardless of genotype.

  3. Establishment of Multiplex Solid-Phase Strip PCR Test for Detection of 24 Ocular Infectious Disease Pathogens.

    Science.gov (United States)

    Nakano, Satoko; Sugita, Sunao; Tomaru, Yasuhiro; Hono, Ayumi; Nakamuro, Takako; Kubota, Toshiaki; Takase, Hiroshi; Mochizuki, Manabu; Takahashi, Masayo; Shimizu, Norio

    2017-03-01

    To establish and evaluate a new multiplex solid-phase strip polymerase chain reaction (strip PCR) for concurrent detection of common ocular infectious disease pathogens. A new multiplex strip PCR was established to detect 24 common ocular infectious disease pathogens: herpes simplex virus (HSV) 1, HSV2, varicella-zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), human herpes virus (HHV) 6, HHV7, HHV8, human T-cell lymphotropic virus (HTLV)-1, adenovirus, Mycobacterium tuberculosis, Treponema pallidum, Propionibacterium acnes (P. acnes), bacterial 16S ribosomal RNA (rRNA), Candida species (Candida sp.), C. glabrata, C. krusei, Aspergillus, Fusarium, fungal 28S rRNA, Toxoplasma (T. gondii), Toxocara, Chlamydia trachomatis (C. trachomatis), and Acanthamoeba. Strip PCR was tested with a negative control (distilled water) and standard positive control DNA. Cutoffs of quantification cycle (Cq) values were determined with noninfectious ocular samples to avoid false-positives caused by contamination with P. acnes, bacterial 16S, and fungal 28S from reagents and ocular surfaces. A pilot study to evaluate the strip PCR was performed using infectious ocular samples (aqueous humor, vitreous, cornea, and tears) by strip PCR and previously developed capillary-type multiplex PCR and quantitative real-time PCR (qPCR). Strip PCR was verified with negative and positive controls. Strip PCR rapidly detected HSV1, HSV2, VZV, EBV, CMV, HHV6, HHV7, HTLV-1, adenovirus, P. acnes, bacterial 16S, Candida sp., C. glabrata, Aspergillus, fungal 28S, T. gondii, C. trachomatis, and Acanthamoeba in patient samples. The sensitivity was comparable to that of qPCR. Our novel strip PCR assay is a simple, rapid, and high-sensitivity method for detecting ocular infectious disease pathogens.

  4. Development of floating strip micromegas detectors

    Energy Technology Data Exchange (ETDEWEB)

    Bortfeldt, Jonathan

    2014-04-28

    Micromegas are high-rate capable, high-resolution micro-pattern gaseous detectors. Square meter sized resistive strip Micromegas are foreseen as replacement of the currently used precision tracking detectors in the Small Wheel, which is part of the forward region of the ATLAS muon spectrometer. The replacement is necessary to ensure tracking and triggering performance of the muon spectrometer after the luminosity increase of the Large Hadron Collider beyond its design value of 10{sup 34} cm{sup -2}s{sup -1} around 2020. In this thesis a novel discharge tolerant floating strip Micromegas detector is presented and described. By individually powering copper anode strips, the effects of a discharge are confined to a small region of the detector. This reduces the impact of discharges on the efficiency by three orders of magnitude, compared to a standard Micromegas. The physics of the detector is studied and discussed in detail. Several detectors are developed: A 6.4 x 6.4 cm{sup 2} floating strip Micromegas with exchangeable SMD capacitors and resistors allows for an optimization of the floating strip principle. The discharge behavior is investigated on this device in depth. The microscopic structure of discharges is quantitatively explained by a detailed detector simulation. A 48 x 50 cm{sup 2} floating strip Micromegas is studied in high energy pion beams. Its homogeneity with respect to pulse height, efficiency and spatial resolution is investigated. The good performance in high-rate background environments is demonstrated in cosmic muon tracking measurements with a 6.4 x 6.4 cm{sup 2} floating strip Micromegas under lateral irradiation with 550 kHz 20 MeV proton beams. A floating strip Micromegas doublet with low material budget is developed for ion tracking without limitations from multiple scattering in imaging applications during medical ion therapy. Highly efficient tracking of 20 MeV protons at particle rates of 550 kHz is possible. The reconstruction of the

  5. Genotyping common FSHR polymorphisms based on competitive amplification of differentially melting amplicons (CADMA)

    DEFF Research Database (Denmark)

    Borgbo, Tanni; Sommer Kristensen, Lasse; Lindgren, Ida

    2014-01-01

    gene: rs6165 (c.919A > G, p. Thr307Ala, FSHR 307) and rs6166 (c.2039A > G, p. Asn680Ser, FSHR 680). To evaluate the reliability of the new CADMA-based assays, the genotyping results were compared with two conventional PCR based genotyping methods; allele-specific PCR (AS-PCR) and Sanger sequencing......-based genotyping results. Comparing the CADMA-based assays to (AS-PCR) and Sanger sequencing, the CADMA based assays showed an improved analytical sensitivity and a wider applicability. CONCLUSIONS: The new assays provide a reliable, fast and user-friendly genotyping method facilitating a wider implication....... RESULTS: The genotype frequencies for both polymorphisms were 35 % (TT), 42 % (CT), and 23 % (CC), respectively. A 100 % accordance was observed between the CADMA-based genotyping results and sequencing results, whereas 5 discrepancies were observed between the AS-PCR results and the CADMA...

  6. Properties isotropy of magnesium alloy strip workpieces

    Directory of Open Access Journals (Sweden)

    Р. Кавалла

    2016-12-01

    Full Text Available The paper discusses the issue of obtaining high quality cast workpieces of magnesium alloys produced by strip roll-casting. Producing strips of magnesium alloys by combining the processes of casting and rolling when liquid melt is fed continuously to fast rolls is quite promising and economic. In the process of sheet stamping considerable losses of metal occur on festoons formed due to anisotropy of properties of foil workpiece, as defined by the macro- and microstructure and modes of rolling and annealing. The principal causes of anisotropic mechanical properties of metal strips produced by the combined casting and rolling technique are the character of distribution of intermetallic compounds in the strip, orientation of phases of metal defects and the residual tensions. One of the tasks in increasing the output of fit products during stamping operations consists in minimizing the amount of defects. To lower the level of anisotropy in mechanical properties various ways of treating the melt during casting are suggested. Designing the technology of producing strips of magnesium alloys opens a possibility of using them in automobile industry to manufacture light-weight body elements instead of those made of steel.

  7. Superconducting nano-strip particle detectors

    International Nuclear Information System (INIS)

    Cristiano, R; Ejrnaes, M; Casaburi, A; Zen, N; Ohkubo, M

    2015-01-01

    We review progress in the development and applications of superconducting nano-strip particle detectors. Particle detectors based on superconducting nano-strips stem from the parent devices developed for single photon detection (SSPD) and share with them ultra-fast response times (sub-nanosecond) and the ability to operate at a relatively high temperature (2–5 K) compared with other cryogenic detectors. SSPDs have been used in the detection of electrons, neutral and charged ions, and biological macromolecules; nevertheless, the development of superconducting nano-strip particle detectors has mainly been driven by their use in time-of-flight mass spectrometers (TOF-MSs) where the goal of 100% efficiency at large mass values can be achieved. Special emphasis will be given to this case, reporting on the great progress which has been achieved and which permits us to overcome the limitations of existing mass spectrometers represented by low detection efficiency at large masses and charge/mass ambiguity. Furthermore, such progress could represent a breakthrough in the field. In this review article we will introduce the device concept and detection principle, stressing the peculiarities of the nano-strip particle detector as well as its similarities with photon detectors. The development of parallel strip configuration is introduced and extensively discussed, since it has contributed to the significant progress of TOF-MS applications. (paper)

  8. Area specific stripping factors for AGS. A method for extracting stripping factors from survey data

    International Nuclear Information System (INIS)

    Aage, H.K.; Korsbech, U.

    2006-04-01

    In order to use Airborne Gamma-ray Spectrometry (AGS) for contamination mapping, for source search etc. one must to be able to eliminate the contribution to the spectra from natural radioactivity. This in general is done by a stripping technique. The parameters for performing a stripping have until recently been measured by recording gamma spectra at special calibration sites (pads). This may be cumbersome and the parameters may not be correct when used at low gamma energies for environmental spectra. During 2000-2001 DTU tested with success a new technique for Carborne Gamma-ray Spectrometry (CGS) where the spectra from the surveyed area (or from a similar area) were used for calculating the stripping parameters. It was possible to calculate usable stripping ratios for a number of low energy windows - and weak source signals not detectable by other means were discovered with the ASS technique. In this report it is shown that the ASS technique also works for AGS data, and it has been used for recent Danish AGS tests with point sources. (Check of calibration of AGS parameters.) By using the ASS technique with the Boden data (Barents Rescue) an exercise source was detected that has not been detected by any of the teams during the exercise. The ASS technique therefore seems to be better for search for radiation anomalies than any other method known presently. The experiences also tell that although the stripping can be performed correctly at any altitude there is a variation of the stripping parameters with altitude that has not yet been quite understood. However, even with the oddly variations the stripping worked as expected. It was also observed that one might calculate a single common set of usable stripping factors for all altitudes from the entire data set i.e. some average a, b and c values. When those stripping factors were used the stripping technique still worked well. (au)

  9. Area specific stripping factors for AGS. A method for extracting stripping factors from survey data

    Energy Technology Data Exchange (ETDEWEB)

    Aage, H.K.; Korsbech, U. [Technical Univ. of Denmark (Denmark)

    2006-04-15

    In order to use Airborne Gamma-ray Spectrometry (AGS) for contamination mapping, for source search etc. one must to be able to eliminate the contribution to the spectra from natural radioactivity. This in general is done by a stripping technique. The parameters for performing a stripping have until recently been measured by recording gamma spectra at special calibration sites (pads). This may be cumbersome and the parameters may not be correct when used at low gamma energies for environmental spectra. During 2000-2001 DTU tested with success a new technique for Carborne Gamma-ray Spectrometry (CGS) where the spectra from the surveyed area (or from a similar area) were used for calculating the stripping parameters. It was possible to calculate usable stripping ratios for a number of low energy windows - and weak source signals not detectable by other means were discovered with the ASS technique. In this report it is shown that the ASS technique also works for AGS data, and it has been used for recent Danish AGS tests with point sources. (Check of calibration of AGS parameters.) By using the ASS technique with the Boden data (Barents Rescue) an exercise source was detected that has not been detected by any of the teams during the exercise. The ASS technique therefore seems to be better for search for radiation anomalies than any other method known presently. The experiences also tell that although the stripping can be performed correctly at any altitude there is a variation of the stripping parameters with altitude that has not yet been quite understood. However, even with the oddly variations the stripping worked as expected. It was also observed that one might calculate a single common set of usable stripping factors for all altitudes from the entire data set i.e. some average a, b and c values. When those stripping factors were used the stripping technique still worked well. (au)

  10. Single-Use Sensor Strips for Reliable Field Analysis of Gunshot Residue

    Science.gov (United States)

    2013-10-13

    determined in a single GSR assay. Wearable textile -based printed electrodes were also examined towards a ’Lab-on-Sleeve’ forensic field analysis. New...Example of the different cyclic square-wave stripping voltammetric signals obtained with “swiping” samples at a bare SPCE electrode . Score plot of the...A) The Forensic Finger exhibiting the three electrode surface screen-printed onto a flexible nitrile finger cot (bottom left inset), as well as a

  11. Measurement of the enzymes lactate dehydrogenase and creatine kinase using reflectance spectroscopy and reagent strips.

    OpenAIRE

    Stevens, J F; Tsang, W; Newall, R G

    1983-01-01

    Two new methods for the assay of total activities of lactate dehydrogenase and creatine kinase are described, in which the enzyme activities are measured from a solid-state reagent strip during a kinetic reaction, the reaction being monitored in the ultra-violet region of the spectrum by reflectance spectroscopy. The performances of these methods are evaluated, and compared to conventional "wet" chemistry methods. The solid-phase reagent methods demonstrated precision and accuracy acceptable ...

  12. Comparison of two enzyme-linked immunosorbent assays and one rapid immunoblot assay for detection of herpes simplex virus type 2-specific antibodies in serum

    NARCIS (Netherlands)

    Groen, J; Van Dijk, G; Niesters, H G; Van Der Meijden, W I; Osterhaus, A D

    The sensitivities and specificities of three immunoassays for the detection of herpes simplex virus type 2 (HSV-2)-specific immunoglobulin G antibodies in serum, including the one-strip rapid immunoblot assay (RIBA; Chiron Corporation) and two indirect enzyme immunosorbent assays (EIA; Gull

  13. Genotype to phenotype

    National Research Council Canada - National Science Library

    Malcolm, Sue; Goodship, Timothy H. J

    2001-01-01

    ... Disorders Molecular Genetics of Hypertension Human Gene EvolutionAnalysis of Multifactorial Disease Transcription Factors Molecular Genetics of Cancer, Second edition Genotype to Phenotype, second e...

  14. Analysis of 'Coma strip' galaxy redshift catalog

    International Nuclear Information System (INIS)

    Klypin, A.A.; Karachentsev, I.D.; Lebedev, V.S.

    1990-01-01

    We present results of the analysis of a galaxy redshift catalog made at the 6-m telescope by Karachentsev and Kopylov (1990. Mon. Not. R. astr. Soc., 243, 390). The catalog covers a long narrow strip on the sky (10 arcmin by 63 0 ) and lists 283 galaxies up to limiting blue magnitude m B = 17.6. The strip goes through the core of Coma cluster and this is called the 'Coma strip' catalog. The catalog is almost two times deeper than the CfA redshift survey and creates the possibility of studying the galaxy distribution on scales of 100-250 Mpc. Due to the small number of galaxies in the catalog, we were able to estimate only very general and stable parameters of the distribution. (author)

  15. Colorimetric analysis of saliva–alcohol test strips by smartphone-based instruments using machine-learning algorithms

    Science.gov (United States)

    Strip lateral flow assays, similar to a home pregnancy test, are used widely in food safety applications to provide rapid and accurate tests for the presence of specific foodborne pathogens or other contaminants. Though these tests are very rapid, they are not very sensitive, are not quantitative, a...

  16. Enzyme-Based Test Strips for Visual or Photographic Detection and Quantitation of Gaseous Sulfur Mustard.

    Science.gov (United States)

    Bidmanova, Sarka; Steiner, Mark-Steven; Stepan, Martin; Vymazalova, Kamila; Gruber, Michael A; Duerkop, Axel; Damborsky, Jiri; Prokop, Zbynek; Wolfbeis, Otto S

    2016-06-07

    Sulfur mustard is a chemical agent of high military and terroristic significance. No effective antidote exists, and sulfur mustard can be fairly easily produced in large quantity. Rapid field testing of sulfur mustard is highly desirable. Existing analytical devices for its detection are available but can suffer from low selectivity, laborious sample preparation, and/or the need for complex instrumentation. We describe a new kind of test strip for rapid detection of gaseous sulfur mustard that is based on its degradation by the enzyme haloalkane dehalogenase that is accompanied by a change of local pH. This change can be detected using pH indicators contained in the strips whose color changes from blue-green to yellow within 10 min. In addition to visual read-out, we also demonstrate quantitative reflectometric readout by using a conventional digital camera based on red-green-blue data acquisition. Organic haloalkanes, such as 1,2-dichloroethane, have a negligible interfering effect. The visual limit of detection is 20 μg/L, and the one for red-green-blue read-out is as low as 3 μg/L. The assays have good reproducibility ±6% and ±2% for interday assays and intraday assays, respectively. The strips can be stored for at least 6 months without loss of function. They are disposable and can be produced fairly rapidly and at low costs. Hence, they represent a promising tool for in-field detection of sulfur mustard.

  17. Wokker. Notes on a Surrealist comic strip

    Directory of Open Access Journals (Sweden)

    Roger Sabin

    2012-05-01

    Full Text Available This essay explores the creation and development of a British comic strip, Wokker (1971-1999, and its connections with the surrealist movement. Although the strip is remarkable for its content and formalist properties, it remains obscure both because of its publishing circumstances, and because it does not fit easily into a history of comics. Rather it can be argued that its conceptual roots can be traced to the artistic ferment that happened in Paris in the 1920s (with Breton as a key reference point, and that it represents a very English, and late-flowering, example of the surrealist idea.

  18. slice of LEP beamtube with getter strip

    CERN Multimedia

    1989-01-01

    A section of the LEP beam pipe. This is the chamber in which LEP's counter-rotating electron and positron beams travel. It is made of lead-clad aluminium. The beams circulate in the oval cross-section part of the chamber. In the rectangular cross-section part, LEP's innovative getter-strip vacuum pump is installed. After heating to purify the surface of the getter, the strip acts like molecular sticky tape, trapping any stray molecules left behind after the accelerator's traditional vacuum pumps have done their job.

  19. Spray Rolling Aluminum Strip for Transportation Applications

    Energy Technology Data Exchange (ETDEWEB)

    Kevin M. McHugh; Y. Lin; Y. Zhou; E. J. Lavernia; J.-P. Delplanque; S. B. Johnson

    2005-02-01

    Spray rolling is a novel strip casting technology in which molten aluminum alloy is atomized and deposited into the roll gap of mill rolls to produce aluminum strip. A combined experimental/modeling approach has been followed in developing this technology with active participation from industry. The feasibility of this technology has been demonstrated at the laboratory scale and it is currently being scaled-up. This paper provides an overview of the process and compares the microstructure and properties of spray-rolled 2124 aluminum alloy with commercial ingot-processed material

  20. Silicon strip detectors for the LHCb experiment

    OpenAIRE

    Steinkamp, O

    2005-01-01

    The LHCb experiment is a single-arm magnetic spectrometer. Silicon micro-strip detectors are employed in a significant fraction of the tracking system. The Vertex Locator consists of 21 detector stations that operate inside the LHC beam pipe and are separated from the beam vacuum by a thin aluminium foil. The Silicon Tracker is a large-surface silicon micro-strip detector that covers the full acceptance of the experiment in a single tracking station upstream of the spectrometer magnet and the...

  1. CMS Silicon Strip Tracker Operation and Performance

    CERN Document Server

    Boudoul, Gaelle

    2011-01-01

    The Silicon Strip Tracker (SST) of the CMS experiment is, with 9.6 million readout channels, the largest strip tracker ever built. In order to correctly interpret and reconstruct the events recorded it needs to be precisely calibrated, thus ensuring that it fully contributes to the physics research program of the CMS experiment. In 2009 and 2010, the performance of the SST has been carefully studied using cosmic muons and tracks from proton-proton collisions at centre-of-mass energies of 900 GeV, 2.36 TeV and 7 TeV. In this paper, we present some results of the detector performance.

  2. Development of a colloidal gold immunochromatographic strip for rapid detection of Streptococcus agalactiae in tilapia.

    Science.gov (United States)

    Wen-de, Wu; Min, Li; Ming, Chen; Li-Ping, Li; Rui, Wang; Hai-Lan, Chen; Fu-Yan, Chen; Qiang, Mi; Wan-Wen, Liang; Han-Zhong, Chen

    2017-05-15

    A colloidal gold immunochromatographic strip was developed for rapid detection of Streptococcus agalactiae (S. agalactiae) infection in tilapia. The monoclonal antibodies (mAb) 4C12 and 3A9 were used to target S. agalactiae as colloidal gold-mAb conjugate and captured antibody, respectively. The colloidal gold immunochromatographic strip was assembled via routine procedures. Optimal pH and minimum antibody levels in the reaction system for gold colloidal-mAb 4C12 conjugation were pH 7.4 and 18μg/mL, respectively. Optimal concentrations of the captured antibody 3A9 and goat anti-mouse antibody were 0.6mg/mL and 2mg/mL, respectively. The sensitivity of the strip for detecting S. agalactiae was 1.5×10 5 colony forming units (CFU). No cross-reaction was observed with other commonly encountered bacteria, including Pseudomonas fluorescens, Aeromonas hydrophila, Vibrio anguillarum and Streptococcus iniae. The assay time for S. agalactiae was less than 15min. Tilapia samples artificially infected with S. agalactiae were tested using the newly developed strip. The results indicated that blood, brain, kidney, spleen, metanephros and intestine specimens of infected fish can be used for S. agalactiae detection. The validity of the strip was maintained for 6 months at 4°C. These findings suggested that the immunochromatographic strip was effective for spot and rapid detection of S. agalactiae infected tilapia. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. 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.

  4. (Cyamopsis tetragonoloba) genotypes

    Indian Academy of Sciences (India)

    Molecular assessment of genetic diversity in cluster bean. (Cyamopsis tetragonoloba) genotypes. Rakesh Pathak, S. K. Singh, Manjit Singh and A. Henry. J. Genet. 89, 243–246. Figure 1. RAPD profile of 1–16 Cyamopsis tetragonoloba genotypes amplified with arbitrary primer OPA-16. Figure 2. RAPD profile of 17–32 ...

  5. (Prunus armeniaca L.) genotypes

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... Table 2. Leaf stomatal frequency, stomata size and stomatal conductance of apricot genotypes. Stomatal conductance (mmol m-2 s-1). Apricot genotype. Stomata frequency. (number/mm2). Stomata size. (μm). 2006. 2007. Orange Red. 349.0 a. 71.6 abc. 192 a-d. 176 bc. Palstein. 311.7 ab. 76.6 abc.

  6. KRITIK SOSIAL DALAM KOMIK STRIP PAK BEI

    Directory of Open Access Journals (Sweden)

    Yudhi Novriansyah

    2016-08-01

    Full Text Available This research aimed to do interpret the marking which flange social criticism and know laboring ideology in story of Comic Strip Pak Bei. Research based on theory of structural semiotic according to Ferdinand De Saussure. Using analysis of Syntagmatic as first level of meaning to the text network and also picture, and analysis of Paradigmatic as second level of meaning or implicit meaning (connota-tion, myth, ideology Analysis done to six Comic choice edition of Strip Pak Bei period of November 2004 - Februari 2005 which tend to flange social criticism. At band of syntagmatic, result of research indicate that story theme lifted from social problems that happened in major society. The fact clear progressively when connected by Intertextual with information and texts which have preexisted. At band of Paradigmatic, social criticism tend to emerge dimly, is not transparent. Because of Comic Strip Pak Bei expand in the middle of Java cultural domination that developing myth of criticize as action menacing compatibility and orderliness of society. Story of Comic Strip Pak Bei also confirm dominant ideology in Java society culture, namely ideology of Patriarkhi and Feudalism which still go into effect until now. This prove ideology idea according to Louis Althusser which not again opposition between class, but have been owned and practiced by all social class.

  7. Trees for strip-mined lands

    Science.gov (United States)

    George Hart; William R. Byrnes

    1960-01-01

    Open-pit or strip mining has become an important method of mining bituminous coal in Pennsylvania. In 1958 some 19.5 million tons of soft coal - 29 percent of the total bituminous production in the State - were produced by this method.

  8. Asset Stripping in a Mature Market Economy

    DEFF Research Database (Denmark)

    Klarskov Jeppesen, Kim; Møller, Ulrik Gorm

    2011-01-01

    Purpose – The purpose of this paper is to document a Danish fraud scheme, in which a large number of limited companies were stripped of their assets leaving them with nothing but tax debt, eventually causing the Danish Tax and Customs Administration to lose large sums. Furthermore, the purpose is...... the social supervisory system of a mature market economy. Originality/value – The paper contributes to the knowledge about asset stripping by documenting and analysing the phenomenon in a mature market economy context.......Purpose – The purpose of this paper is to document a Danish fraud scheme, in which a large number of limited companies were stripped of their assets leaving them with nothing but tax debt, eventually causing the Danish Tax and Customs Administration to lose large sums. Furthermore, the purpose...... is to analyse why the asset-stripping schemes occurred in a mature market economy with a strong corporate governance system and a low level of corruption. Design/methodology/approach – The research is conducted as a longitudinal single case study based on documentary research. Findings – The Danish case...

  9. Linear sweep anodic stripping voltammetry: Determination of ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Chemical Sciences; Volume 127; Issue 6. Linear sweep anodic stripping voltammetry: Determination of Chromium (VI) using synthesized gold nanoparticles modified screen-printed electrode. Salamatu Aliyu Tukur Nor Azah Yusof Reza Hajian. Regular Articles Volume 127 Issue 6 June 2015 pp ...

  10. Comic Strips to Accompany Science Museum Exhibits

    Science.gov (United States)

    Chung, Beom Sun; Park, Eun-mi; Kim, Sang-Hee; Cho, Sook-kyoung; Chung, Min Suk

    2016-01-01

    Science museums make the effort to create exhibits with amusing explanations. However, existing explanation signs with lengthy text are not appealing, and as such, visitors do not pay attention to them. In contrast, conspicuous comic strips composed of simple drawings and humors can attract science museum visitors. This study attempted to reveal…

  11. Nanoscale Test Strips for Multiplexed Blood Analysis

    Science.gov (United States)

    Chan, Eugene

    2015-01-01

    A critical component of the DNA Medicine Institute's Reusable Handheld Electrolyte and Lab Technology for Humans (rHEALTH) sensor are nanoscale test strips, or nanostrips, that enable multiplexed blood analysis. Nanostrips are conceptually similar to the standard urinalysis test strip, but the strips are shrunk down a billionfold to the microscale. Each nanostrip can have several sensor pads that fluoresce in response to different targets in a sample. The strips carry identification tags that permit differentiation of a specific panel from hundreds of other nanostrip panels during a single measurement session. In Phase I of the project, the company fabricated, tested, and demonstrated functional parathyroid hormone and vitamin D nanostrips for bone metabolism, and thrombin aptamer and immunoglobulin G antibody nanostrips. In Phase II, numerous nanostrips were developed to address key space flight-based medical needs: assessment of bone metabolism, immune response, cardiac status, liver metabolism, and lipid profiles. This unique approach holds genuine promise for space-based portable biodiagnostics and for point-of-care (POC) health monitoring and diagnostics here on Earth.

  12. Ductility of reinforced concrete columns confined with stapled strips

    International Nuclear Information System (INIS)

    Tahir, M.F.; Khan, Q.U.Z.; Shabbir, F.; Sharif, M.B.; Ijaz, N.

    2015-01-01

    Response of three 150x150x450mm short reinforced concrete (RC) columns confined with different types of confining steel was investigated. Standard stirrups, strips and stapled strips, each having same cross-sectional area, were employed as confining steel around four comer column bars. Experimental work was aimed at probing into the affect of stapled strip confinement on post elastic behavior and ductility level under cyclic axial load. Ductility ratios, strength enhancement factor and core concrete strengths were compared to study the affect of confinement. Results indicate that strength enhancement in RC columns due to strip and stapled strip confinement was not remarkable as compared to stirrup confined column. It was found that as compared to stirrup confined column, stapled strip confinement enhanced the ductility of RC column by 183% and observed axial capacity of stapled strip confined columns was 41 % higher than the strip confined columns. (author)

  13. Laboratory testing of Alcoscan saliva-alcohol test strips

    Science.gov (United States)

    1986-10-01

    This report describes a laboratory evaluation of Alcoscan saliva-alcohol test strips. The objectives of this work were: (1) to determine the precision and accuracy of the Alcoscan strips; and (2) to determine what effect extreme ambient temperatures ...

  14. Imaging of Low Compressibility Strips in the Quantum Hall Liquid

    OpenAIRE

    Finkelstein, G.; Glicofridis, P. I.; Tessmer, S. H.; Ashoori, R. C.; Melloch, M. R.

    1999-01-01

    Using Subsurface Charge Accumulation scanning microscopy we image strips of low compressibility corresponding to several integer Quantum Hall filling factors. We study in detail the strips at Landau level filling factors $\

  15. Dual Strip-Excited Dielectric Resonator Antenna with Parasitic Strips for Radiation Pattern Reconfigurability

    Directory of Open Access Journals (Sweden)

    M. Kamran Saleem

    2014-01-01

    Full Text Available A novel pattern reconfigurable antenna concept utilizing rectangular dielectric resonator antenna (DRA placed over dielectric substrate backed by a ground plane is presented. A dual strip excitation scheme is utilized and both excitation strips are connected together by means of a 50 Ω microstrip feed network placed over the substrate. The four vertical metallic parasitic strips are placed at corner of DRA each having a corresponding ground pad to provide a short/open circuit between the parasitic strip and antenna ground plane, through which a shift of 90° in antenna radiation pattern in elevation plane is achieved. A fractional bandwidth of approximately 40% at center frequency of 1.6 GHz is achieved. The DRA peak realized gain in whole frequency band of operation is found to be above 4 dB. The antenna configuration along with simulation and measured results are presented.

  16. Parallel superconducting strip-line detectors: reset behaviour in the single-strip switch regime

    International Nuclear Information System (INIS)

    Casaburi, A; Heath, R M; Tanner, M G; Hadfield, R H; Cristiano, R; Ejrnaes, M; Nappi, C

    2014-01-01

    Superconducting strip-line detectors (SSLDs) are an important emerging technology for the detection of single molecules in time-of-flight mass spectrometry (TOF-MS). We present an experimental investigation of a SSLD laid out in a parallel configuration, designed to address selected single strip-lines operating in the single-strip switch regime. Fast laser pulses were tightly focused onto the device, allowing controllable nucleation of a resistive region at a specific location and study of the subsequent device response dynamics. We observed that in this regime, although the strip-line returns to the superconducting state after triggering, no effective recovery of the bias current occurs, in qualitative agreement with a phenomenological circuit simulation that we performed. Moreover, from theoretical considerations and by looking at the experimental pulse amplitude distribution histogram, we have the first confirmation of the fact that the phenomenological London model governs the current redistribution in these large area devices also after detection events. (paper)

  17. Parallel superconducting strip-line detectors: reset behaviour in the single-strip switch regime

    Science.gov (United States)

    Casaburi, A.; Heath, R. M.; Tanner, M. G.; Cristiano, R.; Ejrnaes, M.; Nappi, C.; Hadfield, R. H.

    2014-04-01

    Superconducting strip-line detectors (SSLDs) are an important emerging technology for the detection of single molecules in time-of-flight mass spectrometry (TOF-MS). We present an experimental investigation of a SSLD laid out in a parallel configuration, designed to address selected single strip-lines operating in the single-strip switch regime. Fast laser pulses were tightly focused onto the device, allowing controllable nucleation of a resistive region at a specific location and study of the subsequent device response dynamics. We observed that in this regime, although the strip-line returns to the superconducting state after triggering, no effective recovery of the bias current occurs, in qualitative agreement with a phenomenological circuit simulation that we performed. Moreover, from theoretical considerations and by looking at the experimental pulse amplitude distribution histogram, we have the first confirmation of the fact that the phenomenological London model governs the current redistribution in these large area devices also after detection events.

  18. Electrical results of double-sided silicon strip modules for the ATLAS Upgrade Strip Tracker

    CERN Document Server

    Gonzalez-Sevilla, S; The ATLAS collaboration; Cadoux, F; Clark, A; Ferrere, D; Ikegami, Y; Hara, K; La Marra, D; Pelleriti, G; Pohl, M; Takubo, Y; Terada, S; Unno, Y; Weber, M

    2012-01-01

    A double-sided silicon strip module has been designed for the short-strip barrel region of the future ATLAS inner tracker for the High Luminosity LHC. University of Geneva and KEK have produced first module prototypes with common components and similar assembly procedures and jigs. This note reports on the electrical performance of the modules tested. The data acquisition system is described. Results from individual and combined module readout are shown.

  19. Development of colloidal gold immunochromatographic strips for detection of Riemerella anatipestifer.

    Directory of Open Access Journals (Sweden)

    Wanwan Hou

    Full Text Available Riemerella anatipestifer is one of the most important bacterial pathogen of ducks and causes a contagious septicemia. R. anatipestifer infection causes serositis syndromes similar to other bacterial infections in ducks, including infection by Escherichia coli, Salmonella enterica and Pasteurella multocida. Clinically differentiating R. anatipestifer infections from other bacterial pathogen infections is usually difficult. In this study, MAb 1G2F10, a monoclonal antibody against R. anatipestifer GroEL, was used to develop a colloidal gold immunochromatographic strip. Colloidal gold particles were prepared by chemical synthesis to an average diameter of 20 ± 5.26 nm by transmission electron microscope imaging. MAb 1G2F10 was conjugated to colloidal gold particles and the formation of antibody-colloidal gold conjugates was monitored by UV/Vis spectroscopy. Immunochromatographic strips were assembled in regular sequence through different accessories sticked on PVC plate. Strips specifically detected R. anatipestifer within 10 min, but did not detect E. coli, S. enterica and P. multocida. The detection limit for R. anatipestifer was 1 × 10(6 colony forming units, which was 500 times higher than a conventional agglutination test. Accuracy was 100% match to multiplex PCR. Assay stability and reproducibility were excellent after storage at 4°C for 6 months. The immunochromatographic strips prepared in this study offer a specific, sensitive, and rapid detection method for R. anatipestifer, which is of great importance for the prevention and control of R. anatipestifer infections.

  20. Testbeam evaluation of silicon strip modules for ATLAS Phase - II Strip Tracker Upgrade

    CERN Document Server

    Blue, Andrew; The ATLAS collaboration; Ai, Xiaocong; Allport, Phillip; Arling, Jan-Hendrik; Atkin, Ryan Justin; Bruni, Lucrezia Stella; Carli, Ina; Casse, Gianluigi; Chen, Liejian; Chisholm, Andrew; Cormier, Kyle James Read; Cunningham, William Reilly; Dervan, Paul; Diez Cornell, Sergio; Dolezal, Zdenek; Dopke, Jens; Dreyer, Etienne; Dreyling-Eschweiler, Jan Linus Roderik; Escobar, Carlos; Fabiani, Veronica; Fadeyev, Vitaliy; Fernandez Tejero, Javier; Fleta Corral, Maria Celeste; Gallop, Bruce; Garcia-Argos, Carlos; Greenall, Ashley; Gregor, Ingrid-Maria; Greig, Graham George; Guescini, Francesco; Hara, Kazuhiko; Hauser, Marc Manuel; Huang, Yanping; Hunter, Robert Francis Holub; Keller, John; Klein, Christoph; Kodys, Peter; Koffas, Thomas; Kotek, Zdenek; Kroll, Jiri; Kuehn, Susanne; Lee, Steven Juhyung; Liu, Yi; Lohwasser, Kristin; Meszarosova, Lucia; Mikestikova, Marcela; Mi\\~nano Moya, Mercedes; Mori, Riccardo; Moser, Brian; Nikolopoulos, Konstantinos; Peschke, Richard; Pezzullo, Giuseppe; Phillips, Peter William; Poley, Anne-luise; Queitsch-Maitland, Michaela; Ravotti, Federico; Rodriguez Rodriguez, Daniel

    2018-01-01

    The planned HL-LHC (High Luminosity LHC) is being designed to maximise the physics potential of the LHC with 10 years of operation at instantaneous luminosities of \\mbox{$7.5\\times10^{34}\\;\\mathrm{cm}^{-2}\\mathrm{s}^{-1}$}. A consequence of this increased luminosity is the expected radiation damage requiring the tracking detectors to withstand hadron equivalences to over $1x10^{15}$ 1 MeV neutron equivalent per $cm^{2}$ in the ATLAS Strips system. The silicon strip tracker exploits the concept of modularity. Fast readout electronics, deploying 130nm CMOS front-end electronics are glued on top of a silicon sensor to make a module. The radiation hard n-in-p micro-strip sensors used have been developed by the ATLAS ITk Strip Sensor collaboration and produced by Hamamatsu Photonics. A series of tests were performed at the DESY-II test beam facility to investigate the detailed performance of a strip module with both 2.5cm and 5cm length strips before irradiation. The DURANTA telescope was used to obtain a pointing...

  1. Conveyorized Photoresist Stripping Replacement for Flex Circuit Fabrication

    Energy Technology Data Exchange (ETDEWEB)

    Megan Donahue

    2009-02-24

    A replacement conveyorized photoresist stripping system was characterized to replace the ASI photoresist stripping system. This system uses the qualified ADF-25c chemistry for the fabrication of flex circuits, while the ASI uses the qualified potassium hydroxide chemistry. The stripping process removes photoresist, which is used to protect the copper traces being formed during the etch process.

  2. 7 CFR 29.6128 - Straight Stripped (X Group).

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Straight Stripped (X Group). 29.6128 Section 29.6128... REGULATIONS TOBACCO INSPECTION Standards Grades § 29.6128 Straight Stripped (X Group). This group consists of..., and tolerances X1 Fine Quality Straight Stripped. Heavy, ripe, firm, semielastic, normal strength and...

  3. 21 CFR 880.2200 - Liquid crystal forehead temperature strip.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Liquid crystal forehead temperature strip. 880... Personal Use Monitoring Devices § 880.2200 Liquid crystal forehead temperature strip. (a) Identification. A liquid crystal forehead temperature strip is a device applied to the forehead that is used to indicate...

  4. Evaluation of two rapid immunochromatographic assays for diagnosis of dengue among Vietnamese febrile patients

    NARCIS (Netherlands)

    Nga, Tran Thi Thanh; Thai, Khoa T. D.; Phuong, Hoang Lan; Giao, Phan Trong; Hung, Le Quoc; Binh, Tran Quang; Mai, Vo Thi Chi; van Nam, Nguyen; de Vries, Peter J.

    2007-01-01

    Results from two dengue rapid tests, the PanBio Duo cassette and the SD Bioline strip test, were compared to those of enzyme-linked immunosorbent assays (Focus Diagnostics) from sera of 200 Vietnamese febrile patients. The PanBio assay was superior, with sensitivity and specificity values for

  5. Clinical performance of the VERIS HCV assay for hepatitis C virus RNA quantification.

    Science.gov (United States)

    Izquierdo, Laure; Prégermain, Corinne; Hottelet, Corinne; Decombe, Gwenaëlle; Roque-Afonso, Anne-Marie

    2017-08-01

    Diagnosis of hepatitis C virus (HCV) infection and treatment monitoring rely on detection/quantification of HCV RNA and real-time polymerase chain reaction (PCR) techniques are expected to equivalently quantify the different HCV genotypes. The clinical performance of the VERIS HCV assay for HCV RNA quantification was compared to that of the Abbott RealTime HCV assay. Qualitative concordance and quantitative comparison were evaluated on a first panel of 286 clinical samples containing HCV genotypes 1-6. Forty additional genotype 4 samples were tested to explore genotype 4 HCV RNA underquantification. Qualitative discrepancies were observed for low viral loads (HCV RNA quantification by the VERIS HCV assay and the Abbott RealTime HCV assay was well correlated for all HCV genotypes, except genotype 4 where 5' UTR RNA folding may impact quantification. Nevertheless, this underestimation of HCV RNA levels had no impact on clinical use. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Bird community response to filter strips in Maryland

    Science.gov (United States)

    Blank, P.J.; Dively, G.P.; Gill, D.E.; Rewa, C.A.

    2011-01-01

    Filter strips are strips of herbaceous vegetation planted along agricultural field margins adjacent to streams or wetlands and are designed to intercept sediment, nutrients, and agrichemicals. Roughly 16,000 ha of filter strips have been established in Maryland through the United States Department of Agriculture's Conservation Reserve Enhancement Program. Filter strips often represent the only uncultivated herbaceous areas on farmland in Maryland and therefore may be important habitat for early-successional bird species. Most filter strips in Maryland are planted to either native warm-season grasses or cool-season grasses and range in width from 10.7 m to 91.4 m. From 2004 to 2007 we studied the breeding and wintering bird communities in filter strips adjacent to wooded edges and non-buffered field edges and the effect that grass type and width of filter strips had on bird community composition. We used 5 bird community metrics (total bird density, species richness, scrub-shrub bird density, grassland bird density, and total avian conservation value), species-specific densities, nest densities, and nest survival estimates to assess the habitat value of filter strips for birds. Breeding and wintering bird community metrics were greater in filter strips than in non-buffered field edges but did not differ between cool-season and warm-season grass filter strips. Most breeding bird community metrics were negatively related to the percent cover of orchardgrass (Dactylis glomerata) in ???1 yr. Breeding bird density was greater in narrow (60 m) filter strips. Our results suggest that narrow filter strips adjacent to wooded edges can provide habitat for many bird species but that wide filter strips provide better habitat for grassland birds, particularly obligate grassland species. If bird conservation is an objective, avoid planting orchardgrass in filter strips and reduce or eliminate orchardgrass from filter strips through management practices. Copyright ?? 2011 The

  7. APOE Genotyping, Cardiovascular Disease

    Science.gov (United States)

    ... it ordered? As a test to evaluate lipid metabolism or cardiovascular risk, APOE genotyping is ordered when someone has: Significantly elevated cholesterol and triglyceride levels that do not respond to dietary and ...

  8. Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

    Directory of Open Access Journals (Sweden)

    Joaquim Manoel da Silva

    Full Text Available High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

  9. Ammonia recovery from anaerobically digested cattle manure by steam stripping.

    Science.gov (United States)

    Zeng, L; Mangan, C; Li, X

    2006-01-01

    Ammonia recovery from anaerobically digested cattle manure effluents through steam stripping was studied at a stripping tower temperature of 98-99 degrees C and a steam-water ratio approximately 56-72 g/L. The digested manure effluents were first treated by microfiltration and then the permeate was used as feed in steam stripping. The stripping performance was evaluated under different feed pH values, ammonia concentrations and temperatures. The increase of the initial feed pH does not significantly improve ammonia stripping efficiency due to the fact that the stripped effluent pH is increased during steam stripping. This suggests that steam stripping of anaerobically digested manure effluents for ammonia recovery may not need pre-raised pH. In contrast, the pH value of the synthetic ammonia wastewater containing NH4Cl dramatically decreases after steam stripping. Increasing the feed temperature slightly improves ammonia stripping efficiency, but reduces the concentration of the recovered ammonia in the condensate due to an increased condensate volume at a higher feed temperature. Therefore, the feed temperature should be controlled at an optimum point that can compromise the condensate ammonia concentration and the ammonia stripping efficiency. Experimental results indicate that recovery of ammonia from anaerobically digested cattle manure effluents as NH4OH is technically feasible.

  10. Dual deflectable beam strip engine development.

    Science.gov (United States)

    Dulgeroff, C. R.; Zuccaro, D. E.; Kami, S.; Schnelker, D. E.; Ward, J. W.

    1972-01-01

    This paper describes a dual beam thruster that has been designed, constructed, and tested. The system is suitable for two-axes attitude control and is comprised of two orthogonal strips, each capable of producing 0.30 mlb thrust and beam deflections of more than plus or minus 20 deg. The nominal specific impulse for the thruster is 5000 sec, and the thrust level from each strip can be varied from 0 to 100%. Neutralizer filaments that were developed and life tested over 2000 hours producing more than 40 mA of electron emission per watt of input power are also discussed. The system power required for clean ionizers is approximately 200 W.

  11. Nuclear reactor spring strip grid spacer

    International Nuclear Information System (INIS)

    Patterson, J.F.; Flora, B.S.

    1980-01-01

    An improved and novel grid spacer was developed for use in nuclear reactor fuel assemblies. It is comprised of a series of intersecting support strips and a peripheral support band attached to the ends of the support strips. Each of the openings into which the fuel element is inserted has a number of protruding dimples and springs extending in different directions. The dimples coact with the springs to secure the fuel rods in the openings. Compared with previous designs, this design gives more positive alignment of the support stips while allowing greater flexibility to counterbalance the effects of thermal expansion. The springs are arranged in alternating directions so that the reaction forces tend to counterbalance each other, which in turn minimizes the reaction loads on the supporting structure. (D.N.)

  12. L-strip proximity fed ga

    Directory of Open Access Journals (Sweden)

    Ashish Singh

    2014-03-01

    Full Text Available In this article, the analysis of dualband L-strip fed compact semi-circular disk microstrip patch antenna has been presented using circuit theory concept. The antenna parameters such as return loss, VSWR and radiation pattern are calculated. The effect of geometric dimensions of the proposed antenna such as length of vertical and horizontal portion of L-strip is investigated. It is found that antenna resonate at two distinct modes i.e. 1.3 GHz and 6.13 GHz for lower and upper resonance frequencies respectively. The bandwidth of the proposed antenna at lower resonance frequency is 6.61% (simulated and 10.64% (theoretical whereas at upper resonance frequency, it is 6.02% (simulated and 9.06 % (theoretical. The theoretical results are compared with IE3D simulation results as well as experimental results and they are in close agreement.

  13. Strip-till seeder for sugar beets

    Directory of Open Access Journals (Sweden)

    Peter Schulze Lammers

    2014-06-01

    Full Text Available Strip-till save costs by reducing tillage on the area of sugar beet rows only. The seeding system is characterized by a deep loosening of soil with a tine combined with a share and by following tools generating fine-grained soil as seed bed. In cooperation with the Kverneland company group Soest/Germany a strip tiller combined with precision seeder was designed and tested in field experiments. Tilling and seeding was performed in one path on fields with straw and mustard mulch. Even the plant development was slower as compared to conventional sawn sugar beets the yield was on equivalent level. Further field experiments are planned to attest constant yield, cost and energy efficiency of the seeding system.

  14. Continuous liquid sheet generator for ion stripping

    International Nuclear Information System (INIS)

    Gavin, B.; Batson, P.; Leemann, B.; Rude, B.

    1984-10-01

    Many of the technical problems of generating a large thin liquid sheet from 0.02 to 0.20 μm thick (3 to 40 μgm/cm 2 ) have been solved. It is shown that this perennial sheet is stable and consonant in dimension. Several ion beam species from the SuperHILAC have been used for evaluation; at 0.11 MeV/n. In one of three modes this sheet serves as an equivalent substitute for a carbon foil. The second mode is characterized by a solid-like charge state distribution but with a varying fraction of unstripped ions. The third mode gives stripping performance akin to a vapor stripping medium. 9 references, 7 figures

  15. Strengthening Bridges with Prestressed CFRP Strips

    Science.gov (United States)

    Siwowski, Tomasz; Żółtowski, Piotr

    2012-06-01

    Limitation of bridge's carrying bearing capacity due to aging and deterioration is a common problem faced by road administration and drivers. Rehabilitation of bridges including strengthening may be applied in order to maintain or upgrade existing bridge parameters. The case studies of strengthening of two small bridges with high modulus prestressed CFRP strips have been presented in the paper. The first one - reinforced concrete slab bridge - and the other - composite steel-concrete girder bridge - have been successfully upgraded with quite new technology. In both cases the additional CFRP reinforcement let increasing of bridge carrying capacity from 15 till 40 metric tons. The CFRP strip prestressing system named Neoxe Prestressing System (NPS), developed by multi-disciplinary team and tested at full scale in Rzeszow University of Technology, has been also described in the paper.

  16. The extent of the stop coannihilation strip

    Energy Technology Data Exchange (ETDEWEB)

    Ellis, John [King' s College London, Theoretical Particle Physics and Cosmology Group, Department of Physics, London (United Kingdom); CERN, Theory Division, Geneva 23 (Switzerland); Olive, Keith A. [University of Minnesota, School of Physics and Astronomy, Minneapolis, MN (United States); University of Minnesota, William I. Fine Theoretical Physics Institute, School of Physics and Astronomy, Minneapolis, MN (United States); Zheng, Jiaming [University of Minnesota, School of Physics and Astronomy, Minneapolis, MN (United States)

    2014-07-15

    Many supersymmetric models such as the constrained minimal supersymmetric extension of the Standard Model (CMSSM) feature a strip in parameter space where the lightest neutralino χ is identified as the lightest supersymmetric particle, the lighter stop squark t{sub 1} is the next-to-lightest supersymmetric particle (NLSP), and the relic χ cold darkmatter density is brought into the range allowed by astrophysics and cosmology by coannihilation with the lighter stop squark t{sub 1} NLSP. We calculate the stop coannihilation strip in the CMSSM, incorporating Sommerfeld enhancement effects, and we explore the relevant phenomenological constraints and phenomenological signatures. In particular, we show that the t{sub 1} may weigh several TeV, and its lifetime may be in the nanosecond range, features that are more general than the specific CMSSM scenarios that we study in this paper. (orig.)

  17. Antenna with distributed strip and integrated electronic components

    Science.gov (United States)

    Rodenbeck, Christopher T [Albuquerque, NM; Payne, Jason A [Albuquerque, NM; Ottesen, Cory W [Albuquerque, NM

    2008-08-05

    An antenna comprises electrical conductors arranged to form a radiating element including a folded line configuration and a distributed strip configuration, where the radiating element can be in proximity to a ground conductor and/or arranged as a dipole. Embodiments of the antenna include conductor patterns formed on a printed wiring board, having a ground plane, spacedly adjacent to and coplanar with the radiating element. An antenna can comprise a distributed strip patterned on a printed wiring board, integrated with electronic components mounted on top of or below the distributed strip, and substantially within the extents of the distributed strip. Mounting of electronic components on top of or below the distributed strip has little effect on the performance of the antenna, and allows for realizing the combination of the antenna and integrated components in a compact form. An embodiment of the invention comprises an antenna including a distributed strip, integrated with a battery mounted on the distributed strip.

  18. Cathode readout with stripped resistive drift tubes

    International Nuclear Information System (INIS)

    Bychkov, V.N.; Kekelidze, G.D.; Novikov, E.A.; Peshekhonov, V.D.; Shafranov, M.D.; Zhiltsov, V.E.

    1995-01-01

    A straw tube drift chamber prototype has been constructed and tested. The straw tube material is mylar film covered with a carbon layer with a resistivity of 0.5, 30 and 70 kΩ/□. Both the anode wire and the cathode strip signals were detected to study the behaviour of the chamber in the presence of X-ray ionization. The construction and the results of the study are presented. (orig.)

  19. Neutralization of H- beams by magnetic stripping

    International Nuclear Information System (INIS)

    Jason, A.J.; Hudgings, D.W.; van Dyck, O.B.

    1981-01-01

    The stability of H - beams passing through strong magnetic fields has been relevant to accelerator transport problems and, recently, to neutral beam preparation techniques. The H - electron detachment rate was measured as a function of rest-frame electric field and provides parameters for a theoretical lifetime expression. The limitations imposed on H - transport by magnetic stripping, and neutral-beam preparation in emittance growth, magnetic fields, and beam energies are discussed. Application techniques are also briefly discussed

  20. Ram pressure stripping of tilted galaxies

    Czech Academy of Sciences Publication Activity Database

    Jáchym, Pavel; Köppen, J.; Palouš, Jan; Combes, F.

    2009-01-01

    Roč. 500, č. 2 (2009), s. 693-703 ISSN 0004-6361 R&D Projects: GA MŠk(CZ) LC06014; GA ČR GP205/08/P556 Institutional research plan: CEZ:AV0Z10030501 Keywords : interstellar medium * clusters of galaxies * gas stripping Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 4.179, year: 2009

  1. CLOSED-LOOP STRIPPING ANALYSIS (CLSA) OF ...

    Science.gov (United States)

    Synthetic musk compounds have been found in surface water, fish tissues, and human breast milk. Current techniques for separating these compounds from fish tissues require tedious sample clean-upprocedures A simple method for the deterrnination of these compounds in fish tissues has been developed. Closed-loop stripping of saponified fish tissues in a I -L Wheaton purge-and-trap vessel is used to strip compounds with high vapor pressures such as synthetic musks from the matrix onto a solid sorbent (Abselut Nexus). This technique is useful for screening biological tissues that contain lipids for musk compounds. Analytes are desorbed from the sorbent trap sequentially with polar and nonpolar solvents, concentrated, and directly analyzed by high resolution gas chromatography coupled to a mass spectrometer operating in the selected ion monitoring mode. In this paper, we analyzed two homogenized samples of whole fish tissues with spiked synthetic musk compounds using closed-loop stripping analysis (CLSA) and pressurized liquid extraction (PLE). The analytes were not recovered quantitatively but the extraction yield was sufficiently reproducible for at least semi-quantitative purposes (screening). The method was less expensive to implement and required significantly less sample preparation than the PLE technique. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water,

  2. Deuteron stripping reactions with Tabakin potential

    International Nuclear Information System (INIS)

    Osman, A.

    1976-05-01

    Deuteron stripping reactions are considered. Due to the strong repulsion between nucleons at very short distances, we have investigated the nuclear short-range correlations. The neutron proton nuclear potential in the deuteron is taken as a short-range repulsive core surrounded by a long-range attractive potential. The neutron-proton potential is taken as the Tabakin separable potential to take into account the short-range correlations. The differential cross-sections for deuteron stripping reactions have been calculated in two different cases by taking Yamaguchi or Breit et al type parameters for the Tabakin potential used. The angular distributions for different (d,p) stripping reactions on the different target nuclei 28 Si, 32 , 34 S, 36 Ar, 40 , 48 Ca, 50 , 52 , 54 Cr have been calculated using the DWBA calculations. Our present theoretical calculations for the angular distributions of the different reactions cosidered have been fitted to the experimental data, where good agreement is obtained. The extracted spectroscopic factors from the present work are found to be more reliable

  3. Noise analysis due to strip resistance in the ATLAS SCT silicon strip module

    International Nuclear Information System (INIS)

    Kipnis, I.

    1996-08-01

    The module is made out of four 6 cm x 6 cm single sided Si microstrip detectors. Two detectors are butt glued to form a 12 cm long mechanical unit and strips of the two detectors are electrically connected to form 12 cm long strips. The butt gluing is followed by a back to back attachment. The module in this note is the Rφ module where the electronics is oriented parallel to the strip direction and bonded directly to the strips. This module concept provides the maximum signal-to-noise ratio, particularly when the front-end electronics is placed near the middle rather than at the end. From the noise analysis, it is concluded that the worst-case ΔENC (far-end injection) between end- and center-tapped modules will be 120 to 210 el. rms (9 to 15%) for a non-irradiated detector and 75 to 130 el. rms (5 to 9%) for an irradiated detector, for a metal strip resistance of 10 to 20 Ω/cm

  4. Preparation of Colloidal Gold Immunochromatographic Strip for Detection of Paragonimiasis skrjabini

    Science.gov (United States)

    Zhang, Jianwei; Wang, Guangxi; Chen, Wenbi; Chen, Lin; Zhang, Xilin

    2014-01-01

    Background Paragonimiasis is a food-borne trematodiasis, a serious public health issue and a neglected tropical disease. Paragonimus skrjabini is a unique species found in China. Unlike paragonimiasis westermani, it is nearly impossible to make a definitive diagnosis for paragonimiasis skrjabini by finding eggs in sputum or feces. Immunodiagnosis is the best choice to detect paragonimiasis skrjabini. There is an urgent need to develop a novel, rapid and simple immunoassay for large-scale screening patients in endemic areas. Methodology/Principal Findings To develop a rapid, simple immunodiagnostic assay for paragonimiasis, rabbit anti-human IgG was conjugated to colloidal gold particles and used to detect antibodies in the sera of paragonimiasis patients. The synthesis and identification of colloidal gold particles and antibody-colloidal gold conjugates were performed. The size of colloidal gold particles was examined using a transmission electron microscope (TEM). The average diameter of colloidal gold particles was 17.46 nm with a range of 14.32–21.80 nm according to the TEM images. The formation of antibody-colloidal gold conjugates was monitored by UV/Vis spectroscopy. Excretory-secretory (ES) antigen of Paragonimus skrjabini was coated on nitrocellulose membrane as the capture line. Recombinant Staphylococcus protein A was used to prepare the control line. This rapid gold immunochromatographic strip was assembled in regular sequence through different accessories sticked on PVC board. The relative sensitivity and specificity of the strip was 94.4% (51/54) and 94.1% (32/34) respectively using ELISA as the standard method. Its stability and reproducibility were quite excellent after storage of the strip at 4°C for 6 months. Conclusions/Significance Immunochromatographic strip prepared in this study can be used in a rapid one-step immunochromatographic assay, which is instantaneous and convenient. PMID:24643068

  5. Preparation of colloidal gold immunochromatographic strip for detection of Paragonimiasis skrjabini.

    Directory of Open Access Journals (Sweden)

    Ying Wang

    Full Text Available BACKGROUND: Paragonimiasis is a food-borne trematodiasis, a serious public health issue and a neglected tropical disease. Paragonimus skrjabini is a unique species found in China. Unlike paragonimiasis westermani, it is nearly impossible to make a definitive diagnosis for paragonimiasis skrjabini by finding eggs in sputum or feces. Immunodiagnosis is the best choice to detect paragonimiasis skrjabini. There is an urgent need to develop a novel, rapid and simple immunoassay for large-scale screening patients in endemic areas. METHODOLOGY/PRINCIPAL FINDINGS: To develop a rapid, simple immunodiagnostic assay for paragonimiasis, rabbit anti-human IgG was conjugated to colloidal gold particles and used to detect antibodies in the sera of paragonimiasis patients. The synthesis and identification of colloidal gold particles and antibody-colloidal gold conjugates were performed. The size of colloidal gold particles was examined using a transmission electron microscope (TEM. The average diameter of colloidal gold particles was 17.46 nm with a range of 14.32-21.80 nm according to the TEM images. The formation of antibody-colloidal gold conjugates was monitored by UV/Vis spectroscopy. Excretory-secretory (ES antigen of Paragonimus skrjabini was coated on nitrocellulose membrane as the capture line. Recombinant Staphylococcus protein A was used to prepare the control line. This rapid gold immunochromatographic strip was assembled in regular sequence through different accessories sticked on PVC board. The relative sensitivity and specificity of the strip was 94.4% (51/54 and 94.1% (32/34 respectively using ELISA as the standard method. Its stability and reproducibility were quite excellent after storage of the strip at 4°C for 6 months. CONCLUSIONS/SIGNIFICANCE: Immunochromatographic strip prepared in this study can be used in a rapid one-step immunochromatographic assay, which is instantaneous and convenient.

  6. Hepatitis C virus genotypes in Bahawalpur

    International Nuclear Information System (INIS)

    Qazi, M.A.; Fayyaz, M.; Chaudhry, G.M.D.; Jamil, A.

    2006-01-01

    This study was conducted at Medical Unit-II Bahawal Victoria Hospital / Quaid-e-Azam Medical College Bahawalpur from May 1st , 2005 to December 31st 2005. The objective of this study was to determine hepatitis C virus (HCV) genotypes in Bahawalpur, Pakistan. In consecutive 105 anti-HCV (ELISA-3) positive patients, complete history and physical examination was performed. Liver function tests, complete blood counts and platelet count, blood sugar fasting and 2 hours after breakfast, prothrombin time, serum albumin, serum globulin and abdominal ultrasound were carried out in all the patients. Tru cut biopsy was performed on 17 patients. We studied HCV RNA in all these patients by Nested PCR method. HCV RNA was detected in 98 patients and geno typing assay was done by genotype specific PCR. Among total of 105 anti-HCV positive patients, HCV-RNA was detected in 98 patients. Out of these 98 patients there were 57 (58.2%) males and 41 (42.8%) females. Their age range was 18-75 years. The age 18-29 years 26 (26.5%), 30-39 years 35 (35.7%) and 40-75 37 (37.8%), while 10 (10.2%) patients were diabetics and 34 (34.7%) patients were obese. Liver cirrhosis was present in 10 (10.2%) patients. Forty two (43.9%) patients were symptomatic while 56 (57.1%) were asymptomatic. Out of 98 patients 11 (11.2%) were un type-able and 87 (88.8%) were type able. 70/98 (71.4%) were genotype 3; 10/98 (10.2%) were genotype 1; 03/98 (3.1%) were genotype 2; 03/98 (3.1%) were mixed genotype 2 and 3; 01/98 (1%) were mixed genotype 3a and 3b. Genotype 3 is the most common HCV virus in our area which shows that both virological and biochemical response will be better. Because HCV genotype 3 is more frequent among the drug users which points towards unsafe injection practices in our area. (author)

  7. Performance of Bemisia tabaci Biotype B on Soybean Genotypes.

    Science.gov (United States)

    Cruz, P L; Baldin, E L L

    2017-04-01

    Bemisia tabaci (Genn.) (Hemiptera: Aleyrodidae) has been recognized as an important pest of many agricultural systems including soybean [Glycine max (L.) Merrill] crops. As an alternative to chemical control, the use of resistant genotypes represents an important tool for integrated pest management (IPM). This study aimed to evaluate the biological development of Bemisia tabaci biotype B confined on 13 soybean genotypes under greenhouse conditions. Initially, the nymphal period, complete development period (egg-adult), and the viability of the silverleaf whitefly nymphs were evaluated in all genotypes. Then, four genotypes promising for resistance ('Jackson,' UX-2569-159, 'P98Y11,' and 'TMG132 RR') and a susceptible genotype (PI-227687) were selected for further assays, where two insect populations were compared: a first population from the initial rearing (cabbage plants) and another corresponding to insects previously reared out on the selected genotypes. In addition to the parameters evaluated in preliminary tests, we also determined the viability and incubation period of eggs. Moderate levels of resistance (antibiosis/antixenosis) to B. tabaci biotype B were found in three genotypes. 'P98Y11' and 'TMG132 RR' were less suitable for insect development, extending the development cycle, and UX-2569-159 caused high nymphal mortality. We did not observe a significant increase in the level of plant resistance by the use of previously stressed insects. This suggests that the evaluation of a single whitefly generation may be sufficient to make correct decisions on promising soybean genotypes.

  8. Detection and genotyping of human papillomavirus in gynaecologic outpatients of Messina, eastern Sicily, Italy.

    Science.gov (United States)

    Giuffrè, Giuseppe; Simone, Angela; Todaro, Paolo; Le Donne, Maria; Caruso, Carmela; Pizzo, Alfonsa; Granese, Domenico

    2010-03-01

    In order to determine the prevalence of human papillomavirus (HPV) infection in sexually active female population in Messina, we tested cervical scrapes of women referred to university clinics for routine gynaecologic care. Between March and December 2008, a total of 680 cervical samples of 598 patients (573 Italian from province of Messina and 25 resident aliens) were examined consecutively from laboratory of molecular biology at the Department of Human Pathology. For each sample, cervical cells were collected by centrifugation and DNA was extracted (QIAamp DNA mini kit, Qiagen), followed by a PCR-based HPV DNA assay and reverse dot blot genotyping (HPV-HS Bio plus HPV-strip, AB Analytica or HPV-type, AB Analytica). The overall rate of HPV DNA detection in Italian patients (mean age 34 years; range 15-69) was 70.5% (404/573), with 163 cases of multiple infections (40.3%). In 335 patients (82.9%) a high-risk HPV infection was detected. In this group the coexistence of a low-risk HPV infection was documented in 97 cases while 65 patients exhibited only a low-risk HPV infection. HPV-16 was the most prevalent (33.4%), followed by HPV-6 (28.0%), HPV-31 (24.3%), HPV-58 (11.4%), HPV-66 (11.1%), HPV-53 (6.4%), HPV-18 (6.2%), HPV-56 (5.4%), HPV-33 (5.2%) while the other genotypes identified (HPV-11, -40, -42, -43, -44, -54, -61, -70, -81, -26, -35, -39, -45, -51, -52, -59, -68, -73, -82) were below 5%. HPV prevalence (any type) was 78.7% at age or =45 years. A significant association (chi2=12.718; P=0.006) between HPV DNA detection and the younger age was encountered. Since available data on the prevalence and distribution of HPV infection in Italy are somewhat discordant, this study represents a helpful contribution to the knowledge on the circulation of precise genotypes in east Sicily in order to improve new HPV vaccines.

  9. High pressure water jet cutting and stripping

    Science.gov (United States)

    Hoppe, David T.; Babai, Majid K.

    1991-01-01

    High pressure water cutting techniques have a wide range of applications to the American space effort. Hydroblasting techniques are commonly used during the refurbishment of the reusable solid rocket motors. The process can be controlled to strip a thermal protective ablator without incurring any damage to the painted surface underneath by using a variation of possible parameters. Hydroblasting is a technique which is easily automated. Automation removes personnel from the hostile environment of the high pressure water. Computer controlled robots can perform the same task in a fraction of the time that would be required by manual operation.

  10. The CMS Si-Strip Tracker

    CERN Document Server

    Sguazzoni, Giacomo

    2004-01-01

    The Compact Muon Solenoid (CMS) experiment at LHC features the largest Silicon Strip Tracker (SST) ever build. This device is immersed in a 4T magnetic field and, in conjunction with a Pixel system, it allows the momentum of the charged particles to be measured and the heavy-flavour final states to be tagged despite the hostile radiation environment. The impact of operating conditions and physics requirements on the SST layout and design choices is discussed and the expected performances are reviewed. The SST collaboration is now facing the production of the ~15000 modules and their assembly into the SST substructures. A status is given.

  11. The CMS Si-strip Tracker

    CERN Document Server

    Sguazzoni, Giacomo

    2004-01-01

    The Compact Muon Solenoid (CMS) experiment at LHC features the largest Silicon Strip Tracker (SST) ever build. This device is immersed in a 4T magnetic field and, in conjunction with a Pixel system, it allows the momentum of the charged particles to be measured and the heavy-flavour final states to be tagged despite the hostile radiation environment. The impact of operating conditions and physics requirements on the SST layout and design choices is discussed and the expected performances are reviewed. The SST collaboration is now facing the production of the ~15000 modules and their assembly into the SST substructures. A status is given.

  12. Tritium stripping by a catalytic exchange stripper

    International Nuclear Information System (INIS)

    Heung, L.K.; Gibson, G.W.; Ortman, M.S.

    1991-01-01

    A catalytic exchange process for stripping elemental tritium from gas streams has been demonstrated. The process uses a catalyzed isotopic exchange reaction between tritium in the gas phase and protium or deuterium in the solid phase on alumina. The reaction is catalyzed by platinum deposited on the alumina. The process has been tested with both tritium and deuterium. Decontamination factors (ration of inlet and outlet tritium concentrations) as high as 1000 have been achieved, depending on inlet concentration. The test results and some demonstrated applications are presented

  13. Comparative study of corneal strip extensometry and inflation tests

    OpenAIRE

    Elsheikh, Ahmed; Anderson, Kevin

    2005-01-01

    Strip extensometry tests are usually considered less reliable than trephinate inflation tests in studying corneal biomechanics. In spite of the evident simplicity of strip extensometry tests, several earlier studies preferred inflation tests in determining the constitutive relationship of the cornea and its other material properties, such as Young's modulus and the hysteresis behaviour. In this research, the deficiencies of the strip tests are discussed and a mathematical procedure presented ...

  14. DEVELOPMENT OF DEFORMATION STRIPS WHILE STRETCHING OF CYLINDRICAL SAMPLES

    Directory of Open Access Journals (Sweden)

    Y. V. Vasilevich

    2011-01-01

    Full Text Available Deformation strips have been experimentally revealed and described while stretching of cylindrical samples by means of computer thermography. It has been established that temperature of shift strip surface grows smoothly up to the stage of crack origin in material defect. Sharp growth of surface temperature occurs when tensile stresses reach tensile strength. Change in surface temperature occurs wavy after destruction (while cooling the sample. Processes of material destruction origin and development  characterize temperature changes in deformation strips.

  15. Axiom turkey genotyping array

    Science.gov (United States)

    The Axiom®Turkey Genotyping Array interrogates 643,845 probesets on the array, covering 643,845 SNPs. The array development was led by Dr. Julie Long of the USDA-ARS Beltsville Agricultural Research Center under a public-private partnership with Hendrix Genetics, Aviagen, and Affymetrix. The Turk...

  16. (Phaseolus vulgaris L) Genotypes

    African Journals Online (AJOL)

    Bruening 2001; Ho 1988). At whole plant level, the differences in drought resistance among drought-resistant and susceptible genotypes are related to the ability to accumulate biomass, remobilization of stored biomass to reproductive organs and the subsequent capacity to establish new reproductive sinks (Koç et al. 2003 ...

  17. Stability of barotropic vortex strip on a rotating sphere.

    Science.gov (United States)

    Sohn, Sung-Ik; Sakajo, Takashi; Kim, Sun-Chul

    2018-02-01

    We study the stability of a barotropic vortex strip on a rotating sphere, as a simple model of jet streams. The flow is approximated by a piecewise-continuous vorticity distribution by zonal bands of uniform vorticity. The linear stability analysis shows that the vortex strip becomes stable as the strip widens or the rotation speed increases. When the vorticity constants in the upper and the lower regions of the vortex strip have the same positive value, the inner flow region of the vortex strip becomes the most unstable. However, when the upper and the lower vorticity constants in the polar regions have different signs, a complex pattern of instability is found, depending on the wavenumber of perturbations, and interestingly, a boundary far away from the vortex strip can be unstable. We also compute the nonlinear evolution of the vortex strip on the rotating sphere and compare with the linear stability analysis. When the width of the vortex strip is small, we observe a good agreement in the growth rate of perturbation at an early time, and the eigenvector corresponding to the unstable eigenvalue coincides with the most unstable part of the flow. We demonstrate that a large structure of rolling-up vortex cores appears in the vortex strip after a long-time evolution. Furthermore, the geophysical relevance of the model to jet streams of Jupiter, Saturn and Earth is examined.

  18. Strip type radiation detector and method of making same

    International Nuclear Information System (INIS)

    Jantsch, O.; Feigt, I.; Willig, W.R.

    1976-01-01

    An improved strip detector and a method for making such a detector in which a high resistivity N conduction semiconductor body has electrode strips formed thereon by diffusion is described. The strips are formed so as to be covered by an oxide layer at the surface point of the PN junction and in which the opposite side of the semiconductor body then has a substantial amount of material etched away to form a thin semiconductor upon which strip electrodes which are perpendicular to the electrodes on the first side are then placed

  19. Strip defect recognition in electrical tests of silicon microstrip sensors

    Energy Technology Data Exchange (ETDEWEB)

    Valentan, Manfred, E-mail: valentan@mpp.mpg.de

    2017-02-11

    This contribution describes the measurement procedure and data analysis of AC-coupled double-sided silicon microstrip sensors with polysilicon resistor biasing. The most thorough test of a strip sensor is an electrical measurement of all strips of the sensor; the measured observables include e.g. the strip's current and the coupling capacitance. These measurements are performed to find defective strips, e.g. broken capacitors (pinholes) or implant shorts between two adjacent strips. When a strip has a defect, its observables will show a deviation from the “typical value”. To recognize and quantify certain defects, it is necessary to determine these typical values, i.e. the values the observables would have without the defect. As a novel approach, local least-median-of-squares linear fits are applied to determine these “would-be” values of the observables. A least-median-of-squares fit is robust against outliers, i.e. it ignores the observable values of defective strips. Knowing the typical values allows to recognize, distinguish and quantify a whole range of strip defects. This contribution explains how the various defects appear in the data and in which order the defects can be recognized. The method has been used to find strip defects on 30 double-sided trapezoidal microstrip sensors for the Belle II Silicon Vertex Detector, which have been measured at the Institute of High Energy Physics, Vienna (Austria).

  20. Stability of barotropic vortex strip on a rotating sphere

    Science.gov (United States)

    Sohn, Sung-Ik; Sakajo, Takashi; Kim, Sun-Chul

    2018-02-01

    We study the stability of a barotropic vortex strip on a rotating sphere, as a simple model of jet streams. The flow is approximated by a piecewise-continuous vorticity distribution by zonal bands of uniform vorticity. The linear stability analysis shows that the vortex strip becomes stable as the strip widens or the rotation speed increases. When the vorticity constants in the upper and the lower regions of the vortex strip have the same positive value, the inner flow region of the vortex strip becomes the most unstable. However, when the upper and the lower vorticity constants in the polar regions have different signs, a complex pattern of instability is found, depending on the wavenumber of perturbations, and interestingly, a boundary far away from the vortex strip can be unstable. We also compute the nonlinear evolution of the vortex strip on the rotating sphere and compare with the linear stability analysis. When the width of the vortex strip is small, we observe a good agreement in the growth rate of perturbation at an early time, and the eigenvector corresponding to the unstable eigenvalue coincides with the most unstable part of the flow. We demonstrate that a large structure of rolling-up vortex cores appears in the vortex strip after a long-time evolution. Furthermore, the geophysical relevance of the model to jet streams of Jupiter, Saturn and Earth is examined.

  1. Pavement Stripping in Saudi Arabia: Prediction and Prevention

    Directory of Open Access Journals (Sweden)

    H.I. Al-Abdul Wahhab

    2004-12-01

    Full Text Available Pavement weathering or stripping is a major distress in highway networks in arid regions. Using the Saudi Arabian road network as a case study area, seventeen road test sections were selected, out of which eight were stripped and nine were non-stripped. Aggregates from quarries used to build these sections were also collected and subjected to detailed physical and chemical tests to evaluate the ability of these tests to distinguish between stripped and non-stripped sections. The modified Lottman test was used to distinguish between compacted mixes. In addition, the Swedish Rolling Bottle test, was also found to be effective in being able to distinguish between different asphalt-aggregates for stripping potential. Eleven anti-stripping liquid additives, lime and cement, in addition to two polymers, were evaluated for their ability to reduce/eliminate stripping potential of stripping-prone aggregates. It was found that EE-2 Polymer, Portland cement, and their combination were effective with all aggregate sources.

  2. Sensitive and Quantitative Detection of C-Reaction Protein Based on Immunofluorescent Nanospheres Coupled with Lateral Flow Test Strip.

    Science.gov (United States)

    Hu, Jiao; Zhang, Zhi-Ling; Wen, Cong-Ying; Tang, Man; Wu, Ling-Ling; Liu, Cui; Zhu, Lian; Pang, Dai-Wen

    2016-06-21

    Sensitive and quantitative detection of protein biomarkers with a point-of-care (POC) assay is significant for early diagnosis, treatment, and prognosis of diseases. In this paper, a quantitative lateral flow assay with high sensitivity for protein biomarkers was established by utilizing fluorescent nanospheres (FNs) as reporters. Each fluorescent nanosphere (FN) contains 332 ± 8 CdSe/ZnS quantum dots (QDs), leading to its superstrong luminescence, 380-fold higher than that of one QD. Then a detection limit of 27.8 pM C-reaction protein (CRP) could be achieved with an immunofluorescent nanosphere (IFN)-based lateral flow test strip. The assay was 257-fold more sensitive than that with a conventional Au-based lateral flow test strip for CRP detection. Besides, the fluorescence intensity of FNs and bioactivity of IFNs were stable during 6 months of storage. Hence, the assay owns good reproducibility (intra-assay variability of 5.3% and interassay variability of 6.6%). Furthermore, other cancer biomarkers (PSA, CEA, AFP) showed negative results by this method, validating the excellent specificity of the method. Then the assay was successfully applied to quantitatively detect CRP in peripheral blood plasma samples from lung cancer and breast cancer patients, and healthy people, facilitating the diagnosis of lung cancer. It holds a good prospect of POC protein biomarker detection.

  3. Designs, formats and applications of lateral flow assay: A literature review

    Directory of Open Access Journals (Sweden)

    Muhammad Sajid

    2015-11-01

    Full Text Available This manuscript provides a brief overview of latest research involving the use of lateral flow assay for qualitative and quantitative analysis in different areas. The excellent features and versatility of detection formats make these strips an ideal choice for point of care applications. We outline and critically discuss detection formats, molecular recognition probes, labels, and detection systems used in lateral flow assay. Applications in different fields along with selected examples from the literature have been included to show analytical performance of these devices. At the end, we summarize accomplishments, weaknesses and future challenges in the area of lateral flow strips.

  4. Highly sensitive multianalyte immunochromatographic test strip for rapid chemiluminescent detection of ractopamine and salbutamol

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Hongfei; Han, Jing; Yang, Shijia; Wang, Zhenxing; Wang, Lin; Fu, Zhifeng, E-mail: fuzf@swu.edu.cn

    2014-08-11

    Graphical abstract: A multianalyte immunochromatographic test strip was developed for the rapid detection of two β{sub 2}-agonists. Due to the application of chemiluminescent detection, this quantitative method shows much higher sensitivity. - Highlights: • An immunochromatographic test strip was developed for detection of multiple β{sub 2}-agonists. • The whole assay process can be completed within 20 min. • The proposed method shows much higher sensitivity due to the application of CL detection. • It is a portable analytical tool suitable for field analysis and rapid screening. - Abstract: A novel immunochromatographic assay (ICA) was proposed for rapid and multiple assay of β{sub 2}-agonists, by utilizing ractopamine (RAC) and salbutamol (SAL) as the models. Owing to the introduction of chemiluminescent (CL) approach, the proposed protocol shows much higher sensitivity. In this work, the described ICA was based on a competitive format, and horseradish peroxidase-tagged antibodies were used as highly sensitive CL probes. Quantitative analysis of β{sub 2}-agonists was achieved by recording the CL signals of the probes captured on the two test zones of the nitrocellulose membrane. Under the optimum conditions, RAC and SAL could be detected within the linear ranges of 0.50–40 and 0.10–50 ng mL{sup −1}, with the detection limits of 0.20 and 0.040 ng mL{sup −1} (S/N = 3), respectively. The whole process for multianalyte immunoassay of RAC and SAL can be completed within 20 min. Furthermore, the test strip was validated with spiked swine urine samples and the results showed that this method was reliable in measuring β{sub 2}-agonists in swine urine. This CL-based multianalyte test strip shows a series of advantages such as high sensitivity, ideal selectivity, simple manipulation, high assay efficiency and low cost. Thus, it opens up new pathway for rapid screening and field analysis, and shows a promising prospect in food safety.

  5. Measurement of the enzymes lactate dehydrogenase and creatine kinase using reflectance spectroscopy and reagent strips.

    Science.gov (United States)

    Stevens, J F; Tsang, W; Newall, R G

    1983-01-01

    Two new methods for the assay of total activities of lactate dehydrogenase and creatine kinase are described, in which the enzyme activities are measured from a solid-state reagent strip during a kinetic reaction, the reaction being monitored in the ultra-violet region of the spectrum by reflectance spectroscopy. The performances of these methods are evaluated, and compared to conventional "wet" chemistry methods. The solid-phase reagent methods demonstrated precision and accuracy acceptable for diagnostic purposes, and were easy to use by trained operators. PMID:6655069

  6. Solute diffusion through stripped mouse duodenum.

    Science.gov (United States)

    Takeuchi, T; Ham, M; Mizumori, M; Guth, P H; Engel, E; Kaunitz, J D; Akiba, Y

    2007-12-01

    We measured villous cell intracellular pH (pH(i)) and solute diffusion between the bathing media and the epithelial cells in stripped, chambered mouse duodenum. Apical perfusion of a high CO2 solution rapidly acidified the upper villous cells with recovery after its removal. Apical zoniporide (ZP) enhanced CO(2)-induced acidification. Serosal ZP, dimethylamiloride (DMA) or stilbene anion transport inhibitors failed to alter CO(2)-induced acidification, whereas serosal high CO(2) buffer acidified the upper villous cells. Serosal 5-hydroxytryptamine rapidly acidified the upper villous cells. All serosally-perfused fluorescent compounds stained the crypt area, but not the villi or villous cells. In contrast, intravenous carboxyfluorescein quickly diffused into the interstitial space of the entire mucosa, and mucosally perfused fluorescent compound rapidly penetrated the epithelial cell layer. In muscle-stripped duodenum mounted in a small-aperture perfusion chamber, serosal solutes can readily diffuse only to the crypt cell region, whereas access to the villous epithelial cells is diffusion-limited. In contrast, rapid villous cell responses to serosally applied solutes are best explained by neural reflexes. Limited viability of the villous cells and impaired structural stability of the villi further limit long-term, villous cell functional studies of mucosal preparations mounted in small aperture diffusion chambers.

  7. Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

    1995-11-01

    Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

  8. [Determination of hepatitis C virus genotypes among hepatitis C patients in Eastern Black Sea Region, Turkey].

    Science.gov (United States)

    Buruk, Celal Kurtuluş; Bayramoğlu, Gülçin; Reis, Ahu; Kaklıkkaya, Neşe; Tosun, Ilknur; Aydın, Faruk

    2013-10-01

    Hepatitis C virus (HCV), the major cause of transfusion-associated hepatitis, is an important public health problem in the world as well as in Turkey. HCV is grouped as six distinct genotypes and a large number of closely-related subtypes. Genotyping of HCV is an important tool for providing epidemiological data, prediction of prognosis, and optimization of antiviral therapy. This study was carried out to determine the distribution of HCV genotypes in hepatitis C patients residing in different provinces of the Eastern Black Sea Region, Turkey. A total of 304 HCV-RNA positive cases (151 male, 153 female; age range: 11-93 years, mean age: 55.2 ± 13.3 years) who were admitted to the Molecular Microbiology Unit of Department of Medical Microbiology, Karadeniz Technical University Faculty of Medicine, between January 2009 to December 2012, were included in the study. HCV genotypes were detected in plasma samples of the patients by using commercial assays [INNO-LiPA HCV II (Innogenetics, Belgium) or Abbott RealTime HCV Genotype II (Abbott Molecular Inc, USA)]. Due to the ambiguous genotyping results in some samples with these methods, an in-house multiplex polymerase chain reaction (PCR) assay with genotype-specific primers was also used in the study. Similar to the previous reports from Turkey, our results showed that four HCV genotypes (1, 2, 3, and 4) prevailed in the Eastern Black Sea Region and the predominant genotype and subtype were genotype 1 (92.8%) and 1b (87.5%), respectively. Distribution of genotypes were observed to vary according to the province. Prevalences of subtype 1a, genotype 2, 3, and 4 were noted as 5.3%, 1.6%, 4.9%, and 0.7%, respectively. Furthermore, the samples from Giresun, Gumushane and Bayburt provinces, which are relatively less immigrated, had higher genotype 1, and the prevalence rates in the region was affected by the presence of non-citizen residents. This study is the first report on distribution of HCV genotypes in chronic hepatitis

  9. Europium (III) chelate microparticle-based lateral flow immunoassay strips for rapid and quantitative detection of antibody to hepatitis B core antigen.

    Science.gov (United States)

    Liang, Rong-Liang; Deng, Qiao-Ting; Chen, Zhen-Hua; Xu, Xu-Ping; Zhou, Jian-Wei; Liang, Jun-Yu; Dong, Zhi-Ning; Liu, Tian-Cai; Wu, Ying-Song

    2017-10-26

    Quantitative hepatitis B core antigen (anti-HBc) measurements could play an important role in evaluating therapeutic outcomes and optimizing the antiviral therapy of chronic hepatitis B infection. In this study, we have developed a simple and rapid fluorescence point-of-care test based on a lateral flow immunoassay (LFIA) method integrated with Eu (III) chelate microparticles to quantitatively determine anti-HBc concentrations in serum. This assay is based on a direct competitive immunoassay performed on lateral flow test strips with an assay time of 15 min. The Eu (III) chelate microparticle-based LFIA assay could quantitatively detect anti-HBc levels with a limit of detection of 0.31 IU mL -1 , and exhibited a wide linear range (0.63-640 IU mL -1 ). The intra- and inter-assay coefficients of variation for anti-HBc were both less than 10% and a satisfactory dilution test and accuracy were demonstrated. There were no statistically significant differences in sensitivity or specificity in serum samples between the Eu (III) chelate microparticle-based LFIA strips and the Abbott Architect kit. A simple, rapid and effective quantitative detection of anti-HBc was possible using the Eu (III) chelate microparticle-based LFIA strips. The strips will provide diagnostic value for clinical application.

  10. Hollow Au-Ag Nanoparticles Labeled Immunochromatography Strip for Highly Sensitive Detection of Clenbuterol

    Science.gov (United States)

    Wang, Jingyun; Zhang, Lei; Huang, Youju; Dandapat, Anirban; Dai, Liwei; Zhang, Ganggang; Lu, Xuefei; Zhang, Jiawei; Lai, Weihua; Chen, Tao

    2017-01-01

    The probe materials play a significant role in improving the detection efficiency and sensitivity of lateral-flow immunochromatographic test strip (ICTS). Unlike conventional ICTS assay usually uses single-component, solid gold nanoparticles as labeled probes, in our present study, a bimetallic, hollow Au-Ag nanoparticles (NPs) labeled ICTS was successfully developed for the detection of clenbuterol (CLE). The hollow Au-Ag NPs with different Au/Ag mole ratio and tunable size were synthesized by varying the volume ratio of [HAuCl4]:[Ag NPs] via the galvanic replacement reaction. The surface of hollow Ag-Au NPs was functionalized with 11-mercaptoundecanoic acid (MUA) for further covalently bonded with anti-CLE monoclonal antibody. Overall size of the Au-Ag NPs, size of the holes within individual NPs and also Au/Ag mole ratio have been systematically optimized to amplify both the visual inspection signals and the quantitative data. The sensitivity of optimized hollow Au-Ag NPs probes has been achieved even as low as 2 ppb in a short time (within 15 min), which is superior over the detection performance of conventional test strip using Au NPs. The optimized hollow Au-Ag NPs labeled test strip can be used as an ideal candidate for the rapid screening of CLE in food samples.

  11. Aptamer-Based Lateral Flow Test Strip for Rapid Detection of Zearalenone in Corn Samples.

    Science.gov (United States)

    Wu, Shijia; Liu, Lihong; Duan, Nuo; Li, Qian; Zhou, You; Wang, Zhouping

    2018-02-28

    An aptamer-based lateral flow test strip was developed for the detection of zearalenone (ZEN). This assay was based on the competition for the aptamer between ZEN and its complementary sequence. Several experimental conditions that could influence sensitivity have been investigated, including the concentration of aptamer and NaCl used in the probe preparation, the mole ratio of streptavidin and biotinylated DNA used in the preparation of test line and control line, and the loading quantity of gold nanoparticles-aptamer conjugates (AuNPs-Apt). Under the optimal experimental conditions, we successfully detected ZEN within a detection range of 5-200 ng/mL and the visual limit of detection of 20 ng/mL. This aptamer-based strip was successfully applied to the determination of ZEN in spiked corn samples, and the recoveries were from 93.4% to 114.2%. All detections can be achieved within 5 min. The results demonstrated that the developed aptamer-based lateral flow test strip is a potential alternative tool for the rapid and sensitive detection of ZEN.

  12. Evaluation of silicon micro strip detectors with large read-out pitch

    International Nuclear Information System (INIS)

    Senyo, K.; Yamamura, K.; Tsuboyama, T.; Avrillon, S.; Asano, Y.; Bozek, A.; Natkaniec, Z.; Palka, H.; Rozanska, M.; Rybicki, K.

    1996-01-01

    For the development of the silicon micro-strip detector with the pitch of the readout strips as large as 250 μm on the ohmic side, we made samples with different structures. Charge collection was evaluated to optimize the width of implant strips, aluminum read-out strips, and/or the read-out scheme among strips. (orig.)

  13. Genotyping of Brucella species using clade specific SNPs

    Directory of Open Access Journals (Sweden)

    Foster Jeffrey T

    2012-06-01

    Full Text Available Abstract Background Brucellosis is a worldwide disease of mammals caused by Alphaproteobacteria in the genus Brucella. The genus is genetically monomorphic, requiring extensive genotyping to differentiate isolates. We utilized two different genotyping strategies to characterize isolates. First, we developed a microarray-based assay based on 1000 single nucleotide polymorphisms (SNPs that were identified from whole genome comparisons of two B. abortus isolates , one B. melitensis, and one B. suis. We then genotyped a diverse collection of 85 Brucella strains at these SNP loci and generated a phylogenetic tree of relationships. Second, we developed a selective primer-extension assay system using capillary electrophoresis that targeted 17 high value SNPs across 8 major branches of the phylogeny and determined their genotypes in a large collection ( n = 340 of diverse isolates. Results Our 1000 SNP microarray readily distinguished B. abortus, B. melitensis, and B. suis, differentiating B. melitensis and B. suis into two clades each. Brucella abortus was divided into four major clades. Our capillary-based SNP genotyping confirmed all major branches from the microarray assay and assigned all samples to defined lineages. Isolates from these lineages and closely related isolates, among the most commonly encountered lineages worldwide, can now be quickly and easily identified and genetically characterized. Conclusions We have identified clade-specific SNPs in Brucella that can be used for rapid assignment into major groups below the species level in the three main Brucella species. Our assays represent SNP genotyping approaches that can reliably determine the evolutionary relationships of bacterial isolates without the need for whole genome sequencing of all isolates.

  14. Comparison of two enzyme-linked immunosorbent assays and one rapid immunoblot assay for detection of herpes simplex virus type 2-specific antibodies in serum

    NARCIS (Netherlands)

    J. Groen (Jan); G. van Dijk (Grietje); H.G.M. Niesters (Bert); W.I. van der Meijden (Willem); A.D.M.E. Osterhaus (Albert)

    1998-01-01

    textabstractThe sensitivities and specificities of three immunoassays for the detection of herpes simplex virus type 2 (HSV-2)-specific immunoglobulin G antibodies in serum, including the one-strip rapid immunoblot assay (RIBA; Chiron Corporation) and two indirect enzyme

  15. Quantum dot-based immunochromatography test strip for rapid, quantitative and sensitive detection of alpha fetoprotein.

    Science.gov (United States)

    Yang, Qiuhua; Gong, Xiaoqun; Song, Tao; Yang, Jiumin; Zhu, Shengjiang; Li, Yunhong; Cui, Ye; Li, Yingxin; Zhang, Bingbo; Chang, Jin

    2011-12-15

    Rapid, quantitative detection of tumor markers with high sensitivity and specificity is critical to clinical diagnosis and treatment of cancer. We describe here a novel portable fluorescent biosensor that integrates quantum dot (QD) with an immunochromatography test strip (ICTS) and a home-made test strip reader for detection of tumor markers in human serum. Alpha fetoprotein (AFP), which is valuable for diagnosis of primary hepatic carcinoma, is used as a model tumor marker to demonstrate the performance of the proposed immunosensor. The principle of this sensor is on the basis of a sandwich immunoreaction that was performed on an ICTS. The fluorescence intensity of captured QD labels on the test line and control line served as signals was determined by the home-made test strip reader. The strong luminescence and robust photostability of QDs combined with the promising advantages of an ICTS and sensitive detection with the test strip reader result in good performance. Under optimal conditions, this biosensor is capable of detecting as low as 1 ng/mL AFP standard analyte in 10 min with only 50 μL sample volume. Furthermore, 1000 clinical human serum samples were tested by both the QD-based ICTS and a commercial electrochemiluminescence immunoassay AFP kit simultaneously to estimate the sensitivity, specificity and concordance of the assays. Results showed high consistency except for 24 false positive cases (false positive rate 3.92%) and 17 false negative cases (false negative rate 4.38%); the error rate was 4.10% in all. This demonstrates that the QD-based ICTS is capable of rapid, sensitive, and quantitative detection of AFP and shows a great promise for point-of-care testing of other tumor markers. Copyright © 2011 Elsevier B.V. All rights reserved.

  16. 25 CFR 170.445 - What is a strip map?

    Science.gov (United States)

    2010-04-01

    ... BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR LAND AND WATER INDIAN RESERVATION ROADS PROGRAM Planning, Design, and Construction of Indian Reservation Roads Program Facilities Irr Inventory § 170.445 What is a strip map? A strip map is a graphic representation of a section of road or other...

  17. Determination of residual stresses in roll compacted titanium strips

    CSIR Research Space (South Africa)

    Mothosi, KL

    2017-01-01

    Full Text Available induced during roll compaction of titanium strips were measured for strips of different densities. The different densities were achieved by rolling two different particle size (100 and 325 mesh) titanium powders varying the roll gap (0.1, 0.3 and 0.5 mm...

  18. Hollow Mill for Extraction of Stripped Titanium Screws: An Easy ...

    African Journals Online (AJOL)

    Removal of jammed titanium screws can be difficult due to the problem of stripping of the hexagonal heads of the screws. We present a technique of extraction of stripped screws with the use of a standard 4.5 mm stainless steel hollow mill in a patient of peri‑implant fracture of the radius fixed with a titanium locking plate 2 ...

  19. Hollow Mill for Extraction of Stripped Titanium Screws: An Easy ...

    African Journals Online (AJOL)

    screws. We present a technique of extraction of stripped screws with the use of a standard 4.5 mm stainless steel hollow mill in a patient of peri-implant fracture of the radius fixed with a titanium locking plate 2 years back. The technique is quick, safe, and cost effective. Key words: Hollow mill, stripped screws, titanium locked.

  20. Great saphenous vein stripping using nasogastric tube | Ademola ...

    African Journals Online (AJOL)

    Method and result: We describe the use of nasogastric tube in the stripping of GSV. This simple technique has been successfully applied in three patients. Conclusion: There is a need to carry out a prospective study regarding the application of this technique of GSV stripping. Keywords: Great saphenous vein, crossectomy, ...

  1. Reforestation of strip-mined lands in West Virginia

    Science.gov (United States)

    H. Spencer Potter; Sidney Weitzman; George R., Jr. Trimble

    1951-01-01

    The early 1940's witnessed a striking increase in strip-mining throughout the eastern coal region. West Virginia, with its extensive coal resources, naturally was caught in the full current of this shift in mining methods. Today the raw gash on the hillside - almost infallibly the mark of a strip-mine operation - is a familiar sight in the State.

  2. Using Comic Strips as a Book Report Alternative

    Science.gov (United States)

    Reading Teacher, 2012

    2012-01-01

    Comic strips are great to share with parents, younger students, and peers. This article presents an activity where students use a six-paneled comic strip to summarize a story. This activity allows for multiple interpretations and enhances comprehension by drawing attention to story elements.

  3. Temperature sensitivity of the oxygenation reaction of stripped ...

    African Journals Online (AJOL)

    Temperature sensitivity of the oxygenation reaction of stripped haemolysates from the freshwater fishes Labeo capensis and Ciarias gariepinus. ... of the mudfish Labeo capensis and the catfish Clarias gariepinus, stripped by gel filtration chromatography and buffered at 23°C in 0,05 M Hepes (pH 7,48), were determined at ...

  4. Tape Stripping Technique for Stratum Corneum Protein Analysis

    DEFF Research Database (Denmark)

    Clausen, Maja-Lisa; Slotved, H.-C.; Krogfelt, Karen Angeliki

    2016-01-01

    The aim of this study was to investigate the amount of protein in stratum corneum in atopic dermatitis (AD) patients and healthy controls, using tape stripping technique. Furthermore, to compare two different methods for protein assessment. Tape stripping was performed in AD patients and healthy ...

  5. Quality Tests of Double-Sided Silicon Strip Detectors

    CERN Document Server

    Cambon, T; CERN. Geneva; Fintz, P; Guillaume, G; Jundt, F; Kuhn, C; Lutz, Jean Robert; Pagès, P; Pozdniakov, S; Rami, F; Sparavec, K; Dulinski, W; Arnold, L

    1997-01-01

    The quality of the SiO2 insulator (AC coupling between metal and implanted strips) of double-sided Silicon strip detectors has been studied by using a probe station. Some tests performed on 23 wafers are described and the results are discussed. Remark This note seems to cause problems with ghostview but it can be printed without any problem.

  6. Stripping foils for the PSB H- injection system

    CERN Document Server

    Aiba, M; Goddard, B; Weterings, W

    2009-01-01

    Beam physics considerations for the stripping foil of the PSB H- injection system are described, including the arguments for the foil type, thickness, geometry and positioning. The foil performance considerations are described, including expected stripping efficiency, emittance growth, energy straggling, temperature and lifetime. The required movement ranges and tolerances are detailed, together with the assumptions used.

  7. Coiled sheet metal strip opens into tubular configuration

    Science.gov (United States)

    Park, J. J.

    1966-01-01

    Copper alloy is converted into a spring material that can be rolled into a compact coil which will spontaneously open to form a tube in the long direction of the strip. The copper alloy is passed through a furnace at a prescribed temperature while restraining the strip in the desired tubular configuration.

  8. Optical fiber cable chemical stripping fixture

    Science.gov (United States)

    Kolasinski, John R. (Inventor); Coleman, Alexander M. (Inventor)

    1995-01-01

    An elongated fixture handle member is connected to a fixture body member with both members having interconnecting longitudinal central axial bores for the passage of an optical cable therethrough. The axial bore of the fixture body member, however, terminates in a shoulder stop for the outer end of a jacket of the optical cable covering both an optical fiber and a coating therefor, with an axial bore of reduced diameter continuing from the shoulder stop forward for a predetermined desired length to the outer end of the fixture body member. A subsequent insertion of the fixture body member including the above optical fiber elements into a chemical stripping solution results in a softening of the exposed external coating thereat which permits easy removal thereof from the optical fiber while leaving a desired length coated fiber intact within the fixture body member.

  9. Digital autoradiography using silicon strip detectors

    Energy Technology Data Exchange (ETDEWEB)

    Overdick, M.

    1998-05-01

    Spatially resolving radiation detection systems operating in real time can be used to acquire autoradiographic images. An overview over alternatives to traditional autoradiography is given and the special features of these filmless methods are discussed. On this basis the design of a system for digital autoradiography using silicon strip detectors is presented. Special emphasis is put on the physical background of the detection process in the semiconductor and on the self-triggering read-out technique. The practical performance of the system is analyzed with respect to energy and spatial resolution. This analysis is complemented by case studies from cell biology (especially electrophoresis), botany and mineralogy. Also the results from a time-resolved autoradiographic experiment are presented. (orig.) 80 refs.

  10. Silicon strip detectors for the ATLAS upgrade

    CERN Document Server

    Gonzalez Sevilla, S; The ATLAS collaboration

    2011-01-01

    The Large Hadron Collider at CERN will extend its current physics program by increasing the peak luminosity by one order of magnitude. For ATLAS, one of the two general-purpose experiments of the LHC, an upgrade scenario will imply the complete replacement of its internal tracker due to the harsh conditions in terms of particle rates and radiation doses. New radiation-hard prototype n-in-p silicon sensors have been produced for the short-strip region of the future ATLAS tracker. The sensors have been irradiated up to the fluences expected in the high-luminous LHC collider. This paper summarizes recent results on the performance of the irradiated n-in-p detectors.

  11. Dynamic underground stripping. Innovative technology summary report

    International Nuclear Information System (INIS)

    1995-04-01

    Dynamic Underground Stripping (DUS) is a combination of technologies targeted to remediate soil and ground water contaminated with organic compounds. DUS is effective both above and below the water table and is especially well suited for sites with interbedded sand and clay layers. The main technologies comprising DUS are steam injection at the periphery of a contaminated area to heat permeable subsurface areas, vaporize volatile compounds bound to the soil, and drive contaminants to centrally located vacuum extraction wells; electrical heating of less permeable sediments to vaporize contaminants and drive them into the steam zone; and underground imaging such as Electrical Resistance Tomography to delineate heated areas to ensure total cleanup and process control. A full-scale demonstration was conducted on a gasoline spill site at Lawrence Livermore National Laboratory in Livermore, California from November 1992 through December 1993

  12. Evaluation of anatomy comic strips for further production and applications.

    Science.gov (United States)

    Shin, Dong Sun; Kim, Dae Hyun; Park, Jin Seo; Jang, Hae Gwon; Chung, Min Suk

    2013-09-01

    The corresponding author of the study has been sketching comic strips to explain anatomy in a humorous manner. All the anatomy comic strips, including those in Korean (650 episodes) and English (451 episodes), can be viewed on the homepage (http://anatomy.co.kr). Such comic strips were created with the aim of assisting medical students. However, their impact was unknown, and therefore, we surveyed the students' responses. We noted that anatomy grades were better in the students who read the comic strips. The comics helped the trainees chat with individuals with and without a medical background. The authors also considered comments on the problems with the comic strips and attempted to find solutions. The episodes are being currently used and further produced for educational purposes. To support this effort, the readers' valuable opinions will be continuously collected and assessed.

  13. Evaluation of anatomy comic strips for further production and applications

    Science.gov (United States)

    Shin, Dong Sun; Kim, Dae Hyun; Park, Jin Seo; Jang, Hae Gwon

    2013-01-01

    The corresponding author of the study has been sketching comic strips to explain anatomy in a humorous manner. All the anatomy comic strips, including those in Korean (650 episodes) and English (451 episodes), can be viewed on the homepage (http://anatomy.co.kr). Such comic strips were created with the aim of assisting medical students. However, their impact was unknown, and therefore, we surveyed the students' responses. We noted that anatomy grades were better in the students who read the comic strips. The comics helped the trainees chat with individuals with and without a medical background. The authors also considered comments on the problems with the comic strips and attempted to find solutions. The episodes are being currently used and further produced for educational purposes. To support this effort, the readers' valuable opinions will be continuously collected and assessed. PMID:24179697

  14. Comparative study of corneal strip extensometry and inflation tests.

    Science.gov (United States)

    Elsheikh, Ahmed; Anderson, Kevin

    2005-06-22

    Strip extensometry tests are usually considered less reliable than trephinate inflation tests in studying corneal biomechanics. In spite of the evident simplicity of strip extensometry tests, several earlier studies preferred inflation tests in determining the constitutive relationship of the cornea and its other material properties, such as Young's modulus and the hysteresis behaviour. In this research, the deficiencies of the strip tests are discussed and a mathematical procedure presented to take account of these deficiencies when obtaining the corneal material properties. The study also involves testing 10 pairs of porcine corneas using both strip extensometry and trephinate inflation techniques and the results are subjected to mathematical back analysis in order to determine the stress-strain behaviour. The behaviour obtained from the strip extensometry tests and using the new mathematical analysis procedure is shown to match closely the inflation test results.

  15. Superconducting strip detectors as position sensitive particle detectors

    Energy Technology Data Exchange (ETDEWEB)

    Scherschel, M. (Lab. fuer Festkoerperphysik, ETH-Hoenggerberg, Zuerich (Switzerland) Paul Scherrer Inst., Solid State Div., Villigen (Switzerland)); Finkbeiner, F. (Paul Scherrer Inst., Solid State Div., Villigen (Switzerland)); Zhao, S.P. (Paul Scherrer Inst., Solid State Div., Villigen (Switzerland)); Jaggi, A. (Paul Scherrer Inst., Solid State Div., Villigen (Switzerland)); Maier, T. (Paul Scherrer Inst., Solid State Div., Villigen (Switzerland)); Lerch, P. (Paul Scherrer Inst., Solid State Div., Villigen (Switzerland)); Zehnder, A. (Paul Scherrer Inst., Solid State Div., Villigen (Switzerland)); Ott, H.R. (Lab. fuer Festkoerperphysik, ETH-Hoenggerberg, Zuerich (Switzerland) Paul Scherrer Inst., Solid State Div., Villigen (Switzerland))

    1994-02-01

    The feasibility of using of current-biased superconducting strips for radiation detection is investigated. Narrow Ta strips are exposed to 5.5 MeV [alpha]-particle radiation and the rise-time of the induced voltage pulses is measured as function of temperature and bias current. The rise-time of the voltage signal strongly depends on the site on the strip which is hit by the [alpha]-particle. In order to determine the spatial resolution of a superconducting strip detector, position-sensitive measurements were performed. The maximum lateral resolution estimated so far is 25[mu]m in a 7[mu]m wide, 340 nm thick and 0.6 mm long Ta-strip. (orig.)

  16. Development and application of potentiometric stripping analysis

    Directory of Open Access Journals (Sweden)

    Babincev Ljiljana M.

    2017-01-01

    Full Text Available This paper focuses on the voltammetric determination of lead, cadmium and zinc in water. Two ways of determining were investigated: individually and all three metals simultaneously. The experiments were performed using the Potentiometric Stripping Analysis (PSA. Determination of metals in real samples was preceded by preliminary tests. Preliminary investigations were performed in order to determine the optimal conditions of measurement. It was concluded that the process of determining was for most part influenced by: pH, time of metals extraction, stirring rate of the solution and the thickness of the mercury layer on the working electrode. The smallest concentrations of metals which can be determined using this method are: for lead 22.48 μg dm-3, for cadmium 16.23 μg dm-3 and for zinc 18.75 μg dm-3. The obtained results deviated from the actual 1.12% for lead, 1.91% for cadmium and 1.81% for zinc. All tests (individually and simultaneously were conducted from model solution with concentration as follows: 44.96 μg dm-3 for lead, 32.47 μg dm-3 for cadmium and 37.50 μg dm-3 for zinc. The results of individual measurements deviated by 1.02% lead, 1.90% for cadmium and 1.89% for zinc. Simultaneously the contents were lower than real for: -4.58% for lead, cadmium for -1.91% and -1.89% for zinc. For the conditions determined, except for lead, deviations did not exceed ±2% . This indicates that Potentiometric Stripping Analysis is a good way of individual and simultaneous determination of lead, cadmium and zinc and for determination of their concentrations in water (river and groundwater.

  17. Study of inter-strip gap effects and efficiency for full energy detection of double sided silicon strip detectors

    International Nuclear Information System (INIS)

    Fisichella, M.; Forneris, J.; Grassi, L.

    2015-01-01

    We performed a characterization of Double Sided Silicon Strip Detectors (DSSSD) with the aim to carry out a systematic study of the inter-strip effects on the energy measurement of charged particles. The dependence of the DSSSD response on ion, energy and applied bias has been investigated. (author)

  18. Vaccine-induced cross-genotype reactive neutralizing antibodies against hepatitis C virus

    DEFF Research Database (Denmark)

    Meunier, Jean-Christophe; Gottwein, Judith M; Houghton, Michael

    2011-01-01

    We detected cross-reactive neutralizing antibodies (NtAb) against hepatitis C virus (HCV) in chimpanzees vaccinated with HCV-1 (genotype 1a) recombinant E1/E2 envelope glycoproteins. Five vaccinated chimpanzees, protected following HCV-1 challenge, were initially studied using the heterologous H77...... (genotype 1a) HCVpp assay. All animals had developed NtAb after the second vaccination; 4 animals had reciprocal titers of =200 at the time of challenge. Using genotypes 1a-6a HCV pseudoparticles (HCVpp) and cell culture-derived HCV (HCVcc) assays, cross-reactive NtAb were detected against 1a, 4a, 5a, and 6...

  19. Determination of the algal growth-limiting nutrients in strip mine ponds

    International Nuclear Information System (INIS)

    Bucknavage, M.J.; Aharrah, E.C.

    1984-01-01

    Using both a test organism, Ankistrodesmus falcatus, and natural phytoplankton, the Printz Algal Assay Bottle Test was used to determine the algal growth limiting nutrients in two strip mine ponds. Nitrogen, phosphorus, and iron were investigated, singly and in combination, as possible limiting nutrients. A synthetic chelator, Na 2 EDTA, was also used in the assay to test for the presence of metal toxicants and/or trace metal limitation. Because bacteria have a major influence on water chemistry, a separate assay incorporating the natural bacteria population was performed. In both ponds, assay results using test alga indicate phosphorus to be the primary limiting nutrient and nitrogen as a secondary factor. The presence of EDTA in combination with phosphate containing treatment promoted a higher algal concentration in both ponds. Iron was determined to be a secondary limiting nutrient in only one of the ponds. Natural phytoplankton of the two ponds responded in a similar manner to nutrient increases. Only one pond had the same results produced by both assays. Nutrient availability was influenced by the presence of bacteria in one pond but not in the other

  20. Microstructural research on hot strips of low carbon steel produced by a compact strip production line under different thermal histories

    International Nuclear Information System (INIS)

    Yu Hao; Chen Qixiang; Kang Yonglin; Sun Yi

    2005-01-01

    Coupons with the same composition and thickness (4.0 mm nominal gauge) obtained from hot strips of low carbon steel underwent a series of investigations to analyze the microstructural characteristics and mechanisms responsible for their differences in mechanical properties. Two different industrial technologies were adopted, although the strips used in this research were produced on the same Compact Strip Production (CSP) line. One of the strips was produced with a routine γ→α CSP thermal history, but the other with a γ→α→γ* conventional thermal history. The only difference between them was that one technology had a α→γ* thermal history. Different specimens of both types of strips were prepared for metallographic observation, tensile tests, electron back-scattered diffraction tests and positron annihilation technique tests. Experimental results showed that the differences in mechanical properties could be ascribed to dissimilarities not only in the grain size and textural components but also in dislocation density

  1. New Concept of Cultivation Using Limited Strip-Tillage with Strip Shallow Irrigation

    Directory of Open Access Journals (Sweden)

    Yazid Ismi Intara

    2014-04-01

    Full Text Available Normal 0 false false false IN X-NONE X-NONE Dry land is one of land resources which potentially used for food crop cultivation, especially in the areas which have light to medium technical obstacles. The development of technology to improve soil quality in marginal lands to be productive lands is still widely open for agricultural development in Indonesia. Rooting medium quality can be improved by changing soil tillage method and observing the proper crop irrigation technology. It can be the solution for crop cultivation in clay loam soil. This study aimed to obtain water movement model in a minimally-tilled clay soil with strip shallow irrigation. The concept is limited soil-tillage with strip shallow irrigation method, water supply technique, and crop water requirement. Method used in this study includes developing water movement model (software development in a minimally-tilled clay soil with subsurface irrigation. In the final stages, research also conducted water movement analysis testing apparatus in the laboratory, field validation of the subsurface irrigation performance, and cultivation technique testing to chili pepper growth (Capsicum annuumL.. The development of water movement simulation on a limited strip-tillage with subsurface irrigation uses the concept to quantify the amount of water in the soil. The analysis of movement pattern was demonstrated on contour patterns. It showed that the wetting process can reach depth zone – 5 cm to the rooting zone. It was an important discovery on the development of minimum stripe tillage soil with subsurface irrigation. Specifically, it can be concluded that: the result of fitting by eyes to diffusivity graphic and water content obtained the required parameter values for soil physical properties. It was then simulated on horizontal water movement model on a minimum strip-tillage with strip shallow irrigation /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso

  2. The production of rare earth elements group via tributyl phosphate extraction and precipitation stripping using oxalic acid

    Directory of Open Access Journals (Sweden)

    Esmaeil Jorjani

    2016-11-01

    Full Text Available In this study, solvent extraction and precipitation stripping were used to produce rare earth elements (REEs. Tributyl phosphate (TBP was used to extract yttrium, lanthanum, cerium, and neodymium from an aqueous solution produced by nitric acid leaching of apatite concentrate. In the extraction stage, the effects of TBP concentration, pH, contact time, temperature, and phase ratio were investigated. The results show that about 95%, 90%, 87% and 80% of neodymium, cerium, lanthanum, and yttrium, respectively, can be extracted in optimum conditions of extraction. Hot, deionized water was used to scrub the impurities from the loaded organic phase. The results showed that three stages of scrubbing with a phase ratio (Va/Vo of five removed about 80%, 30%, 27%, and 15% of Ca, Mg, Fe, and P, respectively, from loaded TBP, while less than 9% of total REEs was lost. The effects on precipitation stripping of oxalic acid concentration, contact time, and phase ratio were investigated. The results showed that precipitation stripping is a viable alternative to traditional acid stripping in the REEs production process. Mixed REEs oxide with an assay of about 90% can be achieved as a final product.

  3. Development of an immunochromatographic strip incorporating anti-mitragynine monoclonal antibody conjugated to colloidal gold for kratom alkaloids detection.

    Science.gov (United States)

    Limsuwanchote, Supattra; Putalun, Waraporn; Tanaka, Hiroyuki; Morimoto, Satoshi; Keawpradub, Niwat; Wungsintaweekul, Juraithip

    2017-12-29

    A lateral flow-based immunochromatographic strip was developed for the rapid detection of mitragynine (MG), a dominant alkaloid found in the leaves of kratom. Monoclonal antibody (mAb) against MG (anti-MG mAb) was conjugated to colloidal gold and used as a recognition probe. MG-ovalbumin conjugate (MG-OVA) and goat anti-mouse IgG were immobilized on the strip to produce a test zone and control zone, respectively. Based on the principle of a competitive assay, MG in a test sample competed with MG-OVA resident in the test zone to bind with colloidal gold-anti-MG mAb, resulting in an inverse relation of color intensity at the test zone and MG amount. The limit of detection (LOD) of the immunochromatographic strip is determined at 1 mg/mL of MG by visual assessment and 0.60 mg/mL by Image J analysis. The developed immunochromatographic strip can determine MG in kratom cocktails and kratom leaf samples. It could serve as a rapid and simple diagnostic kit for the detection of MG in kratom samples. Copyright © 2017 John Wiley & Sons, Ltd.

  4. Disposable lateral flow-through strip for smartphone-camera to quantitatively detect alkaline phosphatase activity in milk.

    Science.gov (United States)

    Yu, Ling; Shi, ZhuanZhuan; Fang, Can; Zhang, YuanYuan; Liu, YingShuai; Li, ChangMing

    2015-07-15

    A disposable lateral flow-through strip was developed for smartphone to fast one-step quantitatively detect alkaline phosphatase (ALP) activity in raw milk. The strip comprises two functional components, a conjugation pad loaded with phosphotyrosine-coated gold nanoparticles (AuNPs@Cys-Try-p) and a testing line coated with anti-phosphotryosine antibody (anti-Tyr-p mAb). The dephosphorylation activity of ALP at the testing zone can be quantitatively assayed by monitoring the accumulated AuNPs-induced color changes by smartphone camera, thus providing a highly convenient portable detection method. A trace amount of ALP as low as 0.1UL(-1) with a linear dynamic range of 0.1-150UL(-1) (R(2)=0.999) in pasteurized milk and raw milk can be one-step detected by the developed flow-through strip within 10min, demonstrating the potential of smartphone-based portable sensing device for pathogen detection. This bio-hazards free lateral flow-through testing strip can be also used to fabricate rapid, sensitive and inexpensive enzyme or immunosensors for broad portable clinic diagnosis and food contamination analysis, particularly in point-of-care and daily food quality inspection. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Smartphone-Based Dual-Modality Imaging System for Quantitative Detection of Color or Fluorescent Lateral Flow Immunochromatographic Strips.

    Science.gov (United States)

    Hou, Yafei; Wang, Kan; Xiao, Kun; Qin, Weijian; Lu, Wenting; Tao, Wei; Cui, Daxiang

    2017-12-01

    Nowadays, lateral flow immunochromatographic assays are increasingly popular as a diagnostic tool for point-of-care (POC) test based on their simplicity, specificity, and sensitivity. Hence, quantitative detection and pluralistic popular application are urgently needed in medical examination. In this study, a smartphone-based dual-modality imaging system was developed for quantitative detection of color or fluorescent lateral flow test strips, which can be operated anywhere at any time. In this system, the white and ultra-violet (UV) light of optical device was designed, which was tunable with different strips, and the Sobel operator algorithm was used in the software, which could enhance the identification ability to recognize the test area from the background boundary information. Moreover, this technology based on extraction of the components from RGB format (red, green, and blue) of color strips or only red format of the fluorescent strips can obviously improve the high-signal intensity and sensitivity. Fifty samples were used to evaluate the accuracy of this system, and the ideal detection limit was calculated separately from detection of human chorionic gonadotropin (HCG) and carcinoembryonic antigen (CEA). The results indicated that smartphone-controlled dual-modality imaging system could provide various POC diagnoses, which becomes a potential technology for developing the next-generation of portable system in the near future.

  6. Smartphone-Based Dual-Modality Imaging System for Quantitative Detection of Color or Fluorescent Lateral Flow Immunochromatographic Strips

    Science.gov (United States)

    Hou, Yafei; Wang, Kan; Xiao, Kun; Qin, Weijian; Lu, Wenting; Tao, Wei; Cui, Daxiang

    2017-04-01

    Nowadays, lateral flow immunochromatographic assays are increasingly popular as a diagnostic tool for point-of-care (POC) test based on their simplicity, specificity, and sensitivity. Hence, quantitative detection and pluralistic popular application are urgently needed in medical examination. In this study, a smartphone-based dual-modality imaging system was developed for quantitative detection of color or fluorescent lateral flow test strips, which can be operated anywhere at any time. In this system, the white and ultra-violet (UV) light of optical device was designed, which was tunable with different strips, and the Sobel operator algorithm was used in the software, which could enhance the identification ability to recognize the test area from the background boundary information. Moreover, this technology based on extraction of the components from RGB format (red, green, and blue) of color strips or only red format of the fluorescent strips can obviously improve the high-signal intensity and sensitivity. Fifty samples were used to evaluate the accuracy of this system, and the ideal detection limit was calculated separately from detection of human chorionic gonadotropin (HCG) and carcinoembryonic antigen (CEA). The results indicated that smartphone-controlled dual-modality imaging system could provide various POC diagnoses, which becomes a potential technology for developing the next-generation of portable system in the near future.

  7. The use of next-generation sequencing for the determination of rare blood group genotypes

    DEFF Research Database (Denmark)

    Jakobsen, M. A.; Dellgren, C.; Sheppard, C.

    2018-01-01

    Objectives: Next-generation sequencing (NGS) for the determination of rare blood group genotypes was tested in 72 individuals from different ethnicities. Background: Traditional serological-based antigen detection methods, as well as genotyping based on specific single nucleotide polymorphisms...... (SNPs) or single nucleotide variants (SNVs), are limited to detecting only a limited number of known antigens or alleles. NGS methods do not have this limitation. Methods: NGS using Ion torrent Personal Genome Machine (PGM) was performed with a customised Ampliseq panel targeting 15 different blood...... genotypes using commercial SNP assays. However, particularly for the Kidd, Duffy and Lutheran blood group systems, several SNVs were detected by the NGS assay that revealed additional coding information compared to other methods. Furthermore, the NGS assay allowed for the detection of genotypes related...

  8. Membrane air stripping utilizing a plate and frame configuration

    International Nuclear Information System (INIS)

    Boswell, S.T.

    1991-01-01

    Membrane air stripping has recently been proposed as a possible method to remove volatile organic chemicals (VOCs) and radon from drinking water supplies. Current and anticipated regulatory requirements, driven by health consequences, make the removal of these contaminants mandatory. This work examines the use of plate and frame membrane air stripping for the removal of VOCs and radon from a water supply. The theoretical basis of membrane air stripping and a literature review are included. The advantages of membrane air stripping versus other methods of removal, as well as the advantages of a plate and frame configuration versus a hollow fiber configuration for membrane air stripping are discussed. Multiple regression/correlation techniques are used to model mass transfer coefficients and fluid resistances. An economic evaluation is performed using the developed models. The costs of comparable membrane and packed tower air stripping systems are 4.86 cents per thousand gallons versus 4.36 cents per thousand gallons, respectively. This work indicates that plate and frame membrane air stripping may, in fact, prove to be an economical alternative to packed tower aeration and carbon adsorption for the removal of VOCs and radon

  9. Inadvertent Screw Stripping During Ankle Fracture Fixation in Elderly Bone

    Science.gov (United States)

    Dinah, A. Feroz; Mears, Simon C.; Knight, Trevor A.; Soin, Sandeep P.; Campbell, John T.; Belkoff, Stephen M.

    2011-01-01

    Poor screw purchase because of osteoporosis presents difficulties in ankle fracture fixation. The aim of our study was to determine if cortical thickness, unicortical versus bicortical purchase, and bone mineral density are predictors of inadvertent screw stripping and overtightening. Ten paired cadaver ankles (average donor age, 81.7 years; range, 50-97 years) were used for the study. Computed tomography scanning with phantoms of known density was used to determine the bone density along the distal fibula. A standard small-fragment, 7-hole, one-third tubular plate was applied to the lateral surface of the fibula, with 3 proximal bicortical cortical screws and 2 distal unicortical cancellous screws. A posterior plate, in which all 5 screws were cortical and achieved bicortical purchase, was subsequently applied to the same bones and positioned so that the screw holes did not overlap. A torque sensor was used to measure the torque of each screw during insertion (Ti) and then stripping (Ts). The effect of bone density, screw location, cortical thickness, and unicortical versus bicortical purchase on Ti and Ts was checked for significance (P screws were inadvertently stripped and 12% were overtightened. Despite 21% of the screws being stripped or being at risk for stripping, we found no significant predictors to warn of impending screw stripping. Additional work is needed to identify clinically useful predictors of screw stripping. PMID:23569675

  10. Infectious hepatitis C viruses of genotype 3A and 4A and uses thereof

    DEFF Research Database (Denmark)

    2015-01-01

    (strain S52) or genotype 4a (strain ED43). The invention therefore relates to the use of the nucleic acid sequences and polypeptides encoded by all or part of the sequences in the development of vaccines and diagnostic assays for HCV and in the development of screening assays for the identification...

  11. Reductive stripping process for uranium recovery from organic extracts

    Science.gov (United States)

    Hurst, F.J. Jr.

    1983-06-16

    In the reductive stripping of uranium from an organic extractant in a uranium recovery process, the use of phosphoric acid having a molarity in the range of 8 to 10 increases the efficiency of the reductive stripping and allows the strip step to operate with lower aqueous to organic recycle ratios and shorter retention time in the mixer stages. Under these operating conditions, less solvent is required in the process, and smaller, less expensive process equipment can be utilized. The high strength H/sub 3/PO/sub 4/ is available from the evaporator stage of the process.

  12. New technology for the production of magnesium strips and sheets

    Directory of Open Access Journals (Sweden)

    R. Kawalla

    2008-07-01

    Full Text Available A new production technology for magnesium strip, based on twin-roll-casting and strip rolling was developed in Freiberg Germany. By means of this economic method it is possible to produce strips in deep drawing quality with good forming properties in order to satisfy the request for low cost Mg sheets in the automotive and electronic industry. Both, coils as single sheets, were manufactured and rolled to a thickness of 1mm(0,5 mm. The technology of the new process and the properties of the twin-roll-casted material and the final sheets are presented.

  13. Dual Immunomagnetic Nanobeads-Based Lateral Flow Test Strip for Simultaneous Quantitative Detection of Carcinoembryonic Antigen and Neuron Specific Enolase

    Science.gov (United States)

    Lu, Wenting; Wang, Kan; Xiao, Kun; Qin, Weijian; Hou, Yafei; Xu, Hao; Yan, Xinyu; Chen, Yanrong; Cui, Daxiang; He, Jinghua

    2017-01-01

    A novel immunomagnetic nanobeads -based lateral flow test strip was developed for the simultaneous quantitative detection of neuron specific enolase (NSE) and carcinoembryonic antigen (CEA), which are sensitive and specific in the clinical diagnosis of small cell lung cancer. Using this nanoscale method, high saturation magnetization, carboxyl-modified magnetic nanobeads were successfully synthesized. To obtain the immunomagnetic probes, a covalent bioconjugation of the magnetic nanobeads with the antibody of NSE and CEA was carried out. The detection area contained test line 1 and test line 2 which captured the immune complexes sensitively and formed sandwich complexes. In this assay, cross-reactivity results were negative and both NSE and CEA were detected simultaneously with no obvious influence on each other. The magnetic signal intensity of the nitrocellulose membrane was measured by a magnetic assay reader. For quantitative analysis, the calculated limit of detection was 0.094 ng/mL for NSE and 0.045 ng/mL for CEA. One hundred thirty clinical samples were used to validate the test strip which exhibited high sensitivity and specificity. This dual lateral flow test strip not only provided an easy, rapid, simultaneous quantitative detection strategy for NSE and CEA, but may also be valuable in automated and portable diagnostic applications. PMID:28186176

  14. Distribution of HCV genotypes among different exposure categories in Brazil

    Directory of Open Access Journals (Sweden)

    Oliveira M.L.A.

    1999-01-01

    Full Text Available Hepatitis C virus (HCV infection is widespread and responsible for more than 60% of chronic hepatitis cases. HCV presents a genetic variability which has led to viral classification into at least 6 genotypes and a series of subtypes. These variants present characteristic geographical distribution, but their association with different responses to treatment with interferon and severity of disease still remains controversial. The aim of this study was to investigate the patterns of distribution of HCV genotypes among different exposure categories in Brazil. Two hundred and fifty anti-HCV positive samples were submitted to HCV-RNA detection by RT-PCR and their genotype was determined by restriction fragment length polymorphism (RFLP analysis. In addition, the genotype/subtype of 60 samples was also determined by a reverse hybridization assay. HCV 1 was the most prevalent (72.0%, followed by type 3 (25.3%, HCV 2 (2.0% and HCV 4 (0.7%. The HCV genotype distribution varied among the different exposure categories, with HCV 1 being more frequent among blood donors, hemophiliacs and hemodialysis patients. A high frequency of HCV 3 was observed in cirrhotic patients, blood donors from the South of Brazil and injecting drug users (IDUs. The general distribution of the HCV genotype in Brazil is similar to that in other regions of the world.

  15. Profile of a science comic strip author

    CERN Multimedia

    Anaïs Schaeffer

    2014-01-01

    After studying visual arts, Lison Bernet worked as a lock keeper, waitress, grape picker, farm labourer and chef before finally returning to her first love: drawing. Today a scientific illustrator, Lison is the author of the cartoon strip "La BD du LHC", which she draws every month for LHC France (by CNRS/IN2P3 and CEA/Irfu, see here).   © Lison Bernet. Lison’s career path might seem somewhat chaotic, but it is a reflection of the artist herself: original and passionate. “I never do anything by half measures. When I got into cooking for example [Lison took a chef training course for adults], I became completely wrapped up in it. I even went as far as cooking roasts during my lunch hour, just for practice…” says Lison. On completing the course, Lison got a job as a chef on a canal boat. And it was then that she got the drawing bug again. “I started keeping an illustrated travel diary,” she says. &ldquo...

  16. Operation of the CMS silicon strip tracker

    CERN Document Server

    Gotra, Yuri

    2011-01-01

    The CMS Silicon Strip Tracker (SST), comprising 9.6 million readout channels from 15148 modules covering an area of about 200 square meters, needs to be precisely calibrated in order to correctly interpret and reconstruct the events recorded from the detector, ensuring that the SST performance fully meets the physics research program of the CMS experiment. Calibration constants may be derived from promptly reconstructed events as well as from pedestal runs gathered just before the acquisition of physics runs. These calibration procedures were exercised in summer and winter 2009, when the CMS detector was commissioned using cosmic muons and proton-proton collisions at a center-of-mass energies of 900 GeV and 2.36 TeV. During these data taking periods the performance of the SST was carefully studied: the noise of the detector, the data integrity, the signal-to-noise ratio, the hit reconstruction efficiency, the calibration workflows have been all checked for stability and for different conditions, at the module...

  17. An improved rolled strip pulse forming line.

    Science.gov (United States)

    Li, Song; Qian, Bao-Liang; Yang, Han-Wu; Gao, Jing-Ming; Liu, Zhao-Xi

    2013-06-01

    The rolled strip pulse forming line (RSPFL) has advantages of compactness, portability, and long pulse achievability which could well meet the requirements of industrial application of the pulse power technology. In this paper, an improved RSPFL with an additional insulator between the grounded conductors is investigated numerically and experimentally. Results demonstrate that the jitter on the flat-top of the output voltage waveform is reduced to 3.8% due to the improved structure. Theoretical analysis shows that the electromagnetic coupling between the conductors of the RSPFL strongly influences the output voltage waveform. Therefore, the new structure was designed to minimize the detrimental effect of the electromagnetic coupling. Simulation results show that the electromagnetic coupling can be efficiently reduced in the improved RSPFL. Experimental results illustrate that the improved RSPFL, with dimensions and weight of Φ 290 × 250 mm and 16 kg, when used as a simple pulse forming line, could generate a well shaped quasi-square pulse with output power of hundreds of MW and pulse duration of 250 ns. Importantly, the improved RSPFL was successfully used as a Blumlein pulse forming line, and a 10.8 kV, 260 ns quasi-square pulse was obtained on a 2 Ω dummy load. Experiments show reasonable agreement with numerical analysis.

  18. Microbead agglutination based assays

    KAUST Repository

    Kodzius, Rimantas

    2013-01-21

    We report a simple and rapid room temperature assay for point-of-care (POC) testing that is based on specific agglutination. Agglutination tests are based on aggregation of microbeads in the presence of a specific analyte thus enabling the macroscopic observation. Such tests are most often used to explore antibody-antigen reactions. Agglutination has been used for protein assays using a biotin/streptavidin system as well as a hybridization based assay. The agglutination systems are prone to selftermination of the linking analyte, prone to active site saturation and loss of agglomeration at high analyte concentrations. We investigated the molecular target/ligand interaction, explaining the common agglutination problems related to analyte self-termination, linkage of the analyte to the same bead instead of different microbeads. We classified the agglutination process into three kinds of assays: a two- component assay, a three-component assay and a stepped three- component assay. Although we compared these three kinds of assays for recognizing DNA and protein molecules, the assay can be used for virtually any molecule, including ions and metabolites. In total, the optimized assay permits detecting analytes with high sensitivity in a short time, 5 min, at room temperature. Such a system is appropriate for POC testing.

  19. A greenhouse screening assay for Botrytis tulipae resistance in tulips

    NARCIS (Netherlands)

    Straathof, T.P.; Mes, J.J.; Eikelboom, W.; Tuyl, van J.M.

    2002-01-01

    As a leaf pathogen, Botrytis tulipae severely affects tulip bulb production. Chemical control is not desired for environmental reasons. Thus, resistant cultivars can play an important role in the control of this disease. To select genotypes resistant to B. tulipae, a reliable screening assay is

  20. Viral fitness does not correlate with three genotype displacement events involving infectious hematopoietic necrosis virus

    Science.gov (United States)

    Kell, Alison M.; Wargo, Andrew R.; Kurath, Gael

    2014-01-01

    Viral genotype displacement events are characterized by the replacement of a previously dominant virus genotype by a novel genotype of the same virus species in a given geographic region. We examine here the fitness of three pairs of infectious hematopoietic necrosis virus (IHNV) genotypes involved in three major genotype displacement events in Washington state over the last 30 years to determine whether increased virus fitness correlates with displacement. Fitness was assessed using in vivo assays to measure viral replication in single infection, simultaneous co-infection, and sequential superinfection in the natural host, steelhead trout. In addition, virion stability of each genotype was measured in freshwater and seawater environments at various temperatures. By these methods, we found no correlation between increased viral fitness and displacement in the field. These results suggest that other pressures likely exist in the field with important consequences for IHNV evolution.

  1. Phenotypic and genotypic screening of rice genotypes at seedling ...

    African Journals Online (AJOL)

    Selection for salinity tolerance genotypes of rice based on phenotypic performance alone is less reliable and will delay progress in breeding. Recent advent of molecular markers, microsatellites or simple sequence repeats (SSRs) are used to find out salt tolerant rice genotypes. Three selected SSR markers; RM7075, ...

  2. Common genotypes of hepatitis B virus

    International Nuclear Information System (INIS)

    Idrees, M.; Khan, S.; Riazuddin, S.

    2004-01-01

    Objective: To find out the frequency of common genotypes of hepatitis-B virus (HBV). Subjects and Methods: HBV genotypes were determined in 112 HBV DNA positive sera by a simple and precise molecular genotyping system base on PCR using type-specific primers for the determination of genotypes of HBV A through H. Results: Four genotypes (A,B,C and D) out of total eight reported genotypes so far were identified. Genotypes A, B and C were predominant. HBV genotype C was the most predominant in this collection, appearing in 46 samples (41.7%). However, the genotypes of a total of 5 (4.46%) samples could not be determined with the present genotyping system. Mixed genotypes were seen in 8(7.14% HBV) isolates. Five of these were infected with genotypes A/D whereas two were with genotypes C/D. One patient was infected with 4 genotypes (A/B/C/D). Genotype A (68%) was predominant in Sindh genotype C was most predominant in North West Frontier Province (NWFP) (68.96) whereas genotype C and B were dominant in Punjab (39.65% and 25.86% respectively). Conclusion: All the four common genotypes of HBV found worldwide (A,B,C and D) were isolated. Genotype C is the predominant Genotypes B and C are predominant in Punjab and N.W.F.P. whereas genotype A is predominant in Sindh. (author)

  3. Nanoscale Test Strips for Multiplexed Blood Analysis, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of our nanoscale test strips, or nanostrips, is to provide rapid, low-cost, powerful multiplexed analyses in a diminutive form so that whole body health...

  4. Acrylamide content and color development in fried potato strips

    DEFF Research Database (Denmark)

    Pedreschi, F.; Kaack, K.; Granby, Kit

    2006-01-01

    and 45 min; 90 degrees C for 3 and 10 min); (iii) immersed in a citric acid solution of 10 g/L for an hour; (iv) immersed in a sodium pyrophosphate solution of 10 g/L for an hour. Acrylamide content and color was determined in the potato strips after frying. Immersed strips in water for 120 min showed...... (13 5, 327 and 564 mu m acrylamide/kg for 150, 170 and 190 degrees C, respectively). Potato strip immersion in citric acid solution of 10 g/L reduced much more the acrylamide formation after frying than the strip immersion in sodium pyrophosphate solution of 10 g/L (53% vs. 17%, respectively, average...

  5. Digital simulation of anodic stripping voltammetry from thin film electrodes

    International Nuclear Information System (INIS)

    Magallanes, J.F.

    1984-01-01

    The anodic stripping voltammetry (ASV) is routinely applied to control of Cu(II) in heavy water in the primary cooling loop of the Nuclear Power Reactor. The anodic stripping voltammetry (ASV) is a very well-known technique in electroanalytical chemistry. However, due to the complexity of the phenomena, it is practised with the fundamentals of empiric considerations. A geometric model for the anodic stripping voltammetry (ASV) from thin film electrodes which can be calculated by explicit digital simulation method is proposed as a possibility of solving the electrochemically reversible, cuasi-reversible and irreversible reactions under linear potential scan and multiple potential scans. (Until now the analytical mathematical method was applied to reversible reactions). All the results are compared with analytical solutions and experimental results and it permits to conclude that the anodic stripping voltammetry (ASV) can be studied with the simplicity and potentialities of explicit digital simulation methods. (M.E.L.) [es

  6. Data acquisition software for the CMS strip tracker

    International Nuclear Information System (INIS)

    Bainbridge, R; Cripps, N; Fulcher, J; Radicci, V; Wingham, M; Baulieu, G; Bel, S; Delaere, C; Drouhin, F; Gill, K; Mirabito, L; Cole, J; Jesus, A C A; Giassi, A; Giordano, D; Gross, L; Hahn, K; Mersi, S; Nikolic, M; Tkaczyk, S

    2008-01-01

    The CMS silicon strip tracker, providing a sensitive area of approximately 200 m 2 and comprising 10 million readout channels, has recently been completed at the tracker integration facility at CERN. The strip tracker community is currently working to develop and integrate the online and offline software frameworks, known as XDAQ and CMSSW respectively, for the purposes of data acquisition and detector commissioning and monitoring. Recent developments have seen the integration of many new services and tools within the online data acquisition system, such as event building, online distributed analysis, an online monitoring framework, and data storage management. We review the various software components that comprise the strip tracker data acquisition system, the software architectures used for stand-alone and global data-taking modes. Our experiences in commissioning and operating one of the largest ever silicon micro-strip tracking systems are also reviewed

  7. The Construction of the CMS Tracker Silicon Strip Modules

    CERN Document Server

    Chiorboli, Massimiliano

    2006-01-01

    The procedures followed for the construction of the Silicon Strip Modules to be used in the CMS Tracker Detector are described. The steps of the production chain are described, and the results are given.

  8. Stability of flow over axisymmetric bodies with porous suction strips

    Science.gov (United States)

    Nayfeh, A. H.; Reed, H. L.

    1982-01-01

    Linear triple deck, closed form solutions for mean-flow quantities are developed for axisymmetric incompressible flow past a body with porous strips. The solutions account for upstream influence and are linear superpositions of the flow past the body without suction plus the perturbations due to the suction strips. Flow past the suctionless body is calculated using the Transition Analysis Program System, and a simple linear optimization scheme to determine number, spacing, and mass flow rate through the strips on an axisymmetric body is developed using the linear, triple-deck, closed-form solutions. The theory is demonstrated by predicting optimal strip distributions, and the effect of various adverse pressure-gradient situations on stability is studied.

  9. The New Silicon Strip Detectors for the CMS Tracker Upgrade

    CERN Document Server

    Dragicevic, Marko

    2010-01-01

    The first introductory part of the thesis describes the concept of the CMS experiment. The tasks of the various detector systems and their technical implementations in CMS are explained. To facilitate the understanding of the basic principles of silicon strip sensors, the subsequent chapter discusses the fundamentals in semiconductor technology, with particular emphasis on silicon. The necessary process steps to manufacture strip sensors in a so-called planar process are described in detail. Furthermore, the effects of irradiation on silicon strip sensors are discussed. To conclude the introductory part of the thesis, the design of the silicon strip sensors of the CMS Tracker are described in detail. The choice of the substrate material and the complex geometry of the sensors are reviewed and the quality assurance procedures for the production of the sensors are presented. Furthermore the design of the detector modules are described. The main part of this thesis starts with a discussion on the demands on the ...

  10. Results of Laboratory Testing of Advanced Power Strips: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Earle, L.; Sparn, B.

    2012-08-01

    This paper describes the results of a laboratory investigation to evaluate the technical performance of advanced power strip (APS) devices when subjected to a range of home entertainment center and home office usage scenarios.

  11. Continuous Strip Reduction Test Simulating Tribological Conditions in Ironing

    DEFF Research Database (Denmark)

    Üstünyagiz, Esmeray; Nielsen, Chris Valentin; Christiansen, Peter

    2017-01-01

    materials, surface roughnesses, normal pressure, sliding length, sliding speed, interface temperature and lubrication. This paper proposes a new Strip Reduction Test (SRT) for industrial ironing processes that is capable of replicating the highly severe tribological conditions that are experienced during...

  12. Nanoscale Test Strips for Multiplexed Blood Analysis, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The goal of our nanoscale test strips, or nanostrips, is to provide rapid, low-cost, powerful multiplexed analyses in a diminutive form so that whole body health...

  13. High Pressure Water Stripping Using Multi-Orifice Nozzles

    Science.gov (United States)

    Hoppe, David

    1999-01-01

    The use of multi-orifice rotary nozzles greatly increases the speed and stripping effectiveness of high pressure water blasting systems, but also greatly increases the complexity of selecting and optimizing the operating parameters. The rotational speed of the nozzle must be coupled with its transverse velocity as it passes across the surface of the substrate being stripped. The radial and angular positions of each orifice must be included in the analysis of the nozzle configuration. Orifices at the outer edge of the nozzle head move at a faster rate than the orifices located near the center. The energy transmitted to the surface from the impact force of the water stream from an outer orifice is therefore spread over a larger area than energy from an inner orifice. Utilizing a larger diameter orifice in the outer radial positions increases the total energy transmitted from the outer orifice to compensate for the wider distribution of energy. The total flow rate from the combination of all orifices must be monitored and should be kept below the pump capacity while choosing orifice to insert in each position. The energy distribution from the orifice pattern is further complicated since the rotary path of all the orifices in the nozzle head pass through the center section. All orifices contribute to the stripping in the center of the path while only the outer most orifice contributes to the stripping at the edge of the nozzle. Additional orifices contribute to the stripping from the outer edge toward the center section. With all these parameters to configure and each parameter change affecting the others, a computer model was developed to track and coordinate these parameters. The computer simulation graphically indicates the cumulative affect from each parameter selected. The result from the proper choices in parameters is a well designed, highly efficient stripping system. A poorly chosen set of parameters will cause the nozzle to strip aggressively in some areas

  14. HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples

    Directory of Open Access Journals (Sweden)

    Alyssa M. Cornall

    2017-12-01

    Full Text Available Purpose: To compare human papillomavirus genotype-specific performance of two genotyping assays, Anyplex II HPV28 (Seegene and EuroArray HPV (EuroImmun, with Linear Array HPV (Roche. Methods: DNA extracted from clinican-collected cervical brush specimens in PreservCyt medium (Hologic, from 403 women undergoing management for detected cytological abnormalities, was tested on the three assays. Genotype-specific agreement were assessed by Cohen's kappa statistic and Fisher's z-test of significance between proportions. Results: Agreement between Linear Array and the other 2 assays was substantial to almost perfect (κ = 0.60 − 1.00 for most genotypes, and was almost perfect (κ = 0.81 – 0.98 for almost all high-risk genotypes. Linear Array overall detected most genotypes more frequently, however this was only statistically significant for HPV51 (EuroArray; p = 0.0497, HPV52 (Anyplex II; p = 0.039 and HPV61 (Anyplex II; p=0.047. EuroArray detected signficantly more HPV26 (p = 0.002 and Anyplex II detected more HPV42 (p = 0.035 than Linear Array. Each assay performed differently for HPV68 detection: EuroArray and LA were in moderate to substantial agreement with Anyplex II (κ = 0.46 and 0.62, respectively, but were in poor disagreement with each other (κ = −0.01. Conclusions: EuroArray and Anyplex II had similar sensitivity to Linear Array for most high-risk genotypes, with slightly lower sensitivity for HPV 51 or 52. Keywords: Human papillomavirus, Genotyping, Linear Array, Anyplex II, EuroArray, Cervix

  15. Pt-MWCNT modified carbon electrode strip for rapid and quantitative detection of H2O2 in food

    Directory of Open Access Journals (Sweden)

    Tai-Cheng Chou

    2018-04-01

    Full Text Available A single-use screen-printed carbon electrode strip was designed and fabricated. Nanohybrids, prepared by deposition of platinum (Pt nanoparticles on multi-wall carbon nanotube (MWCNT, was modified on the surface of screen-printed carbon electrode for the development of a fast, sensitive and cost-effective hydrogen peroxide (H2O2 detection amperometric sensor strip. With Pt-MWCNT nanohybrids surface modification, current generated in response to H2O2 by the screen-printed carbon electrode strip was enhanced 100 fold with an applied potential of 300 mV. Quality of as-prepared electrode strip was assured by the low coefficient of variation (CV (<5% of currents measured at 5 s. Three linear detection ranges with sensitivity of 75.2, 120.7, and 142.8 μA mM−1 cm−2 were observed for H2O2 concentration in the range of 1–15 mM, 0.1–1 mM, and 10–100 μM, respectively. The lowest H2O2 concentration could be measured by the as-prepared strip was 10 μM. H2O2 levels in green tea infusion and pressed Tofu could be rapidly detected with results comparable to that measured by ferrous oxidation xylenol orange (FOX assay and peroxidase colorimetric method. Keywords: Platinum-multi-wall carbon nanotube (Pt-MWCNT, Disposable carbon electrode, Hydrogen peroxide (H2O2, Amperometric sensor

  16. The CMS Silicon Strip Tracker: Design and Production Status

    CERN Document Server

    Affolder, A A

    2004-01-01

    The CMS Silicon Strip Tracker (SST) will be equipped with 15000 silicon micro-strip detector modules covering a surface of 200 m^2. This paper details the SST layout and updates the status of construction. Progress in the fabrication of module components is detailed, with focus on the front-end hybrid and silicon sensor production. The assembly of over 2200 modules using industrial methods is described; the quality assurance protocols have resulted in modules of extremely high mechanical and electrical quality.

  17. Area Strip Mine Reclamation Using Dredged Material: A Field Demonstration.

    Science.gov (United States)

    1980-07-01

    reclamation of abandoned strip mine spoils.l1 Regraded areas can be seeded or planted with cuttings or seedlings ; however, most strip mine areas are...Helianthus petiolaris PLAINS THREE-AWN GRASS Aristida oligantha PRICKLEY LETTUCE Lactuca scariola QUACK GRASS Agropyron repens RED TOP Agrostis alba REED...Arctium minus FILD THISTLE Cirsiumn vlare BUL THISTLE Cirsiun aulgare A9’ COMMON SOW THISTLE Sonchus uliginosus PRICKLY LETTUCE Lactuca scariola A10

  18. An analysis of stripping to isolated analog resonances

    International Nuclear Information System (INIS)

    Pessoa, E.F.; Toledo Piza, A.F.R. de.

    1983-04-01

    The Feshbach projection formalism is used to calculate the form factors for the (d,n) stripping process to isolated analog resonances. These are used in a standard DWBA stripping calculation in which the radial integration over all space is accomplished by including outerspace contributions evaluated along the complex contours of Vincent and Fortune. It turns out that the shape and magnitude of the predicted cross section is quite insensitive to the continuum proton wave emanating from the resonant residual state. (Author) [pt

  19. Optimising carbon electrode materials for adsorptive stripping voltammetry

    OpenAIRE

    Chaisiwamongkhol, K; Batchelor-McAuley, C; Sokolov, S; Holter, J; Young, N; Compton, R

    2017-01-01

    Different types of carbon electrode materials for adsorptive stripping voltammetry are studied through the use of cyclic voltammetry. Capsaicin is utilised as a model compound for adsorptive stripping voltammetry using unmodified and modified basal plane pyrolytic graphite (BPPG) electrodes modified with multi-walled carbon nanotubes, carbon black or graphene nanoplatelets, screen printed carbon electrodes (SPE), carbon nanotube modified screen printed electrodes, and carbon paste electrodes....

  20. Radioreceptor opioid assay

    International Nuclear Information System (INIS)

    Miller, R.J.; Chang, K.-J.

    1981-01-01

    A radioreceptor assay is described for assaying opioid drugs in biological fluids. The method enables the assay of total opioid activity, being specific for opioids as a class but lacking specificity within the class. A radio-iodinated opioid and the liquid test sample are incubated with an opiate receptor material. The percentage inhibition of the binding of the radio-iodinated compound to the opiate receptor is calculated and the opioid activity of the test liquid determined from a standard curve. Examples of preparing radio-iodinated opioids and assaying opioid activity are given. A test kit for the assay is described. Compared to other methods, this assay is cheap, easy and rapid. (U.K.)

  1. An epidemiologic survey of methicillin-resistant Staphylococcus aureus by combined use of mec-HVR genotyping and toxin genotyping in a university hospital in Japan.

    Science.gov (United States)

    Nishi, Junichiro; Yoshinaga, Masao; Miyanohara, Hiroaki; Kawahara, Motoshi; Kawabata, Masaharu; Motoya, Toshiro; Owaki, Tetsuhiro; Oiso, Shigeru; Kawakami, Masayuki; Kamewari, Shigeko; Koyama, Yumiko; Wakimoto, Naoko; Tokuda, Koichi; Manago, Kunihiro; Maruyama, Ikuro

    2002-09-01

    To evaluate the usefulness of an assay using two polymerase chain reaction-based genotyping methods in the practical surveillance of methicillin-resistant Staphylococcus aureus (MRSA). Nosocomial infection and colonization were surveyed monthly in a university hospital in Japan for 20 months. Genotyping with mec-HVR is based on the size of the mec-associated hypervariable region amplified by polymerase chain reaction. Toxin genotyping uses a multiplex polymerase chain reaction method to amplify eight staphylococcal toxin genes. Eight hundred nine MRSA isolates were classified into 49 genotypes. We observed differing prevalences of genotypes for different hospital wards, and could rapidly demonstrate the similarity of genotype for outbreak isolates. The incidence of genotype D: SEC/TSST1 was significantly higher in isolates causing nosocomial infections (49.5%; 48 of 97) than in nasal isolates (31.4%; 54 of 172) (P = .004), suggesting that this genotype may represent the nosocomial strains. The combined use of these two genotyping methods resulted in improved discriminatory ability and should be further investigated.

  2. Absolute nuclear material assay

    Science.gov (United States)

    Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

    2010-07-13

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  3. Absolute nuclear material assay

    Science.gov (United States)

    Prasad, Manoj K [Pleasanton, CA; Snyderman, Neal J [Berkeley, CA; Rowland, Mark S [Alamo, CA

    2012-05-15

    A method of absolute nuclear material assay of an unknown source comprising counting neutrons from the unknown source and providing an absolute nuclear material assay utilizing a model to optimally compare to the measured count distributions. In one embodiment, the step of providing an absolute nuclear material assay comprises utilizing a random sampling of analytically computed fission chain distributions to generate a continuous time-evolving sequence of event-counts by spreading the fission chain distribution in time.

  4. A new strips tracker for the upgraded ATLAS ITk detector

    Science.gov (United States)

    David, C.

    2018-01-01

    The ATLAS detector has been designed and developed to function in the environment of the present Large Hadron Collider (LHC). At the next-generation tracking detector proposed for the High Luminosity LHC (HL-LHC), the so-called ATLAS Phase-II Upgrade, the fluences and radiation levels will be higher by as much as a factor of ten. The new sub-detectors must thus be faster, of larger area, more segmented and more radiation hard while the amount of inactive material should be minimized and the power supply to the front-end systems should be increased. For those reasons, the current inner tracker of the ATLAS detector will be fully replaced by an all-silicon tracking system that consists of a pixel detector at small radius close to the beam line and a large area strip tracker surrounding it. This document gives an overview of the design of the strip inner tracker (Strip ITk) and summarises the intensive R&D activities performed over the last years by the numerous institutes within the Strips ITk collaboration. These studies are accompanied with a strong prototyping effort to contribute to the optimisation of the Strip ITk's structure and components. This effort culminated recently in the release of the ATLAS Strips ITk Technical Design Report (TDR).

  5. Efficient ozone, sulfate, and ammonium free resist stripping process

    Science.gov (United States)

    Dattilo, Davide; Dietze, Uwe

    2014-07-01

    In recent years, photomask resist strip and cleaning technology development was substantially driven by the industry's need to prevent surface haze formation through the elimination of sulfuric acid and ammonium hydroxide from these processes. As a result, conventional SPM (H2SO4 + H2O2) was replaced with Ozone water (DIO3) for resist stripping and organic removal to eliminate chemical haze formation [1, 2]. However, it has been shown that DIO3 basted strip and clean process causes oxidative degradation of photomask materials [3, 4]. Such material damage can affect optical properties of funcitional mask layers, causeing CD line-width, phase, transmission and reflection changes, adversely affecting image transfer during the Lithography process. To overcome Ozone induced surface damage, SUSS MicroTec successfully developed a highly efficient strip process, where photolysis of DIO3 is leading to highly reactive hydroxyl radical formation, as the main contribution to hydrocarbon removal without surface damage [5]. This technology has been further extended to a final clean process, which is utilizing pure DI water for residual organic material removal during final clean [6]. Recently, SUS MicroTec did also successfully release strip and clean processes which completely remove NH4OH, eliminating any chemicals known today to induce haze [7]. In this paper we show the benefits of these new technologies for highly efficient sulfate and ammonium free stripping and cleaning processes.

  6. Development of a thin steel strip casting process. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Williams, R.S.

    1994-04-01

    This is a comprehensive effort to develop direct strip casting to the point where a pilot scale program for casting carbon steel strip could be initiated. All important aspects of the technology were being investigated, however the program was terminated early due to a change in the business strategy of the primary contractor, Armco Inc. (focus to be directed at specialty steels, not low carbon steel). At termination, the project was on target on all milestones and under budget. Major part was casting of strip at the experiment casting facility. A new caster, capable of producing direct cast strip of up to 12 in. wide in heats of 1000 and 3000 lb, was used. A total of 81 1000-1200 lb heats were cast as well as one test heat of 3000 lb. Most produced strip of from 0.016 to 0.085 in. thick. Process reliability was excellent for short casting times; quality was generally poor from modern hot strip mill standards, but the practices necessary for good surface quality were identified.

  7. Tricyclic antidepressant radioreceptor assay

    International Nuclear Information System (INIS)

    Innis, R.B.; Tune, L.; Rock, R.; Depaulo, R.; U'Prichard, D.C.; Snyder, S.M.

    1979-01-01

    A receptor assay for tricyclic antidepressants described here is based on the ability of these drugs to compete with [ 3 H]-3-guinuclidnyl benzilate ( 3 H-QNB) for binding to muscarinic cholinergic receptors in rat brain membranes. The assay is sensitive, in that it can detect, for example, 2ng/ml nortriptyline in plasma. Seven plasma samples from depressed patients treated with nortriptyline were assayed with the radioreceptor and gas liquid chromatographic methods, and the results from these two methods were almost identical. This assay should be used cautiously, if at all, in patients treated with other drugs that have potent anticholinergic effects. (Auth.)

  8. HBV Genotypic Variability in Cuba

    Science.gov (United States)

    Loureiro, Carmen L.; Aguilar, Julio C.; Aguiar, Jorge; Muzio, Verena; Pentón, Eduardo; Garcia, Daymir; Guillen, Gerardo; Pujol, Flor H.

    2015-01-01

    The genetic diversity of HBV in human population is often a reflection of its genetic admixture. The aim of this study was to explore the genotypic diversity of HBV in Cuba. The S genomic region of Cuban HBV isolates was sequenced and for selected isolates the complete genome or precore-core sequence was analyzed. The most frequent genotype was A (167/250, 67%), mainly A2 (149, 60%) but also A1 and one A4. A total of 77 isolates were classified as genotype D (31%), with co-circulation of several subgenotypes (56 D4, 2 D1, 5 D2, 7 D3/6 and 7 D7). Three isolates belonged to genotype E, two to H and one to B3. Complete genome sequence analysis of selected isolates confirmed the phylogenetic analysis performed with the S region. Mutations or polymorphisms in precore region were more common among genotype D compared to genotype A isolates. The HBV genotypic distribution in this Caribbean island correlates with the Y lineage genetic background of the population, where a European and African origin prevails. HBV genotypes E, B3 and H isolates might represent more recent introductions. PMID:25742179

  9. Genotyping with CRISPR-Cas-derived RNA-guided endonucleases.

    Science.gov (United States)

    Kim, Jong Min; Kim, Daesik; Kim, Seokjoong; Kim, Jin-Soo

    2014-01-01

    Restriction fragment length polymorphism (RFLP) analysis is one of the oldest, most convenient and least expensive methods of genotyping, but is limited by the availability of restriction endonuclease sites. Here we present a novel method of employing CRISPR/Cas-derived RNA-guided engineered nucleases (RGENs) in RFLP analysis. We prepare RGENs by complexing recombinant Cas9 protein derived from Streptococcus pyogenes with in vitro transcribed guide RNAs that are complementary to the DNA sequences of interest. Then, we genotype recurrent mutations found in cancer and small insertions or deletions (indels) induced in cultured cells and animals by RGENs and other engineered nucleases such as transcription activator-like effector nucleases (TALENs). Unlike T7 endonuclease I or Surveyor assays that are widely used for genotyping engineered nuclease-induced mutations, RGEN-mediated RFLP analysis can detect homozygous mutant clones that contain identical biallelic indel sequences and is not limited by sequence polymorphisms near the nuclease target sites.

  10. SNP high-throughput screening in grapevine using the SNPlex™ genotyping system

    Directory of Open Access Journals (Sweden)

    Velasco Riccardo

    2008-01-01

    Full Text Available Abstract Background Until recently, only a small number of low- and mid-throughput methods have been used for single nucleotide polymorphism (SNP discovery and genotyping in grapevine (Vitis vinifera L.. However, following completion of the sequence of the highly heterozygous genome of Pinot Noir, it has been possible to identify millions of electronic SNPs (eSNPs thus providing a valuable source for high-throughput genotyping methods. Results Herein we report the first application of the SNPlex™ genotyping system in grapevine aiming at the anchoring of an eukaryotic genome. This approach combines robust SNP detection with automated assay readout and data analysis. 813 candidate eSNPs were developed from non-repetitive contigs of the assembled genome of Pinot Noir and tested in 90 progeny of Syrah × Pinot Noir cross. 563 new SNP-based markers were obtained and mapped. The efficiency rate of 69% was enhanced to 80% when multiple displacement amplification (MDA methods were used for preparation of genomic DNA for the SNPlex assay. Conclusion Unlike other SNP genotyping methods used to investigate thousands of SNPs in a few genotypes, or a few SNPs in around a thousand genotypes, the SNPlex genotyping system represents a good compromise to investigate several hundred SNPs in a hundred or more samples simultaneously. Therefore, the use of the SNPlex assay, coupled with whole genome amplification (WGA, is a good solution for future applications in well-equipped laboratories.

  11. Discrepancy between Hepatitis C Virus Genotypes and NS4-Based Serotypes: Association with Their Subgenomic Sequences

    Directory of Open Access Journals (Sweden)

    Nan Nwe Win

    2017-01-01

    Full Text Available Determination of hepatitis C virus (HCV genotypes plays an important role in the direct-acting agent era. Discrepancies between HCV genotyping and serotyping assays are occasionally observed. Eighteen samples with discrepant results between genotyping and serotyping methods were analyzed. HCV serotyping and genotyping were based on the HCV nonstructural 4 (NS4 region and 5′-untranslated region (5′-UTR, respectively. HCV core and NS4 regions were chosen to be sequenced and were compared with the genotyping and serotyping results. Deep sequencing was also performed for the corresponding HCV NS4 regions. Seventeen out of 18 discrepant samples could be sequenced by the Sanger method. Both HCV core and NS4 sequences were concordant with that of genotyping in the 5′-UTR in all 17 samples. In cloning analysis of the HCV NS4 region, there were several amino acid variations, but each sequence was much closer to the peptide with the same genotype. Deep sequencing revealed that minor clones with different subgenotypes existed in two of the 17 samples. Genotyping by genome amplification showed high consistency, while several false reactions were detected by serotyping. The deep sequencing method also provides accurate genotyping results and may be useful for analyzing discrepant cases. HCV genotyping should be correctly determined before antiviral treatment.

  12. Usefulness of Dried Blood Spots (DBS) to perform hepatitis C virus genotyping in drug users in Senegal.

    Science.gov (United States)

    Ndiaye, O; Gozlan, J; Diop-Ndiaye, H; Sall, A S; Chapelain, S; Leprêtre, A; Maynart, M; Gueye, M; Lo, G; Thiam, M; Ba, I; Lacombe, K; Girard, P M; Mboup, S; Kane, C T

    2017-03-01

    The aim of this pilot study was to analyze the Hepatitis C Virus (HCV) genotypes circulating in Senegal among Drug User (DUs), using Dried Blood Spots (DBS) as RNA source for molecular assays. Heroin and/or cocaine users (n = 506) were recruited in Dakar from April to July 2011, using a Respondent Driven Sampling (RDS) method. DBS preparation consisted of five drops of whole blood from finger applied to a Whatman paper card. HCV infection was screened by the detection of anti-HCV antibodies, using a rapid immune-chromatographic test. HCV RNA was quantified on anti-HCV positive DBS, using the Abbott RealTime HCV® Genotyping was performed on DBS with detectable viral load with Versant® HCV Genotype 2.0 Assay (LiPA) and Abbott RealTime HCV Genotype II assay®. Among the 506 participants, 120 were tested as positive for anti-HCV antibodies and their samples were analyzed for HCV RNA viral load and genotype. Out of the 120 DBS tested, HCV RNA was detected on 25 (20.8%). The median viral load was 15,058 IU/ml (ranging from 710 to 766,740 IU/ml). All positive DBS were suitable for the genotyping assay, that showed a predominance of genotype 1 (21/25) including 16 genotypes 1a and 5 genotypes 1b. HCV genotype 1 prevails in a DU population in Dakar. DBS could be useful for HCV RNA genotyping, but optimal storage conditions should required avoiding RNA impairment. Acknowledging this limitation, DBS could be a great interest for detecting and genotyping HCV viremic patients. J. Med. Virol. 89:484-488, 2017. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  13. Novel approach based on one-tube nested PCR and a lateral flow strip for highly sensitive diagnosis of tuberculous meningitis.

    Science.gov (United States)

    Sun, Yajuan; Chen, Jiajun; Li, Jia; Xu, Yawei; Jin, Hui; Xu, Na; Yin, Rui; Hu, Guohua

    2017-01-01

    Rapid and sensitive detection of Mycobacterium tuberculosis (M. Tb) in cerebrospinal fluid is crucial in the diagnosis of tuberculous meningitis (TBM), but conventional diagnostic technologies have limited sensitivity and specificity or are time-consuming. In this work, a novel, highly sensitive molecular diagnostic method, one-tube nested PCR-lateral flow strip test (OTNPCR-LFST), was developed for detecting M. tuberculosis. This one-tube nested PCR maintains the sensitivity of conventional two-step nested PCR and reduces both the chance of cross-contamination and the time required for analysis. The PCR product was detected by a lateral flow strip assay, which provided a basis for migration of the test to a point-of-care (POC) microfluidic format. The developed assay had an improved sensitivity compared with traditional PCR, and the limit of detection was up to 1 fg DNA isolated from M. tuberculosis. The assay was also specific for M. tuberculosis, and no cross-reactions were found in other non-target bacteria. The application of this technique to clinical samples was successfully evaluated, and OTNPCR-LFST showed 89% overall sensitivity and 100% specificity for TBM patients. This one-tube nested PCR-lateral flow strip assay is useful for detecting M. tuberculosis in TBM due to its rapidity, high sensitivity and simple manipulation.

  14. Novel approach based on one-tube nested PCR and a lateral flow strip for highly sensitive diagnosis of tuberculous meningitis.

    Directory of Open Access Journals (Sweden)

    Yajuan Sun

    Full Text Available Rapid and sensitive detection of Mycobacterium tuberculosis (M. Tb in cerebrospinal fluid is crucial in the diagnosis of tuberculous meningitis (TBM, but conventional diagnostic technologies have limited sensitivity and specificity or are time-consuming. In this work, a novel, highly sensitive molecular diagnostic method, one-tube nested PCR-lateral flow strip test (OTNPCR-LFST, was developed for detecting M. tuberculosis. This one-tube nested PCR maintains the sensitivity of conventional two-step nested PCR and reduces both the chance of cross-contamination and the time required for analysis. The PCR product was detected by a lateral flow strip assay, which provided a basis for migration of the test to a point-of-care (POC microfluidic format. The developed assay had an improved sensitivity compared with traditional PCR, and the limit of detection was up to 1 fg DNA isolated from M. tuberculosis. The assay was also specific for M. tuberculosis, and no cross-reactions were found in other non-target bacteria. The application of this technique to clinical samples was successfully evaluated, and OTNPCR-LFST showed 89% overall sensitivity and 100% specificity for TBM patients. This one-tube nested PCR-lateral flow strip assay is useful for detecting M. tuberculosis in TBM due to its rapidity, high sensitivity and simple manipulation.

  15. Test-beam evaluation of heavily irradiated silicon strip modules for ATLAS Phase-II Strip Tracker Upgrade

    CERN Document Server

    Blue, Andrew; The ATLAS collaboration

    2018-01-01

    The planned HL-LHC (High Luminosity LHC) is being designed to maximise the physics potential of the LHC with 10 years of operation at instantaneous luminosities of 7.5x1034cm−2s−1. A consequence of this increased luminosity is the expected radiation damage requiring the tracking detectors to withstand hadron equivalences to over 1x1015 1 MeV neutron equivalent per cm2 in the ATLAS Strips system. The silicon strip tracker exploits the concept of modularity. Fast readout electronics, deploying 130nm CMOS front-end electronics are glued on top of a silicon sensor to make a module. The radiation hard n-in-p micro-strip sensors used have been developed by the ATLAS ITk Strip Sensor collaboration and produced by Hamamatsu Photonics. A series of tests were performed at the DESY-II and CERN SPS test beam facilities to investigate the detailed performance of a strip module with both 2.5cm and 5cm length strips before and after irradiation with 8x1014neqcm−2 protons and a total ionising dose of 37.2MRad. The DURA...

  16. Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea

    Directory of Open Access Journals (Sweden)

    Deulvot Chrystel

    2010-08-01

    Full Text Available Abstract Background Single Nucleotide Polymorphisms (SNPs can be used as genetic markers for applications such as genetic diversity studies or genetic mapping. New technologies now allow genotyping hundreds to thousands of SNPs in a single reaction. In order to evaluate the potential of these technologies in pea, we selected a custom 384-SNP set using SNPs discovered in Pisum through the resequencing of gene fragments in different genotypes and by compiling genomic sequence data present in databases. We then designed an Illumina GoldenGate assay to genotype both a Pisum germplasm collection and a genetic mapping population with the SNP set. Results We obtained clear allelic data for more than 92% of the SNPs (356 out of 384. Interestingly, the technique was successful for all the genotypes present in the germplasm collection, including those from species or subspecies different from the P. sativum ssp sativum used to generate sequences. By genotyping the mapping population with the SNP set, we obtained a genetic map and map positions for 37 new gene markers. Conclusion Our results show that the Illumina GoldenGate assay can be used successfully for high-throughput SNP genotyping of diverse germplasm in pea. This genotyping approach will simplify genotyping procedures for association mapping or diversity studies purposes and open new perspectives in legume genomics.

  17. Endogenous Locus Reporter Assays.

    Science.gov (United States)

    Liu, Yaping; Hermes, Jeffrey; Li, Jing; Tudor, Matthew

    2018-01-01

    Reporter gene assays are widely used in high-throughput screening (HTS) to identify compounds that modulate gene expression. Traditionally a reporter gene assay is built by cloning an endogenous promoter sequence or synthetic response elements in the regulatory region of a reporter gene to monitor transcriptional activity of a specific biological process (exogenous reporter assay). In contrast, an endogenous locus reporter has a reporter gene inserted in the endogenous gene locus that allows the reporter gene to be expressed under the control of the same regulatory elements as the endogenous gene, thus more accurately reflecting the changes seen in the regulation of the actual gene. In this chapter, we introduce some of the considerations behind building a reporter gene assay for high-throughput compound screening and describe the methods we have utilized to establish 1536-well format endogenous locus reporter and exogenous reporter assays for the screening of compounds that modulate Myc pathway activity.

  18. Biomarker assessment of the effects of strip mine contamination on channel catfish

    International Nuclear Information System (INIS)

    Martin, L.K. Jr.; Black, M.C.

    1994-01-01

    A suite of biomarkers were used to evaluate acute (1 day) to semi-chronic (3 month) heavy metal-induced toxicity in channel catfish, Ictalurus punctatus, caged at an abandoned strip mine and a noncontaminated reference site. Assays performed include indicators of metabolic, hematological, osmoregulatory, and genotoxic stress. Two cage designs were utilized to evaluate the importance of exposure routes; one allowing exclusive contact with the water column and the other allowing contact with water and sediments. Significant DNA strand breakage was observed in catfish exposed in both regimes, but DNA repair was observed only in water-exposed catfish. Transient increases in hemoglobin, ALAD, and hematocrit levels were observed at 1 month for both exposure regimes, followed by a return to control levels for the duration of the study. Environmental conditions (i.e., changes in water quality and temperature) may have contributed to the variable plasma chloride and glucose levels observed in all catfish exposed to strip mine wastes. Further analysis of the data with non-metric clustering techniques and correlations with tissue metal residues may yield more insights into causal relationships

  19. Associating Symptom Phenotype and Genotype in Preeclampsia.

    Science.gov (United States)

    Founds, Sandra A; Tsigas, Eleni; Ren, Dianxu; Barmada, M Michael

    2018-03-01

    Preeclampsia is a complex genetic disorder with an incompletely understood pathogenesis. Its phenotype may be better elucidated by integrating symptoms. This study aimed to identify symptoms by gestational age and associations with novel preeclampsia candidate genes. Women with a history of preeclampsia recruited from The Preeclampsia Registry completed clinical/demographic, symptom surveys and provided medical records. DNA extracted from saliva was processed with multiplexed assays for eight single-nucleotide polymorphisms (SNPs) selected to tag candidate genes and/or located in symptom susceptibility regions. Groups with versus without symptoms were compared using χ 2 . Associations between SNPs and symptoms were analyzed as genotype categories and presence/absence of the variant allele. Logistic regression modeling was conducted with exploratory p = .05. In 114 participants, 113 reported at least 1 of the 18 symptoms. Symptoms varied by trimester. Nine symptoms were associated with seven SNPs. Visual disturbances were associated with three SNPs and nausea/vomiting with two SNPs. Modeling adjustment for maternal age and parity resulted in 15 associations between 9 symptoms and 8 SNPs. Medical records demonstrated 100% concordance with self-reported diagnosis and 48% concordance with reported severity. Findings indicated novel symptom-genotype associations in preeclampsia. The small sample was self-selected, but results support future studies including medical records review. When validated, these results may lead to holistic phenotyping of women to characterize subsets of preeclampsia. This approach may optimize health in pregnancy and later life for mothers and offspring through prediction, prevention, and precision nursing care.

  20. Echinococcus granulosus genotypes in Iran

    Science.gov (United States)

    Sharafi, Seyedeh Maryam; Rostami-Nejad, Mohammad; Moazeni, Mohammad; Yousefi, Morteza; Saneie, Behnam; Hosseini-Safa, Ahmad

    2014-01-01

    Hydatidosis, caused by Echinococcus granulosus is one of the most important zoonotic diseases, throughout most parts of the world. Hydatidosis is endemic in Iran and responsible for approximately 1% of admission to surgical wards. There are extensive genetic variations within E. granulosus and 10 different genotypes (G1–G10) within this parasite have been reported. Identification of strains is important for improvement of control and prevention of the disease. No new review article presented the situation of Echinococcus granulosus genotypes in Iran in the recent years; therefore in this paper we reviewed the different studies regarding Echinococcus granulosus genotypes in Iran. PMID:24834298

  1. HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples.

    Science.gov (United States)

    Cornall, Alyssa M; Poljak, Marin; Garland, Suzanne M; Phillips, Samuel; Machalek, Dorothy A; Tan, Jeffrey H; Quinn, Michael A; Tabrizi, Sepehr N

    2017-12-01

    To compare human papillomavirus genotype-specific performance of two genotyping assays, Anyplex II HPV28 (Seegene) and EuroArray HPV (EuroImmun), with Linear Array HPV (Roche). DNA extracted from clinican-collected cervical brush specimens in PreservCyt medium (Hologic), from 403 women undergoing management for detected cytological abnormalities, was tested on the three assays. Genotype-specific agreement were assessed by Cohen's kappa statistic and Fisher's z-test of significance between proportions. Agreement between Linear Array and the other 2 assays was substantial to almost perfect (κ = 0.60 - 1.00) for most genotypes, and was almost perfect (κ = 0.81 - 0.98) for almost all high-risk genotypes. Linear Array overall detected most genotypes more frequently, however this was only statistically significant for HPV51 (EuroArray; p = 0.0497), HPV52 (Anyplex II; p = 0.039) and HPV61 (Anyplex II; p=0.047). EuroArray detected signficantly more HPV26 (p = 0.002) and Anyplex II detected more HPV42 (p = 0.035) than Linear Array. Each assay performed differently for HPV68 detection: EuroArray and LA were in moderate to substantial agreement with Anyplex II (κ = 0.46 and 0.62, respectively), but were in poor disagreement with each other (κ = -0.01). EuroArray and Anyplex II had similar sensitivity to Linear Array for most high-risk genotypes, with slightly lower sensitivity for HPV 51 or 52. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  2. Solid phase assays

    International Nuclear Information System (INIS)

    Reese, M.G.; Johnson, L.R.; Ransom, D.K.

    1980-01-01

    In a solid phase assay for quantitative determination of biological and other analytes, a sample such as serum is contacted with a receptor for the analyte being assayed, the receptor being supported on a solid support. No tracer for the analyte is added to the sample before contacting with the receptor; instead the tracer is contacted with the receptor after unbound analyte has been removed from the receptor. The assay can be otherwise performed in a conventional manner but can give greater sensitivity. (author)

  3. STRIPPED ELLIPTICAL GALAXIES AS PROBES OF ICM PHYSICS. I. TAILS, WAKES, AND FLOW PATTERNS IN AND AROUND STRIPPED ELLIPTICALS

    Energy Technology Data Exchange (ETDEWEB)

    Roediger, E. [Hamburger Sternwarte, Universität Hamburg, Gojensbergsweg 112, D-21029 Hamburg (Germany); Kraft, R. P.; Nulsen, P. E. J.; Forman, W. R.; Machacek, M.; Randall, S.; Jones, C. [Harvard/Smithsonian Center for Astrophysics, 60 Garden Street MS-4, Cambridge, MA 02138 (United States); Churazov, E. [MPI für Astrophysik, Karl-Schwarzschild-Str. 1, Garching, D-85741 (Germany); Kokotanekova, R., E-mail: eroediger@hs.uni-hamburg.de [AstroMundus Master Programme, University of Innsbruck, Technikerstr. 25/8, 6020 Innsbruck (Austria)

    2015-06-10

    Elliptical cluster galaxies are progressively stripped of their atmospheres due to their motion through the intracluster medium (ICM). Deep X-ray observations reveal the fine-structure of the galaxy’s remnant atmosphere and its gas tail and wake. This fine-structure depends on dynamic conditions (galaxy potential, initial gas contents, orbit through the host cluster), orbital stage (early infall, pre-/post-pericenter passage), and ICM plasma properties (thermal conductivity, viscosity, magnetic field structure). We aim to disentangle dynamic and plasma effects in order to use stripped ellipticals as probes of ICM plasma properties. This first paper of a series investigates the hydrodynamics of progressive gas stripping by means of inviscid hydrodynamical simulations. We distinguish a long-lasting initial relaxation phase and a quasi-steady stripping phase. During quasi-steady stripping, the ICM flow around the remnant atmosphere resembles the flow around solid bodies, including a “deadwater” region in the near wake. Gas is stripped from the remnant atmosphere predominantly at its sides via Kelvin–Helmholtz instabilities. The downstream atmosphere is largely shielded from the ICM wind and thus shaped into a tail. Observationally, both this “remnant tail” and the stripped gas in the wake can appear as a “tail”, but only in the wake can galactic gas mix with the ambient ICM. While the qualitative results are generic, the simulations presented here are tailored to the Virgo elliptical galaxy M89 (NGC 4552) for the most direct comparison to observations. Papers II and III of this series describe the effect of viscosity and compare to Chandra and XMM-Newton observations, respectively.

  4. Acrylamide content and color development in fried potato strips

    DEFF Research Database (Denmark)

    Pedreschi, F.; Kaack, K.; Granby, Kit

    2006-01-01

    Acrylamide formation and changes in color of fried potato strips was investigated in relation to frying temperature and three treatments before frying. Potato strips (0.8 x 0.8 x 5 cm) of Bintje variety were fried at 150, 170 and 190 degrees C until reaching moisture contents of similar to 40 g...... water/100 g (total basis). Prior to frying, potato strips were treated in one of the following ways: (i) immersed in distilled water for 0 min (control), 60 min and 120 min; (ii) blanched in hot water at six different time-temperature combinations (50 degrees C for 40 and 80 min; 70 degrees C for 10...... and 45 min; 90 degrees C for 3 and 10 min); (iii) immersed in a citric acid solution of 10 g/L for an hour; (iv) immersed in a sodium pyrophosphate solution of 10 g/L for an hour. Acrylamide content and color was determined in the potato strips after frying. Immersed strips in water for 120 min showed...

  5. Prototype indicator strip for tank ammunition. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Bates, B.; Griest, W.

    1993-10-31

    Combustible nitrocellulose ordnance casings offer advantages of: light weight, low cost, low detectability, and quick cycling of rounds by immediate disposal. However, mechanical strength is degraded with time by the action of humidity and nitroester diffusion through the casing to adhesives. The primary development effort of this study is a means to detect nitroester migration to the crucial skive joint which binds an assortment of warhead choices to propellant casings. This work has developed a prototype colorimetric indicator strip which, when applied in a field environment, produces a purple tint proportional to casing nitroester concentration, and inversely proportional to remaining adhesive joint strength. This work addressed the three steps in indicator strip use: (1) A suggested protocol for indicator strip preparation was developed. Various coatings, support reagents, and backings were examined resulting in a choice of polyethylene tape coating over separate AB- and C-impregnated cellulose punches. Various methods of punch creation and impregnation were tried resulting in stirred aqueous solutions and suspensions of AB and C, respectively. (2) Suggested protocols for indicator strip application to lab backings and field casings were developed. After chemical stripper was applied to the alumina-polyurethane paint on casings, C and AB punches were stacked and double-tape sealed. (3) A means for indicator strip monitoring was developed. From known time of indicator reaction, casing humidity, and indicator color, a means for field concentration determination was determined. Lab time-lapse photography was used to calibrate the indicator at a single level of humidity.

  6. Theoretical study of H- stripping with a wiggler magnet

    International Nuclear Information System (INIS)

    Hutson, R.L.

    1991-01-01

    The first step for injecting protons into the LAMPF Proton Storage Ring (PSR) at LANL is to strip a beam of 800-MeV H - ions to H 0 with a 1.8-T dipole magnet. Because of the finite lifetime of energetic H - ions in the magnetic field, their trajectories bend before stripping causing the angular spread of the beam, and therefore its emittance, to grow during the stripping process. In the case of the PSR, the horizontal beam emittance grows by a factor of roughly three during injection. As a consequence, beam losses in the ring are significantly greater than they would be if there were not emittance growth. A speculative technique is proposed in which the beam divergence growth and resulting emittance growth is reduced by stripping the H - in a wiggler magnet whose transverse field alternates in direction as a function of position along the beam axis. The wiggler field configuration is adjusted so that the angular beam spread introduced during passage through one unidirectional-field increment of path is relatively small and so that 99.99% of the beam is stripped after passing through the whole magnet. With careful field design the net added angular beam spread is reduced because the incremental angular spreads are painted back and forth over the same small range. In the hypothetical case described, the calculated emittance growth and beam loss increase are significantly smaller than those calculated for a conventional stripper magnet. 3 refs., 3 figs

  7. Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

    Science.gov (United States)

    Wang, Chaolong; Zhan, Xiaowei; Liang, Liming; Abecasis, Gonçalo R.; Lin, Xihong

    2015-01-01

    Accurate estimation of individual ancestry is important in genetic association studies, especially when a large number of samples are collected from multiple sources. However, existing approaches developed for genome-wide SNP data do not work well with modest amounts of genetic data, such as in targeted sequencing or exome chip genotyping experiments. We propose a statistical framework to estimate individual ancestry in a principal component ancestry map generated by a reference set of individuals. This framework extends and improves upon our previous method for estimating ancestry using low-coverage sequence reads (LASER 1.0) to analyze either genotyping or sequencing data. In particular, we introduce a projection Procrustes analysis approach that uses high-dimensional principal components to estimate ancestry in a low-dimensional reference space. Using extensive simulations and empirical data examples, we show that our new method (LASER 2.0), combined with genotype imputation on the reference individuals, can substantially outperform LASER 1.0 in estimating fine-scale genetic ancestry. Specifically, LASER 2.0 can accurately estimate fine-scale ancestry within Europe using either exome chip genotypes or targeted sequencing data with off-target coverage as low as 0.05×. Under the framework of LASER 2.0, we can estimate individual ancestry in a shared reference space for samples assayed at different loci or by different techniques. Therefore, our ancestry estimation method will accelerate discovery in disease association studies not only by helping model ancestry within individual studies but also by facilitating combined analysis of genetic data from multiple sources. PMID:26027497

  8. Diagnosis of rinderpest in Tanzania by a rapid chromatographic strip-test.

    Science.gov (United States)

    Wambura, P N; Moshy, D W; Mbise, A N; Mollel, G O; Taylor, W P; Anderson, J; Bruning, A

    2000-06-01

    A simple chromatographic strip-test based on Clearview technology, is under development as a pen-side test for the detection of rinderpest antigen in eye swabs taken from cattle in the field. An outbreak of rinderpest occurred in the northern zone of Tanzania from late February to June 1997. The affected cattle exhibited very mild clinical signs, which made clinical diagnosis difficult. One hundred and seven eye swabs were collected from cattle suspected of infection with rinderpest. These were tested in the field using a prototype of the pen-side test and 13 (12.15%) of the samples were found to be positive for the presence of rinderpest antigen. These were confirmed by ICE. The positive cases were predominantly found in the Ngorongoro district. This demonstrates the usefulness of such a simple, rapid pen-side diagnostic assay, particularly when clinically 'mild' strains of rinderpest are present.

  9. Comparison of cobas HCV GT against Versant HCV Genotype 2.0 (LiPA) with confirmation by Sanger sequencing.

    Science.gov (United States)

    Yusrina, Falah; Chua, Cui Wen; Lee, Chun Kiat; Chiu, Lily; Png, Tracy Si-Yu; Khoo, Mui Joo; Yan, Gabriel; Lee, Guan Huei; Yan, Benedict; Lee, Hong Kai

    2018-05-01

    Correct identification of infecting hepatitis C virus (HCV) genotype is helpful for targeted antiviral therapy. Here, we compared the HCV genotyping performance of the cobas HCV GT assay against the Versant HCV Genotype 2.0 (LiPA) assay, using 97 archived serum samples. In the event of discrepant or indeterminate results produced by either assay, the core and NS5B regions were sequenced. Of the 97 samples tested by the cobas, 25 (26%) were deemed indeterminate. Sequencing analyses confirmed 21 (84%) of the 25 samples as genotype 6 viruses with either subtype 6m, 6n, 6v, 6xa, or unknown subtype. Of the 97 samples tested by the LiPA, thirteen (13%) were deemed indeterminate. Seven (7%) were assigned with genotype 1, with unavailable/inconclusive results from the core region of the LiPA. Notably, the 7 samples were later found to be either genotype 3 or 6 by sequencing analyses. Moreover, 1 sample by the LiPA was assigned as genotypes 4 (cobas: indeterminate) but were later found to be genotype 3 by sequencing analyses, highlighting its limitation in assigning the correct genotype. The cobas showed similar or slightly higher accuracy (100%; 95% CI 94-100%) compared to the LiPA (99%; 95% CI 92-100%). Twenty-six percent of the 97 samples tested by the cobas had indeterminate results, mainly due to its limitation in identifying genotype 6 other than subtypes 6a and 6b. This presents a significant assay limitation in Southeast Asia, where genotype 6 infection is highly prevalent. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Nafion/2,2'-bipyridyl-modified bismuth film electrode for anodic stripping voltammetry

    International Nuclear Information System (INIS)

    Torma, Ferenc; Kadar, Mihaly; Toth, Klara; Tatar, Eniko

    2008-01-01

    This paper describes the fabrication, characterisation and the application of a Nafion/2,2'-bipyridyl/bismuth composite film-coated glassy carbon electrode (NC(Bpy)BiFE) for the anodic stripping voltammetric determination of trace metal ions (Zn 2+ , Cd 2+ and Pb 2+ ). The NC(Bpy)BiFE electrode is prepared by first applying a 2.5 mm 3 drop of a coating solution containing 0.5 wt% Nafion and 0.1% (w/v) 2,2'-bipyridil (Bpy) onto the surface of a glassy carbon electrode, while the Bi film was plated in situ simultaneously with the target metal ions at -1.4 V. The main advantage of the polymer coated bismuth film electrode is that the sensitivity of the stripping responses is increased considerably due to the incorporation of the neutral chelating agent of 2,2'-bipyridyl (Bpy) in the Nafion film, while the Nafion coating improved the mechanical stability of the bismuth film and its resistance to the interference of surfactants. The key experimental parameters relevant to both the electrode fabrication and the voltammetric measurement were optimized on the basis of the stripping signals. With a 2 min deposition time in the presence of oxygen, linear calibration curves were obtained in a wide concentration range (about 2-0.001 μM) with detection limits of 8.6 nM (0.56 μg dm -3 ) for Zn 2+ , 1.1 nM (0.12 μg dm -3 ) for Cd 2+ and 0.37 nM (0.077 μg dm -3 ) for Pb 2+ . For nine successive preconcentration/determination/electrode renewal experiments the standard deviations were between 3 and 5% at 1.2 μM for zinc and 0.3-0.3 μM concentration level for lead and cadmium, respectively, and the method exhibited excellent selectivity in the presence of the excess of several potential interfering metal ions. The analytical utility of the stripping voltammetric method elaborated was tested in the assay of heavy metals in some real samples and the method was validated by ICP-MS technique

  11. Lateral flow assays.

    Science.gov (United States)

    Koczula, Katarzyna M; Gallotta, Andrea

    2016-06-30

    Lateral flow assays (LFAs) are the technology behind low-cost, simple, rapid and portable detection devices popular in biomedicine, agriculture, food and environmental sciences. This review presents an overview of the principle of the method and the critical components of the assay, focusing on lateral flow immunoassays. This type of assay has recently attracted considerable interest because of its potential to provide instantaneous diagnosis directly to patients. The range and interpretation of results and parameters used for evaluation of the assay will also be discussed. The main advantages and disadvantages of LFAs will be summarized and relevant future improvements to testing devices and strategies will be proposed. Finally, the major recent advances and future diagnostic applications in the LFA field will be explored. © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  12. Lateral flow assays

    Science.gov (United States)

    Koczula, Katarzyna M.

    2016-01-01

    Lateral flow assays (LFAs) are the technology behind low-cost, simple, rapid and portable detection devices popular in biomedicine, agriculture, food and environmental sciences. This review presents an overview of the principle of the method and the critical components of the assay, focusing on lateral flow immunoassays. This type of assay has recently attracted considerable interest because of its potential to provide instantaneous diagnosis directly to patients. The range and interpretation of results and parameters used for evaluation of the assay will also be discussed. The main advantages and disadvantages of LFAs will be summarized and relevant future improvements to testing devices and strategies will be proposed. Finally, the major recent advances and future diagnostic applications in the LFA field will be explored. PMID:27365041

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

    Directory of Open Access Journals (Sweden)

    Nicole Thomsen

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

  14. Hepatitis C virus deep sequencing for sub-genotype identification in mixed infections: A real-life experience.

    Science.gov (United States)

    Del Campo, José A; Parra-Sánchez, Manuel; Figueruela, Blanca; García-Rey, Silvia; Quer, Josep; Gregori, Josep; Bernal, Samuel; Grande, Lourdes; Palomares, José C; Romero-Gómez, Manuel

    2018-02-01

    The effectiveness of the new generation of hepatitis C treatments named direct-acting antiviral agents (DAAs) depends on the genotype, subtype, and resistance-associated substitutions present in individual patients. The aim of this study was to evaluate a massive sequencing platform for the analysis of genotypes and subtypes of hepatitis C virus (HCV) in order to optimize therapy. A total of 84 patients with hepatitis C were analyzed. The routine genotyping methodology for HCV used at the study institution (Versant HCV Assay, LiPA) was compared with a deep sequencing platform (454/GS-Junior and Illumina MiSeq). The mean viral load in these HCV patients was 6.89×10 6 ±7.02×10 5 . Viral genotypes analyzed by LiPA were distributed as follows: 26% genotype 1a (22/84), 55% genotype 1b (46/84), 1% genotype 1 (1/84), 2.5% genotype 3 (2/84), 6% genotype 3a (5/84), 6% genotype 4a/c/d (5/84). When analyzed by deep sequencing, the samples were distributed as follows: 27% genotype 1a (23/84), 56% genotype 1b (47/84), 8% genotype 3a (7/84), 5% genotype 4d (4/84), 2.5% genotype 4f (2/84). Six of the 84 patients (7%) were infected with more than one subtype. Among these, 33% (2/6) failed DAA-based triple therapy. The detection of mixed infection could explain some treatment failures. Accurate determination of viral genotypes and subtypes would allow optimal patient management and improve the effectiveness of DAA therapy. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  15. Phonon thermal conductance of disordered graphene strips with armchair edges

    International Nuclear Information System (INIS)

    Shi Lipeng; Xiong Shijie

    2009-01-01

    Based on the model of lattice dynamics together with the transfer matrix technique, we investigate the thermal conductances of phonons in quasi-one-dimensional disordered graphene strips with armchair edges using Landauer formalism for thermal transport. It is found that the contributions to thermal conductance from the phonon transport near von Hove singularities is significantly suppressed by the presence of disorder, on the contrary to the effect of disorder on phonon modes in other frequency regions. Besides the magnitude, for different widths of the strips, the thermal conductance also shows different temperature dependence. At low temperatures, the thermal conductance displays quantized features of both pure and disordered graphene strips implying that the transmission of phonon modes at low frequencies are almost unaffected by the disorder

  16. Efficiency measurements for 3D silicon strip detectors

    Energy Technology Data Exchange (ETDEWEB)

    Parzefall, Ulrich, E-mail: ulrich.parzefall@physik.uni-freiburg.d [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Dalla Betta, Gian-Franco [INFN Trento and Universita di Trento, via Sommarive 14, 38050 Povo di Trento (Italy); Boscardin, Maurizio [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy); Eckert, Simon [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Eklund, Lars; Fleta, Celeste [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Jakobs, Karl; Koehler, Michael; Kuehn, Susanne; Pahn, Gregor [Physikalisches Institut, Universitaet Freiburg, Hermann-Herder-Str. 3, D-79104 Freiburg (Germany); Parkes, Chris; Pennicard, David [University of Glasgow, Department of Physics and Astronomy, Glasgow G12 8QQ (United Kingdom); Ronchin, Sabina [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy); Zoboli, Andrea [INFN Trento and Universita di Trento, via Sommarive 14, 38050 Povo di Trento (Italy); Zorzi, Nicola [FBK-irst, Center for Materials and Microsystems, via Sommarive 18, 38050 Povo di Trento (Italy)

    2010-11-01

    Silicon strip detectors are widely used as part of the inner tracking layers in particle physics experiments. For applications at the luminosity upgrade of the Large Hadron Collider (LHC), the sLHC, silicon detectors with extreme radiation hardness are required. The 3D detector design, where electrodes are processed from underneath the strips into the silicon bulk material, provides a way to enhance the radiation tolerance of standard planar silicon strip detectors. Detectors with several innovative 3D designs that constitute a simpler and more cost-effective processing than the 3D design initially proposed were connected to read-out electronics from LHC experiments and subsequently tested. Results on the amount of charge collected, the noise and the uniformity of charge collection are given.

  17. Synchronizing a Triple Dragline Stripping System in Thick Overburden

    Directory of Open Access Journals (Sweden)

    Erdem Bülent

    2017-06-01

    Full Text Available This study addresses the use of combined stripping systems to investigate the technical feasibility of extracting thick coal seams underlying deep overburden strata. The possibility of using multiple draglines in tandem with bucket wheel excavator systems is explored. Pit geometry design alternatives incorporating a triple dragline excavation fleet with bucket wheel excavator-cross pit spreader subsystems (BWE+XPS are examined. A production simulation algorithm, which emphasizes synchronizing excavator units in the triple dragline system, is developed. The combined methodology is evaluated in Sector-D of the Afşin-Elbistan lignite basin, one of the most important resources for electricity production in Turkey. The results reveal that a combined stripping fleet may successfully perform overburden stripping at the predetermined rate and uncover coal seams.

  18. Performance studies of the CMS Strip Tracker before installation

    Energy Technology Data Exchange (ETDEWEB)

    Adam, W.; et al.

    2009-06-01

    In March 2007 the assembly of the Silicon Strip Tracker was completed at the Tracker Integration Facility at CERN. Nearly 15% of the detector was instrumented using cables, fiber optics, power supplies, and electronics intended for the operation at the LHC. A local chiller was used to circulate the coolant for low temperature operation. In order to understand the efficiency and alignment of the strip tracker modules, a cosmic ray trigger was implemented. From March through July 4.5 million triggers were recorded. This period, referred to as the Sector Test, provided practical experience with the operation of the Tracker, especially safety, data acquisition, power, and cooling systems. This paper describes the performance of the strip system during the Sector Test, which consisted of five distinct periods defined by the coolant temperature. Significant emphasis is placed on comparisons between the data and results from Monte Carlo studies.

  19. Performance studies of the CMS Strip Tracker before installation

    CERN Document Server

    Adam, Wolfgang; Dragicevic, Marko; Friedl, Markus; Fruhwirth, R; Hansel, S; Hrubec, Josef; Krammer, Manfred; Oberegger, Margit; Pernicka, Manfred; Schmid, Siegfried; Stark, Roland; Steininger, Helmut; Uhl, Dieter; Waltenberger, Wolfgang; Widl, Edmund; Van Mechelen, Pierre; Cardaci, Marco; Beaumont, Willem; de Langhe, Eric; de Wolf, Eddi A; Delmeire, Evelyne; Hashemi, Majid; Bouhali, Othmane; Charaf, Otman; Clerbaux, Barbara; Dewulf, Jean-Paul; Elgammal, Sherif; Hammad, Gregory Habib; de Lentdecker, Gilles; Marage, Pierre Edouard; Vander Velde, Catherine; Vanlaer, Pascal; Wickens, John; Adler, Volker; Devroede, Olivier; De Weirdt, Stijn; D'Hondt, Jorgen; Goorens, Robert; Heyninck, Jan; Maes, Joris; Mozer, Matthias Ulrich; Tavernier, Stefaan; Van Lancker, Luc; Van Mulders, Petra; Villella, Ilaria; Wastiels, C; Bonnet, Jean-Luc; Bruno, Giacomo; De Callatay, Bernard; Florins, Benoit; Giammanco, Andrea; Gregoire, Ghislain; Keutgen, Thomas; Kcira, Dorian; Lemaitre, Vincent; Michotte, Daniel; Militaru, Otilia; Piotrzkowski, Krzysztof; Quertermont, L; Roberfroid, Vincent; Rouby, Xavier; Teyssier, Daniel; Daubie, Evelyne; Anttila, Erkki; Czellar, Sandor; Engstrom, Pauli; Harkonen, J; Karimaki, V; Kostesmaa, J; Kuronen, Auli; Lampen, Tapio; Linden, Tomas; Luukka, Panja-Riina; Maenpaa, T; Michal, Sebastien; Tuominen, Eija; Tuominiemi, Jorma; Ageron, Michel; Baulieu, Guillaume; Bonnevaux, Alain; Boudoul, Gaelle; Chabanat, Eric; Chabert, Eric Christian; Chierici, Roberto; Contardo, Didier; Della Negra, Rodolphe; Dupasquier, Thierry; Gelin, Georges; Giraud, Noël; Guillot, Gérard; Estre, Nicolas; Haroutunian, Roger; Lumb, Nicholas; Perries, Stephane; Schirra, Florent; Trocme, Benjamin; Vanzetto, Sylvain; Agram, Jean-Laurent; Blaes, Reiner; Drouhin, Frédéric; Ernenwein, Jean-Pierre; Fontaine, Jean-Charles; Berst, Jean-Daniel; Brom, Jean-Marie; Didierjean, Francois; Goerlach, Ulrich; Graehling, Philippe; Gross, Laurent; Hosselet, J; Juillot, Pierre; Lounis, Abdenour; Maazouzi, Chaker; Olivetto, Christian; Strub, Roger; Van Hove, Pierre; Anagnostou, Georgios; Brauer, Richard; Esser, Hans; Feld, Lutz; Karpinski, Waclaw; Klein, Katja; Kukulies, Christoph; Olzem, Jan; Ostapchuk, Andrey; Pandoulas, Demetrios; Pierschel, Gerhard; Raupach, Frank; Schael, Stefan; Schwering, Georg; Sprenger, Daniel; Thomas, Maarten; Weber, Markus; Wittmer, Bruno; Wlochal, Michael; Beissel, Franz; Bock, E; Flugge, G; Gillissen, C; Hermanns, Thomas; Heydhausen, Dirk; Jahn, Dieter; Kaussen, Gordon; Linn, Alexander; Perchalla, Lars; Poettgens, Michael; Pooth, Oliver; Stahl, Achim; Zoeller, Marc Henning; Buhmann, Peter; Butz, Erik; Flucke, Gero; Hamdorf, Richard Helmut; Hauk, Johannes; Klanner, Robert; Pein, Uwe; Schleper, Peter; Steinbruck, G; Blum, P; De Boer, Wim; Dierlamm, Alexander; Dirkes, Guido; Fahrer, Manuel; Frey, Martin; Furgeri, Alexander; Hartmann, Frank; Heier, Stefan; Hoffmann, Karl-Heinz; Kaminski, Jochen; Ledermann, Bernhard; Liamsuwan, Thiansin; Muller, S; Muller, Th; Schilling, Frank-Peter; Simonis, Hans-Jürgen; Steck, Pia; Zhukov, Valery; Cariola, P; De Robertis, Giuseppe; Ferorelli, Raffaele; Fiore, Luigi; Preda, M; Sala, Giuliano; Silvestris, Lucia; Tempesta, Paolo; Zito, Giuseppe; Creanza, Donato; De Filippis, Nicola; De Palma, Mauro; Giordano, Domenico; Maggi, Giorgio; Manna, Norman; My, Salvatore; Selvaggi, Giovanna; Albergo, Sebastiano; Chiorboli, Massimiliano; Costa, Salvatore; Galanti, Mario; Giudice, Nunzio; Guardone, Nunzio; Noto, Francesco; Potenza, Renato; Saizu, Mirela Angela; Sparti, V; Sutera, Concetta; Tricomi, Alessia; Tuve, Cristina; Brianzi, Mirko; Civinini, Carlo; Maletta, Fernando; Manolescu, Florentina; Meschini, Marco; Paoletti, Simone; Sguazzoni, Giacomo; Broccolo, B; Ciulli, Vitaliano; D'Alessandro, Raffaello; Focardi, Ettore; Frosali, Simone; Genta, Chiara; Landi, Gregorio; Lenzi, Piergiulio; Macchiolo, Anna; Magini, Nicolo; Parrini, Giuliano; Scarlini, Enrico; Cerati, Giuseppe Benedetto; Azzi, Patrizia; Bacchetta, Nicola; Candelori, Andrea; Dorigo, Tommaso; Kaminsky, A; Karaevski, S; Khomenkov, Volodymyr; Reznikov, Sergey; Tessaro, Mario; Bisello, Dario; De Mattia, Marco; Giubilato, Piero; Loreti, Maurizio; Mattiazzo, Serena; Nigro, Massimo; Paccagnella, Alessandro; Pantano, Devis; Pozzobon, Nicola; Tosi, Mia; Bilei, Gian Mario; Checcucci, Bruno; Fano, Livio; Servoli, Leonello; Ambroglini, Filippo; Babucci, Ezio; Benedetti, Daniele; Biasini, Maurizio; Caponeri, Benedetta; Covarelli, Roberto; Giorgi, Marco; Lariccia, Paolo; Mantovani, Giancarlo; Marcantonini, Marta; Postolache, Vasile; Santocchia, Attilio; Spiga, Daniele; Bagliesi, Giuseppe; Balestri, Gabriele; Berretta, Luca; Bianucci, S; Boccali, Tommaso; Bosi, Filippo; Bracci, Fabrizio; Castaldi, Rino; Ceccanti, Marco; Cecchi, Roberto; Cerri, Claudio; Cucoanes, Andi Sebastian; Dell'Orso, Roberto; Dobur, Didar; Dutta, Suchandra; Giassi, Alessandro; Giusti, Simone; Kartashov, Dmitry; Kraan, Aafke; Lomtadze, Teimuraz; Lungu, George-Adrian; Magazzu, Guido; Mammini, Paolo; Mariani, Filippo; Martinelli, Giovanni; Moggi, Andrea; Palla, Fabrizio; Palmonari, Francesco; Petragnani, Giulio; Profeti, Alessandro; Raffaelli, Fabrizio; Rizzi, Domenico; Sanguinetti, Giulio; Sarkar, Subir; Sentenac, Daniel; Serban, Alin Titus; Slav, Adrian; Soldani, A; Spagnolo, Paolo; Tenchini, Roberto; Tolaini, Sergio; Venturi, Andrea; Verdini, Piero Giorgio; Vos, Marcel; Zaccarelli, Luciano; Avanzini, Carlo; Basti, Andrea; Benucci, Leonardo; Bocci, Andrea; Cazzola, Ugo; Fiori, Francesco; Linari, Stefano; Massa, Maurizio; Messineo, Alberto; Segneri, Gabriele; Tonelli, Guido; Azzurri, Paolo; Bernardini, Jacopo; Borrello, Laura; Calzolari, Federico; Foa, Lorenzo; Gennai, Simone; Ligabue, Franco; Petrucciani, Giovanni; Rizzi, Andrea; Yang, Zong-Chang; Benotto, Franco; Demaria, Natale; Dumitrache, Floarea; Farano, R; Borgia, Maria Assunta; Castello, Roberto; Costa, Marco; Migliore, Ernesto; Romero, Alessandra; Abbaneo, Duccio; Abbas, M; Ahmed, Ijaz; Akhtar, I; Albert, Eric; Bloch, Christoph; Breuker, Horst; Butt, Shahid Aleem; Buchmuller, Oliver; Cattai, Ariella; Delaere, Christophe; Delattre, Michel; Edera, Laura Maria; Engstrom, Pauli; Eppard, Michael; Gateau, Maryline; Gill, Karl; Giolo-Nicollerat, Anne-Sylvie; Grabit, Robert; Honma, Alan; Huhtinen, Mika; Kloukinas, Kostas; Kortesmaa, Jarmo; Kottelat, Luc-Joseph; Kuronen, Auli; Leonardo, Nuno; Ljuslin, Christer; Mannelli, Marcello; Masetti, Lorenzo; Marchioro, Alessandro; Mersi, Stefano; Michal, Sebastien; Mirabito, Laurent; Muffat-Joly, Jeannine; Onnela, Antti; Paillard, Christian; Pal, Imre; Pernot, Jean-Francois; Petagna, Paolo; Petit, Patrick; Piccut, C; Pioppi, Michele; Postema, Hans; Ranieri, Riccardo; Ricci, Daniel; Rolandi, Gigi; Ronga, Frederic Jean; Sigaud, Christophe; Syed, A; Siegrist, Patrice; Tropea, Paola; Troska, Jan; Tsirou, Andromachi; Vander Donckt, Muriel; Vasey, François; Alagoz, Enver; Amsler, Claude; Chiochia, Vincenzo; Regenfus, Christian; Robmann, Peter; Rochet, Jacky; Rommerskirchen, Tanja; Schmidt, Alexander; Steiner, Stefan; Wilke, Lotte; Church, Ivan; Cole, Joanne; Coughlan, John A; Gay, Arnaud; Taghavi, S; Tomalin, Ian R; Bainbridge, Robert; Cripps, Nicholas; Fulcher, Jonathan; Hall, Geoffrey; Noy, Matthew; Pesaresi, Mark; Radicci, Valeria; Raymond, David Mark; Sharp, Peter; Stoye, Markus; Wingham, Matthew; Zorba, Osman; Goitom, Israel; Hobson, Peter R; Reid, Ivan; Teodorescu, Liliana; Hanson, Gail; Jeng, Geng-Yuan; Liu, Haidong; Pasztor, Gabriella; Satpathy, Asish; Stringer, Robert; Mangano, Boris; Affolder, K; Affolder, T; Allen, Andrea; Barge, Derek; Burke, Samuel; Callahan, D; Campagnari, Claudio; Crook, A; D'Alfonso, Mariarosaria; Dietch, J; Garberson, Jeffrey; Hale, David; Incandela, H; Incandela, Joe; Jaditz, Stephen; Kalavase, Puneeth; Kreyer, Steven Lawrence; Kyre, Susanne; Lamb, James; Mc Guinness, C; Mills, C; Nguyen, Harold; Nikolic, Milan; Lowette, Steven; Rebassoo, Finn; Ribnik, Jacob; Richman, Jeffrey; Rubinstein, Noah; Sanhueza, S; Shah, Yousaf Syed; Simms, L; Staszak, D; Stoner, J; Stuart, David; Swain, Sanjay Kumar; Vlimant, Jean-Roch; White, Dean; Ulmer, Keith; Wagner, Stephen Robert; Bagby, Linda; Bhat, Pushpalatha C; Burkett, Kevin; Cihangir, Selcuk; Gutsche, Oliver; Jensen, Hans; Johnson, Mark; Luzhetskiy, Nikolay; Mason, David; Miao, Ting; Moccia, Stefano; Noeding, Carsten; Ronzhin, Anatoly; Skup, Ewa; Spalding, William J; Spiegel, Leonard; Tkaczyk, Slawek; Yumiceva, Francisco; Zatserklyaniy, Andriy; Zerev, E; Anghel, Ioana Maria; Bazterra, Victor Eduardo; Gerber, Cecilia Elena; Khalatian, S; Shabalina, Elizaveta; Baringer, Philip; Bean, Alice; Chen, Jie; Hinchey, Carl Louis; Martin, Christophe; Moulik, Tania; Robinson, Richard; Gritsan, Andrei; Lae, Chung Khim; Tran, Nhan Viet; Everaerts, Pieter; Hahn, Kristan Allan; Harris, Philip; Nahn, Steve; Rudolph, Matthew; Sung, Kevin; Betchart, Burton; Demina, Regina; Gotra, Yury; Korjenevski, Sergey; Miner, Daniel Carl; Orbaker, Douglas; Christofek, Leonard; Hooper, Ryan; Landsberg, Greg; Nguyen, Duong; Narain, Meenakshi; Speer, Thomas; Tsang, Ka Vang

    2009-01-01

    In March 2007 the assembly of the Silicon Strip Tracker was completed at the Tracker Integration Facility at CERN. Nearly 15% of the detector was instrumented using cables, fiber optics, power supplies, and electronics intended for the operation at the LHC. A local chiller was used to circulate the coolant for low temperature operation. In order to understand the efficiency and alignment of the strip tracker modules, a cosmic ray trigger was implemented. From March through July 4.5 million triggers were recorded. This period, referred to as the Sector Test, provided practical experience with the operation of the Tracker, especially safety, data acquisition, power, and cooling systems. This paper describes the performance of the strip system during the Sector Test, which consisted of five distinct periods defined by the coolant temperature. Significant emphasis is placed on comparisons between the data and results from Monte Carlo studies.

  20. Nonlinear Vibration Analysis of Moving Strip with Inertial Boundary Condition

    Directory of Open Access Journals (Sweden)

    Chong-yi Gao

    2015-01-01

    Full Text Available According to the movement mechanism of strip and rollers in tandem mill, the strip between two stands was simplified to axially moving Euler beam and the rollers were simplified to the inertial component on the fixed axis rotation, namely, inertial boundary. Nonlinear vibration mechanical model of Euler beam with inertial boundary conditions was established. The transverse and longitudinal motion equations were derived based on Hamilton’s principle. Kantorovich averaging method was employed to discretize the motion equations and the inertial boundary equations, and the solutions were obtained using the modified iteration method. Depending on numerical calculation, the amplitude-frequency responses of Euler beam were determined. The axial velocity, tension, and rotational inertia have strong influences on the vibration characteristics. The results would provide an important theoretical reference to control and analyze the vertical vibration of moving strip in continuous rolling process.

  1. An integrated electrochemical device based on immunochromatographic test strip and enzyme labels for sensitive detection of disease-related biomarkers

    Energy Technology Data Exchange (ETDEWEB)

    Zou, Zhexiang; Wang, Jun; Wang, Hua; Li, Yao Q.; Lin, Yuehe

    2012-05-30

    A novel electrochemical biosensing device that integrates an immunochromatographic test strip and a screen-printed electrode (SPE) connected to a portable electrochemical analyzer was presented for rapid, sensitive, and quantitative detection of disease-related biomarker in human blood samples. The principle of the sensor is based on sandwich immunoreactions between a biomarker and a pair of its antibodies on the test strip, followed by highly sensitive square-wave voltammetry (SWV) detection. Horseradish peroxidase (HRP) was used as a signal reporter for electrochemical readout. Hepatitis B surface antigen (HBsAg) was employed as a model protein biomarker to demonstrate the analytical performance of the sensor in this study. Some critical parameters governing the performance of the sensor were investigated in detail. The sensor was further utilized to detect HBsAg in human plasma with an average recovery of 91.3%. In comparison, a colorimetric immunochromatographic test strip assay (ITSA) was also conducted. The result shows that the SWV detection in the electrochemical sensor is much more sensitive for the quantitative determination of HBsAg than the colorimetric detection, indicating that such a sensor is a promising platform for rapid and sensitive point-of-care testing/screening of disease-related biomarkers in a large population

  2. Total protein concentration and diagnostic test results for gray wolf (Canis lupus) serum using Nobuto filter paper strips

    Science.gov (United States)

    Jara, Rocio F.; Sepúlveda, Carolina; Ip, Hon S.; Samuel, Michael D.

    2015-01-01

    Nobuto filter paper strips are widely used for storing blood-serum samples, but the recovery of proteins from these strips following rehydration is unknown. Poor recovery of proteins could reduce the concentration of antibodies and antigens and reduce the sensitivity of diagnostic assays. We compared the protein concentration, and its association with test sensitivity, of eluted Nobuto strip samples with paired sera. We collected and froze serum from five gray wolves (Canis lupus) for 8 mo. When thawed, we used a spectrophotometer (absorbance 280 nm) to determine the serum protein concentration for paired sera and Nobuto eluates for each animal in 2-fold serial dilutions. Total protein concentration was similar for both sample storage methods (Nobuto eluates and control sera), except for the undiluted samples in which Nobuto eluates had higher total protein concentrations. Both sample storage methods appear to produce similar results using the SNAP® 4Dx® Test to detect antibodies against pathogens causing Lyme disease, anaplasmosis, and ehrlichiosis as well as antigen for canine heartworm disease.

  3. Comparison of Three Different Commercial Kits for the Human Papilloma Virus Genotyping.

    Science.gov (United States)

    Lim, Yong Kwan; Choi, Jee-Hye; Park, Serah; Kweon, Oh Joo; Park, Ae Ja

    2016-11-01

    High-risk type human papilloma virus (HPV) is the most important cause of cervical cancer. Recently, real-time polymerase chain reaction and reverse blot hybridization assay-based HPV DNA genotyping kits are developed. So, we compared the performances of different three HPV genotyping kits using different analytical principles and methods. Two hundred positive and 100 negative cervical swab specimens were used. DNA was extracted and all samples were tested by the MolecuTech REBA HPV-ID, Anyplex II HPV28 Detection, and HPVDNAChip. Direct sequencing was performed as a reference method for confirming high-risk HPV genotypes 16, 18, 45, 52, and 58. Although high-level agreement results were observed in negative samples, three kits showed decreased interassay agreement as screening setting in positive samples. Comparing the genotyping results, three assays showed acceptable sensitivity and specificity for the detection of HPV 16 and 18. Otherwise, various sensitivities showed in the detection of HPV 45, 52, and 58. The three assays had dissimilar performance of HPV screening capacity and exhibited moderate level of concordance in HPV genotyping. These discrepant results were unavoidable due to difference in type-specific analytical sensitivity and lack of standardization; therefore, we suggested that the efforts to standardization of HPV genotyping kits and adjusting analytical sensitivity would be important for the best clinical performance. © 2016 Wiley Periodicals, Inc.

  4. ISM stripping from cluster galaxies and inhomogeneities in cooling flows

    Science.gov (United States)

    Soker, Noam; Bregman, Joel N.; Sarazin, Craig L.

    1990-01-01

    Analyses of the x ray surface brightness profiles of cluster cooling flows suggest that the mass flow rate decreases towards the center of the cluster. It is often suggested that this decrease results from thermal instabilities, in which denser blobs of gas cool rapidly and drop below x ray emitting temperatures. If the seeds for the thermal instabilities are entropy perturbations, these perturbations must enter the flow already in the nonlinear regime. Otherwise, the blobs would take too long to cool. Here, researchers suggest that such nonlinear perturbations might start as blobs of interstellar gas which are stripped out of cluster galaxies. Assuming that most of the gas produced by stellar mass loss in cluster galaxies is stripped from the galaxies, the total rate of such stripping is roughly M sub Interstellar Matter (ISM) approx. 100 solar mass yr(-1). It is interesting that the typical rates of cooling in cluster cooling flows are M sub cool approx. 100 solar mass yr(-1). Thus, it is possible that a substantial portion of the cooling gas originates as blobs of interstellar gas stripped from galaxies. The magnetic fields within and outside of the low entropy perturbations can help to maintain their identities, both by suppressing thermal conduction and through the dynamical effects of magnetic tension. One significant question concerning this scenario is: Why are cooling flows seen only in a fraction of clusters, although one would expect gas stripping to be very common. It may be that the density perturbations only survive and cool efficiently in clusters with a very high intracluster gas density and with the focusing effect of a central dominant galaxy. Inhomogeneities in the intracluster medium caused by the stripping of interstellar gas from galaxies can have a number of other effects on clusters. For example, these density fluctuations may disrupt the propagation of radio jets through the intracluster gas, and this may be one mechanism for producing Wide

  5. Silicon strip detector qualification for the CMS experiment

    International Nuclear Information System (INIS)

    Kaussen, Gordon

    2008-01-01

    To provide the best spatial resolution for the particle trajectory reconstruction and a very fast readout, the inner tracking system of CMS is build up of silicon detectors with a pixel tracker in the center surrounded by a strip tracker. The silicon strip tracker consists of so-called modules representing the smallest detection unit of the tracking device. These modules are mounted on higher-level structures called shells in the tracker inner barrel (TIB), rods in the tracker outer barrel (TOB), disks in the tracker inner disks (TID) and petals in the tracker end caps (TEC). The performance of the participating two shells of the TIB, four rods of the TOB and two petals of the TEC (representing about 1% of the final strip tracker) could be studied in different magnetic fields over a period of approximately two month using cosmic muon signals. The last test before inserting the tracker in the CMS experiment was the Tracker Slice Test performed in spring/summer 2007 at the Tracker Integration Facility (TIF) at CERN after installing all subdetectors in the tracker support tube. Approximately 25% of the strip tracker +z side was powered and read out using a cosmic ray trigger built up of scintillation counters. In total, about 5 million muon events were recorded under various operating conditions. These events together with results from commissioning runs were used to study the detector response like cluster charges, signal-to-noise ratios and single strip noise behaviour as well as to identify faulty channels which turned out to be in the order of a few per mille. The performance of the silicon strip tracker during these different construction stages is discussed in this thesis with a special emphasis on the tracker end caps. (orig.)

  6. Experimental evidence that wildflower strips increase pollinator visits to crops.

    Science.gov (United States)

    Feltham, Hannah; Park, Kirsty; Minderman, Jeroen; Goulson, Dave

    2015-08-01

    Wild bees provide a free and potentially diverse ecosystem service to farmers growing pollination-dependent crops. While many crops benefit from insect pollination, soft fruit crops, including strawberries are highly dependent on this ecosystem service to produce viable fruit. However, as a result of intensive farming practices and declining pollinator populations, farmers are increasingly turning to commercially reared bees to ensure that crops are adequately pollinated throughout the season. Wildflower strips are a commonly used measure aimed at the conservation of wild pollinators. It has been suggested that commercial crops may also benefit from the presence of noncrop flowers; however, the efficacy and economic benefits of sowing flower strips for crops remain relatively unstudied. In a study system that utilizes both wild and commercial pollinators, we test whether wildflower strips increase the number of visits to adjacent commercial strawberry crops by pollinating insects. We quantified this by experimentally sowing wildflower strips approximately 20 meters away from the crop and recording the number of pollinator visits to crops with, and without, flower strips. Between June and August 2013, we walked 292 crop transects at six farms in Scotland, recording a total of 2826 pollinators. On average, the frequency of pollinator visits was 25% higher for crops with adjacent flower strips compared to those without, with a combination of wild and commercial bumblebees (Bombus spp.) accounting for 67% of all pollinators observed. This effect was independent of other confounding effects, such as the number of flowers on the crop, date, and temperature. Synthesis and applications. This study provides evidence that soft fruit farmers can increase the number of pollinators that visit their crops by sowing inexpensive flower seed mixes nearby. By investing in this management option, farmers have the potential to increase and sustain pollinator populations over time.

  7. Silicon strip detector qualification for the CMS experiment

    Energy Technology Data Exchange (ETDEWEB)

    Kaussen, Gordon

    2008-10-06

    To provide the best spatial resolution for the particle trajectory reconstruction and a very fast readout, the inner tracking system of CMS is build up of silicon detectors with a pixel tracker in the center surrounded by a strip tracker. The silicon strip tracker consists of so-called modules representing the smallest detection unit of the tracking device. These modules are mounted on higher-level structures called shells in the tracker inner barrel (TIB), rods in the tracker outer barrel (TOB), disks in the tracker inner disks (TID) and petals in the tracker end caps (TEC). The performance of the participating two shells of the TIB, four rods of the TOB and two petals of the TEC (representing about 1% of the final strip tracker) could be studied in different magnetic fields over a period of approximately two month using cosmic muon signals. The last test before inserting the tracker in the CMS experiment was the Tracker Slice Test performed in spring/summer 2007 at the Tracker Integration Facility (TIF) at CERN after installing all subdetectors in the tracker support tube. Approximately 25% of the strip tracker +z side was powered and read out using a cosmic ray trigger built up of scintillation counters. In total, about 5 million muon events were recorded under various operating conditions. These events together with results from commissioning runs were used to study the detector response like cluster charges, signal-to-noise ratios and single strip noise behaviour as well as to identify faulty channels which turned out to be in the order of a few per mille. The performance of the silicon strip tracker during these different construction stages is discussed in this thesis with a special emphasis on the tracker end caps. (orig.)

  8. A visual strip sensor for determination of iron

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Sanjukta A., E-mail: sanjuktaak301@gmail.com [Analytical Chemistry Division, BARC, Trombay, Mumbai 400085 (India); Thakur, Neha; Parab, Harshala J.; Pandey, Shailaja P. [Analytical Chemistry Division, BARC, Trombay, Mumbai 400085 (India); Shinde, Rakesh N.; Pandey, Ashok K. [Radiochemistry Division, BARC, Trombay, Mumbai 400085 (India); Kumar, Sangita D.; Reddy, A.V.R. [Analytical Chemistry Division, BARC, Trombay, Mumbai 400085 (India)

    2014-12-03

    Highlights: • A visual strip sensor for on-site detection of iron has been developed and made. • The sensor is easy to synthesize, portable and recyclable with shelf life >1 year. • Visual detection limit for iron using the present sensor is 50 ng mL{sup −1}. • Visual strip sensor was applied to ground water and fruit juices. - Abstract: A visual strip has been developed for sensing iron in different aqueous samples like natural water and fruit juices. The sensor has been synthesized by UV-radiation induced graft polymerization of acrylamide monomer in microporous poly(propylene) base. For physical immobilization of iron selective reagent, the in situ polymerization of acrylamide has been carried out in the presence of 1,10-phenanthroline. The loaded strip on interaction with Fe(II) in aqueous solution turned into orange red color and the intensity of the color was found to be directly proportional to the amount of Fe(II) in the aqueous sample. The minimal sensor response with naked eye was found for 50 ng mL{sup −1} of Fe in 15 min of interaction. However, as low as 20 ng mL{sup −1} Fe could be quantified using a spectrophotometer. The detection limit calculated using the 3s/S criteria, where ‘s’ is the standard deviation of the absorbance of blank reagent loaded strip and ‘S’ is the slope of the linear calibration plot, was 1.0 ng mL{sup −1}. The strip was applied to measure Fe in a variety of samples such as ground water and fruit juices.

  9. A plane mirror experiment inspired by a comic strip

    Science.gov (United States)

    Lúcio Prados Ribeiro, Jair

    2016-01-01

    A comic strip about a plane mirror was used in a high school optics test, and it was perceived that a large portion of the students believed that the mirror should be larger than the object so the virtual image could be entirely visible. Inspired on the comic strip, an experimental demonstration with flat mirrors was developed, in order to readdress this topic learning. Students were encouraged to create their own investigation of the phenomenon with a simple instrumental apparatus and also suggest different experimental approaches.

  10. The CMS Silicon Strip Tracker performance using cosmic ray data

    CERN Document Server

    Borrello, L

    2010-01-01

    The CMS Silicon Strip Tracker is the largest tracking system based on silicon detector technology ever built for high energy physics experiment. It consists of 24,244 single-sided micro-strip sensors for a total active area of 198 $m^2$ and about 10 million readout channels. The SST was installed inside CMS in December 2007, commissioned during summer 2008 and then it participated along with other CMS subdetectors in several cosmic muon data taking runs. The commissioning strategy, operational experience and detector performance results will be presented.

  11. Stability of flow over plates with porous suction strips

    Science.gov (United States)

    Reed, H. L.; Nayfeh, A. H.

    1981-01-01

    This paper addresses the stability of two-dimensional, incompressible boundary-layer flow over plates with suction through porous strips. The mean flow is calculated using linearized triple-deck, closed-form solutions. The stability results of the triple-deck theory are shown to be in good agreement with those of the interacting boundary layers. Then different configurations of number, spacing, and mass flow rate through such porous strips are analyzed and compared with nonsimilar uniform-suction stability results from the point of view of applicability to laminar flow control.

  12. The Las Vegas Strip as a Genuinely Invented Global Landscape

    Directory of Open Access Journals (Sweden)

    Daniel Ortega

    2004-12-01

    Full Text Available Las Vegas, Nevada, is typically recognised as a place via a single urban gesture, that gesture being Las Vegas Boulevard, which is more commonly referred to as "The Strip". In constructing a thesis around the theme, "Here or There? Interconnections between the Global and the Local", one cannot ignore the invitation to discuss globalisation and its effects on a particular local fabric. For the purpose of this text, globalisation can be thought of as what Carmona et al describe as an intricate series of events leading to the world "becoming increasingly interconnected, with centralised decision making exploiting economies of scale and standardisation" (2003: 101. The centralised decision-making process for The Strip is evident in the strategy to develop individually themed casino resorts along Las Vegas Boulevard that respond to a competitive economy, thus creating a newly standardised landscape. If we also understand that globalisation can be thought of as the development of an interconnected world where economic, political and cultural boundaries can be easily crossed, this work can begin to define how the Las Vegas Strip is a genuinely invented global landscape. This paper addresses the "here-ness" as well as the "there-ness" of The Strip, while offering a dialectical framework for establishing a meaning of place by having 'there' placed 'here'. By employing semiological interpretations of real landscapes from around the globe (for example, Venturi et al, 1972, The Strip becomes a newly invented landscape of "simulations" (Baudrillard, 1988. As such, The Strip acts as a narrative that forms a unique place, opening the door to questions of authenticity and identity. This paper concludes by focusing on the question of "Here or There?" as an appropriate deviation from the assumed role that the post-modern landscape of the Las Vegas Strip plays. This work is intended to be a point of departure from the frequent criticism of the Las Vegas Strip as

  13. Beam test of CSES silicon strip detector module

    Science.gov (United States)

    Zhang, Da-Li; Lu, Hong; Wang, Huan-Yu; Li, Xin-Qiao; Xu, Yan-Bing; An, Zheng-Hua; Yu, Xiao-xia; Wang, Hui; Shi, Feng; Wang, Ping; Zhao, Xiao-Yun

    2017-05-01

    The silicon-strip tracker of the China Seismo-Electromagnetic Satellite (CSES) consists of two double-sided silicon strip detectors (DSSDs) which provide incident particle tracking information. A low-noise analog ASIC VA140 was used in this study for DSSD signal readout. A beam test on the DSSD module was performed at the Beijing Test Beam Facility of the Beijing Electron Positron Collider (BEPC) using a 400-800 MeV/c proton beam. The pedestal analysis results, RMSE noise, gain correction, and intensity distribution of incident particles of the DSSD module are presented. Supported by the XXX Civil Space Programme

  14. Genotyping of the fish rhabdovirus, viral haemorrhagic septicaemia virus, by restriction fragment length polymorphisms

    DEFF Research Database (Denmark)

    Einer-Jensen, Katja; Winton, J.; Lorenzen, Niels

    2005-01-01

    The aim of this study was to develop a standardized molecular assay that used limited resources and equipment for routine genotyping of isolates of the fish rhabdovirus, viral haemorrhagic septicaemia virus (VHSV). Computer generated restriction maps, based on 62 unique full-length (1524 nt......-gene by a set of three restriction enzymes was predicted to accurately enable the assignment of the VHSV isolates into the four major genotypes discovered to date. Further sub-typing of the isolates into the recently described sub-lineages of genotype I was possible by applying three additional enzymes...

  15. Validation of a Diagnostic Microarray for Human Papillomavirus: Coverage of 102 Genotypes

    Directory of Open Access Journals (Sweden)

    Sarah Tuttleton Arron

    2011-01-01

    Full Text Available Papillomaviruses have been implicated in a variety of human diseases ranging from common warts to invasive carcinoma of the anogenital mucosa. Existing assays for genotyping human papillomavirus are restricted to a small number of types. Here, we present a comprehensive, accurate microarray strategy for detection and genotyping of 102 human papillomavirus types and validate its use in a panel of 91 anal swabs. This array has equal performance to traditional dot blot analysis with the benefits of added genotype coverage and the ability to calibrate readout over a range of sensitivity or specificity values.

  16. Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants

    DEFF Research Database (Denmark)

    Serre, Stéphanie B N; Jensen, Sanne B; Ghanem, Lubna

    2016-01-01

    Hepatitis C virus (HCV) NS3 protease inhibitors (PIs) are important components of novel HCV therapy regimens. Studies of PI resistance initially focused on genotype 1. Therefore, knowledge on determinants of PI resistance for the highly prevalent genotypes 2-6 remains limited. Using Huh7.5 cell...... selected under telaprevir/boceprevir conferred less resistance to certain newer PIs. In a single-cycle production assay, across genotypes, PI treatment primarily decreased viral replication, which was rescued by PI resistance substitutions. Identified substitutions resulted in differential effects on viral...... cycle, which is of interest for clinical and virological HCV research....

  17. Application of high-resolution DNA melting for genotyping in lepidopteran non-model species: Ostrinia furnacalis (Crambidae.

    Directory of Open Access Journals (Sweden)

    FengBo Li

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

  18. Transforming microbial genotyping: a robotic pipeline for genotyping bacterial strains.

    Directory of Open Access Journals (Sweden)

    Brian O'Farrell

    Full Text Available Microbial genotyping increasingly deals with large numbers of samples, and data are commonly evaluated by unstructured approaches, such as spread-sheets. The efficiency, reliability and throughput of genotyping would benefit from the automation of manual manipulations within the context of sophisticated data storage. We developed a medium- throughput genotyping pipeline for MultiLocus Sequence Typing (MLST of bacterial pathogens. This pipeline was implemented through a combination of four automated liquid handling systems, a Laboratory Information Management System (LIMS consisting of a variety of dedicated commercial operating systems and programs, including a Sample Management System, plus numerous Python scripts. All tubes and microwell racks were bar-coded and their locations and status were recorded in the LIMS. We also created a hierarchical set of items that could be used to represent bacterial species, their products and experiments. The LIMS allowed reliable, semi-automated, traceable bacterial genotyping from initial single colony isolation and sub-cultivation through DNA extraction and normalization to PCRs, sequencing and MLST sequence trace evaluation. We also describe robotic sequencing to facilitate cherrypicking of sequence dropouts. This pipeline is user-friendly, with a throughput of 96 strains within 10 working days at a total cost of 200,000 items were processed by two to three people. Our sophisticated automated pipeline can be implemented by a small microbiology group without extensive external support, and provides a general framework for semi-automated bacterial genotyping of large numbers of samples at low cost.

  19. Rapid and quantitative detection of C-reactive protein using quantum dots and immunochromatographic test strips

    Directory of Open Access Journals (Sweden)

    Cheng X

    2014-12-01

    Full Text Available Xianglin Cheng,1,* Xu Pu,2,* Pen Jun,3 XiaoBo Zhu,3 Di Zhu,4 Ming Chen1 1Department of Laboratory Medicine, First Affiliated Hospital of Yangtze University, Jingzhou, 2Department of Laboratory Medicine, RenMin Hospital of Wuhan University, Wuhan, 3Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, People’s Republic of China; 4Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA *These authors contributed equally to this study and share first authorship Background: Rapid immunochromatographic tests can detect disease markers in 10–15 minutes, which facilitates clinical diagnosis and treatment programs. However, most immunochromatographic tests employ gold nanoparticles as reporters, and these have only moderate sensitivity and act as qualitative methods for analyzing high biomarker concentrations. Methods: In this study, we introduce quantum dots (QDs as fluorescent probes and immunochromatographic strips to develop quantitative fluorescence point-of-care tests (QF-POCT to analyze C-reactive protein (CRP levels. Goat anti-rabbit IgG and rabbit IgG were used as control antibodies, and mouse monoclonal CRP antibody pairs were used for disease marker detection. One monoclonal CRP antibody was conjugated with QDs and served as a signal antibody, and the other monoclonal CRP antibody was dispensed onto the nitrocellulose membrane and served as a capturing antibody. In the presence of CRP, the fluorescence intensity of the monoclonal antibody-CRP-monoclonal antibody sandwich complex captured on the nitrocellulose membrane was determined using the fluorescence strip reader. Results: QF-POCT assays could quantitatively analyze the concentration of CRP in 15 minutes had a detection limit of 0.25 mg/L, and had a wide detection linearity range (0.5–300 mg/L. The intra-assay and interassay

  20. Univariate stability analysis methods for determining genotype ...

    African Journals Online (AJOL)

    Twenty two different stability statistics were used for analyzing genotype × environment (GE) interaction of durum wheat experimental data (20 genotypes in 15 environments). Combined analysis of variance indicated that GE interaction significantly influenced genotypes yield. According to type I stability concept, genotypes ...

  1. Acute barrier disruption by adhesive tapes is influenced by pressure, time and anatomical location: integrity and cohesion assessed by sequential tape stripping. A randomized, controlled study.

    Science.gov (United States)

    Breternitz, M; Flach, M; Prässler, J; Elsner, P; Fluhr, J W

    2007-02-01

    Tape stripping is an established procedure in stratum corneum (SC) physiology research. Adhesive films are pressed to the surface of the skin and then removed. The superficial layers of the SC adhere to the film and are accessible for further investigations. Although this method is widely used, only scant information about standardization is known. Various protocols are used but are difficult to compare. The aim of the present study was to investigate the effects of the type of tape, pressure, time, anatomical site and type of applied pressure. Twelve healthy volunteers (age range 20-31 years) were entered in a randomized, controlled study with sequential tape stripping at the volar forearm, upper arm, cheek and back. Different methods (roller, stamp, thumb, stretched skin), total duration of applied pressure (2 s, 10 s), degrees of pressure (2 N stamp, 7 N stamp) and different tapes (D-Squame, Corneofix, Blenderm) were investigated and the impact on barrier function assessed by transepidermal water loss measurements. Furthermore, measurements of SC hydration, skin colour and skin surface pH were performed. Spectroscopic measurements and a Bradford protein assay to determine the mass of removed SC were carried out in parallel. The degree of barrier disruption, irritation and SC cohesion is influenced by the character of adhesive tapes, total duration of applied pressure (2 s, 10 s; 2 N, 7 N), the kind of method for pressure application (roller, stamp, thumb, stretched skin), anatomical site and condition before stripping (occlusion vs. nonocclusion). The spectroscopic assessment and Bradford protein assay determination showed a significant correlation (P tape strips on the volar forearm and then discarding the first and second strips. This approach allows the performance of a standardized study with a reasonable amount of resources.

  2. Assay for identification of heterozygous single-nucleotide polymorphism (Ala67Thr in human poliovirus receptor gene

    Directory of Open Access Journals (Sweden)

    Shyam Sundar Nandi

    2016-01-01

    Results: A new SNP assay for detection of heterozygous Ala67Thr genotype was developed and validated by testing 150 DNA samples. Heterozygous CD155 was detected in 27.33 per cent (41/150 of DNA samples tested by both SNP detection assay and sequencing. Interpretation & conclusions: The SNP detection assay was successfully developed for identification of Ala67Thr polymorphism in human PVR/CD155 gene. The SNP assay will be useful for large scale screening of DNA samples.

  3. Comparsion of an immunochromatographic strip with ELISA for simultaneous detection of thiamphenicol, florfenicol and chloramphenicol in food samples.

    Science.gov (United States)

    Guo, Lingling; Song, Shanshan; Liu, Liqiang; Peng, Juan; Kuang, Hua; Xu, Chuanlai

    2015-09-01

    Rapid and sensitive indirect competitive enzyme-linked immunosorbent assays (ic-ELISA) and gold nanoparticle immunochromatographic strip tests were developed to detect thiamphenicol (TAP), florfenicol (FF) and chloramphenicol (CAP) in milk and honey samples. The generic monoclonal antibody for TAP, FF and CAP was prepared based on a hapten [D-threo-1-(4-aminophenyl)-2- dichloroacetylamino-1,3-propanediol], and the haptenwas linked to a carrier protein using the diazotization method. After the optimization of several parameters (coating, pH, sodium chloride content and methanol content), the ic-ELISA was established. The quantitative working range for TAP was 0.11-1.36 ng/mL, with an IC50 of 0.39 ng/mL. The optimized ELISA showed cross-reactivity to CAP (300%) and FF (15.6%), with IC50 values of 0.13 and 2.5 ng/mL, respectively. The analytical recovery of TAP, FF and CAP in milk and honey samples in the ic-ELISA ranged from 81.2 to 112.9%. Based on this monoclonal antibody, a rapid and sensitive immunochromatographic test strip was also developed. This strip had a detection limit of 1 ng/mL for TAP, FF and CAP in milk and honey samples. Moreover, the test was completed within 10 min. Our results showed that the proposed ic-ELISA and immunochromatographic test strip method are highly useful screening tools for TAP, FF and CAP detection in milk and honey samples. Copyright © 2015 John Wiley & Sons, Ltd.

  4. Genotypic, physiological, and biochemical characterization of potentially pathogenic Acanthamoeba isolated from the environment in Cairo, Egypt.

    Science.gov (United States)

    Tawfeek, Gihan Mostafa; Bishara, Sawsan Abdel-Hamid; Sarhan, Rania Mohammad; ElShabrawi Taher, Eman; ElSaady Khayyal, Amira

    2016-05-01

    Acanthamoebae are the most common opportunistic amphizoic protozoa that cause life-threatening granulomatous amoebic encephalitis in immunocompromised individuals and sight-threatening amoebic keratitis (AK) in contact lens wearers. The present work aimed to determine the presence of Acanthamoeba isolates in different environmental sources: water, soil, and dust in Cairo, Egypt and to characterize the pathogenic potential of the isolated Acanthamoeba using physiological and biochemical assays as well as determination of the genotypes in an attempt to correlate pathogenicity with certain genotypes. The study included the collection of 22 corneal scrapings from patients complaining of symptoms and signs indicative of acanthamoeba keratitis (AK) and 75 environmental samples followed by cultivation on non-nutrient agar plates preseeded with E. coli. Positive samples for Acanthamoeba were subjected to osmo- and thermo-tolerance assays and zymography analysis. Potentially pathogenic isolates were subjected to PCR amplification using genus-specific primer pair. Isolates were classified at the genotype level based on the sequence analysis of Acanthamoeba 18S rRNA gene (diagnostic fragment 3). The total detection rate for Acanthamoeba in environmental samples was 33.3 %, 31.4 % in water, 40 % in soil, and 20 % in dust samples. Three and two Acanthamoeba isolates from water and soil sources, respectively, had the potential for pathogenicity as they exhibited full range of pathogenic traits. Other 12 isolates were designated as weak potential pathogens. Only ten of the environmental isolates were positive in PCR and were classified by genotype analysis into T4 genotype (70 %), T3 (10 %) and T5 (20 %). Potential pathogens belonged to genotypes T4 (from water) and T5 (from soil) while weak potential pathogens belonged to genotypes T3 (from water) and T4 (from water and soil). Additionally, T7 genotype was isolated from keratitis patients. There is a considerable

  5. Expression of Hepatitis B virus surface antigen (HBsAg from genotypes A, D and F and influence of amino acid variations related or not to genotypes on HBsAg detection

    Directory of Open Access Journals (Sweden)

    Natalia M. Araujo

    Full Text Available The impact of hepatitis B virus (HBV genotypes on the sensitivity of surface antigen (HBsAg detection assays has been poorly investigated. Here, plasmids carrying consensus or variant coding sequences for HBV surface proteins from genotypes A, D and F, were constructed. HBsAg levels were evaluated in medium and extracts of transfected CHO cells by a commercial polyclonal-based assay. We show that HBsAg detection values of consensus forms from genotypes D and F were, respectively, 37% and 30% lower than those obtained by genotype A. However, the presence of two single variations, T143M in genotype A, and T125M in genotype D, produced a decrease of 44% and an increase of 34%, respectively, on HBsAg mean values in comparison with their consensus forms. In conclusion, HBsAg detection levels varied among HBV genotypes. However, unique amino acid substitutions not linked to genotypes, such as T125M and T143M described here, should have more implications in HBV immunological diagnostics than the set of variations characteristic of each HBV genotype.

  6. Assay method and compositions

    International Nuclear Information System (INIS)

    1977-01-01

    Methods are described for measuring catecholamine levels in human and animal body fluids and tissues using the catechol-O-methyl-transferase (COMT) radioassay. The assay involves incubating the biological sample with COMT and the tritiated methyl donor, S-adenosyl-L-methionine( 3 H)-methyl. The O-methylated ( 3 H) epinephrine and/or norepinephrine are extracted and oxidised to vanillin- 3 H which in turn is extracted and its radioactivity counted. When analysing dopamine levels the assay is extended by vanillin- 3 H and raising the pH of the aqueous periodate phase from which O-methylated ( 3 H) dopamine is extracted and counted. The assay may be modified depending on whether measurements of undifferentiated total endogenous catecholamine levels or differential analyses of the catecholamine levels are being performed. The sensitivity of the assay can be as low as 5 picograms for norepinephrine and epinephrine and 12 picograms for dopamine. The assemblance of the essential components of the assay into a kit for use in laboratories is also described. (U.K.)

  7. Análise de vinte genótipos de sorgo (Sorghum bicolor (L. Moench, de portes médio e alto, pertencentes ao ensaio nacional Analysis of twenty genotypes of sorghum (Sorghum bicolor (L. Moench of medium and high status from the national assay

    Directory of Open Access Journals (Sweden)

    Domingos Marcelo Cenachi Pesce

    2000-08-01

    Full Text Available Os vinte genótipos de sorgo estudados foram cultivados e ensilados aos 104 dias de idade, em estádio de grão pastoso, em silos de laboratório de "PVC", com 10 cm de diâmetro e 40 cm de comprimento. Os silos foram abertos aos 150 dias após a ensilagem. O delineamento adotado foi o inteiramente casualizado. No material estudado (verde e ensilado, foram determinados os valores de fibra em detergente neutro (FDN, fibra em detergente ácido (FDA, hemicelulose, celulose, lignina, cinzas totais, matéria seca (MS, proteína bruta (PB e carboidratos solúveis em álcool, que apresentaram valores médios de 61,8; 34,2; 27,5; 29,5; 4,6; 3,8; 25,7; 7,7; e 8,5% no material original e de 55,9; 32,6; 23,3; 28,5; 3,9; 4,0; 27,5; 8,6; e 0,8% nas silagens, respectivamente. Os valores de hemicelulose e celulose diminuíram com a ensilagem, indicando que tais frações forneceram carboidratos adicionais para a fermentação. Os teores de carboidratos solúveis do material original foram altos para todos os genótipos, sendo intensamente consumidos no silo, garantindo bom padrão de fermentação. Nas silagens, os valores de pH foram, em média, 3,5 e os teores de nitrogênio amoniacal, inferiores a 8%, em todos os genótipos. As silagens estudadas apresentaram-se iguais para todas as características pesquisadas.The twenty studied genotypes of sorghum were cultivated and ensiled at 104 days of age, at dough grain phase, using "PVC" lab silos, presenting 10 cm diameter and 40 cm length. The silos were opened at 150 days after ensiling. A completely randomized experimental design was used. In the studied material (fresh and ensiled the values of neutral detergent fiber (NDF, acid detergent fiber (ADF, hemicellulose, cellulose, lignin, total ash, dry matter (DM, crude protein (CP and alcool soluble carbohydrates were determined. The mean values were of 61.8, 34.2, 27.5, 29.5, 4.6, 3.8, 25.7, 7.7 and 8.5% in the fresh matter and of 55.9, 32.6, 23.3, 28.5, 3.9, 4

  8. Radioreceptor assay for insulin

    International Nuclear Information System (INIS)

    Suzuki, Kazuo

    1975-01-01

    Radioreceptor assay of insulin was discussed from the aspects of the measuring method, its merits and problems to be solved, and its clinical application. Rat liver 10 x g pellet was used as receptor site, and enzymatic degradation of insulin by the system contained in this fraction was inhibited by adding 1 mM p-CMB. 125 I-labelled porcine insulin was made by lactoperoxidase method under overnight incubation at 4 0 C and later purification by Sephadex G-25 column and Whatman CF-11 cellulose powder. Dog pancreatic vein serum insulin during and after the glucose load was determined by radioreceptor assay and radioimmunoassay resulting that both measurements accorded considerably. Radioreceptor assay would clarify the pathology of disorders of glucose metabolism including diabetes. (Tsukamoto, Y.)

  9. Rover waste assay system

    International Nuclear Information System (INIS)

    Akers, D.W.; Stoots, C.M.; Kraft, N.C.; Marts, D.J.

    1997-01-01

    The Rover Waste Assay System (RWAS) is a nondestructive assay system designed for the rapid assay of highly-enriched 235 U contaminated piping, tank sections, and debris from the Rover nuclear rocket fuel processing facility at the Idaho Chemical Processing Plant. A scanning system translates a NaI(Tl) detector/collimator system over the structural components where both relative and calibrated measurements for 137 Cs are made. Uranium-235 concentrations are in operation and is sufficiently automated that most functions are performed by the computer system. These functions include system calibration, problem identification, collimator control, data analysis, and reporting. Calibration of the system was done through a combination of measurements on calibration standards and benchmarked modeling. A description of the system is presented along with the methods and uncertainties associated with the calibration and analysis of the system for components from the Rover facility. 4 refs., 2 figs., 4 tabs

  10. Hepatitis C genotype distribution in patient and blood donor samples in South Africa for the period 2008-2012.

    Science.gov (United States)

    Prabdial-Sing, N; Chirwa, T; Thaver, J; Smuts, H; Vermeulen, M; Suchard, M; Puren, A J

    2016-11-01

    There are limited molecular epidemiological studies of hepatitis C at a national level in South Africa. The introduction of newer treatment modalities for hepatitis C requires knowledge of the genotypes as these may have different prognostic and therapeutic implications. This retrospective study describes genotype distributions of patients attending specialist clinics and a blood donor group studied during the period 2008-2012 in South Africa. Residual samples from diagnostic viral load testing from specialist clinics in South Africa (n=941) and from the South African National Blood Service (n=294) were analysed quantitatively by real-time PCR and genotyped using the Versant line probe assay or sequencing. Genotype 1 was predominant in blood donors (34%), whilst genotype 5a was prevalent in patients (36%). In the blood donor group, genotype 4 was detected for the first time. Genotype 2 was rare in the patient group and not detected in blood donors. Genotype 1 was the predominant genotype in the younger age groups (less than 30 years), whereas genotype 5a was found at higher proportions in the older age groups for both the patient and blood donor groups, comprising more than 60% of genotypes in those older than 50 years. Genotypes 1 and 5 were at highest proportions across all provinces compared to other genotypes. In blood donors, genotype 1 was predominant among Caucasians (43%) and genotype 5a among Blacks (54%). Such information is required for planning the impact on the health sector with regard to newly emerging therapies for hepatitis C and burden of disease. © 2016 John Wiley & Sons Ltd.

  11. Young tourists visiting strip clubs and paying for sex

    DEFF Research Database (Denmark)

    Hesse, Morten; Tutenges, Sébastien

    2011-01-01

    it for the first time. Among the men who attended strip clubs, 32% reported having done it for the first time. Stripclub patronage and paying for sex were both associated with higher levels of drinking, use of Viagra, and with having done the same thing before the holiday. Paying for sex was uniquely associated...

  12. Beam tests of ATLAS SCT silicon strip detector modules

    Czech Academy of Sciences Publication Activity Database

    Campabadal, F.; Fleta, C.; Key, M.; Böhm, Jan; Mikeštíková, Marcela; Šťastný, Jan

    2005-01-01

    Roč. 538, - (2005), s. 384-407 ISSN 0168-9002 R&D Projects: GA MŠk(CZ) 1P04LA212 Institutional research plan: CEZ:AV0Z10100502 Keywords : ATLAS * silicon * micro-strip * beam * test Subject RIV: BF - Elementary Particles and High Energy Physics Impact factor: 1.224, year: 2005

  13. Anodic Stripping Voltammetry for Arsenic Determination on Composite Gold Electrode

    Czech Academy of Sciences Publication Activity Database

    Navrátil, Tomáš; Kopanica, M.; Krista, J.

    2003-01-01

    Roč. 48, č. 2 (2003), s. 265-272 ISSN 0009-2223 Grant - others:GIT(AR) 101/02/U111/CZ Institutional research plan: CEZ:AV0Z4040901 Keywords : arsenic determination * stripping voltammetry * composite gold electrode Subject RIV: CG - Electrochemistry Impact factor: 0.415, year: 2003

  14. Visual method for detecting critical damage in railway contact strips

    Science.gov (United States)

    Judek, S.; Skibicki, J.

    2018-05-01

    Ensuring an uninterrupted supply of power in the electric traction is vital for the safety of this important transport system. For this purpose, monitoring and diagnostics of the technical condition of the vehicle’s power supply elements are becoming increasingly common. This paper presents a new visual method for detecting contact strip damage, based on measurement and analysis of the movement of the overhead contact line (OCL) wire. A measurement system configuration with a 2D camera was proposed. The experimental method has shown that contact strips damage can be detected by transverse displacement signal analysis. It has been proven that the velocity signal numerically established on that basis has a comparable level in the case of identical damage, regardless of its location on the surface of the contact strip. The proposed method belongs to the group of contact-less measurements, so it does not require interference with the structure of the catenary network nor the mounting of sensors in its vicinity. Measurement of displacements of the contact wire in 2D space makes it possible to combine the functions of existing diagnostic stands assessing the correctness of the mean contact force control adjustment of the current collector with the elements of the contact strip diagnostics, which involves detecting their damage which may result in overhead contact line rupture.

  15. Nutrient removal by prairie filter strips in agricultural landscapes

    Science.gov (United States)

    X. Zhou; M.J. Helmers; H. Asbjornsen; R. Kolka; M.D. Tomer; R.M. Cruse

    2014-01-01

    Nitrogen (N) and phosphorus (P) from agricultural landscapes have been identified as primary sources of excess nutrients in aquatic systems. The main objective of this study was to evaluate the effectiveness of prairie filter strips (PFS) in removing nutrients from cropland runoff in 12 small watersheds in central Iowa. Four treatments with PFS of different spatial...

  16. Metallurgical analysis of spalled work roll of hot strip mill

    International Nuclear Information System (INIS)

    Khan, M.M.; Khan, M.A.

    1993-01-01

    In this study failure analysis of four work roll of the Hot Strip Mill is carried out. The microstructure is correlated with the chemical composition of shell and roll-life. It was concluded that for the longer service of the roll, cementite, graphite and martensite should be balanced (as per working requirement of the mill). (author)

  17. Effectiveness of anti-strip agents in asphalt mixtures.

    Science.gov (United States)

    2012-07-01

    Since the late 1970s there has been much research performed to better understand the stripping phenomenon in asphalt mixtures. : As a result, there have been changes in both materials and technology over the past 30 years to improve the resistance to...

  18. Strip-Search Case Testing Balance between Privacy, Student Safety

    Science.gov (United States)

    Robelen, Erik W.

    2009-01-01

    As it weighs the high-profile case of a 13-year-old girl strip-searched at school, the U.S. Supreme Court is grappling with where to draw the line between protecting student privacy rights and allowing school officials to take steps to ensure a safe environment. During oral arguments, several of the justices seemed sympathetic to the challenges…

  19. Evaluation of Questionnaire, Reagent Strip and Egg Count as ...

    African Journals Online (AJOL)

    A longitudinal study covering 55 months evaluated the three diagnostic tools used for confirmation of prevalence of urinary schistosomiasis among 1151 consented primary school pupils in 13 communities of Edo State, Nigeria. Questionnaire, reagent strip method and parasitological examination were employed.

  20. Qualification of submerged-arc narrow strip cladding process

    International Nuclear Information System (INIS)

    Ayres, P.S.; Gottschling, J.D.; Jeffers, G.K.

    1975-08-01

    An unique narrow strip cladding process for use on both plate and forging material for nuclear components was developed. The qualification testing of this low-heat input process for cladding nuclear components, including those of SA508 Class 2 material is described. The theory that explains the acceptable results of these tests is also given. (auth)

  1. Qualification of submerged-arc narrow strip cladding process

    International Nuclear Information System (INIS)

    Ayres, P.S.; Gottschling, J.D.; Jeffers, G.K.

    1976-03-01

    Babcock and Wilcox has developed an unique narrow strip cladding process for use on both plate and forging material for nuclear components. The qualification testing of this low-heat input process for cladding nuclear components is described, including those of SA508 Class 2 material. The theory that explains the acceptable results of these tests is also given

  2. Effectiveness of buffer strips in the Netherlands : research plan

    NARCIS (Netherlands)

    Noij, G.J.

    2006-01-01

    On 1 July 2004 the European Commission and the Netherlands reached an agreement about the implementation of the Nitrates Directive for the nearby future. In this decree narrow fertilizer-free strips of 0.25 – 1.501 m are prescribed, depending on the type of crop and the method of herbicide

  3. Digital Images of Breast Biopsies using a Silicon Strip Detector

    International Nuclear Information System (INIS)

    Montano, Luis M.; Diaz, Claudia C.; Leyva, Antonio; Cabal, Fatima; Ortiz, Carlos M.

    2006-01-01

    In our study we have used a silicon strip detector to obtain digital images of some breast tissues with micro calcifications. Some of those images will be shown and we will discuss the perspectives of using this technique as an improvement of breast cancer diagnostics

  4. Magnetic stray fields of periodically arranged Co-Crmicro strips

    NARCIS (Netherlands)

    te Lintelo, J.G.T.; te Lintelo, J.G.T.

    1993-01-01

    Research was carried out on magnetic stray fields of Co-Cr micro strips. This investigation was motivated by the search for increasing bit density and miniaturisation in magnetic data storage and magnetic sensor devices. In these devices the magnetisation is patterned, i.e. by writing bits or

  5. Results of Laboratory Testing of Advanced Power Strips

    Energy Technology Data Exchange (ETDEWEB)

    Earle, L. [National Renewable Energy Lab. (NREL), Golden, CO (United States); Sparn, B. [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2012-08-01

    Presented at the ACEEE Summer Study on Energy Efficiency in Buildings on August 12-17, 2012, this presentation reports on laboratory tests of 20 currently available advanced power strip products, which reduce wasteful electricity use of miscellaneous electric loads in buildings.

  6. Impact of radiation on breakdown performance of Si strip detectors

    CERN Document Server

    Bhardwaj, A; Chatterji, S; Ranjan, Kirti; Shivpuri, E K; Srivastava-Ajay, K

    2002-01-01

    The very intense radiation environment of high luminosity future colliding beam experiments, like Large Hadron Collider (LHC etc.) makes radiation hardness the most urgent demand for Si detectors. The radiation hardness of Si strip detectors especially developed for LHC experiment was investigated with respect to ionizing and nonionizing radiation using computer simulations. (10 refs).

  7. Consideration of Factors Affecting Strip Effluent PH and Sodium Content

    Energy Technology Data Exchange (ETDEWEB)

    Peters, T. [Savannah River Site (SRS), Aiken, SC (United States)

    2015-07-29

    A number of factors were investigated to determine possible reasons for why the Strip Effluent (SE) can sometimes have higher than expected pH values and/or sodium content, both of which have prescribed limits. All of the factors likely have some impact on the pH values and Na content.

  8. Mechanistic modeling & effectiveness of buffer strips for pesticide regulatory frameworks

    Science.gov (United States)

    Vegetative Filter Strips (VFS) have been used as an effective conservation practice in agricultural areas for controlling and mitigate the effect of sediment, nutrients and pesticides loads into water bodies. In addition to the agricultural sector, another important use of VFS for controlling plague...

  9. Development of the H1 backward silicon strip detector

    International Nuclear Information System (INIS)

    Eick, W.; Hansen, K.; Lange, W.; Prell, S.; Zimmermann, W.; Bullough, M.A.; Greenwood, N.M.; Lucas, A.D.; Newton, A.M.; Wilburn, C.D.; Horisberger, R.; Pitzl, D.; Haynes, W.J.; Noyes, G.

    1996-10-01

    The development and first results are described of a silicon strip detector telescope for the HERA experiment H1 designed to measure the polar angle of deep inelastic scattered electrons at small Bjorken x and low momentum transfers Q 2 . (orig.)

  10. Engineering analyses of large precision cathode strip chambers for GEM

    Energy Technology Data Exchange (ETDEWEB)

    Horvath, J.A.; Belser, F.C.; Pratuch, S.M.; Wuest, C.R. [Lawrence Livermore National Lab., CA (United States); Mitselmakher, G. [Superconducting Super Collider Lab., Dallas, TX (United States); Gordeev, A. [Institute of Theoretical and Experimental Physics, Moscow (Russian Federation); Johnson, C.V. [Lawrence Livermore National Lab., CA (United States)]|[Superconducting Super Collider Lab., Dallas, TX (United States); Polychronakos, V.A. [Brookhaven National Lab., Upton, NY (United States); Golutvin, I.A. [Joint Institute for Nuclear Research, Dubna (Russian Federation)

    1993-10-21

    Structural analyses of large precision cathode strip chambers performed up to the date of this publication are documented. Mechanical property data for typical chamber materials are included. This information, originally intended to be an appendix to the {open_quotes}CSC Structural Design Bible,{close_quotes} is presented as a guide for future designers of large chambers.

  11. Vibration control of an elastic strip by a singular force

    Indian Academy of Sciences (India)

    MS received 10 September 2008; revised 27 August 2009; accepted 17 December. 2009. Abstract. Vibration characteristics of an elastic plate in the shape of an infinite strip are changed by applying a lateral concentrated force to the plate. The homo- geneous, isotropic, elastic plate is infinite in the x-direction and the sides ...

  12. Vibration control of an elastic strip by a singular force

    Indian Academy of Sciences (India)

    Vibration characteristics of an elastic plate in the shape of an infinite strip are changed by applying a lateral concentrated force to the plate. The homogeneous, isotropic, elastic plate is infinite in the -direction and the sides are simply supported. The size of the force is changed in proportion to the displacement measured at ...

  13. Low material budget floating strip Micromegas for ion transmission radiography

    Energy Technology Data Exchange (ETDEWEB)

    Bortfeldt, J., E-mail: jonathan.bortfeldt@cern.ch [LMU Munich, LS Schaile, Am Coulombwall 1, D-85748 Garching (Germany); Biebel, O.; Flierl, B.; Hertenberger, R.; Klitzner, F.; Lösel, Ph. [LMU Munich, LS Schaile, Am Coulombwall 1, D-85748 Garching (Germany); Magallanes, L. [LMU Munich, LS Parodi, Am Coulombwall 1, D-85748 Garching (Germany); University Hospital Heidelberg, Im Neuenheimer Feld 672, D-69120 Heidelberg (Germany); Müller, R. [LMU Munich, LS Schaile, Am Coulombwall 1, D-85748 Garching (Germany); Parodi, K. [LMU Munich, LS Parodi, Am Coulombwall 1, D-85748 Garching (Germany); Heidelberg Ion-Beam Therapy Center, Im Neuenheimer Feld 450, D-69120 Heidelberg (Germany); Schlüter, T. [LMU Munich, Excellence Cluster Universe, Boltzmannstr. 2, D-85748 Garching (Germany); Voss, B. [GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstr. 1, D-64291 Darmstadt (Germany); Zibell, A. [JMU Würzburg, Sanderring 2, D-97070 Würzburg (Germany)

    2017-02-11

    Floating strip Micromegas are high-accuracy and discharge insensitive gaseous detectors, able to track single particles at fluxes of 7 MHz/cm{sup 2} with 100 μm resolution. We developed low-material-budget detectors with one-dimensional strip readout, suitable for tracking at highest particle rates as encountered in medical ion transmission radiography or inner tracker applications. Recently we additionally developed Kapton-based floating strip Micromegas with two-dimensional strip readout, featuring an overall thickness of 0.011 X{sub 0}. These detectors were tested in high-rate proton and carbon-ion beams at the tandem accelerator in Garching and the Heidelberg Ion-Beam Therapy Center, operated with an optimized Ne:CF{sub 4} gas mixture. By coupling the Micromegas detectors to a new scintillator based range detector, ion transmission radiographies of PMMA and tissue-equivalent phantoms were acquired. The range detector with 18 layers is read out via wavelength shifting fibers, coupled to a multi-anode photomultiplier. We present the performance of the Micromegas detectors with respect to timing and single plane track reconstruction using the μTPC method. We discuss the range resolution of the scintillator range telescope and present the image reconstruction capabilities of the combined system.

  14. Paint stripping with high power flattened Gaussian beams

    CSIR Research Space (South Africa)

    Forbes, A

    2009-08-01

    Full Text Available In this paper the researchers present results on improved paint stripping performance with an intra-cavity generated Flattened Gaussian Beam (FGB). A resonator with suitable diffractive optical elements was designed in order to produce a single mode...

  15. A Harmonic Algorithm for the 3D Strip Packing Problem

    NARCIS (Netherlands)

    N. Bansal (Nikhil); X. Han; K. Iwama; M. Sviridenko; G. Zhang (Guochuan)

    2013-01-01

    htmlabstractIn the three-dimensional (3D) strip packing problem, we are given a set of 3D rectangular items and a 3D box $B$. The goal is to pack all the items in $B$ such that the height of the packing is minimized. We consider the most basic version of the problem, where the items must be packed

  16. MUST: A silicon strip detector array for radioactive beam experiments

    CERN Document Server

    Blumenfeld, Y; Sauvestre, J E; Maréchal, F; Ottini, S; Alamanos, N; Barbier, A; Beaumel, D; Bonnereau, B; Charlet, D; Clavelin, J F; Courtat, P; Delbourgo-Salvador, P; Douet, R; Engrand, M; Ethvignot, T; Gillibert, A; Khan, E; Lapoux, V; Lagoyannis, A; Lavergne, L; Lebon, S; Lelong, P; Lesage, A; Le Ven, V; Lhenry, I; Martin, J M; Musumarra, A; Pita, S; Petizon, L; Pollacco, E; Pouthas, J; Richard, A; Rougier, D; Santonocito, D; Scarpaci, J A; Sida, J L; Soulet, C; Stutzmann, J S; Suomijärvi, T; Szmigiel, M; Volkov, P; Voltolini, G

    1999-01-01

    A new and innovative array, MUST, based on silicon strip technology and dedicated to the study of reactions induced by radioactive beams on light particles is described. The detector consists of 8 silicon strip - Si(Li) telescopes used to identify recoiling light charged particles through time of flight, energy loss and energy measurements and to determine precisely their scattering angle through X, Y position measurements. Each 60x60 mm sup 2 double sided silicon strip detector with 60 vertical and 60 horizontal strips yields an X-Y position resolution of 1 mm, an energy resolution of 50 keV, a time resolution of around 1 ns and a 500 keV energy threshold for protons. The backing Si(Li) detectors stop protons up to 25 MeV with a resolution of approximately 50 keV. CsI crystals read out by photo-diodes which stop protons up to 70 MeV are added to the telescopes for applications where higher energy particles need to be detected. The dedicated electronics in VXIbus standard allow us to house the 968 logic and a...

  17. Radioreceptor assay for GH

    International Nuclear Information System (INIS)

    Tsushima, Toshio; Matsuzaki, Fukashi

    1975-01-01

    Radioreceptor assay (RRA) of growth hormone (GH) was studied using the protein which specifically bound to GH presenting in the liver of rabbits. 100,000g pellet of the liver homogenate was used as receptor source. The factors which affected the results of RRA such as salt, temperature and incubation time, were discussed. As same as in other RRA methods, serum protein inhibited non-specifically 125 I-GH binding in this method. In this assay, serum GH less than 5ng/ml could not be detected. The difference between the value obtained by RRA and that by radioimmunoassay was compared with reference to the patients with acromegalia. (Tsukamoto, Y.)

  18. TOLERANCE OF PEANUT GENOTYPES TO ACIDIC SOIL CONDITION

    Directory of Open Access Journals (Sweden)

    Astanto Kasno

    2013-06-01

    Full Text Available The acidic soil is generally less productive due to soil pH ranging from 3.1 to 5.0. However, it could be solved through soil amelioration, planting tolerant varieties to acidic soil condition, and a combination of both. Twenty peanut genotypes including two check varieties (Jerapah and Talam 1 were evaluated on dolomite-ameliorated and non ameliorated soil. In the greenhouse, the treatments were laid out in factorial design with four replications, while in the field using strip plot design with three replications. Assessment of tolerance was using Stressed Tolerance Index (STI according to Fernandez (1992. Results showed that dolomite application at dose equivalent to 0.5 x exchangeable Al was optimal in improving peanut growth, and peanut yield on acidic soil. Lines of GH3 (G/92088/92088-02-B-2-8-1 and GH 4 (G/92088/ 92088-02-B-2-8-2 genotypes had high STI with average yield of 2.47 tha-1 and 2.62 t ha-1 of dry pods and potential yield of 4.05 t ha-1 and 3.73 t ha-1 of dry pods, respectively as well as check varieties (Jerapah and Talam-1. It is concluded that peanut genotype of G/92088//92088-02-B-2-8-1 and G/92088//920 88- 02-B-2-8-2 were adaptable and tolerance to acidic, and tolerance of peanuts on acidic soil condition were probably controlled by the buffering mechanisms.

  19. Use of moisture induced stress testing to evaluate stripping potential of hot mix asphalt (HMA).

    Science.gov (United States)

    2012-07-01

    Stripping of hot mix asphalt (HMA) in the field is an ongoing issue for many Departments of Transportation : (DOTs). A leading cause of stripping is hydraulic scouring. The Moisture Induced Stress Tester (MIST) is a recently : developed technology th...

  20. Performance of the carbon stripping foils in the Argonne FN tandem

    International Nuclear Information System (INIS)

    Den Hartog, P.K.; Munson, F.; Heath, C.; Thomas, G.

    1980-01-01

    Carbon stripping foils produced by the glow discharge cracking of ethylene were produced and the foils were tested in the Argonne FN tandem accelerator. The results are presented and the characteristics of stripping media are discussed

  1. Computerized Decision Support Improves Medication Review Effectiveness : An Experiment Evaluating the STRIP Assistant's Usability

    NARCIS (Netherlands)

    Meulendijk, Michiel C; Spruit, Marco R; Drenth-van Maanen, A Clara; Numans, Mattijs E; Brinkkemper, Sjaak; Jansen, Paul A F; Knol, Wilma

    BACKGROUND: Polypharmacy poses threats to patients' health. The Systematic Tool to Reduce Inappropriate Prescribing (STRIP) is a drug optimization process for conducting medication reviews in primary care. To effectively and efficiently incorporate this method into daily practice, the STRIP

  2. Computerized decision support improves medication review effectiveness: an experiment evaluating the STRIP Assistant’s usability

    NARCIS (Netherlands)

    Meulendijk, M.; Spruit, M.; Drenth-van Maanen, C.; Numans, M.; Brinkkemper, S.; Jansen, P.; Knol, W

    2015-01-01

    Background Polypharmacy poses threats to patients’ health. The Systematic Tool to Reduce Inappropriate Prescribing (STRIP) is a drug optimization process for conducting medication reviews in primary care. To effectively and efficiently incorporate this method into daily practice, the STRIP

  3. Tools for applying lead tape to flat conductor cabling for chemical stripping

    Science.gov (United States)

    Angele, W.

    1969-01-01

    Two tools facilitate chemical stripping of insulation on flat conductor cabling. A tape pressing tool and a taping fixture apply adhesive lead tape with the proper amount of pressure to protect the remaining insulation from the chemical stripping solution.

  4. Extraction and stripping of neodymium (III) and dysprosium (III) by TRUEX solvent

    International Nuclear Information System (INIS)

    Rout, Alok; Venkatesan, K.A.; Antony, M.P.; Srinivasan, T.G.; Vasudeva Rao, P.R.

    2009-01-01

    McCabe-Thiele diagram for the extraction and stripping of Nd (III) and Dy (III) by TRUEX solvent has been constructed to determine the number of stages required for complete extraction and stripping. (author)

  5. Validation of the DNATyper™15 PCR Genotyping System for Forensic Application

    Directory of Open Access Journals (Sweden)

    Jian Ye

    2015-01-01

    Full Text Available We describe the optimization and validation of the DNATyper™15 multiplex polymerase chain reaction (PCR genotyping system for autosomal short tandem repeat (STR amplification at 14 autosomal loci (D6S1043, D21S11, D7S820, CSF1PO, D2S1338, D3S1358, D13S317, D8S1179, D16S539, Penta E, D5S818, vWA, D18S51, and FGA and  amelogenin, a sex-determining locus. Several DNATyper™15 assay variables were optimized, including hot start Taq polymerase concentration, Taq polymerase activation time, magnesium concentration, primer concentration, annealing temperature, reaction volume, and cycle number. The performance of the assay was validated with respect to species specificity, sensitivity to template concentration, stability, accuracy, influence of the DNA extraction methods, and the ability to genotype the mixture samples. The performance of the DNATyper™15 system on casework samples was compared with that of two widely used STR amplification kits, Identifiler™ (Applied Biosystems, Carlsbad, CA, USA and PowerPlex 16 ® (Promega, Madison, WI, USA. The conditions for PCR-based DNATyper™15 genotyping were optimized. Contamination from forensically relevant nonhuman DNA was not found to impact genotyping results, and full profiles were generated for all the reactions containing ≥ 0.125 ng of DNA template. No significant difference in performance was observed even after the DNATyper™15 assay components were subjected to 20 freeze-thaw cycles. The performances of DNATyper™15, Identifiler™, and PowerPlex 16 ® were comparable in terms of sensitivity and the ability to genotype the mixed samples and case-type samples, with the assays giving the same genotyping results for all the shared loci. The DNA extraction methods did not affect the performance of any of the systems. Our results demonstrate that the DNATyper™15 system is suitable for genotyping in both forensic DNA database work and case-type samples.

  6. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    OBJECTIVE: To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN: Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURCES...... circumference in response to weight loss intervention were not significantly different between FTO genotypes. Sensitivity analyses indicated that differential changes in body mass index, body weight, and waist circumference by FTO genotype did not differ by intervention type, intervention length, ethnicity......, sample size, sex, and baseline body mass index and age category. CONCLUSIONS: We have observed that carriage of the FTO minor allele was not associated with differential change in adiposity after weight loss interventions. These findings show that individuals carrying the minor allele respond equally...

  7. Pros and cons of flowers strips for farmers. A review

    Directory of Open Access Journals (Sweden)

    Uyttenbroeck, R.

    2016-01-01

    Full Text Available Description of the subject. To counteract environmental problems due to agricultural intensification, European farmers can apply agri-environmental schemes in their fields. Flower strips are one example of these schemes, with the aim of supporting biodiversity, leading to an increase in "useful" species groups such as pollinators for crop pollination and natural enemies for pest control. However, to our knowledge, a complete appraisal of the pros and cons of flower strips, from a farmer's point of view, does not yet exist. It is proposed that better and more complete information could increase the adoption and implementation of such agri-environmental schemes. Objectives. This study aims 1 to assess the pros and cons of flower strips, from a farmer's point of view, and 2 to highlight the knowledge gaps that exist in the scientific literature, for the different types of pros and cons. Method. We listed the different components of the appraisal of pros and cons and conducted a systematic screening of the scientific literature on flower strips and these components. Results. The largest part of the 31 selected studies was concerning agronomical and ecological processes, such as pollination and animal pest control. Most of them indicated positive effects of flower strips. For many components of the appraisal, mostly economic and social ones, few or no studies were found. Conclusions. While a positive balance of pros and cons, from a farmer's point of view, came from our literature screening, large research gaps still remain and more research is required, especially in the economic and social components of the evaluation.

  8. The Examination of Fatty Acid Taste with Edible Strips

    Science.gov (United States)

    Ebba, Sahbina; Abarintos, Ray A.; Kim, Dae G.; Tiyouh, Melissa; Stull, Judith C.; Movalia, Ankur; Smutzer, Gregory

    2012-01-01

    The objective of this study was to determine whether humans could detect long-chain fatty acids when these lipid molecules are delivered to the oral cavity by edible taste strips. For suprathreshold studies, up to 1.7 umoles of stearic acid or linoleic acid were incorporated into 0.03 mm thick, one-inch square taste strips. Normalized taste intensity values for stearic acid were in the barely detectable range, with values equal to, or slightly above control strips. One-third of test subjects described the taste quality as oily/fatty/waxy. Approximately 75% of test subjects could detect the presence of linoleic acid when this fatty acid was incorporated into dissolvable strips. Normalized taste intensity values for linoleic acid were in the weak to moderate range. The most commonly reported taste quality responses for linoleic acid were fatty/oily/waxy, or bitter. When nasal airflow was obstructed, the perceived taste intensity of linoleic acid decreased by approximately 40 percent. Taste intensity values and taste quality responses for linoleic acid were then compared among tasters and non-tasters of 6-n-propylthiouracil (PROP). Individuals who could detect the bitter taste of PROP reported higher taste intensity values for linoleic acid compared with PROP non-tasters. However, taste quality responses for linoleic acid were similar among both PROP tasters and PROP non-tasters. These results indicate that humans can detect long-chain fatty acids by both olfactory and non-olfactory pathways when these hydrophobic molecules are delivered to the oral cavity by means of edible taste strips. These studies further show that genetic variation in taste sensitivity to PROP affects chemosensory responses to the cis-unsaturated fatty acid linoleic acid in the oral cavity. PMID:22521910

  9. Comparison of blood glucose test strips in the detection of neonatal hypoglycaemia

    OpenAIRE

    Wilkins, B H; Kalra, D

    1982-01-01

    Blood glucose levels were estimated in 101 neonatal blood samples using three glucose test strip methods and the results compared with those from a laboratory. BM-test-glycemie 20-800 test strips and Reflotest-hypoglycemie test strips gave a rapid and reliable estimate of blood glucose level in the range 0-8 mmol/l (0-140 mg/100 ml). Dextrostix test strips tended to overestimate all blood glucose levels.

  10. Prevalence and Genotypic Distribution of Hepatitis C Virus in Peshawar KPK, Pakistan

    Directory of Open Access Journals (Sweden)

    Tanweer Kumar

    2017-01-01

    Full Text Available This present study was planned to obtain an up-to-date picture of Hepatitis C virus (HCV infection and its genotypes distribution in Peshawar, Khyber Pakhtunkhwa, Pakistan, as well as of the relationship between HCV genotypes and demographic and clinical parameters, and the risk factors in patients with an HCV subtype. Samples (blood from 1978 individuals were collected and were tested using a strip-based method called the immunochromatographic test (ICT for the existence of antibodies against HCV. It was observed that 158 of the 1978 individuals (7.9% harbored antibodies in their blood against HCV, among which the female percentage (53.2% was higher than that of the male (46.8%. Among the different age groups, the highest number of incidences of HCV antibodies was found in the age group of 31–40 years (26.6%. ICT positive samples were further screened by polymerase chain reaction (PCR to determine the existence of active HCV-RNA, and it was found that 6.21% (123 of the total population (1978 tested, was positive, among which the female rate (56.91% was observed to be higher than that of the male (43.09%. The highest incidence recorded was in the age group of 41–50 years (33.3%. HCV RNA positive individuals were genotyped: genotype 3a (45.5% was dominant among the other detected genotypes, followed by 1a (11.4%, 3b (4.9%, and 2a (4.1%. It was concluded that the highest prevalence of HCV was found in females, and that the dominant genotype of the screened individuals was 3a genotype.

  11. Heated oligonucleotide ligation assay (HOLA): an affordable single nucleotide polymorphism assay.

    Science.gov (United States)

    Black, W C; Gorrochotegui-Escalante, N; Duteau, N M

    2006-03-01

    Most single nucleotide polymorphism (SNP) detection requires expensive equipment and reagents. The oligonucleotide ligation assay (OLA) is an inexpensive SNP assay that detects ligation between a biotinylated "allele-specific detector" and a 3' fluorescein-labeled "reporter" oligonucleotide. No ligation occurs unless the 3' detector nucleotide is complementary to the SNP nucleotide. The original OLA used chemical denaturation and neutralization. Heated OLA (HOLA) instead uses a thermal stable ligase and cycles of denaturing and hybridization for ligation and SNP detection. The cost per genotype is approximately US$1.25 with two-allele SNPs or approximately US$1.75 with three-allele SNPs. We illustrate the development of HOLA for SNP detection in the Early Trypsin and Abundant Trypsin loci in the mosquito Aedes aegypti (L.) and at the a-glycerophosphate dehydrogenase locus in the mosquito Anopheles gambiae s.s.

  12. Occurrence of Acanthamoeba Genotypes in Wastewater Samples in Tehran, Iran

    Directory of Open Access Journals (Sweden)

    Massoud BEHNIA

    2017-12-01

    Full Text Available AbstractBackground: Acanthamoeba spp. is potentially pathogenic free-living amoeba that can exist in various water sources. The presence of this amoeba in water sources could be a health hazard as Acanthamoeba could lead to severe diseases such as Acanthamoeba keratitis and encephalitis. This study aimed to determine the genotypes of isolated Acanthamoeba spp. in raw wastewater samples in Tehran, Iran.Methods: Overall, 90 raw wastewater samples were collected from water treatment facilities in west and south of Tehran, Iran during 2014-2016. Water samples were filtered and cultured on non-nutrient agar (NNA medium enriched with Escherichia coli. Morphological and molecular analyses were done on positive strains. The pathogenic ability of the isolated strains was determined using physical assays.Results: Totally, 6 out of 90 (6.7% samples were positive for Acanthamoeba, according to morphological characteristics of double-walled cysts. Genotyping and sequencing of the positive strains showed Acanthamoeba belonging to T4 (83% and T11 (17% genotypes. In vitro pathogenicity tests were revealed that five isolates were classified as non-pathogenic strains and one strain belonging to T4 genotype was classified as the highly pathogenic amoebae.Conclusion: The current research reflected a low contamination of wastewater sources to Acanthamoeba. More studies regarding the contamination of wastewaters before and after treatment are required in different places of the country.

  13. A high-resolution melting analysis for genotyping urogenital Chlamydia trachomatis.

    Science.gov (United States)

    Li, Jian-Hong; Yin, Yue-Ping; Zheng, He-Ping; Zhong, Ming-Ying; Peng, Rui-Rui; Wang, Baoxi; Chen, Xiang-Sheng

    2010-12-01

    We have developed a high-resolution melting analysis (HRMA) for the genotyping of Chlamydia trachomatis and applied it specifically to the 11 sexually transmitted infection-related genotypes: D through K and L1 through L3. The variable segment 2 (VS2) was selected as the target for HRMA genotype identification. Eleven C. trachomatis genotypes were amplified by a nested real-time polymerase chain reaction (PCR) in the presence of the LCGreen saturating dye and showed no cross-reaction with 10 pathogenic bacteria or commensals from urogenital tract. The detection limit of HRMA method was 100 elementary bodies (EB)/mL. All of the 11 genotypes can be distinguished from each other by following an HRMA workflow. Genotype F, G, H, I, J, K, L2, and L3 could be directly identified from each other, whereas D, E, and L1 could be distinguished from each other by a second analysis with fewer curves or by heteroduplex formation with a known reference strain. In the validation panel of 36 C. trachomatis-positive urogenital samples genotyped by VS1-VS2 sequencing, nested real-time VS2 PCR followed by HRMA was able to discriminate between all samples correctly. This assay requires no fluorescence-labeled probes or separate post-PCR analysis and provides a simple and rapid approach for genotyping the C. trachomatis strains that are the most commonly sexually transmitted. Copyright © 2010 Elsevier Inc. All rights reserved.

  14. Hyaluronic Acid Assays

    DEFF Research Database (Denmark)

    Itenov, Theis Skovsgaard; Kirkby, Nikolai S; Bestle, Morten H

    2016-01-01

    BACKGROUD: Hyaluronic acid (HA) is proposed as a marker of functional liver capacity. The aim of the present study was to compare a new turbidimetric assay for measuring HA with the current standard method. METHODS: HA was measured by a particle-enhanced turbidimetric immunoassay (PETIA) and enzyme...

  15. FLUIDICS DEVICE FOR ASSAY

    DEFF Research Database (Denmark)

    2007-01-01

    The present invention relates to a device for use in performing assays on standard laboratory solid supports whereon chemical entities are attached. The invention furthermore relates to the use of such a device and a kit comprising such a device. The device according to the present invention is a...

  16. Sediment removal by prairie filter strips in row-cropped ephemeral watersheds

    Science.gov (United States)

    Matthew J. Helmers; Xiaobo Zhou; Heidi Asbjornsen; Randy Kolka; Mark D. Tomer; Richard M. Cruse

    2012-01-01

    Twelve small watersheds in central Iowa were used to evaluate the eff ectiveness of prairie filter strips (PFS) in trapping sediment from agricultural runoff. Four treatments with PFS of different size and location (100% rowcrop, 10% PFS of total watershed area at footslope, 10% PFS at footslope and in contour strips, 20% PFS at footslope and in contour strips)...

  17. 77 FR 73010 - Polyethylene Terephthalate Film, Sheet, and Strip From the United Arab Emirates; Preliminary...

    Science.gov (United States)

    2012-12-07

    ... International Trade Administration Polyethylene Terephthalate Film, Sheet, and Strip From the United Arab... terephthalate film, sheet, and strip (PET Film) from the United Arab Emirates (UAE). The period of review (POR... Terephthalate Film, Sheet, and Strip from the United Arab Emirates'' (Preliminary Decision Memorandum), dated...

  18. 78 FR 77649 - Polyethylene Terephthalate Film, Sheet, and Strip From the United Arab Emirates; Preliminary...

    Science.gov (United States)

    2013-12-24

    ... International Trade Administration Polyethylene Terephthalate Film, Sheet, and Strip From the United Arab... antidumping duty order on polyethylene terephthalate film, sheet, and strip (PET Film) from the United Arab... Strip from the United Arab Emirates'' (Preliminary Decision Memorandum), dated concurrently with this...

  19. 76 FR 11509 - Brass Sheet and Strip From France, Germany, Italy, and Japan

    Science.gov (United States)

    2011-03-02

    ... COMMISSION Brass Sheet and Strip From France, Germany, Italy, and Japan AGENCY: United States International... brass sheet and strip from France, Germany, Italy, and Japan. SUMMARY: The Commission hereby gives... strip from France, Germany, Italy, and Japan would be likely to lead to continuation or recurrence of...

  20. 77 FR 23508 - Brass Sheet and Strip From France, Germany, Italy, and Japan

    Science.gov (United States)

    2012-04-19

    ... COMMISSION Brass Sheet and Strip From France, Germany, Italy, and Japan Determination On the basis of the... revocation of the antidumping duty orders on brass sheet and strip from France, Germany, Italy, and Japan...), entitled Brass Sheet and Strip from France, Germany, Italy, and Japan: Investigation Nos. 731-TA-313, 314...

  1. A design aid for sizing filter strips using buffer area ratio

    Science.gov (United States)

    M.G. Dosskey; M.J. Helmers; D.E. Eisenhauer

    2011-01-01

    Nonuniform field runoff can reduce the effectiveness of filter strips that are a uniform size along a field margin. Effectiveness can be improved by placing more filter strip where the runoff load is greater and less where the load is smaller. A modeling analysis was conducted of the relationship between pollutant trapping efficiency and the ratio of filter strip area...

  2. Effect of Strip Mining on Water Quality in Small Streams in Eastern Kentucky, 1967-1975

    Science.gov (United States)

    Kenneth L. Dyer; Willie R. Curtis

    1977-01-01

    Eight years of streamflow data are analyzed to show the effects of strip mining on chemical quality of water in six first-order streams in Breathitt County, Kentucky. All these watersheds were unmined in August, 1967, but five have since been strip mined. The accumulated data from this case history study indicate that strip mining causes large increases in the...

  3. Flexible Faraday Cage with a Twist: Surface Charge on a Mobius Strip

    Science.gov (United States)

    Stewart, Sean

    2007-01-01

    Once an intriguing topological novelty known only to mathematicians, the Mobius strip has become a source of fascination and inspiration to the layperson and artist alike. Principal among its features are the two strange properties that the Mobius strip is a surface with only one side and one edge. A Mobius strip is readily formed by taking a long…

  4. Rapid fluorescent lateral-flow immunoassay for hepatitis B virus genotyping.

    Science.gov (United States)

    Song, Liu-Wei; Wang, Ying-Bin; Fang, Lin-Lin; Wu, Yong; Yang, Lin; Chen, Jie-Yu; Ge, Sheng-Xiang; Zhang, Jing; Xiong, You-Zheng; Deng, Xiu-Mei; Min, Xiao-Ping; Zhang, Jun; Chen, Pei-Jer; Yuan, Quan; Xia, Ning-Shao

    2015-01-01

    Hepatitis B virus (HBV) genotyping plays an important role in the clinical management of chronic hepatitis B (CHB) patients. However, the current nucleic acid based techniques are expensive, time-consuming, and inconvenient. Here, we developed a novel DNA-independent HBV genotyping tool based on a one-step fluorescent lateral flow immunoassay (LFIA). Epitope-targeting immunization and screening techniques were used to develop HBV genotype specific monoclonal antibodies (mAbs). These mAbs were used to develop a multitest LFIA with a matched scanning luminoscope for HBV genotyping (named the GT-LFIA). The performance of this novel assay was carefully evaluated in well-characterized clinical cohorts. The GT-LFIA, which can specifically differentiate HBV genotypes A, B, C, and D in a pretreatment-free single test, was successfully developed using four genotype specific mAbs. The detection limits of the GT-LFIA for HBV genotypes A, B, C, and D were 2.5-10.0 IU HBV surface antigen/mL, respectively. Among the sera from 456 CHB patients, 439 (96.3%; 95% confidence interval (CI), 94.1-97.8%) were genotype-differentiable by the GT-LFIA and 437 (99.5%; 95% CI, 98.4-99.9%) were consistent with viral genome sequencing. In the 21 patients receiving nucleos(t)ide analogue therapy, for end-of-treatment specimens that were HBV DNA undetectable and were not applicable for DNA-dependent genotyping, the GT-LFIA presented genotyping results that were consistent with those obtained in pretreatment specimens by viral genome sequencing and the GT-LFIA. In conclusion, the novel GT-LFIA is a convenient, fast, and reliable tool for differential HBV genotyping, especially in patients with low or undetectable HBV DNA levels.

  5. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  6. Dual-Quantum-Dots-Labeled Lateral Flow Strip Rapidly Quantifies Procalcitonin and C-reactive Protein

    Science.gov (United States)

    Qi, XiaoPing; Huang, YunYe; Lin, ZhongShi; Xu, Liang; Yu, Hao

    2016-03-01

    In the article, a dual-quantum-dots-labeled (dual-QDs-labeled) lateral flow strip (LFS) method was developed for the simultaneous and rapid quantitative detection of procalcitonin (PCT) and C-reactive protein (CRP) in the blood. Two QD-antibody conjugates with different fluorescence emission spectra were produced and sprayed on the LFS to capture PCT and CRP in the blood. Furthermore, a double antibody sandwich method for PCT and, meanwhile, a competitive inhibition method for CRP were employed in the LFS. For PCT and CRP in serum assayed by the dual-QDs-labeled LFS, their detection sensitivities reached 0.1 and 1 ng/mL, respectively, and their linear quantitative detection ranges were from 0.3 to 200 ng/mL and from 50 to 250 μg/mL, respectively. There was little evidence that the PCT and CRP assays would be interfered with each other. The correlations for testing CRP and PCT in clinical samples were 99.75 and 97.02 %, respectively, between the dual-QDs-labeled LFS we developed and commercial methods. The rapid quantification of PCT and CRP on dual-QDs-labeled LFS is of great clinical value to distinguish inflammation, bacterial infection, or viral infection and to provide guidance for the use of antibiotics or other medicines.

  7. Resistance of solanum species to phytophthora infestans evaluated in the detached-leaf and whole-plant assays

    International Nuclear Information System (INIS)

    Akhtar, K.P.; Saleem, M.Y.; Asghar, M.

    2012-01-01

    The reaction of 82 tomato genotypes belonging to 8 Solanum and a Lycopersicon species against Phytophthora infestans causing late blight was determined using detached-leaf and whole-plant assays. None of the test genotypes was immune or highly resistant. Of the 82 commercial and wild genotypes only TMS-2 (male-sterile and characterized by indeterminate growth) belonging to Lycopersicon esculentum was resistant with severity index of 2.4 in the detached-leaf assay on 0-5 scale (where 5 was highly susceptible) and percent disease index (%DI) of 23.3% under the whole-plant assay. Among the remaining genotypes, 41 were susceptible and 40 were highly susceptible under the detached-leaf assay, while 18 were susceptible and 63 were highly susceptible under the whole-plant assay. However, there was a significant difference in %DI for genotypes under the whole-plant assay. The response of whole-plants to inoculation with P. infestans in the detached-leaf assay was similar in all cases. The overall screening results indicate that TMS-2 is a good source of resistance and it can be useful for the development of tomato hybrid cultivars resistant to late blight. (author)

  8. Removal of nitrogen from swine manure by ammonia stripping; Reduccion del contenido en nitrogeno amoniacal del purin procino mediante la tecnica de stripping

    Energy Technology Data Exchange (ETDEWEB)

    Hidalgo, M. D.; Alamo, J. del; Nunez, U.; Irusta, R. [Grupo de Tecnologia Ambiental . Laboratorio de Analisis y Estudios Medioambientales. Valladolid (Spain)

    2001-07-01

    Lab scale experiments were undertaken to investigate air stripping as method for removing ammonia from cattle effluents and, more concretely, from the liquid fraction of swine manure. The effects of packet size, influent pH, air to liquid flow ratio and liquid recirculation flow in the stripping tower were investigated. The high ammonia removal efficiency of the air stripping method indicates that it could provide an interim solution for current waste management problems in the swine industry. (Author) 5 refs.

  9. SCREENING SOYBEAN GENOTYPES FOR PROMISCUOUS ...

    African Journals Online (AJOL)

    ACSS

    2016-02-25

    Feb 25, 2016 ... Symbiotic potential, competitiveness and compatibility of indigenous. Bradyrhizobium Japonicum isolates to three soybean genotypes of two distinct agro- climatic regions of Rajasthan, India. Saudi. Journal of Biological Sciences 17: 303- 310. Muhammad, A. 2010. Response of a promiscuous soybean ...

  10. FTO genotype and weight loss

    DEFF Research Database (Denmark)

    Livingstone, Katherine M; Celis-Morales, Carlos; Papandonatos, George D

    2016-01-01

    : Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION: Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after...

  11. Fabrication and evaluation of a sequence-specific oligonucleotide miniarray for molecular genotyping

    Directory of Open Access Journals (Sweden)

    Iqbal J

    2008-01-01

    Full Text Available Purpose: Molecular genotyping relies on the identification of specific microbial DNA sequences. Accurate genotyping not only requires discrimination between low- and high-risk pathogens for effective diagnosis or disease management but also requires the identity of the specific strain or type of the microbe involved in pathogenesis. The majority of these assays require DNA amplification followed by genome identification either through sequencing or hybridization to specific oligonucleotide probes. We evaluated the use of a DNA microchip assay as a simple and easy-to-use procedure for genotyping. Methods: Various methodological parameters were optimized for single-base mismatch discrimination on a DNA microarray. The fabrication procedures involved substrate chemistry for immobilization. The effect of various buffers and features associated with oligonucleotide sequences were standardized. The assay was evaluated on a low-density genotyping chip containing the sequences of various (Human Papilloma Virus HPV subtypes. Results: The specific subtype was identified with high specificity by hybridization in miniaturized condition. Conclusions: The DNA microchip provides a rapid and cost-effective genotyping procedure for microbial organisms and can be implemented easily in any laboratory.

  12. Acetohydroxyacid synthase (AHAS) in vivo assay for screening imidazolinone-resistance in sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Vega, T; Breccia, G; Gil, M; Zorzoli, R; Picardi, L; Nestares, G

    2012-12-01

    The objective of this work was to evaluate the in vivo acetohydroxyacid synthase (AHAS) activity response to imidazolinones and its possible use as a selection method for evaluating AHAS inhibitor resistance. In vivo AHAS assay and the comparison of parameters from dose-response curves have been used as a valid tool for comparing sunflower lines and hybrids differing in imidazolinone resistance. The sunflower resistant genotypes evaluated here were 100-fold and 20-fold more resistant compared with the susceptible line for imazethapyr and imazapyr, respectively. This assay also allowed discrimination of homozygous from heterozygous genotypes for I(mr1) locus that codify for the catalytic subunit of AHAS. The in vivo AHAS assay described in this study was useful for the selection of sunflower genotypes differing in herbicide resistance and could be a useful tool when breeding for imidazolinone resistance in sunflower. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  13. The new silicon strip detectors for the CMS tracker upgrade

    International Nuclear Information System (INIS)

    Dragicevic, M.

    2010-01-01

    The first introductory part of the thesis describes the concept of the CMS experiment. The tasks of the various detector systems and their technical implementations in CMS are explained. To facilitate the understanding of the basic principles of silicon strip sensors, the subsequent chapter discusses the fundamentals in semiconductor technology, with particular emphasis on silicon. The necessary process steps to manufacture strip sensors in a so-called planar process are described in detail. Furthermore, the effects of irradiation on silicon strip sensors are discussed. To conclude the introductory part of the thesis, the design of the silicon strip sensors of the CMS Tracker are described in detail. The choice of the substrate material and the complex geometry of the sensors are reviewed and the quality assurance procedures for the production of the sensors are presented. Furthermore the design of the detector modules are described. The main part of this thesis starts with a discussion on the demands on the tracker caused by the increase in luminosity which is proposed as an upgrade to the LHC accelerator (sLHC). This chapter motivates the work I have conducted and clarifies why the solutions proposed by myself are important contributions to the upgrade of the CMS tracker. The following chapters present the concepts that are necessary to operate the silicon strip sensors at sLHC luminosities and additional improvements to the construction and quality assurance of the sensors and the detector modules. The most important concepts and works presented in chapters 7 to 9 are: Development of a software framework to enable the flexible and quick design of test structures and sensors. Selecting a suitable sensor material which is sufficiently radiation hard. Design, implementation and production of a standard set of test structures to enable the quality assurance of such sensors and any future developments. Electrical characterisation of the test structures and analysis

  14. A SERS-based lateral flow assay biosensor for highly sensitive detection of HIV-1 DNA.

    Science.gov (United States)

    Fu, Xiuli; Cheng, Ziyi; Yu, Jimin; Choo, Priscilla; Chen, Lingxin; Choo, Jaebum

    2016-04-15

    User-friendly lateral flow (LF) strips have been extensively used for point-of-care (POC) self-diagnostics, but they have some limitations in their detection sensitivity and quantitative analysis because they only identify the high cut-off value of a biomarker by utilizing color changes that are detected with the naked eye. To resolve these problems associated with LF strips, we developed a novel surface-enhanced Raman scattering (SERS)-based LF assay for the quantitative analysis of a specific biomarker in the low concentration range. Herein, human immunodeficiency virus type 1 (HIV-1) DNA was chosen as the specific biomarker. Raman reporter-labeled gold nanoparticles (AuNPs) were employed as SERS nano tags for targeting and detecting the HIV-1 DNA marker, as opposed to using bare AuNPs in LF strips. It was possible to quantitatively analyze HIV-1 DNA with high sensitivity by monitoring the characteristic Raman peak intensity of the DNA-conjugated AuNPs. Under optimized conditions, the detection limit of our SERS-based lateral flow assay was 0.24 pg/mL, which was at least 1000 times more sensitive compared to colorimetric or fluorescent detection methods. These results demonstrate the potential feasibility of the proposed SERS-based lateral flow assay to quantitatively detect a broad range of genetic diseases with high sensitivity. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Dual isotope assays

    International Nuclear Information System (INIS)

    Smith, G.F.W.; Stevens, R.A.J.; Jacoby, B.

    1980-01-01

    Dual isotope assays for thyroid function are performed by carrying out a radio-immunoassay for two of thyroxine (T4), tri-iodothyronine (T3), thyroid stimulating hormone (TSH), and thyroxine binding globulin (TBG), by a method wherein a version of one of the thyroid components, preferably T4 or T3 is labelled with Selenium-75 and the version of the other thyroid component is labelled with a different radionuclide, preferably Iodine-125. (author)

  16. Cytotoxicity assay automation

    Science.gov (United States)

    Levinthal, E. C.; Payne, R. O.

    1971-01-01

    The design and construction of a system to automatically test HLP antigens are described. Major efforts were made to test and evaluate the performance of such a system, and compare its performance with nonautomatic tissue typing techniques. The system is based on the fluorochromatic cytotoxicity assay. Results show the system will work but is subject to malfunctions after a few samplings, and poses problems in showing correctly the necessary readings.

  17. Application of DNA Aptamers and Quantum Dots to Lateral Flow Test Strips for Detection of Foodborne Pathogens with Improved Sensitivity versus Colloidal Gold

    Directory of Open Access Journals (Sweden)

    John G. Bruno

    2014-04-01

    Full Text Available Preliminary studies aimed at improving the sensitivity of foodborne pathogen detection via lateral flow (LF test strips by use of high affinity DNA aptamers for capture and reporter functions when coupled to red-emitting quantum dots (Qdot 655 are reported. A variety of DNA aptamers developed against Escherichia coli, Listeria monocytogenes, and Salmonella enterica were paired in capture and reporter combinations to determine which yielded the strongest detection of their cognate bacteria using a colloidal gold screening system. Several promising sandwich combinations were identified for each of the three bacterial LF strip systems. The best E. coli aptamer-LF system was further studied and yielded a visible limit of detection (LOD of ~3,000 E. coli 8739 and ~6,000 E. coli O157:H7 in buffer. These LODs were reduced to ~300–600 bacterial cells per test respectively by switching to a Qdot 655 aptamer-LF system. Novel aspects of these assays such as the use of high levels of detergents to avoid quantum dot agglutination and enhance migration in analytical membranes, identification of optimal analytical membrane types, UV-immobilization of capture aptamers, and novel dual biotin/digoxigenin-end labeled aptamer streptavidin-colloidal gold or -Qdot 655 conjugates plus anti-digoxigenin antibody control lines are also discussed. In general, this work provides proof-of-principle for highly sensitive aptamer-Qdot LF strip assays for rapid foodborne pathogen detection.

  18. HCV genotypes and age distribution in patients of Vienna and surrounding areas.

    Science.gov (United States)

    Haushofer, A C; Kopty, C; Hauer, R; Brunner, H; Halbmayer, W M

    2001-01-01

    Chronic hepatitis C (CHC) can result in liver cirrhosis and hepatocellular carcinoma. Determination of the hepatitis C virus (HCV) genotype/subtype may be of prognostic value to estimate the risk of development of liver cirrhosis. The HCV genotype/subtype was determined in patients with CHC and possible associations with age, source of HCV transmission, duration of HCV infection, and development of liver cirrhosis were investigated. A total of 250 consecutive patients with CHC were studied. HCV genotypes/subtypes were determined with a commercially available assay based on the reverse-hybridization principle. Source of HCV transmission and duration of HCV infection were taken from the patient documentation and liver cirrhosis was diagnosed by clinical, biochemical, and sonographic data. HCV genotypes 1, 2, 3, 4, and 5 were found in 74.8, 2.8, 16, 5.2, and 0.4% of the patients. Most frequent subtypes were 1b (54%), 1a (15.6%), and 3a (15.6%). Patients with genotype 1 (mean, 52.8 years) or 2 (mean, 51.0 years) were significantly older than patients with genotype 3 (mean, 37.2 years) or genotype 4 (mean, 37.2 years). Patients with subtype 1b (mean, 58.1 years) were significantly older than patients with subtype 1a (mean, 40.8 years) or 3a (mean, 37.5 years). The main sources of HCV infection were intravenous drug abuse in 30.0% of all patients (genotype 1 in 53.3%; genotype 3 in 40%) or transfusion of blood and blood products in 21.6% of all patients (genotype 1 in 83.4%). The source of transmission, however, remained unknown in 44.8% of all patients. The prevalence of genotype 1 was significantly higher in patients with long duration (more than 20 years) of CHC. In none of the patients with genotype 2 or 3, duration of CHC for more than 20 years was observed. The prevalence of genotype 4 was significantly higher in patients with short duration (less than 10 years) of CHC. Liver cirrhosis was diagnosed in 13.6% of all patients (97.1% of patients with genotype 1

  19. Concurrent quantitation of the A and D genotypes of hepatitis B virus

    NARCIS (Netherlands)

    Tanic, Nikola; Stanojevic, Boban; Tanic, Nasta; Schaefer, Stephan; Niesters, Hubert G. M.; Bozic, Milena; Dimitrijevic, Bogomir

    2009-01-01

    Hepatitis B virus (HBV) infection is a global health problem associated with severe liver disorders. Viral load and HBV genotype affect the clinical outcome, guide antiviral therapy and provide long term prognosis for HBV infected patients. Various types of detection and quantitation assays are

  20. Molecular diagnosis of MDR-TB using GenoType MTBDR plus 96 ...

    African Journals Online (AJOL)

    This three month laboratory- based study (1st September-30th November, 2011) was carried out at the TB laboratories of the University College Hospital, Ibadan, Nigeria to determine the magnitude of MDR-TB using molecular based GenoType MTBDRplus 96 assay. Two sputum samples were collected from each subject.